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planktoscope/flows/main.json

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Add files via upload
2020-01-08 14:32:46 +01:00
[
{
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"id": "eaae323a.31b3",
update to main.json to fix camera bugs
2020-09-15 17:33:49 +02:00
"type": "tab",
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"label": "Home",
update to main.json to fix camera bugs
2020-09-15 17:33:49 +02:00
"disabled": false,
"info": ""
},
{
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"id": "b771c342.49603",
"type": "tab",
"label": "Sample",
"disabled": false,
"info": ""
update to main.json to fix camera bugs
2020-09-15 17:33:49 +02:00
},
{
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"id": "bccd1f23.87219",
"type": "tab",
"label": "Optic Configuration",
"disabled": false,
"info": ""
Add files via upload
2020-01-08 14:32:46 +01:00
},
{
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"id": "baa1e3d9.cb29d",
"type": "tab",
"label": "Fluidic Acquisition",
"disabled": false,
"info": ""
Update flows.json
2020-07-14 18:22:31 +02:00
},
{
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"id": "cb95299c.2817c8",
"type": "tab",
"label": "Segmentation",
"disabled": false,
"info": ""
update to main.json to fix camera bugs
2020-09-15 17:33:49 +02:00
},
{
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"id": "c1660bc.e7ff7f8",
"type": "tab",
"label": "Gallery",
"disabled": false,
"info": ""
update to main.json to fix camera bugs
2020-09-15 17:33:49 +02:00
},
{
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"id": "1371dec5.76e671",
"type": "tab",
"label": "Settings",
"disabled": false,
"info": ""
update to main.json to fix camera bugs
2020-09-15 17:33:49 +02:00
},
{
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"id": "1c24ad9c.bebec2",
update to main.json to fix camera bugs
2020-09-15 17:33:49 +02:00
"type": "subflow",
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"name": "Config",
"info": "An input to this subflow will get the configuration to be saved to disk.\n\nOn startup, this node outputs the loaded configuration",
update to main.json to fix camera bugs
2020-09-15 17:33:49 +02:00
"category": "",
"in": [
{
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"x": 440,
"y": 860,
update to main.json to fix camera bugs
2020-09-15 17:33:49 +02:00
"wires": [
{
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"id": "b584292a.24b08"
update to main.json to fix camera bugs
2020-09-15 17:33:49 +02:00
}
]
}
],
"out": [
{
Main.json: UI upgrade
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"x": 1240,
"y": 300,
update to main.json to fix camera bugs
2020-09-15 17:33:49 +02:00
"wires": [
{
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"id": "ad541674.4791c8",
update to main.json to fix camera bugs
2020-09-15 17:33:49 +02:00
"port": 0
}
]
Update flows.json
2020-07-14 18:22:31 +02:00
}
],
update to main.json to fix camera bugs
2020-09-15 17:33:49 +02:00
"env": [],
"color": "#DDAA99"
Update flows.json
2020-07-14 18:22:31 +02:00
},
{
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"id": "da2c279f.cbe318",
"type": "ui_group",
"name": "Controller",
"tab": null,
"order": 6,
"disp": true,
"width": 6,
"collapse": false
update to main.json to fix camera bugs
2020-09-15 17:33:49 +02:00
},
{
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"id": "833bc5bb.217ba8",
"type": "ui_group",
"name": "Preview",
"tab": "181bb236.1e94be",
"order": 1,
"disp": true,
"width": 14,
"collapse": false
update to main.json to fix camera bugs
2020-09-15 17:33:49 +02:00
},
{
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"id": "3a6bb13f.c9703e",
"type": "ui_tab",
"name": "Home",
"icon": "home",
"order": 1,
"disabled": false,
"hidden": false
update to main.json to fix camera bugs
2020-09-15 17:33:49 +02:00
},
{
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"id": "181bb236.1e94be",
"type": "ui_tab",
"name": "Optic Configuration",
"icon": "fa-eye",
"order": 3,
"disabled": false,
"hidden": false
update to main.json to fix camera bugs
2020-09-15 17:33:49 +02:00
},
{
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"id": "c9194f02.9d5e9",
"type": "ui_tab",
"name": "Fluidic Acquisition",
"icon": "fa-flask",
"order": 4,
"disabled": false,
"hidden": false
Extraction and refactor of the python code from node-red flow The rationale for this rewrite is to improve the readability, the modularity, the reliability and the future-proofing of the main python script. All in all, this is now 124 commits that are going to be squashed and merged together, spanning more than two weeks of development and testing. Please test away this release and break things. An upgrading guide will be published in the coming days, along with a new image for people to use if they don't want to upgrade on their own. Read along if you want to know all the goodies! As a starter, the python script was extracted from the main flow, and now lives in its own files at `PlantonScope/scripts/*`. We set up the auto formatting of the code by using [Black](https://github.com/psf/black). This make the code clearer and uniform. We are using the default settings, so if you just install Black and set your editor to format on save using it, you should be good to go. The code is separated in four main processes, each with a specific set of responsibilities: - The main process controls all the others, starts everything up and cleans up on shutdown - The stepper process manages the stepper movements. It's now possible to have simultaneous movements of both motors (this closes #38 ). - The imager process controls the camera and the streaming server via a state machine. - The segmenter process manages the segmentation and its outputs. The segmentation happens recursively in all folders in `/home/pi/PlanktonScope/img/`. Each folder has its own output archive, and bug #26 is now closed. Those processes communicates together using MQTT and json messages. Each message is adressed to one topic. The high level topic controls which process receives the message. The details of each topic is at the end of this commit message. Every imaging sessions has now its own folder, under the `img` root. Metadata are saved individually for every session, in a JSON file in the same directory as the pictures. The configuration is not parsed from `config.json` anymore and passed directly through MQTT messages to the concerned process. A new configuration file has been created: `hardware.json`. This file contains information related to your specific hardware configuration. You can choose to reverse the connection of the motors for example, but you can also define specific speed limits and steps number for your pump and focus stage. This will make it easier for people who wants to experiment with different kind of hardware. It's not necessary to have this file though. If it doesn't exists, the default configuration will be applied. The code is architectured around 6 modules and about 10 classes. I encourage you to have a look at the files, they're pretty straightforward to understand. There is a lot of work left around the node-red code refactoring, dashboard ui improvements, better and clearer LED messages, OLED screen integration and finer control of the segmentation process, but this is quite good for now. Here is the topic lists for MQTT and the corresponding messages. - actuator : This topic adresses the stepper control thread No publication under this topic should happen from the python process - actuator/pump : Control of the pump The message is a json object {"action":"move", "direction":"FORWARD", "volume":10, "flowrate":1} to move 10mL forward at 1mL/min action can be "move" or "stop" Receive only - actuator/focus : Control of the focus stage The message is a json object, speed is optional {"action":"move", "direction":"UP", "distance":0.26, "speed":1} to move up 10mm action can be "move" or "stop" Receive only - imager/image : This topic adresses the imaging thread Is a json object with {"action":"image","sleep":5,"volume":1,"nb_frame":200} sleep in seconds, volume in mL Can also receive a config update message: {"action":"config","config":[...]} Can also receive a camera settings message: {"action":"settings","iso":100,"shutter_speed":40} Receive only - segmenter/segment : This topic adresses the segmenter process Is a json object with {"action":"segment"} Receive only - status : This topics sends feedback to Node-Red No publication or receive at this level - status/pump : State of the pump Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/focus : State of the focus stage Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/imager : State of the imager Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Completed or 12_11_15_0.1.jpg has been imaged. Publish only - status/segmenter : Status of the segmentation - status/segmenter/name - status/segmenter/object_id - status/segmenter/metric Here is the original commit history: * Extract python main.py from flow * Fix bug in server addresses These addresses should be the loopback device instead of the network address of the device. Using the loopback address will not necessitate to update the script when the network address changes. * clean up picamera import * changes to main python and flow: update MQTT requests address to localhost (bugfix) update streaming output address to nothing update main flow to remove python script references and location * Automatically initialise imaging led on startup to off state. * Add the ability to invert outputs of the motor We added a key to config.json "hardware_config" with a subkey "stepper_reverse". If this key is present in the config file and set to 1, the output of the motors are inversed (stepper2 becomes the pump motor and stepper1 the focus motor) * move all non main script to a subfolder * add __init__.py to package * light module rewrite * json cleanup and absolute path for config file * light.py forgot to import subprocess #oups * Add command to turn the leds off * Auto formatting of main.py I've used Black with default settings, see https://github.com/psf/black * First commit of stepper.py Pump parameters still needs to be checked and tuned. * addition of hardware details in config.json * Introduce hardware.json to replace the `hardware_config` of config.json * stepper.py: calibration, typos * creates the MQTT_Client class * pump_max_speed is now in ml/min to help readability * forgot to add self to the class def * addition of threading capabilities to stepper.py (UNTESTED) * mqtt: fix topic bug * remove counter * mqtt add doc about topics * stepper.py creates an "actuator/*/state" topic * stepper.py: rename mqtt_client to pump_client * mqtt.py: add details about topics * stepper.py: rename pump_client to actuator_client * topic was not split properly and a part was lost * switch to f-strings for mqtt.py * cosmetic update * stepper.py: folder name will be planktoscope change calls * hardware.json became more straightforward * stepper.py syntax bugs * stepper.py addition of a received stop command * stepper.py: update to max travel distance * stepper.py: several typos here * rename folder * main.py: reword to reflect folder rename * main.py: remove logic that has been moved to stepper.py and mqtt.py * main.py: update to add mqtt imaging client * mqtt.py: make command and args local to class and output more verbose * make stepper.py a class * main.py: instantiate stepper class and call it * main.py: name mqtt client * update to main.json to reflect main.py changes * fix bugs around pump control * update flows to latest version from Thibault * distance can be a small value, and definitevely should be a float. * unify mqtt topics * unify mqtt output in the main flow * first logger implementation, uses loguru * mqtt: add reason to on_connect * mqtt: add on_disconnect handler * stepper: add more logger calls for debug mainly * main: add levels for logger * imager.py: first move of the imager logic * imager: time import cleanup * imager: morphocut import cleanup * imager: skimage import cleanup * imager: finishing import cleanup * imager: Class creation - WIP Also provides a fix for #26 (see line 190). * imager: threading is needed for Condition() * streamer: get the streamer server its own file * imager: creates start_camera and get the server creation out * imager: subclass multiprocessing.Process * imager: get Pipeline creation its own function * imager: cleanup of self calls * main: code removal and corresponding calls to newly created classes * imager: various formatting changes * main: management of signal shutdown * add requirements.txt * mqtt: messages are now json objects Also, addition of a flag on receiving a new message * mqtt: make message private and add logic to synchronise * stepper: creates the stepper class * stepper: use the new class * stepper: uses the new logic * stepper: add the shutdown event * stepper: add shutdown method * main: add shutdown event * imager: graceful shutdown * stepper: nicer way of checking the Eevnt * self is a required first argument for a method in a class Especially if you use said class private members! * python: various typos and small errors in import * stepper: create mqtt client during init * stepper: instanciate the mqtt client inside run Otherwise it's not accessible from inside the loop. It's a PITA, more information at https://stackoverflow.com/questions/17172878/using-pythons-multiprocessing-process-class * stepper: little bugs and typos all around * mqtt: add shutdown method * mqtt: add connect in init * stepper: fix bugs, sanitize inputs * stepper: work on delay prediction improvements * stepper: json is mean, double quote are mandatory inside * mqtt: add details about message exchanged * imager: first implementation of json messages * main.json: add new tab for RPi management + json for payloads * imager: add state_machine class * stepper: publish last will * imager: major refactor * main: make streaming server process a daemon * mqtt: insert debug statement on close * main: reorder imports * imager: make it work! Reinsert the streaming server logic in there, because there is a problem with the synchronisation part otherwise. Also, eventually, StreamingOuput() will have to be made not global Final very critical learning: it's super duper important to make sure the memory split is at least 256Meg for the GPU. Chaos ensues otherwise * main: changes to accomodate the streamer/imager fusino * imager_state_machine: insert states transition description * stepper: cleanup of code * segmenter: creation of the class * python: include segmenter changes * remove unused files * stepper: check existence of hardware.json * main.json: changes to reflect the python script evolution * remove unecessary TODOs and add some others * main: add check for config and directories * imager: update_config is implemented and we have better management of directories now * segmenter: now work recursively in all folders * flow: the configuration is now sent via mqtt * segmenter: better manage pipeline error * segmenter: declaration of archive_fn in init * imager: small bugs and typos * main: add uniqueID output * imager: add the camera settings message We can now update the ISO, shutter speed and resolution from Node-Red * package.json: update dependencies
2020-09-28 11:05:27 +02:00
},
{
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"id": "8d16beb8.9b3fb",
"type": "ui_tab",
"name": "Segmentation",
"icon": "fa-crop",
"order": 5,
"disabled": false,
"hidden": false
Extraction and refactor of the python code from node-red flow The rationale for this rewrite is to improve the readability, the modularity, the reliability and the future-proofing of the main python script. All in all, this is now 124 commits that are going to be squashed and merged together, spanning more than two weeks of development and testing. Please test away this release and break things. An upgrading guide will be published in the coming days, along with a new image for people to use if they don't want to upgrade on their own. Read along if you want to know all the goodies! As a starter, the python script was extracted from the main flow, and now lives in its own files at `PlantonScope/scripts/*`. We set up the auto formatting of the code by using [Black](https://github.com/psf/black). This make the code clearer and uniform. We are using the default settings, so if you just install Black and set your editor to format on save using it, you should be good to go. The code is separated in four main processes, each with a specific set of responsibilities: - The main process controls all the others, starts everything up and cleans up on shutdown - The stepper process manages the stepper movements. It's now possible to have simultaneous movements of both motors (this closes #38 ). - The imager process controls the camera and the streaming server via a state machine. - The segmenter process manages the segmentation and its outputs. The segmentation happens recursively in all folders in `/home/pi/PlanktonScope/img/`. Each folder has its own output archive, and bug #26 is now closed. Those processes communicates together using MQTT and json messages. Each message is adressed to one topic. The high level topic controls which process receives the message. The details of each topic is at the end of this commit message. Every imaging sessions has now its own folder, under the `img` root. Metadata are saved individually for every session, in a JSON file in the same directory as the pictures. The configuration is not parsed from `config.json` anymore and passed directly through MQTT messages to the concerned process. A new configuration file has been created: `hardware.json`. This file contains information related to your specific hardware configuration. You can choose to reverse the connection of the motors for example, but you can also define specific speed limits and steps number for your pump and focus stage. This will make it easier for people who wants to experiment with different kind of hardware. It's not necessary to have this file though. If it doesn't exists, the default configuration will be applied. The code is architectured around 6 modules and about 10 classes. I encourage you to have a look at the files, they're pretty straightforward to understand. There is a lot of work left around the node-red code refactoring, dashboard ui improvements, better and clearer LED messages, OLED screen integration and finer control of the segmentation process, but this is quite good for now. Here is the topic lists for MQTT and the corresponding messages. - actuator : This topic adresses the stepper control thread No publication under this topic should happen from the python process - actuator/pump : Control of the pump The message is a json object {"action":"move", "direction":"FORWARD", "volume":10, "flowrate":1} to move 10mL forward at 1mL/min action can be "move" or "stop" Receive only - actuator/focus : Control of the focus stage The message is a json object, speed is optional {"action":"move", "direction":"UP", "distance":0.26, "speed":1} to move up 10mm action can be "move" or "stop" Receive only - imager/image : This topic adresses the imaging thread Is a json object with {"action":"image","sleep":5,"volume":1,"nb_frame":200} sleep in seconds, volume in mL Can also receive a config update message: {"action":"config","config":[...]} Can also receive a camera settings message: {"action":"settings","iso":100,"shutter_speed":40} Receive only - segmenter/segment : This topic adresses the segmenter process Is a json object with {"action":"segment"} Receive only - status : This topics sends feedback to Node-Red No publication or receive at this level - status/pump : State of the pump Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/focus : State of the focus stage Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/imager : State of the imager Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Completed or 12_11_15_0.1.jpg has been imaged. Publish only - status/segmenter : Status of the segmentation - status/segmenter/name - status/segmenter/object_id - status/segmenter/metric Here is the original commit history: * Extract python main.py from flow * Fix bug in server addresses These addresses should be the loopback device instead of the network address of the device. Using the loopback address will not necessitate to update the script when the network address changes. * clean up picamera import * changes to main python and flow: update MQTT requests address to localhost (bugfix) update streaming output address to nothing update main flow to remove python script references and location * Automatically initialise imaging led on startup to off state. * Add the ability to invert outputs of the motor We added a key to config.json "hardware_config" with a subkey "stepper_reverse". If this key is present in the config file and set to 1, the output of the motors are inversed (stepper2 becomes the pump motor and stepper1 the focus motor) * move all non main script to a subfolder * add __init__.py to package * light module rewrite * json cleanup and absolute path for config file * light.py forgot to import subprocess #oups * Add command to turn the leds off * Auto formatting of main.py I've used Black with default settings, see https://github.com/psf/black * First commit of stepper.py Pump parameters still needs to be checked and tuned. * addition of hardware details in config.json * Introduce hardware.json to replace the `hardware_config` of config.json * stepper.py: calibration, typos * creates the MQTT_Client class * pump_max_speed is now in ml/min to help readability * forgot to add self to the class def * addition of threading capabilities to stepper.py (UNTESTED) * mqtt: fix topic bug * remove counter * mqtt add doc about topics * stepper.py creates an "actuator/*/state" topic * stepper.py: rename mqtt_client to pump_client * mqtt.py: add details about topics * stepper.py: rename pump_client to actuator_client * topic was not split properly and a part was lost * switch to f-strings for mqtt.py * cosmetic update * stepper.py: folder name will be planktoscope change calls * hardware.json became more straightforward * stepper.py syntax bugs * stepper.py addition of a received stop command * stepper.py: update to max travel distance * stepper.py: several typos here * rename folder * main.py: reword to reflect folder rename * main.py: remove logic that has been moved to stepper.py and mqtt.py * main.py: update to add mqtt imaging client * mqtt.py: make command and args local to class and output more verbose * make stepper.py a class * main.py: instantiate stepper class and call it * main.py: name mqtt client * update to main.json to reflect main.py changes * fix bugs around pump control * update flows to latest version from Thibault * distance can be a small value, and definitevely should be a float. * unify mqtt topics * unify mqtt output in the main flow * first logger implementation, uses loguru * mqtt: add reason to on_connect * mqtt: add on_disconnect handler * stepper: add more logger calls for debug mainly * main: add levels for logger * imager.py: first move of the imager logic * imager: time import cleanup * imager: morphocut import cleanup * imager: skimage import cleanup * imager: finishing import cleanup * imager: Class creation - WIP Also provides a fix for #26 (see line 190). * imager: threading is needed for Condition() * streamer: get the streamer server its own file * imager: creates start_camera and get the server creation out * imager: subclass multiprocessing.Process * imager: get Pipeline creation its own function * imager: cleanup of self calls * main: code removal and corresponding calls to newly created classes * imager: various formatting changes * main: management of signal shutdown * add requirements.txt * mqtt: messages are now json objects Also, addition of a flag on receiving a new message * mqtt: make message private and add logic to synchronise * stepper: creates the stepper class * stepper: use the new class * stepper: uses the new logic * stepper: add the shutdown event * stepper: add shutdown method * main: add shutdown event * imager: graceful shutdown * stepper: nicer way of checking the Eevnt * self is a required first argument for a method in a class Especially if you use said class private members! * python: various typos and small errors in import * stepper: create mqtt client during init * stepper: instanciate the mqtt client inside run Otherwise it's not accessible from inside the loop. It's a PITA, more information at https://stackoverflow.com/questions/17172878/using-pythons-multiprocessing-process-class * stepper: little bugs and typos all around * mqtt: add shutdown method * mqtt: add connect in init * stepper: fix bugs, sanitize inputs * stepper: work on delay prediction improvements * stepper: json is mean, double quote are mandatory inside * mqtt: add details about message exchanged * imager: first implementation of json messages * main.json: add new tab for RPi management + json for payloads * imager: add state_machine class * stepper: publish last will * imager: major refactor * main: make streaming server process a daemon * mqtt: insert debug statement on close * main: reorder imports * imager: make it work! Reinsert the streaming server logic in there, because there is a problem with the synchronisation part otherwise. Also, eventually, StreamingOuput() will have to be made not global Final very critical learning: it's super duper important to make sure the memory split is at least 256Meg for the GPU. Chaos ensues otherwise * main: changes to accomodate the streamer/imager fusino * imager_state_machine: insert states transition description * stepper: cleanup of code * segmenter: creation of the class * python: include segmenter changes * remove unused files * stepper: check existence of hardware.json * main.json: changes to reflect the python script evolution * remove unecessary TODOs and add some others * main: add check for config and directories * imager: update_config is implemented and we have better management of directories now * segmenter: now work recursively in all folders * flow: the configuration is now sent via mqtt * segmenter: better manage pipeline error * segmenter: declaration of archive_fn in init * imager: small bugs and typos * main: add uniqueID output * imager: add the camera settings message We can now update the ISO, shutter speed and resolution from Node-Red * package.json: update dependencies
2020-09-28 11:05:27 +02:00
},
Flow updates
2020-10-06 17:22:25 +02:00
{
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"id": "d9cd733b.ab73d",
"type": "ui_tab",
"name": "Settings",
"icon": "fa-cogs",
"order": 7,
"disabled": false,
"hidden": false
Flow updates
2020-10-06 17:22:25 +02:00
},
Extraction and refactor of the python code from node-red flow The rationale for this rewrite is to improve the readability, the modularity, the reliability and the future-proofing of the main python script. All in all, this is now 124 commits that are going to be squashed and merged together, spanning more than two weeks of development and testing. Please test away this release and break things. An upgrading guide will be published in the coming days, along with a new image for people to use if they don't want to upgrade on their own. Read along if you want to know all the goodies! As a starter, the python script was extracted from the main flow, and now lives in its own files at `PlantonScope/scripts/*`. We set up the auto formatting of the code by using [Black](https://github.com/psf/black). This make the code clearer and uniform. We are using the default settings, so if you just install Black and set your editor to format on save using it, you should be good to go. The code is separated in four main processes, each with a specific set of responsibilities: - The main process controls all the others, starts everything up and cleans up on shutdown - The stepper process manages the stepper movements. It's now possible to have simultaneous movements of both motors (this closes #38 ). - The imager process controls the camera and the streaming server via a state machine. - The segmenter process manages the segmentation and its outputs. The segmentation happens recursively in all folders in `/home/pi/PlanktonScope/img/`. Each folder has its own output archive, and bug #26 is now closed. Those processes communicates together using MQTT and json messages. Each message is adressed to one topic. The high level topic controls which process receives the message. The details of each topic is at the end of this commit message. Every imaging sessions has now its own folder, under the `img` root. Metadata are saved individually for every session, in a JSON file in the same directory as the pictures. The configuration is not parsed from `config.json` anymore and passed directly through MQTT messages to the concerned process. A new configuration file has been created: `hardware.json`. This file contains information related to your specific hardware configuration. You can choose to reverse the connection of the motors for example, but you can also define specific speed limits and steps number for your pump and focus stage. This will make it easier for people who wants to experiment with different kind of hardware. It's not necessary to have this file though. If it doesn't exists, the default configuration will be applied. The code is architectured around 6 modules and about 10 classes. I encourage you to have a look at the files, they're pretty straightforward to understand. There is a lot of work left around the node-red code refactoring, dashboard ui improvements, better and clearer LED messages, OLED screen integration and finer control of the segmentation process, but this is quite good for now. Here is the topic lists for MQTT and the corresponding messages. - actuator : This topic adresses the stepper control thread No publication under this topic should happen from the python process - actuator/pump : Control of the pump The message is a json object {"action":"move", "direction":"FORWARD", "volume":10, "flowrate":1} to move 10mL forward at 1mL/min action can be "move" or "stop" Receive only - actuator/focus : Control of the focus stage The message is a json object, speed is optional {"action":"move", "direction":"UP", "distance":0.26, "speed":1} to move up 10mm action can be "move" or "stop" Receive only - imager/image : This topic adresses the imaging thread Is a json object with {"action":"image","sleep":5,"volume":1,"nb_frame":200} sleep in seconds, volume in mL Can also receive a config update message: {"action":"config","config":[...]} Can also receive a camera settings message: {"action":"settings","iso":100,"shutter_speed":40} Receive only - segmenter/segment : This topic adresses the segmenter process Is a json object with {"action":"segment"} Receive only - status : This topics sends feedback to Node-Red No publication or receive at this level - status/pump : State of the pump Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/focus : State of the focus stage Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/imager : State of the imager Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Completed or 12_11_15_0.1.jpg has been imaged. Publish only - status/segmenter : Status of the segmentation - status/segmenter/name - status/segmenter/object_id - status/segmenter/metric Here is the original commit history: * Extract python main.py from flow * Fix bug in server addresses These addresses should be the loopback device instead of the network address of the device. Using the loopback address will not necessitate to update the script when the network address changes. * clean up picamera import * changes to main python and flow: update MQTT requests address to localhost (bugfix) update streaming output address to nothing update main flow to remove python script references and location * Automatically initialise imaging led on startup to off state. * Add the ability to invert outputs of the motor We added a key to config.json "hardware_config" with a subkey "stepper_reverse". If this key is present in the config file and set to 1, the output of the motors are inversed (stepper2 becomes the pump motor and stepper1 the focus motor) * move all non main script to a subfolder * add __init__.py to package * light module rewrite * json cleanup and absolute path for config file * light.py forgot to import subprocess #oups * Add command to turn the leds off * Auto formatting of main.py I've used Black with default settings, see https://github.com/psf/black * First commit of stepper.py Pump parameters still needs to be checked and tuned. * addition of hardware details in config.json * Introduce hardware.json to replace the `hardware_config` of config.json * stepper.py: calibration, typos * creates the MQTT_Client class * pump_max_speed is now in ml/min to help readability * forgot to add self to the class def * addition of threading capabilities to stepper.py (UNTESTED) * mqtt: fix topic bug * remove counter * mqtt add doc about topics * stepper.py creates an "actuator/*/state" topic * stepper.py: rename mqtt_client to pump_client * mqtt.py: add details about topics * stepper.py: rename pump_client to actuator_client * topic was not split properly and a part was lost * switch to f-strings for mqtt.py * cosmetic update * stepper.py: folder name will be planktoscope change calls * hardware.json became more straightforward * stepper.py syntax bugs * stepper.py addition of a received stop command * stepper.py: update to max travel distance * stepper.py: several typos here * rename folder * main.py: reword to reflect folder rename * main.py: remove logic that has been moved to stepper.py and mqtt.py * main.py: update to add mqtt imaging client * mqtt.py: make command and args local to class and output more verbose * make stepper.py a class * main.py: instantiate stepper class and call it * main.py: name mqtt client * update to main.json to reflect main.py changes * fix bugs around pump control * update flows to latest version from Thibault * distance can be a small value, and definitevely should be a float. * unify mqtt topics * unify mqtt output in the main flow * first logger implementation, uses loguru * mqtt: add reason to on_connect * mqtt: add on_disconnect handler * stepper: add more logger calls for debug mainly * main: add levels for logger * imager.py: first move of the imager logic * imager: time import cleanup * imager: morphocut import cleanup * imager: skimage import cleanup * imager: finishing import cleanup * imager: Class creation - WIP Also provides a fix for #26 (see line 190). * imager: threading is needed for Condition() * streamer: get the streamer server its own file * imager: creates start_camera and get the server creation out * imager: subclass multiprocessing.Process * imager: get Pipeline creation its own function * imager: cleanup of self calls * main: code removal and corresponding calls to newly created classes * imager: various formatting changes * main: management of signal shutdown * add requirements.txt * mqtt: messages are now json objects Also, addition of a flag on receiving a new message * mqtt: make message private and add logic to synchronise * stepper: creates the stepper class * stepper: use the new class * stepper: uses the new logic * stepper: add the shutdown event * stepper: add shutdown method * main: add shutdown event * imager: graceful shutdown * stepper: nicer way of checking the Eevnt * self is a required first argument for a method in a class Especially if you use said class private members! * python: various typos and small errors in import * stepper: create mqtt client during init * stepper: instanciate the mqtt client inside run Otherwise it's not accessible from inside the loop. It's a PITA, more information at https://stackoverflow.com/questions/17172878/using-pythons-multiprocessing-process-class * stepper: little bugs and typos all around * mqtt: add shutdown method * mqtt: add connect in init * stepper: fix bugs, sanitize inputs * stepper: work on delay prediction improvements * stepper: json is mean, double quote are mandatory inside * mqtt: add details about message exchanged * imager: first implementation of json messages * main.json: add new tab for RPi management + json for payloads * imager: add state_machine class * stepper: publish last will * imager: major refactor * main: make streaming server process a daemon * mqtt: insert debug statement on close * main: reorder imports * imager: make it work! Reinsert the streaming server logic in there, because there is a problem with the synchronisation part otherwise. Also, eventually, StreamingOuput() will have to be made not global Final very critical learning: it's super duper important to make sure the memory split is at least 256Meg for the GPU. Chaos ensues otherwise * main: changes to accomodate the streamer/imager fusino * imager_state_machine: insert states transition description * stepper: cleanup of code * segmenter: creation of the class * python: include segmenter changes * remove unused files * stepper: check existence of hardware.json * main.json: changes to reflect the python script evolution * remove unecessary TODOs and add some others * main: add check for config and directories * imager: update_config is implemented and we have better management of directories now * segmenter: now work recursively in all folders * flow: the configuration is now sent via mqtt * segmenter: better manage pipeline error * segmenter: declaration of archive_fn in init * imager: small bugs and typos * main: add uniqueID output * imager: add the camera settings message We can now update the ISO, shutter speed and resolution from Node-Red * package.json: update dependencies
2020-09-28 11:05:27 +02:00
{
Main.json: UI upgrade
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"id": "4248342d.e55fac",
update to main.json to fix camera bugs
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"type": "ui_group",
Main.json: UI upgrade
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"name": "Optic Characterization",
"tab": "181bb236.1e94be",
"order": 2,
update to main.json to fix camera bugs
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"disp": true,
Main.json: UI upgrade
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"width": 10,
update to main.json to fix camera bugs
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"collapse": false
},
{
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"id": "858a0e3c.987fe",
update to main.json to fix camera bugs
2020-09-15 17:33:49 +02:00
"type": "ui_group",
Main.json: UI upgrade
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"name": "Preview",
"tab": "c9194f02.9d5e9",
"order": 1,
update to main.json to fix camera bugs
2020-09-15 17:33:49 +02:00
"disp": true,
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"width": "14",
update to main.json to fix camera bugs
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"collapse": false
},
{
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"id": "64903b47.4034e4",
update to main.json to fix camera bugs
2020-09-15 17:33:49 +02:00
"type": "ui_group",
"z": "",
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"name": "Navigation",
"tab": "8d16beb8.9b3fb",
"order": 2,
"disp": false,
"width": "6",
update to main.json to fix camera bugs
2020-09-15 17:33:49 +02:00
"collapse": false
},
{
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"id": "3da7da8f.179606",
update to main.json to fix camera bugs
2020-09-15 17:33:49 +02:00
"type": "ui_group",
Main.json: UI upgrade
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"name": "Processor",
"tab": "d9cd733b.ab73d",
Extraction and refactor of the python code from node-red flow The rationale for this rewrite is to improve the readability, the modularity, the reliability and the future-proofing of the main python script. All in all, this is now 124 commits that are going to be squashed and merged together, spanning more than two weeks of development and testing. Please test away this release and break things. An upgrading guide will be published in the coming days, along with a new image for people to use if they don't want to upgrade on their own. Read along if you want to know all the goodies! As a starter, the python script was extracted from the main flow, and now lives in its own files at `PlantonScope/scripts/*`. We set up the auto formatting of the code by using [Black](https://github.com/psf/black). This make the code clearer and uniform. We are using the default settings, so if you just install Black and set your editor to format on save using it, you should be good to go. The code is separated in four main processes, each with a specific set of responsibilities: - The main process controls all the others, starts everything up and cleans up on shutdown - The stepper process manages the stepper movements. It's now possible to have simultaneous movements of both motors (this closes #38 ). - The imager process controls the camera and the streaming server via a state machine. - The segmenter process manages the segmentation and its outputs. The segmentation happens recursively in all folders in `/home/pi/PlanktonScope/img/`. Each folder has its own output archive, and bug #26 is now closed. Those processes communicates together using MQTT and json messages. Each message is adressed to one topic. The high level topic controls which process receives the message. The details of each topic is at the end of this commit message. Every imaging sessions has now its own folder, under the `img` root. Metadata are saved individually for every session, in a JSON file in the same directory as the pictures. The configuration is not parsed from `config.json` anymore and passed directly through MQTT messages to the concerned process. A new configuration file has been created: `hardware.json`. This file contains information related to your specific hardware configuration. You can choose to reverse the connection of the motors for example, but you can also define specific speed limits and steps number for your pump and focus stage. This will make it easier for people who wants to experiment with different kind of hardware. It's not necessary to have this file though. If it doesn't exists, the default configuration will be applied. The code is architectured around 6 modules and about 10 classes. I encourage you to have a look at the files, they're pretty straightforward to understand. There is a lot of work left around the node-red code refactoring, dashboard ui improvements, better and clearer LED messages, OLED screen integration and finer control of the segmentation process, but this is quite good for now. Here is the topic lists for MQTT and the corresponding messages. - actuator : This topic adresses the stepper control thread No publication under this topic should happen from the python process - actuator/pump : Control of the pump The message is a json object {"action":"move", "direction":"FORWARD", "volume":10, "flowrate":1} to move 10mL forward at 1mL/min action can be "move" or "stop" Receive only - actuator/focus : Control of the focus stage The message is a json object, speed is optional {"action":"move", "direction":"UP", "distance":0.26, "speed":1} to move up 10mm action can be "move" or "stop" Receive only - imager/image : This topic adresses the imaging thread Is a json object with {"action":"image","sleep":5,"volume":1,"nb_frame":200} sleep in seconds, volume in mL Can also receive a config update message: {"action":"config","config":[...]} Can also receive a camera settings message: {"action":"settings","iso":100,"shutter_speed":40} Receive only - segmenter/segment : This topic adresses the segmenter process Is a json object with {"action":"segment"} Receive only - status : This topics sends feedback to Node-Red No publication or receive at this level - status/pump : State of the pump Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/focus : State of the focus stage Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/imager : State of the imager Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Completed or 12_11_15_0.1.jpg has been imaged. Publish only - status/segmenter : Status of the segmentation - status/segmenter/name - status/segmenter/object_id - status/segmenter/metric Here is the original commit history: * Extract python main.py from flow * Fix bug in server addresses These addresses should be the loopback device instead of the network address of the device. Using the loopback address will not necessitate to update the script when the network address changes. * clean up picamera import * changes to main python and flow: update MQTT requests address to localhost (bugfix) update streaming output address to nothing update main flow to remove python script references and location * Automatically initialise imaging led on startup to off state. * Add the ability to invert outputs of the motor We added a key to config.json "hardware_config" with a subkey "stepper_reverse". If this key is present in the config file and set to 1, the output of the motors are inversed (stepper2 becomes the pump motor and stepper1 the focus motor) * move all non main script to a subfolder * add __init__.py to package * light module rewrite * json cleanup and absolute path for config file * light.py forgot to import subprocess #oups * Add command to turn the leds off * Auto formatting of main.py I've used Black with default settings, see https://github.com/psf/black * First commit of stepper.py Pump parameters still needs to be checked and tuned. * addition of hardware details in config.json * Introduce hardware.json to replace the `hardware_config` of config.json * stepper.py: calibration, typos * creates the MQTT_Client class * pump_max_speed is now in ml/min to help readability * forgot to add self to the class def * addition of threading capabilities to stepper.py (UNTESTED) * mqtt: fix topic bug * remove counter * mqtt add doc about topics * stepper.py creates an "actuator/*/state" topic * stepper.py: rename mqtt_client to pump_client * mqtt.py: add details about topics * stepper.py: rename pump_client to actuator_client * topic was not split properly and a part was lost * switch to f-strings for mqtt.py * cosmetic update * stepper.py: folder name will be planktoscope change calls * hardware.json became more straightforward * stepper.py syntax bugs * stepper.py addition of a received stop command * stepper.py: update to max travel distance * stepper.py: several typos here * rename folder * main.py: reword to reflect folder rename * main.py: remove logic that has been moved to stepper.py and mqtt.py * main.py: update to add mqtt imaging client * mqtt.py: make command and args local to class and output more verbose * make stepper.py a class * main.py: instantiate stepper class and call it * main.py: name mqtt client * update to main.json to reflect main.py changes * fix bugs around pump control * update flows to latest version from Thibault * distance can be a small value, and definitevely should be a float. * unify mqtt topics * unify mqtt output in the main flow * first logger implementation, uses loguru * mqtt: add reason to on_connect * mqtt: add on_disconnect handler * stepper: add more logger calls for debug mainly * main: add levels for logger * imager.py: first move of the imager logic * imager: time import cleanup * imager: morphocut import cleanup * imager: skimage import cleanup * imager: finishing import cleanup * imager: Class creation - WIP Also provides a fix for #26 (see line 190). * imager: threading is needed for Condition() * streamer: get the streamer server its own file * imager: creates start_camera and get the server creation out * imager: subclass multiprocessing.Process * imager: get Pipeline creation its own function * imager: cleanup of self calls * main: code removal and corresponding calls to newly created classes * imager: various formatting changes * main: management of signal shutdown * add requirements.txt * mqtt: messages are now json objects Also, addition of a flag on receiving a new message * mqtt: make message private and add logic to synchronise * stepper: creates the stepper class * stepper: use the new class * stepper: uses the new logic * stepper: add the shutdown event * stepper: add shutdown method * main: add shutdown event * imager: graceful shutdown * stepper: nicer way of checking the Eevnt * self is a required first argument for a method in a class Especially if you use said class private members! * python: various typos and small errors in import * stepper: create mqtt client during init * stepper: instanciate the mqtt client inside run Otherwise it's not accessible from inside the loop. It's a PITA, more information at https://stackoverflow.com/questions/17172878/using-pythons-multiprocessing-process-class * stepper: little bugs and typos all around * mqtt: add shutdown method * mqtt: add connect in init * stepper: fix bugs, sanitize inputs * stepper: work on delay prediction improvements * stepper: json is mean, double quote are mandatory inside * mqtt: add details about message exchanged * imager: first implementation of json messages * main.json: add new tab for RPi management + json for payloads * imager: add state_machine class * stepper: publish last will * imager: major refactor * main: make streaming server process a daemon * mqtt: insert debug statement on close * main: reorder imports * imager: make it work! Reinsert the streaming server logic in there, because there is a problem with the synchronisation part otherwise. Also, eventually, StreamingOuput() will have to be made not global Final very critical learning: it's super duper important to make sure the memory split is at least 256Meg for the GPU. Chaos ensues otherwise * main: changes to accomodate the streamer/imager fusino * imager_state_machine: insert states transition description * stepper: cleanup of code * segmenter: creation of the class * python: include segmenter changes * remove unused files * stepper: check existence of hardware.json * main.json: changes to reflect the python script evolution * remove unecessary TODOs and add some others * main: add check for config and directories * imager: update_config is implemented and we have better management of directories now * segmenter: now work recursively in all folders * flow: the configuration is now sent via mqtt * segmenter: better manage pipeline error * segmenter: declaration of archive_fn in init * imager: small bugs and typos * main: add uniqueID output * imager: add the camera settings message We can now update the ISO, shutter speed and resolution from Node-Red * package.json: update dependencies
2020-09-28 11:05:27 +02:00
"order": 1,
update to main.json to fix camera bugs
2020-09-15 17:33:49 +02:00
"disp": true,
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"width": "6",
update to main.json to fix camera bugs
2020-09-15 17:33:49 +02:00
"collapse": false
},
{
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"id": "cc8bc4eb.651868",
update to main.json to fix camera bugs
2020-09-15 17:33:49 +02:00
"type": "ui_base",
"theme": {
"name": "theme-dark",
"lightTheme": {
"default": "#0094CE",
Main.json: UI upgrade
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"baseColor": "#5900ce",
update to main.json to fix camera bugs
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"baseFont": "-apple-system,BlinkMacSystemFont,Segoe UI,Roboto,Oxygen-Sans,Ubuntu,Cantarell,Helvetica Neue,sans-serif",
Main.json: UI upgrade
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"edited": false,
update to main.json to fix camera bugs
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"reset": false
},
"darkTheme": {
"default": "#097479",
"baseColor": "#097479",
"baseFont": "-apple-system,BlinkMacSystemFont,Segoe UI,Roboto,Oxygen-Sans,Ubuntu,Cantarell,Helvetica Neue,sans-serif",
"edited": true,
"reset": false
},
"customTheme": {
"name": "Untitled Theme 1",
"default": "#4B7930",
"baseColor": "#4B7930",
"baseFont": "-apple-system,BlinkMacSystemFont,Segoe UI,Roboto,Oxygen-Sans,Ubuntu,Cantarell,Helvetica Neue,sans-serif"
},
"themeState": {
"base-color": {
"default": "#097479",
"value": "#097479",
Main.json: UI upgrade
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"edited": true
update to main.json to fix camera bugs
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},
"page-titlebar-backgroundColor": {
"value": "#097479",
"edited": false
},
"page-backgroundColor": {
"value": "#111111",
"edited": false
},
"page-sidebar-backgroundColor": {
"value": "#333333",
"edited": false
},
"group-textColor": {
"value": "#0eb8c0",
"edited": false
},
"group-borderColor": {
"value": "#555555",
"edited": false
},
"group-backgroundColor": {
"value": "#333333",
"edited": false
},
"widget-textColor": {
"value": "#eeeeee",
"edited": false
},
"widget-backgroundColor": {
"value": "#097479",
"edited": false
},
"widget-borderColor": {
"value": "#333333",
"edited": false
},
"base-font": {
"value": "-apple-system,BlinkMacSystemFont,Segoe UI,Roboto,Oxygen-Sans,Ubuntu,Cantarell,Helvetica Neue,sans-serif"
}
},
"angularTheme": {
"primary": "indigo",
"accents": "blue",
"warn": "red",
"background": "grey"
Update flows.json
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}
update to main.json to fix camera bugs
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},
"site": {
Main.json: UI upgrade
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"name": "Node-RED Dashboard",
update to main.json to fix camera bugs
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"hideToolbar": "false",
flow: remove ability to swipe between tabs and tooltip improvement
2020-10-19 10:14:05 +02:00
"allowSwipe": "false",
update to main.json to fix camera bugs
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"lockMenu": "false",
"allowTempTheme": "true",
"dateFormat": "DD/MM/YYYY",
"sizes": {
Main.json: UI upgrade
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"sx": 56,
"sy": 56,
"gx": 5,
"gy": 5,
"cx": 5,
"cy": 5,
"px": 5,
"py": 5
update to main.json to fix camera bugs
2020-09-15 17:33:49 +02:00
}
}
Update flows.json
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},
Extraction and refactor of the python code from node-red flow The rationale for this rewrite is to improve the readability, the modularity, the reliability and the future-proofing of the main python script. All in all, this is now 124 commits that are going to be squashed and merged together, spanning more than two weeks of development and testing. Please test away this release and break things. An upgrading guide will be published in the coming days, along with a new image for people to use if they don't want to upgrade on their own. Read along if you want to know all the goodies! As a starter, the python script was extracted from the main flow, and now lives in its own files at `PlantonScope/scripts/*`. We set up the auto formatting of the code by using [Black](https://github.com/psf/black). This make the code clearer and uniform. We are using the default settings, so if you just install Black and set your editor to format on save using it, you should be good to go. The code is separated in four main processes, each with a specific set of responsibilities: - The main process controls all the others, starts everything up and cleans up on shutdown - The stepper process manages the stepper movements. It's now possible to have simultaneous movements of both motors (this closes #38 ). - The imager process controls the camera and the streaming server via a state machine. - The segmenter process manages the segmentation and its outputs. The segmentation happens recursively in all folders in `/home/pi/PlanktonScope/img/`. Each folder has its own output archive, and bug #26 is now closed. Those processes communicates together using MQTT and json messages. Each message is adressed to one topic. The high level topic controls which process receives the message. The details of each topic is at the end of this commit message. Every imaging sessions has now its own folder, under the `img` root. Metadata are saved individually for every session, in a JSON file in the same directory as the pictures. The configuration is not parsed from `config.json` anymore and passed directly through MQTT messages to the concerned process. A new configuration file has been created: `hardware.json`. This file contains information related to your specific hardware configuration. You can choose to reverse the connection of the motors for example, but you can also define specific speed limits and steps number for your pump and focus stage. This will make it easier for people who wants to experiment with different kind of hardware. It's not necessary to have this file though. If it doesn't exists, the default configuration will be applied. The code is architectured around 6 modules and about 10 classes. I encourage you to have a look at the files, they're pretty straightforward to understand. There is a lot of work left around the node-red code refactoring, dashboard ui improvements, better and clearer LED messages, OLED screen integration and finer control of the segmentation process, but this is quite good for now. Here is the topic lists for MQTT and the corresponding messages. - actuator : This topic adresses the stepper control thread No publication under this topic should happen from the python process - actuator/pump : Control of the pump The message is a json object {"action":"move", "direction":"FORWARD", "volume":10, "flowrate":1} to move 10mL forward at 1mL/min action can be "move" or "stop" Receive only - actuator/focus : Control of the focus stage The message is a json object, speed is optional {"action":"move", "direction":"UP", "distance":0.26, "speed":1} to move up 10mm action can be "move" or "stop" Receive only - imager/image : This topic adresses the imaging thread Is a json object with {"action":"image","sleep":5,"volume":1,"nb_frame":200} sleep in seconds, volume in mL Can also receive a config update message: {"action":"config","config":[...]} Can also receive a camera settings message: {"action":"settings","iso":100,"shutter_speed":40} Receive only - segmenter/segment : This topic adresses the segmenter process Is a json object with {"action":"segment"} Receive only - status : This topics sends feedback to Node-Red No publication or receive at this level - status/pump : State of the pump Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/focus : State of the focus stage Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/imager : State of the imager Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Completed or 12_11_15_0.1.jpg has been imaged. Publish only - status/segmenter : Status of the segmentation - status/segmenter/name - status/segmenter/object_id - status/segmenter/metric Here is the original commit history: * Extract python main.py from flow * Fix bug in server addresses These addresses should be the loopback device instead of the network address of the device. Using the loopback address will not necessitate to update the script when the network address changes. * clean up picamera import * changes to main python and flow: update MQTT requests address to localhost (bugfix) update streaming output address to nothing update main flow to remove python script references and location * Automatically initialise imaging led on startup to off state. * Add the ability to invert outputs of the motor We added a key to config.json "hardware_config" with a subkey "stepper_reverse". If this key is present in the config file and set to 1, the output of the motors are inversed (stepper2 becomes the pump motor and stepper1 the focus motor) * move all non main script to a subfolder * add __init__.py to package * light module rewrite * json cleanup and absolute path for config file * light.py forgot to import subprocess #oups * Add command to turn the leds off * Auto formatting of main.py I've used Black with default settings, see https://github.com/psf/black * First commit of stepper.py Pump parameters still needs to be checked and tuned. * addition of hardware details in config.json * Introduce hardware.json to replace the `hardware_config` of config.json * stepper.py: calibration, typos * creates the MQTT_Client class * pump_max_speed is now in ml/min to help readability * forgot to add self to the class def * addition of threading capabilities to stepper.py (UNTESTED) * mqtt: fix topic bug * remove counter * mqtt add doc about topics * stepper.py creates an "actuator/*/state" topic * stepper.py: rename mqtt_client to pump_client * mqtt.py: add details about topics * stepper.py: rename pump_client to actuator_client * topic was not split properly and a part was lost * switch to f-strings for mqtt.py * cosmetic update * stepper.py: folder name will be planktoscope change calls * hardware.json became more straightforward * stepper.py syntax bugs * stepper.py addition of a received stop command * stepper.py: update to max travel distance * stepper.py: several typos here * rename folder * main.py: reword to reflect folder rename * main.py: remove logic that has been moved to stepper.py and mqtt.py * main.py: update to add mqtt imaging client * mqtt.py: make command and args local to class and output more verbose * make stepper.py a class * main.py: instantiate stepper class and call it * main.py: name mqtt client * update to main.json to reflect main.py changes * fix bugs around pump control * update flows to latest version from Thibault * distance can be a small value, and definitevely should be a float. * unify mqtt topics * unify mqtt output in the main flow * first logger implementation, uses loguru * mqtt: add reason to on_connect * mqtt: add on_disconnect handler * stepper: add more logger calls for debug mainly * main: add levels for logger * imager.py: first move of the imager logic * imager: time import cleanup * imager: morphocut import cleanup * imager: skimage import cleanup * imager: finishing import cleanup * imager: Class creation - WIP Also provides a fix for #26 (see line 190). * imager: threading is needed for Condition() * streamer: get the streamer server its own file * imager: creates start_camera and get the server creation out * imager: subclass multiprocessing.Process * imager: get Pipeline creation its own function * imager: cleanup of self calls * main: code removal and corresponding calls to newly created classes * imager: various formatting changes * main: management of signal shutdown * add requirements.txt * mqtt: messages are now json objects Also, addition of a flag on receiving a new message * mqtt: make message private and add logic to synchronise * stepper: creates the stepper class * stepper: use the new class * stepper: uses the new logic * stepper: add the shutdown event * stepper: add shutdown method * main: add shutdown event * imager: graceful shutdown * stepper: nicer way of checking the Eevnt * self is a required first argument for a method in a class Especially if you use said class private members! * python: various typos and small errors in import * stepper: create mqtt client during init * stepper: instanciate the mqtt client inside run Otherwise it's not accessible from inside the loop. It's a PITA, more information at https://stackoverflow.com/questions/17172878/using-pythons-multiprocessing-process-class * stepper: little bugs and typos all around * mqtt: add shutdown method * mqtt: add connect in init * stepper: fix bugs, sanitize inputs * stepper: work on delay prediction improvements * stepper: json is mean, double quote are mandatory inside * mqtt: add details about message exchanged * imager: first implementation of json messages * main.json: add new tab for RPi management + json for payloads * imager: add state_machine class * stepper: publish last will * imager: major refactor * main: make streaming server process a daemon * mqtt: insert debug statement on close * main: reorder imports * imager: make it work! Reinsert the streaming server logic in there, because there is a problem with the synchronisation part otherwise. Also, eventually, StreamingOuput() will have to be made not global Final very critical learning: it's super duper important to make sure the memory split is at least 256Meg for the GPU. Chaos ensues otherwise * main: changes to accomodate the streamer/imager fusino * imager_state_machine: insert states transition description * stepper: cleanup of code * segmenter: creation of the class * python: include segmenter changes * remove unused files * stepper: check existence of hardware.json * main.json: changes to reflect the python script evolution * remove unecessary TODOs and add some others * main: add check for config and directories * imager: update_config is implemented and we have better management of directories now * segmenter: now work recursively in all folders * flow: the configuration is now sent via mqtt * segmenter: better manage pipeline error * segmenter: declaration of archive_fn in init * imager: small bugs and typos * main: add uniqueID output * imager: add the camera settings message We can now update the ISO, shutter speed and resolution from Node-Red * package.json: update dependencies
2020-09-28 11:05:27 +02:00
{
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"id": "36739a35.7cce36",
Extraction and refactor of the python code from node-red flow The rationale for this rewrite is to improve the readability, the modularity, the reliability and the future-proofing of the main python script. All in all, this is now 124 commits that are going to be squashed and merged together, spanning more than two weeks of development and testing. Please test away this release and break things. An upgrading guide will be published in the coming days, along with a new image for people to use if they don't want to upgrade on their own. Read along if you want to know all the goodies! As a starter, the python script was extracted from the main flow, and now lives in its own files at `PlantonScope/scripts/*`. We set up the auto formatting of the code by using [Black](https://github.com/psf/black). This make the code clearer and uniform. We are using the default settings, so if you just install Black and set your editor to format on save using it, you should be good to go. The code is separated in four main processes, each with a specific set of responsibilities: - The main process controls all the others, starts everything up and cleans up on shutdown - The stepper process manages the stepper movements. It's now possible to have simultaneous movements of both motors (this closes #38 ). - The imager process controls the camera and the streaming server via a state machine. - The segmenter process manages the segmentation and its outputs. The segmentation happens recursively in all folders in `/home/pi/PlanktonScope/img/`. Each folder has its own output archive, and bug #26 is now closed. Those processes communicates together using MQTT and json messages. Each message is adressed to one topic. The high level topic controls which process receives the message. The details of each topic is at the end of this commit message. Every imaging sessions has now its own folder, under the `img` root. Metadata are saved individually for every session, in a JSON file in the same directory as the pictures. The configuration is not parsed from `config.json` anymore and passed directly through MQTT messages to the concerned process. A new configuration file has been created: `hardware.json`. This file contains information related to your specific hardware configuration. You can choose to reverse the connection of the motors for example, but you can also define specific speed limits and steps number for your pump and focus stage. This will make it easier for people who wants to experiment with different kind of hardware. It's not necessary to have this file though. If it doesn't exists, the default configuration will be applied. The code is architectured around 6 modules and about 10 classes. I encourage you to have a look at the files, they're pretty straightforward to understand. There is a lot of work left around the node-red code refactoring, dashboard ui improvements, better and clearer LED messages, OLED screen integration and finer control of the segmentation process, but this is quite good for now. Here is the topic lists for MQTT and the corresponding messages. - actuator : This topic adresses the stepper control thread No publication under this topic should happen from the python process - actuator/pump : Control of the pump The message is a json object {"action":"move", "direction":"FORWARD", "volume":10, "flowrate":1} to move 10mL forward at 1mL/min action can be "move" or "stop" Receive only - actuator/focus : Control of the focus stage The message is a json object, speed is optional {"action":"move", "direction":"UP", "distance":0.26, "speed":1} to move up 10mm action can be "move" or "stop" Receive only - imager/image : This topic adresses the imaging thread Is a json object with {"action":"image","sleep":5,"volume":1,"nb_frame":200} sleep in seconds, volume in mL Can also receive a config update message: {"action":"config","config":[...]} Can also receive a camera settings message: {"action":"settings","iso":100,"shutter_speed":40} Receive only - segmenter/segment : This topic adresses the segmenter process Is a json object with {"action":"segment"} Receive only - status : This topics sends feedback to Node-Red No publication or receive at this level - status/pump : State of the pump Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/focus : State of the focus stage Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/imager : State of the imager Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Completed or 12_11_15_0.1.jpg has been imaged. Publish only - status/segmenter : Status of the segmentation - status/segmenter/name - status/segmenter/object_id - status/segmenter/metric Here is the original commit history: * Extract python main.py from flow * Fix bug in server addresses These addresses should be the loopback device instead of the network address of the device. Using the loopback address will not necessitate to update the script when the network address changes. * clean up picamera import * changes to main python and flow: update MQTT requests address to localhost (bugfix) update streaming output address to nothing update main flow to remove python script references and location * Automatically initialise imaging led on startup to off state. * Add the ability to invert outputs of the motor We added a key to config.json "hardware_config" with a subkey "stepper_reverse". If this key is present in the config file and set to 1, the output of the motors are inversed (stepper2 becomes the pump motor and stepper1 the focus motor) * move all non main script to a subfolder * add __init__.py to package * light module rewrite * json cleanup and absolute path for config file * light.py forgot to import subprocess #oups * Add command to turn the leds off * Auto formatting of main.py I've used Black with default settings, see https://github.com/psf/black * First commit of stepper.py Pump parameters still needs to be checked and tuned. * addition of hardware details in config.json * Introduce hardware.json to replace the `hardware_config` of config.json * stepper.py: calibration, typos * creates the MQTT_Client class * pump_max_speed is now in ml/min to help readability * forgot to add self to the class def * addition of threading capabilities to stepper.py (UNTESTED) * mqtt: fix topic bug * remove counter * mqtt add doc about topics * stepper.py creates an "actuator/*/state" topic * stepper.py: rename mqtt_client to pump_client * mqtt.py: add details about topics * stepper.py: rename pump_client to actuator_client * topic was not split properly and a part was lost * switch to f-strings for mqtt.py * cosmetic update * stepper.py: folder name will be planktoscope change calls * hardware.json became more straightforward * stepper.py syntax bugs * stepper.py addition of a received stop command * stepper.py: update to max travel distance * stepper.py: several typos here * rename folder * main.py: reword to reflect folder rename * main.py: remove logic that has been moved to stepper.py and mqtt.py * main.py: update to add mqtt imaging client * mqtt.py: make command and args local to class and output more verbose * make stepper.py a class * main.py: instantiate stepper class and call it * main.py: name mqtt client * update to main.json to reflect main.py changes * fix bugs around pump control * update flows to latest version from Thibault * distance can be a small value, and definitevely should be a float. * unify mqtt topics * unify mqtt output in the main flow * first logger implementation, uses loguru * mqtt: add reason to on_connect * mqtt: add on_disconnect handler * stepper: add more logger calls for debug mainly * main: add levels for logger * imager.py: first move of the imager logic * imager: time import cleanup * imager: morphocut import cleanup * imager: skimage import cleanup * imager: finishing import cleanup * imager: Class creation - WIP Also provides a fix for #26 (see line 190). * imager: threading is needed for Condition() * streamer: get the streamer server its own file * imager: creates start_camera and get the server creation out * imager: subclass multiprocessing.Process * imager: get Pipeline creation its own function * imager: cleanup of self calls * main: code removal and corresponding calls to newly created classes * imager: various formatting changes * main: management of signal shutdown * add requirements.txt * mqtt: messages are now json objects Also, addition of a flag on receiving a new message * mqtt: make message private and add logic to synchronise * stepper: creates the stepper class * stepper: use the new class * stepper: uses the new logic * stepper: add the shutdown event * stepper: add shutdown method * main: add shutdown event * imager: graceful shutdown * stepper: nicer way of checking the Eevnt * self is a required first argument for a method in a class Especially if you use said class private members! * python: various typos and small errors in import * stepper: create mqtt client during init * stepper: instanciate the mqtt client inside run Otherwise it's not accessible from inside the loop. It's a PITA, more information at https://stackoverflow.com/questions/17172878/using-pythons-multiprocessing-process-class * stepper: little bugs and typos all around * mqtt: add shutdown method * mqtt: add connect in init * stepper: fix bugs, sanitize inputs * stepper: work on delay prediction improvements * stepper: json is mean, double quote are mandatory inside * mqtt: add details about message exchanged * imager: first implementation of json messages * main.json: add new tab for RPi management + json for payloads * imager: add state_machine class * stepper: publish last will * imager: major refactor * main: make streaming server process a daemon * mqtt: insert debug statement on close * main: reorder imports * imager: make it work! Reinsert the streaming server logic in there, because there is a problem with the synchronisation part otherwise. Also, eventually, StreamingOuput() will have to be made not global Final very critical learning: it's super duper important to make sure the memory split is at least 256Meg for the GPU. Chaos ensues otherwise * main: changes to accomodate the streamer/imager fusino * imager_state_machine: insert states transition description * stepper: cleanup of code * segmenter: creation of the class * python: include segmenter changes * remove unused files * stepper: check existence of hardware.json * main.json: changes to reflect the python script evolution * remove unecessary TODOs and add some others * main: add check for config and directories * imager: update_config is implemented and we have better management of directories now * segmenter: now work recursively in all folders * flow: the configuration is now sent via mqtt * segmenter: better manage pipeline error * segmenter: declaration of archive_fn in init * imager: small bugs and typos * main: add uniqueID output * imager: add the camera settings message We can now update the ISO, shutter speed and resolution from Node-Red * package.json: update dependencies
2020-09-28 11:05:27 +02:00
"type": "ui_tab",
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"name": "Gallery",
"icon": "fa fa-file-image-o",
"order": 6,
Extraction and refactor of the python code from node-red flow The rationale for this rewrite is to improve the readability, the modularity, the reliability and the future-proofing of the main python script. All in all, this is now 124 commits that are going to be squashed and merged together, spanning more than two weeks of development and testing. Please test away this release and break things. An upgrading guide will be published in the coming days, along with a new image for people to use if they don't want to upgrade on their own. Read along if you want to know all the goodies! As a starter, the python script was extracted from the main flow, and now lives in its own files at `PlantonScope/scripts/*`. We set up the auto formatting of the code by using [Black](https://github.com/psf/black). This make the code clearer and uniform. We are using the default settings, so if you just install Black and set your editor to format on save using it, you should be good to go. The code is separated in four main processes, each with a specific set of responsibilities: - The main process controls all the others, starts everything up and cleans up on shutdown - The stepper process manages the stepper movements. It's now possible to have simultaneous movements of both motors (this closes #38 ). - The imager process controls the camera and the streaming server via a state machine. - The segmenter process manages the segmentation and its outputs. The segmentation happens recursively in all folders in `/home/pi/PlanktonScope/img/`. Each folder has its own output archive, and bug #26 is now closed. Those processes communicates together using MQTT and json messages. Each message is adressed to one topic. The high level topic controls which process receives the message. The details of each topic is at the end of this commit message. Every imaging sessions has now its own folder, under the `img` root. Metadata are saved individually for every session, in a JSON file in the same directory as the pictures. The configuration is not parsed from `config.json` anymore and passed directly through MQTT messages to the concerned process. A new configuration file has been created: `hardware.json`. This file contains information related to your specific hardware configuration. You can choose to reverse the connection of the motors for example, but you can also define specific speed limits and steps number for your pump and focus stage. This will make it easier for people who wants to experiment with different kind of hardware. It's not necessary to have this file though. If it doesn't exists, the default configuration will be applied. The code is architectured around 6 modules and about 10 classes. I encourage you to have a look at the files, they're pretty straightforward to understand. There is a lot of work left around the node-red code refactoring, dashboard ui improvements, better and clearer LED messages, OLED screen integration and finer control of the segmentation process, but this is quite good for now. Here is the topic lists for MQTT and the corresponding messages. - actuator : This topic adresses the stepper control thread No publication under this topic should happen from the python process - actuator/pump : Control of the pump The message is a json object {"action":"move", "direction":"FORWARD", "volume":10, "flowrate":1} to move 10mL forward at 1mL/min action can be "move" or "stop" Receive only - actuator/focus : Control of the focus stage The message is a json object, speed is optional {"action":"move", "direction":"UP", "distance":0.26, "speed":1} to move up 10mm action can be "move" or "stop" Receive only - imager/image : This topic adresses the imaging thread Is a json object with {"action":"image","sleep":5,"volume":1,"nb_frame":200} sleep in seconds, volume in mL Can also receive a config update message: {"action":"config","config":[...]} Can also receive a camera settings message: {"action":"settings","iso":100,"shutter_speed":40} Receive only - segmenter/segment : This topic adresses the segmenter process Is a json object with {"action":"segment"} Receive only - status : This topics sends feedback to Node-Red No publication or receive at this level - status/pump : State of the pump Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/focus : State of the focus stage Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/imager : State of the imager Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Completed or 12_11_15_0.1.jpg has been imaged. Publish only - status/segmenter : Status of the segmentation - status/segmenter/name - status/segmenter/object_id - status/segmenter/metric Here is the original commit history: * Extract python main.py from flow * Fix bug in server addresses These addresses should be the loopback device instead of the network address of the device. Using the loopback address will not necessitate to update the script when the network address changes. * clean up picamera import * changes to main python and flow: update MQTT requests address to localhost (bugfix) update streaming output address to nothing update main flow to remove python script references and location * Automatically initialise imaging led on startup to off state. * Add the ability to invert outputs of the motor We added a key to config.json "hardware_config" with a subkey "stepper_reverse". If this key is present in the config file and set to 1, the output of the motors are inversed (stepper2 becomes the pump motor and stepper1 the focus motor) * move all non main script to a subfolder * add __init__.py to package * light module rewrite * json cleanup and absolute path for config file * light.py forgot to import subprocess #oups * Add command to turn the leds off * Auto formatting of main.py I've used Black with default settings, see https://github.com/psf/black * First commit of stepper.py Pump parameters still needs to be checked and tuned. * addition of hardware details in config.json * Introduce hardware.json to replace the `hardware_config` of config.json * stepper.py: calibration, typos * creates the MQTT_Client class * pump_max_speed is now in ml/min to help readability * forgot to add self to the class def * addition of threading capabilities to stepper.py (UNTESTED) * mqtt: fix topic bug * remove counter * mqtt add doc about topics * stepper.py creates an "actuator/*/state" topic * stepper.py: rename mqtt_client to pump_client * mqtt.py: add details about topics * stepper.py: rename pump_client to actuator_client * topic was not split properly and a part was lost * switch to f-strings for mqtt.py * cosmetic update * stepper.py: folder name will be planktoscope change calls * hardware.json became more straightforward * stepper.py syntax bugs * stepper.py addition of a received stop command * stepper.py: update to max travel distance * stepper.py: several typos here * rename folder * main.py: reword to reflect folder rename * main.py: remove logic that has been moved to stepper.py and mqtt.py * main.py: update to add mqtt imaging client * mqtt.py: make command and args local to class and output more verbose * make stepper.py a class * main.py: instantiate stepper class and call it * main.py: name mqtt client * update to main.json to reflect main.py changes * fix bugs around pump control * update flows to latest version from Thibault * distance can be a small value, and definitevely should be a float. * unify mqtt topics * unify mqtt output in the main flow * first logger implementation, uses loguru * mqtt: add reason to on_connect * mqtt: add on_disconnect handler * stepper: add more logger calls for debug mainly * main: add levels for logger * imager.py: first move of the imager logic * imager: time import cleanup * imager: morphocut import cleanup * imager: skimage import cleanup * imager: finishing import cleanup * imager: Class creation - WIP Also provides a fix for #26 (see line 190). * imager: threading is needed for Condition() * streamer: get the streamer server its own file * imager: creates start_camera and get the server creation out * imager: subclass multiprocessing.Process * imager: get Pipeline creation its own function * imager: cleanup of self calls * main: code removal and corresponding calls to newly created classes * imager: various formatting changes * main: management of signal shutdown * add requirements.txt * mqtt: messages are now json objects Also, addition of a flag on receiving a new message * mqtt: make message private and add logic to synchronise * stepper: creates the stepper class * stepper: use the new class * stepper: uses the new logic * stepper: add the shutdown event * stepper: add shutdown method * main: add shutdown event * imager: graceful shutdown * stepper: nicer way of checking the Eevnt * self is a required first argument for a method in a class Especially if you use said class private members! * python: various typos and small errors in import * stepper: create mqtt client during init * stepper: instanciate the mqtt client inside run Otherwise it's not accessible from inside the loop. It's a PITA, more information at https://stackoverflow.com/questions/17172878/using-pythons-multiprocessing-process-class * stepper: little bugs and typos all around * mqtt: add shutdown method * mqtt: add connect in init * stepper: fix bugs, sanitize inputs * stepper: work on delay prediction improvements * stepper: json is mean, double quote are mandatory inside * mqtt: add details about message exchanged * imager: first implementation of json messages * main.json: add new tab for RPi management + json for payloads * imager: add state_machine class * stepper: publish last will * imager: major refactor * main: make streaming server process a daemon * mqtt: insert debug statement on close * main: reorder imports * imager: make it work! Reinsert the streaming server logic in there, because there is a problem with the synchronisation part otherwise. Also, eventually, StreamingOuput() will have to be made not global Final very critical learning: it's super duper important to make sure the memory split is at least 256Meg for the GPU. Chaos ensues otherwise * main: changes to accomodate the streamer/imager fusino * imager_state_machine: insert states transition description * stepper: cleanup of code * segmenter: creation of the class * python: include segmenter changes * remove unused files * stepper: check existence of hardware.json * main.json: changes to reflect the python script evolution * remove unecessary TODOs and add some others * main: add check for config and directories * imager: update_config is implemented and we have better management of directories now * segmenter: now work recursively in all folders * flow: the configuration is now sent via mqtt * segmenter: better manage pipeline error * segmenter: declaration of archive_fn in init * imager: small bugs and typos * main: add uniqueID output * imager: add the camera settings message We can now update the ISO, shutter speed and resolution from Node-Red * package.json: update dependencies
2020-09-28 11:05:27 +02:00
"disabled": false,
"hidden": false
},
{
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"id": "c0ebfc57.42527",
Extraction and refactor of the python code from node-red flow The rationale for this rewrite is to improve the readability, the modularity, the reliability and the future-proofing of the main python script. All in all, this is now 124 commits that are going to be squashed and merged together, spanning more than two weeks of development and testing. Please test away this release and break things. An upgrading guide will be published in the coming days, along with a new image for people to use if they don't want to upgrade on their own. Read along if you want to know all the goodies! As a starter, the python script was extracted from the main flow, and now lives in its own files at `PlantonScope/scripts/*`. We set up the auto formatting of the code by using [Black](https://github.com/psf/black). This make the code clearer and uniform. We are using the default settings, so if you just install Black and set your editor to format on save using it, you should be good to go. The code is separated in four main processes, each with a specific set of responsibilities: - The main process controls all the others, starts everything up and cleans up on shutdown - The stepper process manages the stepper movements. It's now possible to have simultaneous movements of both motors (this closes #38 ). - The imager process controls the camera and the streaming server via a state machine. - The segmenter process manages the segmentation and its outputs. The segmentation happens recursively in all folders in `/home/pi/PlanktonScope/img/`. Each folder has its own output archive, and bug #26 is now closed. Those processes communicates together using MQTT and json messages. Each message is adressed to one topic. The high level topic controls which process receives the message. The details of each topic is at the end of this commit message. Every imaging sessions has now its own folder, under the `img` root. Metadata are saved individually for every session, in a JSON file in the same directory as the pictures. The configuration is not parsed from `config.json` anymore and passed directly through MQTT messages to the concerned process. A new configuration file has been created: `hardware.json`. This file contains information related to your specific hardware configuration. You can choose to reverse the connection of the motors for example, but you can also define specific speed limits and steps number for your pump and focus stage. This will make it easier for people who wants to experiment with different kind of hardware. It's not necessary to have this file though. If it doesn't exists, the default configuration will be applied. The code is architectured around 6 modules and about 10 classes. I encourage you to have a look at the files, they're pretty straightforward to understand. There is a lot of work left around the node-red code refactoring, dashboard ui improvements, better and clearer LED messages, OLED screen integration and finer control of the segmentation process, but this is quite good for now. Here is the topic lists for MQTT and the corresponding messages. - actuator : This topic adresses the stepper control thread No publication under this topic should happen from the python process - actuator/pump : Control of the pump The message is a json object {"action":"move", "direction":"FORWARD", "volume":10, "flowrate":1} to move 10mL forward at 1mL/min action can be "move" or "stop" Receive only - actuator/focus : Control of the focus stage The message is a json object, speed is optional {"action":"move", "direction":"UP", "distance":0.26, "speed":1} to move up 10mm action can be "move" or "stop" Receive only - imager/image : This topic adresses the imaging thread Is a json object with {"action":"image","sleep":5,"volume":1,"nb_frame":200} sleep in seconds, volume in mL Can also receive a config update message: {"action":"config","config":[...]} Can also receive a camera settings message: {"action":"settings","iso":100,"shutter_speed":40} Receive only - segmenter/segment : This topic adresses the segmenter process Is a json object with {"action":"segment"} Receive only - status : This topics sends feedback to Node-Red No publication or receive at this level - status/pump : State of the pump Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/focus : State of the focus stage Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/imager : State of the imager Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Completed or 12_11_15_0.1.jpg has been imaged. Publish only - status/segmenter : Status of the segmentation - status/segmenter/name - status/segmenter/object_id - status/segmenter/metric Here is the original commit history: * Extract python main.py from flow * Fix bug in server addresses These addresses should be the loopback device instead of the network address of the device. Using the loopback address will not necessitate to update the script when the network address changes. * clean up picamera import * changes to main python and flow: update MQTT requests address to localhost (bugfix) update streaming output address to nothing update main flow to remove python script references and location * Automatically initialise imaging led on startup to off state. * Add the ability to invert outputs of the motor We added a key to config.json "hardware_config" with a subkey "stepper_reverse". If this key is present in the config file and set to 1, the output of the motors are inversed (stepper2 becomes the pump motor and stepper1 the focus motor) * move all non main script to a subfolder * add __init__.py to package * light module rewrite * json cleanup and absolute path for config file * light.py forgot to import subprocess #oups * Add command to turn the leds off * Auto formatting of main.py I've used Black with default settings, see https://github.com/psf/black * First commit of stepper.py Pump parameters still needs to be checked and tuned. * addition of hardware details in config.json * Introduce hardware.json to replace the `hardware_config` of config.json * stepper.py: calibration, typos * creates the MQTT_Client class * pump_max_speed is now in ml/min to help readability * forgot to add self to the class def * addition of threading capabilities to stepper.py (UNTESTED) * mqtt: fix topic bug * remove counter * mqtt add doc about topics * stepper.py creates an "actuator/*/state" topic * stepper.py: rename mqtt_client to pump_client * mqtt.py: add details about topics * stepper.py: rename pump_client to actuator_client * topic was not split properly and a part was lost * switch to f-strings for mqtt.py * cosmetic update * stepper.py: folder name will be planktoscope change calls * hardware.json became more straightforward * stepper.py syntax bugs * stepper.py addition of a received stop command * stepper.py: update to max travel distance * stepper.py: several typos here * rename folder * main.py: reword to reflect folder rename * main.py: remove logic that has been moved to stepper.py and mqtt.py * main.py: update to add mqtt imaging client * mqtt.py: make command and args local to class and output more verbose * make stepper.py a class * main.py: instantiate stepper class and call it * main.py: name mqtt client * update to main.json to reflect main.py changes * fix bugs around pump control * update flows to latest version from Thibault * distance can be a small value, and definitevely should be a float. * unify mqtt topics * unify mqtt output in the main flow * first logger implementation, uses loguru * mqtt: add reason to on_connect * mqtt: add on_disconnect handler * stepper: add more logger calls for debug mainly * main: add levels for logger * imager.py: first move of the imager logic * imager: time import cleanup * imager: morphocut import cleanup * imager: skimage import cleanup * imager: finishing import cleanup * imager: Class creation - WIP Also provides a fix for #26 (see line 190). * imager: threading is needed for Condition() * streamer: get the streamer server its own file * imager: creates start_camera and get the server creation out * imager: subclass multiprocessing.Process * imager: get Pipeline creation its own function * imager: cleanup of self calls * main: code removal and corresponding calls to newly created classes * imager: various formatting changes * main: management of signal shutdown * add requirements.txt * mqtt: messages are now json objects Also, addition of a flag on receiving a new message * mqtt: make message private and add logic to synchronise * stepper: creates the stepper class * stepper: use the new class * stepper: uses the new logic * stepper: add the shutdown event * stepper: add shutdown method * main: add shutdown event * imager: graceful shutdown * stepper: nicer way of checking the Eevnt * self is a required first argument for a method in a class Especially if you use said class private members! * python: various typos and small errors in import * stepper: create mqtt client during init * stepper: instanciate the mqtt client inside run Otherwise it's not accessible from inside the loop. It's a PITA, more information at https://stackoverflow.com/questions/17172878/using-pythons-multiprocessing-process-class * stepper: little bugs and typos all around * mqtt: add shutdown method * mqtt: add connect in init * stepper: fix bugs, sanitize inputs * stepper: work on delay prediction improvements * stepper: json is mean, double quote are mandatory inside * mqtt: add details about message exchanged * imager: first implementation of json messages * main.json: add new tab for RPi management + json for payloads * imager: add state_machine class * stepper: publish last will * imager: major refactor * main: make streaming server process a daemon * mqtt: insert debug statement on close * main: reorder imports * imager: make it work! Reinsert the streaming server logic in there, because there is a problem with the synchronisation part otherwise. Also, eventually, StreamingOuput() will have to be made not global Final very critical learning: it's super duper important to make sure the memory split is at least 256Meg for the GPU. Chaos ensues otherwise * main: changes to accomodate the streamer/imager fusino * imager_state_machine: insert states transition description * stepper: cleanup of code * segmenter: creation of the class * python: include segmenter changes * remove unused files * stepper: check existence of hardware.json * main.json: changes to reflect the python script evolution * remove unecessary TODOs and add some others * main: add check for config and directories * imager: update_config is implemented and we have better management of directories now * segmenter: now work recursively in all folders * flow: the configuration is now sent via mqtt * segmenter: better manage pipeline error * segmenter: declaration of archive_fn in init * imager: small bugs and typos * main: add uniqueID output * imager: add the camera settings message We can now update the ISO, shutter speed and resolution from Node-Red * package.json: update dependencies
2020-09-28 11:05:27 +02:00
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Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
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Extraction and refactor of the python code from node-red flow The rationale for this rewrite is to improve the readability, the modularity, the reliability and the future-proofing of the main python script. All in all, this is now 124 commits that are going to be squashed and merged together, spanning more than two weeks of development and testing. Please test away this release and break things. An upgrading guide will be published in the coming days, along with a new image for people to use if they don't want to upgrade on their own. Read along if you want to know all the goodies! As a starter, the python script was extracted from the main flow, and now lives in its own files at `PlantonScope/scripts/*`. We set up the auto formatting of the code by using [Black](https://github.com/psf/black). This make the code clearer and uniform. We are using the default settings, so if you just install Black and set your editor to format on save using it, you should be good to go. The code is separated in four main processes, each with a specific set of responsibilities: - The main process controls all the others, starts everything up and cleans up on shutdown - The stepper process manages the stepper movements. It's now possible to have simultaneous movements of both motors (this closes #38 ). - The imager process controls the camera and the streaming server via a state machine. - The segmenter process manages the segmentation and its outputs. The segmentation happens recursively in all folders in `/home/pi/PlanktonScope/img/`. Each folder has its own output archive, and bug #26 is now closed. Those processes communicates together using MQTT and json messages. Each message is adressed to one topic. The high level topic controls which process receives the message. The details of each topic is at the end of this commit message. Every imaging sessions has now its own folder, under the `img` root. Metadata are saved individually for every session, in a JSON file in the same directory as the pictures. The configuration is not parsed from `config.json` anymore and passed directly through MQTT messages to the concerned process. A new configuration file has been created: `hardware.json`. This file contains information related to your specific hardware configuration. You can choose to reverse the connection of the motors for example, but you can also define specific speed limits and steps number for your pump and focus stage. This will make it easier for people who wants to experiment with different kind of hardware. It's not necessary to have this file though. If it doesn't exists, the default configuration will be applied. The code is architectured around 6 modules and about 10 classes. I encourage you to have a look at the files, they're pretty straightforward to understand. There is a lot of work left around the node-red code refactoring, dashboard ui improvements, better and clearer LED messages, OLED screen integration and finer control of the segmentation process, but this is quite good for now. Here is the topic lists for MQTT and the corresponding messages. - actuator : This topic adresses the stepper control thread No publication under this topic should happen from the python process - actuator/pump : Control of the pump The message is a json object {"action":"move", "direction":"FORWARD", "volume":10, "flowrate":1} to move 10mL forward at 1mL/min action can be "move" or "stop" Receive only - actuator/focus : Control of the focus stage The message is a json object, speed is optional {"action":"move", "direction":"UP", "distance":0.26, "speed":1} to move up 10mm action can be "move" or "stop" Receive only - imager/image : This topic adresses the imaging thread Is a json object with {"action":"image","sleep":5,"volume":1,"nb_frame":200} sleep in seconds, volume in mL Can also receive a config update message: {"action":"config","config":[...]} Can also receive a camera settings message: {"action":"settings","iso":100,"shutter_speed":40} Receive only - segmenter/segment : This topic adresses the segmenter process Is a json object with {"action":"segment"} Receive only - status : This topics sends feedback to Node-Red No publication or receive at this level - status/pump : State of the pump Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/focus : State of the focus stage Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/imager : State of the imager Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Completed or 12_11_15_0.1.jpg has been imaged. Publish only - status/segmenter : Status of the segmentation - status/segmenter/name - status/segmenter/object_id - status/segmenter/metric Here is the original commit history: * Extract python main.py from flow * Fix bug in server addresses These addresses should be the loopback device instead of the network address of the device. Using the loopback address will not necessitate to update the script when the network address changes. * clean up picamera import * changes to main python and flow: update MQTT requests address to localhost (bugfix) update streaming output address to nothing update main flow to remove python script references and location * Automatically initialise imaging led on startup to off state. * Add the ability to invert outputs of the motor We added a key to config.json "hardware_config" with a subkey "stepper_reverse". If this key is present in the config file and set to 1, the output of the motors are inversed (stepper2 becomes the pump motor and stepper1 the focus motor) * move all non main script to a subfolder * add __init__.py to package * light module rewrite * json cleanup and absolute path for config file * light.py forgot to import subprocess #oups * Add command to turn the leds off * Auto formatting of main.py I've used Black with default settings, see https://github.com/psf/black * First commit of stepper.py Pump parameters still needs to be checked and tuned. * addition of hardware details in config.json * Introduce hardware.json to replace the `hardware_config` of config.json * stepper.py: calibration, typos * creates the MQTT_Client class * pump_max_speed is now in ml/min to help readability * forgot to add self to the class def * addition of threading capabilities to stepper.py (UNTESTED) * mqtt: fix topic bug * remove counter * mqtt add doc about topics * stepper.py creates an "actuator/*/state" topic * stepper.py: rename mqtt_client to pump_client * mqtt.py: add details about topics * stepper.py: rename pump_client to actuator_client * topic was not split properly and a part was lost * switch to f-strings for mqtt.py * cosmetic update * stepper.py: folder name will be planktoscope change calls * hardware.json became more straightforward * stepper.py syntax bugs * stepper.py addition of a received stop command * stepper.py: update to max travel distance * stepper.py: several typos here * rename folder * main.py: reword to reflect folder rename * main.py: remove logic that has been moved to stepper.py and mqtt.py * main.py: update to add mqtt imaging client * mqtt.py: make command and args local to class and output more verbose * make stepper.py a class * main.py: instantiate stepper class and call it * main.py: name mqtt client * update to main.json to reflect main.py changes * fix bugs around pump control * update flows to latest version from Thibault * distance can be a small value, and definitevely should be a float. * unify mqtt topics * unify mqtt output in the main flow * first logger implementation, uses loguru * mqtt: add reason to on_connect * mqtt: add on_disconnect handler * stepper: add more logger calls for debug mainly * main: add levels for logger * imager.py: first move of the imager logic * imager: time import cleanup * imager: morphocut import cleanup * imager: skimage import cleanup * imager: finishing import cleanup * imager: Class creation - WIP Also provides a fix for #26 (see line 190). * imager: threading is needed for Condition() * streamer: get the streamer server its own file * imager: creates start_camera and get the server creation out * imager: subclass multiprocessing.Process * imager: get Pipeline creation its own function * imager: cleanup of self calls * main: code removal and corresponding calls to newly created classes * imager: various formatting changes * main: management of signal shutdown * add requirements.txt * mqtt: messages are now json objects Also, addition of a flag on receiving a new message * mqtt: make message private and add logic to synchronise * stepper: creates the stepper class * stepper: use the new class * stepper: uses the new logic * stepper: add the shutdown event * stepper: add shutdown method * main: add shutdown event * imager: graceful shutdown * stepper: nicer way of checking the Eevnt * self is a required first argument for a method in a class Especially if you use said class private members! * python: various typos and small errors in import * stepper: create mqtt client during init * stepper: instanciate the mqtt client inside run Otherwise it's not accessible from inside the loop. It's a PITA, more information at https://stackoverflow.com/questions/17172878/using-pythons-multiprocessing-process-class * stepper: little bugs and typos all around * mqtt: add shutdown method * mqtt: add connect in init * stepper: fix bugs, sanitize inputs * stepper: work on delay prediction improvements * stepper: json is mean, double quote are mandatory inside * mqtt: add details about message exchanged * imager: first implementation of json messages * main.json: add new tab for RPi management + json for payloads * imager: add state_machine class * stepper: publish last will * imager: major refactor * main: make streaming server process a daemon * mqtt: insert debug statement on close * main: reorder imports * imager: make it work! Reinsert the streaming server logic in there, because there is a problem with the synchronisation part otherwise. Also, eventually, StreamingOuput() will have to be made not global Final very critical learning: it's super duper important to make sure the memory split is at least 256Meg for the GPU. Chaos ensues otherwise * main: changes to accomodate the streamer/imager fusino * imager_state_machine: insert states transition description * stepper: cleanup of code * segmenter: creation of the class * python: include segmenter changes * remove unused files * stepper: check existence of hardware.json * main.json: changes to reflect the python script evolution * remove unecessary TODOs and add some others * main: add check for config and directories * imager: update_config is implemented and we have better management of directories now * segmenter: now work recursively in all folders * flow: the configuration is now sent via mqtt * segmenter: better manage pipeline error * segmenter: declaration of archive_fn in init * imager: small bugs and typos * main: add uniqueID output * imager: add the camera settings message We can now update the ISO, shutter speed and resolution from Node-Red * package.json: update dependencies
2020-09-28 11:05:27 +02:00
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Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
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Extraction and refactor of the python code from node-red flow The rationale for this rewrite is to improve the readability, the modularity, the reliability and the future-proofing of the main python script. All in all, this is now 124 commits that are going to be squashed and merged together, spanning more than two weeks of development and testing. Please test away this release and break things. An upgrading guide will be published in the coming days, along with a new image for people to use if they don't want to upgrade on their own. Read along if you want to know all the goodies! As a starter, the python script was extracted from the main flow, and now lives in its own files at `PlantonScope/scripts/*`. We set up the auto formatting of the code by using [Black](https://github.com/psf/black). This make the code clearer and uniform. We are using the default settings, so if you just install Black and set your editor to format on save using it, you should be good to go. The code is separated in four main processes, each with a specific set of responsibilities: - The main process controls all the others, starts everything up and cleans up on shutdown - The stepper process manages the stepper movements. It's now possible to have simultaneous movements of both motors (this closes #38 ). - The imager process controls the camera and the streaming server via a state machine. - The segmenter process manages the segmentation and its outputs. The segmentation happens recursively in all folders in `/home/pi/PlanktonScope/img/`. Each folder has its own output archive, and bug #26 is now closed. Those processes communicates together using MQTT and json messages. Each message is adressed to one topic. The high level topic controls which process receives the message. The details of each topic is at the end of this commit message. Every imaging sessions has now its own folder, under the `img` root. Metadata are saved individually for every session, in a JSON file in the same directory as the pictures. The configuration is not parsed from `config.json` anymore and passed directly through MQTT messages to the concerned process. A new configuration file has been created: `hardware.json`. This file contains information related to your specific hardware configuration. You can choose to reverse the connection of the motors for example, but you can also define specific speed limits and steps number for your pump and focus stage. This will make it easier for people who wants to experiment with different kind of hardware. It's not necessary to have this file though. If it doesn't exists, the default configuration will be applied. The code is architectured around 6 modules and about 10 classes. I encourage you to have a look at the files, they're pretty straightforward to understand. There is a lot of work left around the node-red code refactoring, dashboard ui improvements, better and clearer LED messages, OLED screen integration and finer control of the segmentation process, but this is quite good for now. Here is the topic lists for MQTT and the corresponding messages. - actuator : This topic adresses the stepper control thread No publication under this topic should happen from the python process - actuator/pump : Control of the pump The message is a json object {"action":"move", "direction":"FORWARD", "volume":10, "flowrate":1} to move 10mL forward at 1mL/min action can be "move" or "stop" Receive only - actuator/focus : Control of the focus stage The message is a json object, speed is optional {"action":"move", "direction":"UP", "distance":0.26, "speed":1} to move up 10mm action can be "move" or "stop" Receive only - imager/image : This topic adresses the imaging thread Is a json object with {"action":"image","sleep":5,"volume":1,"nb_frame":200} sleep in seconds, volume in mL Can also receive a config update message: {"action":"config","config":[...]} Can also receive a camera settings message: {"action":"settings","iso":100,"shutter_speed":40} Receive only - segmenter/segment : This topic adresses the segmenter process Is a json object with {"action":"segment"} Receive only - status : This topics sends feedback to Node-Red No publication or receive at this level - status/pump : State of the pump Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/focus : State of the focus stage Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/imager : State of the imager Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Completed or 12_11_15_0.1.jpg has been imaged. Publish only - status/segmenter : Status of the segmentation - status/segmenter/name - status/segmenter/object_id - status/segmenter/metric Here is the original commit history: * Extract python main.py from flow * Fix bug in server addresses These addresses should be the loopback device instead of the network address of the device. Using the loopback address will not necessitate to update the script when the network address changes. * clean up picamera import * changes to main python and flow: update MQTT requests address to localhost (bugfix) update streaming output address to nothing update main flow to remove python script references and location * Automatically initialise imaging led on startup to off state. * Add the ability to invert outputs of the motor We added a key to config.json "hardware_config" with a subkey "stepper_reverse". If this key is present in the config file and set to 1, the output of the motors are inversed (stepper2 becomes the pump motor and stepper1 the focus motor) * move all non main script to a subfolder * add __init__.py to package * light module rewrite * json cleanup and absolute path for config file * light.py forgot to import subprocess #oups * Add command to turn the leds off * Auto formatting of main.py I've used Black with default settings, see https://github.com/psf/black * First commit of stepper.py Pump parameters still needs to be checked and tuned. * addition of hardware details in config.json * Introduce hardware.json to replace the `hardware_config` of config.json * stepper.py: calibration, typos * creates the MQTT_Client class * pump_max_speed is now in ml/min to help readability * forgot to add self to the class def * addition of threading capabilities to stepper.py (UNTESTED) * mqtt: fix topic bug * remove counter * mqtt add doc about topics * stepper.py creates an "actuator/*/state" topic * stepper.py: rename mqtt_client to pump_client * mqtt.py: add details about topics * stepper.py: rename pump_client to actuator_client * topic was not split properly and a part was lost * switch to f-strings for mqtt.py * cosmetic update * stepper.py: folder name will be planktoscope change calls * hardware.json became more straightforward * stepper.py syntax bugs * stepper.py addition of a received stop command * stepper.py: update to max travel distance * stepper.py: several typos here * rename folder * main.py: reword to reflect folder rename * main.py: remove logic that has been moved to stepper.py and mqtt.py * main.py: update to add mqtt imaging client * mqtt.py: make command and args local to class and output more verbose * make stepper.py a class * main.py: instantiate stepper class and call it * main.py: name mqtt client * update to main.json to reflect main.py changes * fix bugs around pump control * update flows to latest version from Thibault * distance can be a small value, and definitevely should be a float. * unify mqtt topics * unify mqtt output in the main flow * first logger implementation, uses loguru * mqtt: add reason to on_connect * mqtt: add on_disconnect handler * stepper: add more logger calls for debug mainly * main: add levels for logger * imager.py: first move of the imager logic * imager: time import cleanup * imager: morphocut import cleanup * imager: skimage import cleanup * imager: finishing import cleanup * imager: Class creation - WIP Also provides a fix for #26 (see line 190). * imager: threading is needed for Condition() * streamer: get the streamer server its own file * imager: creates start_camera and get the server creation out * imager: subclass multiprocessing.Process * imager: get Pipeline creation its own function * imager: cleanup of self calls * main: code removal and corresponding calls to newly created classes * imager: various formatting changes * main: management of signal shutdown * add requirements.txt * mqtt: messages are now json objects Also, addition of a flag on receiving a new message * mqtt: make message private and add logic to synchronise * stepper: creates the stepper class * stepper: use the new class * stepper: uses the new logic * stepper: add the shutdown event * stepper: add shutdown method * main: add shutdown event * imager: graceful shutdown * stepper: nicer way of checking the Eevnt * self is a required first argument for a method in a class Especially if you use said class private members! * python: various typos and small errors in import * stepper: create mqtt client during init * stepper: instanciate the mqtt client inside run Otherwise it's not accessible from inside the loop. It's a PITA, more information at https://stackoverflow.com/questions/17172878/using-pythons-multiprocessing-process-class * stepper: little bugs and typos all around * mqtt: add shutdown method * mqtt: add connect in init * stepper: fix bugs, sanitize inputs * stepper: work on delay prediction improvements * stepper: json is mean, double quote are mandatory inside * mqtt: add details about message exchanged * imager: first implementation of json messages * main.json: add new tab for RPi management + json for payloads * imager: add state_machine class * stepper: publish last will * imager: major refactor * main: make streaming server process a daemon * mqtt: insert debug statement on close * main: reorder imports * imager: make it work! Reinsert the streaming server logic in there, because there is a problem with the synchronisation part otherwise. Also, eventually, StreamingOuput() will have to be made not global Final very critical learning: it's super duper important to make sure the memory split is at least 256Meg for the GPU. Chaos ensues otherwise * main: changes to accomodate the streamer/imager fusino * imager_state_machine: insert states transition description * stepper: cleanup of code * segmenter: creation of the class * python: include segmenter changes * remove unused files * stepper: check existence of hardware.json * main.json: changes to reflect the python script evolution * remove unecessary TODOs and add some others * main: add check for config and directories * imager: update_config is implemented and we have better management of directories now * segmenter: now work recursively in all folders * flow: the configuration is now sent via mqtt * segmenter: better manage pipeline error * segmenter: declaration of archive_fn in init * imager: small bugs and typos * main: add uniqueID output * imager: add the camera settings message We can now update the ISO, shutter speed and resolution from Node-Red * package.json: update dependencies
2020-09-28 11:05:27 +02:00
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Extraction and refactor of the python code from node-red flow The rationale for this rewrite is to improve the readability, the modularity, the reliability and the future-proofing of the main python script. All in all, this is now 124 commits that are going to be squashed and merged together, spanning more than two weeks of development and testing. Please test away this release and break things. An upgrading guide will be published in the coming days, along with a new image for people to use if they don't want to upgrade on their own. Read along if you want to know all the goodies! As a starter, the python script was extracted from the main flow, and now lives in its own files at `PlantonScope/scripts/*`. We set up the auto formatting of the code by using [Black](https://github.com/psf/black). This make the code clearer and uniform. We are using the default settings, so if you just install Black and set your editor to format on save using it, you should be good to go. The code is separated in four main processes, each with a specific set of responsibilities: - The main process controls all the others, starts everything up and cleans up on shutdown - The stepper process manages the stepper movements. It's now possible to have simultaneous movements of both motors (this closes #38 ). - The imager process controls the camera and the streaming server via a state machine. - The segmenter process manages the segmentation and its outputs. The segmentation happens recursively in all folders in `/home/pi/PlanktonScope/img/`. Each folder has its own output archive, and bug #26 is now closed. Those processes communicates together using MQTT and json messages. Each message is adressed to one topic. The high level topic controls which process receives the message. The details of each topic is at the end of this commit message. Every imaging sessions has now its own folder, under the `img` root. Metadata are saved individually for every session, in a JSON file in the same directory as the pictures. The configuration is not parsed from `config.json` anymore and passed directly through MQTT messages to the concerned process. A new configuration file has been created: `hardware.json`. This file contains information related to your specific hardware configuration. You can choose to reverse the connection of the motors for example, but you can also define specific speed limits and steps number for your pump and focus stage. This will make it easier for people who wants to experiment with different kind of hardware. It's not necessary to have this file though. If it doesn't exists, the default configuration will be applied. The code is architectured around 6 modules and about 10 classes. I encourage you to have a look at the files, they're pretty straightforward to understand. There is a lot of work left around the node-red code refactoring, dashboard ui improvements, better and clearer LED messages, OLED screen integration and finer control of the segmentation process, but this is quite good for now. Here is the topic lists for MQTT and the corresponding messages. - actuator : This topic adresses the stepper control thread No publication under this topic should happen from the python process - actuator/pump : Control of the pump The message is a json object {"action":"move", "direction":"FORWARD", "volume":10, "flowrate":1} to move 10mL forward at 1mL/min action can be "move" or "stop" Receive only - actuator/focus : Control of the focus stage The message is a json object, speed is optional {"action":"move", "direction":"UP", "distance":0.26, "speed":1} to move up 10mm action can be "move" or "stop" Receive only - imager/image : This topic adresses the imaging thread Is a json object with {"action":"image","sleep":5,"volume":1,"nb_frame":200} sleep in seconds, volume in mL Can also receive a config update message: {"action":"config","config":[...]} Can also receive a camera settings message: {"action":"settings","iso":100,"shutter_speed":40} Receive only - segmenter/segment : This topic adresses the segmenter process Is a json object with {"action":"segment"} Receive only - status : This topics sends feedback to Node-Red No publication or receive at this level - status/pump : State of the pump Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/focus : State of the focus stage Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/imager : State of the imager Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Completed or 12_11_15_0.1.jpg has been imaged. Publish only - status/segmenter : Status of the segmentation - status/segmenter/name - status/segmenter/object_id - status/segmenter/metric Here is the original commit history: * Extract python main.py from flow * Fix bug in server addresses These addresses should be the loopback device instead of the network address of the device. Using the loopback address will not necessitate to update the script when the network address changes. * clean up picamera import * changes to main python and flow: update MQTT requests address to localhost (bugfix) update streaming output address to nothing update main flow to remove python script references and location * Automatically initialise imaging led on startup to off state. * Add the ability to invert outputs of the motor We added a key to config.json "hardware_config" with a subkey "stepper_reverse". If this key is present in the config file and set to 1, the output of the motors are inversed (stepper2 becomes the pump motor and stepper1 the focus motor) * move all non main script to a subfolder * add __init__.py to package * light module rewrite * json cleanup and absolute path for config file * light.py forgot to import subprocess #oups * Add command to turn the leds off * Auto formatting of main.py I've used Black with default settings, see https://github.com/psf/black * First commit of stepper.py Pump parameters still needs to be checked and tuned. * addition of hardware details in config.json * Introduce hardware.json to replace the `hardware_config` of config.json * stepper.py: calibration, typos * creates the MQTT_Client class * pump_max_speed is now in ml/min to help readability * forgot to add self to the class def * addition of threading capabilities to stepper.py (UNTESTED) * mqtt: fix topic bug * remove counter * mqtt add doc about topics * stepper.py creates an "actuator/*/state" topic * stepper.py: rename mqtt_client to pump_client * mqtt.py: add details about topics * stepper.py: rename pump_client to actuator_client * topic was not split properly and a part was lost * switch to f-strings for mqtt.py * cosmetic update * stepper.py: folder name will be planktoscope change calls * hardware.json became more straightforward * stepper.py syntax bugs * stepper.py addition of a received stop command * stepper.py: update to max travel distance * stepper.py: several typos here * rename folder * main.py: reword to reflect folder rename * main.py: remove logic that has been moved to stepper.py and mqtt.py * main.py: update to add mqtt imaging client * mqtt.py: make command and args local to class and output more verbose * make stepper.py a class * main.py: instantiate stepper class and call it * main.py: name mqtt client * update to main.json to reflect main.py changes * fix bugs around pump control * update flows to latest version from Thibault * distance can be a small value, and definitevely should be a float. * unify mqtt topics * unify mqtt output in the main flow * first logger implementation, uses loguru * mqtt: add reason to on_connect * mqtt: add on_disconnect handler * stepper: add more logger calls for debug mainly * main: add levels for logger * imager.py: first move of the imager logic * imager: time import cleanup * imager: morphocut import cleanup * imager: skimage import cleanup * imager: finishing import cleanup * imager: Class creation - WIP Also provides a fix for #26 (see line 190). * imager: threading is needed for Condition() * streamer: get the streamer server its own file * imager: creates start_camera and get the server creation out * imager: subclass multiprocessing.Process * imager: get Pipeline creation its own function * imager: cleanup of self calls * main: code removal and corresponding calls to newly created classes * imager: various formatting changes * main: management of signal shutdown * add requirements.txt * mqtt: messages are now json objects Also, addition of a flag on receiving a new message * mqtt: make message private and add logic to synchronise * stepper: creates the stepper class * stepper: use the new class * stepper: uses the new logic * stepper: add the shutdown event * stepper: add shutdown method * main: add shutdown event * imager: graceful shutdown * stepper: nicer way of checking the Eevnt * self is a required first argument for a method in a class Especially if you use said class private members! * python: various typos and small errors in import * stepper: create mqtt client during init * stepper: instanciate the mqtt client inside run Otherwise it's not accessible from inside the loop. It's a PITA, more information at https://stackoverflow.com/questions/17172878/using-pythons-multiprocessing-process-class * stepper: little bugs and typos all around * mqtt: add shutdown method * mqtt: add connect in init * stepper: fix bugs, sanitize inputs * stepper: work on delay prediction improvements * stepper: json is mean, double quote are mandatory inside * mqtt: add details about message exchanged * imager: first implementation of json messages * main.json: add new tab for RPi management + json for payloads * imager: add state_machine class * stepper: publish last will * imager: major refactor * main: make streaming server process a daemon * mqtt: insert debug statement on close * main: reorder imports * imager: make it work! Reinsert the streaming server logic in there, because there is a problem with the synchronisation part otherwise. Also, eventually, StreamingOuput() will have to be made not global Final very critical learning: it's super duper important to make sure the memory split is at least 256Meg for the GPU. Chaos ensues otherwise * main: changes to accomodate the streamer/imager fusino * imager_state_machine: insert states transition description * stepper: cleanup of code * segmenter: creation of the class * python: include segmenter changes * remove unused files * stepper: check existence of hardware.json * main.json: changes to reflect the python script evolution * remove unecessary TODOs and add some others * main: add check for config and directories * imager: update_config is implemented and we have better management of directories now * segmenter: now work recursively in all folders * flow: the configuration is now sent via mqtt * segmenter: better manage pipeline error * segmenter: declaration of archive_fn in init * imager: small bugs and typos * main: add uniqueID output * imager: add the camera settings message We can now update the ISO, shutter speed and resolution from Node-Red * package.json: update dependencies
2020-09-28 11:05:27 +02:00
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2020-11-24 17:25:15 +01:00
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Extraction and refactor of the python code from node-red flow The rationale for this rewrite is to improve the readability, the modularity, the reliability and the future-proofing of the main python script. All in all, this is now 124 commits that are going to be squashed and merged together, spanning more than two weeks of development and testing. Please test away this release and break things. An upgrading guide will be published in the coming days, along with a new image for people to use if they don't want to upgrade on their own. Read along if you want to know all the goodies! As a starter, the python script was extracted from the main flow, and now lives in its own files at `PlantonScope/scripts/*`. We set up the auto formatting of the code by using [Black](https://github.com/psf/black). This make the code clearer and uniform. We are using the default settings, so if you just install Black and set your editor to format on save using it, you should be good to go. The code is separated in four main processes, each with a specific set of responsibilities: - The main process controls all the others, starts everything up and cleans up on shutdown - The stepper process manages the stepper movements. It's now possible to have simultaneous movements of both motors (this closes #38 ). - The imager process controls the camera and the streaming server via a state machine. - The segmenter process manages the segmentation and its outputs. The segmentation happens recursively in all folders in `/home/pi/PlanktonScope/img/`. Each folder has its own output archive, and bug #26 is now closed. Those processes communicates together using MQTT and json messages. Each message is adressed to one topic. The high level topic controls which process receives the message. The details of each topic is at the end of this commit message. Every imaging sessions has now its own folder, under the `img` root. Metadata are saved individually for every session, in a JSON file in the same directory as the pictures. The configuration is not parsed from `config.json` anymore and passed directly through MQTT messages to the concerned process. A new configuration file has been created: `hardware.json`. This file contains information related to your specific hardware configuration. You can choose to reverse the connection of the motors for example, but you can also define specific speed limits and steps number for your pump and focus stage. This will make it easier for people who wants to experiment with different kind of hardware. It's not necessary to have this file though. If it doesn't exists, the default configuration will be applied. The code is architectured around 6 modules and about 10 classes. I encourage you to have a look at the files, they're pretty straightforward to understand. There is a lot of work left around the node-red code refactoring, dashboard ui improvements, better and clearer LED messages, OLED screen integration and finer control of the segmentation process, but this is quite good for now. Here is the topic lists for MQTT and the corresponding messages. - actuator : This topic adresses the stepper control thread No publication under this topic should happen from the python process - actuator/pump : Control of the pump The message is a json object {"action":"move", "direction":"FORWARD", "volume":10, "flowrate":1} to move 10mL forward at 1mL/min action can be "move" or "stop" Receive only - actuator/focus : Control of the focus stage The message is a json object, speed is optional {"action":"move", "direction":"UP", "distance":0.26, "speed":1} to move up 10mm action can be "move" or "stop" Receive only - imager/image : This topic adresses the imaging thread Is a json object with {"action":"image","sleep":5,"volume":1,"nb_frame":200} sleep in seconds, volume in mL Can also receive a config update message: {"action":"config","config":[...]} Can also receive a camera settings message: {"action":"settings","iso":100,"shutter_speed":40} Receive only - segmenter/segment : This topic adresses the segmenter process Is a json object with {"action":"segment"} Receive only - status : This topics sends feedback to Node-Red No publication or receive at this level - status/pump : State of the pump Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/focus : State of the focus stage Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/imager : State of the imager Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Completed or 12_11_15_0.1.jpg has been imaged. Publish only - status/segmenter : Status of the segmentation - status/segmenter/name - status/segmenter/object_id - status/segmenter/metric Here is the original commit history: * Extract python main.py from flow * Fix bug in server addresses These addresses should be the loopback device instead of the network address of the device. Using the loopback address will not necessitate to update the script when the network address changes. * clean up picamera import * changes to main python and flow: update MQTT requests address to localhost (bugfix) update streaming output address to nothing update main flow to remove python script references and location * Automatically initialise imaging led on startup to off state. * Add the ability to invert outputs of the motor We added a key to config.json "hardware_config" with a subkey "stepper_reverse". If this key is present in the config file and set to 1, the output of the motors are inversed (stepper2 becomes the pump motor and stepper1 the focus motor) * move all non main script to a subfolder * add __init__.py to package * light module rewrite * json cleanup and absolute path for config file * light.py forgot to import subprocess #oups * Add command to turn the leds off * Auto formatting of main.py I've used Black with default settings, see https://github.com/psf/black * First commit of stepper.py Pump parameters still needs to be checked and tuned. * addition of hardware details in config.json * Introduce hardware.json to replace the `hardware_config` of config.json * stepper.py: calibration, typos * creates the MQTT_Client class * pump_max_speed is now in ml/min to help readability * forgot to add self to the class def * addition of threading capabilities to stepper.py (UNTESTED) * mqtt: fix topic bug * remove counter * mqtt add doc about topics * stepper.py creates an "actuator/*/state" topic * stepper.py: rename mqtt_client to pump_client * mqtt.py: add details about topics * stepper.py: rename pump_client to actuator_client * topic was not split properly and a part was lost * switch to f-strings for mqtt.py * cosmetic update * stepper.py: folder name will be planktoscope change calls * hardware.json became more straightforward * stepper.py syntax bugs * stepper.py addition of a received stop command * stepper.py: update to max travel distance * stepper.py: several typos here * rename folder * main.py: reword to reflect folder rename * main.py: remove logic that has been moved to stepper.py and mqtt.py * main.py: update to add mqtt imaging client * mqtt.py: make command and args local to class and output more verbose * make stepper.py a class * main.py: instantiate stepper class and call it * main.py: name mqtt client * update to main.json to reflect main.py changes * fix bugs around pump control * update flows to latest version from Thibault * distance can be a small value, and definitevely should be a float. * unify mqtt topics * unify mqtt output in the main flow * first logger implementation, uses loguru * mqtt: add reason to on_connect * mqtt: add on_disconnect handler * stepper: add more logger calls for debug mainly * main: add levels for logger * imager.py: first move of the imager logic * imager: time import cleanup * imager: morphocut import cleanup * imager: skimage import cleanup * imager: finishing import cleanup * imager: Class creation - WIP Also provides a fix for #26 (see line 190). * imager: threading is needed for Condition() * streamer: get the streamer server its own file * imager: creates start_camera and get the server creation out * imager: subclass multiprocessing.Process * imager: get Pipeline creation its own function * imager: cleanup of self calls * main: code removal and corresponding calls to newly created classes * imager: various formatting changes * main: management of signal shutdown * add requirements.txt * mqtt: messages are now json objects Also, addition of a flag on receiving a new message * mqtt: make message private and add logic to synchronise * stepper: creates the stepper class * stepper: use the new class * stepper: uses the new logic * stepper: add the shutdown event * stepper: add shutdown method * main: add shutdown event * imager: graceful shutdown * stepper: nicer way of checking the Eevnt * self is a required first argument for a method in a class Especially if you use said class private members! * python: various typos and small errors in import * stepper: create mqtt client during init * stepper: instanciate the mqtt client inside run Otherwise it's not accessible from inside the loop. It's a PITA, more information at https://stackoverflow.com/questions/17172878/using-pythons-multiprocessing-process-class * stepper: little bugs and typos all around * mqtt: add shutdown method * mqtt: add connect in init * stepper: fix bugs, sanitize inputs * stepper: work on delay prediction improvements * stepper: json is mean, double quote are mandatory inside * mqtt: add details about message exchanged * imager: first implementation of json messages * main.json: add new tab for RPi management + json for payloads * imager: add state_machine class * stepper: publish last will * imager: major refactor * main: make streaming server process a daemon * mqtt: insert debug statement on close * main: reorder imports * imager: make it work! Reinsert the streaming server logic in there, because there is a problem with the synchronisation part otherwise. Also, eventually, StreamingOuput() will have to be made not global Final very critical learning: it's super duper important to make sure the memory split is at least 256Meg for the GPU. Chaos ensues otherwise * main: changes to accomodate the streamer/imager fusino * imager_state_machine: insert states transition description * stepper: cleanup of code * segmenter: creation of the class * python: include segmenter changes * remove unused files * stepper: check existence of hardware.json * main.json: changes to reflect the python script evolution * remove unecessary TODOs and add some others * main: add check for config and directories * imager: update_config is implemented and we have better management of directories now * segmenter: now work recursively in all folders * flow: the configuration is now sent via mqtt * segmenter: better manage pipeline error * segmenter: declaration of archive_fn in init * imager: small bugs and typos * main: add uniqueID output * imager: add the camera settings message We can now update the ISO, shutter speed and resolution from Node-Red * package.json: update dependencies
2020-09-28 11:05:27 +02:00
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Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
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2020-10-06 17:22:25 +02:00
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2020-11-24 17:25:15 +01:00
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Extraction and refactor of the python code from node-red flow The rationale for this rewrite is to improve the readability, the modularity, the reliability and the future-proofing of the main python script. All in all, this is now 124 commits that are going to be squashed and merged together, spanning more than two weeks of development and testing. Please test away this release and break things. An upgrading guide will be published in the coming days, along with a new image for people to use if they don't want to upgrade on their own. Read along if you want to know all the goodies! As a starter, the python script was extracted from the main flow, and now lives in its own files at `PlantonScope/scripts/*`. We set up the auto formatting of the code by using [Black](https://github.com/psf/black). This make the code clearer and uniform. We are using the default settings, so if you just install Black and set your editor to format on save using it, you should be good to go. The code is separated in four main processes, each with a specific set of responsibilities: - The main process controls all the others, starts everything up and cleans up on shutdown - The stepper process manages the stepper movements. It's now possible to have simultaneous movements of both motors (this closes #38 ). - The imager process controls the camera and the streaming server via a state machine. - The segmenter process manages the segmentation and its outputs. The segmentation happens recursively in all folders in `/home/pi/PlanktonScope/img/`. Each folder has its own output archive, and bug #26 is now closed. Those processes communicates together using MQTT and json messages. Each message is adressed to one topic. The high level topic controls which process receives the message. The details of each topic is at the end of this commit message. Every imaging sessions has now its own folder, under the `img` root. Metadata are saved individually for every session, in a JSON file in the same directory as the pictures. The configuration is not parsed from `config.json` anymore and passed directly through MQTT messages to the concerned process. A new configuration file has been created: `hardware.json`. This file contains information related to your specific hardware configuration. You can choose to reverse the connection of the motors for example, but you can also define specific speed limits and steps number for your pump and focus stage. This will make it easier for people who wants to experiment with different kind of hardware. It's not necessary to have this file though. If it doesn't exists, the default configuration will be applied. The code is architectured around 6 modules and about 10 classes. I encourage you to have a look at the files, they're pretty straightforward to understand. There is a lot of work left around the node-red code refactoring, dashboard ui improvements, better and clearer LED messages, OLED screen integration and finer control of the segmentation process, but this is quite good for now. Here is the topic lists for MQTT and the corresponding messages. - actuator : This topic adresses the stepper control thread No publication under this topic should happen from the python process - actuator/pump : Control of the pump The message is a json object {"action":"move", "direction":"FORWARD", "volume":10, "flowrate":1} to move 10mL forward at 1mL/min action can be "move" or "stop" Receive only - actuator/focus : Control of the focus stage The message is a json object, speed is optional {"action":"move", "direction":"UP", "distance":0.26, "speed":1} to move up 10mm action can be "move" or "stop" Receive only - imager/image : This topic adresses the imaging thread Is a json object with {"action":"image","sleep":5,"volume":1,"nb_frame":200} sleep in seconds, volume in mL Can also receive a config update message: {"action":"config","config":[...]} Can also receive a camera settings message: {"action":"settings","iso":100,"shutter_speed":40} Receive only - segmenter/segment : This topic adresses the segmenter process Is a json object with {"action":"segment"} Receive only - status : This topics sends feedback to Node-Red No publication or receive at this level - status/pump : State of the pump Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/focus : State of the focus stage Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/imager : State of the imager Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Completed or 12_11_15_0.1.jpg has been imaged. Publish only - status/segmenter : Status of the segmentation - status/segmenter/name - status/segmenter/object_id - status/segmenter/metric Here is the original commit history: * Extract python main.py from flow * Fix bug in server addresses These addresses should be the loopback device instead of the network address of the device. Using the loopback address will not necessitate to update the script when the network address changes. * clean up picamera import * changes to main python and flow: update MQTT requests address to localhost (bugfix) update streaming output address to nothing update main flow to remove python script references and location * Automatically initialise imaging led on startup to off state. * Add the ability to invert outputs of the motor We added a key to config.json "hardware_config" with a subkey "stepper_reverse". If this key is present in the config file and set to 1, the output of the motors are inversed (stepper2 becomes the pump motor and stepper1 the focus motor) * move all non main script to a subfolder * add __init__.py to package * light module rewrite * json cleanup and absolute path for config file * light.py forgot to import subprocess #oups * Add command to turn the leds off * Auto formatting of main.py I've used Black with default settings, see https://github.com/psf/black * First commit of stepper.py Pump parameters still needs to be checked and tuned. * addition of hardware details in config.json * Introduce hardware.json to replace the `hardware_config` of config.json * stepper.py: calibration, typos * creates the MQTT_Client class * pump_max_speed is now in ml/min to help readability * forgot to add self to the class def * addition of threading capabilities to stepper.py (UNTESTED) * mqtt: fix topic bug * remove counter * mqtt add doc about topics * stepper.py creates an "actuator/*/state" topic * stepper.py: rename mqtt_client to pump_client * mqtt.py: add details about topics * stepper.py: rename pump_client to actuator_client * topic was not split properly and a part was lost * switch to f-strings for mqtt.py * cosmetic update * stepper.py: folder name will be planktoscope change calls * hardware.json became more straightforward * stepper.py syntax bugs * stepper.py addition of a received stop command * stepper.py: update to max travel distance * stepper.py: several typos here * rename folder * main.py: reword to reflect folder rename * main.py: remove logic that has been moved to stepper.py and mqtt.py * main.py: update to add mqtt imaging client * mqtt.py: make command and args local to class and output more verbose * make stepper.py a class * main.py: instantiate stepper class and call it * main.py: name mqtt client * update to main.json to reflect main.py changes * fix bugs around pump control * update flows to latest version from Thibault * distance can be a small value, and definitevely should be a float. * unify mqtt topics * unify mqtt output in the main flow * first logger implementation, uses loguru * mqtt: add reason to on_connect * mqtt: add on_disconnect handler * stepper: add more logger calls for debug mainly * main: add levels for logger * imager.py: first move of the imager logic * imager: time import cleanup * imager: morphocut import cleanup * imager: skimage import cleanup * imager: finishing import cleanup * imager: Class creation - WIP Also provides a fix for #26 (see line 190). * imager: threading is needed for Condition() * streamer: get the streamer server its own file * imager: creates start_camera and get the server creation out * imager: subclass multiprocessing.Process * imager: get Pipeline creation its own function * imager: cleanup of self calls * main: code removal and corresponding calls to newly created classes * imager: various formatting changes * main: management of signal shutdown * add requirements.txt * mqtt: messages are now json objects Also, addition of a flag on receiving a new message * mqtt: make message private and add logic to synchronise * stepper: creates the stepper class * stepper: use the new class * stepper: uses the new logic * stepper: add the shutdown event * stepper: add shutdown method * main: add shutdown event * imager: graceful shutdown * stepper: nicer way of checking the Eevnt * self is a required first argument for a method in a class Especially if you use said class private members! * python: various typos and small errors in import * stepper: create mqtt client during init * stepper: instanciate the mqtt client inside run Otherwise it's not accessible from inside the loop. It's a PITA, more information at https://stackoverflow.com/questions/17172878/using-pythons-multiprocessing-process-class * stepper: little bugs and typos all around * mqtt: add shutdown method * mqtt: add connect in init * stepper: fix bugs, sanitize inputs * stepper: work on delay prediction improvements * stepper: json is mean, double quote are mandatory inside * mqtt: add details about message exchanged * imager: first implementation of json messages * main.json: add new tab for RPi management + json for payloads * imager: add state_machine class * stepper: publish last will * imager: major refactor * main: make streaming server process a daemon * mqtt: insert debug statement on close * main: reorder imports * imager: make it work! Reinsert the streaming server logic in there, because there is a problem with the synchronisation part otherwise. Also, eventually, StreamingOuput() will have to be made not global Final very critical learning: it's super duper important to make sure the memory split is at least 256Meg for the GPU. Chaos ensues otherwise * main: changes to accomodate the streamer/imager fusino * imager_state_machine: insert states transition description * stepper: cleanup of code * segmenter: creation of the class * python: include segmenter changes * remove unused files * stepper: check existence of hardware.json * main.json: changes to reflect the python script evolution * remove unecessary TODOs and add some others * main: add check for config and directories * imager: update_config is implemented and we have better management of directories now * segmenter: now work recursively in all folders * flow: the configuration is now sent via mqtt * segmenter: better manage pipeline error * segmenter: declaration of archive_fn in init * imager: small bugs and typos * main: add uniqueID output * imager: add the camera settings message We can now update the ISO, shutter speed and resolution from Node-Red * package.json: update dependencies
2020-09-28 11:05:27 +02:00
"disp": true,
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"width": 10,
Extraction and refactor of the python code from node-red flow The rationale for this rewrite is to improve the readability, the modularity, the reliability and the future-proofing of the main python script. All in all, this is now 124 commits that are going to be squashed and merged together, spanning more than two weeks of development and testing. Please test away this release and break things. An upgrading guide will be published in the coming days, along with a new image for people to use if they don't want to upgrade on their own. Read along if you want to know all the goodies! As a starter, the python script was extracted from the main flow, and now lives in its own files at `PlantonScope/scripts/*`. We set up the auto formatting of the code by using [Black](https://github.com/psf/black). This make the code clearer and uniform. We are using the default settings, so if you just install Black and set your editor to format on save using it, you should be good to go. The code is separated in four main processes, each with a specific set of responsibilities: - The main process controls all the others, starts everything up and cleans up on shutdown - The stepper process manages the stepper movements. It's now possible to have simultaneous movements of both motors (this closes #38 ). - The imager process controls the camera and the streaming server via a state machine. - The segmenter process manages the segmentation and its outputs. The segmentation happens recursively in all folders in `/home/pi/PlanktonScope/img/`. Each folder has its own output archive, and bug #26 is now closed. Those processes communicates together using MQTT and json messages. Each message is adressed to one topic. The high level topic controls which process receives the message. The details of each topic is at the end of this commit message. Every imaging sessions has now its own folder, under the `img` root. Metadata are saved individually for every session, in a JSON file in the same directory as the pictures. The configuration is not parsed from `config.json` anymore and passed directly through MQTT messages to the concerned process. A new configuration file has been created: `hardware.json`. This file contains information related to your specific hardware configuration. You can choose to reverse the connection of the motors for example, but you can also define specific speed limits and steps number for your pump and focus stage. This will make it easier for people who wants to experiment with different kind of hardware. It's not necessary to have this file though. If it doesn't exists, the default configuration will be applied. The code is architectured around 6 modules and about 10 classes. I encourage you to have a look at the files, they're pretty straightforward to understand. There is a lot of work left around the node-red code refactoring, dashboard ui improvements, better and clearer LED messages, OLED screen integration and finer control of the segmentation process, but this is quite good for now. Here is the topic lists for MQTT and the corresponding messages. - actuator : This topic adresses the stepper control thread No publication under this topic should happen from the python process - actuator/pump : Control of the pump The message is a json object {"action":"move", "direction":"FORWARD", "volume":10, "flowrate":1} to move 10mL forward at 1mL/min action can be "move" or "stop" Receive only - actuator/focus : Control of the focus stage The message is a json object, speed is optional {"action":"move", "direction":"UP", "distance":0.26, "speed":1} to move up 10mm action can be "move" or "stop" Receive only - imager/image : This topic adresses the imaging thread Is a json object with {"action":"image","sleep":5,"volume":1,"nb_frame":200} sleep in seconds, volume in mL Can also receive a config update message: {"action":"config","config":[...]} Can also receive a camera settings message: {"action":"settings","iso":100,"shutter_speed":40} Receive only - segmenter/segment : This topic adresses the segmenter process Is a json object with {"action":"segment"} Receive only - status : This topics sends feedback to Node-Red No publication or receive at this level - status/pump : State of the pump Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/focus : State of the focus stage Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/imager : State of the imager Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Completed or 12_11_15_0.1.jpg has been imaged. Publish only - status/segmenter : Status of the segmentation - status/segmenter/name - status/segmenter/object_id - status/segmenter/metric Here is the original commit history: * Extract python main.py from flow * Fix bug in server addresses These addresses should be the loopback device instead of the network address of the device. Using the loopback address will not necessitate to update the script when the network address changes. * clean up picamera import * changes to main python and flow: update MQTT requests address to localhost (bugfix) update streaming output address to nothing update main flow to remove python script references and location * Automatically initialise imaging led on startup to off state. * Add the ability to invert outputs of the motor We added a key to config.json "hardware_config" with a subkey "stepper_reverse". If this key is present in the config file and set to 1, the output of the motors are inversed (stepper2 becomes the pump motor and stepper1 the focus motor) * move all non main script to a subfolder * add __init__.py to package * light module rewrite * json cleanup and absolute path for config file * light.py forgot to import subprocess #oups * Add command to turn the leds off * Auto formatting of main.py I've used Black with default settings, see https://github.com/psf/black * First commit of stepper.py Pump parameters still needs to be checked and tuned. * addition of hardware details in config.json * Introduce hardware.json to replace the `hardware_config` of config.json * stepper.py: calibration, typos * creates the MQTT_Client class * pump_max_speed is now in ml/min to help readability * forgot to add self to the class def * addition of threading capabilities to stepper.py (UNTESTED) * mqtt: fix topic bug * remove counter * mqtt add doc about topics * stepper.py creates an "actuator/*/state" topic * stepper.py: rename mqtt_client to pump_client * mqtt.py: add details about topics * stepper.py: rename pump_client to actuator_client * topic was not split properly and a part was lost * switch to f-strings for mqtt.py * cosmetic update * stepper.py: folder name will be planktoscope change calls * hardware.json became more straightforward * stepper.py syntax bugs * stepper.py addition of a received stop command * stepper.py: update to max travel distance * stepper.py: several typos here * rename folder * main.py: reword to reflect folder rename * main.py: remove logic that has been moved to stepper.py and mqtt.py * main.py: update to add mqtt imaging client * mqtt.py: make command and args local to class and output more verbose * make stepper.py a class * main.py: instantiate stepper class and call it * main.py: name mqtt client * update to main.json to reflect main.py changes * fix bugs around pump control * update flows to latest version from Thibault * distance can be a small value, and definitevely should be a float. * unify mqtt topics * unify mqtt output in the main flow * first logger implementation, uses loguru * mqtt: add reason to on_connect * mqtt: add on_disconnect handler * stepper: add more logger calls for debug mainly * main: add levels for logger * imager.py: first move of the imager logic * imager: time import cleanup * imager: morphocut import cleanup * imager: skimage import cleanup * imager: finishing import cleanup * imager: Class creation - WIP Also provides a fix for #26 (see line 190). * imager: threading is needed for Condition() * streamer: get the streamer server its own file * imager: creates start_camera and get the server creation out * imager: subclass multiprocessing.Process * imager: get Pipeline creation its own function * imager: cleanup of self calls * main: code removal and corresponding calls to newly created classes * imager: various formatting changes * main: management of signal shutdown * add requirements.txt * mqtt: messages are now json objects Also, addition of a flag on receiving a new message * mqtt: make message private and add logic to synchronise * stepper: creates the stepper class * stepper: use the new class * stepper: uses the new logic * stepper: add the shutdown event * stepper: add shutdown method * main: add shutdown event * imager: graceful shutdown * stepper: nicer way of checking the Eevnt * self is a required first argument for a method in a class Especially if you use said class private members! * python: various typos and small errors in import * stepper: create mqtt client during init * stepper: instanciate the mqtt client inside run Otherwise it's not accessible from inside the loop. It's a PITA, more information at https://stackoverflow.com/questions/17172878/using-pythons-multiprocessing-process-class * stepper: little bugs and typos all around * mqtt: add shutdown method * mqtt: add connect in init * stepper: fix bugs, sanitize inputs * stepper: work on delay prediction improvements * stepper: json is mean, double quote are mandatory inside * mqtt: add details about message exchanged * imager: first implementation of json messages * main.json: add new tab for RPi management + json for payloads * imager: add state_machine class * stepper: publish last will * imager: major refactor * main: make streaming server process a daemon * mqtt: insert debug statement on close * main: reorder imports * imager: make it work! Reinsert the streaming server logic in there, because there is a problem with the synchronisation part otherwise. Also, eventually, StreamingOuput() will have to be made not global Final very critical learning: it's super duper important to make sure the memory split is at least 256Meg for the GPU. Chaos ensues otherwise * main: changes to accomodate the streamer/imager fusino * imager_state_machine: insert states transition description * stepper: cleanup of code * segmenter: creation of the class * python: include segmenter changes * remove unused files * stepper: check existence of hardware.json * main.json: changes to reflect the python script evolution * remove unecessary TODOs and add some others * main: add check for config and directories * imager: update_config is implemented and we have better management of directories now * segmenter: now work recursively in all folders * flow: the configuration is now sent via mqtt * segmenter: better manage pipeline error * segmenter: declaration of archive_fn in init * imager: small bugs and typos * main: add uniqueID output * imager: add the camera settings message We can now update the ISO, shutter speed and resolution from Node-Red * package.json: update dependencies
2020-09-28 11:05:27 +02:00
"collapse": false
},
{
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"id": "707d9797.c8e798",
Extraction and refactor of the python code from node-red flow The rationale for this rewrite is to improve the readability, the modularity, the reliability and the future-proofing of the main python script. All in all, this is now 124 commits that are going to be squashed and merged together, spanning more than two weeks of development and testing. Please test away this release and break things. An upgrading guide will be published in the coming days, along with a new image for people to use if they don't want to upgrade on their own. Read along if you want to know all the goodies! As a starter, the python script was extracted from the main flow, and now lives in its own files at `PlantonScope/scripts/*`. We set up the auto formatting of the code by using [Black](https://github.com/psf/black). This make the code clearer and uniform. We are using the default settings, so if you just install Black and set your editor to format on save using it, you should be good to go. The code is separated in four main processes, each with a specific set of responsibilities: - The main process controls all the others, starts everything up and cleans up on shutdown - The stepper process manages the stepper movements. It's now possible to have simultaneous movements of both motors (this closes #38 ). - The imager process controls the camera and the streaming server via a state machine. - The segmenter process manages the segmentation and its outputs. The segmentation happens recursively in all folders in `/home/pi/PlanktonScope/img/`. Each folder has its own output archive, and bug #26 is now closed. Those processes communicates together using MQTT and json messages. Each message is adressed to one topic. The high level topic controls which process receives the message. The details of each topic is at the end of this commit message. Every imaging sessions has now its own folder, under the `img` root. Metadata are saved individually for every session, in a JSON file in the same directory as the pictures. The configuration is not parsed from `config.json` anymore and passed directly through MQTT messages to the concerned process. A new configuration file has been created: `hardware.json`. This file contains information related to your specific hardware configuration. You can choose to reverse the connection of the motors for example, but you can also define specific speed limits and steps number for your pump and focus stage. This will make it easier for people who wants to experiment with different kind of hardware. It's not necessary to have this file though. If it doesn't exists, the default configuration will be applied. The code is architectured around 6 modules and about 10 classes. I encourage you to have a look at the files, they're pretty straightforward to understand. There is a lot of work left around the node-red code refactoring, dashboard ui improvements, better and clearer LED messages, OLED screen integration and finer control of the segmentation process, but this is quite good for now. Here is the topic lists for MQTT and the corresponding messages. - actuator : This topic adresses the stepper control thread No publication under this topic should happen from the python process - actuator/pump : Control of the pump The message is a json object {"action":"move", "direction":"FORWARD", "volume":10, "flowrate":1} to move 10mL forward at 1mL/min action can be "move" or "stop" Receive only - actuator/focus : Control of the focus stage The message is a json object, speed is optional {"action":"move", "direction":"UP", "distance":0.26, "speed":1} to move up 10mm action can be "move" or "stop" Receive only - imager/image : This topic adresses the imaging thread Is a json object with {"action":"image","sleep":5,"volume":1,"nb_frame":200} sleep in seconds, volume in mL Can also receive a config update message: {"action":"config","config":[...]} Can also receive a camera settings message: {"action":"settings","iso":100,"shutter_speed":40} Receive only - segmenter/segment : This topic adresses the segmenter process Is a json object with {"action":"segment"} Receive only - status : This topics sends feedback to Node-Red No publication or receive at this level - status/pump : State of the pump Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/focus : State of the focus stage Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/imager : State of the imager Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Completed or 12_11_15_0.1.jpg has been imaged. Publish only - status/segmenter : Status of the segmentation - status/segmenter/name - status/segmenter/object_id - status/segmenter/metric Here is the original commit history: * Extract python main.py from flow * Fix bug in server addresses These addresses should be the loopback device instead of the network address of the device. Using the loopback address will not necessitate to update the script when the network address changes. * clean up picamera import * changes to main python and flow: update MQTT requests address to localhost (bugfix) update streaming output address to nothing update main flow to remove python script references and location * Automatically initialise imaging led on startup to off state. * Add the ability to invert outputs of the motor We added a key to config.json "hardware_config" with a subkey "stepper_reverse". If this key is present in the config file and set to 1, the output of the motors are inversed (stepper2 becomes the pump motor and stepper1 the focus motor) * move all non main script to a subfolder * add __init__.py to package * light module rewrite * json cleanup and absolute path for config file * light.py forgot to import subprocess #oups * Add command to turn the leds off * Auto formatting of main.py I've used Black with default settings, see https://github.com/psf/black * First commit of stepper.py Pump parameters still needs to be checked and tuned. * addition of hardware details in config.json * Introduce hardware.json to replace the `hardware_config` of config.json * stepper.py: calibration, typos * creates the MQTT_Client class * pump_max_speed is now in ml/min to help readability * forgot to add self to the class def * addition of threading capabilities to stepper.py (UNTESTED) * mqtt: fix topic bug * remove counter * mqtt add doc about topics * stepper.py creates an "actuator/*/state" topic * stepper.py: rename mqtt_client to pump_client * mqtt.py: add details about topics * stepper.py: rename pump_client to actuator_client * topic was not split properly and a part was lost * switch to f-strings for mqtt.py * cosmetic update * stepper.py: folder name will be planktoscope change calls * hardware.json became more straightforward * stepper.py syntax bugs * stepper.py addition of a received stop command * stepper.py: update to max travel distance * stepper.py: several typos here * rename folder * main.py: reword to reflect folder rename * main.py: remove logic that has been moved to stepper.py and mqtt.py * main.py: update to add mqtt imaging client * mqtt.py: make command and args local to class and output more verbose * make stepper.py a class * main.py: instantiate stepper class and call it * main.py: name mqtt client * update to main.json to reflect main.py changes * fix bugs around pump control * update flows to latest version from Thibault * distance can be a small value, and definitevely should be a float. * unify mqtt topics * unify mqtt output in the main flow * first logger implementation, uses loguru * mqtt: add reason to on_connect * mqtt: add on_disconnect handler * stepper: add more logger calls for debug mainly * main: add levels for logger * imager.py: first move of the imager logic * imager: time import cleanup * imager: morphocut import cleanup * imager: skimage import cleanup * imager: finishing import cleanup * imager: Class creation - WIP Also provides a fix for #26 (see line 190). * imager: threading is needed for Condition() * streamer: get the streamer server its own file * imager: creates start_camera and get the server creation out * imager: subclass multiprocessing.Process * imager: get Pipeline creation its own function * imager: cleanup of self calls * main: code removal and corresponding calls to newly created classes * imager: various formatting changes * main: management of signal shutdown * add requirements.txt * mqtt: messages are now json objects Also, addition of a flag on receiving a new message * mqtt: make message private and add logic to synchronise * stepper: creates the stepper class * stepper: use the new class * stepper: uses the new logic * stepper: add the shutdown event * stepper: add shutdown method * main: add shutdown event * imager: graceful shutdown * stepper: nicer way of checking the Eevnt * self is a required first argument for a method in a class Especially if you use said class private members! * python: various typos and small errors in import * stepper: create mqtt client during init * stepper: instanciate the mqtt client inside run Otherwise it's not accessible from inside the loop. It's a PITA, more information at https://stackoverflow.com/questions/17172878/using-pythons-multiprocessing-process-class * stepper: little bugs and typos all around * mqtt: add shutdown method * mqtt: add connect in init * stepper: fix bugs, sanitize inputs * stepper: work on delay prediction improvements * stepper: json is mean, double quote are mandatory inside * mqtt: add details about message exchanged * imager: first implementation of json messages * main.json: add new tab for RPi management + json for payloads * imager: add state_machine class * stepper: publish last will * imager: major refactor * main: make streaming server process a daemon * mqtt: insert debug statement on close * main: reorder imports * imager: make it work! Reinsert the streaming server logic in there, because there is a problem with the synchronisation part otherwise. Also, eventually, StreamingOuput() will have to be made not global Final very critical learning: it's super duper important to make sure the memory split is at least 256Meg for the GPU. Chaos ensues otherwise * main: changes to accomodate the streamer/imager fusino * imager_state_machine: insert states transition description * stepper: cleanup of code * segmenter: creation of the class * python: include segmenter changes * remove unused files * stepper: check existence of hardware.json * main.json: changes to reflect the python script evolution * remove unecessary TODOs and add some others * main: add check for config and directories * imager: update_config is implemented and we have better management of directories now * segmenter: now work recursively in all folders * flow: the configuration is now sent via mqtt * segmenter: better manage pipeline error * segmenter: declaration of archive_fn in init * imager: small bugs and typos * main: add uniqueID output * imager: add the camera settings message We can now update the ISO, shutter speed and resolution from Node-Red * package.json: update dependencies
2020-09-28 11:05:27 +02:00
"type": "ui_group",
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"name": "Fluidic Manual Manipulation",
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Extraction and refactor of the python code from node-red flow The rationale for this rewrite is to improve the readability, the modularity, the reliability and the future-proofing of the main python script. All in all, this is now 124 commits that are going to be squashed and merged together, spanning more than two weeks of development and testing. Please test away this release and break things. An upgrading guide will be published in the coming days, along with a new image for people to use if they don't want to upgrade on their own. Read along if you want to know all the goodies! As a starter, the python script was extracted from the main flow, and now lives in its own files at `PlantonScope/scripts/*`. We set up the auto formatting of the code by using [Black](https://github.com/psf/black). This make the code clearer and uniform. We are using the default settings, so if you just install Black and set your editor to format on save using it, you should be good to go. The code is separated in four main processes, each with a specific set of responsibilities: - The main process controls all the others, starts everything up and cleans up on shutdown - The stepper process manages the stepper movements. It's now possible to have simultaneous movements of both motors (this closes #38 ). - The imager process controls the camera and the streaming server via a state machine. - The segmenter process manages the segmentation and its outputs. The segmentation happens recursively in all folders in `/home/pi/PlanktonScope/img/`. Each folder has its own output archive, and bug #26 is now closed. Those processes communicates together using MQTT and json messages. Each message is adressed to one topic. The high level topic controls which process receives the message. The details of each topic is at the end of this commit message. Every imaging sessions has now its own folder, under the `img` root. Metadata are saved individually for every session, in a JSON file in the same directory as the pictures. The configuration is not parsed from `config.json` anymore and passed directly through MQTT messages to the concerned process. A new configuration file has been created: `hardware.json`. This file contains information related to your specific hardware configuration. You can choose to reverse the connection of the motors for example, but you can also define specific speed limits and steps number for your pump and focus stage. This will make it easier for people who wants to experiment with different kind of hardware. It's not necessary to have this file though. If it doesn't exists, the default configuration will be applied. The code is architectured around 6 modules and about 10 classes. I encourage you to have a look at the files, they're pretty straightforward to understand. There is a lot of work left around the node-red code refactoring, dashboard ui improvements, better and clearer LED messages, OLED screen integration and finer control of the segmentation process, but this is quite good for now. Here is the topic lists for MQTT and the corresponding messages. - actuator : This topic adresses the stepper control thread No publication under this topic should happen from the python process - actuator/pump : Control of the pump The message is a json object {"action":"move", "direction":"FORWARD", "volume":10, "flowrate":1} to move 10mL forward at 1mL/min action can be "move" or "stop" Receive only - actuator/focus : Control of the focus stage The message is a json object, speed is optional {"action":"move", "direction":"UP", "distance":0.26, "speed":1} to move up 10mm action can be "move" or "stop" Receive only - imager/image : This topic adresses the imaging thread Is a json object with {"action":"image","sleep":5,"volume":1,"nb_frame":200} sleep in seconds, volume in mL Can also receive a config update message: {"action":"config","config":[...]} Can also receive a camera settings message: {"action":"settings","iso":100,"shutter_speed":40} Receive only - segmenter/segment : This topic adresses the segmenter process Is a json object with {"action":"segment"} Receive only - status : This topics sends feedback to Node-Red No publication or receive at this level - status/pump : State of the pump Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/focus : State of the focus stage Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/imager : State of the imager Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Completed or 12_11_15_0.1.jpg has been imaged. Publish only - status/segmenter : Status of the segmentation - status/segmenter/name - status/segmenter/object_id - status/segmenter/metric Here is the original commit history: * Extract python main.py from flow * Fix bug in server addresses These addresses should be the loopback device instead of the network address of the device. Using the loopback address will not necessitate to update the script when the network address changes. * clean up picamera import * changes to main python and flow: update MQTT requests address to localhost (bugfix) update streaming output address to nothing update main flow to remove python script references and location * Automatically initialise imaging led on startup to off state. * Add the ability to invert outputs of the motor We added a key to config.json "hardware_config" with a subkey "stepper_reverse". If this key is present in the config file and set to 1, the output of the motors are inversed (stepper2 becomes the pump motor and stepper1 the focus motor) * move all non main script to a subfolder * add __init__.py to package * light module rewrite * json cleanup and absolute path for config file * light.py forgot to import subprocess #oups * Add command to turn the leds off * Auto formatting of main.py I've used Black with default settings, see https://github.com/psf/black * First commit of stepper.py Pump parameters still needs to be checked and tuned. * addition of hardware details in config.json * Introduce hardware.json to replace the `hardware_config` of config.json * stepper.py: calibration, typos * creates the MQTT_Client class * pump_max_speed is now in ml/min to help readability * forgot to add self to the class def * addition of threading capabilities to stepper.py (UNTESTED) * mqtt: fix topic bug * remove counter * mqtt add doc about topics * stepper.py creates an "actuator/*/state" topic * stepper.py: rename mqtt_client to pump_client * mqtt.py: add details about topics * stepper.py: rename pump_client to actuator_client * topic was not split properly and a part was lost * switch to f-strings for mqtt.py * cosmetic update * stepper.py: folder name will be planktoscope change calls * hardware.json became more straightforward * stepper.py syntax bugs * stepper.py addition of a received stop command * stepper.py: update to max travel distance * stepper.py: several typos here * rename folder * main.py: reword to reflect folder rename * main.py: remove logic that has been moved to stepper.py and mqtt.py * main.py: update to add mqtt imaging client * mqtt.py: make command and args local to class and output more verbose * make stepper.py a class * main.py: instantiate stepper class and call it * main.py: name mqtt client * update to main.json to reflect main.py changes * fix bugs around pump control * update flows to latest version from Thibault * distance can be a small value, and definitevely should be a float. * unify mqtt topics * unify mqtt output in the main flow * first logger implementation, uses loguru * mqtt: add reason to on_connect * mqtt: add on_disconnect handler * stepper: add more logger calls for debug mainly * main: add levels for logger * imager.py: first move of the imager logic * imager: time import cleanup * imager: morphocut import cleanup * imager: skimage import cleanup * imager: finishing import cleanup * imager: Class creation - WIP Also provides a fix for #26 (see line 190). * imager: threading is needed for Condition() * streamer: get the streamer server its own file * imager: creates start_camera and get the server creation out * imager: subclass multiprocessing.Process * imager: get Pipeline creation its own function * imager: cleanup of self calls * main: code removal and corresponding calls to newly created classes * imager: various formatting changes * main: management of signal shutdown * add requirements.txt * mqtt: messages are now json objects Also, addition of a flag on receiving a new message * mqtt: make message private and add logic to synchronise * stepper: creates the stepper class * stepper: use the new class * stepper: uses the new logic * stepper: add the shutdown event * stepper: add shutdown method * main: add shutdown event * imager: graceful shutdown * stepper: nicer way of checking the Eevnt * self is a required first argument for a method in a class Especially if you use said class private members! * python: various typos and small errors in import * stepper: create mqtt client during init * stepper: instanciate the mqtt client inside run Otherwise it's not accessible from inside the loop. It's a PITA, more information at https://stackoverflow.com/questions/17172878/using-pythons-multiprocessing-process-class * stepper: little bugs and typos all around * mqtt: add shutdown method * mqtt: add connect in init * stepper: fix bugs, sanitize inputs * stepper: work on delay prediction improvements * stepper: json is mean, double quote are mandatory inside * mqtt: add details about message exchanged * imager: first implementation of json messages * main.json: add new tab for RPi management + json for payloads * imager: add state_machine class * stepper: publish last will * imager: major refactor * main: make streaming server process a daemon * mqtt: insert debug statement on close * main: reorder imports * imager: make it work! Reinsert the streaming server logic in there, because there is a problem with the synchronisation part otherwise. Also, eventually, StreamingOuput() will have to be made not global Final very critical learning: it's super duper important to make sure the memory split is at least 256Meg for the GPU. Chaos ensues otherwise * main: changes to accomodate the streamer/imager fusino * imager_state_machine: insert states transition description * stepper: cleanup of code * segmenter: creation of the class * python: include segmenter changes * remove unused files * stepper: check existence of hardware.json * main.json: changes to reflect the python script evolution * remove unecessary TODOs and add some others * main: add check for config and directories * imager: update_config is implemented and we have better management of directories now * segmenter: now work recursively in all folders * flow: the configuration is now sent via mqtt * segmenter: better manage pipeline error * segmenter: declaration of archive_fn in init * imager: small bugs and typos * main: add uniqueID output * imager: add the camera settings message We can now update the ISO, shutter speed and resolution from Node-Red * package.json: update dependencies
2020-09-28 11:05:27 +02:00
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Extraction and refactor of the python code from node-red flow The rationale for this rewrite is to improve the readability, the modularity, the reliability and the future-proofing of the main python script. All in all, this is now 124 commits that are going to be squashed and merged together, spanning more than two weeks of development and testing. Please test away this release and break things. An upgrading guide will be published in the coming days, along with a new image for people to use if they don't want to upgrade on their own. Read along if you want to know all the goodies! As a starter, the python script was extracted from the main flow, and now lives in its own files at `PlantonScope/scripts/*`. We set up the auto formatting of the code by using [Black](https://github.com/psf/black). This make the code clearer and uniform. We are using the default settings, so if you just install Black and set your editor to format on save using it, you should be good to go. The code is separated in four main processes, each with a specific set of responsibilities: - The main process controls all the others, starts everything up and cleans up on shutdown - The stepper process manages the stepper movements. It's now possible to have simultaneous movements of both motors (this closes #38 ). - The imager process controls the camera and the streaming server via a state machine. - The segmenter process manages the segmentation and its outputs. The segmentation happens recursively in all folders in `/home/pi/PlanktonScope/img/`. Each folder has its own output archive, and bug #26 is now closed. Those processes communicates together using MQTT and json messages. Each message is adressed to one topic. The high level topic controls which process receives the message. The details of each topic is at the end of this commit message. Every imaging sessions has now its own folder, under the `img` root. Metadata are saved individually for every session, in a JSON file in the same directory as the pictures. The configuration is not parsed from `config.json` anymore and passed directly through MQTT messages to the concerned process. A new configuration file has been created: `hardware.json`. This file contains information related to your specific hardware configuration. You can choose to reverse the connection of the motors for example, but you can also define specific speed limits and steps number for your pump and focus stage. This will make it easier for people who wants to experiment with different kind of hardware. It's not necessary to have this file though. If it doesn't exists, the default configuration will be applied. The code is architectured around 6 modules and about 10 classes. I encourage you to have a look at the files, they're pretty straightforward to understand. There is a lot of work left around the node-red code refactoring, dashboard ui improvements, better and clearer LED messages, OLED screen integration and finer control of the segmentation process, but this is quite good for now. Here is the topic lists for MQTT and the corresponding messages. - actuator : This topic adresses the stepper control thread No publication under this topic should happen from the python process - actuator/pump : Control of the pump The message is a json object {"action":"move", "direction":"FORWARD", "volume":10, "flowrate":1} to move 10mL forward at 1mL/min action can be "move" or "stop" Receive only - actuator/focus : Control of the focus stage The message is a json object, speed is optional {"action":"move", "direction":"UP", "distance":0.26, "speed":1} to move up 10mm action can be "move" or "stop" Receive only - imager/image : This topic adresses the imaging thread Is a json object with {"action":"image","sleep":5,"volume":1,"nb_frame":200} sleep in seconds, volume in mL Can also receive a config update message: {"action":"config","config":[...]} Can also receive a camera settings message: {"action":"settings","iso":100,"shutter_speed":40} Receive only - segmenter/segment : This topic adresses the segmenter process Is a json object with {"action":"segment"} Receive only - status : This topics sends feedback to Node-Red No publication or receive at this level - status/pump : State of the pump Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/focus : State of the focus stage Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/imager : State of the imager Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Completed or 12_11_15_0.1.jpg has been imaged. Publish only - status/segmenter : Status of the segmentation - status/segmenter/name - status/segmenter/object_id - status/segmenter/metric Here is the original commit history: * Extract python main.py from flow * Fix bug in server addresses These addresses should be the loopback device instead of the network address of the device. Using the loopback address will not necessitate to update the script when the network address changes. * clean up picamera import * changes to main python and flow: update MQTT requests address to localhost (bugfix) update streaming output address to nothing update main flow to remove python script references and location * Automatically initialise imaging led on startup to off state. * Add the ability to invert outputs of the motor We added a key to config.json "hardware_config" with a subkey "stepper_reverse". If this key is present in the config file and set to 1, the output of the motors are inversed (stepper2 becomes the pump motor and stepper1 the focus motor) * move all non main script to a subfolder * add __init__.py to package * light module rewrite * json cleanup and absolute path for config file * light.py forgot to import subprocess #oups * Add command to turn the leds off * Auto formatting of main.py I've used Black with default settings, see https://github.com/psf/black * First commit of stepper.py Pump parameters still needs to be checked and tuned. * addition of hardware details in config.json * Introduce hardware.json to replace the `hardware_config` of config.json * stepper.py: calibration, typos * creates the MQTT_Client class * pump_max_speed is now in ml/min to help readability * forgot to add self to the class def * addition of threading capabilities to stepper.py (UNTESTED) * mqtt: fix topic bug * remove counter * mqtt add doc about topics * stepper.py creates an "actuator/*/state" topic * stepper.py: rename mqtt_client to pump_client * mqtt.py: add details about topics * stepper.py: rename pump_client to actuator_client * topic was not split properly and a part was lost * switch to f-strings for mqtt.py * cosmetic update * stepper.py: folder name will be planktoscope change calls * hardware.json became more straightforward * stepper.py syntax bugs * stepper.py addition of a received stop command * stepper.py: update to max travel distance * stepper.py: several typos here * rename folder * main.py: reword to reflect folder rename * main.py: remove logic that has been moved to stepper.py and mqtt.py * main.py: update to add mqtt imaging client * mqtt.py: make command and args local to class and output more verbose * make stepper.py a class * main.py: instantiate stepper class and call it * main.py: name mqtt client * update to main.json to reflect main.py changes * fix bugs around pump control * update flows to latest version from Thibault * distance can be a small value, and definitevely should be a float. * unify mqtt topics * unify mqtt output in the main flow * first logger implementation, uses loguru * mqtt: add reason to on_connect * mqtt: add on_disconnect handler * stepper: add more logger calls for debug mainly * main: add levels for logger * imager.py: first move of the imager logic * imager: time import cleanup * imager: morphocut import cleanup * imager: skimage import cleanup * imager: finishing import cleanup * imager: Class creation - WIP Also provides a fix for #26 (see line 190). * imager: threading is needed for Condition() * streamer: get the streamer server its own file * imager: creates start_camera and get the server creation out * imager: subclass multiprocessing.Process * imager: get Pipeline creation its own function * imager: cleanup of self calls * main: code removal and corresponding calls to newly created classes * imager: various formatting changes * main: management of signal shutdown * add requirements.txt * mqtt: messages are now json objects Also, addition of a flag on receiving a new message * mqtt: make message private and add logic to synchronise * stepper: creates the stepper class * stepper: use the new class * stepper: uses the new logic * stepper: add the shutdown event * stepper: add shutdown method * main: add shutdown event * imager: graceful shutdown * stepper: nicer way of checking the Eevnt * self is a required first argument for a method in a class Especially if you use said class private members! * python: various typos and small errors in import * stepper: create mqtt client during init * stepper: instanciate the mqtt client inside run Otherwise it's not accessible from inside the loop. It's a PITA, more information at https://stackoverflow.com/questions/17172878/using-pythons-multiprocessing-process-class * stepper: little bugs and typos all around * mqtt: add shutdown method * mqtt: add connect in init * stepper: fix bugs, sanitize inputs * stepper: work on delay prediction improvements * stepper: json is mean, double quote are mandatory inside * mqtt: add details about message exchanged * imager: first implementation of json messages * main.json: add new tab for RPi management + json for payloads * imager: add state_machine class * stepper: publish last will * imager: major refactor * main: make streaming server process a daemon * mqtt: insert debug statement on close * main: reorder imports * imager: make it work! Reinsert the streaming server logic in there, because there is a problem with the synchronisation part otherwise. Also, eventually, StreamingOuput() will have to be made not global Final very critical learning: it's super duper important to make sure the memory split is at least 256Meg for the GPU. Chaos ensues otherwise * main: changes to accomodate the streamer/imager fusino * imager_state_machine: insert states transition description * stepper: cleanup of code * segmenter: creation of the class * python: include segmenter changes * remove unused files * stepper: check existence of hardware.json * main.json: changes to reflect the python script evolution * remove unecessary TODOs and add some others * main: add check for config and directories * imager: update_config is implemented and we have better management of directories now * segmenter: now work recursively in all folders * flow: the configuration is now sent via mqtt * segmenter: better manage pipeline error * segmenter: declaration of archive_fn in init * imager: small bugs and typos * main: add uniqueID output * imager: add the camera settings message We can now update the ISO, shutter speed and resolution from Node-Red * package.json: update dependencies
2020-09-28 11:05:27 +02:00
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Extraction and refactor of the python code from node-red flow The rationale for this rewrite is to improve the readability, the modularity, the reliability and the future-proofing of the main python script. All in all, this is now 124 commits that are going to be squashed and merged together, spanning more than two weeks of development and testing. Please test away this release and break things. An upgrading guide will be published in the coming days, along with a new image for people to use if they don't want to upgrade on their own. Read along if you want to know all the goodies! As a starter, the python script was extracted from the main flow, and now lives in its own files at `PlantonScope/scripts/*`. We set up the auto formatting of the code by using [Black](https://github.com/psf/black). This make the code clearer and uniform. We are using the default settings, so if you just install Black and set your editor to format on save using it, you should be good to go. The code is separated in four main processes, each with a specific set of responsibilities: - The main process controls all the others, starts everything up and cleans up on shutdown - The stepper process manages the stepper movements. It's now possible to have simultaneous movements of both motors (this closes #38 ). - The imager process controls the camera and the streaming server via a state machine. - The segmenter process manages the segmentation and its outputs. The segmentation happens recursively in all folders in `/home/pi/PlanktonScope/img/`. Each folder has its own output archive, and bug #26 is now closed. Those processes communicates together using MQTT and json messages. Each message is adressed to one topic. The high level topic controls which process receives the message. The details of each topic is at the end of this commit message. Every imaging sessions has now its own folder, under the `img` root. Metadata are saved individually for every session, in a JSON file in the same directory as the pictures. The configuration is not parsed from `config.json` anymore and passed directly through MQTT messages to the concerned process. A new configuration file has been created: `hardware.json`. This file contains information related to your specific hardware configuration. You can choose to reverse the connection of the motors for example, but you can also define specific speed limits and steps number for your pump and focus stage. This will make it easier for people who wants to experiment with different kind of hardware. It's not necessary to have this file though. If it doesn't exists, the default configuration will be applied. The code is architectured around 6 modules and about 10 classes. I encourage you to have a look at the files, they're pretty straightforward to understand. There is a lot of work left around the node-red code refactoring, dashboard ui improvements, better and clearer LED messages, OLED screen integration and finer control of the segmentation process, but this is quite good for now. Here is the topic lists for MQTT and the corresponding messages. - actuator : This topic adresses the stepper control thread No publication under this topic should happen from the python process - actuator/pump : Control of the pump The message is a json object {"action":"move", "direction":"FORWARD", "volume":10, "flowrate":1} to move 10mL forward at 1mL/min action can be "move" or "stop" Receive only - actuator/focus : Control of the focus stage The message is a json object, speed is optional {"action":"move", "direction":"UP", "distance":0.26, "speed":1} to move up 10mm action can be "move" or "stop" Receive only - imager/image : This topic adresses the imaging thread Is a json object with {"action":"image","sleep":5,"volume":1,"nb_frame":200} sleep in seconds, volume in mL Can also receive a config update message: {"action":"config","config":[...]} Can also receive a camera settings message: {"action":"settings","iso":100,"shutter_speed":40} Receive only - segmenter/segment : This topic adresses the segmenter process Is a json object with {"action":"segment"} Receive only - status : This topics sends feedback to Node-Red No publication or receive at this level - status/pump : State of the pump Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/focus : State of the focus stage Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/imager : State of the imager Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Completed or 12_11_15_0.1.jpg has been imaged. Publish only - status/segmenter : Status of the segmentation - status/segmenter/name - status/segmenter/object_id - status/segmenter/metric Here is the original commit history: * Extract python main.py from flow * Fix bug in server addresses These addresses should be the loopback device instead of the network address of the device. Using the loopback address will not necessitate to update the script when the network address changes. * clean up picamera import * changes to main python and flow: update MQTT requests address to localhost (bugfix) update streaming output address to nothing update main flow to remove python script references and location * Automatically initialise imaging led on startup to off state. * Add the ability to invert outputs of the motor We added a key to config.json "hardware_config" with a subkey "stepper_reverse". If this key is present in the config file and set to 1, the output of the motors are inversed (stepper2 becomes the pump motor and stepper1 the focus motor) * move all non main script to a subfolder * add __init__.py to package * light module rewrite * json cleanup and absolute path for config file * light.py forgot to import subprocess #oups * Add command to turn the leds off * Auto formatting of main.py I've used Black with default settings, see https://github.com/psf/black * First commit of stepper.py Pump parameters still needs to be checked and tuned. * addition of hardware details in config.json * Introduce hardware.json to replace the `hardware_config` of config.json * stepper.py: calibration, typos * creates the MQTT_Client class * pump_max_speed is now in ml/min to help readability * forgot to add self to the class def * addition of threading capabilities to stepper.py (UNTESTED) * mqtt: fix topic bug * remove counter * mqtt add doc about topics * stepper.py creates an "actuator/*/state" topic * stepper.py: rename mqtt_client to pump_client * mqtt.py: add details about topics * stepper.py: rename pump_client to actuator_client * topic was not split properly and a part was lost * switch to f-strings for mqtt.py * cosmetic update * stepper.py: folder name will be planktoscope change calls * hardware.json became more straightforward * stepper.py syntax bugs * stepper.py addition of a received stop command * stepper.py: update to max travel distance * stepper.py: several typos here * rename folder * main.py: reword to reflect folder rename * main.py: remove logic that has been moved to stepper.py and mqtt.py * main.py: update to add mqtt imaging client * mqtt.py: make command and args local to class and output more verbose * make stepper.py a class * main.py: instantiate stepper class and call it * main.py: name mqtt client * update to main.json to reflect main.py changes * fix bugs around pump control * update flows to latest version from Thibault * distance can be a small value, and definitevely should be a float. * unify mqtt topics * unify mqtt output in the main flow * first logger implementation, uses loguru * mqtt: add reason to on_connect * mqtt: add on_disconnect handler * stepper: add more logger calls for debug mainly * main: add levels for logger * imager.py: first move of the imager logic * imager: time import cleanup * imager: morphocut import cleanup * imager: skimage import cleanup * imager: finishing import cleanup * imager: Class creation - WIP Also provides a fix for #26 (see line 190). * imager: threading is needed for Condition() * streamer: get the streamer server its own file * imager: creates start_camera and get the server creation out * imager: subclass multiprocessing.Process * imager: get Pipeline creation its own function * imager: cleanup of self calls * main: code removal and corresponding calls to newly created classes * imager: various formatting changes * main: management of signal shutdown * add requirements.txt * mqtt: messages are now json objects Also, addition of a flag on receiving a new message * mqtt: make message private and add logic to synchronise * stepper: creates the stepper class * stepper: use the new class * stepper: uses the new logic * stepper: add the shutdown event * stepper: add shutdown method * main: add shutdown event * imager: graceful shutdown * stepper: nicer way of checking the Eevnt * self is a required first argument for a method in a class Especially if you use said class private members! * python: various typos and small errors in import * stepper: create mqtt client during init * stepper: instanciate the mqtt client inside run Otherwise it's not accessible from inside the loop. It's a PITA, more information at https://stackoverflow.com/questions/17172878/using-pythons-multiprocessing-process-class * stepper: little bugs and typos all around * mqtt: add shutdown method * mqtt: add connect in init * stepper: fix bugs, sanitize inputs * stepper: work on delay prediction improvements * stepper: json is mean, double quote are mandatory inside * mqtt: add details about message exchanged * imager: first implementation of json messages * main.json: add new tab for RPi management + json for payloads * imager: add state_machine class * stepper: publish last will * imager: major refactor * main: make streaming server process a daemon * mqtt: insert debug statement on close * main: reorder imports * imager: make it work! Reinsert the streaming server logic in there, because there is a problem with the synchronisation part otherwise. Also, eventually, StreamingOuput() will have to be made not global Final very critical learning: it's super duper important to make sure the memory split is at least 256Meg for the GPU. Chaos ensues otherwise * main: changes to accomodate the streamer/imager fusino * imager_state_machine: insert states transition description * stepper: cleanup of code * segmenter: creation of the class * python: include segmenter changes * remove unused files * stepper: check existence of hardware.json * main.json: changes to reflect the python script evolution * remove unecessary TODOs and add some others * main: add check for config and directories * imager: update_config is implemented and we have better management of directories now * segmenter: now work recursively in all folders * flow: the configuration is now sent via mqtt * segmenter: better manage pipeline error * segmenter: declaration of archive_fn in init * imager: small bugs and typos * main: add uniqueID output * imager: add the camera settings message We can now update the ISO, shutter speed and resolution from Node-Red * package.json: update dependencies
2020-09-28 11:05:27 +02:00
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Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
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update to main.json to fix camera bugs
2020-09-15 17:33:49 +02:00
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Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
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update to main.json to fix camera bugs
2020-09-15 17:33:49 +02:00
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Main.json: UI upgrade
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{
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update to main.json to fix camera bugs
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"payload": "",
Main.json: UI upgrade
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update to main.json to fix camera bugs
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"y": 100,
Main.json: UI upgrade
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"wires": []
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{
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"name": "Disk Usage",
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update to main.json to fix camera bugs
2020-09-15 17:33:49 +02:00
"wires": [
Update flows.json
2020-07-14 18:22:31 +02:00
[
Main.json: UI upgrade
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"45e1912a.36a23",
"84ac8611.1a6ac8"
],
[],
[]
Update flows.json
2020-07-14 18:22:31 +02:00
]
},
{
Main.json: UI upgrade
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"id": "45e1912a.36a23",
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"title": "Disk",
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{
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update to main.json to fix camera bugs
2020-09-15 17:33:49 +02:00
"type": "ui_chart",
Main.json: UI upgrade
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"z": "1371dec5.76e671",
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"group": "3da7da8f.179606",
"order": 2,
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update to main.json to fix camera bugs
2020-09-15 17:33:49 +02:00
"chartType": "line",
"legend": "false",
"xformat": "HH:mm:ss",
Main.json: UI upgrade
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"interpolate": "linear",
update to main.json to fix camera bugs
2020-09-15 17:33:49 +02:00
"nodata": "",
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"dot": false,
update to main.json to fix camera bugs
2020-09-15 17:33:49 +02:00
"ymin": "",
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Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"useOldStyle": true,
update to main.json to fix camera bugs
2020-09-15 17:33:49 +02:00
"outputs": 1,
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"x": 510,
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update to main.json to fix camera bugs
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"wires": [
[]
]
},
{
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
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update to main.json to fix camera bugs
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"colors": [
Main.json: UI upgrade
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"#1f77b4",
"#aec7e8",
"#ff7f0e",
"#2ca02c",
"#98df8a",
"#d62728",
"#ff9896",
"#9467bd",
"#c5b0d5"
update to main.json to fix camera bugs
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],
Main.json: UI upgrade
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"useOldStyle": true,
"outputs": 1,
"x": 510,
"y": 320,
"wires": [
[]
]
update to main.json to fix camera bugs
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},
{
Main.json: UI upgrade
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"id": "84ac8611.1a6ac8",
"type": "ui_chart",
"z": "1371dec5.76e671",
"name": "",
"group": "405183bc.d8991c",
"order": 2,
"width": 0,
"height": 0,
"label": "",
"chartType": "line",
"legend": "false",
"xformat": "HH:mm:ss",
"interpolate": "linear",
"nodata": "",
"dot": false,
"ymin": "",
"ymax": "",
"removeOlder": "4",
"removeOlderPoints": "",
"removeOlderUnit": "3600",
"cutout": 0,
"useOneColor": false,
"useUTC": false,
update to main.json to fix camera bugs
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"colors": [
Main.json: UI upgrade
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"#1f77b4",
"#aec7e8",
"#ff7f0e",
"#2ca02c",
"#98df8a",
"#d62728",
"#ff9896",
"#9467bd",
"#c5b0d5"
update to main.json to fix camera bugs
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],
Main.json: UI upgrade
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"useOldStyle": true,
"outputs": 1,
"x": 510,
"y": 420,
"wires": [
[]
]
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},
{
Main.json: UI upgrade
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"id": "1cd5b4c0.46af9b",
"type": "inject",
"z": "1371dec5.76e671",
"name": "",
"props": [
{
"p": "payload",
"v": "",
"vt": "date"
},
{
"p": "topic",
"v": "",
"vt": "string"
}
],
"repeat": "60",
"crontab": "",
"once": false,
"onceDelay": "",
"topic": "",
"payload": "",
"payloadType": "date",
"x": 90,
"y": 260,
Update flows.json
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"wires": [
[
Main.json: UI upgrade
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"3910d662.fa1f7a",
"c2b8d8b.0d90328",
"55749fd8.3aca5",
"ddcbbfa5.cd158"
]
]
},
{
"id": "8485d05.444903",
"type": "ui_switch",
"z": "1371dec5.76e671",
"name": "fan_state",
"label": "Fan",
"tooltip": "",
"group": "3ca00bf9.e5cac4",
"order": 6,
"width": 3,
"height": 1,
"passthru": true,
"decouple": "false",
"topic": "",
"style": "",
"onvalue": "on",
"onvalueType": "str",
"onicon": "",
"oncolor": "",
"offvalue": "off",
"offvalueType": "str",
"officon": "",
"offcolor": "",
"x": 940,
"y": 40,
"wires": [
[
"2549f778.4eb828"
]
]
},
{
"id": "2549f778.4eb828",
"type": "python3-function",
"z": "1371dec5.76e671",
"name": "fan.py",
"func": "#!/usr/bin/python\nimport smbus\nimport sys\n\nstate = msg[\"payload\"]\n\nbus = smbus.SMBus(1)\n\nDEVICE_ADDRESS = 0x0d\n\nif state == \"off\":\n bus.write_byte_data(DEVICE_ADDRESS, 0x08, 0x00)\n bus.write_byte_data(DEVICE_ADDRESS, 0x08, 0x00)\nif state == \"on\":\n bus.write_byte_data(DEVICE_ADDRESS, 0x08, 0x01)\n bus.write_byte_data(DEVICE_ADDRESS, 0x08, 0x01)",
"outputs": 1,
"x": 1090,
"y": 40,
"wires": [
[]
]
},
{
"id": "a113b518.830008",
"type": "ui_button",
"z": "1371dec5.76e671",
"name": "",
"group": "1be83144.4fe4bf",
"order": 10,
"width": 7,
"height": 1,
"passthru": false,
"label": "Reboot",
"tooltip": "",
"color": "",
"bgcolor": "#AD1625",
"icon": "refresh",
"payload": "reboot",
"payloadType": "str",
"topic": "reboot",
"x": 800,
"y": 260,
"wires": [
[
"ee57d11c.ed1dd"
]
]
},
{
"id": "d9a924bc.0ca078",
"type": "exec",
"z": "1371dec5.76e671",
"command": "sudo",
"addpay": true,
"append": "now",
"useSpawn": "false",
"timer": "2",
"oldrc": false,
"name": "cmd",
"x": 1190,
"y": 260,
"wires": [
[],
Update flows.json
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[],
[]
]
},
{
Main.json: UI upgrade
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"id": "552d8bbb.cc4ca4",
"type": "ui_button",
"z": "1371dec5.76e671",
"name": "",
"group": "1be83144.4fe4bf",
"order": 8,
"width": 7,
"height": 1,
"passthru": false,
"label": "Shutdown",
"tooltip": "",
"color": "",
"bgcolor": "#AD1625",
"icon": "standby",
"payload": "shutdown",
"payloadType": "str",
"topic": "shutdown",
"x": 800,
"y": 340,
"wires": [
[
"ee57d11c.ed1dd"
]
]
},
{
"id": "ee57d11c.ed1dd",
"type": "python3-function",
"z": "1371dec5.76e671",
"name": "action",
"func": "#!/usr/bin/python\nimport smbus\nimport time\nbus = smbus.SMBus(1)\ntime.sleep(1)\n#turn off fan RGB\nbus.write_byte_data(0x0d, 0x07, 0x00)\nbus.write_byte_data(0x0d, 0x07, 0x00)\n\n#msg[\"payload\"] = str(msg[\"topic\"])+' now'\nreturn msg",
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"outputs": 1,
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"x": 1010,
"y": 300,
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"wires": [
Main.json: UI upgrade
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[
"b7ab1ada.1f4158",
"d9a924bc.0ca078"
]
Update flows.json
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]
},
{
Main.json: UI upgrade
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"id": "b7ab1ada.1f4158",
"type": "exec",
"z": "1371dec5.76e671",
"command": "i2cdetect -y 1",
"addpay": false,
"append": "",
"useSpawn": "false",
"timer": "1",
"oldrc": false,
"name": "i2c update",
"x": 1200,
"y": 340,
Add files via upload
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"wires": [
Main.json: UI upgrade
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[],
[],
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[]
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]
},
{
Main.json: UI upgrade
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"id": "bc503fa5.f46dd",
update to main.json to fix camera bugs
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"type": "switch",
Main.json: UI upgrade
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"z": "1371dec5.76e671",
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"name": "",
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"property": "payload",
"propertyType": "msg",
"rules": [
{
"t": "gt",
"v": "45",
"vt": "num"
},
{
"t": "lte",
Flow updates
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"v": "35",
update to main.json to fix camera bugs
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"vt": "num"
}
],
"checkall": "true",
"repair": false,
"outputs": 2,
Main.json: UI upgrade
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"x": 570,
"y": 40,
Add files via upload
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"wires": [
[
Main.json: UI upgrade
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"a25d6486.e1ce28"
update to main.json to fix camera bugs
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],
[
Main.json: UI upgrade
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"5d4f3e71.1bad4"
Add files via upload
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]
]
},
{
Main.json: UI upgrade
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"id": "5d4f3e71.1bad4",
update to main.json to fix camera bugs
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"type": "change",
Main.json: UI upgrade
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"z": "1371dec5.76e671",
Update flows.json
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"name": "",
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"rules": [
{
"t": "set",
"p": "payload",
"pt": "msg",
"to": "off",
"tot": "str"
}
],
"action": "",
"property": "",
"from": "",
"to": "",
"reg": false,
Main.json: UI upgrade
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"x": 740,
"y": 60,
Update flows.json
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"wires": [
[
Main.json: UI upgrade
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"8485d05.444903"
Update flows.json
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]
]
},
{
Main.json: UI upgrade
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"id": "a25d6486.e1ce28",
"type": "change",
"z": "1371dec5.76e671",
update to main.json to fix camera bugs
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"name": "",
Main.json: UI upgrade
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"rules": [
{
"t": "set",
"p": "payload",
"pt": "msg",
"to": "on",
"tot": "str"
}
],
"action": "",
"property": "",
"from": "",
"to": "",
"reg": false,
"x": 740,
"y": 20,
Update flows.json
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"wires": [
[
Main.json: UI upgrade
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"8485d05.444903"
Update flows.json
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]
]
},
{
Main.json: UI upgrade
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"id": "6a84252a.d52a0c",
"type": "ui_template",
"z": "bccd1f23.87219",
"group": "833bc5bb.217ba8",
"name": "Stream Pi Camera",
"order": 1,
"width": 14,
"height": 9,
"format": "<center>\n <img src=\"http://planktoscope.local:8000/stream.mjpg\"\n width=\"100%\" height=\"100%\">\n</center>",
"storeOutMessages": true,
"fwdInMessages": true,
"resendOnRefresh": false,
"templateScope": "local",
"x": 110,
"y": 100,
Update flows.json
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"wires": [
[]
]
},
{
Main.json: UI upgrade
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"id": "dc48dc42.98d18",
"type": "function",
"z": "bccd1f23.87219",
"name": "set global",
"func": "global.set(msg.topic,msg.payload);",
"outputs": 1,
"noerr": 0,
"initialize": "",
"finalize": "",
"x": 880,
update to main.json to fix camera bugs
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"y": 340,
Update flows.json
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"wires": [
[]
]
},
{
Main.json: UI upgrade
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"id": "f59a2f0d.5e9af",
"type": "ui_numeric",
"z": "baa1e3d9.cb29d",
"name": "acq_minimum_mesh",
"label": "Min fraction size (μm)",
"tooltip": "",
"group": "404c301a.19c4e",
"order": 2,
update to main.json to fix camera bugs
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"width": 5,
Main.json: UI upgrade
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"height": 1,
"wrap": false,
"passthru": true,
"topic": "acq_minimum_mesh",
update to main.json to fix camera bugs
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"format": "{{value}}",
"min": 0,
Main.json: UI upgrade
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"max": "300",
"step": "10",
"x": 600,
"y": 120,
Update flows.json
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"wires": [
[
Main.json: UI upgrade
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"fb887036.12429"
]
Update flows.json
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]
},
{
Main.json: UI upgrade
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"id": "6008a8bb.259f08",
"type": "ui_numeric",
"z": "baa1e3d9.cb29d",
"name": "acq_maximum_mesh",
"label": "Max fraction size (μm)",
"tooltip": "",
"group": "404c301a.19c4e",
Update flows.json
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"order": 3,
update to main.json to fix camera bugs
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"width": 5,
Main.json: UI upgrade
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"height": 1,
"wrap": false,
"passthru": true,
"topic": "acq_maximum_mesh",
Update flows.json
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"format": "{{value}}",
Main.json: UI upgrade
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"min": "200",
"max": "2000",
"step": "100",
"x": 600,
"y": 160,
"wires": [
[
"fb887036.12429"
]
]
Update flows.json
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},
{
Main.json: UI upgrade
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"id": "6b34c456.83178c",
"type": "ui_text_input",
"z": "baa1e3d9.cb29d",
"name": "acq_id",
"label": "Acquisition unique ID*",
"tooltip": "",
"group": "4322c187.e73e5",
"order": 2,
"width": 5,
"height": 1,
"passthru": true,
"mode": "text",
"delay": 300,
"topic": "acq_id",
"x": 650,
"y": 240,
Update flows.json
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"wires": [
Main.json: UI upgrade
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[
"fb887036.12429"
]
Update flows.json
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]
},
{
Main.json: UI upgrade
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"id": "7789839d.69b48c",
"type": "ui_template",
"z": "eaae323a.31b3",
"group": "4e0cd5ea.17e59c",
"name": "Optic Configuration",
"order": 1,
"width": 4,
update to main.json to fix camera bugs
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"height": 4,
Main.json: UI upgrade
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"format": "<md-button ng-click=\"send({payload:'Optic Configuration'})\" style=\"height:100%;\">\n <i class=\"fa fa-eye fa-5x\"></i>\n <div style=\"margin-top:30px;\">Optic Configuration</div>\n</md-button>",
"storeOutMessages": true,
"fwdInMessages": true,
"templateScope": "local",
"x": 130,
"y": 100,
Update flows.json
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"wires": [
Main.json: UI upgrade
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[
"2a65c3ec.49a6bc"
]
Update flows.json
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]
},
{
Main.json: UI upgrade
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"id": "6ea6c306.f9c12c",
"type": "ui_template",
"z": "eaae323a.31b3",
"group": "ef590206.24f6",
"name": "Fluidic Acquisition",
"order": 1,
"width": 4,
"height": 4,
"format": "<md-button ng-click=\"send({payload:'Fluidic Acquisition'})\" style=\"height:100%;\">\n <i class=\"fa fa-flask fa-5x\"></i>\n <div style=\"margin-top:30px;\">Fluidic Acquisition</div>\n</md-button>",
"storeOutMessages": true,
"fwdInMessages": true,
"templateScope": "local",
"x": 130,
"y": 140,
Update flows.json
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"wires": [
[
Main.json: UI upgrade
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"2a65c3ec.49a6bc"
Update flows.json
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]
]
},
{
Main.json: UI upgrade
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"id": "bb9eb153.9e36c",
"type": "ui_template",
"z": "eaae323a.31b3",
"group": "ae8f6620.073358",
"name": "Segmentation",
"order": 1,
"width": 4,
update to main.json to fix camera bugs
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"height": 4,
Main.json: UI upgrade
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"format": "<md-button ng-click=\"send({payload:'Segmentation'})\" style=\"height:100%;\">\n <i class=\"fa fa-crop fa-5x\"></i>\n <div style=\"margin-top:30px;\">Segmentation</div>\n</md-button>",
"storeOutMessages": true,
"fwdInMessages": true,
"templateScope": "local",
"x": 140,
"y": 180,
Update flows.json
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"wires": [
Main.json: UI upgrade
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[
"2a65c3ec.49a6bc"
]
Update flows.json
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]
},
{
Main.json: UI upgrade
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"id": "eaf8ee7f.96f44",
"type": "ui_template",
"z": "eaae323a.31b3",
"group": "196518b2.4d53b7",
"name": "Gallery",
"order": 1,
"width": 4,
"height": 4,
"format": "<md-button ng-click=\"send({payload:'Gallery'})\" style=\"height:100%;\">\n <i class=\"fa fa-file-image-o fa-5x\"></i>\n <div style=\"margin-top:30px;\">Gallery</div>\n</md-button>",
"storeOutMessages": true,
"fwdInMessages": true,
"templateScope": "local",
"x": 160,
"y": 220,
Update flows.json
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"wires": [
[
Main.json: UI upgrade
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"2a65c3ec.49a6bc"
Update flows.json
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]
]
},
{
Main.json: UI upgrade
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"id": "811cd88c.daf528",
Update flows.json
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"type": "ui_button",
Main.json: UI upgrade
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"z": "bccd1f23.87219",
"name": "down",
"group": "fbd92986.1028c8",
"order": 5,
"width": 0,
"height": 0,
"passthru": true,
"label": "",
"tooltip": "",
"color": "",
"bgcolor": "",
"icon": "arrow_downward",
"payload": "DOWN",
"payloadType": "str",
"topic": "actuator/focus",
"x": 190,
"y": 640,
"wires": [
[
"65ad39d.b6d4d48"
]
]
},
{
"id": "edda4df4.76de2",
"type": "ui_button",
"z": "bccd1f23.87219",
"name": "up",
"group": "fbd92986.1028c8",
Flow updates
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"order": 1,
Main.json: UI upgrade
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"width": 0,
"height": 0,
Add files via upload
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"passthru": false,
Main.json: UI upgrade
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"label": "",
Add files via upload
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"tooltip": "",
update to main.json to fix camera bugs
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"color": "",
"bgcolor": "",
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"icon": "arrow_upwards",
"payload": "UP",
Add files via upload
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"payloadType": "str",
Main.json: UI upgrade
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"topic": "actuator/focus",
"x": 190,
"y": 600,
"wires": [
[
"65ad39d.b6d4d48"
]
]
},
{
"id": "68962547.34a67c",
"type": "ui_text_input",
"z": "bccd1f23.87219",
"name": "pump_manual_volume",
"label": "Volume to pass (ml)",
"tooltip": "",
"group": "707d9797.c8e798",
"order": 3,
"width": 4,
"height": 1,
"passthru": true,
"mode": "number",
"delay": 300,
"topic": "pump_manual_volume",
"x": 320,
"y": 340,
"wires": [
[
"dc48dc42.98d18"
]
]
},
{
"id": "34c81624.df1cea",
"type": "ui_slider",
"z": "bccd1f23.87219",
"name": "pump_flowrate",
"label": "Flowrate (ml/min)*",
"tooltip": "",
"group": "707d9797.c8e798",
"order": 1,
"width": 0,
"height": 0,
"passthru": true,
"outs": "end",
"topic": "pump_flowrate",
"min": 0,
"max": "20",
"step": "0.1",
"x": 340,
"y": 300,
"wires": [
[
"dc48dc42.98d18"
]
]
},
{
"id": "c1b1469.9650eb8",
"type": "ui_template",
"z": "eaae323a.31b3",
"group": "777a7c33.fcd804",
"name": "Settings",
"order": 1,
"width": 4,
"height": 4,
"format": "<md-button ng-click=\"send({payload:'Settings'})\" style=\"height:100%;\">\n <i class=\"fa fa-cogs fa-5x\"></i>\n <div style=\"margin-top:30px;\">Settings</div>\n</md-button>",
"storeOutMessages": true,
"fwdInMessages": true,
"templateScope": "local",
"x": 160,
"y": 260,
"wires": [
[
"2a65c3ec.49a6bc"
]
]
},
{
"id": "18afe75e.288219",
"type": "ui_gauge",
"z": "c1660bc.e7ff7f8",
"name": "",
"group": "c0ebfc57.42527",
"order": 1,
"width": 0,
"height": 0,
"gtype": "gage",
"title": "gauge",
"label": "units",
"format": "{{value}}",
"min": 0,
"max": 10,
"colors": [
"#00b500",
"#e6e600",
"#ca3838"
],
"seg1": "",
"seg2": "",
"x": 720,
"y": 280,
"wires": []
},
{
"id": "abafd6e6.04a5f8",
"type": "ui_template",
"z": "eaae323a.31b3",
"group": "6f97e7ae.270c48",
"name": "Sample",
"order": 1,
"width": 4,
"height": 4,
"format": "<md-button ng-click=\"send({payload:'Sample'})\" style=\"height:100%;\">\n <i class=\"fa fa-eyedropper fa-5x\"></i>\n <div style=\"margin-top:30px;\">Sample</div>\n <br>\n In doubt? Start Here!\n</md-button>",
"storeOutMessages": true,
"fwdInMessages": true,
"resendOnRefresh": false,
"templateScope": "local",
"x": 160,
"y": 60,
Add files via upload
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"wires": [
[
Main.json: UI upgrade
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"2a65c3ec.49a6bc"
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]
]
},
{
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"id": "4557d689.a4fa88",
"type": "ui_text_input",
"z": "b771c342.49603",
"name": "sample_ship",
"label": "Name of the ship",
"tooltip": "",
"group": "3e1ba03d.f01d8",
"order": 2,
"width": 0,
"height": 0,
"passthru": true,
"mode": "text",
"delay": 300,
"topic": "sample_ship",
"x": 650,
"y": 340,
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"wires": [
[
Main.json: UI upgrade
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"9f501f49.45645"
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]
Main.json: UI upgrade
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]
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},
{
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"id": "fcfc31ae.af3af",
"type": "ui_dropdown",
"z": "b771c342.49603",
"name": "sample_sampling_gear",
"label": "Sampling gear",
"tooltip": "",
"place": "Select",
"group": "3e1ba03d.f01d8",
"order": 5,
"width": 0,
"height": 0,
"passthru": true,
"options": [
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{
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"label": "Plankton net",
"value": "net",
"type": "str"
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},
{
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"label": "Niskin bottle 12L",
"value": "niskin_12L",
"type": "str"
},
{
"label": "Niskin bottle 24L",
"value": "niskin_24L",
"type": "str"
},
{
"label": "Pass Hull",
"value": "pass_hull",
"type": "str"
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}
],
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"payload": "",
"topic": "sample_sampling_gear",
"x": 620,
"y": 460,
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"wires": [
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[
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"9f501f49.45645"
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]
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]
},
{
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"id": "82c5fc77.59c97",
"type": "ui_text_input",
"z": "b771c342.49603",
"name": "sample_operator",
"label": "Name of the operator",
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"tooltip": "",
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"group": "3e1ba03d.f01d8",
"order": 4,
"width": 0,
"height": 0,
"passthru": true,
"mode": "text",
"delay": 300,
"topic": "sample_operator",
"x": 640,
"y": 420,
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"wires": [
[
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"9f501f49.45645"
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]
]
},
{
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"id": "9c882b37.fde668",
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"type": "ui_text_input",
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"z": "b771c342.49603",
"name": "sample_project",
"label": "Name of the project*",
"tooltip": "",
"group": "3e1ba03d.f01d8",
"order": 1,
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"width": 0,
"height": 0,
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"passthru": true,
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"mode": "text",
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"delay": 300,
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"topic": "sample_project",
"x": 640,
"y": 300,
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"wires": [
Main.json: UI upgrade
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[
"9f501f49.45645"
]
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]
},
{
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"id": "94eb4221.9b92c",
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"type": "ui_text_input",
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"z": "b771c342.49603",
"name": "sample_id",
"label": "ID of the station*",
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"tooltip": "",
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"group": "3e1ba03d.f01d8",
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"order": 3,
"width": 0,
"height": 0,
"passthru": true,
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"mode": "text",
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"delay": 300,
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"topic": "sample_id",
"x": 660,
"y": 380,
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"wires": [
Main.json: UI upgrade
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[
"9f501f49.45645"
]
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]
},
{
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"id": "9f501f49.45645",
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"type": "function",
Main.json: UI upgrade
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"z": "b771c342.49603",
"name": "set global",
"func": "var value = msg.payload;\nvar key = msg.topic;\n\nglobal.set(key,value);",
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"outputs": 1,
"noerr": 0,
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"initialize": "",
"finalize": "",
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"x": 960,
"y": 520,
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"wires": [
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[]
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]
},
{
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"id": "cc0ca68b.4263a8",
"type": "ui_dropdown",
"z": "baa1e3d9.cb29d",
"name": "acq_celltype",
"label": "Thickness flowcell*",
"tooltip": "",
"place": "Select option",
"group": "404c301a.19c4e",
"order": 1,
"width": 0,
"height": 0,
"passthru": true,
"options": [
{
"label": "200 μm µ-Slide I Luer",
"value": 200,
"type": "num"
},
{
"label": "400 μm µ-Slide I Luer",
"value": 400,
"type": "num"
},
{
"label": "600 μm µ-Slide I Luer",
"value": 600,
"type": "num"
},
{
"label": "800 μm µ-Slide I Luer",
"value": 800,
"type": "num"
}
],
"payload": "",
"topic": "acq_celltype",
"x": 630,
"y": 80,
Add files via upload
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"wires": [
[
Main.json: UI upgrade
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"fb887036.12429"
Update flows.json
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]
]
},
{
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"id": "fb887036.12429",
Update flows.json
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"type": "function",
Main.json: UI upgrade
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"z": "baa1e3d9.cb29d",
"name": "set global",
"func": "var value = msg.payload;\nvar key = msg.topic;\n\nglobal.set(key,value);",
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"outputs": 1,
"noerr": 0,
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"initialize": "",
"finalize": "",
"x": 840,
"y": 180,
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"wires": [
Main.json: UI upgrade
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[]
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]
},
{
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"id": "222c851d.5d0a3a",
"type": "ui_ui_control",
"z": "b771c342.49603",
"name": "",
"events": "change",
"x": 420,
"y": 1000,
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"wires": [
[]
]
},
{
Main.json: UI upgrade
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"id": "52f6b103.1efb6",
"type": "ui_toast",
"z": "b771c342.49603",
"position": "dialog",
"displayTime": "3",
"highlight": "",
"sendall": true,
"outputs": 1,
"ok": "OK",
"cancel": "",
"raw": false,
"topic": "",
"name": "",
"x": 850,
"y": 1120,
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"wires": [
[]
]
},
{
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"id": "986d960a.c75908",
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"type": "function",
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"z": "b771c342.49603",
"name": "Check form",
"func": "var sample_project= global.get(\"sample_project\");\nvar sample_ship= global.get(\"sample_ship\");\nvar sample_id= global.get(\"sample_id\");\nvar sample_operator= global.get(\"sample_operator\");\nvar sample_sampling_gear= global.get(\"sample_sampling_gear\");\nvar object_lat= global.get(\"object_lat\");\nvar object_lon= global.get(\"object_lon\");\nvar sample_day= global.get(\"sample_day\");\nvar sample_hour= global.get(\"sample_hour\");\n\nif (sample_project === undefined || sample_project === \"\") {\n msg.topic = \"Missing entry :\"\n msg.payload = \"Sample project\"\n}\n\nelse if (sample_ship === undefined || sample_ship === \"\") {\n msg.topic = \"Missing entry :\"\n msg.payload = \"Sample ship\"\n}\n\nelse if (sample_id === undefined || sample_id === \"\") {\n msg.topic = \"Missing entry :\"\n msg.payload = \"Sample ID\"\n}\n\nelse if (sample_operator === undefined || sample_operator === \"\") {\n msg.topic = \"Missing entry :\"\n msg.payload = \"Sample operator\"\n}\n\nelse if (sample_sampling_gear === undefined || sample_sampling_gear === \"\") {\n msg.topic = \"Missing entry :\"\n msg.payload = \"Sample sampling gear\"\n}\n\nelse if (object_lat === undefined || object_lat === null) {\n msg.topic = \"Missing entry :\"\n msg.payload = \"Sample latitude\"\n}\n\nelse if (object_lon === undefined || object_lon === null) {\n msg.topic = \"Missing entry :\"\n msg.payload = \"Sample longitude\"\n}\n\nelse if (sample_day === undefined || sample_day === \"\") {\n msg.topic = \"Missing entry :\"\n msg.payload = \"Date\"\n}\n\nelse if (sample_hour === undefined || sample_hour === \"\") {\n msg.topic = \"Missing entry :\"\n msg.payload = \"Time\"\n}\n\nelse {\n msg.topic = \"Change Tab\"\n msg.payload={\"tab\":\"Optic Configuration\"};\n}\nreturn msg;\n",
Update flows.json
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"outputs": 1,
"noerr": 0,
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"x": 430,
"y": 1060,
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"wires": [
[
Main.json: UI upgrade
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"f5e66a2f.0d09d8"
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]
]
},
{
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"id": "18f44504.cac66b",
"type": "gpsd",
"z": "b771c342.49603",
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"name": "",
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"hostname": "localhost",
"port": "2947",
"tpv": true,
"sky": false,
"info": false,
"device": false,
"gst": false,
"att": false,
"x": 290,
"y": 1240,
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"wires": [
Main.json: UI upgrade
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[]
]
},
{
"id": "726a7822.cd6298",
"type": "ui_ui_control",
"z": "b771c342.49603",
"name": "",
"events": "change",
"x": 840,
"y": 1040,
"wires": [
[]
Update flows.json
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]
},
{
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"id": "f5e66a2f.0d09d8",
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"type": "switch",
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"z": "b771c342.49603",
"name": "",
Update flows.json
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"property": "topic",
"propertyType": "msg",
"rules": [
{
"t": "eq",
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"v": "Change Tab",
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"vt": "str"
},
{
"t": "eq",
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"v": "Missing entry :",
Update flows.json
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"vt": "str"
}
],
"checkall": "true",
"repair": false,
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"outputs": 2,
"x": 610,
"y": 1060,
Update flows.json
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"wires": [
[
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"726a7822.cd6298",
"e2b277c1.07283"
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],
[
Main.json: UI upgrade
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"52f6b103.1efb6"
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]
]
},
{
Main.json: UI upgrade
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"id": "2d128018.6a809",
"type": "ui_text_input",
"z": "b771c342.49603",
"name": "object_lat",
"label": "Latitude of throw",
"tooltip": "In decimal degrees",
"group": "cef1e703.bcf3c8",
"order": 1,
"width": 12,
"height": 1,
"passthru": true,
"mode": "number",
"delay": 300,
"topic": "object_lat",
"x": 660,
"y": 520,
Update flows.json
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"wires": [
[
Main.json: UI upgrade
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"9f501f49.45645"
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]
]
},
{
Main.json: UI upgrade
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"id": "4626c0da.e0dd5",
"type": "ui_text_input",
"z": "b771c342.49603",
"name": "object_lon",
"label": "Longitude of throw",
"tooltip": "",
"group": "cef1e703.bcf3c8",
"order": 2,
"width": 12,
"height": 1,
"passthru": true,
"mode": "number",
"delay": 300,
"topic": "object_lon",
"x": 660,
"y": 560,
Update flows.json
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"wires": [
[
Main.json: UI upgrade
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"9f501f49.45645"
Update flows.json
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]
]
},
{
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"id": "f00f321f.77d76",
"type": "ui_date_picker",
"z": "b771c342.49603",
"name": "object_date",
"label": "Date",
"group": "cef1e703.bcf3c8",
"order": 3,
"width": 12,
"height": 1,
"passthru": true,
"topic": "object_date",
"x": 650,
"y": 600,
Update flows.json
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"wires": [
[
Main.json: UI upgrade
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"29f2b365.4327ec"
Update flows.json
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]
]
},
{
Main.json: UI upgrade
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"id": "207fbdbb.2fe2a2",
"type": "ui_text_input",
"z": "b771c342.49603",
"name": "object_time",
"label": "Time :",
"tooltip": "",
"group": "cef1e703.bcf3c8",
"order": 4,
"width": 12,
"height": 1,
"passthru": true,
"mode": "time",
"delay": 300,
"topic": "object_time",
"x": 650,
"y": 640,
Update flows.json
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"wires": [
Main.json: UI upgrade
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[
"1a945afa.d60aad"
]
Update flows.json
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]
},
{
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"id": "6c792043.b6ff9",
"type": "ui_ui_control",
"z": "bccd1f23.87219",
"name": "",
"events": "change",
"x": 840,
"y": 1000,
Update flows.json
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"wires": [
Main.json: UI upgrade
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[]
Update flows.json
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]
},
{
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"id": "902429eb.ceacb8",
"type": "ui_toast",
"z": "bccd1f23.87219",
"position": "dialog",
"displayTime": "3",
"highlight": "",
"sendall": true,
Update flows.json
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"outputs": 1,
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"ok": "OK",
"cancel": "",
"raw": false,
"topic": "",
"name": "",
"x": 1070,
"y": 1100,
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"wires": [
[]
]
},
{
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"id": "fe840e05.b46f3",
Update flows.json
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"type": "function",
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"z": "bccd1f23.87219",
"name": "Check form",
"func": "var acq_fnumber_objective= global.get(\"acq_fnumber_objective\");\n\nif (acq_fnumber_objective === undefined || acq_fnumber_objective === \"\") {\n msg.topic = \"Missing entry :\"\n msg.payload = \"Focal Length of the objective\"\n}\n\nelse {\n msg.topic = \"Change Tab\"\n msg.payload={\"tab\":\"Fluidic Acquisition\"};\n}\nreturn msg;\n",
Update flows.json
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"outputs": 1,
"noerr": 0,
Main.json: UI upgrade
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"x": 670,
"y": 1060,
Update flows.json
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"wires": [
[
Main.json: UI upgrade
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Update flows.json
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"name": "",
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"events": "change",
"x": 1060,
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"wires": [
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},
{
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},
{
"t": "eq",
"v": "Missing entry :",
"vt": "str"
}
Update flows.json
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],
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"checkall": "true",
"repair": false,
"outputs": 2,
"x": 830,
"y": 1060,
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"wires": [
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[
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Update flows.json
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]
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{
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"id": "5846b1d4.7971b",
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"type": "ui_button",
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"z": "bccd1f23.87219",
"name": "Backward",
"group": "707d9797.c8e798",
"order": 2,
"width": 5,
update to main.json to fix camera bugs
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"height": 1,
Update flows.json
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"passthru": false,
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"label": "",
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"tooltip": "",
"color": "",
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"bgcolor": "",
"icon": "arrow_back",
"payload": "BACKWARD",
Update flows.json
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"payloadType": "str",
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"topic": "actuator/pump",
"x": 180,
"y": 220,
Update flows.json
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"wires": [
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"3cb96380.e575ec"
Update flows.json
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]
]
},
{
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"id": "2cab680b.baf888",
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"type": "ui_button",
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"z": "bccd1f23.87219",
"name": "Forward",
"group": "707d9797.c8e798",
"order": 4,
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update to main.json to fix camera bugs
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"height": 1,
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"passthru": true,
"label": "",
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"tooltip": "",
"color": "",
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Update flows.json
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"payloadType": "str",
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"topic": "actuator/pump",
"x": 180,
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Update flows.json
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"wires": [
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"3cb96380.e575ec"
Update flows.json
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"oncolor": "",
"offvalue": "false",
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"x": 280,
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Update flows.json
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"wires": [
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Update flows.json
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],
"icon": "font-awesome/fa-lightbulb-o"
Update flows.json
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},
{
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"id": "cc966678.da8d08",
"type": "ui_dropdown",
"z": "bccd1f23.87219",
"name": "acq_fnumber_objective",
"label": "M12 Lens*",
Update flows.json
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"tooltip": "",
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"place": "Select option",
"group": "4248342d.e55fac",
ui: add counter fields and fields initialize at 0
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"order": 2,
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"width": 0,
"height": 0,
"passthru": true,
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"options": [
{
"label": "f 25mm 1/2\" 5MP IR",
"value": 25,
"type": "num"
},
{
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},
{
"label": "f 12mm 1/2.5\" 5MP IR",
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},
{
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{
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"value": 6,
"type": "num"
}
],
"payload": "",
"topic": "acq_fnumber_objective",
"x": 1080,
"y": 100,
Update flows.json
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"wires": [
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[
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Update flows.json
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]
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{
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"type": "ui_template",
"z": "bccd1f23.87219",
"group": "4248342d.e55fac",
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"order": 3,
Update flows.json
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"width": 0,
"height": 0,
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"format": "<div>\n Magnification : X\n <span id=\"obj_magnification\" ng-bind-html=\"msg.payload\">\n </span>\n</div>",
"storeOutMessages": true,
"fwdInMessages": true,
"templateScope": "local",
"x": 1670,
"y": 100,
Update flows.json
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"wires": [
[]
]
},
{
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"id": "8038414a.34461",
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"type": "function",
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"z": "bccd1f23.87219",
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Update flows.json
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"outputs": 1,
"noerr": 0,
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"initialize": "",
"finalize": "",
"x": 1280,
"y": 100,
Update flows.json
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"wires": [
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Update flows.json
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"storeOutMessages": true,
"fwdInMessages": true,
"resendOnRefresh": false,
"templateScope": "local",
"x": 1680,
"y": 140,
Update flows.json
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"wires": [
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[]
Update flows.json
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]
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"z": "bccd1f23.87219",
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"name": "min_size",
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Update flows.json
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"width": 0,
"height": 0,
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"format": "<div>\n Smallest cells to explore :\n <span id=\"min_size\" ng-bind-html=\"msg.payload\"></span>\n μm\n</div>",
"storeOutMessages": true,
"fwdInMessages": true,
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"x": 1660,
"y": 180,
"wires": [
[]
]
Update flows.json
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},
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"id": "ad87820f.b1d1e",
Update flows.json
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"type": "function",
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"z": "bccd1f23.87219",
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Update flows.json
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"outputs": 1,
"noerr": 0,
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"x": 1490,
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Update flows.json
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"wires": [
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"9b515beb.4aea48"
Update flows.json
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]
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"id": "d68a52ee.82e8e",
Update flows.json
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"type": "function",
Main.json: UI upgrade
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"z": "bccd1f23.87219",
"name": "get process_pixel",
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Update flows.json
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"outputs": 1,
"noerr": 0,
Extraction and refactor of the python code from node-red flow The rationale for this rewrite is to improve the readability, the modularity, the reliability and the future-proofing of the main python script. All in all, this is now 124 commits that are going to be squashed and merged together, spanning more than two weeks of development and testing. Please test away this release and break things. An upgrading guide will be published in the coming days, along with a new image for people to use if they don't want to upgrade on their own. Read along if you want to know all the goodies! As a starter, the python script was extracted from the main flow, and now lives in its own files at `PlantonScope/scripts/*`. We set up the auto formatting of the code by using [Black](https://github.com/psf/black). This make the code clearer and uniform. We are using the default settings, so if you just install Black and set your editor to format on save using it, you should be good to go. The code is separated in four main processes, each with a specific set of responsibilities: - The main process controls all the others, starts everything up and cleans up on shutdown - The stepper process manages the stepper movements. It's now possible to have simultaneous movements of both motors (this closes #38 ). - The imager process controls the camera and the streaming server via a state machine. - The segmenter process manages the segmentation and its outputs. The segmentation happens recursively in all folders in `/home/pi/PlanktonScope/img/`. Each folder has its own output archive, and bug #26 is now closed. Those processes communicates together using MQTT and json messages. Each message is adressed to one topic. The high level topic controls which process receives the message. The details of each topic is at the end of this commit message. Every imaging sessions has now its own folder, under the `img` root. Metadata are saved individually for every session, in a JSON file in the same directory as the pictures. The configuration is not parsed from `config.json` anymore and passed directly through MQTT messages to the concerned process. A new configuration file has been created: `hardware.json`. This file contains information related to your specific hardware configuration. You can choose to reverse the connection of the motors for example, but you can also define specific speed limits and steps number for your pump and focus stage. This will make it easier for people who wants to experiment with different kind of hardware. It's not necessary to have this file though. If it doesn't exists, the default configuration will be applied. The code is architectured around 6 modules and about 10 classes. I encourage you to have a look at the files, they're pretty straightforward to understand. There is a lot of work left around the node-red code refactoring, dashboard ui improvements, better and clearer LED messages, OLED screen integration and finer control of the segmentation process, but this is quite good for now. Here is the topic lists for MQTT and the corresponding messages. - actuator : This topic adresses the stepper control thread No publication under this topic should happen from the python process - actuator/pump : Control of the pump The message is a json object {"action":"move", "direction":"FORWARD", "volume":10, "flowrate":1} to move 10mL forward at 1mL/min action can be "move" or "stop" Receive only - actuator/focus : Control of the focus stage The message is a json object, speed is optional {"action":"move", "direction":"UP", "distance":0.26, "speed":1} to move up 10mm action can be "move" or "stop" Receive only - imager/image : This topic adresses the imaging thread Is a json object with {"action":"image","sleep":5,"volume":1,"nb_frame":200} sleep in seconds, volume in mL Can also receive a config update message: {"action":"config","config":[...]} Can also receive a camera settings message: {"action":"settings","iso":100,"shutter_speed":40} Receive only - segmenter/segment : This topic adresses the segmenter process Is a json object with {"action":"segment"} Receive only - status : This topics sends feedback to Node-Red No publication or receive at this level - status/pump : State of the pump Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/focus : State of the focus stage Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/imager : State of the imager Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Completed or 12_11_15_0.1.jpg has been imaged. Publish only - status/segmenter : Status of the segmentation - status/segmenter/name - status/segmenter/object_id - status/segmenter/metric Here is the original commit history: * Extract python main.py from flow * Fix bug in server addresses These addresses should be the loopback device instead of the network address of the device. Using the loopback address will not necessitate to update the script when the network address changes. * clean up picamera import * changes to main python and flow: update MQTT requests address to localhost (bugfix) update streaming output address to nothing update main flow to remove python script references and location * Automatically initialise imaging led on startup to off state. * Add the ability to invert outputs of the motor We added a key to config.json "hardware_config" with a subkey "stepper_reverse". If this key is present in the config file and set to 1, the output of the motors are inversed (stepper2 becomes the pump motor and stepper1 the focus motor) * move all non main script to a subfolder * add __init__.py to package * light module rewrite * json cleanup and absolute path for config file * light.py forgot to import subprocess #oups * Add command to turn the leds off * Auto formatting of main.py I've used Black with default settings, see https://github.com/psf/black * First commit of stepper.py Pump parameters still needs to be checked and tuned. * addition of hardware details in config.json * Introduce hardware.json to replace the `hardware_config` of config.json * stepper.py: calibration, typos * creates the MQTT_Client class * pump_max_speed is now in ml/min to help readability * forgot to add self to the class def * addition of threading capabilities to stepper.py (UNTESTED) * mqtt: fix topic bug * remove counter * mqtt add doc about topics * stepper.py creates an "actuator/*/state" topic * stepper.py: rename mqtt_client to pump_client * mqtt.py: add details about topics * stepper.py: rename pump_client to actuator_client * topic was not split properly and a part was lost * switch to f-strings for mqtt.py * cosmetic update * stepper.py: folder name will be planktoscope change calls * hardware.json became more straightforward * stepper.py syntax bugs * stepper.py addition of a received stop command * stepper.py: update to max travel distance * stepper.py: several typos here * rename folder * main.py: reword to reflect folder rename * main.py: remove logic that has been moved to stepper.py and mqtt.py * main.py: update to add mqtt imaging client * mqtt.py: make command and args local to class and output more verbose * make stepper.py a class * main.py: instantiate stepper class and call it * main.py: name mqtt client * update to main.json to reflect main.py changes * fix bugs around pump control * update flows to latest version from Thibault * distance can be a small value, and definitevely should be a float. * unify mqtt topics * unify mqtt output in the main flow * first logger implementation, uses loguru * mqtt: add reason to on_connect * mqtt: add on_disconnect handler * stepper: add more logger calls for debug mainly * main: add levels for logger * imager.py: first move of the imager logic * imager: time import cleanup * imager: morphocut import cleanup * imager: skimage import cleanup * imager: finishing import cleanup * imager: Class creation - WIP Also provides a fix for #26 (see line 190). * imager: threading is needed for Condition() * streamer: get the streamer server its own file * imager: creates start_camera and get the server creation out * imager: subclass multiprocessing.Process * imager: get Pipeline creation its own function * imager: cleanup of self calls * main: code removal and corresponding calls to newly created classes * imager: various formatting changes * main: management of signal shutdown * add requirements.txt * mqtt: messages are now json objects Also, addition of a flag on receiving a new message * mqtt: make message private and add logic to synchronise * stepper: creates the stepper class * stepper: use the new class * stepper: uses the new logic * stepper: add the shutdown event * stepper: add shutdown method * main: add shutdown event * imager: graceful shutdown * stepper: nicer way of checking the Eevnt * self is a required first argument for a method in a class Especially if you use said class private members! * python: various typos and small errors in import * stepper: create mqtt client during init * stepper: instanciate the mqtt client inside run Otherwise it's not accessible from inside the loop. It's a PITA, more information at https://stackoverflow.com/questions/17172878/using-pythons-multiprocessing-process-class * stepper: little bugs and typos all around * mqtt: add shutdown method * mqtt: add connect in init * stepper: fix bugs, sanitize inputs * stepper: work on delay prediction improvements * stepper: json is mean, double quote are mandatory inside * mqtt: add details about message exchanged * imager: first implementation of json messages * main.json: add new tab for RPi management + json for payloads * imager: add state_machine class * stepper: publish last will * imager: major refactor * main: make streaming server process a daemon * mqtt: insert debug statement on close * main: reorder imports * imager: make it work! Reinsert the streaming server logic in there, because there is a problem with the synchronisation part otherwise. Also, eventually, StreamingOuput() will have to be made not global Final very critical learning: it's super duper important to make sure the memory split is at least 256Meg for the GPU. Chaos ensues otherwise * main: changes to accomodate the streamer/imager fusino * imager_state_machine: insert states transition description * stepper: cleanup of code * segmenter: creation of the class * python: include segmenter changes * remove unused files * stepper: check existence of hardware.json * main.json: changes to reflect the python script evolution * remove unecessary TODOs and add some others * main: add check for config and directories * imager: update_config is implemented and we have better management of directories now * segmenter: now work recursively in all folders * flow: the configuration is now sent via mqtt * segmenter: better manage pipeline error * segmenter: declaration of archive_fn in init * imager: small bugs and typos * main: add uniqueID output * imager: add the camera settings message We can now update the ISO, shutter speed and resolution from Node-Red * package.json: update dependencies
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"initialize": "",
"finalize": "",
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"x": 1490,
"y": 140,
Update flows.json
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"wires": [
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[
"3d2360ad.e41e7"
]
Update flows.json
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]
},
{
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"id": "238f26b1.e2089a",
Update flows.json
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"type": "function",
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"z": "bccd1f23.87219",
"name": "get sug_min",
"func": "var sug_min = global.get(\"sug_min\");\nmsg.payload = sug_min;\nreturn msg;",
Update flows.json
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"outputs": 1,
"noerr": 0,
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"x": 1470,
"y": 180,
Update flows.json
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"wires": [
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[
"8e66977b.9166a8"
]
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]
},
{
Main.json: UI upgrade
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"id": "6e0f6d36.a6b854",
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"type": "function",
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"z": "bccd1f23.87219",
"name": "get sug_max",
"func": "var sug_max = global.get(\"sug_max\");\nmsg.payload = sug_max;\nreturn msg;",
Update flows.json
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"outputs": 1,
"noerr": 0,
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"x": 1470,
"y": 220,
"wires": [
[
"26b32f2c.c64fc"
]
]
},
{
"id": "bb2bb7ce.1d1458",
"type": "ui_template",
"z": "baa1e3d9.cb29d",
"group": "858a0e3c.987fe",
"name": "Stream Pi Camera",
"order": 1,
"width": 14,
"height": 11,
"format": "<center>\n <img src=\"http://planktoscope.local:8000/stream.mjpg\"\n width=\"100%\" height=\"100%\">\n</center>",
"storeOutMessages": true,
"fwdInMessages": true,
"resendOnRefresh": false,
"templateScope": "local",
"x": 910,
"y": 40,
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"wires": [
[]
]
},
{
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"id": "d0c5b57d.590818",
"type": "ui_ui_control",
"z": "baa1e3d9.cb29d",
"name": "",
"events": "change",
"x": 1020,
"y": 80,
"wires": [
[]
]
},
{
"id": "16de754c.cc969b",
"type": "ui_button",
"z": "b771c342.49603",
"name": "",
"group": "5517c651.b2f668",
"order": 1,
"width": 12,
"height": 1,
"passthru": false,
"label": "Previous",
Update flows.json
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"tooltip": "",
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"color": "#097479",
"bgcolor": "white",
"icon": "keyboard_return",
"payload": "{\"tab\":\"Home\"}",
"payloadType": "json",
"topic": "",
"x": 280,
"y": 1000,
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"wires": [
[
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"222c851d.5d0a3a"
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]
]
},
{
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"id": "84f3d040.5f7ea",
"type": "ui_button",
"z": "b771c342.49603",
"name": "",
"group": "5517c651.b2f668",
"order": 2,
"width": 12,
"height": 1,
"passthru": false,
"label": "Continue",
Update flows.json
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"tooltip": "",
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"color": "#097479",
"bgcolor": "white",
"icon": "keyboard_tab",
"payload": "{\"tab\":\"Home\"}",
"payloadType": "json",
"topic": "",
"x": 280,
"y": 1060,
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"wires": [
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[
"986d960a.c75908"
]
Update flows.json
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]
},
{
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"id": "f61aaed5.1e64",
"type": "ui_button",
"z": "bccd1f23.87219",
"name": "",
"group": "7a0b4877.a5d268",
"order": 1,
"width": 5,
"height": 1,
"passthru": false,
"label": "Previous",
Update flows.json
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"tooltip": "",
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"color": "#097479",
"bgcolor": "white",
"icon": "keyboard_return",
"payload": "{\"tab\":\"Sample\"}",
"payloadType": "json",
"topic": "",
"x": 500,
"y": 1000,
Update flows.json
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"wires": [
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[
"6c792043.b6ff9"
]
]
},
{
"id": "9ba6ec0a.22c96",
"type": "ui_button",
"z": "bccd1f23.87219",
"name": "",
"group": "7a0b4877.a5d268",
"order": 2,
"width": 5,
"height": 1,
"passthru": false,
"label": "Continue",
"tooltip": "",
"color": "#097479",
"bgcolor": "white",
"icon": "keyboard_tab",
"payload": "{\"tab\":\"Home\"}",
"payloadType": "json",
"topic": "",
"x": 500,
"y": 1060,
"wires": [
[
"fe840e05.b46f3"
]
]
},
{
"id": "c72f8fae.23bd4",
"type": "ui_button",
"z": "baa1e3d9.cb29d",
"name": "",
"group": "b7919ae2.c01788",
"order": 1,
"width": 5,
"height": 1,
"passthru": false,
"label": "Previous",
"tooltip": "",
"color": "#097479",
"bgcolor": "white",
"icon": "keyboard_return",
"payload": "{\"tab\":\"Optic Configuration\"}",
"payloadType": "json",
"topic": "",
"x": 880,
"y": 80,
"wires": [
[
"d0c5b57d.590818"
]
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]
},
{
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"id": "389bef3.d94c61",
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"type": "ui_text_input",
Main.json: UI upgrade
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"z": "baa1e3d9.cb29d",
"name": "acq_volume",
"label": "Volume to pass (ml)",
Update flows.json
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"tooltip": "",
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"group": "4322c187.e73e5",
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"order": 1,
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"width": 5,
"height": 1,
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"passthru": true,
"mode": "number",
"delay": 300,
Main.json: UI upgrade
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"topic": "acq_volume",
"x": 630,
"y": 200,
Update flows.json
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"wires": [
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[
"fb887036.12429"
]
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]
},
{
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"id": "b4d324de.a2bd28",
"type": "ui_worldmap",
"z": "b771c342.49603",
"d": true,
"group": "da2c279f.cbe318",
"order": 6,
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"width": 0,
"height": 0,
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"name": "",
"lat": "1.5",
"lon": "1.5",
"zoom": "4",
"layer": "OSM grey",
"cluster": "1",
"maxage": "",
"usermenu": "hide",
"layers": "hide",
"panit": "false",
"panlock": "false",
"zoomlock": "false",
"hiderightclick": "true",
"coords": "deg",
"showgrid": "false",
"path": "/worldmap",
"x": 840,
"y": 920,
"wires": []
},
{
"id": "cf3e1477.25af68",
"type": "function",
"z": "b771c342.49603",
"d": true,
"name": "set point",
"func": "var sample_id= global.get(\"sample_id\");\nvar object_lat= global.get(\"object_lat\");\nvar object_lon= global.get(\"object_lon\");\n\nif (sample_id === undefined || sample_id === \"\") {\n msg.topic = \"Missing entry :\"\n msg.payload = \"Sample ID\"\n}\nelse if (object_lat === undefined || object_lat === null) {\n msg.topic = \"Missing entry :\"\n msg.payload = \"Sample latitude\"\n}\n\nelse if (object_lon === undefined || object_lon === null) {\n msg.topic = \"Missing entry :\"\n msg.payload = \"Sample longitude\"\n}\n\nelse {\n msg.topic = \"Place\"\n msg.payload={\"name\":sample_id, \"lat\":object_lat, \"lon\":object_lon}\n}\nreturn msg;\n",
"outputs": 1,
"noerr": 0,
"x": 420,
"y": 960,
"wires": [
[
"105e9b1b.725865"
]
]
},
{
"id": "d7a44df2.0fb29",
"type": "ui_button",
"z": "b771c342.49603",
"d": true,
"name": "",
"group": "da2c279f.cbe318",
"order": 5,
"width": 5,
"height": 1,
"passthru": false,
"label": "Place",
"tooltip": "",
"color": "#333333",
"bgcolor": "white",
"icon": "",
"payload": "",
"payloadType": "str",
"topic": "",
"x": 270,
"y": 960,
"wires": [
[
"cf3e1477.25af68"
]
]
},
{
"id": "105e9b1b.725865",
"type": "switch",
"z": "b771c342.49603",
"d": true,
"name": "",
"property": "topic",
"propertyType": "msg",
"rules": [
Update flows.json
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{
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"t": "eq",
"v": "Place",
"vt": "str"
Update flows.json
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},
{
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"t": "eq",
"v": "Missing entry :",
"vt": "str"
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}
],
Main.json: UI upgrade
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"checkall": "true",
"repair": false,
"outputs": 2,
"x": 610,
"y": 960,
Update flows.json
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"wires": [
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[
"b4d324de.a2bd28"
],
[
"10c9c12a.feae6f"
]
Update flows.json
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]
},
{
Main.json: UI upgrade
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"id": "10c9c12a.feae6f",
"type": "ui_toast",
"z": "b771c342.49603",
"d": true,
"position": "dialog",
"displayTime": "3",
"highlight": "",
"sendall": true,
"outputs": 1,
"ok": "OK",
"cancel": "",
"raw": false,
"topic": "",
"name": "",
"x": 850,
"y": 980,
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"wires": [
[]
]
},
{
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"id": "f07dec1d.147ce",
Update flows.json
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"type": "ui_text_input",
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"z": "baa1e3d9.cb29d",
"name": "comment",
"label": "Comment",
"tooltip": "",
"group": "567a49a4.244cb8",
"order": 5,
Update flows.json
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"width": 0,
"height": 0,
"passthru": true,
"mode": "text",
"delay": 300,
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"topic": "comment",
"x": 640,
"y": 280,
Update flows.json
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"wires": [
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[
"fb887036.12429"
]
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]
},
{
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"id": "8bd55b54.8e3938",
"type": "file",
"z": "baa1e3d9.cb29d",
"name": "logs.json",
"filename": "/var/www/logs.json",
"appendNewline": false,
"createDir": false,
"overwriteFile": "false",
"encoding": "none",
"x": 2000,
"y": 1340,
Update flows.json
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"wires": [
[
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"20a2d27e.7ccafe"
Update flows.json
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]
]
},
{
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"id": "99fd2803.0843a8",
Update flows.json
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"type": "function",
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"z": "baa1e3d9.cb29d",
"name": "get global",
"func": "msg.payload = {\n \"comment\":global.get(\"comment\"),\n \"sample_project\":global.get(\"sample_project\"),\n \"sample_ship\":global.get(\"sample_ship\"),\n \"sample_operator\":global.get(\"sample_operator\"),\n \"sample_id\":global.get(\"sample_id\"),\n \"sample_sampling_gear\":global.get(\"sample_sampling_gear\"),\n \n \"sample_hour\":global.get(\"sample_hour\"),\n \"sample_minute\":global.get(\"sample_minute\"),\n \"sample_day\":global.get(\"sample_day\"),\n \"sample_month\":global.get(\"sample_month\"),\n \"sample_year\":global.get(\"sample_year\"),\n \n \"object_lat\":global.get(\"object_lat\"),\n \"object_lon\":global.get(\"object_lon\"),\n \n \"acq_id\":global.get(\"acq_id\"),\n \"acq_fnumber_objective\":global.get(\"acq_fnumber_objective\"),\n \"acq_celltype\":global.get(\"acq_celltype\"),\n \"acq_maximum_mesh\":global.get(\"acq_maximum_mesh\"),\n \"acq_minimum_mesh\":global.get(\"acq_minimum_mesh\"),\n \"process_pixel\":global.get(\"process_pixel\"),\n \n \"acq_camera\":global.get(\"acq_camera\"),\n \"acq_instrument\":global.get(\"acq_instrument\"),\n \"acq_software\":global.get(\"acq_software\"),\n \"acq_instrument_ID\":global.get(\"acq_instrument_ID\"),\n \"acq_volume\":global.get(\"acq_volume\"),\n \"acq_flowrate\":global.get(\"sug_flowrate\")\n }\n\nreturn msg;",
Update flows.json
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"outputs": 1,
"noerr": 0,
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"x": 1820,
"y": 1340,
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"wires": [
[
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"8bd55b54.8e3938"
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]
]
},
{
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"id": "ae692178.d44d1",
"type": "python3-function",
"z": "baa1e3d9.cb29d",
"name": "pump.py",
"func": "from adafruit_motor import stepper\nfrom adafruit_motorkit import MotorKit\nfrom time import sleep\n\nkit = MotorKit()\npump_stepper = kit.stepper1\npump_stepper.release()\n\nstate = str(msg[\"state\"])\nvolume = int(msg[\"volume\"])\norientation = str(msg[\"orientation\"])\nflowrate = float(msg[\"flowrate\"])\n\n\nif(state==\"free\"):\n #35000steps will pass 69ml if sleep(0.05) in between 2 steps\n #1ml is about 35000/69=507steps\n nb_step=volume*507 \n #nb_step=vol*460 if sleep(0) in between 2 steps\n \n duration=(volume*60)/flowrate\n \n delay=(duration/nb_step)-0.005\n \nif(state==\"canceled\"):\n nb_step=0\n \nfor i in range(nb_step):\n pump_stepper.onestep(direction=stepper.BACKWARD, style=stepper.DOUBLE)\n sleep(delay)\n \nsleep(1)\npump_stepper.release()\n\nmsg[\"topic\"] = \"pump\"\nmsg[\"payload\"] = \"done\"\n\nreturn msg",
Update flows.json
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"outputs": 1,
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"x": 1240,
"y": 1260,
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"wires": [
[
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"783209c7.51c5a8"
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]
]
},
{
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"id": "a3fd6b29.2ef5f8",
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"type": "function",
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"z": "baa1e3d9.cb29d",
"name": "pump.js",
"func": "state = global.get(\"state\");\n\nif (state == null){\n state=\"free\"\n}\n\nif(state===\"free\"||state===\"canceled\"){\n volume = global.get(\"acq_volume\");\n flowrate = global.get(\"sug_flowrate\");\n duration=(((volume*60)/flowrate)-2)*1000\n global.set(\"duration\",duration);\n \n msg.volume = volume;\n msg.orientation = \"forward\";\n msg.flowrate = flowrate;\n msg.rgb = {r:0, g:255, b:255}\n msg.state = state\n \n return msg;\n \n \n}",
Update flows.json
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"outputs": 1,
"noerr": 0,
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"x": 1040,
"y": 1360,
"wires": [
[
"ae692178.d44d1",
"e0f9efda.fa4ce"
]
],
"info": "### Focusing\n##### focus.py `nb_step` `orientation`\n\n- `nb_step` : **integer** (from 1 to 100000) - number of step to perform by the stage (about 31um/step)\n- `orientation` : **string** - orientation of the focus either `up` or `down`\n\nExample:\n\n python3.7 $HOME/PlanktonScope/scripts/focus.py 650 up\n"
},
{
"id": "e0f9efda.fa4ce",
"type": "python3-function",
"z": "baa1e3d9.cb29d",
"name": "actuate RGB",
"func": "import smbus\nfrom time import sleep\n\nbus = smbus.SMBus(1)\n\nrgb=msg['rgb']\nbus.write_byte_data(0x0d, 0x00, 0)\nbus.write_byte_data(0x0d, 0x01, rgb[\"r\"])\nbus.write_byte_data(0x0d, 0x02, rgb[\"g\"])\nbus.write_byte_data(0x0d, 0x03, rgb[\"b\"])\nbus.write_byte_data(0x0d, 0x00, 1)\nbus.write_byte_data(0x0d, 0x01, rgb[\"r\"])\nbus.write_byte_data(0x0d, 0x02, rgb[\"g\"])\nbus.write_byte_data(0x0d, 0x03, rgb[\"b\"])\nbus.write_byte_data(0x0d, 0x00, 2)\nbus.write_byte_data(0x0d, 0x01, rgb[\"r\"])\nbus.write_byte_data(0x0d, 0x02, rgb[\"g\"])\nbus.write_byte_data(0x0d, 0x03, rgb[\"b\"])\nreturn msg;",
"outputs": 1,
"x": 1250,
"y": 1200,
Update flows.json
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"wires": [
[
Main.json: UI upgrade
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"3b498e72.6e6292"
Update flows.json
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]
]
},
{
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"id": "7baf5071.dc3b2",
"type": "exec",
"z": "baa1e3d9.cb29d",
"command": "i2cdetect -y 1",
"addpay": false,
"append": "",
"useSpawn": "false",
"timer": "1",
"oldrc": false,
"name": "i2c update",
"x": 1570,
"y": 1200,
"wires": [
[],
[],
[]
]
},
{
"id": "783209c7.51c5a8",
"type": "link out",
"z": "baa1e3d9.cb29d",
"name": "",
"links": [
"e1354861.0bb648",
"2bc762dd.1115ce",
"a50134c.ed45ac8",
"f0ef065a.362028"
],
"x": 1335,
"y": 1260,
"wires": []
},
{
"id": "3b498e72.6e6292",
Update flows.json
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"type": "function",
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"z": "baa1e3d9.cb29d",
"name": "set busy",
"func": "global.set(\"state\",\"busy\");\nreturn msg;",
Update flows.json
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"outputs": 1,
"noerr": 0,
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"x": 1420,
"y": 1200,
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"wires": [
[
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"7baf5071.dc3b2"
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]
]
},
{
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"id": "cd56bb1c.8ce378",
"type": "ui_toast",
"z": "baa1e3d9.cb29d",
"position": "dialog",
"displayTime": "3",
"highlight": "",
"sendall": true,
Update flows.json
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"outputs": 1,
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"ok": "OK",
"cancel": "",
"raw": false,
"topic": "",
"name": "",
"x": 1010,
"y": 1200,
"wires": [
[]
]
},
{
"id": "c82e467c.99e208",
"type": "switch",
"z": "baa1e3d9.cb29d",
"name": "",
"property": "topic",
"propertyType": "msg",
"rules": [
{
"t": "eq",
"v": "Missing entry :",
"vt": "str"
},
{
"t": "eq",
"v": "Start",
"vt": "str"
}
],
"checkall": "true",
"repair": false,
"outputs": 2,
"x": 850,
"y": 1220,
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"wires": [
[
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"cd56bb1c.8ce378"
],
[
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"a642fc0b.b6dd7"
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]
]
},
{
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"id": "c6bd5987.c48f78",
"type": "http request",
"z": "baa1e3d9.cb29d",
"name": "Start timelapse",
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"paytoqs": false,
"url": "http://127.0.0.1/html/cmd_pipe.php?cmd=tl%201",
"tls": "",
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"proxy": "",
"authType": "",
"x": 1100,
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"wires": [
[]
]
},
{
"id": "8c15fd05.81b5",
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"type": "function",
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"z": "baa1e3d9.cb29d",
"name": "get duration acquisition",
"func": "msg.delay = global.get(\"duration\");\n\nreturn msg;",
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"outputs": 1,
"noerr": 0,
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"x": 1290,
"y": 1360,
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"wires": [
[
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"2ff9c0cb.7288b",
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]
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{
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"id": "2ff9c0cb.7288b",
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"rateUnits": "second",
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"randomLast": "5",
"randomUnits": "seconds",
"drop": false,
"x": 1510,
"y": 1360,
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"wires": [
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[
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]
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]
},
{
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"id": "a642fc0b.b6dd7",
"type": "delay",
"z": "baa1e3d9.cb29d",
"name": "",
"pauseType": "delay",
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{
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"group": "b5d61bc7.54fe48",
"order": 1,
"width": 10,
"height": 2,
"gtype": "donut",
"title": "",
"label": "%",
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"format": "{{value}}",
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"min": 0,
"max": "100",
"colors": [
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"#ffffff",
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],
"seg1": "",
"seg2": "",
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"wires": []
},
{
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"op1type": "str",
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"duration": "-1",
"extend": false,
"units": "s",
"reset": "done",
"bytopic": "all",
"outputs": 1,
"x": 1960,
"y": 1600,
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"wires": [
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[
"e98903d2.f35c1"
]
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]
},
{
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"id": "3475ecd5.6655f4",
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"type": "function",
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"z": "baa1e3d9.cb29d",
"name": "stop",
"func": "global.set(\"time_to_wait\",0);\nmsg.payload=\"done\";\nreturn msg;",
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"outputs": 1,
"noerr": 0,
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"x": 1810,
"y": 1500,
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"wires": [
[
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"34929df1.bfe602",
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]
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{
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"id": "e98903d2.f35c1",
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"type": "function",
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"z": "baa1e3d9.cb29d",
"name": "pulse",
"func": "var time_to_wait= global.get(\"time_to_wait\");\n\nif (time_to_wait === undefined || time_to_wait === \"\"|| time_to_wait == NaN) {\n time_to_wait=0\n global.set(\"time_to_wait\",time_to_wait);\n}else {\n time_to_wait++;\n global.set(\"time_to_wait\",time_to_wait);\n duration=global.get(\"duration\")/1000;\n percent=(100* time_to_wait/duration).toFixed(0)\n msg.payload=percent;\n return msg;\n \n}",
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"outputs": 1,
"noerr": 0,
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"x": 2110,
"y": 1600,
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"wires": [
[
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"6aaa3bc6.b7dda4"
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]
]
},
{
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"id": "f0ef065a.362028",
"type": "link in",
"z": "baa1e3d9.cb29d",
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"wires": [
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[]
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},
{
"id": "e6a12f33.c7768",
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"type": "function",
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"z": "baa1e3d9.cb29d",
"name": "mkdir",
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"outputs": 1,
"noerr": 0,
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"x": 1770,
"y": 1140,
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"wires": [
[
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"43c69256.b9633c"
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]
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]
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},
{
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"id": "43c69256.b9633c",
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"outputs": 1,
"noerr": 0,
"x": 2330,
"y": 1240,
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"wires": [
[
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"83a1d49e.a29a48"
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]
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},
{
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"id": "9dcdbf1f.4aa21",
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"rateUnits": "second",
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"randomLast": "5",
"randomUnits": "seconds",
"drop": false,
"x": 2090,
"y": 1260,
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"wires": [
[
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"517f13e8.e0793c"
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]
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{
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"id": "83a1d49e.a29a48",
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"command": "mv",
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"timer": "",
"oldrc": false,
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"name": "",
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"x": 2480,
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{
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"outputs": 1,
"noerr": 0,
"x": 2330,
"y": 1320,
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"wires": [
[
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"87cff57.f6d3708"
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]
]
},
{
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"id": "87cff57.f6d3708",
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"command": "mv",
"addpay": true,
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"timer": "",
"oldrc": false,
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"name": "",
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"x": 2480,
"y": 1340,
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{
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"outputs": 1,
"noerr": 0,
"x": 1430,
"y": 620,
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"wires": [
[]
]
},
{
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"id": "29be525e.0c87fe",
"type": "ui_template",
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"outputs": 1,
"noerr": 0,
"initialize": "",
"finalize": "",
"x": 720,
"y": 380,
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"wires": [
[
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"29be525e.0c87fe",
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]
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"id": "295bd912.8d2556",
"type": "debug",
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"name": "",
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"active": true,
"tosidebar": true,
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"tostatus": false,
"complete": "payload",
"targetType": "msg",
"statusVal": "",
"statusType": "auto",
"x": 950,
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"wires": []
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"id": "7ca7754c.0f731c",
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"name": "",
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"repeat": "",
"crontab": "",
"once": false,
"onceDelay": 0.1,
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"topic": "",
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"payload": "",
"payloadType": "date",
"x": 120,
"y": 420,
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"wires": [
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[
"4c6d21e3.0173c"
]
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]
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{
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"id": "cbb8afed.0a026",
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"name": "LED Output",
"pin": "40",
"set": true,
"level": "0",
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"out": "out",
"x": 450,
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"y": 40,
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"wires": []
},
{
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"outputs": 1,
"noerr": 0,
"x": 280,
"y": 420,
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"wires": [
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[
"c82b48ad.8b5478"
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]
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"id": "a256071b.25a008",
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"appendNewline": true,
"createDir": true,
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"wires": [
Extraction and refactor of the python code from node-red flow The rationale for this rewrite is to improve the readability, the modularity, the reliability and the future-proofing of the main python script. All in all, this is now 124 commits that are going to be squashed and merged together, spanning more than two weeks of development and testing. Please test away this release and break things. An upgrading guide will be published in the coming days, along with a new image for people to use if they don't want to upgrade on their own. Read along if you want to know all the goodies! As a starter, the python script was extracted from the main flow, and now lives in its own files at `PlantonScope/scripts/*`. We set up the auto formatting of the code by using [Black](https://github.com/psf/black). This make the code clearer and uniform. We are using the default settings, so if you just install Black and set your editor to format on save using it, you should be good to go. The code is separated in four main processes, each with a specific set of responsibilities: - The main process controls all the others, starts everything up and cleans up on shutdown - The stepper process manages the stepper movements. It's now possible to have simultaneous movements of both motors (this closes #38 ). - The imager process controls the camera and the streaming server via a state machine. - The segmenter process manages the segmentation and its outputs. The segmentation happens recursively in all folders in `/home/pi/PlanktonScope/img/`. Each folder has its own output archive, and bug #26 is now closed. Those processes communicates together using MQTT and json messages. Each message is adressed to one topic. The high level topic controls which process receives the message. The details of each topic is at the end of this commit message. Every imaging sessions has now its own folder, under the `img` root. Metadata are saved individually for every session, in a JSON file in the same directory as the pictures. The configuration is not parsed from `config.json` anymore and passed directly through MQTT messages to the concerned process. A new configuration file has been created: `hardware.json`. This file contains information related to your specific hardware configuration. You can choose to reverse the connection of the motors for example, but you can also define specific speed limits and steps number for your pump and focus stage. This will make it easier for people who wants to experiment with different kind of hardware. It's not necessary to have this file though. If it doesn't exists, the default configuration will be applied. The code is architectured around 6 modules and about 10 classes. I encourage you to have a look at the files, they're pretty straightforward to understand. There is a lot of work left around the node-red code refactoring, dashboard ui improvements, better and clearer LED messages, OLED screen integration and finer control of the segmentation process, but this is quite good for now. Here is the topic lists for MQTT and the corresponding messages. - actuator : This topic adresses the stepper control thread No publication under this topic should happen from the python process - actuator/pump : Control of the pump The message is a json object {"action":"move", "direction":"FORWARD", "volume":10, "flowrate":1} to move 10mL forward at 1mL/min action can be "move" or "stop" Receive only - actuator/focus : Control of the focus stage The message is a json object, speed is optional {"action":"move", "direction":"UP", "distance":0.26, "speed":1} to move up 10mm action can be "move" or "stop" Receive only - imager/image : This topic adresses the imaging thread Is a json object with {"action":"image","sleep":5,"volume":1,"nb_frame":200} sleep in seconds, volume in mL Can also receive a config update message: {"action":"config","config":[...]} Can also receive a camera settings message: {"action":"settings","iso":100,"shutter_speed":40} Receive only - segmenter/segment : This topic adresses the segmenter process Is a json object with {"action":"segment"} Receive only - status : This topics sends feedback to Node-Red No publication or receive at this level - status/pump : State of the pump Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/focus : State of the focus stage Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/imager : State of the imager Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Completed or 12_11_15_0.1.jpg has been imaged. Publish only - status/segmenter : Status of the segmentation - status/segmenter/name - status/segmenter/object_id - status/segmenter/metric Here is the original commit history: * Extract python main.py from flow * Fix bug in server addresses These addresses should be the loopback device instead of the network address of the device. Using the loopback address will not necessitate to update the script when the network address changes. * clean up picamera import * changes to main python and flow: update MQTT requests address to localhost (bugfix) update streaming output address to nothing update main flow to remove python script references and location * Automatically initialise imaging led on startup to off state. * Add the ability to invert outputs of the motor We added a key to config.json "hardware_config" with a subkey "stepper_reverse". If this key is present in the config file and set to 1, the output of the motors are inversed (stepper2 becomes the pump motor and stepper1 the focus motor) * move all non main script to a subfolder * add __init__.py to package * light module rewrite * json cleanup and absolute path for config file * light.py forgot to import subprocess #oups * Add command to turn the leds off * Auto formatting of main.py I've used Black with default settings, see https://github.com/psf/black * First commit of stepper.py Pump parameters still needs to be checked and tuned. * addition of hardware details in config.json * Introduce hardware.json to replace the `hardware_config` of config.json * stepper.py: calibration, typos * creates the MQTT_Client class * pump_max_speed is now in ml/min to help readability * forgot to add self to the class def * addition of threading capabilities to stepper.py (UNTESTED) * mqtt: fix topic bug * remove counter * mqtt add doc about topics * stepper.py creates an "actuator/*/state" topic * stepper.py: rename mqtt_client to pump_client * mqtt.py: add details about topics * stepper.py: rename pump_client to actuator_client * topic was not split properly and a part was lost * switch to f-strings for mqtt.py * cosmetic update * stepper.py: folder name will be planktoscope change calls * hardware.json became more straightforward * stepper.py syntax bugs * stepper.py addition of a received stop command * stepper.py: update to max travel distance * stepper.py: several typos here * rename folder * main.py: reword to reflect folder rename * main.py: remove logic that has been moved to stepper.py and mqtt.py * main.py: update to add mqtt imaging client * mqtt.py: make command and args local to class and output more verbose * make stepper.py a class * main.py: instantiate stepper class and call it * main.py: name mqtt client * update to main.json to reflect main.py changes * fix bugs around pump control * update flows to latest version from Thibault * distance can be a small value, and definitevely should be a float. * unify mqtt topics * unify mqtt output in the main flow * first logger implementation, uses loguru * mqtt: add reason to on_connect * mqtt: add on_disconnect handler * stepper: add more logger calls for debug mainly * main: add levels for logger * imager.py: first move of the imager logic * imager: time import cleanup * imager: morphocut import cleanup * imager: skimage import cleanup * imager: finishing import cleanup * imager: Class creation - WIP Also provides a fix for #26 (see line 190). * imager: threading is needed for Condition() * streamer: get the streamer server its own file * imager: creates start_camera and get the server creation out * imager: subclass multiprocessing.Process * imager: get Pipeline creation its own function * imager: cleanup of self calls * main: code removal and corresponding calls to newly created classes * imager: various formatting changes * main: management of signal shutdown * add requirements.txt * mqtt: messages are now json objects Also, addition of a flag on receiving a new message * mqtt: make message private and add logic to synchronise * stepper: creates the stepper class * stepper: use the new class * stepper: uses the new logic * stepper: add the shutdown event * stepper: add shutdown method * main: add shutdown event * imager: graceful shutdown * stepper: nicer way of checking the Eevnt * self is a required first argument for a method in a class Especially if you use said class private members! * python: various typos and small errors in import * stepper: create mqtt client during init * stepper: instanciate the mqtt client inside run Otherwise it's not accessible from inside the loop. It's a PITA, more information at https://stackoverflow.com/questions/17172878/using-pythons-multiprocessing-process-class * stepper: little bugs and typos all around * mqtt: add shutdown method * mqtt: add connect in init * stepper: fix bugs, sanitize inputs * stepper: work on delay prediction improvements * stepper: json is mean, double quote are mandatory inside * mqtt: add details about message exchanged * imager: first implementation of json messages * main.json: add new tab for RPi management + json for payloads * imager: add state_machine class * stepper: publish last will * imager: major refactor * main: make streaming server process a daemon * mqtt: insert debug statement on close * main: reorder imports * imager: make it work! Reinsert the streaming server logic in there, because there is a problem with the synchronisation part otherwise. Also, eventually, StreamingOuput() will have to be made not global Final very critical learning: it's super duper important to make sure the memory split is at least 256Meg for the GPU. Chaos ensues otherwise * main: changes to accomodate the streamer/imager fusino * imager_state_machine: insert states transition description * stepper: cleanup of code * segmenter: creation of the class * python: include segmenter changes * remove unused files * stepper: check existence of hardware.json * main.json: changes to reflect the python script evolution * remove unecessary TODOs and add some others * main: add check for config and directories * imager: update_config is implemented and we have better management of directories now * segmenter: now work recursively in all folders * flow: the configuration is now sent via mqtt * segmenter: better manage pipeline error * segmenter: declaration of archive_fn in init * imager: small bugs and typos * main: add uniqueID output * imager: add the camera settings message We can now update the ISO, shutter speed and resolution from Node-Red * package.json: update dependencies
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[
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"3cd4bf1e.11ae3"
Extraction and refactor of the python code from node-red flow The rationale for this rewrite is to improve the readability, the modularity, the reliability and the future-proofing of the main python script. All in all, this is now 124 commits that are going to be squashed and merged together, spanning more than two weeks of development and testing. Please test away this release and break things. An upgrading guide will be published in the coming days, along with a new image for people to use if they don't want to upgrade on their own. Read along if you want to know all the goodies! As a starter, the python script was extracted from the main flow, and now lives in its own files at `PlantonScope/scripts/*`. We set up the auto formatting of the code by using [Black](https://github.com/psf/black). This make the code clearer and uniform. We are using the default settings, so if you just install Black and set your editor to format on save using it, you should be good to go. The code is separated in four main processes, each with a specific set of responsibilities: - The main process controls all the others, starts everything up and cleans up on shutdown - The stepper process manages the stepper movements. It's now possible to have simultaneous movements of both motors (this closes #38 ). - The imager process controls the camera and the streaming server via a state machine. - The segmenter process manages the segmentation and its outputs. The segmentation happens recursively in all folders in `/home/pi/PlanktonScope/img/`. Each folder has its own output archive, and bug #26 is now closed. Those processes communicates together using MQTT and json messages. Each message is adressed to one topic. The high level topic controls which process receives the message. The details of each topic is at the end of this commit message. Every imaging sessions has now its own folder, under the `img` root. Metadata are saved individually for every session, in a JSON file in the same directory as the pictures. The configuration is not parsed from `config.json` anymore and passed directly through MQTT messages to the concerned process. A new configuration file has been created: `hardware.json`. This file contains information related to your specific hardware configuration. You can choose to reverse the connection of the motors for example, but you can also define specific speed limits and steps number for your pump and focus stage. This will make it easier for people who wants to experiment with different kind of hardware. It's not necessary to have this file though. If it doesn't exists, the default configuration will be applied. The code is architectured around 6 modules and about 10 classes. I encourage you to have a look at the files, they're pretty straightforward to understand. There is a lot of work left around the node-red code refactoring, dashboard ui improvements, better and clearer LED messages, OLED screen integration and finer control of the segmentation process, but this is quite good for now. Here is the topic lists for MQTT and the corresponding messages. - actuator : This topic adresses the stepper control thread No publication under this topic should happen from the python process - actuator/pump : Control of the pump The message is a json object {"action":"move", "direction":"FORWARD", "volume":10, "flowrate":1} to move 10mL forward at 1mL/min action can be "move" or "stop" Receive only - actuator/focus : Control of the focus stage The message is a json object, speed is optional {"action":"move", "direction":"UP", "distance":0.26, "speed":1} to move up 10mm action can be "move" or "stop" Receive only - imager/image : This topic adresses the imaging thread Is a json object with {"action":"image","sleep":5,"volume":1,"nb_frame":200} sleep in seconds, volume in mL Can also receive a config update message: {"action":"config","config":[...]} Can also receive a camera settings message: {"action":"settings","iso":100,"shutter_speed":40} Receive only - segmenter/segment : This topic adresses the segmenter process Is a json object with {"action":"segment"} Receive only - status : This topics sends feedback to Node-Red No publication or receive at this level - status/pump : State of the pump Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/focus : State of the focus stage Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/imager : State of the imager Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Completed or 12_11_15_0.1.jpg has been imaged. Publish only - status/segmenter : Status of the segmentation - status/segmenter/name - status/segmenter/object_id - status/segmenter/metric Here is the original commit history: * Extract python main.py from flow * Fix bug in server addresses These addresses should be the loopback device instead of the network address of the device. Using the loopback address will not necessitate to update the script when the network address changes. * clean up picamera import * changes to main python and flow: update MQTT requests address to localhost (bugfix) update streaming output address to nothing update main flow to remove python script references and location * Automatically initialise imaging led on startup to off state. * Add the ability to invert outputs of the motor We added a key to config.json "hardware_config" with a subkey "stepper_reverse". If this key is present in the config file and set to 1, the output of the motors are inversed (stepper2 becomes the pump motor and stepper1 the focus motor) * move all non main script to a subfolder * add __init__.py to package * light module rewrite * json cleanup and absolute path for config file * light.py forgot to import subprocess #oups * Add command to turn the leds off * Auto formatting of main.py I've used Black with default settings, see https://github.com/psf/black * First commit of stepper.py Pump parameters still needs to be checked and tuned. * addition of hardware details in config.json * Introduce hardware.json to replace the `hardware_config` of config.json * stepper.py: calibration, typos * creates the MQTT_Client class * pump_max_speed is now in ml/min to help readability * forgot to add self to the class def * addition of threading capabilities to stepper.py (UNTESTED) * mqtt: fix topic bug * remove counter * mqtt add doc about topics * stepper.py creates an "actuator/*/state" topic * stepper.py: rename mqtt_client to pump_client * mqtt.py: add details about topics * stepper.py: rename pump_client to actuator_client * topic was not split properly and a part was lost * switch to f-strings for mqtt.py * cosmetic update * stepper.py: folder name will be planktoscope change calls * hardware.json became more straightforward * stepper.py syntax bugs * stepper.py addition of a received stop command * stepper.py: update to max travel distance * stepper.py: several typos here * rename folder * main.py: reword to reflect folder rename * main.py: remove logic that has been moved to stepper.py and mqtt.py * main.py: update to add mqtt imaging client * mqtt.py: make command and args local to class and output more verbose * make stepper.py a class * main.py: instantiate stepper class and call it * main.py: name mqtt client * update to main.json to reflect main.py changes * fix bugs around pump control * update flows to latest version from Thibault * distance can be a small value, and definitevely should be a float. * unify mqtt topics * unify mqtt output in the main flow * first logger implementation, uses loguru * mqtt: add reason to on_connect * mqtt: add on_disconnect handler * stepper: add more logger calls for debug mainly * main: add levels for logger * imager.py: first move of the imager logic * imager: time import cleanup * imager: morphocut import cleanup * imager: skimage import cleanup * imager: finishing import cleanup * imager: Class creation - WIP Also provides a fix for #26 (see line 190). * imager: threading is needed for Condition() * streamer: get the streamer server its own file * imager: creates start_camera and get the server creation out * imager: subclass multiprocessing.Process * imager: get Pipeline creation its own function * imager: cleanup of self calls * main: code removal and corresponding calls to newly created classes * imager: various formatting changes * main: management of signal shutdown * add requirements.txt * mqtt: messages are now json objects Also, addition of a flag on receiving a new message * mqtt: make message private and add logic to synchronise * stepper: creates the stepper class * stepper: use the new class * stepper: uses the new logic * stepper: add the shutdown event * stepper: add shutdown method * main: add shutdown event * imager: graceful shutdown * stepper: nicer way of checking the Eevnt * self is a required first argument for a method in a class Especially if you use said class private members! * python: various typos and small errors in import * stepper: create mqtt client during init * stepper: instanciate the mqtt client inside run Otherwise it's not accessible from inside the loop. It's a PITA, more information at https://stackoverflow.com/questions/17172878/using-pythons-multiprocessing-process-class * stepper: little bugs and typos all around * mqtt: add shutdown method * mqtt: add connect in init * stepper: fix bugs, sanitize inputs * stepper: work on delay prediction improvements * stepper: json is mean, double quote are mandatory inside * mqtt: add details about message exchanged * imager: first implementation of json messages * main.json: add new tab for RPi management + json for payloads * imager: add state_machine class * stepper: publish last will * imager: major refactor * main: make streaming server process a daemon * mqtt: insert debug statement on close * main: reorder imports * imager: make it work! Reinsert the streaming server logic in there, because there is a problem with the synchronisation part otherwise. Also, eventually, StreamingOuput() will have to be made not global Final very critical learning: it's super duper important to make sure the memory split is at least 256Meg for the GPU. Chaos ensues otherwise * main: changes to accomodate the streamer/imager fusino * imager_state_machine: insert states transition description * stepper: cleanup of code * segmenter: creation of the class * python: include segmenter changes * remove unused files * stepper: check existence of hardware.json * main.json: changes to reflect the python script evolution * remove unecessary TODOs and add some others * main: add check for config and directories * imager: update_config is implemented and we have better management of directories now * segmenter: now work recursively in all folders * flow: the configuration is now sent via mqtt * segmenter: better manage pipeline error * segmenter: declaration of archive_fn in init * imager: small bugs and typos * main: add uniqueID output * imager: add the camera settings message We can now update the ISO, shutter speed and resolution from Node-Red * package.json: update dependencies
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]
Update flows.json
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]
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{
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"wires": [
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]
]
},
{
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"id": "3cb96380.e575ec",
"type": "function",
"z": "bccd1f23.87219",
"name": "pump.js",
"func": "state = global.get(\"state\");\n\nif (state == null){state=\"free\"}\n\nvar manual_volume= global.get(\"pump_manual_volume\");\nvar flowrate= global.get(\"pump_flowrate\");\n\nif (manual_volume === undefined || manual_volume === \"\" || manual_volume === null) {\n msg.topic = \"Missing entry :\"\n msg.payload = \"Volume to pass\";\n \n}else if (flowrate === undefined || flowrate === \"\" || flowrate === null) {\n msg.topic = \"Missing entry :\"\n msg.payload = \"Flowrate\";\n \n}else {\n volume = global.get(\"pump_manual_volume\");\n msg.volume = volume;\n flowrate = global.get(\"pump_flowrate\");\n msg.topic = \"actuator/pump\";\n \n if(state===\"free\"){\n // msg.payload is FORWARD or BACKWARD here\n msg.payload={\"action\":\"move\", \n \"direction\":msg.payload,\n \"volume\":volume,\n \"flowrate\":flowrate};\n }\n}\nreturn msg;",
"outputs": 1,
"noerr": 0,
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"x": 360,
"y": 240,
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"wires": [
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]
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],
"info": "### Focusing\n##### focus.py `nb_step` `orientation`\n\n- `nb_step` : **integer** (from 1 to 100000) - number of step to perform by the stage (about 31um/step)\n- `orientation` : **string** - orientation of the focus either `up` or `down`\n\nExample:\n\n python3.7 $HOME/PlanktonScope/scripts/focus.py 650 up\n"
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},
{
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"id": "43fa762d.35bcb",
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"type": "switch",
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"z": "bccd1f23.87219",
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"v": "actuator/pump",
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"vt": "str"
},
{
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"checkall": "true",
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"outputs": 2,
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"x": 490,
"y": 240,
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"wires": [
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],
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"8bcce348.efc1a"
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]
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"id": "8bcce348.efc1a",
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"type": "ui_toast",
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"z": "bccd1f23.87219",
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"position": "dialog",
"displayTime": "3",
"highlight": "",
"sendall": true,
"outputs": 1,
"ok": "OK",
"cancel": "",
"raw": false,
"topic": "",
"name": "",
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"x": 650,
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"wires": [
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{
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"id": "bdc8ce57.de1f08",
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"broker": "8dc3722c.06efa8",
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"wires": []
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},
{
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"id": "3d31ee98.a7d6fa",
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"type": "ui_text_input",
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"z": "bccd1f23.87219",
"name": "focus_distance",
"label": "Distance in µm",
"tooltip": "This will be rounded to the nearest 25µm",
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"order": 4,
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"width": 0,
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"mode": "number",
"delay": 300,
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"topic": "focus_distance",
"x": 400,
"y": 440,
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"wires": [
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[
"dbd6bde.99db64"
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]
},
{
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{
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"v": "Missing entry :",
"vt": "str"
}
],
"checkall": "true",
"repair": false,
"outputs": 2,
"x": 470,
"y": 620,
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"wires": [
[
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],
[
"d71d224f.0585d8"
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]
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},
{
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"id": "d71d224f.0585d8",
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"z": "bccd1f23.87219",
"position": "dialog",
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"highlight": "",
"sendall": true,
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"outputs": 1,
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"ok": "OK",
"cancel": "",
"raw": false,
"topic": "",
"name": "",
"x": 650,
"y": 640,
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"wires": [
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[]
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]
},
{
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"id": "65ad39d.b6d4d48",
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"type": "function",
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"z": "bccd1f23.87219",
"name": "focus.js",
"func": "state = global.get(\"state\");\n\nif (state == null){state=\"free\"}\n\nvar distance = global.get(\"focus_distance\");\n\nif (distance === undefined || distance === \"\" || distance === null) {\n msg.topic = \"Missing entry :\"\n msg.payload = \"Distance\";\n}else {\n distance = global.get(\"focus_distance\");\n if(state===\"free\"){\n // msg.payload is UP or DOWN here\n msg.payload={\"action\":\"move\", \n \"direction\":msg.payload,\n \"distance\":(distance/1000)};\n }\n}\nreturn msg;",
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"outputs": 1,
"noerr": 0,
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"initialize": "",
"finalize": "",
"x": 320,
"y": 620,
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"wires": [
[
Main.json: UI upgrade
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"1f7cea1d.fbe61e"
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]
]
},
{
Main.json: UI upgrade
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"id": "1962d999.4a97e6",
"type": "ui_button",
"z": "bccd1f23.87219",
"name": "stop focus",
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"icon": "",
"payload": "{\"action\":\"stop\"}",
"payloadType": "json",
"topic": "actuator/focus",
"x": 180,
"y": 680,
Update flows.json
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"wires": [
[
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"fd05f252.5a90c"
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]
]
},
{
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"id": "62030521.88317c",
"type": "mqtt out",
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"broker": "8dc3722c.06efa8",
"x": 630,
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{
"id": "dbd6bde.99db64",
Update flows.json
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"type": "function",
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"z": "bccd1f23.87219",
"name": "round distance",
"func": "// Here we change the focus_distance to 25 µm increment\nif (msg.payload%25 <= 12.5){\n msg.payload = msg.payload - msg.payload%25\n}\nelse {\n msg.payload = msg.payload + msg.payload%25\n}\nreturn msg;",
Update flows.json
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"outputs": 1,
"noerr": 0,
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"initialize": "",
"finalize": "",
"x": 620,
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Update flows.json
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"3d31ee98.a7d6fa",
"69d4ea6c.4c1e2c",
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Update flows.json
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{
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main.json: add machine name and output disable for steppers
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"width": 0,
"height": 0,
"passthru": false,
"label": "UP 1mm",
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"color": "",
"bgcolor": "",
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"payload": "{\"action\":\"move\",\"direction\":\"UP\",\"distance\":1}",
"payloadType": "json",
"topic": "actuator/focus",
"x": 180,
"y": 520,
Update flows.json
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"wires": [
[
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"62030521.88317c"
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]
]
},
{
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"id": "c0663029.2d03b",
"type": "ui_button",
"z": "bccd1f23.87219",
Update flows.json
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"name": "",
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"group": "fbd92986.1028c8",
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"passthru": false,
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"color": "",
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"payload": "{\"action\":\"move\",\"direction\":\"DOWN\",\"distance\":1}",
"payloadType": "json",
"topic": "actuator/focus",
"x": 170,
"y": 560,
Update flows.json
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"wires": [
Main.json: UI upgrade
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[
"62030521.88317c"
]
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]
},
{
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"id": "69d4ea6c.4c1e2c",
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"outs": "end",
"topic": "focus_distance",
"min": "25",
"max": "2000",
"step": "25",
"x": 400,
"y": 500,
Update flows.json
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"wires": [
[
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"3d31ee98.a7d6fa"
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]
]
},
{
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"id": "71f55a58.d7eaf4",
"type": "inject",
"z": "bccd1f23.87219",
"name": "Default: 500µm",
"props": [
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"crontab": "",
"once": true,
"onceDelay": 0.1,
"topic": "",
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"payloadType": "num",
"x": 120,
"y": 440,
Update flows.json
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"wires": [
[
Main.json: UI upgrade
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"3d31ee98.a7d6fa",
"69d4ea6c.4c1e2c"
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]
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]
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},
{
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"id": "9a1d0e7c.2d5a1",
Update flows.json
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"type": "inject",
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"z": "bccd1f23.87219",
"name": "Default: OFF",
Extraction and refactor of the python code from node-red flow The rationale for this rewrite is to improve the readability, the modularity, the reliability and the future-proofing of the main python script. All in all, this is now 124 commits that are going to be squashed and merged together, spanning more than two weeks of development and testing. Please test away this release and break things. An upgrading guide will be published in the coming days, along with a new image for people to use if they don't want to upgrade on their own. Read along if you want to know all the goodies! As a starter, the python script was extracted from the main flow, and now lives in its own files at `PlantonScope/scripts/*`. We set up the auto formatting of the code by using [Black](https://github.com/psf/black). This make the code clearer and uniform. We are using the default settings, so if you just install Black and set your editor to format on save using it, you should be good to go. The code is separated in four main processes, each with a specific set of responsibilities: - The main process controls all the others, starts everything up and cleans up on shutdown - The stepper process manages the stepper movements. It's now possible to have simultaneous movements of both motors (this closes #38 ). - The imager process controls the camera and the streaming server via a state machine. - The segmenter process manages the segmentation and its outputs. The segmentation happens recursively in all folders in `/home/pi/PlanktonScope/img/`. Each folder has its own output archive, and bug #26 is now closed. Those processes communicates together using MQTT and json messages. Each message is adressed to one topic. The high level topic controls which process receives the message. The details of each topic is at the end of this commit message. Every imaging sessions has now its own folder, under the `img` root. Metadata are saved individually for every session, in a JSON file in the same directory as the pictures. The configuration is not parsed from `config.json` anymore and passed directly through MQTT messages to the concerned process. A new configuration file has been created: `hardware.json`. This file contains information related to your specific hardware configuration. You can choose to reverse the connection of the motors for example, but you can also define specific speed limits and steps number for your pump and focus stage. This will make it easier for people who wants to experiment with different kind of hardware. It's not necessary to have this file though. If it doesn't exists, the default configuration will be applied. The code is architectured around 6 modules and about 10 classes. I encourage you to have a look at the files, they're pretty straightforward to understand. There is a lot of work left around the node-red code refactoring, dashboard ui improvements, better and clearer LED messages, OLED screen integration and finer control of the segmentation process, but this is quite good for now. Here is the topic lists for MQTT and the corresponding messages. - actuator : This topic adresses the stepper control thread No publication under this topic should happen from the python process - actuator/pump : Control of the pump The message is a json object {"action":"move", "direction":"FORWARD", "volume":10, "flowrate":1} to move 10mL forward at 1mL/min action can be "move" or "stop" Receive only - actuator/focus : Control of the focus stage The message is a json object, speed is optional {"action":"move", "direction":"UP", "distance":0.26, "speed":1} to move up 10mm action can be "move" or "stop" Receive only - imager/image : This topic adresses the imaging thread Is a json object with {"action":"image","sleep":5,"volume":1,"nb_frame":200} sleep in seconds, volume in mL Can also receive a config update message: {"action":"config","config":[...]} Can also receive a camera settings message: {"action":"settings","iso":100,"shutter_speed":40} Receive only - segmenter/segment : This topic adresses the segmenter process Is a json object with {"action":"segment"} Receive only - status : This topics sends feedback to Node-Red No publication or receive at this level - status/pump : State of the pump Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/focus : State of the focus stage Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/imager : State of the imager Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Completed or 12_11_15_0.1.jpg has been imaged. Publish only - status/segmenter : Status of the segmentation - status/segmenter/name - status/segmenter/object_id - status/segmenter/metric Here is the original commit history: * Extract python main.py from flow * Fix bug in server addresses These addresses should be the loopback device instead of the network address of the device. Using the loopback address will not necessitate to update the script when the network address changes. * clean up picamera import * changes to main python and flow: update MQTT requests address to localhost (bugfix) update streaming output address to nothing update main flow to remove python script references and location * Automatically initialise imaging led on startup to off state. * Add the ability to invert outputs of the motor We added a key to config.json "hardware_config" with a subkey "stepper_reverse". If this key is present in the config file and set to 1, the output of the motors are inversed (stepper2 becomes the pump motor and stepper1 the focus motor) * move all non main script to a subfolder * add __init__.py to package * light module rewrite * json cleanup and absolute path for config file * light.py forgot to import subprocess #oups * Add command to turn the leds off * Auto formatting of main.py I've used Black with default settings, see https://github.com/psf/black * First commit of stepper.py Pump parameters still needs to be checked and tuned. * addition of hardware details in config.json * Introduce hardware.json to replace the `hardware_config` of config.json * stepper.py: calibration, typos * creates the MQTT_Client class * pump_max_speed is now in ml/min to help readability * forgot to add self to the class def * addition of threading capabilities to stepper.py (UNTESTED) * mqtt: fix topic bug * remove counter * mqtt add doc about topics * stepper.py creates an "actuator/*/state" topic * stepper.py: rename mqtt_client to pump_client * mqtt.py: add details about topics * stepper.py: rename pump_client to actuator_client * topic was not split properly and a part was lost * switch to f-strings for mqtt.py * cosmetic update * stepper.py: folder name will be planktoscope change calls * hardware.json became more straightforward * stepper.py syntax bugs * stepper.py addition of a received stop command * stepper.py: update to max travel distance * stepper.py: several typos here * rename folder * main.py: reword to reflect folder rename * main.py: remove logic that has been moved to stepper.py and mqtt.py * main.py: update to add mqtt imaging client * mqtt.py: make command and args local to class and output more verbose * make stepper.py a class * main.py: instantiate stepper class and call it * main.py: name mqtt client * update to main.json to reflect main.py changes * fix bugs around pump control * update flows to latest version from Thibault * distance can be a small value, and definitevely should be a float. * unify mqtt topics * unify mqtt output in the main flow * first logger implementation, uses loguru * mqtt: add reason to on_connect * mqtt: add on_disconnect handler * stepper: add more logger calls for debug mainly * main: add levels for logger * imager.py: first move of the imager logic * imager: time import cleanup * imager: morphocut import cleanup * imager: skimage import cleanup * imager: finishing import cleanup * imager: Class creation - WIP Also provides a fix for #26 (see line 190). * imager: threading is needed for Condition() * streamer: get the streamer server its own file * imager: creates start_camera and get the server creation out * imager: subclass multiprocessing.Process * imager: get Pipeline creation its own function * imager: cleanup of self calls * main: code removal and corresponding calls to newly created classes * imager: various formatting changes * main: management of signal shutdown * add requirements.txt * mqtt: messages are now json objects Also, addition of a flag on receiving a new message * mqtt: make message private and add logic to synchronise * stepper: creates the stepper class * stepper: use the new class * stepper: uses the new logic * stepper: add the shutdown event * stepper: add shutdown method * main: add shutdown event * imager: graceful shutdown * stepper: nicer way of checking the Eevnt * self is a required first argument for a method in a class Especially if you use said class private members! * python: various typos and small errors in import * stepper: create mqtt client during init * stepper: instanciate the mqtt client inside run Otherwise it's not accessible from inside the loop. It's a PITA, more information at https://stackoverflow.com/questions/17172878/using-pythons-multiprocessing-process-class * stepper: little bugs and typos all around * mqtt: add shutdown method * mqtt: add connect in init * stepper: fix bugs, sanitize inputs * stepper: work on delay prediction improvements * stepper: json is mean, double quote are mandatory inside * mqtt: add details about message exchanged * imager: first implementation of json messages * main.json: add new tab for RPi management + json for payloads * imager: add state_machine class * stepper: publish last will * imager: major refactor * main: make streaming server process a daemon * mqtt: insert debug statement on close * main: reorder imports * imager: make it work! Reinsert the streaming server logic in there, because there is a problem with the synchronisation part otherwise. Also, eventually, StreamingOuput() will have to be made not global Final very critical learning: it's super duper important to make sure the memory split is at least 256Meg for the GPU. Chaos ensues otherwise * main: changes to accomodate the streamer/imager fusino * imager_state_machine: insert states transition description * stepper: cleanup of code * segmenter: creation of the class * python: include segmenter changes * remove unused files * stepper: check existence of hardware.json * main.json: changes to reflect the python script evolution * remove unecessary TODOs and add some others * main: add check for config and directories * imager: update_config is implemented and we have better management of directories now * segmenter: now work recursively in all folders * flow: the configuration is now sent via mqtt * segmenter: better manage pipeline error * segmenter: declaration of archive_fn in init * imager: small bugs and typos * main: add uniqueID output * imager: add the camera settings message We can now update the ISO, shutter speed and resolution from Node-Red * package.json: update dependencies
2020-09-28 11:05:27 +02:00
"props": [
{
"p": "payload"
}
],
Update flows.json
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"repeat": "",
"crontab": "",
"once": true,
"onceDelay": 0.1,
update to main.json to fix camera bugs
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"topic": "",
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"payload": "false",
"payloadType": "bool",
"x": 110,
"y": 40,
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"wires": [
[
Main.json: UI upgrade
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"961d27e7.da65c8"
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]
Main.json: UI upgrade
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]
Update flows.json
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},
{
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"id": "16aa0238.209276",
"type": "ui_slider",
"z": "bccd1f23.87219",
"name": "Iso slider",
"label": "ISO",
"tooltip": "Possible values are 100, 200, 320, 400, 500, 640, 800. 500 by default.",
"group": "4248342d.e55fac",
"order": 10,
"width": 0,
"height": 0,
"passthru": true,
"outs": "end",
"topic": "imager/image",
"min": "100",
"max": "800",
"step": "20",
"x": 360,
"y": 820,
Update flows.json
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"wires": [
[
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"bb090334.1e21a8"
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]
]
},
{
Main.json: UI upgrade
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"id": "bb090334.1e21a8",
Update flows.json
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"type": "function",
Main.json: UI upgrade
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"z": "bccd1f23.87219",
"name": "round iso",
"func": "// Iso should be one of 60, 100, 200, 320, 400, 500, 640, 800\n\nif (msg.payload <= 80){\n msg.payload = 60;\n return msg;\n}\n\nif (msg.payload <= 150){\n msg.payload = 100;\n return msg;\n}\n\nif (msg.payload <= 260){\n msg.payload = 200;\n return msg;\n}\n\nif (msg.payload <= 360){\n msg.payload = 320;\n return msg;\n}\n\nif (msg.payload <= 450){\n msg.payload = 400;\n return msg;\n}\n\nif (msg.payload <= 565){\n msg.payload = 500;\n return msg;\n}\n\nif (msg.payload <= 700){\n msg.payload = 640;\n return msg;\n}\n\n\nif (700 < msg.payload){\n msg.payload = 800;\n return msg;\n}\n",
Update flows.json
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"outputs": 1,
"noerr": 0,
Extraction and refactor of the python code from node-red flow The rationale for this rewrite is to improve the readability, the modularity, the reliability and the future-proofing of the main python script. All in all, this is now 124 commits that are going to be squashed and merged together, spanning more than two weeks of development and testing. Please test away this release and break things. An upgrading guide will be published in the coming days, along with a new image for people to use if they don't want to upgrade on their own. Read along if you want to know all the goodies! As a starter, the python script was extracted from the main flow, and now lives in its own files at `PlantonScope/scripts/*`. We set up the auto formatting of the code by using [Black](https://github.com/psf/black). This make the code clearer and uniform. We are using the default settings, so if you just install Black and set your editor to format on save using it, you should be good to go. The code is separated in four main processes, each with a specific set of responsibilities: - The main process controls all the others, starts everything up and cleans up on shutdown - The stepper process manages the stepper movements. It's now possible to have simultaneous movements of both motors (this closes #38 ). - The imager process controls the camera and the streaming server via a state machine. - The segmenter process manages the segmentation and its outputs. The segmentation happens recursively in all folders in `/home/pi/PlanktonScope/img/`. Each folder has its own output archive, and bug #26 is now closed. Those processes communicates together using MQTT and json messages. Each message is adressed to one topic. The high level topic controls which process receives the message. The details of each topic is at the end of this commit message. Every imaging sessions has now its own folder, under the `img` root. Metadata are saved individually for every session, in a JSON file in the same directory as the pictures. The configuration is not parsed from `config.json` anymore and passed directly through MQTT messages to the concerned process. A new configuration file has been created: `hardware.json`. This file contains information related to your specific hardware configuration. You can choose to reverse the connection of the motors for example, but you can also define specific speed limits and steps number for your pump and focus stage. This will make it easier for people who wants to experiment with different kind of hardware. It's not necessary to have this file though. If it doesn't exists, the default configuration will be applied. The code is architectured around 6 modules and about 10 classes. I encourage you to have a look at the files, they're pretty straightforward to understand. There is a lot of work left around the node-red code refactoring, dashboard ui improvements, better and clearer LED messages, OLED screen integration and finer control of the segmentation process, but this is quite good for now. Here is the topic lists for MQTT and the corresponding messages. - actuator : This topic adresses the stepper control thread No publication under this topic should happen from the python process - actuator/pump : Control of the pump The message is a json object {"action":"move", "direction":"FORWARD", "volume":10, "flowrate":1} to move 10mL forward at 1mL/min action can be "move" or "stop" Receive only - actuator/focus : Control of the focus stage The message is a json object, speed is optional {"action":"move", "direction":"UP", "distance":0.26, "speed":1} to move up 10mm action can be "move" or "stop" Receive only - imager/image : This topic adresses the imaging thread Is a json object with {"action":"image","sleep":5,"volume":1,"nb_frame":200} sleep in seconds, volume in mL Can also receive a config update message: {"action":"config","config":[...]} Can also receive a camera settings message: {"action":"settings","iso":100,"shutter_speed":40} Receive only - segmenter/segment : This topic adresses the segmenter process Is a json object with {"action":"segment"} Receive only - status : This topics sends feedback to Node-Red No publication or receive at this level - status/pump : State of the pump Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/focus : State of the focus stage Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/imager : State of the imager Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Completed or 12_11_15_0.1.jpg has been imaged. Publish only - status/segmenter : Status of the segmentation - status/segmenter/name - status/segmenter/object_id - status/segmenter/metric Here is the original commit history: * Extract python main.py from flow * Fix bug in server addresses These addresses should be the loopback device instead of the network address of the device. Using the loopback address will not necessitate to update the script when the network address changes. * clean up picamera import * changes to main python and flow: update MQTT requests address to localhost (bugfix) update streaming output address to nothing update main flow to remove python script references and location * Automatically initialise imaging led on startup to off state. * Add the ability to invert outputs of the motor We added a key to config.json "hardware_config" with a subkey "stepper_reverse". If this key is present in the config file and set to 1, the output of the motors are inversed (stepper2 becomes the pump motor and stepper1 the focus motor) * move all non main script to a subfolder * add __init__.py to package * light module rewrite * json cleanup and absolute path for config file * light.py forgot to import subprocess #oups * Add command to turn the leds off * Auto formatting of main.py I've used Black with default settings, see https://github.com/psf/black * First commit of stepper.py Pump parameters still needs to be checked and tuned. * addition of hardware details in config.json * Introduce hardware.json to replace the `hardware_config` of config.json * stepper.py: calibration, typos * creates the MQTT_Client class * pump_max_speed is now in ml/min to help readability * forgot to add self to the class def * addition of threading capabilities to stepper.py (UNTESTED) * mqtt: fix topic bug * remove counter * mqtt add doc about topics * stepper.py creates an "actuator/*/state" topic * stepper.py: rename mqtt_client to pump_client * mqtt.py: add details about topics * stepper.py: rename pump_client to actuator_client * topic was not split properly and a part was lost * switch to f-strings for mqtt.py * cosmetic update * stepper.py: folder name will be planktoscope change calls * hardware.json became more straightforward * stepper.py syntax bugs * stepper.py addition of a received stop command * stepper.py: update to max travel distance * stepper.py: several typos here * rename folder * main.py: reword to reflect folder rename * main.py: remove logic that has been moved to stepper.py and mqtt.py * main.py: update to add mqtt imaging client * mqtt.py: make command and args local to class and output more verbose * make stepper.py a class * main.py: instantiate stepper class and call it * main.py: name mqtt client * update to main.json to reflect main.py changes * fix bugs around pump control * update flows to latest version from Thibault * distance can be a small value, and definitevely should be a float. * unify mqtt topics * unify mqtt output in the main flow * first logger implementation, uses loguru * mqtt: add reason to on_connect * mqtt: add on_disconnect handler * stepper: add more logger calls for debug mainly * main: add levels for logger * imager.py: first move of the imager logic * imager: time import cleanup * imager: morphocut import cleanup * imager: skimage import cleanup * imager: finishing import cleanup * imager: Class creation - WIP Also provides a fix for #26 (see line 190). * imager: threading is needed for Condition() * streamer: get the streamer server its own file * imager: creates start_camera and get the server creation out * imager: subclass multiprocessing.Process * imager: get Pipeline creation its own function * imager: cleanup of self calls * main: code removal and corresponding calls to newly created classes * imager: various formatting changes * main: management of signal shutdown * add requirements.txt * mqtt: messages are now json objects Also, addition of a flag on receiving a new message * mqtt: make message private and add logic to synchronise * stepper: creates the stepper class * stepper: use the new class * stepper: uses the new logic * stepper: add the shutdown event * stepper: add shutdown method * main: add shutdown event * imager: graceful shutdown * stepper: nicer way of checking the Eevnt * self is a required first argument for a method in a class Especially if you use said class private members! * python: various typos and small errors in import * stepper: create mqtt client during init * stepper: instanciate the mqtt client inside run Otherwise it's not accessible from inside the loop. It's a PITA, more information at https://stackoverflow.com/questions/17172878/using-pythons-multiprocessing-process-class * stepper: little bugs and typos all around * mqtt: add shutdown method * mqtt: add connect in init * stepper: fix bugs, sanitize inputs * stepper: work on delay prediction improvements * stepper: json is mean, double quote are mandatory inside * mqtt: add details about message exchanged * imager: first implementation of json messages * main.json: add new tab for RPi management + json for payloads * imager: add state_machine class * stepper: publish last will * imager: major refactor * main: make streaming server process a daemon * mqtt: insert debug statement on close * main: reorder imports * imager: make it work! Reinsert the streaming server logic in there, because there is a problem with the synchronisation part otherwise. Also, eventually, StreamingOuput() will have to be made not global Final very critical learning: it's super duper important to make sure the memory split is at least 256Meg for the GPU. Chaos ensues otherwise * main: changes to accomodate the streamer/imager fusino * imager_state_machine: insert states transition description * stepper: cleanup of code * segmenter: creation of the class * python: include segmenter changes * remove unused files * stepper: check existence of hardware.json * main.json: changes to reflect the python script evolution * remove unecessary TODOs and add some others * main: add check for config and directories * imager: update_config is implemented and we have better management of directories now * segmenter: now work recursively in all folders * flow: the configuration is now sent via mqtt * segmenter: better manage pipeline error * segmenter: declaration of archive_fn in init * imager: small bugs and typos * main: add uniqueID output * imager: add the camera settings message We can now update the ISO, shutter speed and resolution from Node-Red * package.json: update dependencies
2020-09-28 11:05:27 +02:00
"initialize": "",
"finalize": "",
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"x": 520,
"y": 820,
Update flows.json
2020-07-14 18:22:31 +02:00
"wires": [
[
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"16aa0238.209276",
"8ea9dc9a.c7d87"
Update flows.json
2020-07-14 18:22:31 +02:00
]
]
},
{
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"id": "8ea9dc9a.c7d87",
"type": "function",
"z": "bccd1f23.87219",
"name": "Encapsulate settings",
"func": "msg.payload = {\n \"action\":\"settings\", \n \"settings\":{\"iso\":msg.payload}\n}\nmsg.topic = \"imager/image\"\nreturn msg;",
"outputs": 1,
"noerr": 0,
"initialize": "",
"finalize": "",
"x": 720,
"y": 820,
Update flows.json
2020-07-14 18:22:31 +02:00
"wires": [
[
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"845e06e1.0d812"
Update flows.json
2020-07-14 18:22:31 +02:00
]
]
},
{
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"id": "5765a825.a595c8",
"type": "ui_slider",
"z": "bccd1f23.87219",
"name": "Shutter speed slider",
"label": "Shutter Speed",
"tooltip": "In microseconds, up to 2500µs, 10µs by default",
"group": "4248342d.e55fac",
"order": 9,
"width": 0,
"height": 0,
"passthru": true,
"outs": "end",
"topic": "imager/image",
"min": "10",
"max": "2500",
"step": "10",
"x": 390,
"y": 880,
Update flows.json
2020-07-14 18:22:31 +02:00
"wires": [
[
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"c38509b.fb08af8"
Update flows.json
2020-07-14 18:22:31 +02:00
]
]
},
{
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"id": "c38509b.fb08af8",
"type": "function",
"z": "bccd1f23.87219",
"name": "Encapsulate settings",
"func": "msg.payload = {\n \"action\":\"settings\", \n \"settings\":{\"shutter_speed\":msg.payload}\n}\nmsg.topic = \"imager/image\"\nreturn msg;",
"outputs": 1,
"noerr": 0,
"initialize": "",
"finalize": "",
"x": 720,
"y": 880,
Update flows.json
2020-07-14 18:22:31 +02:00
"wires": [
[
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"845e06e1.0d812"
Update flows.json
2020-07-14 18:22:31 +02:00
]
]
},
{
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"id": "845e06e1.0d812",
"type": "mqtt out",
"z": "bccd1f23.87219",
Update flows.json
2020-07-14 18:22:31 +02:00
"name": "",
Main.json: UI upgrade
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"topic": "",
"qos": "",
"retain": "",
"broker": "8dc3722c.06efa8",
"x": 930,
"y": 840,
Update flows.json
2020-07-14 18:22:31 +02:00
"wires": []
},
{
Main.json: UI upgrade
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"id": "2350e507.d4e302",
"type": "inject",
"z": "bccd1f23.87219",
"name": "Default: 10µs",
"props": [
{
"p": "payload"
}
],
"repeat": "",
"crontab": "",
"once": true,
"onceDelay": "1",
"topic": "",
"payload": "10",
"payloadType": "num",
"x": 110,
"y": 880,
Update flows.json
2020-07-14 18:22:31 +02:00
"wires": [
[
Main.json: UI upgrade
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"5765a825.a595c8"
Update flows.json
2020-07-14 18:22:31 +02:00
]
]
},
{
Main.json: UI upgrade
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"id": "2edd922b.a471a6",
"type": "inject",
"z": "bccd1f23.87219",
"name": "Default: ISO 100",
"props": [
{
"p": "payload"
}
],
"repeat": "",
"crontab": "",
"once": true,
"onceDelay": "1",
"topic": "",
"payload": "100",
"payloadType": "num",
"x": 120,
"y": 820,
Update flows.json
2020-07-14 18:22:31 +02:00
"wires": [
[
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"16aa0238.209276"
]
]
update to main.json to fix camera bugs
2020-09-15 17:33:49 +02:00
},
{
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"id": "96ff24f0.955f",
"type": "ui_template",
"z": "bccd1f23.87219",
"group": "4248342d.e55fac",
"name": "Camera Settings",
"order": 8,
"width": 0,
"height": 0,
"format": "<center>\nCamera Settings\n</center>",
"storeOutMessages": true,
"fwdInMessages": true,
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"templateScope": "local",
"x": 360,
Extraction and refactor of the python code from node-red flow The rationale for this rewrite is to improve the readability, the modularity, the reliability and the future-proofing of the main python script. All in all, this is now 124 commits that are going to be squashed and merged together, spanning more than two weeks of development and testing. Please test away this release and break things. An upgrading guide will be published in the coming days, along with a new image for people to use if they don't want to upgrade on their own. Read along if you want to know all the goodies! As a starter, the python script was extracted from the main flow, and now lives in its own files at `PlantonScope/scripts/*`. We set up the auto formatting of the code by using [Black](https://github.com/psf/black). This make the code clearer and uniform. We are using the default settings, so if you just install Black and set your editor to format on save using it, you should be good to go. The code is separated in four main processes, each with a specific set of responsibilities: - The main process controls all the others, starts everything up and cleans up on shutdown - The stepper process manages the stepper movements. It's now possible to have simultaneous movements of both motors (this closes #38 ). - The imager process controls the camera and the streaming server via a state machine. - The segmenter process manages the segmentation and its outputs. The segmentation happens recursively in all folders in `/home/pi/PlanktonScope/img/`. Each folder has its own output archive, and bug #26 is now closed. Those processes communicates together using MQTT and json messages. Each message is adressed to one topic. The high level topic controls which process receives the message. The details of each topic is at the end of this commit message. Every imaging sessions has now its own folder, under the `img` root. Metadata are saved individually for every session, in a JSON file in the same directory as the pictures. The configuration is not parsed from `config.json` anymore and passed directly through MQTT messages to the concerned process. A new configuration file has been created: `hardware.json`. This file contains information related to your specific hardware configuration. You can choose to reverse the connection of the motors for example, but you can also define specific speed limits and steps number for your pump and focus stage. This will make it easier for people who wants to experiment with different kind of hardware. It's not necessary to have this file though. If it doesn't exists, the default configuration will be applied. The code is architectured around 6 modules and about 10 classes. I encourage you to have a look at the files, they're pretty straightforward to understand. There is a lot of work left around the node-red code refactoring, dashboard ui improvements, better and clearer LED messages, OLED screen integration and finer control of the segmentation process, but this is quite good for now. Here is the topic lists for MQTT and the corresponding messages. - actuator : This topic adresses the stepper control thread No publication under this topic should happen from the python process - actuator/pump : Control of the pump The message is a json object {"action":"move", "direction":"FORWARD", "volume":10, "flowrate":1} to move 10mL forward at 1mL/min action can be "move" or "stop" Receive only - actuator/focus : Control of the focus stage The message is a json object, speed is optional {"action":"move", "direction":"UP", "distance":0.26, "speed":1} to move up 10mm action can be "move" or "stop" Receive only - imager/image : This topic adresses the imaging thread Is a json object with {"action":"image","sleep":5,"volume":1,"nb_frame":200} sleep in seconds, volume in mL Can also receive a config update message: {"action":"config","config":[...]} Can also receive a camera settings message: {"action":"settings","iso":100,"shutter_speed":40} Receive only - segmenter/segment : This topic adresses the segmenter process Is a json object with {"action":"segment"} Receive only - status : This topics sends feedback to Node-Red No publication or receive at this level - status/pump : State of the pump Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/focus : State of the focus stage Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/imager : State of the imager Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Completed or 12_11_15_0.1.jpg has been imaged. Publish only - status/segmenter : Status of the segmentation - status/segmenter/name - status/segmenter/object_id - status/segmenter/metric Here is the original commit history: * Extract python main.py from flow * Fix bug in server addresses These addresses should be the loopback device instead of the network address of the device. Using the loopback address will not necessitate to update the script when the network address changes. * clean up picamera import * changes to main python and flow: update MQTT requests address to localhost (bugfix) update streaming output address to nothing update main flow to remove python script references and location * Automatically initialise imaging led on startup to off state. * Add the ability to invert outputs of the motor We added a key to config.json "hardware_config" with a subkey "stepper_reverse". If this key is present in the config file and set to 1, the output of the motors are inversed (stepper2 becomes the pump motor and stepper1 the focus motor) * move all non main script to a subfolder * add __init__.py to package * light module rewrite * json cleanup and absolute path for config file * light.py forgot to import subprocess #oups * Add command to turn the leds off * Auto formatting of main.py I've used Black with default settings, see https://github.com/psf/black * First commit of stepper.py Pump parameters still needs to be checked and tuned. * addition of hardware details in config.json * Introduce hardware.json to replace the `hardware_config` of config.json * stepper.py: calibration, typos * creates the MQTT_Client class * pump_max_speed is now in ml/min to help readability * forgot to add self to the class def * addition of threading capabilities to stepper.py (UNTESTED) * mqtt: fix topic bug * remove counter * mqtt add doc about topics * stepper.py creates an "actuator/*/state" topic * stepper.py: rename mqtt_client to pump_client * mqtt.py: add details about topics * stepper.py: rename pump_client to actuator_client * topic was not split properly and a part was lost * switch to f-strings for mqtt.py * cosmetic update * stepper.py: folder name will be planktoscope change calls * hardware.json became more straightforward * stepper.py syntax bugs * stepper.py addition of a received stop command * stepper.py: update to max travel distance * stepper.py: several typos here * rename folder * main.py: reword to reflect folder rename * main.py: remove logic that has been moved to stepper.py and mqtt.py * main.py: update to add mqtt imaging client * mqtt.py: make command and args local to class and output more verbose * make stepper.py a class * main.py: instantiate stepper class and call it * main.py: name mqtt client * update to main.json to reflect main.py changes * fix bugs around pump control * update flows to latest version from Thibault * distance can be a small value, and definitevely should be a float. * unify mqtt topics * unify mqtt output in the main flow * first logger implementation, uses loguru * mqtt: add reason to on_connect * mqtt: add on_disconnect handler * stepper: add more logger calls for debug mainly * main: add levels for logger * imager.py: first move of the imager logic * imager: time import cleanup * imager: morphocut import cleanup * imager: skimage import cleanup * imager: finishing import cleanup * imager: Class creation - WIP Also provides a fix for #26 (see line 190). * imager: threading is needed for Condition() * streamer: get the streamer server its own file * imager: creates start_camera and get the server creation out * imager: subclass multiprocessing.Process * imager: get Pipeline creation its own function * imager: cleanup of self calls * main: code removal and corresponding calls to newly created classes * imager: various formatting changes * main: management of signal shutdown * add requirements.txt * mqtt: messages are now json objects Also, addition of a flag on receiving a new message * mqtt: make message private and add logic to synchronise * stepper: creates the stepper class * stepper: use the new class * stepper: uses the new logic * stepper: add the shutdown event * stepper: add shutdown method * main: add shutdown event * imager: graceful shutdown * stepper: nicer way of checking the Eevnt * self is a required first argument for a method in a class Especially if you use said class private members! * python: various typos and small errors in import * stepper: create mqtt client during init * stepper: instanciate the mqtt client inside run Otherwise it's not accessible from inside the loop. It's a PITA, more information at https://stackoverflow.com/questions/17172878/using-pythons-multiprocessing-process-class * stepper: little bugs and typos all around * mqtt: add shutdown method * mqtt: add connect in init * stepper: fix bugs, sanitize inputs * stepper: work on delay prediction improvements * stepper: json is mean, double quote are mandatory inside * mqtt: add details about message exchanged * imager: first implementation of json messages * main.json: add new tab for RPi management + json for payloads * imager: add state_machine class * stepper: publish last will * imager: major refactor * main: make streaming server process a daemon * mqtt: insert debug statement on close * main: reorder imports * imager: make it work! Reinsert the streaming server logic in there, because there is a problem with the synchronisation part otherwise. Also, eventually, StreamingOuput() will have to be made not global Final very critical learning: it's super duper important to make sure the memory split is at least 256Meg for the GPU. Chaos ensues otherwise * main: changes to accomodate the streamer/imager fusino * imager_state_machine: insert states transition description * stepper: cleanup of code * segmenter: creation of the class * python: include segmenter changes * remove unused files * stepper: check existence of hardware.json * main.json: changes to reflect the python script evolution * remove unecessary TODOs and add some others * main: add check for config and directories * imager: update_config is implemented and we have better management of directories now * segmenter: now work recursively in all folders * flow: the configuration is now sent via mqtt * segmenter: better manage pipeline error * segmenter: declaration of archive_fn in init * imager: small bugs and typos * main: add uniqueID output * imager: add the camera settings message We can now update the ISO, shutter speed and resolution from Node-Red * package.json: update dependencies
2020-09-28 11:05:27 +02:00
"y": 780,
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"wires": [
[]
]
Extraction and refactor of the python code from node-red flow The rationale for this rewrite is to improve the readability, the modularity, the reliability and the future-proofing of the main python script. All in all, this is now 124 commits that are going to be squashed and merged together, spanning more than two weeks of development and testing. Please test away this release and break things. An upgrading guide will be published in the coming days, along with a new image for people to use if they don't want to upgrade on their own. Read along if you want to know all the goodies! As a starter, the python script was extracted from the main flow, and now lives in its own files at `PlantonScope/scripts/*`. We set up the auto formatting of the code by using [Black](https://github.com/psf/black). This make the code clearer and uniform. We are using the default settings, so if you just install Black and set your editor to format on save using it, you should be good to go. The code is separated in four main processes, each with a specific set of responsibilities: - The main process controls all the others, starts everything up and cleans up on shutdown - The stepper process manages the stepper movements. It's now possible to have simultaneous movements of both motors (this closes #38 ). - The imager process controls the camera and the streaming server via a state machine. - The segmenter process manages the segmentation and its outputs. The segmentation happens recursively in all folders in `/home/pi/PlanktonScope/img/`. Each folder has its own output archive, and bug #26 is now closed. Those processes communicates together using MQTT and json messages. Each message is adressed to one topic. The high level topic controls which process receives the message. The details of each topic is at the end of this commit message. Every imaging sessions has now its own folder, under the `img` root. Metadata are saved individually for every session, in a JSON file in the same directory as the pictures. The configuration is not parsed from `config.json` anymore and passed directly through MQTT messages to the concerned process. A new configuration file has been created: `hardware.json`. This file contains information related to your specific hardware configuration. You can choose to reverse the connection of the motors for example, but you can also define specific speed limits and steps number for your pump and focus stage. This will make it easier for people who wants to experiment with different kind of hardware. It's not necessary to have this file though. If it doesn't exists, the default configuration will be applied. The code is architectured around 6 modules and about 10 classes. I encourage you to have a look at the files, they're pretty straightforward to understand. There is a lot of work left around the node-red code refactoring, dashboard ui improvements, better and clearer LED messages, OLED screen integration and finer control of the segmentation process, but this is quite good for now. Here is the topic lists for MQTT and the corresponding messages. - actuator : This topic adresses the stepper control thread No publication under this topic should happen from the python process - actuator/pump : Control of the pump The message is a json object {"action":"move", "direction":"FORWARD", "volume":10, "flowrate":1} to move 10mL forward at 1mL/min action can be "move" or "stop" Receive only - actuator/focus : Control of the focus stage The message is a json object, speed is optional {"action":"move", "direction":"UP", "distance":0.26, "speed":1} to move up 10mm action can be "move" or "stop" Receive only - imager/image : This topic adresses the imaging thread Is a json object with {"action":"image","sleep":5,"volume":1,"nb_frame":200} sleep in seconds, volume in mL Can also receive a config update message: {"action":"config","config":[...]} Can also receive a camera settings message: {"action":"settings","iso":100,"shutter_speed":40} Receive only - segmenter/segment : This topic adresses the segmenter process Is a json object with {"action":"segment"} Receive only - status : This topics sends feedback to Node-Red No publication or receive at this level - status/pump : State of the pump Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/focus : State of the focus stage Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/imager : State of the imager Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Completed or 12_11_15_0.1.jpg has been imaged. Publish only - status/segmenter : Status of the segmentation - status/segmenter/name - status/segmenter/object_id - status/segmenter/metric Here is the original commit history: * Extract python main.py from flow * Fix bug in server addresses These addresses should be the loopback device instead of the network address of the device. Using the loopback address will not necessitate to update the script when the network address changes. * clean up picamera import * changes to main python and flow: update MQTT requests address to localhost (bugfix) update streaming output address to nothing update main flow to remove python script references and location * Automatically initialise imaging led on startup to off state. * Add the ability to invert outputs of the motor We added a key to config.json "hardware_config" with a subkey "stepper_reverse". If this key is present in the config file and set to 1, the output of the motors are inversed (stepper2 becomes the pump motor and stepper1 the focus motor) * move all non main script to a subfolder * add __init__.py to package * light module rewrite * json cleanup and absolute path for config file * light.py forgot to import subprocess #oups * Add command to turn the leds off * Auto formatting of main.py I've used Black with default settings, see https://github.com/psf/black * First commit of stepper.py Pump parameters still needs to be checked and tuned. * addition of hardware details in config.json * Introduce hardware.json to replace the `hardware_config` of config.json * stepper.py: calibration, typos * creates the MQTT_Client class * pump_max_speed is now in ml/min to help readability * forgot to add self to the class def * addition of threading capabilities to stepper.py (UNTESTED) * mqtt: fix topic bug * remove counter * mqtt add doc about topics * stepper.py creates an "actuator/*/state" topic * stepper.py: rename mqtt_client to pump_client * mqtt.py: add details about topics * stepper.py: rename pump_client to actuator_client * topic was not split properly and a part was lost * switch to f-strings for mqtt.py * cosmetic update * stepper.py: folder name will be planktoscope change calls * hardware.json became more straightforward * stepper.py syntax bugs * stepper.py addition of a received stop command * stepper.py: update to max travel distance * stepper.py: several typos here * rename folder * main.py: reword to reflect folder rename * main.py: remove logic that has been moved to stepper.py and mqtt.py * main.py: update to add mqtt imaging client * mqtt.py: make command and args local to class and output more verbose * make stepper.py a class * main.py: instantiate stepper class and call it * main.py: name mqtt client * update to main.json to reflect main.py changes * fix bugs around pump control * update flows to latest version from Thibault * distance can be a small value, and definitevely should be a float. * unify mqtt topics * unify mqtt output in the main flow * first logger implementation, uses loguru * mqtt: add reason to on_connect * mqtt: add on_disconnect handler * stepper: add more logger calls for debug mainly * main: add levels for logger * imager.py: first move of the imager logic * imager: time import cleanup * imager: morphocut import cleanup * imager: skimage import cleanup * imager: finishing import cleanup * imager: Class creation - WIP Also provides a fix for #26 (see line 190). * imager: threading is needed for Condition() * streamer: get the streamer server its own file * imager: creates start_camera and get the server creation out * imager: subclass multiprocessing.Process * imager: get Pipeline creation its own function * imager: cleanup of self calls * main: code removal and corresponding calls to newly created classes * imager: various formatting changes * main: management of signal shutdown * add requirements.txt * mqtt: messages are now json objects Also, addition of a flag on receiving a new message * mqtt: make message private and add logic to synchronise * stepper: creates the stepper class * stepper: use the new class * stepper: uses the new logic * stepper: add the shutdown event * stepper: add shutdown method * main: add shutdown event * imager: graceful shutdown * stepper: nicer way of checking the Eevnt * self is a required first argument for a method in a class Especially if you use said class private members! * python: various typos and small errors in import * stepper: create mqtt client during init * stepper: instanciate the mqtt client inside run Otherwise it's not accessible from inside the loop. It's a PITA, more information at https://stackoverflow.com/questions/17172878/using-pythons-multiprocessing-process-class * stepper: little bugs and typos all around * mqtt: add shutdown method * mqtt: add connect in init * stepper: fix bugs, sanitize inputs * stepper: work on delay prediction improvements * stepper: json is mean, double quote are mandatory inside * mqtt: add details about message exchanged * imager: first implementation of json messages * main.json: add new tab for RPi management + json for payloads * imager: add state_machine class * stepper: publish last will * imager: major refactor * main: make streaming server process a daemon * mqtt: insert debug statement on close * main: reorder imports * imager: make it work! Reinsert the streaming server logic in there, because there is a problem with the synchronisation part otherwise. Also, eventually, StreamingOuput() will have to be made not global Final very critical learning: it's super duper important to make sure the memory split is at least 256Meg for the GPU. Chaos ensues otherwise * main: changes to accomodate the streamer/imager fusino * imager_state_machine: insert states transition description * stepper: cleanup of code * segmenter: creation of the class * python: include segmenter changes * remove unused files * stepper: check existence of hardware.json * main.json: changes to reflect the python script evolution * remove unecessary TODOs and add some others * main: add check for config and directories * imager: update_config is implemented and we have better management of directories now * segmenter: now work recursively in all folders * flow: the configuration is now sent via mqtt * segmenter: better manage pipeline error * segmenter: declaration of archive_fn in init * imager: small bugs and typos * main: add uniqueID output * imager: add the camera settings message We can now update the ISO, shutter speed and resolution from Node-Red * package.json: update dependencies
2020-09-28 11:05:27 +02:00
},
{
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"id": "f782a471.447748",
"type": "inject",
"z": "bccd1f23.87219",
"name": "Default: 5mL/min",
"props": [
{
"p": "payload"
}
],
"repeat": "",
"crontab": "",
"once": true,
"onceDelay": 0.1,
Extraction and refactor of the python code from node-red flow The rationale for this rewrite is to improve the readability, the modularity, the reliability and the future-proofing of the main python script. All in all, this is now 124 commits that are going to be squashed and merged together, spanning more than two weeks of development and testing. Please test away this release and break things. An upgrading guide will be published in the coming days, along with a new image for people to use if they don't want to upgrade on their own. Read along if you want to know all the goodies! As a starter, the python script was extracted from the main flow, and now lives in its own files at `PlantonScope/scripts/*`. We set up the auto formatting of the code by using [Black](https://github.com/psf/black). This make the code clearer and uniform. We are using the default settings, so if you just install Black and set your editor to format on save using it, you should be good to go. The code is separated in four main processes, each with a specific set of responsibilities: - The main process controls all the others, starts everything up and cleans up on shutdown - The stepper process manages the stepper movements. It's now possible to have simultaneous movements of both motors (this closes #38 ). - The imager process controls the camera and the streaming server via a state machine. - The segmenter process manages the segmentation and its outputs. The segmentation happens recursively in all folders in `/home/pi/PlanktonScope/img/`. Each folder has its own output archive, and bug #26 is now closed. Those processes communicates together using MQTT and json messages. Each message is adressed to one topic. The high level topic controls which process receives the message. The details of each topic is at the end of this commit message. Every imaging sessions has now its own folder, under the `img` root. Metadata are saved individually for every session, in a JSON file in the same directory as the pictures. The configuration is not parsed from `config.json` anymore and passed directly through MQTT messages to the concerned process. A new configuration file has been created: `hardware.json`. This file contains information related to your specific hardware configuration. You can choose to reverse the connection of the motors for example, but you can also define specific speed limits and steps number for your pump and focus stage. This will make it easier for people who wants to experiment with different kind of hardware. It's not necessary to have this file though. If it doesn't exists, the default configuration will be applied. The code is architectured around 6 modules and about 10 classes. I encourage you to have a look at the files, they're pretty straightforward to understand. There is a lot of work left around the node-red code refactoring, dashboard ui improvements, better and clearer LED messages, OLED screen integration and finer control of the segmentation process, but this is quite good for now. Here is the topic lists for MQTT and the corresponding messages. - actuator : This topic adresses the stepper control thread No publication under this topic should happen from the python process - actuator/pump : Control of the pump The message is a json object {"action":"move", "direction":"FORWARD", "volume":10, "flowrate":1} to move 10mL forward at 1mL/min action can be "move" or "stop" Receive only - actuator/focus : Control of the focus stage The message is a json object, speed is optional {"action":"move", "direction":"UP", "distance":0.26, "speed":1} to move up 10mm action can be "move" or "stop" Receive only - imager/image : This topic adresses the imaging thread Is a json object with {"action":"image","sleep":5,"volume":1,"nb_frame":200} sleep in seconds, volume in mL Can also receive a config update message: {"action":"config","config":[...]} Can also receive a camera settings message: {"action":"settings","iso":100,"shutter_speed":40} Receive only - segmenter/segment : This topic adresses the segmenter process Is a json object with {"action":"segment"} Receive only - status : This topics sends feedback to Node-Red No publication or receive at this level - status/pump : State of the pump Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/focus : State of the focus stage Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/imager : State of the imager Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Completed or 12_11_15_0.1.jpg has been imaged. Publish only - status/segmenter : Status of the segmentation - status/segmenter/name - status/segmenter/object_id - status/segmenter/metric Here is the original commit history: * Extract python main.py from flow * Fix bug in server addresses These addresses should be the loopback device instead of the network address of the device. Using the loopback address will not necessitate to update the script when the network address changes. * clean up picamera import * changes to main python and flow: update MQTT requests address to localhost (bugfix) update streaming output address to nothing update main flow to remove python script references and location * Automatically initialise imaging led on startup to off state. * Add the ability to invert outputs of the motor We added a key to config.json "hardware_config" with a subkey "stepper_reverse". If this key is present in the config file and set to 1, the output of the motors are inversed (stepper2 becomes the pump motor and stepper1 the focus motor) * move all non main script to a subfolder * add __init__.py to package * light module rewrite * json cleanup and absolute path for config file * light.py forgot to import subprocess #oups * Add command to turn the leds off * Auto formatting of main.py I've used Black with default settings, see https://github.com/psf/black * First commit of stepper.py Pump parameters still needs to be checked and tuned. * addition of hardware details in config.json * Introduce hardware.json to replace the `hardware_config` of config.json * stepper.py: calibration, typos * creates the MQTT_Client class * pump_max_speed is now in ml/min to help readability * forgot to add self to the class def * addition of threading capabilities to stepper.py (UNTESTED) * mqtt: fix topic bug * remove counter * mqtt add doc about topics * stepper.py creates an "actuator/*/state" topic * stepper.py: rename mqtt_client to pump_client * mqtt.py: add details about topics * stepper.py: rename pump_client to actuator_client * topic was not split properly and a part was lost * switch to f-strings for mqtt.py * cosmetic update * stepper.py: folder name will be planktoscope change calls * hardware.json became more straightforward * stepper.py syntax bugs * stepper.py addition of a received stop command * stepper.py: update to max travel distance * stepper.py: several typos here * rename folder * main.py: reword to reflect folder rename * main.py: remove logic that has been moved to stepper.py and mqtt.py * main.py: update to add mqtt imaging client * mqtt.py: make command and args local to class and output more verbose * make stepper.py a class * main.py: instantiate stepper class and call it * main.py: name mqtt client * update to main.json to reflect main.py changes * fix bugs around pump control * update flows to latest version from Thibault * distance can be a small value, and definitevely should be a float. * unify mqtt topics * unify mqtt output in the main flow * first logger implementation, uses loguru * mqtt: add reason to on_connect * mqtt: add on_disconnect handler * stepper: add more logger calls for debug mainly * main: add levels for logger * imager.py: first move of the imager logic * imager: time import cleanup * imager: morphocut import cleanup * imager: skimage import cleanup * imager: finishing import cleanup * imager: Class creation - WIP Also provides a fix for #26 (see line 190). * imager: threading is needed for Condition() * streamer: get the streamer server its own file * imager: creates start_camera and get the server creation out * imager: subclass multiprocessing.Process * imager: get Pipeline creation its own function * imager: cleanup of self calls * main: code removal and corresponding calls to newly created classes * imager: various formatting changes * main: management of signal shutdown * add requirements.txt * mqtt: messages are now json objects Also, addition of a flag on receiving a new message * mqtt: make message private and add logic to synchronise * stepper: creates the stepper class * stepper: use the new class * stepper: uses the new logic * stepper: add the shutdown event * stepper: add shutdown method * main: add shutdown event * imager: graceful shutdown * stepper: nicer way of checking the Eevnt * self is a required first argument for a method in a class Especially if you use said class private members! * python: various typos and small errors in import * stepper: create mqtt client during init * stepper: instanciate the mqtt client inside run Otherwise it's not accessible from inside the loop. It's a PITA, more information at https://stackoverflow.com/questions/17172878/using-pythons-multiprocessing-process-class * stepper: little bugs and typos all around * mqtt: add shutdown method * mqtt: add connect in init * stepper: fix bugs, sanitize inputs * stepper: work on delay prediction improvements * stepper: json is mean, double quote are mandatory inside * mqtt: add details about message exchanged * imager: first implementation of json messages * main.json: add new tab for RPi management + json for payloads * imager: add state_machine class * stepper: publish last will * imager: major refactor * main: make streaming server process a daemon * mqtt: insert debug statement on close * main: reorder imports * imager: make it work! Reinsert the streaming server logic in there, because there is a problem with the synchronisation part otherwise. Also, eventually, StreamingOuput() will have to be made not global Final very critical learning: it's super duper important to make sure the memory split is at least 256Meg for the GPU. Chaos ensues otherwise * main: changes to accomodate the streamer/imager fusino * imager_state_machine: insert states transition description * stepper: cleanup of code * segmenter: creation of the class * python: include segmenter changes * remove unused files * stepper: check existence of hardware.json * main.json: changes to reflect the python script evolution * remove unecessary TODOs and add some others * main: add check for config and directories * imager: update_config is implemented and we have better management of directories now * segmenter: now work recursively in all folders * flow: the configuration is now sent via mqtt * segmenter: better manage pipeline error * segmenter: declaration of archive_fn in init * imager: small bugs and typos * main: add uniqueID output * imager: add the camera settings message We can now update the ISO, shutter speed and resolution from Node-Red * package.json: update dependencies
2020-09-28 11:05:27 +02:00
"topic": "",
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"payload": "5",
"payloadType": "num",
"x": 130,
"y": 300,
Extraction and refactor of the python code from node-red flow The rationale for this rewrite is to improve the readability, the modularity, the reliability and the future-proofing of the main python script. All in all, this is now 124 commits that are going to be squashed and merged together, spanning more than two weeks of development and testing. Please test away this release and break things. An upgrading guide will be published in the coming days, along with a new image for people to use if they don't want to upgrade on their own. Read along if you want to know all the goodies! As a starter, the python script was extracted from the main flow, and now lives in its own files at `PlantonScope/scripts/*`. We set up the auto formatting of the code by using [Black](https://github.com/psf/black). This make the code clearer and uniform. We are using the default settings, so if you just install Black and set your editor to format on save using it, you should be good to go. The code is separated in four main processes, each with a specific set of responsibilities: - The main process controls all the others, starts everything up and cleans up on shutdown - The stepper process manages the stepper movements. It's now possible to have simultaneous movements of both motors (this closes #38 ). - The imager process controls the camera and the streaming server via a state machine. - The segmenter process manages the segmentation and its outputs. The segmentation happens recursively in all folders in `/home/pi/PlanktonScope/img/`. Each folder has its own output archive, and bug #26 is now closed. Those processes communicates together using MQTT and json messages. Each message is adressed to one topic. The high level topic controls which process receives the message. The details of each topic is at the end of this commit message. Every imaging sessions has now its own folder, under the `img` root. Metadata are saved individually for every session, in a JSON file in the same directory as the pictures. The configuration is not parsed from `config.json` anymore and passed directly through MQTT messages to the concerned process. A new configuration file has been created: `hardware.json`. This file contains information related to your specific hardware configuration. You can choose to reverse the connection of the motors for example, but you can also define specific speed limits and steps number for your pump and focus stage. This will make it easier for people who wants to experiment with different kind of hardware. It's not necessary to have this file though. If it doesn't exists, the default configuration will be applied. The code is architectured around 6 modules and about 10 classes. I encourage you to have a look at the files, they're pretty straightforward to understand. There is a lot of work left around the node-red code refactoring, dashboard ui improvements, better and clearer LED messages, OLED screen integration and finer control of the segmentation process, but this is quite good for now. Here is the topic lists for MQTT and the corresponding messages. - actuator : This topic adresses the stepper control thread No publication under this topic should happen from the python process - actuator/pump : Control of the pump The message is a json object {"action":"move", "direction":"FORWARD", "volume":10, "flowrate":1} to move 10mL forward at 1mL/min action can be "move" or "stop" Receive only - actuator/focus : Control of the focus stage The message is a json object, speed is optional {"action":"move", "direction":"UP", "distance":0.26, "speed":1} to move up 10mm action can be "move" or "stop" Receive only - imager/image : This topic adresses the imaging thread Is a json object with {"action":"image","sleep":5,"volume":1,"nb_frame":200} sleep in seconds, volume in mL Can also receive a config update message: {"action":"config","config":[...]} Can also receive a camera settings message: {"action":"settings","iso":100,"shutter_speed":40} Receive only - segmenter/segment : This topic adresses the segmenter process Is a json object with {"action":"segment"} Receive only - status : This topics sends feedback to Node-Red No publication or receive at this level - status/pump : State of the pump Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/focus : State of the focus stage Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/imager : State of the imager Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Completed or 12_11_15_0.1.jpg has been imaged. Publish only - status/segmenter : Status of the segmentation - status/segmenter/name - status/segmenter/object_id - status/segmenter/metric Here is the original commit history: * Extract python main.py from flow * Fix bug in server addresses These addresses should be the loopback device instead of the network address of the device. Using the loopback address will not necessitate to update the script when the network address changes. * clean up picamera import * changes to main python and flow: update MQTT requests address to localhost (bugfix) update streaming output address to nothing update main flow to remove python script references and location * Automatically initialise imaging led on startup to off state. * Add the ability to invert outputs of the motor We added a key to config.json "hardware_config" with a subkey "stepper_reverse". If this key is present in the config file and set to 1, the output of the motors are inversed (stepper2 becomes the pump motor and stepper1 the focus motor) * move all non main script to a subfolder * add __init__.py to package * light module rewrite * json cleanup and absolute path for config file * light.py forgot to import subprocess #oups * Add command to turn the leds off * Auto formatting of main.py I've used Black with default settings, see https://github.com/psf/black * First commit of stepper.py Pump parameters still needs to be checked and tuned. * addition of hardware details in config.json * Introduce hardware.json to replace the `hardware_config` of config.json * stepper.py: calibration, typos * creates the MQTT_Client class * pump_max_speed is now in ml/min to help readability * forgot to add self to the class def * addition of threading capabilities to stepper.py (UNTESTED) * mqtt: fix topic bug * remove counter * mqtt add doc about topics * stepper.py creates an "actuator/*/state" topic * stepper.py: rename mqtt_client to pump_client * mqtt.py: add details about topics * stepper.py: rename pump_client to actuator_client * topic was not split properly and a part was lost * switch to f-strings for mqtt.py * cosmetic update * stepper.py: folder name will be planktoscope change calls * hardware.json became more straightforward * stepper.py syntax bugs * stepper.py addition of a received stop command * stepper.py: update to max travel distance * stepper.py: several typos here * rename folder * main.py: reword to reflect folder rename * main.py: remove logic that has been moved to stepper.py and mqtt.py * main.py: update to add mqtt imaging client * mqtt.py: make command and args local to class and output more verbose * make stepper.py a class * main.py: instantiate stepper class and call it * main.py: name mqtt client * update to main.json to reflect main.py changes * fix bugs around pump control * update flows to latest version from Thibault * distance can be a small value, and definitevely should be a float. * unify mqtt topics * unify mqtt output in the main flow * first logger implementation, uses loguru * mqtt: add reason to on_connect * mqtt: add on_disconnect handler * stepper: add more logger calls for debug mainly * main: add levels for logger * imager.py: first move of the imager logic * imager: time import cleanup * imager: morphocut import cleanup * imager: skimage import cleanup * imager: finishing import cleanup * imager: Class creation - WIP Also provides a fix for #26 (see line 190). * imager: threading is needed for Condition() * streamer: get the streamer server its own file * imager: creates start_camera and get the server creation out * imager: subclass multiprocessing.Process * imager: get Pipeline creation its own function * imager: cleanup of self calls * main: code removal and corresponding calls to newly created classes * imager: various formatting changes * main: management of signal shutdown * add requirements.txt * mqtt: messages are now json objects Also, addition of a flag on receiving a new message * mqtt: make message private and add logic to synchronise * stepper: creates the stepper class * stepper: use the new class * stepper: uses the new logic * stepper: add the shutdown event * stepper: add shutdown method * main: add shutdown event * imager: graceful shutdown * stepper: nicer way of checking the Eevnt * self is a required first argument for a method in a class Especially if you use said class private members! * python: various typos and small errors in import * stepper: create mqtt client during init * stepper: instanciate the mqtt client inside run Otherwise it's not accessible from inside the loop. It's a PITA, more information at https://stackoverflow.com/questions/17172878/using-pythons-multiprocessing-process-class * stepper: little bugs and typos all around * mqtt: add shutdown method * mqtt: add connect in init * stepper: fix bugs, sanitize inputs * stepper: work on delay prediction improvements * stepper: json is mean, double quote are mandatory inside * mqtt: add details about message exchanged * imager: first implementation of json messages * main.json: add new tab for RPi management + json for payloads * imager: add state_machine class * stepper: publish last will * imager: major refactor * main: make streaming server process a daemon * mqtt: insert debug statement on close * main: reorder imports * imager: make it work! Reinsert the streaming server logic in there, because there is a problem with the synchronisation part otherwise. Also, eventually, StreamingOuput() will have to be made not global Final very critical learning: it's super duper important to make sure the memory split is at least 256Meg for the GPU. Chaos ensues otherwise * main: changes to accomodate the streamer/imager fusino * imager_state_machine: insert states transition description * stepper: cleanup of code * segmenter: creation of the class * python: include segmenter changes * remove unused files * stepper: check existence of hardware.json * main.json: changes to reflect the python script evolution * remove unecessary TODOs and add some others * main: add check for config and directories * imager: update_config is implemented and we have better management of directories now * segmenter: now work recursively in all folders * flow: the configuration is now sent via mqtt * segmenter: better manage pipeline error * segmenter: declaration of archive_fn in init * imager: small bugs and typos * main: add uniqueID output * imager: add the camera settings message We can now update the ISO, shutter speed and resolution from Node-Red * package.json: update dependencies
2020-09-28 11:05:27 +02:00
"wires": [
[
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"34c81624.df1cea"
Extraction and refactor of the python code from node-red flow The rationale for this rewrite is to improve the readability, the modularity, the reliability and the future-proofing of the main python script. All in all, this is now 124 commits that are going to be squashed and merged together, spanning more than two weeks of development and testing. Please test away this release and break things. An upgrading guide will be published in the coming days, along with a new image for people to use if they don't want to upgrade on their own. Read along if you want to know all the goodies! As a starter, the python script was extracted from the main flow, and now lives in its own files at `PlantonScope/scripts/*`. We set up the auto formatting of the code by using [Black](https://github.com/psf/black). This make the code clearer and uniform. We are using the default settings, so if you just install Black and set your editor to format on save using it, you should be good to go. The code is separated in four main processes, each with a specific set of responsibilities: - The main process controls all the others, starts everything up and cleans up on shutdown - The stepper process manages the stepper movements. It's now possible to have simultaneous movements of both motors (this closes #38 ). - The imager process controls the camera and the streaming server via a state machine. - The segmenter process manages the segmentation and its outputs. The segmentation happens recursively in all folders in `/home/pi/PlanktonScope/img/`. Each folder has its own output archive, and bug #26 is now closed. Those processes communicates together using MQTT and json messages. Each message is adressed to one topic. The high level topic controls which process receives the message. The details of each topic is at the end of this commit message. Every imaging sessions has now its own folder, under the `img` root. Metadata are saved individually for every session, in a JSON file in the same directory as the pictures. The configuration is not parsed from `config.json` anymore and passed directly through MQTT messages to the concerned process. A new configuration file has been created: `hardware.json`. This file contains information related to your specific hardware configuration. You can choose to reverse the connection of the motors for example, but you can also define specific speed limits and steps number for your pump and focus stage. This will make it easier for people who wants to experiment with different kind of hardware. It's not necessary to have this file though. If it doesn't exists, the default configuration will be applied. The code is architectured around 6 modules and about 10 classes. I encourage you to have a look at the files, they're pretty straightforward to understand. There is a lot of work left around the node-red code refactoring, dashboard ui improvements, better and clearer LED messages, OLED screen integration and finer control of the segmentation process, but this is quite good for now. Here is the topic lists for MQTT and the corresponding messages. - actuator : This topic adresses the stepper control thread No publication under this topic should happen from the python process - actuator/pump : Control of the pump The message is a json object {"action":"move", "direction":"FORWARD", "volume":10, "flowrate":1} to move 10mL forward at 1mL/min action can be "move" or "stop" Receive only - actuator/focus : Control of the focus stage The message is a json object, speed is optional {"action":"move", "direction":"UP", "distance":0.26, "speed":1} to move up 10mm action can be "move" or "stop" Receive only - imager/image : This topic adresses the imaging thread Is a json object with {"action":"image","sleep":5,"volume":1,"nb_frame":200} sleep in seconds, volume in mL Can also receive a config update message: {"action":"config","config":[...]} Can also receive a camera settings message: {"action":"settings","iso":100,"shutter_speed":40} Receive only - segmenter/segment : This topic adresses the segmenter process Is a json object with {"action":"segment"} Receive only - status : This topics sends feedback to Node-Red No publication or receive at this level - status/pump : State of the pump Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/focus : State of the focus stage Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/imager : State of the imager Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Completed or 12_11_15_0.1.jpg has been imaged. Publish only - status/segmenter : Status of the segmentation - status/segmenter/name - status/segmenter/object_id - status/segmenter/metric Here is the original commit history: * Extract python main.py from flow * Fix bug in server addresses These addresses should be the loopback device instead of the network address of the device. Using the loopback address will not necessitate to update the script when the network address changes. * clean up picamera import * changes to main python and flow: update MQTT requests address to localhost (bugfix) update streaming output address to nothing update main flow to remove python script references and location * Automatically initialise imaging led on startup to off state. * Add the ability to invert outputs of the motor We added a key to config.json "hardware_config" with a subkey "stepper_reverse". If this key is present in the config file and set to 1, the output of the motors are inversed (stepper2 becomes the pump motor and stepper1 the focus motor) * move all non main script to a subfolder * add __init__.py to package * light module rewrite * json cleanup and absolute path for config file * light.py forgot to import subprocess #oups * Add command to turn the leds off * Auto formatting of main.py I've used Black with default settings, see https://github.com/psf/black * First commit of stepper.py Pump parameters still needs to be checked and tuned. * addition of hardware details in config.json * Introduce hardware.json to replace the `hardware_config` of config.json * stepper.py: calibration, typos * creates the MQTT_Client class * pump_max_speed is now in ml/min to help readability * forgot to add self to the class def * addition of threading capabilities to stepper.py (UNTESTED) * mqtt: fix topic bug * remove counter * mqtt add doc about topics * stepper.py creates an "actuator/*/state" topic * stepper.py: rename mqtt_client to pump_client * mqtt.py: add details about topics * stepper.py: rename pump_client to actuator_client * topic was not split properly and a part was lost * switch to f-strings for mqtt.py * cosmetic update * stepper.py: folder name will be planktoscope change calls * hardware.json became more straightforward * stepper.py syntax bugs * stepper.py addition of a received stop command * stepper.py: update to max travel distance * stepper.py: several typos here * rename folder * main.py: reword to reflect folder rename * main.py: remove logic that has been moved to stepper.py and mqtt.py * main.py: update to add mqtt imaging client * mqtt.py: make command and args local to class and output more verbose * make stepper.py a class * main.py: instantiate stepper class and call it * main.py: name mqtt client * update to main.json to reflect main.py changes * fix bugs around pump control * update flows to latest version from Thibault * distance can be a small value, and definitevely should be a float. * unify mqtt topics * unify mqtt output in the main flow * first logger implementation, uses loguru * mqtt: add reason to on_connect * mqtt: add on_disconnect handler * stepper: add more logger calls for debug mainly * main: add levels for logger * imager.py: first move of the imager logic * imager: time import cleanup * imager: morphocut import cleanup * imager: skimage import cleanup * imager: finishing import cleanup * imager: Class creation - WIP Also provides a fix for #26 (see line 190). * imager: threading is needed for Condition() * streamer: get the streamer server its own file * imager: creates start_camera and get the server creation out * imager: subclass multiprocessing.Process * imager: get Pipeline creation its own function * imager: cleanup of self calls * main: code removal and corresponding calls to newly created classes * imager: various formatting changes * main: management of signal shutdown * add requirements.txt * mqtt: messages are now json objects Also, addition of a flag on receiving a new message * mqtt: make message private and add logic to synchronise * stepper: creates the stepper class * stepper: use the new class * stepper: uses the new logic * stepper: add the shutdown event * stepper: add shutdown method * main: add shutdown event * imager: graceful shutdown * stepper: nicer way of checking the Eevnt * self is a required first argument for a method in a class Especially if you use said class private members! * python: various typos and small errors in import * stepper: create mqtt client during init * stepper: instanciate the mqtt client inside run Otherwise it's not accessible from inside the loop. It's a PITA, more information at https://stackoverflow.com/questions/17172878/using-pythons-multiprocessing-process-class * stepper: little bugs and typos all around * mqtt: add shutdown method * mqtt: add connect in init * stepper: fix bugs, sanitize inputs * stepper: work on delay prediction improvements * stepper: json is mean, double quote are mandatory inside * mqtt: add details about message exchanged * imager: first implementation of json messages * main.json: add new tab for RPi management + json for payloads * imager: add state_machine class * stepper: publish last will * imager: major refactor * main: make streaming server process a daemon * mqtt: insert debug statement on close * main: reorder imports * imager: make it work! Reinsert the streaming server logic in there, because there is a problem with the synchronisation part otherwise. Also, eventually, StreamingOuput() will have to be made not global Final very critical learning: it's super duper important to make sure the memory split is at least 256Meg for the GPU. Chaos ensues otherwise * main: changes to accomodate the streamer/imager fusino * imager_state_machine: insert states transition description * stepper: cleanup of code * segmenter: creation of the class * python: include segmenter changes * remove unused files * stepper: check existence of hardware.json * main.json: changes to reflect the python script evolution * remove unecessary TODOs and add some others * main: add check for config and directories * imager: update_config is implemented and we have better management of directories now * segmenter: now work recursively in all folders * flow: the configuration is now sent via mqtt * segmenter: better manage pipeline error * segmenter: declaration of archive_fn in init * imager: small bugs and typos * main: add uniqueID output * imager: add the camera settings message We can now update the ISO, shutter speed and resolution from Node-Red * package.json: update dependencies
2020-09-28 11:05:27 +02:00
]
]
},
{
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"id": "73b8252a.5ca754",
"type": "inject",
"z": "bccd1f23.87219",
"name": "Default: 2mL",
"props": [
{
"p": "payload"
}
Extraction and refactor of the python code from node-red flow The rationale for this rewrite is to improve the readability, the modularity, the reliability and the future-proofing of the main python script. All in all, this is now 124 commits that are going to be squashed and merged together, spanning more than two weeks of development and testing. Please test away this release and break things. An upgrading guide will be published in the coming days, along with a new image for people to use if they don't want to upgrade on their own. Read along if you want to know all the goodies! As a starter, the python script was extracted from the main flow, and now lives in its own files at `PlantonScope/scripts/*`. We set up the auto formatting of the code by using [Black](https://github.com/psf/black). This make the code clearer and uniform. We are using the default settings, so if you just install Black and set your editor to format on save using it, you should be good to go. The code is separated in four main processes, each with a specific set of responsibilities: - The main process controls all the others, starts everything up and cleans up on shutdown - The stepper process manages the stepper movements. It's now possible to have simultaneous movements of both motors (this closes #38 ). - The imager process controls the camera and the streaming server via a state machine. - The segmenter process manages the segmentation and its outputs. The segmentation happens recursively in all folders in `/home/pi/PlanktonScope/img/`. Each folder has its own output archive, and bug #26 is now closed. Those processes communicates together using MQTT and json messages. Each message is adressed to one topic. The high level topic controls which process receives the message. The details of each topic is at the end of this commit message. Every imaging sessions has now its own folder, under the `img` root. Metadata are saved individually for every session, in a JSON file in the same directory as the pictures. The configuration is not parsed from `config.json` anymore and passed directly through MQTT messages to the concerned process. A new configuration file has been created: `hardware.json`. This file contains information related to your specific hardware configuration. You can choose to reverse the connection of the motors for example, but you can also define specific speed limits and steps number for your pump and focus stage. This will make it easier for people who wants to experiment with different kind of hardware. It's not necessary to have this file though. If it doesn't exists, the default configuration will be applied. The code is architectured around 6 modules and about 10 classes. I encourage you to have a look at the files, they're pretty straightforward to understand. There is a lot of work left around the node-red code refactoring, dashboard ui improvements, better and clearer LED messages, OLED screen integration and finer control of the segmentation process, but this is quite good for now. Here is the topic lists for MQTT and the corresponding messages. - actuator : This topic adresses the stepper control thread No publication under this topic should happen from the python process - actuator/pump : Control of the pump The message is a json object {"action":"move", "direction":"FORWARD", "volume":10, "flowrate":1} to move 10mL forward at 1mL/min action can be "move" or "stop" Receive only - actuator/focus : Control of the focus stage The message is a json object, speed is optional {"action":"move", "direction":"UP", "distance":0.26, "speed":1} to move up 10mm action can be "move" or "stop" Receive only - imager/image : This topic adresses the imaging thread Is a json object with {"action":"image","sleep":5,"volume":1,"nb_frame":200} sleep in seconds, volume in mL Can also receive a config update message: {"action":"config","config":[...]} Can also receive a camera settings message: {"action":"settings","iso":100,"shutter_speed":40} Receive only - segmenter/segment : This topic adresses the segmenter process Is a json object with {"action":"segment"} Receive only - status : This topics sends feedback to Node-Red No publication or receive at this level - status/pump : State of the pump Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/focus : State of the focus stage Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/imager : State of the imager Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Completed or 12_11_15_0.1.jpg has been imaged. Publish only - status/segmenter : Status of the segmentation - status/segmenter/name - status/segmenter/object_id - status/segmenter/metric Here is the original commit history: * Extract python main.py from flow * Fix bug in server addresses These addresses should be the loopback device instead of the network address of the device. Using the loopback address will not necessitate to update the script when the network address changes. * clean up picamera import * changes to main python and flow: update MQTT requests address to localhost (bugfix) update streaming output address to nothing update main flow to remove python script references and location * Automatically initialise imaging led on startup to off state. * Add the ability to invert outputs of the motor We added a key to config.json "hardware_config" with a subkey "stepper_reverse". If this key is present in the config file and set to 1, the output of the motors are inversed (stepper2 becomes the pump motor and stepper1 the focus motor) * move all non main script to a subfolder * add __init__.py to package * light module rewrite * json cleanup and absolute path for config file * light.py forgot to import subprocess #oups * Add command to turn the leds off * Auto formatting of main.py I've used Black with default settings, see https://github.com/psf/black * First commit of stepper.py Pump parameters still needs to be checked and tuned. * addition of hardware details in config.json * Introduce hardware.json to replace the `hardware_config` of config.json * stepper.py: calibration, typos * creates the MQTT_Client class * pump_max_speed is now in ml/min to help readability * forgot to add self to the class def * addition of threading capabilities to stepper.py (UNTESTED) * mqtt: fix topic bug * remove counter * mqtt add doc about topics * stepper.py creates an "actuator/*/state" topic * stepper.py: rename mqtt_client to pump_client * mqtt.py: add details about topics * stepper.py: rename pump_client to actuator_client * topic was not split properly and a part was lost * switch to f-strings for mqtt.py * cosmetic update * stepper.py: folder name will be planktoscope change calls * hardware.json became more straightforward * stepper.py syntax bugs * stepper.py addition of a received stop command * stepper.py: update to max travel distance * stepper.py: several typos here * rename folder * main.py: reword to reflect folder rename * main.py: remove logic that has been moved to stepper.py and mqtt.py * main.py: update to add mqtt imaging client * mqtt.py: make command and args local to class and output more verbose * make stepper.py a class * main.py: instantiate stepper class and call it * main.py: name mqtt client * update to main.json to reflect main.py changes * fix bugs around pump control * update flows to latest version from Thibault * distance can be a small value, and definitevely should be a float. * unify mqtt topics * unify mqtt output in the main flow * first logger implementation, uses loguru * mqtt: add reason to on_connect * mqtt: add on_disconnect handler * stepper: add more logger calls for debug mainly * main: add levels for logger * imager.py: first move of the imager logic * imager: time import cleanup * imager: morphocut import cleanup * imager: skimage import cleanup * imager: finishing import cleanup * imager: Class creation - WIP Also provides a fix for #26 (see line 190). * imager: threading is needed for Condition() * streamer: get the streamer server its own file * imager: creates start_camera and get the server creation out * imager: subclass multiprocessing.Process * imager: get Pipeline creation its own function * imager: cleanup of self calls * main: code removal and corresponding calls to newly created classes * imager: various formatting changes * main: management of signal shutdown * add requirements.txt * mqtt: messages are now json objects Also, addition of a flag on receiving a new message * mqtt: make message private and add logic to synchronise * stepper: creates the stepper class * stepper: use the new class * stepper: uses the new logic * stepper: add the shutdown event * stepper: add shutdown method * main: add shutdown event * imager: graceful shutdown * stepper: nicer way of checking the Eevnt * self is a required first argument for a method in a class Especially if you use said class private members! * python: various typos and small errors in import * stepper: create mqtt client during init * stepper: instanciate the mqtt client inside run Otherwise it's not accessible from inside the loop. It's a PITA, more information at https://stackoverflow.com/questions/17172878/using-pythons-multiprocessing-process-class * stepper: little bugs and typos all around * mqtt: add shutdown method * mqtt: add connect in init * stepper: fix bugs, sanitize inputs * stepper: work on delay prediction improvements * stepper: json is mean, double quote are mandatory inside * mqtt: add details about message exchanged * imager: first implementation of json messages * main.json: add new tab for RPi management + json for payloads * imager: add state_machine class * stepper: publish last will * imager: major refactor * main: make streaming server process a daemon * mqtt: insert debug statement on close * main: reorder imports * imager: make it work! Reinsert the streaming server logic in there, because there is a problem with the synchronisation part otherwise. Also, eventually, StreamingOuput() will have to be made not global Final very critical learning: it's super duper important to make sure the memory split is at least 256Meg for the GPU. Chaos ensues otherwise * main: changes to accomodate the streamer/imager fusino * imager_state_machine: insert states transition description * stepper: cleanup of code * segmenter: creation of the class * python: include segmenter changes * remove unused files * stepper: check existence of hardware.json * main.json: changes to reflect the python script evolution * remove unecessary TODOs and add some others * main: add check for config and directories * imager: update_config is implemented and we have better management of directories now * segmenter: now work recursively in all folders * flow: the configuration is now sent via mqtt * segmenter: better manage pipeline error * segmenter: declaration of archive_fn in init * imager: small bugs and typos * main: add uniqueID output * imager: add the camera settings message We can now update the ISO, shutter speed and resolution from Node-Red * package.json: update dependencies
2020-09-28 11:05:27 +02:00
],
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"repeat": "",
"crontab": "",
"once": true,
"onceDelay": 0.1,
"topic": "",
"payload": "2",
"payloadType": "num",
Extraction and refactor of the python code from node-red flow The rationale for this rewrite is to improve the readability, the modularity, the reliability and the future-proofing of the main python script. All in all, this is now 124 commits that are going to be squashed and merged together, spanning more than two weeks of development and testing. Please test away this release and break things. An upgrading guide will be published in the coming days, along with a new image for people to use if they don't want to upgrade on their own. Read along if you want to know all the goodies! As a starter, the python script was extracted from the main flow, and now lives in its own files at `PlantonScope/scripts/*`. We set up the auto formatting of the code by using [Black](https://github.com/psf/black). This make the code clearer and uniform. We are using the default settings, so if you just install Black and set your editor to format on save using it, you should be good to go. The code is separated in four main processes, each with a specific set of responsibilities: - The main process controls all the others, starts everything up and cleans up on shutdown - The stepper process manages the stepper movements. It's now possible to have simultaneous movements of both motors (this closes #38 ). - The imager process controls the camera and the streaming server via a state machine. - The segmenter process manages the segmentation and its outputs. The segmentation happens recursively in all folders in `/home/pi/PlanktonScope/img/`. Each folder has its own output archive, and bug #26 is now closed. Those processes communicates together using MQTT and json messages. Each message is adressed to one topic. The high level topic controls which process receives the message. The details of each topic is at the end of this commit message. Every imaging sessions has now its own folder, under the `img` root. Metadata are saved individually for every session, in a JSON file in the same directory as the pictures. The configuration is not parsed from `config.json` anymore and passed directly through MQTT messages to the concerned process. A new configuration file has been created: `hardware.json`. This file contains information related to your specific hardware configuration. You can choose to reverse the connection of the motors for example, but you can also define specific speed limits and steps number for your pump and focus stage. This will make it easier for people who wants to experiment with different kind of hardware. It's not necessary to have this file though. If it doesn't exists, the default configuration will be applied. The code is architectured around 6 modules and about 10 classes. I encourage you to have a look at the files, they're pretty straightforward to understand. There is a lot of work left around the node-red code refactoring, dashboard ui improvements, better and clearer LED messages, OLED screen integration and finer control of the segmentation process, but this is quite good for now. Here is the topic lists for MQTT and the corresponding messages. - actuator : This topic adresses the stepper control thread No publication under this topic should happen from the python process - actuator/pump : Control of the pump The message is a json object {"action":"move", "direction":"FORWARD", "volume":10, "flowrate":1} to move 10mL forward at 1mL/min action can be "move" or "stop" Receive only - actuator/focus : Control of the focus stage The message is a json object, speed is optional {"action":"move", "direction":"UP", "distance":0.26, "speed":1} to move up 10mm action can be "move" or "stop" Receive only - imager/image : This topic adresses the imaging thread Is a json object with {"action":"image","sleep":5,"volume":1,"nb_frame":200} sleep in seconds, volume in mL Can also receive a config update message: {"action":"config","config":[...]} Can also receive a camera settings message: {"action":"settings","iso":100,"shutter_speed":40} Receive only - segmenter/segment : This topic adresses the segmenter process Is a json object with {"action":"segment"} Receive only - status : This topics sends feedback to Node-Red No publication or receive at this level - status/pump : State of the pump Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/focus : State of the focus stage Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/imager : State of the imager Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Completed or 12_11_15_0.1.jpg has been imaged. Publish only - status/segmenter : Status of the segmentation - status/segmenter/name - status/segmenter/object_id - status/segmenter/metric Here is the original commit history: * Extract python main.py from flow * Fix bug in server addresses These addresses should be the loopback device instead of the network address of the device. Using the loopback address will not necessitate to update the script when the network address changes. * clean up picamera import * changes to main python and flow: update MQTT requests address to localhost (bugfix) update streaming output address to nothing update main flow to remove python script references and location * Automatically initialise imaging led on startup to off state. * Add the ability to invert outputs of the motor We added a key to config.json "hardware_config" with a subkey "stepper_reverse". If this key is present in the config file and set to 1, the output of the motors are inversed (stepper2 becomes the pump motor and stepper1 the focus motor) * move all non main script to a subfolder * add __init__.py to package * light module rewrite * json cleanup and absolute path for config file * light.py forgot to import subprocess #oups * Add command to turn the leds off * Auto formatting of main.py I've used Black with default settings, see https://github.com/psf/black * First commit of stepper.py Pump parameters still needs to be checked and tuned. * addition of hardware details in config.json * Introduce hardware.json to replace the `hardware_config` of config.json * stepper.py: calibration, typos * creates the MQTT_Client class * pump_max_speed is now in ml/min to help readability * forgot to add self to the class def * addition of threading capabilities to stepper.py (UNTESTED) * mqtt: fix topic bug * remove counter * mqtt add doc about topics * stepper.py creates an "actuator/*/state" topic * stepper.py: rename mqtt_client to pump_client * mqtt.py: add details about topics * stepper.py: rename pump_client to actuator_client * topic was not split properly and a part was lost * switch to f-strings for mqtt.py * cosmetic update * stepper.py: folder name will be planktoscope change calls * hardware.json became more straightforward * stepper.py syntax bugs * stepper.py addition of a received stop command * stepper.py: update to max travel distance * stepper.py: several typos here * rename folder * main.py: reword to reflect folder rename * main.py: remove logic that has been moved to stepper.py and mqtt.py * main.py: update to add mqtt imaging client * mqtt.py: make command and args local to class and output more verbose * make stepper.py a class * main.py: instantiate stepper class and call it * main.py: name mqtt client * update to main.json to reflect main.py changes * fix bugs around pump control * update flows to latest version from Thibault * distance can be a small value, and definitevely should be a float. * unify mqtt topics * unify mqtt output in the main flow * first logger implementation, uses loguru * mqtt: add reason to on_connect * mqtt: add on_disconnect handler * stepper: add more logger calls for debug mainly * main: add levels for logger * imager.py: first move of the imager logic * imager: time import cleanup * imager: morphocut import cleanup * imager: skimage import cleanup * imager: finishing import cleanup * imager: Class creation - WIP Also provides a fix for #26 (see line 190). * imager: threading is needed for Condition() * streamer: get the streamer server its own file * imager: creates start_camera and get the server creation out * imager: subclass multiprocessing.Process * imager: get Pipeline creation its own function * imager: cleanup of self calls * main: code removal and corresponding calls to newly created classes * imager: various formatting changes * main: management of signal shutdown * add requirements.txt * mqtt: messages are now json objects Also, addition of a flag on receiving a new message * mqtt: make message private and add logic to synchronise * stepper: creates the stepper class * stepper: use the new class * stepper: uses the new logic * stepper: add the shutdown event * stepper: add shutdown method * main: add shutdown event * imager: graceful shutdown * stepper: nicer way of checking the Eevnt * self is a required first argument for a method in a class Especially if you use said class private members! * python: various typos and small errors in import * stepper: create mqtt client during init * stepper: instanciate the mqtt client inside run Otherwise it's not accessible from inside the loop. It's a PITA, more information at https://stackoverflow.com/questions/17172878/using-pythons-multiprocessing-process-class * stepper: little bugs and typos all around * mqtt: add shutdown method * mqtt: add connect in init * stepper: fix bugs, sanitize inputs * stepper: work on delay prediction improvements * stepper: json is mean, double quote are mandatory inside * mqtt: add details about message exchanged * imager: first implementation of json messages * main.json: add new tab for RPi management + json for payloads * imager: add state_machine class * stepper: publish last will * imager: major refactor * main: make streaming server process a daemon * mqtt: insert debug statement on close * main: reorder imports * imager: make it work! Reinsert the streaming server logic in there, because there is a problem with the synchronisation part otherwise. Also, eventually, StreamingOuput() will have to be made not global Final very critical learning: it's super duper important to make sure the memory split is at least 256Meg for the GPU. Chaos ensues otherwise * main: changes to accomodate the streamer/imager fusino * imager_state_machine: insert states transition description * stepper: cleanup of code * segmenter: creation of the class * python: include segmenter changes * remove unused files * stepper: check existence of hardware.json * main.json: changes to reflect the python script evolution * remove unecessary TODOs and add some others * main: add check for config and directories * imager: update_config is implemented and we have better management of directories now * segmenter: now work recursively in all folders * flow: the configuration is now sent via mqtt * segmenter: better manage pipeline error * segmenter: declaration of archive_fn in init * imager: small bugs and typos * main: add uniqueID output * imager: add the camera settings message We can now update the ISO, shutter speed and resolution from Node-Red * package.json: update dependencies
2020-09-28 11:05:27 +02:00
"x": 110,
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"y": 340,
Extraction and refactor of the python code from node-red flow The rationale for this rewrite is to improve the readability, the modularity, the reliability and the future-proofing of the main python script. All in all, this is now 124 commits that are going to be squashed and merged together, spanning more than two weeks of development and testing. Please test away this release and break things. An upgrading guide will be published in the coming days, along with a new image for people to use if they don't want to upgrade on their own. Read along if you want to know all the goodies! As a starter, the python script was extracted from the main flow, and now lives in its own files at `PlantonScope/scripts/*`. We set up the auto formatting of the code by using [Black](https://github.com/psf/black). This make the code clearer and uniform. We are using the default settings, so if you just install Black and set your editor to format on save using it, you should be good to go. The code is separated in four main processes, each with a specific set of responsibilities: - The main process controls all the others, starts everything up and cleans up on shutdown - The stepper process manages the stepper movements. It's now possible to have simultaneous movements of both motors (this closes #38 ). - The imager process controls the camera and the streaming server via a state machine. - The segmenter process manages the segmentation and its outputs. The segmentation happens recursively in all folders in `/home/pi/PlanktonScope/img/`. Each folder has its own output archive, and bug #26 is now closed. Those processes communicates together using MQTT and json messages. Each message is adressed to one topic. The high level topic controls which process receives the message. The details of each topic is at the end of this commit message. Every imaging sessions has now its own folder, under the `img` root. Metadata are saved individually for every session, in a JSON file in the same directory as the pictures. The configuration is not parsed from `config.json` anymore and passed directly through MQTT messages to the concerned process. A new configuration file has been created: `hardware.json`. This file contains information related to your specific hardware configuration. You can choose to reverse the connection of the motors for example, but you can also define specific speed limits and steps number for your pump and focus stage. This will make it easier for people who wants to experiment with different kind of hardware. It's not necessary to have this file though. If it doesn't exists, the default configuration will be applied. The code is architectured around 6 modules and about 10 classes. I encourage you to have a look at the files, they're pretty straightforward to understand. There is a lot of work left around the node-red code refactoring, dashboard ui improvements, better and clearer LED messages, OLED screen integration and finer control of the segmentation process, but this is quite good for now. Here is the topic lists for MQTT and the corresponding messages. - actuator : This topic adresses the stepper control thread No publication under this topic should happen from the python process - actuator/pump : Control of the pump The message is a json object {"action":"move", "direction":"FORWARD", "volume":10, "flowrate":1} to move 10mL forward at 1mL/min action can be "move" or "stop" Receive only - actuator/focus : Control of the focus stage The message is a json object, speed is optional {"action":"move", "direction":"UP", "distance":0.26, "speed":1} to move up 10mm action can be "move" or "stop" Receive only - imager/image : This topic adresses the imaging thread Is a json object with {"action":"image","sleep":5,"volume":1,"nb_frame":200} sleep in seconds, volume in mL Can also receive a config update message: {"action":"config","config":[...]} Can also receive a camera settings message: {"action":"settings","iso":100,"shutter_speed":40} Receive only - segmenter/segment : This topic adresses the segmenter process Is a json object with {"action":"segment"} Receive only - status : This topics sends feedback to Node-Red No publication or receive at this level - status/pump : State of the pump Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/focus : State of the focus stage Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/imager : State of the imager Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Completed or 12_11_15_0.1.jpg has been imaged. Publish only - status/segmenter : Status of the segmentation - status/segmenter/name - status/segmenter/object_id - status/segmenter/metric Here is the original commit history: * Extract python main.py from flow * Fix bug in server addresses These addresses should be the loopback device instead of the network address of the device. Using the loopback address will not necessitate to update the script when the network address changes. * clean up picamera import * changes to main python and flow: update MQTT requests address to localhost (bugfix) update streaming output address to nothing update main flow to remove python script references and location * Automatically initialise imaging led on startup to off state. * Add the ability to invert outputs of the motor We added a key to config.json "hardware_config" with a subkey "stepper_reverse". If this key is present in the config file and set to 1, the output of the motors are inversed (stepper2 becomes the pump motor and stepper1 the focus motor) * move all non main script to a subfolder * add __init__.py to package * light module rewrite * json cleanup and absolute path for config file * light.py forgot to import subprocess #oups * Add command to turn the leds off * Auto formatting of main.py I've used Black with default settings, see https://github.com/psf/black * First commit of stepper.py Pump parameters still needs to be checked and tuned. * addition of hardware details in config.json * Introduce hardware.json to replace the `hardware_config` of config.json * stepper.py: calibration, typos * creates the MQTT_Client class * pump_max_speed is now in ml/min to help readability * forgot to add self to the class def * addition of threading capabilities to stepper.py (UNTESTED) * mqtt: fix topic bug * remove counter * mqtt add doc about topics * stepper.py creates an "actuator/*/state" topic * stepper.py: rename mqtt_client to pump_client * mqtt.py: add details about topics * stepper.py: rename pump_client to actuator_client * topic was not split properly and a part was lost * switch to f-strings for mqtt.py * cosmetic update * stepper.py: folder name will be planktoscope change calls * hardware.json became more straightforward * stepper.py syntax bugs * stepper.py addition of a received stop command * stepper.py: update to max travel distance * stepper.py: several typos here * rename folder * main.py: reword to reflect folder rename * main.py: remove logic that has been moved to stepper.py and mqtt.py * main.py: update to add mqtt imaging client * mqtt.py: make command and args local to class and output more verbose * make stepper.py a class * main.py: instantiate stepper class and call it * main.py: name mqtt client * update to main.json to reflect main.py changes * fix bugs around pump control * update flows to latest version from Thibault * distance can be a small value, and definitevely should be a float. * unify mqtt topics * unify mqtt output in the main flow * first logger implementation, uses loguru * mqtt: add reason to on_connect * mqtt: add on_disconnect handler * stepper: add more logger calls for debug mainly * main: add levels for logger * imager.py: first move of the imager logic * imager: time import cleanup * imager: morphocut import cleanup * imager: skimage import cleanup * imager: finishing import cleanup * imager: Class creation - WIP Also provides a fix for #26 (see line 190). * imager: threading is needed for Condition() * streamer: get the streamer server its own file * imager: creates start_camera and get the server creation out * imager: subclass multiprocessing.Process * imager: get Pipeline creation its own function * imager: cleanup of self calls * main: code removal and corresponding calls to newly created classes * imager: various formatting changes * main: management of signal shutdown * add requirements.txt * mqtt: messages are now json objects Also, addition of a flag on receiving a new message * mqtt: make message private and add logic to synchronise * stepper: creates the stepper class * stepper: use the new class * stepper: uses the new logic * stepper: add the shutdown event * stepper: add shutdown method * main: add shutdown event * imager: graceful shutdown * stepper: nicer way of checking the Eevnt * self is a required first argument for a method in a class Especially if you use said class private members! * python: various typos and small errors in import * stepper: create mqtt client during init * stepper: instanciate the mqtt client inside run Otherwise it's not accessible from inside the loop. It's a PITA, more information at https://stackoverflow.com/questions/17172878/using-pythons-multiprocessing-process-class * stepper: little bugs and typos all around * mqtt: add shutdown method * mqtt: add connect in init * stepper: fix bugs, sanitize inputs * stepper: work on delay prediction improvements * stepper: json is mean, double quote are mandatory inside * mqtt: add details about message exchanged * imager: first implementation of json messages * main.json: add new tab for RPi management + json for payloads * imager: add state_machine class * stepper: publish last will * imager: major refactor * main: make streaming server process a daemon * mqtt: insert debug statement on close * main: reorder imports * imager: make it work! Reinsert the streaming server logic in there, because there is a problem with the synchronisation part otherwise. Also, eventually, StreamingOuput() will have to be made not global Final very critical learning: it's super duper important to make sure the memory split is at least 256Meg for the GPU. Chaos ensues otherwise * main: changes to accomodate the streamer/imager fusino * imager_state_machine: insert states transition description * stepper: cleanup of code * segmenter: creation of the class * python: include segmenter changes * remove unused files * stepper: check existence of hardware.json * main.json: changes to reflect the python script evolution * remove unecessary TODOs and add some others * main: add check for config and directories * imager: update_config is implemented and we have better management of directories now * segmenter: now work recursively in all folders * flow: the configuration is now sent via mqtt * segmenter: better manage pipeline error * segmenter: declaration of archive_fn in init * imager: small bugs and typos * main: add uniqueID output * imager: add the camera settings message We can now update the ISO, shutter speed and resolution from Node-Red * package.json: update dependencies
2020-09-28 11:05:27 +02:00
"wires": [
[
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"68962547.34a67c"
Extraction and refactor of the python code from node-red flow The rationale for this rewrite is to improve the readability, the modularity, the reliability and the future-proofing of the main python script. All in all, this is now 124 commits that are going to be squashed and merged together, spanning more than two weeks of development and testing. Please test away this release and break things. An upgrading guide will be published in the coming days, along with a new image for people to use if they don't want to upgrade on their own. Read along if you want to know all the goodies! As a starter, the python script was extracted from the main flow, and now lives in its own files at `PlantonScope/scripts/*`. We set up the auto formatting of the code by using [Black](https://github.com/psf/black). This make the code clearer and uniform. We are using the default settings, so if you just install Black and set your editor to format on save using it, you should be good to go. The code is separated in four main processes, each with a specific set of responsibilities: - The main process controls all the others, starts everything up and cleans up on shutdown - The stepper process manages the stepper movements. It's now possible to have simultaneous movements of both motors (this closes #38 ). - The imager process controls the camera and the streaming server via a state machine. - The segmenter process manages the segmentation and its outputs. The segmentation happens recursively in all folders in `/home/pi/PlanktonScope/img/`. Each folder has its own output archive, and bug #26 is now closed. Those processes communicates together using MQTT and json messages. Each message is adressed to one topic. The high level topic controls which process receives the message. The details of each topic is at the end of this commit message. Every imaging sessions has now its own folder, under the `img` root. Metadata are saved individually for every session, in a JSON file in the same directory as the pictures. The configuration is not parsed from `config.json` anymore and passed directly through MQTT messages to the concerned process. A new configuration file has been created: `hardware.json`. This file contains information related to your specific hardware configuration. You can choose to reverse the connection of the motors for example, but you can also define specific speed limits and steps number for your pump and focus stage. This will make it easier for people who wants to experiment with different kind of hardware. It's not necessary to have this file though. If it doesn't exists, the default configuration will be applied. The code is architectured around 6 modules and about 10 classes. I encourage you to have a look at the files, they're pretty straightforward to understand. There is a lot of work left around the node-red code refactoring, dashboard ui improvements, better and clearer LED messages, OLED screen integration and finer control of the segmentation process, but this is quite good for now. Here is the topic lists for MQTT and the corresponding messages. - actuator : This topic adresses the stepper control thread No publication under this topic should happen from the python process - actuator/pump : Control of the pump The message is a json object {"action":"move", "direction":"FORWARD", "volume":10, "flowrate":1} to move 10mL forward at 1mL/min action can be "move" or "stop" Receive only - actuator/focus : Control of the focus stage The message is a json object, speed is optional {"action":"move", "direction":"UP", "distance":0.26, "speed":1} to move up 10mm action can be "move" or "stop" Receive only - imager/image : This topic adresses the imaging thread Is a json object with {"action":"image","sleep":5,"volume":1,"nb_frame":200} sleep in seconds, volume in mL Can also receive a config update message: {"action":"config","config":[...]} Can also receive a camera settings message: {"action":"settings","iso":100,"shutter_speed":40} Receive only - segmenter/segment : This topic adresses the segmenter process Is a json object with {"action":"segment"} Receive only - status : This topics sends feedback to Node-Red No publication or receive at this level - status/pump : State of the pump Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/focus : State of the focus stage Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/imager : State of the imager Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Completed or 12_11_15_0.1.jpg has been imaged. Publish only - status/segmenter : Status of the segmentation - status/segmenter/name - status/segmenter/object_id - status/segmenter/metric Here is the original commit history: * Extract python main.py from flow * Fix bug in server addresses These addresses should be the loopback device instead of the network address of the device. Using the loopback address will not necessitate to update the script when the network address changes. * clean up picamera import * changes to main python and flow: update MQTT requests address to localhost (bugfix) update streaming output address to nothing update main flow to remove python script references and location * Automatically initialise imaging led on startup to off state. * Add the ability to invert outputs of the motor We added a key to config.json "hardware_config" with a subkey "stepper_reverse". If this key is present in the config file and set to 1, the output of the motors are inversed (stepper2 becomes the pump motor and stepper1 the focus motor) * move all non main script to a subfolder * add __init__.py to package * light module rewrite * json cleanup and absolute path for config file * light.py forgot to import subprocess #oups * Add command to turn the leds off * Auto formatting of main.py I've used Black with default settings, see https://github.com/psf/black * First commit of stepper.py Pump parameters still needs to be checked and tuned. * addition of hardware details in config.json * Introduce hardware.json to replace the `hardware_config` of config.json * stepper.py: calibration, typos * creates the MQTT_Client class * pump_max_speed is now in ml/min to help readability * forgot to add self to the class def * addition of threading capabilities to stepper.py (UNTESTED) * mqtt: fix topic bug * remove counter * mqtt add doc about topics * stepper.py creates an "actuator/*/state" topic * stepper.py: rename mqtt_client to pump_client * mqtt.py: add details about topics * stepper.py: rename pump_client to actuator_client * topic was not split properly and a part was lost * switch to f-strings for mqtt.py * cosmetic update * stepper.py: folder name will be planktoscope change calls * hardware.json became more straightforward * stepper.py syntax bugs * stepper.py addition of a received stop command * stepper.py: update to max travel distance * stepper.py: several typos here * rename folder * main.py: reword to reflect folder rename * main.py: remove logic that has been moved to stepper.py and mqtt.py * main.py: update to add mqtt imaging client * mqtt.py: make command and args local to class and output more verbose * make stepper.py a class * main.py: instantiate stepper class and call it * main.py: name mqtt client * update to main.json to reflect main.py changes * fix bugs around pump control * update flows to latest version from Thibault * distance can be a small value, and definitevely should be a float. * unify mqtt topics * unify mqtt output in the main flow * first logger implementation, uses loguru * mqtt: add reason to on_connect * mqtt: add on_disconnect handler * stepper: add more logger calls for debug mainly * main: add levels for logger * imager.py: first move of the imager logic * imager: time import cleanup * imager: morphocut import cleanup * imager: skimage import cleanup * imager: finishing import cleanup * imager: Class creation - WIP Also provides a fix for #26 (see line 190). * imager: threading is needed for Condition() * streamer: get the streamer server its own file * imager: creates start_camera and get the server creation out * imager: subclass multiprocessing.Process * imager: get Pipeline creation its own function * imager: cleanup of self calls * main: code removal and corresponding calls to newly created classes * imager: various formatting changes * main: management of signal shutdown * add requirements.txt * mqtt: messages are now json objects Also, addition of a flag on receiving a new message * mqtt: make message private and add logic to synchronise * stepper: creates the stepper class * stepper: use the new class * stepper: uses the new logic * stepper: add the shutdown event * stepper: add shutdown method * main: add shutdown event * imager: graceful shutdown * stepper: nicer way of checking the Eevnt * self is a required first argument for a method in a class Especially if you use said class private members! * python: various typos and small errors in import * stepper: create mqtt client during init * stepper: instanciate the mqtt client inside run Otherwise it's not accessible from inside the loop. It's a PITA, more information at https://stackoverflow.com/questions/17172878/using-pythons-multiprocessing-process-class * stepper: little bugs and typos all around * mqtt: add shutdown method * mqtt: add connect in init * stepper: fix bugs, sanitize inputs * stepper: work on delay prediction improvements * stepper: json is mean, double quote are mandatory inside * mqtt: add details about message exchanged * imager: first implementation of json messages * main.json: add new tab for RPi management + json for payloads * imager: add state_machine class * stepper: publish last will * imager: major refactor * main: make streaming server process a daemon * mqtt: insert debug statement on close * main: reorder imports * imager: make it work! Reinsert the streaming server logic in there, because there is a problem with the synchronisation part otherwise. Also, eventually, StreamingOuput() will have to be made not global Final very critical learning: it's super duper important to make sure the memory split is at least 256Meg for the GPU. Chaos ensues otherwise * main: changes to accomodate the streamer/imager fusino * imager_state_machine: insert states transition description * stepper: cleanup of code * segmenter: creation of the class * python: include segmenter changes * remove unused files * stepper: check existence of hardware.json * main.json: changes to reflect the python script evolution * remove unecessary TODOs and add some others * main: add check for config and directories * imager: update_config is implemented and we have better management of directories now * segmenter: now work recursively in all folders * flow: the configuration is now sent via mqtt * segmenter: better manage pipeline error * segmenter: declaration of archive_fn in init * imager: small bugs and typos * main: add uniqueID output * imager: add the camera settings message We can now update the ISO, shutter speed and resolution from Node-Red * package.json: update dependencies
2020-09-28 11:05:27 +02:00
]
]
},
{
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"id": "8ec68b82.17e3d8",
"type": "ui_button",
"z": "cb95299c.2817c8",
"name": "Start segmentation",
"group": "abeb6dad.635a2",
"order": 1,
Extraction and refactor of the python code from node-red flow The rationale for this rewrite is to improve the readability, the modularity, the reliability and the future-proofing of the main python script. All in all, this is now 124 commits that are going to be squashed and merged together, spanning more than two weeks of development and testing. Please test away this release and break things. An upgrading guide will be published in the coming days, along with a new image for people to use if they don't want to upgrade on their own. Read along if you want to know all the goodies! As a starter, the python script was extracted from the main flow, and now lives in its own files at `PlantonScope/scripts/*`. We set up the auto formatting of the code by using [Black](https://github.com/psf/black). This make the code clearer and uniform. We are using the default settings, so if you just install Black and set your editor to format on save using it, you should be good to go. The code is separated in four main processes, each with a specific set of responsibilities: - The main process controls all the others, starts everything up and cleans up on shutdown - The stepper process manages the stepper movements. It's now possible to have simultaneous movements of both motors (this closes #38 ). - The imager process controls the camera and the streaming server via a state machine. - The segmenter process manages the segmentation and its outputs. The segmentation happens recursively in all folders in `/home/pi/PlanktonScope/img/`. Each folder has its own output archive, and bug #26 is now closed. Those processes communicates together using MQTT and json messages. Each message is adressed to one topic. The high level topic controls which process receives the message. The details of each topic is at the end of this commit message. Every imaging sessions has now its own folder, under the `img` root. Metadata are saved individually for every session, in a JSON file in the same directory as the pictures. The configuration is not parsed from `config.json` anymore and passed directly through MQTT messages to the concerned process. A new configuration file has been created: `hardware.json`. This file contains information related to your specific hardware configuration. You can choose to reverse the connection of the motors for example, but you can also define specific speed limits and steps number for your pump and focus stage. This will make it easier for people who wants to experiment with different kind of hardware. It's not necessary to have this file though. If it doesn't exists, the default configuration will be applied. The code is architectured around 6 modules and about 10 classes. I encourage you to have a look at the files, they're pretty straightforward to understand. There is a lot of work left around the node-red code refactoring, dashboard ui improvements, better and clearer LED messages, OLED screen integration and finer control of the segmentation process, but this is quite good for now. Here is the topic lists for MQTT and the corresponding messages. - actuator : This topic adresses the stepper control thread No publication under this topic should happen from the python process - actuator/pump : Control of the pump The message is a json object {"action":"move", "direction":"FORWARD", "volume":10, "flowrate":1} to move 10mL forward at 1mL/min action can be "move" or "stop" Receive only - actuator/focus : Control of the focus stage The message is a json object, speed is optional {"action":"move", "direction":"UP", "distance":0.26, "speed":1} to move up 10mm action can be "move" or "stop" Receive only - imager/image : This topic adresses the imaging thread Is a json object with {"action":"image","sleep":5,"volume":1,"nb_frame":200} sleep in seconds, volume in mL Can also receive a config update message: {"action":"config","config":[...]} Can also receive a camera settings message: {"action":"settings","iso":100,"shutter_speed":40} Receive only - segmenter/segment : This topic adresses the segmenter process Is a json object with {"action":"segment"} Receive only - status : This topics sends feedback to Node-Red No publication or receive at this level - status/pump : State of the pump Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/focus : State of the focus stage Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/imager : State of the imager Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Completed or 12_11_15_0.1.jpg has been imaged. Publish only - status/segmenter : Status of the segmentation - status/segmenter/name - status/segmenter/object_id - status/segmenter/metric Here is the original commit history: * Extract python main.py from flow * Fix bug in server addresses These addresses should be the loopback device instead of the network address of the device. Using the loopback address will not necessitate to update the script when the network address changes. * clean up picamera import * changes to main python and flow: update MQTT requests address to localhost (bugfix) update streaming output address to nothing update main flow to remove python script references and location * Automatically initialise imaging led on startup to off state. * Add the ability to invert outputs of the motor We added a key to config.json "hardware_config" with a subkey "stepper_reverse". If this key is present in the config file and set to 1, the output of the motors are inversed (stepper2 becomes the pump motor and stepper1 the focus motor) * move all non main script to a subfolder * add __init__.py to package * light module rewrite * json cleanup and absolute path for config file * light.py forgot to import subprocess #oups * Add command to turn the leds off * Auto formatting of main.py I've used Black with default settings, see https://github.com/psf/black * First commit of stepper.py Pump parameters still needs to be checked and tuned. * addition of hardware details in config.json * Introduce hardware.json to replace the `hardware_config` of config.json * stepper.py: calibration, typos * creates the MQTT_Client class * pump_max_speed is now in ml/min to help readability * forgot to add self to the class def * addition of threading capabilities to stepper.py (UNTESTED) * mqtt: fix topic bug * remove counter * mqtt add doc about topics * stepper.py creates an "actuator/*/state" topic * stepper.py: rename mqtt_client to pump_client * mqtt.py: add details about topics * stepper.py: rename pump_client to actuator_client * topic was not split properly and a part was lost * switch to f-strings for mqtt.py * cosmetic update * stepper.py: folder name will be planktoscope change calls * hardware.json became more straightforward * stepper.py syntax bugs * stepper.py addition of a received stop command * stepper.py: update to max travel distance * stepper.py: several typos here * rename folder * main.py: reword to reflect folder rename * main.py: remove logic that has been moved to stepper.py and mqtt.py * main.py: update to add mqtt imaging client * mqtt.py: make command and args local to class and output more verbose * make stepper.py a class * main.py: instantiate stepper class and call it * main.py: name mqtt client * update to main.json to reflect main.py changes * fix bugs around pump control * update flows to latest version from Thibault * distance can be a small value, and definitevely should be a float. * unify mqtt topics * unify mqtt output in the main flow * first logger implementation, uses loguru * mqtt: add reason to on_connect * mqtt: add on_disconnect handler * stepper: add more logger calls for debug mainly * main: add levels for logger * imager.py: first move of the imager logic * imager: time import cleanup * imager: morphocut import cleanup * imager: skimage import cleanup * imager: finishing import cleanup * imager: Class creation - WIP Also provides a fix for #26 (see line 190). * imager: threading is needed for Condition() * streamer: get the streamer server its own file * imager: creates start_camera and get the server creation out * imager: subclass multiprocessing.Process * imager: get Pipeline creation its own function * imager: cleanup of self calls * main: code removal and corresponding calls to newly created classes * imager: various formatting changes * main: management of signal shutdown * add requirements.txt * mqtt: messages are now json objects Also, addition of a flag on receiving a new message * mqtt: make message private and add logic to synchronise * stepper: creates the stepper class * stepper: use the new class * stepper: uses the new logic * stepper: add the shutdown event * stepper: add shutdown method * main: add shutdown event * imager: graceful shutdown * stepper: nicer way of checking the Eevnt * self is a required first argument for a method in a class Especially if you use said class private members! * python: various typos and small errors in import * stepper: create mqtt client during init * stepper: instanciate the mqtt client inside run Otherwise it's not accessible from inside the loop. It's a PITA, more information at https://stackoverflow.com/questions/17172878/using-pythons-multiprocessing-process-class * stepper: little bugs and typos all around * mqtt: add shutdown method * mqtt: add connect in init * stepper: fix bugs, sanitize inputs * stepper: work on delay prediction improvements * stepper: json is mean, double quote are mandatory inside * mqtt: add details about message exchanged * imager: first implementation of json messages * main.json: add new tab for RPi management + json for payloads * imager: add state_machine class * stepper: publish last will * imager: major refactor * main: make streaming server process a daemon * mqtt: insert debug statement on close * main: reorder imports * imager: make it work! Reinsert the streaming server logic in there, because there is a problem with the synchronisation part otherwise. Also, eventually, StreamingOuput() will have to be made not global Final very critical learning: it's super duper important to make sure the memory split is at least 256Meg for the GPU. Chaos ensues otherwise * main: changes to accomodate the streamer/imager fusino * imager_state_machine: insert states transition description * stepper: cleanup of code * segmenter: creation of the class * python: include segmenter changes * remove unused files * stepper: check existence of hardware.json * main.json: changes to reflect the python script evolution * remove unecessary TODOs and add some others * main: add check for config and directories * imager: update_config is implemented and we have better management of directories now * segmenter: now work recursively in all folders * flow: the configuration is now sent via mqtt * segmenter: better manage pipeline error * segmenter: declaration of archive_fn in init * imager: small bugs and typos * main: add uniqueID output * imager: add the camera settings message We can now update the ISO, shutter speed and resolution from Node-Red * package.json: update dependencies
2020-09-28 11:05:27 +02:00
"width": 6,
"height": 1,
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"passthru": false,
"label": "Start segmentation",
"tooltip": "",
"color": "",
"bgcolor": "",
"icon": "",
"payload": "{\"action\":\"segment\"}",
"payloadType": "json",
"topic": "segmenter/segment",
"x": 370,
"y": 260,
"wires": [
[
"16f3cef4.0acac9"
]
]
Extraction and refactor of the python code from node-red flow The rationale for this rewrite is to improve the readability, the modularity, the reliability and the future-proofing of the main python script. All in all, this is now 124 commits that are going to be squashed and merged together, spanning more than two weeks of development and testing. Please test away this release and break things. An upgrading guide will be published in the coming days, along with a new image for people to use if they don't want to upgrade on their own. Read along if you want to know all the goodies! As a starter, the python script was extracted from the main flow, and now lives in its own files at `PlantonScope/scripts/*`. We set up the auto formatting of the code by using [Black](https://github.com/psf/black). This make the code clearer and uniform. We are using the default settings, so if you just install Black and set your editor to format on save using it, you should be good to go. The code is separated in four main processes, each with a specific set of responsibilities: - The main process controls all the others, starts everything up and cleans up on shutdown - The stepper process manages the stepper movements. It's now possible to have simultaneous movements of both motors (this closes #38 ). - The imager process controls the camera and the streaming server via a state machine. - The segmenter process manages the segmentation and its outputs. The segmentation happens recursively in all folders in `/home/pi/PlanktonScope/img/`. Each folder has its own output archive, and bug #26 is now closed. Those processes communicates together using MQTT and json messages. Each message is adressed to one topic. The high level topic controls which process receives the message. The details of each topic is at the end of this commit message. Every imaging sessions has now its own folder, under the `img` root. Metadata are saved individually for every session, in a JSON file in the same directory as the pictures. The configuration is not parsed from `config.json` anymore and passed directly through MQTT messages to the concerned process. A new configuration file has been created: `hardware.json`. This file contains information related to your specific hardware configuration. You can choose to reverse the connection of the motors for example, but you can also define specific speed limits and steps number for your pump and focus stage. This will make it easier for people who wants to experiment with different kind of hardware. It's not necessary to have this file though. If it doesn't exists, the default configuration will be applied. The code is architectured around 6 modules and about 10 classes. I encourage you to have a look at the files, they're pretty straightforward to understand. There is a lot of work left around the node-red code refactoring, dashboard ui improvements, better and clearer LED messages, OLED screen integration and finer control of the segmentation process, but this is quite good for now. Here is the topic lists for MQTT and the corresponding messages. - actuator : This topic adresses the stepper control thread No publication under this topic should happen from the python process - actuator/pump : Control of the pump The message is a json object {"action":"move", "direction":"FORWARD", "volume":10, "flowrate":1} to move 10mL forward at 1mL/min action can be "move" or "stop" Receive only - actuator/focus : Control of the focus stage The message is a json object, speed is optional {"action":"move", "direction":"UP", "distance":0.26, "speed":1} to move up 10mm action can be "move" or "stop" Receive only - imager/image : This topic adresses the imaging thread Is a json object with {"action":"image","sleep":5,"volume":1,"nb_frame":200} sleep in seconds, volume in mL Can also receive a config update message: {"action":"config","config":[...]} Can also receive a camera settings message: {"action":"settings","iso":100,"shutter_speed":40} Receive only - segmenter/segment : This topic adresses the segmenter process Is a json object with {"action":"segment"} Receive only - status : This topics sends feedback to Node-Red No publication or receive at this level - status/pump : State of the pump Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/focus : State of the focus stage Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/imager : State of the imager Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Completed or 12_11_15_0.1.jpg has been imaged. Publish only - status/segmenter : Status of the segmentation - status/segmenter/name - status/segmenter/object_id - status/segmenter/metric Here is the original commit history: * Extract python main.py from flow * Fix bug in server addresses These addresses should be the loopback device instead of the network address of the device. Using the loopback address will not necessitate to update the script when the network address changes. * clean up picamera import * changes to main python and flow: update MQTT requests address to localhost (bugfix) update streaming output address to nothing update main flow to remove python script references and location * Automatically initialise imaging led on startup to off state. * Add the ability to invert outputs of the motor We added a key to config.json "hardware_config" with a subkey "stepper_reverse". If this key is present in the config file and set to 1, the output of the motors are inversed (stepper2 becomes the pump motor and stepper1 the focus motor) * move all non main script to a subfolder * add __init__.py to package * light module rewrite * json cleanup and absolute path for config file * light.py forgot to import subprocess #oups * Add command to turn the leds off * Auto formatting of main.py I've used Black with default settings, see https://github.com/psf/black * First commit of stepper.py Pump parameters still needs to be checked and tuned. * addition of hardware details in config.json * Introduce hardware.json to replace the `hardware_config` of config.json * stepper.py: calibration, typos * creates the MQTT_Client class * pump_max_speed is now in ml/min to help readability * forgot to add self to the class def * addition of threading capabilities to stepper.py (UNTESTED) * mqtt: fix topic bug * remove counter * mqtt add doc about topics * stepper.py creates an "actuator/*/state" topic * stepper.py: rename mqtt_client to pump_client * mqtt.py: add details about topics * stepper.py: rename pump_client to actuator_client * topic was not split properly and a part was lost * switch to f-strings for mqtt.py * cosmetic update * stepper.py: folder name will be planktoscope change calls * hardware.json became more straightforward * stepper.py syntax bugs * stepper.py addition of a received stop command * stepper.py: update to max travel distance * stepper.py: several typos here * rename folder * main.py: reword to reflect folder rename * main.py: remove logic that has been moved to stepper.py and mqtt.py * main.py: update to add mqtt imaging client * mqtt.py: make command and args local to class and output more verbose * make stepper.py a class * main.py: instantiate stepper class and call it * main.py: name mqtt client * update to main.json to reflect main.py changes * fix bugs around pump control * update flows to latest version from Thibault * distance can be a small value, and definitevely should be a float. * unify mqtt topics * unify mqtt output in the main flow * first logger implementation, uses loguru * mqtt: add reason to on_connect * mqtt: add on_disconnect handler * stepper: add more logger calls for debug mainly * main: add levels for logger * imager.py: first move of the imager logic * imager: time import cleanup * imager: morphocut import cleanup * imager: skimage import cleanup * imager: finishing import cleanup * imager: Class creation - WIP Also provides a fix for #26 (see line 190). * imager: threading is needed for Condition() * streamer: get the streamer server its own file * imager: creates start_camera and get the server creation out * imager: subclass multiprocessing.Process * imager: get Pipeline creation its own function * imager: cleanup of self calls * main: code removal and corresponding calls to newly created classes * imager: various formatting changes * main: management of signal shutdown * add requirements.txt * mqtt: messages are now json objects Also, addition of a flag on receiving a new message * mqtt: make message private and add logic to synchronise * stepper: creates the stepper class * stepper: use the new class * stepper: uses the new logic * stepper: add the shutdown event * stepper: add shutdown method * main: add shutdown event * imager: graceful shutdown * stepper: nicer way of checking the Eevnt * self is a required first argument for a method in a class Especially if you use said class private members! * python: various typos and small errors in import * stepper: create mqtt client during init * stepper: instanciate the mqtt client inside run Otherwise it's not accessible from inside the loop. It's a PITA, more information at https://stackoverflow.com/questions/17172878/using-pythons-multiprocessing-process-class * stepper: little bugs and typos all around * mqtt: add shutdown method * mqtt: add connect in init * stepper: fix bugs, sanitize inputs * stepper: work on delay prediction improvements * stepper: json is mean, double quote are mandatory inside * mqtt: add details about message exchanged * imager: first implementation of json messages * main.json: add new tab for RPi management + json for payloads * imager: add state_machine class * stepper: publish last will * imager: major refactor * main: make streaming server process a daemon * mqtt: insert debug statement on close * main: reorder imports * imager: make it work! Reinsert the streaming server logic in there, because there is a problem with the synchronisation part otherwise. Also, eventually, StreamingOuput() will have to be made not global Final very critical learning: it's super duper important to make sure the memory split is at least 256Meg for the GPU. Chaos ensues otherwise * main: changes to accomodate the streamer/imager fusino * imager_state_machine: insert states transition description * stepper: cleanup of code * segmenter: creation of the class * python: include segmenter changes * remove unused files * stepper: check existence of hardware.json * main.json: changes to reflect the python script evolution * remove unecessary TODOs and add some others * main: add check for config and directories * imager: update_config is implemented and we have better management of directories now * segmenter: now work recursively in all folders * flow: the configuration is now sent via mqtt * segmenter: better manage pipeline error * segmenter: declaration of archive_fn in init * imager: small bugs and typos * main: add uniqueID output * imager: add the camera settings message We can now update the ISO, shutter speed and resolution from Node-Red * package.json: update dependencies
2020-09-28 11:05:27 +02:00
},
{
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"id": "27be7971.b3fbce",
"type": "ui_button",
"z": "cb95299c.2817c8",
"name": "Stop segmentation",
"group": "abeb6dad.635a2",
"order": 2,
Extraction and refactor of the python code from node-red flow The rationale for this rewrite is to improve the readability, the modularity, the reliability and the future-proofing of the main python script. All in all, this is now 124 commits that are going to be squashed and merged together, spanning more than two weeks of development and testing. Please test away this release and break things. An upgrading guide will be published in the coming days, along with a new image for people to use if they don't want to upgrade on their own. Read along if you want to know all the goodies! As a starter, the python script was extracted from the main flow, and now lives in its own files at `PlantonScope/scripts/*`. We set up the auto formatting of the code by using [Black](https://github.com/psf/black). This make the code clearer and uniform. We are using the default settings, so if you just install Black and set your editor to format on save using it, you should be good to go. The code is separated in four main processes, each with a specific set of responsibilities: - The main process controls all the others, starts everything up and cleans up on shutdown - The stepper process manages the stepper movements. It's now possible to have simultaneous movements of both motors (this closes #38 ). - The imager process controls the camera and the streaming server via a state machine. - The segmenter process manages the segmentation and its outputs. The segmentation happens recursively in all folders in `/home/pi/PlanktonScope/img/`. Each folder has its own output archive, and bug #26 is now closed. Those processes communicates together using MQTT and json messages. Each message is adressed to one topic. The high level topic controls which process receives the message. The details of each topic is at the end of this commit message. Every imaging sessions has now its own folder, under the `img` root. Metadata are saved individually for every session, in a JSON file in the same directory as the pictures. The configuration is not parsed from `config.json` anymore and passed directly through MQTT messages to the concerned process. A new configuration file has been created: `hardware.json`. This file contains information related to your specific hardware configuration. You can choose to reverse the connection of the motors for example, but you can also define specific speed limits and steps number for your pump and focus stage. This will make it easier for people who wants to experiment with different kind of hardware. It's not necessary to have this file though. If it doesn't exists, the default configuration will be applied. The code is architectured around 6 modules and about 10 classes. I encourage you to have a look at the files, they're pretty straightforward to understand. There is a lot of work left around the node-red code refactoring, dashboard ui improvements, better and clearer LED messages, OLED screen integration and finer control of the segmentation process, but this is quite good for now. Here is the topic lists for MQTT and the corresponding messages. - actuator : This topic adresses the stepper control thread No publication under this topic should happen from the python process - actuator/pump : Control of the pump The message is a json object {"action":"move", "direction":"FORWARD", "volume":10, "flowrate":1} to move 10mL forward at 1mL/min action can be "move" or "stop" Receive only - actuator/focus : Control of the focus stage The message is a json object, speed is optional {"action":"move", "direction":"UP", "distance":0.26, "speed":1} to move up 10mm action can be "move" or "stop" Receive only - imager/image : This topic adresses the imaging thread Is a json object with {"action":"image","sleep":5,"volume":1,"nb_frame":200} sleep in seconds, volume in mL Can also receive a config update message: {"action":"config","config":[...]} Can also receive a camera settings message: {"action":"settings","iso":100,"shutter_speed":40} Receive only - segmenter/segment : This topic adresses the segmenter process Is a json object with {"action":"segment"} Receive only - status : This topics sends feedback to Node-Red No publication or receive at this level - status/pump : State of the pump Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/focus : State of the focus stage Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/imager : State of the imager Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Completed or 12_11_15_0.1.jpg has been imaged. Publish only - status/segmenter : Status of the segmentation - status/segmenter/name - status/segmenter/object_id - status/segmenter/metric Here is the original commit history: * Extract python main.py from flow * Fix bug in server addresses These addresses should be the loopback device instead of the network address of the device. Using the loopback address will not necessitate to update the script when the network address changes. * clean up picamera import * changes to main python and flow: update MQTT requests address to localhost (bugfix) update streaming output address to nothing update main flow to remove python script references and location * Automatically initialise imaging led on startup to off state. * Add the ability to invert outputs of the motor We added a key to config.json "hardware_config" with a subkey "stepper_reverse". If this key is present in the config file and set to 1, the output of the motors are inversed (stepper2 becomes the pump motor and stepper1 the focus motor) * move all non main script to a subfolder * add __init__.py to package * light module rewrite * json cleanup and absolute path for config file * light.py forgot to import subprocess #oups * Add command to turn the leds off * Auto formatting of main.py I've used Black with default settings, see https://github.com/psf/black * First commit of stepper.py Pump parameters still needs to be checked and tuned. * addition of hardware details in config.json * Introduce hardware.json to replace the `hardware_config` of config.json * stepper.py: calibration, typos * creates the MQTT_Client class * pump_max_speed is now in ml/min to help readability * forgot to add self to the class def * addition of threading capabilities to stepper.py (UNTESTED) * mqtt: fix topic bug * remove counter * mqtt add doc about topics * stepper.py creates an "actuator/*/state" topic * stepper.py: rename mqtt_client to pump_client * mqtt.py: add details about topics * stepper.py: rename pump_client to actuator_client * topic was not split properly and a part was lost * switch to f-strings for mqtt.py * cosmetic update * stepper.py: folder name will be planktoscope change calls * hardware.json became more straightforward * stepper.py syntax bugs * stepper.py addition of a received stop command * stepper.py: update to max travel distance * stepper.py: several typos here * rename folder * main.py: reword to reflect folder rename * main.py: remove logic that has been moved to stepper.py and mqtt.py * main.py: update to add mqtt imaging client * mqtt.py: make command and args local to class and output more verbose * make stepper.py a class * main.py: instantiate stepper class and call it * main.py: name mqtt client * update to main.json to reflect main.py changes * fix bugs around pump control * update flows to latest version from Thibault * distance can be a small value, and definitevely should be a float. * unify mqtt topics * unify mqtt output in the main flow * first logger implementation, uses loguru * mqtt: add reason to on_connect * mqtt: add on_disconnect handler * stepper: add more logger calls for debug mainly * main: add levels for logger * imager.py: first move of the imager logic * imager: time import cleanup * imager: morphocut import cleanup * imager: skimage import cleanup * imager: finishing import cleanup * imager: Class creation - WIP Also provides a fix for #26 (see line 190). * imager: threading is needed for Condition() * streamer: get the streamer server its own file * imager: creates start_camera and get the server creation out * imager: subclass multiprocessing.Process * imager: get Pipeline creation its own function * imager: cleanup of self calls * main: code removal and corresponding calls to newly created classes * imager: various formatting changes * main: management of signal shutdown * add requirements.txt * mqtt: messages are now json objects Also, addition of a flag on receiving a new message * mqtt: make message private and add logic to synchronise * stepper: creates the stepper class * stepper: use the new class * stepper: uses the new logic * stepper: add the shutdown event * stepper: add shutdown method * main: add shutdown event * imager: graceful shutdown * stepper: nicer way of checking the Eevnt * self is a required first argument for a method in a class Especially if you use said class private members! * python: various typos and small errors in import * stepper: create mqtt client during init * stepper: instanciate the mqtt client inside run Otherwise it's not accessible from inside the loop. It's a PITA, more information at https://stackoverflow.com/questions/17172878/using-pythons-multiprocessing-process-class * stepper: little bugs and typos all around * mqtt: add shutdown method * mqtt: add connect in init * stepper: fix bugs, sanitize inputs * stepper: work on delay prediction improvements * stepper: json is mean, double quote are mandatory inside * mqtt: add details about message exchanged * imager: first implementation of json messages * main.json: add new tab for RPi management + json for payloads * imager: add state_machine class * stepper: publish last will * imager: major refactor * main: make streaming server process a daemon * mqtt: insert debug statement on close * main: reorder imports * imager: make it work! Reinsert the streaming server logic in there, because there is a problem with the synchronisation part otherwise. Also, eventually, StreamingOuput() will have to be made not global Final very critical learning: it's super duper important to make sure the memory split is at least 256Meg for the GPU. Chaos ensues otherwise * main: changes to accomodate the streamer/imager fusino * imager_state_machine: insert states transition description * stepper: cleanup of code * segmenter: creation of the class * python: include segmenter changes * remove unused files * stepper: check existence of hardware.json * main.json: changes to reflect the python script evolution * remove unecessary TODOs and add some others * main: add check for config and directories * imager: update_config is implemented and we have better management of directories now * segmenter: now work recursively in all folders * flow: the configuration is now sent via mqtt * segmenter: better manage pipeline error * segmenter: declaration of archive_fn in init * imager: small bugs and typos * main: add uniqueID output * imager: add the camera settings message We can now update the ISO, shutter speed and resolution from Node-Red * package.json: update dependencies
2020-09-28 11:05:27 +02:00
"width": 6,
"height": 1,
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"passthru": true,
"label": "Stop segmentation",
"tooltip": "",
"color": "",
"bgcolor": "#AD1625",
"icon": "",
"payload": "{\"action\":\"stop\"}",
"payloadType": "json",
"topic": "segmenter/segment",
"x": 370,
"y": 380,
"wires": [
[
"16f3cef4.0acac9"
]
]
Extraction and refactor of the python code from node-red flow The rationale for this rewrite is to improve the readability, the modularity, the reliability and the future-proofing of the main python script. All in all, this is now 124 commits that are going to be squashed and merged together, spanning more than two weeks of development and testing. Please test away this release and break things. An upgrading guide will be published in the coming days, along with a new image for people to use if they don't want to upgrade on their own. Read along if you want to know all the goodies! As a starter, the python script was extracted from the main flow, and now lives in its own files at `PlantonScope/scripts/*`. We set up the auto formatting of the code by using [Black](https://github.com/psf/black). This make the code clearer and uniform. We are using the default settings, so if you just install Black and set your editor to format on save using it, you should be good to go. The code is separated in four main processes, each with a specific set of responsibilities: - The main process controls all the others, starts everything up and cleans up on shutdown - The stepper process manages the stepper movements. It's now possible to have simultaneous movements of both motors (this closes #38 ). - The imager process controls the camera and the streaming server via a state machine. - The segmenter process manages the segmentation and its outputs. The segmentation happens recursively in all folders in `/home/pi/PlanktonScope/img/`. Each folder has its own output archive, and bug #26 is now closed. Those processes communicates together using MQTT and json messages. Each message is adressed to one topic. The high level topic controls which process receives the message. The details of each topic is at the end of this commit message. Every imaging sessions has now its own folder, under the `img` root. Metadata are saved individually for every session, in a JSON file in the same directory as the pictures. The configuration is not parsed from `config.json` anymore and passed directly through MQTT messages to the concerned process. A new configuration file has been created: `hardware.json`. This file contains information related to your specific hardware configuration. You can choose to reverse the connection of the motors for example, but you can also define specific speed limits and steps number for your pump and focus stage. This will make it easier for people who wants to experiment with different kind of hardware. It's not necessary to have this file though. If it doesn't exists, the default configuration will be applied. The code is architectured around 6 modules and about 10 classes. I encourage you to have a look at the files, they're pretty straightforward to understand. There is a lot of work left around the node-red code refactoring, dashboard ui improvements, better and clearer LED messages, OLED screen integration and finer control of the segmentation process, but this is quite good for now. Here is the topic lists for MQTT and the corresponding messages. - actuator : This topic adresses the stepper control thread No publication under this topic should happen from the python process - actuator/pump : Control of the pump The message is a json object {"action":"move", "direction":"FORWARD", "volume":10, "flowrate":1} to move 10mL forward at 1mL/min action can be "move" or "stop" Receive only - actuator/focus : Control of the focus stage The message is a json object, speed is optional {"action":"move", "direction":"UP", "distance":0.26, "speed":1} to move up 10mm action can be "move" or "stop" Receive only - imager/image : This topic adresses the imaging thread Is a json object with {"action":"image","sleep":5,"volume":1,"nb_frame":200} sleep in seconds, volume in mL Can also receive a config update message: {"action":"config","config":[...]} Can also receive a camera settings message: {"action":"settings","iso":100,"shutter_speed":40} Receive only - segmenter/segment : This topic adresses the segmenter process Is a json object with {"action":"segment"} Receive only - status : This topics sends feedback to Node-Red No publication or receive at this level - status/pump : State of the pump Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/focus : State of the focus stage Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/imager : State of the imager Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Completed or 12_11_15_0.1.jpg has been imaged. Publish only - status/segmenter : Status of the segmentation - status/segmenter/name - status/segmenter/object_id - status/segmenter/metric Here is the original commit history: * Extract python main.py from flow * Fix bug in server addresses These addresses should be the loopback device instead of the network address of the device. Using the loopback address will not necessitate to update the script when the network address changes. * clean up picamera import * changes to main python and flow: update MQTT requests address to localhost (bugfix) update streaming output address to nothing update main flow to remove python script references and location * Automatically initialise imaging led on startup to off state. * Add the ability to invert outputs of the motor We added a key to config.json "hardware_config" with a subkey "stepper_reverse". If this key is present in the config file and set to 1, the output of the motors are inversed (stepper2 becomes the pump motor and stepper1 the focus motor) * move all non main script to a subfolder * add __init__.py to package * light module rewrite * json cleanup and absolute path for config file * light.py forgot to import subprocess #oups * Add command to turn the leds off * Auto formatting of main.py I've used Black with default settings, see https://github.com/psf/black * First commit of stepper.py Pump parameters still needs to be checked and tuned. * addition of hardware details in config.json * Introduce hardware.json to replace the `hardware_config` of config.json * stepper.py: calibration, typos * creates the MQTT_Client class * pump_max_speed is now in ml/min to help readability * forgot to add self to the class def * addition of threading capabilities to stepper.py (UNTESTED) * mqtt: fix topic bug * remove counter * mqtt add doc about topics * stepper.py creates an "actuator/*/state" topic * stepper.py: rename mqtt_client to pump_client * mqtt.py: add details about topics * stepper.py: rename pump_client to actuator_client * topic was not split properly and a part was lost * switch to f-strings for mqtt.py * cosmetic update * stepper.py: folder name will be planktoscope change calls * hardware.json became more straightforward * stepper.py syntax bugs * stepper.py addition of a received stop command * stepper.py: update to max travel distance * stepper.py: several typos here * rename folder * main.py: reword to reflect folder rename * main.py: remove logic that has been moved to stepper.py and mqtt.py * main.py: update to add mqtt imaging client * mqtt.py: make command and args local to class and output more verbose * make stepper.py a class * main.py: instantiate stepper class and call it * main.py: name mqtt client * update to main.json to reflect main.py changes * fix bugs around pump control * update flows to latest version from Thibault * distance can be a small value, and definitevely should be a float. * unify mqtt topics * unify mqtt output in the main flow * first logger implementation, uses loguru * mqtt: add reason to on_connect * mqtt: add on_disconnect handler * stepper: add more logger calls for debug mainly * main: add levels for logger * imager.py: first move of the imager logic * imager: time import cleanup * imager: morphocut import cleanup * imager: skimage import cleanup * imager: finishing import cleanup * imager: Class creation - WIP Also provides a fix for #26 (see line 190). * imager: threading is needed for Condition() * streamer: get the streamer server its own file * imager: creates start_camera and get the server creation out * imager: subclass multiprocessing.Process * imager: get Pipeline creation its own function * imager: cleanup of self calls * main: code removal and corresponding calls to newly created classes * imager: various formatting changes * main: management of signal shutdown * add requirements.txt * mqtt: messages are now json objects Also, addition of a flag on receiving a new message * mqtt: make message private and add logic to synchronise * stepper: creates the stepper class * stepper: use the new class * stepper: uses the new logic * stepper: add the shutdown event * stepper: add shutdown method * main: add shutdown event * imager: graceful shutdown * stepper: nicer way of checking the Eevnt * self is a required first argument for a method in a class Especially if you use said class private members! * python: various typos and small errors in import * stepper: create mqtt client during init * stepper: instanciate the mqtt client inside run Otherwise it's not accessible from inside the loop. It's a PITA, more information at https://stackoverflow.com/questions/17172878/using-pythons-multiprocessing-process-class * stepper: little bugs and typos all around * mqtt: add shutdown method * mqtt: add connect in init * stepper: fix bugs, sanitize inputs * stepper: work on delay prediction improvements * stepper: json is mean, double quote are mandatory inside * mqtt: add details about message exchanged * imager: first implementation of json messages * main.json: add new tab for RPi management + json for payloads * imager: add state_machine class * stepper: publish last will * imager: major refactor * main: make streaming server process a daemon * mqtt: insert debug statement on close * main: reorder imports * imager: make it work! Reinsert the streaming server logic in there, because there is a problem with the synchronisation part otherwise. Also, eventually, StreamingOuput() will have to be made not global Final very critical learning: it's super duper important to make sure the memory split is at least 256Meg for the GPU. Chaos ensues otherwise * main: changes to accomodate the streamer/imager fusino * imager_state_machine: insert states transition description * stepper: cleanup of code * segmenter: creation of the class * python: include segmenter changes * remove unused files * stepper: check existence of hardware.json * main.json: changes to reflect the python script evolution * remove unecessary TODOs and add some others * main: add check for config and directories * imager: update_config is implemented and we have better management of directories now * segmenter: now work recursively in all folders * flow: the configuration is now sent via mqtt * segmenter: better manage pipeline error * segmenter: declaration of archive_fn in init * imager: small bugs and typos * main: add uniqueID output * imager: add the camera settings message We can now update the ISO, shutter speed and resolution from Node-Red * package.json: update dependencies
2020-09-28 11:05:27 +02:00
},
{
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"id": "16f3cef4.0acac9",
"type": "mqtt out",
"z": "cb95299c.2817c8",
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"broker": "8dc3722c.06efa8",
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Extraction and refactor of the python code from node-red flow The rationale for this rewrite is to improve the readability, the modularity, the reliability and the future-proofing of the main python script. All in all, this is now 124 commits that are going to be squashed and merged together, spanning more than two weeks of development and testing. Please test away this release and break things. An upgrading guide will be published in the coming days, along with a new image for people to use if they don't want to upgrade on their own. Read along if you want to know all the goodies! As a starter, the python script was extracted from the main flow, and now lives in its own files at `PlantonScope/scripts/*`. We set up the auto formatting of the code by using [Black](https://github.com/psf/black). This make the code clearer and uniform. We are using the default settings, so if you just install Black and set your editor to format on save using it, you should be good to go. The code is separated in four main processes, each with a specific set of responsibilities: - The main process controls all the others, starts everything up and cleans up on shutdown - The stepper process manages the stepper movements. It's now possible to have simultaneous movements of both motors (this closes #38 ). - The imager process controls the camera and the streaming server via a state machine. - The segmenter process manages the segmentation and its outputs. The segmentation happens recursively in all folders in `/home/pi/PlanktonScope/img/`. Each folder has its own output archive, and bug #26 is now closed. Those processes communicates together using MQTT and json messages. Each message is adressed to one topic. The high level topic controls which process receives the message. The details of each topic is at the end of this commit message. Every imaging sessions has now its own folder, under the `img` root. Metadata are saved individually for every session, in a JSON file in the same directory as the pictures. The configuration is not parsed from `config.json` anymore and passed directly through MQTT messages to the concerned process. A new configuration file has been created: `hardware.json`. This file contains information related to your specific hardware configuration. You can choose to reverse the connection of the motors for example, but you can also define specific speed limits and steps number for your pump and focus stage. This will make it easier for people who wants to experiment with different kind of hardware. It's not necessary to have this file though. If it doesn't exists, the default configuration will be applied. The code is architectured around 6 modules and about 10 classes. I encourage you to have a look at the files, they're pretty straightforward to understand. There is a lot of work left around the node-red code refactoring, dashboard ui improvements, better and clearer LED messages, OLED screen integration and finer control of the segmentation process, but this is quite good for now. Here is the topic lists for MQTT and the corresponding messages. - actuator : This topic adresses the stepper control thread No publication under this topic should happen from the python process - actuator/pump : Control of the pump The message is a json object {"action":"move", "direction":"FORWARD", "volume":10, "flowrate":1} to move 10mL forward at 1mL/min action can be "move" or "stop" Receive only - actuator/focus : Control of the focus stage The message is a json object, speed is optional {"action":"move", "direction":"UP", "distance":0.26, "speed":1} to move up 10mm action can be "move" or "stop" Receive only - imager/image : This topic adresses the imaging thread Is a json object with {"action":"image","sleep":5,"volume":1,"nb_frame":200} sleep in seconds, volume in mL Can also receive a config update message: {"action":"config","config":[...]} Can also receive a camera settings message: {"action":"settings","iso":100,"shutter_speed":40} Receive only - segmenter/segment : This topic adresses the segmenter process Is a json object with {"action":"segment"} Receive only - status : This topics sends feedback to Node-Red No publication or receive at this level - status/pump : State of the pump Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/focus : State of the focus stage Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/imager : State of the imager Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Completed or 12_11_15_0.1.jpg has been imaged. Publish only - status/segmenter : Status of the segmentation - status/segmenter/name - status/segmenter/object_id - status/segmenter/metric Here is the original commit history: * Extract python main.py from flow * Fix bug in server addresses These addresses should be the loopback device instead of the network address of the device. Using the loopback address will not necessitate to update the script when the network address changes. * clean up picamera import * changes to main python and flow: update MQTT requests address to localhost (bugfix) update streaming output address to nothing update main flow to remove python script references and location * Automatically initialise imaging led on startup to off state. * Add the ability to invert outputs of the motor We added a key to config.json "hardware_config" with a subkey "stepper_reverse". If this key is present in the config file and set to 1, the output of the motors are inversed (stepper2 becomes the pump motor and stepper1 the focus motor) * move all non main script to a subfolder * add __init__.py to package * light module rewrite * json cleanup and absolute path for config file * light.py forgot to import subprocess #oups * Add command to turn the leds off * Auto formatting of main.py I've used Black with default settings, see https://github.com/psf/black * First commit of stepper.py Pump parameters still needs to be checked and tuned. * addition of hardware details in config.json * Introduce hardware.json to replace the `hardware_config` of config.json * stepper.py: calibration, typos * creates the MQTT_Client class * pump_max_speed is now in ml/min to help readability * forgot to add self to the class def * addition of threading capabilities to stepper.py (UNTESTED) * mqtt: fix topic bug * remove counter * mqtt add doc about topics * stepper.py creates an "actuator/*/state" topic * stepper.py: rename mqtt_client to pump_client * mqtt.py: add details about topics * stepper.py: rename pump_client to actuator_client * topic was not split properly and a part was lost * switch to f-strings for mqtt.py * cosmetic update * stepper.py: folder name will be planktoscope change calls * hardware.json became more straightforward * stepper.py syntax bugs * stepper.py addition of a received stop command * stepper.py: update to max travel distance * stepper.py: several typos here * rename folder * main.py: reword to reflect folder rename * main.py: remove logic that has been moved to stepper.py and mqtt.py * main.py: update to add mqtt imaging client * mqtt.py: make command and args local to class and output more verbose * make stepper.py a class * main.py: instantiate stepper class and call it * main.py: name mqtt client * update to main.json to reflect main.py changes * fix bugs around pump control * update flows to latest version from Thibault * distance can be a small value, and definitevely should be a float. * unify mqtt topics * unify mqtt output in the main flow * first logger implementation, uses loguru * mqtt: add reason to on_connect * mqtt: add on_disconnect handler * stepper: add more logger calls for debug mainly * main: add levels for logger * imager.py: first move of the imager logic * imager: time import cleanup * imager: morphocut import cleanup * imager: skimage import cleanup * imager: finishing import cleanup * imager: Class creation - WIP Also provides a fix for #26 (see line 190). * imager: threading is needed for Condition() * streamer: get the streamer server its own file * imager: creates start_camera and get the server creation out * imager: subclass multiprocessing.Process * imager: get Pipeline creation its own function * imager: cleanup of self calls * main: code removal and corresponding calls to newly created classes * imager: various formatting changes * main: management of signal shutdown * add requirements.txt * mqtt: messages are now json objects Also, addition of a flag on receiving a new message * mqtt: make message private and add logic to synchronise * stepper: creates the stepper class * stepper: use the new class * stepper: uses the new logic * stepper: add the shutdown event * stepper: add shutdown method * main: add shutdown event * imager: graceful shutdown * stepper: nicer way of checking the Eevnt * self is a required first argument for a method in a class Especially if you use said class private members! * python: various typos and small errors in import * stepper: create mqtt client during init * stepper: instanciate the mqtt client inside run Otherwise it's not accessible from inside the loop. It's a PITA, more information at https://stackoverflow.com/questions/17172878/using-pythons-multiprocessing-process-class * stepper: little bugs and typos all around * mqtt: add shutdown method * mqtt: add connect in init * stepper: fix bugs, sanitize inputs * stepper: work on delay prediction improvements * stepper: json is mean, double quote are mandatory inside * mqtt: add details about message exchanged * imager: first implementation of json messages * main.json: add new tab for RPi management + json for payloads * imager: add state_machine class * stepper: publish last will * imager: major refactor * main: make streaming server process a daemon * mqtt: insert debug statement on close * main: reorder imports * imager: make it work! Reinsert the streaming server logic in there, because there is a problem with the synchronisation part otherwise. Also, eventually, StreamingOuput() will have to be made not global Final very critical learning: it's super duper important to make sure the memory split is at least 256Meg for the GPU. Chaos ensues otherwise * main: changes to accomodate the streamer/imager fusino * imager_state_machine: insert states transition description * stepper: cleanup of code * segmenter: creation of the class * python: include segmenter changes * remove unused files * stepper: check existence of hardware.json * main.json: changes to reflect the python script evolution * remove unecessary TODOs and add some others * main: add check for config and directories * imager: update_config is implemented and we have better management of directories now * segmenter: now work recursively in all folders * flow: the configuration is now sent via mqtt * segmenter: better manage pipeline error * segmenter: declaration of archive_fn in init * imager: small bugs and typos * main: add uniqueID output * imager: add the camera settings message We can now update the ISO, shutter speed and resolution from Node-Red * package.json: update dependencies
2020-09-28 11:05:27 +02:00
"wires": []
},
{
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"id": "6b61b50c.7456d4",
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"z": "1371dec5.76e671",
"name": "Update",
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"label": "Update",
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Extraction and refactor of the python code from node-red flow The rationale for this rewrite is to improve the readability, the modularity, the reliability and the future-proofing of the main python script. All in all, this is now 124 commits that are going to be squashed and merged together, spanning more than two weeks of development and testing. Please test away this release and break things. An upgrading guide will be published in the coming days, along with a new image for people to use if they don't want to upgrade on their own. Read along if you want to know all the goodies! As a starter, the python script was extracted from the main flow, and now lives in its own files at `PlantonScope/scripts/*`. We set up the auto formatting of the code by using [Black](https://github.com/psf/black). This make the code clearer and uniform. We are using the default settings, so if you just install Black and set your editor to format on save using it, you should be good to go. The code is separated in four main processes, each with a specific set of responsibilities: - The main process controls all the others, starts everything up and cleans up on shutdown - The stepper process manages the stepper movements. It's now possible to have simultaneous movements of both motors (this closes #38 ). - The imager process controls the camera and the streaming server via a state machine. - The segmenter process manages the segmentation and its outputs. The segmentation happens recursively in all folders in `/home/pi/PlanktonScope/img/`. Each folder has its own output archive, and bug #26 is now closed. Those processes communicates together using MQTT and json messages. Each message is adressed to one topic. The high level topic controls which process receives the message. The details of each topic is at the end of this commit message. Every imaging sessions has now its own folder, under the `img` root. Metadata are saved individually for every session, in a JSON file in the same directory as the pictures. The configuration is not parsed from `config.json` anymore and passed directly through MQTT messages to the concerned process. A new configuration file has been created: `hardware.json`. This file contains information related to your specific hardware configuration. You can choose to reverse the connection of the motors for example, but you can also define specific speed limits and steps number for your pump and focus stage. This will make it easier for people who wants to experiment with different kind of hardware. It's not necessary to have this file though. If it doesn't exists, the default configuration will be applied. The code is architectured around 6 modules and about 10 classes. I encourage you to have a look at the files, they're pretty straightforward to understand. There is a lot of work left around the node-red code refactoring, dashboard ui improvements, better and clearer LED messages, OLED screen integration and finer control of the segmentation process, but this is quite good for now. Here is the topic lists for MQTT and the corresponding messages. - actuator : This topic adresses the stepper control thread No publication under this topic should happen from the python process - actuator/pump : Control of the pump The message is a json object {"action":"move", "direction":"FORWARD", "volume":10, "flowrate":1} to move 10mL forward at 1mL/min action can be "move" or "stop" Receive only - actuator/focus : Control of the focus stage The message is a json object, speed is optional {"action":"move", "direction":"UP", "distance":0.26, "speed":1} to move up 10mm action can be "move" or "stop" Receive only - imager/image : This topic adresses the imaging thread Is a json object with {"action":"image","sleep":5,"volume":1,"nb_frame":200} sleep in seconds, volume in mL Can also receive a config update message: {"action":"config","config":[...]} Can also receive a camera settings message: {"action":"settings","iso":100,"shutter_speed":40} Receive only - segmenter/segment : This topic adresses the segmenter process Is a json object with {"action":"segment"} Receive only - status : This topics sends feedback to Node-Red No publication or receive at this level - status/pump : State of the pump Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/focus : State of the focus stage Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/imager : State of the imager Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Completed or 12_11_15_0.1.jpg has been imaged. Publish only - status/segmenter : Status of the segmentation - status/segmenter/name - status/segmenter/object_id - status/segmenter/metric Here is the original commit history: * Extract python main.py from flow * Fix bug in server addresses These addresses should be the loopback device instead of the network address of the device. Using the loopback address will not necessitate to update the script when the network address changes. * clean up picamera import * changes to main python and flow: update MQTT requests address to localhost (bugfix) update streaming output address to nothing update main flow to remove python script references and location * Automatically initialise imaging led on startup to off state. * Add the ability to invert outputs of the motor We added a key to config.json "hardware_config" with a subkey "stepper_reverse". If this key is present in the config file and set to 1, the output of the motors are inversed (stepper2 becomes the pump motor and stepper1 the focus motor) * move all non main script to a subfolder * add __init__.py to package * light module rewrite * json cleanup and absolute path for config file * light.py forgot to import subprocess #oups * Add command to turn the leds off * Auto formatting of main.py I've used Black with default settings, see https://github.com/psf/black * First commit of stepper.py Pump parameters still needs to be checked and tuned. * addition of hardware details in config.json * Introduce hardware.json to replace the `hardware_config` of config.json * stepper.py: calibration, typos * creates the MQTT_Client class * pump_max_speed is now in ml/min to help readability * forgot to add self to the class def * addition of threading capabilities to stepper.py (UNTESTED) * mqtt: fix topic bug * remove counter * mqtt add doc about topics * stepper.py creates an "actuator/*/state" topic * stepper.py: rename mqtt_client to pump_client * mqtt.py: add details about topics * stepper.py: rename pump_client to actuator_client * topic was not split properly and a part was lost * switch to f-strings for mqtt.py * cosmetic update * stepper.py: folder name will be planktoscope change calls * hardware.json became more straightforward * stepper.py syntax bugs * stepper.py addition of a received stop command * stepper.py: update to max travel distance * stepper.py: several typos here * rename folder * main.py: reword to reflect folder rename * main.py: remove logic that has been moved to stepper.py and mqtt.py * main.py: update to add mqtt imaging client * mqtt.py: make command and args local to class and output more verbose * make stepper.py a class * main.py: instantiate stepper class and call it * main.py: name mqtt client * update to main.json to reflect main.py changes * fix bugs around pump control * update flows to latest version from Thibault * distance can be a small value, and definitevely should be a float. * unify mqtt topics * unify mqtt output in the main flow * first logger implementation, uses loguru * mqtt: add reason to on_connect * mqtt: add on_disconnect handler * stepper: add more logger calls for debug mainly * main: add levels for logger * imager.py: first move of the imager logic * imager: time import cleanup * imager: morphocut import cleanup * imager: skimage import cleanup * imager: finishing import cleanup * imager: Class creation - WIP Also provides a fix for #26 (see line 190). * imager: threading is needed for Condition() * streamer: get the streamer server its own file * imager: creates start_camera and get the server creation out * imager: subclass multiprocessing.Process * imager: get Pipeline creation its own function * imager: cleanup of self calls * main: code removal and corresponding calls to newly created classes * imager: various formatting changes * main: management of signal shutdown * add requirements.txt * mqtt: messages are now json objects Also, addition of a flag on receiving a new message * mqtt: make message private and add logic to synchronise * stepper: creates the stepper class * stepper: use the new class * stepper: uses the new logic * stepper: add the shutdown event * stepper: add shutdown method * main: add shutdown event * imager: graceful shutdown * stepper: nicer way of checking the Eevnt * self is a required first argument for a method in a class Especially if you use said class private members! * python: various typos and small errors in import * stepper: create mqtt client during init * stepper: instanciate the mqtt client inside run Otherwise it's not accessible from inside the loop. It's a PITA, more information at https://stackoverflow.com/questions/17172878/using-pythons-multiprocessing-process-class * stepper: little bugs and typos all around * mqtt: add shutdown method * mqtt: add connect in init * stepper: fix bugs, sanitize inputs * stepper: work on delay prediction improvements * stepper: json is mean, double quote are mandatory inside * mqtt: add details about message exchanged * imager: first implementation of json messages * main.json: add new tab for RPi management + json for payloads * imager: add state_machine class * stepper: publish last will * imager: major refactor * main: make streaming server process a daemon * mqtt: insert debug statement on close * main: reorder imports * imager: make it work! Reinsert the streaming server logic in there, because there is a problem with the synchronisation part otherwise. Also, eventually, StreamingOuput() will have to be made not global Final very critical learning: it's super duper important to make sure the memory split is at least 256Meg for the GPU. Chaos ensues otherwise * main: changes to accomodate the streamer/imager fusino * imager_state_machine: insert states transition description * stepper: cleanup of code * segmenter: creation of the class * python: include segmenter changes * remove unused files * stepper: check existence of hardware.json * main.json: changes to reflect the python script evolution * remove unecessary TODOs and add some others * main: add check for config and directories * imager: update_config is implemented and we have better management of directories now * segmenter: now work recursively in all folders * flow: the configuration is now sent via mqtt * segmenter: better manage pipeline error * segmenter: declaration of archive_fn in init * imager: small bugs and typos * main: add uniqueID output * imager: add the camera settings message We can now update the ISO, shutter speed and resolution from Node-Red * package.json: update dependencies
2020-09-28 11:05:27 +02:00
"wires": [
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Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"386ce65d.a15d52"
Extraction and refactor of the python code from node-red flow The rationale for this rewrite is to improve the readability, the modularity, the reliability and the future-proofing of the main python script. All in all, this is now 124 commits that are going to be squashed and merged together, spanning more than two weeks of development and testing. Please test away this release and break things. An upgrading guide will be published in the coming days, along with a new image for people to use if they don't want to upgrade on their own. Read along if you want to know all the goodies! As a starter, the python script was extracted from the main flow, and now lives in its own files at `PlantonScope/scripts/*`. We set up the auto formatting of the code by using [Black](https://github.com/psf/black). This make the code clearer and uniform. We are using the default settings, so if you just install Black and set your editor to format on save using it, you should be good to go. The code is separated in four main processes, each with a specific set of responsibilities: - The main process controls all the others, starts everything up and cleans up on shutdown - The stepper process manages the stepper movements. It's now possible to have simultaneous movements of both motors (this closes #38 ). - The imager process controls the camera and the streaming server via a state machine. - The segmenter process manages the segmentation and its outputs. The segmentation happens recursively in all folders in `/home/pi/PlanktonScope/img/`. Each folder has its own output archive, and bug #26 is now closed. Those processes communicates together using MQTT and json messages. Each message is adressed to one topic. The high level topic controls which process receives the message. The details of each topic is at the end of this commit message. Every imaging sessions has now its own folder, under the `img` root. Metadata are saved individually for every session, in a JSON file in the same directory as the pictures. The configuration is not parsed from `config.json` anymore and passed directly through MQTT messages to the concerned process. A new configuration file has been created: `hardware.json`. This file contains information related to your specific hardware configuration. You can choose to reverse the connection of the motors for example, but you can also define specific speed limits and steps number for your pump and focus stage. This will make it easier for people who wants to experiment with different kind of hardware. It's not necessary to have this file though. If it doesn't exists, the default configuration will be applied. The code is architectured around 6 modules and about 10 classes. I encourage you to have a look at the files, they're pretty straightforward to understand. There is a lot of work left around the node-red code refactoring, dashboard ui improvements, better and clearer LED messages, OLED screen integration and finer control of the segmentation process, but this is quite good for now. Here is the topic lists for MQTT and the corresponding messages. - actuator : This topic adresses the stepper control thread No publication under this topic should happen from the python process - actuator/pump : Control of the pump The message is a json object {"action":"move", "direction":"FORWARD", "volume":10, "flowrate":1} to move 10mL forward at 1mL/min action can be "move" or "stop" Receive only - actuator/focus : Control of the focus stage The message is a json object, speed is optional {"action":"move", "direction":"UP", "distance":0.26, "speed":1} to move up 10mm action can be "move" or "stop" Receive only - imager/image : This topic adresses the imaging thread Is a json object with {"action":"image","sleep":5,"volume":1,"nb_frame":200} sleep in seconds, volume in mL Can also receive a config update message: {"action":"config","config":[...]} Can also receive a camera settings message: {"action":"settings","iso":100,"shutter_speed":40} Receive only - segmenter/segment : This topic adresses the segmenter process Is a json object with {"action":"segment"} Receive only - status : This topics sends feedback to Node-Red No publication or receive at this level - status/pump : State of the pump Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/focus : State of the focus stage Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/imager : State of the imager Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Completed or 12_11_15_0.1.jpg has been imaged. Publish only - status/segmenter : Status of the segmentation - status/segmenter/name - status/segmenter/object_id - status/segmenter/metric Here is the original commit history: * Extract python main.py from flow * Fix bug in server addresses These addresses should be the loopback device instead of the network address of the device. Using the loopback address will not necessitate to update the script when the network address changes. * clean up picamera import * changes to main python and flow: update MQTT requests address to localhost (bugfix) update streaming output address to nothing update main flow to remove python script references and location * Automatically initialise imaging led on startup to off state. * Add the ability to invert outputs of the motor We added a key to config.json "hardware_config" with a subkey "stepper_reverse". If this key is present in the config file and set to 1, the output of the motors are inversed (stepper2 becomes the pump motor and stepper1 the focus motor) * move all non main script to a subfolder * add __init__.py to package * light module rewrite * json cleanup and absolute path for config file * light.py forgot to import subprocess #oups * Add command to turn the leds off * Auto formatting of main.py I've used Black with default settings, see https://github.com/psf/black * First commit of stepper.py Pump parameters still needs to be checked and tuned. * addition of hardware details in config.json * Introduce hardware.json to replace the `hardware_config` of config.json * stepper.py: calibration, typos * creates the MQTT_Client class * pump_max_speed is now in ml/min to help readability * forgot to add self to the class def * addition of threading capabilities to stepper.py (UNTESTED) * mqtt: fix topic bug * remove counter * mqtt add doc about topics * stepper.py creates an "actuator/*/state" topic * stepper.py: rename mqtt_client to pump_client * mqtt.py: add details about topics * stepper.py: rename pump_client to actuator_client * topic was not split properly and a part was lost * switch to f-strings for mqtt.py * cosmetic update * stepper.py: folder name will be planktoscope change calls * hardware.json became more straightforward * stepper.py syntax bugs * stepper.py addition of a received stop command * stepper.py: update to max travel distance * stepper.py: several typos here * rename folder * main.py: reword to reflect folder rename * main.py: remove logic that has been moved to stepper.py and mqtt.py * main.py: update to add mqtt imaging client * mqtt.py: make command and args local to class and output more verbose * make stepper.py a class * main.py: instantiate stepper class and call it * main.py: name mqtt client * update to main.json to reflect main.py changes * fix bugs around pump control * update flows to latest version from Thibault * distance can be a small value, and definitevely should be a float. * unify mqtt topics * unify mqtt output in the main flow * first logger implementation, uses loguru * mqtt: add reason to on_connect * mqtt: add on_disconnect handler * stepper: add more logger calls for debug mainly * main: add levels for logger * imager.py: first move of the imager logic * imager: time import cleanup * imager: morphocut import cleanup * imager: skimage import cleanup * imager: finishing import cleanup * imager: Class creation - WIP Also provides a fix for #26 (see line 190). * imager: threading is needed for Condition() * streamer: get the streamer server its own file * imager: creates start_camera and get the server creation out * imager: subclass multiprocessing.Process * imager: get Pipeline creation its own function * imager: cleanup of self calls * main: code removal and corresponding calls to newly created classes * imager: various formatting changes * main: management of signal shutdown * add requirements.txt * mqtt: messages are now json objects Also, addition of a flag on receiving a new message * mqtt: make message private and add logic to synchronise * stepper: creates the stepper class * stepper: use the new class * stepper: uses the new logic * stepper: add the shutdown event * stepper: add shutdown method * main: add shutdown event * imager: graceful shutdown * stepper: nicer way of checking the Eevnt * self is a required first argument for a method in a class Especially if you use said class private members! * python: various typos and small errors in import * stepper: create mqtt client during init * stepper: instanciate the mqtt client inside run Otherwise it's not accessible from inside the loop. It's a PITA, more information at https://stackoverflow.com/questions/17172878/using-pythons-multiprocessing-process-class * stepper: little bugs and typos all around * mqtt: add shutdown method * mqtt: add connect in init * stepper: fix bugs, sanitize inputs * stepper: work on delay prediction improvements * stepper: json is mean, double quote are mandatory inside * mqtt: add details about message exchanged * imager: first implementation of json messages * main.json: add new tab for RPi management + json for payloads * imager: add state_machine class * stepper: publish last will * imager: major refactor * main: make streaming server process a daemon * mqtt: insert debug statement on close * main: reorder imports * imager: make it work! Reinsert the streaming server logic in there, because there is a problem with the synchronisation part otherwise. Also, eventually, StreamingOuput() will have to be made not global Final very critical learning: it's super duper important to make sure the memory split is at least 256Meg for the GPU. Chaos ensues otherwise * main: changes to accomodate the streamer/imager fusino * imager_state_machine: insert states transition description * stepper: cleanup of code * segmenter: creation of the class * python: include segmenter changes * remove unused files * stepper: check existence of hardware.json * main.json: changes to reflect the python script evolution * remove unecessary TODOs and add some others * main: add check for config and directories * imager: update_config is implemented and we have better management of directories now * segmenter: now work recursively in all folders * flow: the configuration is now sent via mqtt * segmenter: better manage pipeline error * segmenter: declaration of archive_fn in init * imager: small bugs and typos * main: add uniqueID output * imager: add the camera settings message We can now update the ISO, shutter speed and resolution from Node-Red * package.json: update dependencies
2020-09-28 11:05:27 +02:00
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Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
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config: update default and flow update bug
2020-11-24 17:26:10 +01:00
"command": "git --git-dir /home/pi/PlanktonScope/.git/ stash",
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"addpay": false,
config: update default and flow update bug
2020-11-24 17:26:10 +01:00
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Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
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Extraction and refactor of the python code from node-red flow The rationale for this rewrite is to improve the readability, the modularity, the reliability and the future-proofing of the main python script. All in all, this is now 124 commits that are going to be squashed and merged together, spanning more than two weeks of development and testing. Please test away this release and break things. An upgrading guide will be published in the coming days, along with a new image for people to use if they don't want to upgrade on their own. Read along if you want to know all the goodies! As a starter, the python script was extracted from the main flow, and now lives in its own files at `PlantonScope/scripts/*`. We set up the auto formatting of the code by using [Black](https://github.com/psf/black). This make the code clearer and uniform. We are using the default settings, so if you just install Black and set your editor to format on save using it, you should be good to go. The code is separated in four main processes, each with a specific set of responsibilities: - The main process controls all the others, starts everything up and cleans up on shutdown - The stepper process manages the stepper movements. It's now possible to have simultaneous movements of both motors (this closes #38 ). - The imager process controls the camera and the streaming server via a state machine. - The segmenter process manages the segmentation and its outputs. The segmentation happens recursively in all folders in `/home/pi/PlanktonScope/img/`. Each folder has its own output archive, and bug #26 is now closed. Those processes communicates together using MQTT and json messages. Each message is adressed to one topic. The high level topic controls which process receives the message. The details of each topic is at the end of this commit message. Every imaging sessions has now its own folder, under the `img` root. Metadata are saved individually for every session, in a JSON file in the same directory as the pictures. The configuration is not parsed from `config.json` anymore and passed directly through MQTT messages to the concerned process. A new configuration file has been created: `hardware.json`. This file contains information related to your specific hardware configuration. You can choose to reverse the connection of the motors for example, but you can also define specific speed limits and steps number for your pump and focus stage. This will make it easier for people who wants to experiment with different kind of hardware. It's not necessary to have this file though. If it doesn't exists, the default configuration will be applied. The code is architectured around 6 modules and about 10 classes. I encourage you to have a look at the files, they're pretty straightforward to understand. There is a lot of work left around the node-red code refactoring, dashboard ui improvements, better and clearer LED messages, OLED screen integration and finer control of the segmentation process, but this is quite good for now. Here is the topic lists for MQTT and the corresponding messages. - actuator : This topic adresses the stepper control thread No publication under this topic should happen from the python process - actuator/pump : Control of the pump The message is a json object {"action":"move", "direction":"FORWARD", "volume":10, "flowrate":1} to move 10mL forward at 1mL/min action can be "move" or "stop" Receive only - actuator/focus : Control of the focus stage The message is a json object, speed is optional {"action":"move", "direction":"UP", "distance":0.26, "speed":1} to move up 10mm action can be "move" or "stop" Receive only - imager/image : This topic adresses the imaging thread Is a json object with {"action":"image","sleep":5,"volume":1,"nb_frame":200} sleep in seconds, volume in mL Can also receive a config update message: {"action":"config","config":[...]} Can also receive a camera settings message: {"action":"settings","iso":100,"shutter_speed":40} Receive only - segmenter/segment : This topic adresses the segmenter process Is a json object with {"action":"segment"} Receive only - status : This topics sends feedback to Node-Red No publication or receive at this level - status/pump : State of the pump Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/focus : State of the focus stage Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/imager : State of the imager Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Completed or 12_11_15_0.1.jpg has been imaged. Publish only - status/segmenter : Status of the segmentation - status/segmenter/name - status/segmenter/object_id - status/segmenter/metric Here is the original commit history: * Extract python main.py from flow * Fix bug in server addresses These addresses should be the loopback device instead of the network address of the device. Using the loopback address will not necessitate to update the script when the network address changes. * clean up picamera import * changes to main python and flow: update MQTT requests address to localhost (bugfix) update streaming output address to nothing update main flow to remove python script references and location * Automatically initialise imaging led on startup to off state. * Add the ability to invert outputs of the motor We added a key to config.json "hardware_config" with a subkey "stepper_reverse". If this key is present in the config file and set to 1, the output of the motors are inversed (stepper2 becomes the pump motor and stepper1 the focus motor) * move all non main script to a subfolder * add __init__.py to package * light module rewrite * json cleanup and absolute path for config file * light.py forgot to import subprocess #oups * Add command to turn the leds off * Auto formatting of main.py I've used Black with default settings, see https://github.com/psf/black * First commit of stepper.py Pump parameters still needs to be checked and tuned. * addition of hardware details in config.json * Introduce hardware.json to replace the `hardware_config` of config.json * stepper.py: calibration, typos * creates the MQTT_Client class * pump_max_speed is now in ml/min to help readability * forgot to add self to the class def * addition of threading capabilities to stepper.py (UNTESTED) * mqtt: fix topic bug * remove counter * mqtt add doc about topics * stepper.py creates an "actuator/*/state" topic * stepper.py: rename mqtt_client to pump_client * mqtt.py: add details about topics * stepper.py: rename pump_client to actuator_client * topic was not split properly and a part was lost * switch to f-strings for mqtt.py * cosmetic update * stepper.py: folder name will be planktoscope change calls * hardware.json became more straightforward * stepper.py syntax bugs * stepper.py addition of a received stop command * stepper.py: update to max travel distance * stepper.py: several typos here * rename folder * main.py: reword to reflect folder rename * main.py: remove logic that has been moved to stepper.py and mqtt.py * main.py: update to add mqtt imaging client * mqtt.py: make command and args local to class and output more verbose * make stepper.py a class * main.py: instantiate stepper class and call it * main.py: name mqtt client * update to main.json to reflect main.py changes * fix bugs around pump control * update flows to latest version from Thibault * distance can be a small value, and definitevely should be a float. * unify mqtt topics * unify mqtt output in the main flow * first logger implementation, uses loguru * mqtt: add reason to on_connect * mqtt: add on_disconnect handler * stepper: add more logger calls for debug mainly * main: add levels for logger * imager.py: first move of the imager logic * imager: time import cleanup * imager: morphocut import cleanup * imager: skimage import cleanup * imager: finishing import cleanup * imager: Class creation - WIP Also provides a fix for #26 (see line 190). * imager: threading is needed for Condition() * streamer: get the streamer server its own file * imager: creates start_camera and get the server creation out * imager: subclass multiprocessing.Process * imager: get Pipeline creation its own function * imager: cleanup of self calls * main: code removal and corresponding calls to newly created classes * imager: various formatting changes * main: management of signal shutdown * add requirements.txt * mqtt: messages are now json objects Also, addition of a flag on receiving a new message * mqtt: make message private and add logic to synchronise * stepper: creates the stepper class * stepper: use the new class * stepper: uses the new logic * stepper: add the shutdown event * stepper: add shutdown method * main: add shutdown event * imager: graceful shutdown * stepper: nicer way of checking the Eevnt * self is a required first argument for a method in a class Especially if you use said class private members! * python: various typos and small errors in import * stepper: create mqtt client during init * stepper: instanciate the mqtt client inside run Otherwise it's not accessible from inside the loop. It's a PITA, more information at https://stackoverflow.com/questions/17172878/using-pythons-multiprocessing-process-class * stepper: little bugs and typos all around * mqtt: add shutdown method * mqtt: add connect in init * stepper: fix bugs, sanitize inputs * stepper: work on delay prediction improvements * stepper: json is mean, double quote are mandatory inside * mqtt: add details about message exchanged * imager: first implementation of json messages * main.json: add new tab for RPi management + json for payloads * imager: add state_machine class * stepper: publish last will * imager: major refactor * main: make streaming server process a daemon * mqtt: insert debug statement on close * main: reorder imports * imager: make it work! Reinsert the streaming server logic in there, because there is a problem with the synchronisation part otherwise. Also, eventually, StreamingOuput() will have to be made not global Final very critical learning: it's super duper important to make sure the memory split is at least 256Meg for the GPU. Chaos ensues otherwise * main: changes to accomodate the streamer/imager fusino * imager_state_machine: insert states transition description * stepper: cleanup of code * segmenter: creation of the class * python: include segmenter changes * remove unused files * stepper: check existence of hardware.json * main.json: changes to reflect the python script evolution * remove unecessary TODOs and add some others * main: add check for config and directories * imager: update_config is implemented and we have better management of directories now * segmenter: now work recursively in all folders * flow: the configuration is now sent via mqtt * segmenter: better manage pipeline error * segmenter: declaration of archive_fn in init * imager: small bugs and typos * main: add uniqueID output * imager: add the camera settings message We can now update the ISO, shutter speed and resolution from Node-Red * package.json: update dependencies
2020-09-28 11:05:27 +02:00
"wires": [
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
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Extraction and refactor of the python code from node-red flow The rationale for this rewrite is to improve the readability, the modularity, the reliability and the future-proofing of the main python script. All in all, this is now 124 commits that are going to be squashed and merged together, spanning more than two weeks of development and testing. Please test away this release and break things. An upgrading guide will be published in the coming days, along with a new image for people to use if they don't want to upgrade on their own. Read along if you want to know all the goodies! As a starter, the python script was extracted from the main flow, and now lives in its own files at `PlantonScope/scripts/*`. We set up the auto formatting of the code by using [Black](https://github.com/psf/black). This make the code clearer and uniform. We are using the default settings, so if you just install Black and set your editor to format on save using it, you should be good to go. The code is separated in four main processes, each with a specific set of responsibilities: - The main process controls all the others, starts everything up and cleans up on shutdown - The stepper process manages the stepper movements. It's now possible to have simultaneous movements of both motors (this closes #38 ). - The imager process controls the camera and the streaming server via a state machine. - The segmenter process manages the segmentation and its outputs. The segmentation happens recursively in all folders in `/home/pi/PlanktonScope/img/`. Each folder has its own output archive, and bug #26 is now closed. Those processes communicates together using MQTT and json messages. Each message is adressed to one topic. The high level topic controls which process receives the message. The details of each topic is at the end of this commit message. Every imaging sessions has now its own folder, under the `img` root. Metadata are saved individually for every session, in a JSON file in the same directory as the pictures. The configuration is not parsed from `config.json` anymore and passed directly through MQTT messages to the concerned process. A new configuration file has been created: `hardware.json`. This file contains information related to your specific hardware configuration. You can choose to reverse the connection of the motors for example, but you can also define specific speed limits and steps number for your pump and focus stage. This will make it easier for people who wants to experiment with different kind of hardware. It's not necessary to have this file though. If it doesn't exists, the default configuration will be applied. The code is architectured around 6 modules and about 10 classes. I encourage you to have a look at the files, they're pretty straightforward to understand. There is a lot of work left around the node-red code refactoring, dashboard ui improvements, better and clearer LED messages, OLED screen integration and finer control of the segmentation process, but this is quite good for now. Here is the topic lists for MQTT and the corresponding messages. - actuator : This topic adresses the stepper control thread No publication under this topic should happen from the python process - actuator/pump : Control of the pump The message is a json object {"action":"move", "direction":"FORWARD", "volume":10, "flowrate":1} to move 10mL forward at 1mL/min action can be "move" or "stop" Receive only - actuator/focus : Control of the focus stage The message is a json object, speed is optional {"action":"move", "direction":"UP", "distance":0.26, "speed":1} to move up 10mm action can be "move" or "stop" Receive only - imager/image : This topic adresses the imaging thread Is a json object with {"action":"image","sleep":5,"volume":1,"nb_frame":200} sleep in seconds, volume in mL Can also receive a config update message: {"action":"config","config":[...]} Can also receive a camera settings message: {"action":"settings","iso":100,"shutter_speed":40} Receive only - segmenter/segment : This topic adresses the segmenter process Is a json object with {"action":"segment"} Receive only - status : This topics sends feedback to Node-Red No publication or receive at this level - status/pump : State of the pump Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/focus : State of the focus stage Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/imager : State of the imager Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Completed or 12_11_15_0.1.jpg has been imaged. Publish only - status/segmenter : Status of the segmentation - status/segmenter/name - status/segmenter/object_id - status/segmenter/metric Here is the original commit history: * Extract python main.py from flow * Fix bug in server addresses These addresses should be the loopback device instead of the network address of the device. Using the loopback address will not necessitate to update the script when the network address changes. * clean up picamera import * changes to main python and flow: update MQTT requests address to localhost (bugfix) update streaming output address to nothing update main flow to remove python script references and location * Automatically initialise imaging led on startup to off state. * Add the ability to invert outputs of the motor We added a key to config.json "hardware_config" with a subkey "stepper_reverse". If this key is present in the config file and set to 1, the output of the motors are inversed (stepper2 becomes the pump motor and stepper1 the focus motor) * move all non main script to a subfolder * add __init__.py to package * light module rewrite * json cleanup and absolute path for config file * light.py forgot to import subprocess #oups * Add command to turn the leds off * Auto formatting of main.py I've used Black with default settings, see https://github.com/psf/black * First commit of stepper.py Pump parameters still needs to be checked and tuned. * addition of hardware details in config.json * Introduce hardware.json to replace the `hardware_config` of config.json * stepper.py: calibration, typos * creates the MQTT_Client class * pump_max_speed is now in ml/min to help readability * forgot to add self to the class def * addition of threading capabilities to stepper.py (UNTESTED) * mqtt: fix topic bug * remove counter * mqtt add doc about topics * stepper.py creates an "actuator/*/state" topic * stepper.py: rename mqtt_client to pump_client * mqtt.py: add details about topics * stepper.py: rename pump_client to actuator_client * topic was not split properly and a part was lost * switch to f-strings for mqtt.py * cosmetic update * stepper.py: folder name will be planktoscope change calls * hardware.json became more straightforward * stepper.py syntax bugs * stepper.py addition of a received stop command * stepper.py: update to max travel distance * stepper.py: several typos here * rename folder * main.py: reword to reflect folder rename * main.py: remove logic that has been moved to stepper.py and mqtt.py * main.py: update to add mqtt imaging client * mqtt.py: make command and args local to class and output more verbose * make stepper.py a class * main.py: instantiate stepper class and call it * main.py: name mqtt client * update to main.json to reflect main.py changes * fix bugs around pump control * update flows to latest version from Thibault * distance can be a small value, and definitevely should be a float. * unify mqtt topics * unify mqtt output in the main flow * first logger implementation, uses loguru * mqtt: add reason to on_connect * mqtt: add on_disconnect handler * stepper: add more logger calls for debug mainly * main: add levels for logger * imager.py: first move of the imager logic * imager: time import cleanup * imager: morphocut import cleanup * imager: skimage import cleanup * imager: finishing import cleanup * imager: Class creation - WIP Also provides a fix for #26 (see line 190). * imager: threading is needed for Condition() * streamer: get the streamer server its own file * imager: creates start_camera and get the server creation out * imager: subclass multiprocessing.Process * imager: get Pipeline creation its own function * imager: cleanup of self calls * main: code removal and corresponding calls to newly created classes * imager: various formatting changes * main: management of signal shutdown * add requirements.txt * mqtt: messages are now json objects Also, addition of a flag on receiving a new message * mqtt: make message private and add logic to synchronise * stepper: creates the stepper class * stepper: use the new class * stepper: uses the new logic * stepper: add the shutdown event * stepper: add shutdown method * main: add shutdown event * imager: graceful shutdown * stepper: nicer way of checking the Eevnt * self is a required first argument for a method in a class Especially if you use said class private members! * python: various typos and small errors in import * stepper: create mqtt client during init * stepper: instanciate the mqtt client inside run Otherwise it's not accessible from inside the loop. It's a PITA, more information at https://stackoverflow.com/questions/17172878/using-pythons-multiprocessing-process-class * stepper: little bugs and typos all around * mqtt: add shutdown method * mqtt: add connect in init * stepper: fix bugs, sanitize inputs * stepper: work on delay prediction improvements * stepper: json is mean, double quote are mandatory inside * mqtt: add details about message exchanged * imager: first implementation of json messages * main.json: add new tab for RPi management + json for payloads * imager: add state_machine class * stepper: publish last will * imager: major refactor * main: make streaming server process a daemon * mqtt: insert debug statement on close * main: reorder imports * imager: make it work! Reinsert the streaming server logic in there, because there is a problem with the synchronisation part otherwise. Also, eventually, StreamingOuput() will have to be made not global Final very critical learning: it's super duper important to make sure the memory split is at least 256Meg for the GPU. Chaos ensues otherwise * main: changes to accomodate the streamer/imager fusino * imager_state_machine: insert states transition description * stepper: cleanup of code * segmenter: creation of the class * python: include segmenter changes * remove unused files * stepper: check existence of hardware.json * main.json: changes to reflect the python script evolution * remove unecessary TODOs and add some others * main: add check for config and directories * imager: update_config is implemented and we have better management of directories now * segmenter: now work recursively in all folders * flow: the configuration is now sent via mqtt * segmenter: better manage pipeline error * segmenter: declaration of archive_fn in init * imager: small bugs and typos * main: add uniqueID output * imager: add the camera settings message We can now update the ISO, shutter speed and resolution from Node-Red * package.json: update dependencies
2020-09-28 11:05:27 +02:00
[]
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},
{
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"id": "c3f72169.9d2b8",
"type": "exec",
"z": "1371dec5.76e671",
config: update default and flow update bug
2020-11-24 17:26:10 +01:00
"command": "git --git-dir /home/pi/PlanktonScope/.git/ pull",
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"addpay": false,
config: update default and flow update bug
2020-11-24 17:26:10 +01:00
"append": "",
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"useSpawn": "false",
"timer": "2",
"oldrc": false,
"name": "git pull",
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Extraction and refactor of the python code from node-red flow The rationale for this rewrite is to improve the readability, the modularity, the reliability and the future-proofing of the main python script. All in all, this is now 124 commits that are going to be squashed and merged together, spanning more than two weeks of development and testing. Please test away this release and break things. An upgrading guide will be published in the coming days, along with a new image for people to use if they don't want to upgrade on their own. Read along if you want to know all the goodies! As a starter, the python script was extracted from the main flow, and now lives in its own files at `PlantonScope/scripts/*`. We set up the auto formatting of the code by using [Black](https://github.com/psf/black). This make the code clearer and uniform. We are using the default settings, so if you just install Black and set your editor to format on save using it, you should be good to go. The code is separated in four main processes, each with a specific set of responsibilities: - The main process controls all the others, starts everything up and cleans up on shutdown - The stepper process manages the stepper movements. It's now possible to have simultaneous movements of both motors (this closes #38 ). - The imager process controls the camera and the streaming server via a state machine. - The segmenter process manages the segmentation and its outputs. The segmentation happens recursively in all folders in `/home/pi/PlanktonScope/img/`. Each folder has its own output archive, and bug #26 is now closed. Those processes communicates together using MQTT and json messages. Each message is adressed to one topic. The high level topic controls which process receives the message. The details of each topic is at the end of this commit message. Every imaging sessions has now its own folder, under the `img` root. Metadata are saved individually for every session, in a JSON file in the same directory as the pictures. The configuration is not parsed from `config.json` anymore and passed directly through MQTT messages to the concerned process. A new configuration file has been created: `hardware.json`. This file contains information related to your specific hardware configuration. You can choose to reverse the connection of the motors for example, but you can also define specific speed limits and steps number for your pump and focus stage. This will make it easier for people who wants to experiment with different kind of hardware. It's not necessary to have this file though. If it doesn't exists, the default configuration will be applied. The code is architectured around 6 modules and about 10 classes. I encourage you to have a look at the files, they're pretty straightforward to understand. There is a lot of work left around the node-red code refactoring, dashboard ui improvements, better and clearer LED messages, OLED screen integration and finer control of the segmentation process, but this is quite good for now. Here is the topic lists for MQTT and the corresponding messages. - actuator : This topic adresses the stepper control thread No publication under this topic should happen from the python process - actuator/pump : Control of the pump The message is a json object {"action":"move", "direction":"FORWARD", "volume":10, "flowrate":1} to move 10mL forward at 1mL/min action can be "move" or "stop" Receive only - actuator/focus : Control of the focus stage The message is a json object, speed is optional {"action":"move", "direction":"UP", "distance":0.26, "speed":1} to move up 10mm action can be "move" or "stop" Receive only - imager/image : This topic adresses the imaging thread Is a json object with {"action":"image","sleep":5,"volume":1,"nb_frame":200} sleep in seconds, volume in mL Can also receive a config update message: {"action":"config","config":[...]} Can also receive a camera settings message: {"action":"settings","iso":100,"shutter_speed":40} Receive only - segmenter/segment : This topic adresses the segmenter process Is a json object with {"action":"segment"} Receive only - status : This topics sends feedback to Node-Red No publication or receive at this level - status/pump : State of the pump Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/focus : State of the focus stage Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/imager : State of the imager Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Completed or 12_11_15_0.1.jpg has been imaged. Publish only - status/segmenter : Status of the segmentation - status/segmenter/name - status/segmenter/object_id - status/segmenter/metric Here is the original commit history: * Extract python main.py from flow * Fix bug in server addresses These addresses should be the loopback device instead of the network address of the device. Using the loopback address will not necessitate to update the script when the network address changes. * clean up picamera import * changes to main python and flow: update MQTT requests address to localhost (bugfix) update streaming output address to nothing update main flow to remove python script references and location * Automatically initialise imaging led on startup to off state. * Add the ability to invert outputs of the motor We added a key to config.json "hardware_config" with a subkey "stepper_reverse". If this key is present in the config file and set to 1, the output of the motors are inversed (stepper2 becomes the pump motor and stepper1 the focus motor) * move all non main script to a subfolder * add __init__.py to package * light module rewrite * json cleanup and absolute path for config file * light.py forgot to import subprocess #oups * Add command to turn the leds off * Auto formatting of main.py I've used Black with default settings, see https://github.com/psf/black * First commit of stepper.py Pump parameters still needs to be checked and tuned. * addition of hardware details in config.json * Introduce hardware.json to replace the `hardware_config` of config.json * stepper.py: calibration, typos * creates the MQTT_Client class * pump_max_speed is now in ml/min to help readability * forgot to add self to the class def * addition of threading capabilities to stepper.py (UNTESTED) * mqtt: fix topic bug * remove counter * mqtt add doc about topics * stepper.py creates an "actuator/*/state" topic * stepper.py: rename mqtt_client to pump_client * mqtt.py: add details about topics * stepper.py: rename pump_client to actuator_client * topic was not split properly and a part was lost * switch to f-strings for mqtt.py * cosmetic update * stepper.py: folder name will be planktoscope change calls * hardware.json became more straightforward * stepper.py syntax bugs * stepper.py addition of a received stop command * stepper.py: update to max travel distance * stepper.py: several typos here * rename folder * main.py: reword to reflect folder rename * main.py: remove logic that has been moved to stepper.py and mqtt.py * main.py: update to add mqtt imaging client * mqtt.py: make command and args local to class and output more verbose * make stepper.py a class * main.py: instantiate stepper class and call it * main.py: name mqtt client * update to main.json to reflect main.py changes * fix bugs around pump control * update flows to latest version from Thibault * distance can be a small value, and definitevely should be a float. * unify mqtt topics * unify mqtt output in the main flow * first logger implementation, uses loguru * mqtt: add reason to on_connect * mqtt: add on_disconnect handler * stepper: add more logger calls for debug mainly * main: add levels for logger * imager.py: first move of the imager logic * imager: time import cleanup * imager: morphocut import cleanup * imager: skimage import cleanup * imager: finishing import cleanup * imager: Class creation - WIP Also provides a fix for #26 (see line 190). * imager: threading is needed for Condition() * streamer: get the streamer server its own file * imager: creates start_camera and get the server creation out * imager: subclass multiprocessing.Process * imager: get Pipeline creation its own function * imager: cleanup of self calls * main: code removal and corresponding calls to newly created classes * imager: various formatting changes * main: management of signal shutdown * add requirements.txt * mqtt: messages are now json objects Also, addition of a flag on receiving a new message * mqtt: make message private and add logic to synchronise * stepper: creates the stepper class * stepper: use the new class * stepper: uses the new logic * stepper: add the shutdown event * stepper: add shutdown method * main: add shutdown event * imager: graceful shutdown * stepper: nicer way of checking the Eevnt * self is a required first argument for a method in a class Especially if you use said class private members! * python: various typos and small errors in import * stepper: create mqtt client during init * stepper: instanciate the mqtt client inside run Otherwise it's not accessible from inside the loop. It's a PITA, more information at https://stackoverflow.com/questions/17172878/using-pythons-multiprocessing-process-class * stepper: little bugs and typos all around * mqtt: add shutdown method * mqtt: add connect in init * stepper: fix bugs, sanitize inputs * stepper: work on delay prediction improvements * stepper: json is mean, double quote are mandatory inside * mqtt: add details about message exchanged * imager: first implementation of json messages * main.json: add new tab for RPi management + json for payloads * imager: add state_machine class * stepper: publish last will * imager: major refactor * main: make streaming server process a daemon * mqtt: insert debug statement on close * main: reorder imports * imager: make it work! Reinsert the streaming server logic in there, because there is a problem with the synchronisation part otherwise. Also, eventually, StreamingOuput() will have to be made not global Final very critical learning: it's super duper important to make sure the memory split is at least 256Meg for the GPU. Chaos ensues otherwise * main: changes to accomodate the streamer/imager fusino * imager_state_machine: insert states transition description * stepper: cleanup of code * segmenter: creation of the class * python: include segmenter changes * remove unused files * stepper: check existence of hardware.json * main.json: changes to reflect the python script evolution * remove unecessary TODOs and add some others * main: add check for config and directories * imager: update_config is implemented and we have better management of directories now * segmenter: now work recursively in all folders * flow: the configuration is now sent via mqtt * segmenter: better manage pipeline error * segmenter: declaration of archive_fn in init * imager: small bugs and typos * main: add uniqueID output * imager: add the camera settings message We can now update the ISO, shutter speed and resolution from Node-Red * package.json: update dependencies
2020-09-28 11:05:27 +02:00
"wires": [
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
[],
[],
[]
Extraction and refactor of the python code from node-red flow The rationale for this rewrite is to improve the readability, the modularity, the reliability and the future-proofing of the main python script. All in all, this is now 124 commits that are going to be squashed and merged together, spanning more than two weeks of development and testing. Please test away this release and break things. An upgrading guide will be published in the coming days, along with a new image for people to use if they don't want to upgrade on their own. Read along if you want to know all the goodies! As a starter, the python script was extracted from the main flow, and now lives in its own files at `PlantonScope/scripts/*`. We set up the auto formatting of the code by using [Black](https://github.com/psf/black). This make the code clearer and uniform. We are using the default settings, so if you just install Black and set your editor to format on save using it, you should be good to go. The code is separated in four main processes, each with a specific set of responsibilities: - The main process controls all the others, starts everything up and cleans up on shutdown - The stepper process manages the stepper movements. It's now possible to have simultaneous movements of both motors (this closes #38 ). - The imager process controls the camera and the streaming server via a state machine. - The segmenter process manages the segmentation and its outputs. The segmentation happens recursively in all folders in `/home/pi/PlanktonScope/img/`. Each folder has its own output archive, and bug #26 is now closed. Those processes communicates together using MQTT and json messages. Each message is adressed to one topic. The high level topic controls which process receives the message. The details of each topic is at the end of this commit message. Every imaging sessions has now its own folder, under the `img` root. Metadata are saved individually for every session, in a JSON file in the same directory as the pictures. The configuration is not parsed from `config.json` anymore and passed directly through MQTT messages to the concerned process. A new configuration file has been created: `hardware.json`. This file contains information related to your specific hardware configuration. You can choose to reverse the connection of the motors for example, but you can also define specific speed limits and steps number for your pump and focus stage. This will make it easier for people who wants to experiment with different kind of hardware. It's not necessary to have this file though. If it doesn't exists, the default configuration will be applied. The code is architectured around 6 modules and about 10 classes. I encourage you to have a look at the files, they're pretty straightforward to understand. There is a lot of work left around the node-red code refactoring, dashboard ui improvements, better and clearer LED messages, OLED screen integration and finer control of the segmentation process, but this is quite good for now. Here is the topic lists for MQTT and the corresponding messages. - actuator : This topic adresses the stepper control thread No publication under this topic should happen from the python process - actuator/pump : Control of the pump The message is a json object {"action":"move", "direction":"FORWARD", "volume":10, "flowrate":1} to move 10mL forward at 1mL/min action can be "move" or "stop" Receive only - actuator/focus : Control of the focus stage The message is a json object, speed is optional {"action":"move", "direction":"UP", "distance":0.26, "speed":1} to move up 10mm action can be "move" or "stop" Receive only - imager/image : This topic adresses the imaging thread Is a json object with {"action":"image","sleep":5,"volume":1,"nb_frame":200} sleep in seconds, volume in mL Can also receive a config update message: {"action":"config","config":[...]} Can also receive a camera settings message: {"action":"settings","iso":100,"shutter_speed":40} Receive only - segmenter/segment : This topic adresses the segmenter process Is a json object with {"action":"segment"} Receive only - status : This topics sends feedback to Node-Red No publication or receive at this level - status/pump : State of the pump Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/focus : State of the focus stage Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/imager : State of the imager Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Completed or 12_11_15_0.1.jpg has been imaged. Publish only - status/segmenter : Status of the segmentation - status/segmenter/name - status/segmenter/object_id - status/segmenter/metric Here is the original commit history: * Extract python main.py from flow * Fix bug in server addresses These addresses should be the loopback device instead of the network address of the device. Using the loopback address will not necessitate to update the script when the network address changes. * clean up picamera import * changes to main python and flow: update MQTT requests address to localhost (bugfix) update streaming output address to nothing update main flow to remove python script references and location * Automatically initialise imaging led on startup to off state. * Add the ability to invert outputs of the motor We added a key to config.json "hardware_config" with a subkey "stepper_reverse". If this key is present in the config file and set to 1, the output of the motors are inversed (stepper2 becomes the pump motor and stepper1 the focus motor) * move all non main script to a subfolder * add __init__.py to package * light module rewrite * json cleanup and absolute path for config file * light.py forgot to import subprocess #oups * Add command to turn the leds off * Auto formatting of main.py I've used Black with default settings, see https://github.com/psf/black * First commit of stepper.py Pump parameters still needs to be checked and tuned. * addition of hardware details in config.json * Introduce hardware.json to replace the `hardware_config` of config.json * stepper.py: calibration, typos * creates the MQTT_Client class * pump_max_speed is now in ml/min to help readability * forgot to add self to the class def * addition of threading capabilities to stepper.py (UNTESTED) * mqtt: fix topic bug * remove counter * mqtt add doc about topics * stepper.py creates an "actuator/*/state" topic * stepper.py: rename mqtt_client to pump_client * mqtt.py: add details about topics * stepper.py: rename pump_client to actuator_client * topic was not split properly and a part was lost * switch to f-strings for mqtt.py * cosmetic update * stepper.py: folder name will be planktoscope change calls * hardware.json became more straightforward * stepper.py syntax bugs * stepper.py addition of a received stop command * stepper.py: update to max travel distance * stepper.py: several typos here * rename folder * main.py: reword to reflect folder rename * main.py: remove logic that has been moved to stepper.py and mqtt.py * main.py: update to add mqtt imaging client * mqtt.py: make command and args local to class and output more verbose * make stepper.py a class * main.py: instantiate stepper class and call it * main.py: name mqtt client * update to main.json to reflect main.py changes * fix bugs around pump control * update flows to latest version from Thibault * distance can be a small value, and definitevely should be a float. * unify mqtt topics * unify mqtt output in the main flow * first logger implementation, uses loguru * mqtt: add reason to on_connect * mqtt: add on_disconnect handler * stepper: add more logger calls for debug mainly * main: add levels for logger * imager.py: first move of the imager logic * imager: time import cleanup * imager: morphocut import cleanup * imager: skimage import cleanup * imager: finishing import cleanup * imager: Class creation - WIP Also provides a fix for #26 (see line 190). * imager: threading is needed for Condition() * streamer: get the streamer server its own file * imager: creates start_camera and get the server creation out * imager: subclass multiprocessing.Process * imager: get Pipeline creation its own function * imager: cleanup of self calls * main: code removal and corresponding calls to newly created classes * imager: various formatting changes * main: management of signal shutdown * add requirements.txt * mqtt: messages are now json objects Also, addition of a flag on receiving a new message * mqtt: make message private and add logic to synchronise * stepper: creates the stepper class * stepper: use the new class * stepper: uses the new logic * stepper: add the shutdown event * stepper: add shutdown method * main: add shutdown event * imager: graceful shutdown * stepper: nicer way of checking the Eevnt * self is a required first argument for a method in a class Especially if you use said class private members! * python: various typos and small errors in import * stepper: create mqtt client during init * stepper: instanciate the mqtt client inside run Otherwise it's not accessible from inside the loop. It's a PITA, more information at https://stackoverflow.com/questions/17172878/using-pythons-multiprocessing-process-class * stepper: little bugs and typos all around * mqtt: add shutdown method * mqtt: add connect in init * stepper: fix bugs, sanitize inputs * stepper: work on delay prediction improvements * stepper: json is mean, double quote are mandatory inside * mqtt: add details about message exchanged * imager: first implementation of json messages * main.json: add new tab for RPi management + json for payloads * imager: add state_machine class * stepper: publish last will * imager: major refactor * main: make streaming server process a daemon * mqtt: insert debug statement on close * main: reorder imports * imager: make it work! Reinsert the streaming server logic in there, because there is a problem with the synchronisation part otherwise. Also, eventually, StreamingOuput() will have to be made not global Final very critical learning: it's super duper important to make sure the memory split is at least 256Meg for the GPU. Chaos ensues otherwise * main: changes to accomodate the streamer/imager fusino * imager_state_machine: insert states transition description * stepper: cleanup of code * segmenter: creation of the class * python: include segmenter changes * remove unused files * stepper: check existence of hardware.json * main.json: changes to reflect the python script evolution * remove unecessary TODOs and add some others * main: add check for config and directories * imager: update_config is implemented and we have better management of directories now * segmenter: now work recursively in all folders * flow: the configuration is now sent via mqtt * segmenter: better manage pipeline error * segmenter: declaration of archive_fn in init * imager: small bugs and typos * main: add uniqueID output * imager: add the camera settings message We can now update the ISO, shutter speed and resolution from Node-Red * package.json: update dependencies
2020-09-28 11:05:27 +02:00
]
},
{
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"id": "9998aa86.74bb",
"type": "exec",
"z": "1371dec5.76e671",
"command": "python3 /home/pi/PlanktonScope/scripts/main.py",
"addpay": false,
"append": "",
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"oldrc": false,
Extraction and refactor of the python code from node-red flow The rationale for this rewrite is to improve the readability, the modularity, the reliability and the future-proofing of the main python script. All in all, this is now 124 commits that are going to be squashed and merged together, spanning more than two weeks of development and testing. Please test away this release and break things. An upgrading guide will be published in the coming days, along with a new image for people to use if they don't want to upgrade on their own. Read along if you want to know all the goodies! As a starter, the python script was extracted from the main flow, and now lives in its own files at `PlantonScope/scripts/*`. We set up the auto formatting of the code by using [Black](https://github.com/psf/black). This make the code clearer and uniform. We are using the default settings, so if you just install Black and set your editor to format on save using it, you should be good to go. The code is separated in four main processes, each with a specific set of responsibilities: - The main process controls all the others, starts everything up and cleans up on shutdown - The stepper process manages the stepper movements. It's now possible to have simultaneous movements of both motors (this closes #38 ). - The imager process controls the camera and the streaming server via a state machine. - The segmenter process manages the segmentation and its outputs. The segmentation happens recursively in all folders in `/home/pi/PlanktonScope/img/`. Each folder has its own output archive, and bug #26 is now closed. Those processes communicates together using MQTT and json messages. Each message is adressed to one topic. The high level topic controls which process receives the message. The details of each topic is at the end of this commit message. Every imaging sessions has now its own folder, under the `img` root. Metadata are saved individually for every session, in a JSON file in the same directory as the pictures. The configuration is not parsed from `config.json` anymore and passed directly through MQTT messages to the concerned process. A new configuration file has been created: `hardware.json`. This file contains information related to your specific hardware configuration. You can choose to reverse the connection of the motors for example, but you can also define specific speed limits and steps number for your pump and focus stage. This will make it easier for people who wants to experiment with different kind of hardware. It's not necessary to have this file though. If it doesn't exists, the default configuration will be applied. The code is architectured around 6 modules and about 10 classes. I encourage you to have a look at the files, they're pretty straightforward to understand. There is a lot of work left around the node-red code refactoring, dashboard ui improvements, better and clearer LED messages, OLED screen integration and finer control of the segmentation process, but this is quite good for now. Here is the topic lists for MQTT and the corresponding messages. - actuator : This topic adresses the stepper control thread No publication under this topic should happen from the python process - actuator/pump : Control of the pump The message is a json object {"action":"move", "direction":"FORWARD", "volume":10, "flowrate":1} to move 10mL forward at 1mL/min action can be "move" or "stop" Receive only - actuator/focus : Control of the focus stage The message is a json object, speed is optional {"action":"move", "direction":"UP", "distance":0.26, "speed":1} to move up 10mm action can be "move" or "stop" Receive only - imager/image : This topic adresses the imaging thread Is a json object with {"action":"image","sleep":5,"volume":1,"nb_frame":200} sleep in seconds, volume in mL Can also receive a config update message: {"action":"config","config":[...]} Can also receive a camera settings message: {"action":"settings","iso":100,"shutter_speed":40} Receive only - segmenter/segment : This topic adresses the segmenter process Is a json object with {"action":"segment"} Receive only - status : This topics sends feedback to Node-Red No publication or receive at this level - status/pump : State of the pump Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/focus : State of the focus stage Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/imager : State of the imager Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Completed or 12_11_15_0.1.jpg has been imaged. Publish only - status/segmenter : Status of the segmentation - status/segmenter/name - status/segmenter/object_id - status/segmenter/metric Here is the original commit history: * Extract python main.py from flow * Fix bug in server addresses These addresses should be the loopback device instead of the network address of the device. Using the loopback address will not necessitate to update the script when the network address changes. * clean up picamera import * changes to main python and flow: update MQTT requests address to localhost (bugfix) update streaming output address to nothing update main flow to remove python script references and location * Automatically initialise imaging led on startup to off state. * Add the ability to invert outputs of the motor We added a key to config.json "hardware_config" with a subkey "stepper_reverse". If this key is present in the config file and set to 1, the output of the motors are inversed (stepper2 becomes the pump motor and stepper1 the focus motor) * move all non main script to a subfolder * add __init__.py to package * light module rewrite * json cleanup and absolute path for config file * light.py forgot to import subprocess #oups * Add command to turn the leds off * Auto formatting of main.py I've used Black with default settings, see https://github.com/psf/black * First commit of stepper.py Pump parameters still needs to be checked and tuned. * addition of hardware details in config.json * Introduce hardware.json to replace the `hardware_config` of config.json * stepper.py: calibration, typos * creates the MQTT_Client class * pump_max_speed is now in ml/min to help readability * forgot to add self to the class def * addition of threading capabilities to stepper.py (UNTESTED) * mqtt: fix topic bug * remove counter * mqtt add doc about topics * stepper.py creates an "actuator/*/state" topic * stepper.py: rename mqtt_client to pump_client * mqtt.py: add details about topics * stepper.py: rename pump_client to actuator_client * topic was not split properly and a part was lost * switch to f-strings for mqtt.py * cosmetic update * stepper.py: folder name will be planktoscope change calls * hardware.json became more straightforward * stepper.py syntax bugs * stepper.py addition of a received stop command * stepper.py: update to max travel distance * stepper.py: several typos here * rename folder * main.py: reword to reflect folder rename * main.py: remove logic that has been moved to stepper.py and mqtt.py * main.py: update to add mqtt imaging client * mqtt.py: make command and args local to class and output more verbose * make stepper.py a class * main.py: instantiate stepper class and call it * main.py: name mqtt client * update to main.json to reflect main.py changes * fix bugs around pump control * update flows to latest version from Thibault * distance can be a small value, and definitevely should be a float. * unify mqtt topics * unify mqtt output in the main flow * first logger implementation, uses loguru * mqtt: add reason to on_connect * mqtt: add on_disconnect handler * stepper: add more logger calls for debug mainly * main: add levels for logger * imager.py: first move of the imager logic * imager: time import cleanup * imager: morphocut import cleanup * imager: skimage import cleanup * imager: finishing import cleanup * imager: Class creation - WIP Also provides a fix for #26 (see line 190). * imager: threading is needed for Condition() * streamer: get the streamer server its own file * imager: creates start_camera and get the server creation out * imager: subclass multiprocessing.Process * imager: get Pipeline creation its own function * imager: cleanup of self calls * main: code removal and corresponding calls to newly created classes * imager: various formatting changes * main: management of signal shutdown * add requirements.txt * mqtt: messages are now json objects Also, addition of a flag on receiving a new message * mqtt: make message private and add logic to synchronise * stepper: creates the stepper class * stepper: use the new class * stepper: uses the new logic * stepper: add the shutdown event * stepper: add shutdown method * main: add shutdown event * imager: graceful shutdown * stepper: nicer way of checking the Eevnt * self is a required first argument for a method in a class Especially if you use said class private members! * python: various typos and small errors in import * stepper: create mqtt client during init * stepper: instanciate the mqtt client inside run Otherwise it's not accessible from inside the loop. It's a PITA, more information at https://stackoverflow.com/questions/17172878/using-pythons-multiprocessing-process-class * stepper: little bugs and typos all around * mqtt: add shutdown method * mqtt: add connect in init * stepper: fix bugs, sanitize inputs * stepper: work on delay prediction improvements * stepper: json is mean, double quote are mandatory inside * mqtt: add details about message exchanged * imager: first implementation of json messages * main.json: add new tab for RPi management + json for payloads * imager: add state_machine class * stepper: publish last will * imager: major refactor * main: make streaming server process a daemon * mqtt: insert debug statement on close * main: reorder imports * imager: make it work! Reinsert the streaming server logic in there, because there is a problem with the synchronisation part otherwise. Also, eventually, StreamingOuput() will have to be made not global Final very critical learning: it's super duper important to make sure the memory split is at least 256Meg for the GPU. Chaos ensues otherwise * main: changes to accomodate the streamer/imager fusino * imager_state_machine: insert states transition description * stepper: cleanup of code * segmenter: creation of the class * python: include segmenter changes * remove unused files * stepper: check existence of hardware.json * main.json: changes to reflect the python script evolution * remove unecessary TODOs and add some others * main: add check for config and directories * imager: update_config is implemented and we have better management of directories now * segmenter: now work recursively in all folders * flow: the configuration is now sent via mqtt * segmenter: better manage pipeline error * segmenter: declaration of archive_fn in init * imager: small bugs and typos * main: add uniqueID output * imager: add the camera settings message We can now update the ISO, shutter speed and resolution from Node-Red * package.json: update dependencies
2020-09-28 11:05:27 +02:00
"name": "",
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"x": 860,
"y": 940,
Extraction and refactor of the python code from node-red flow The rationale for this rewrite is to improve the readability, the modularity, the reliability and the future-proofing of the main python script. All in all, this is now 124 commits that are going to be squashed and merged together, spanning more than two weeks of development and testing. Please test away this release and break things. An upgrading guide will be published in the coming days, along with a new image for people to use if they don't want to upgrade on their own. Read along if you want to know all the goodies! As a starter, the python script was extracted from the main flow, and now lives in its own files at `PlantonScope/scripts/*`. We set up the auto formatting of the code by using [Black](https://github.com/psf/black). This make the code clearer and uniform. We are using the default settings, so if you just install Black and set your editor to format on save using it, you should be good to go. The code is separated in four main processes, each with a specific set of responsibilities: - The main process controls all the others, starts everything up and cleans up on shutdown - The stepper process manages the stepper movements. It's now possible to have simultaneous movements of both motors (this closes #38 ). - The imager process controls the camera and the streaming server via a state machine. - The segmenter process manages the segmentation and its outputs. The segmentation happens recursively in all folders in `/home/pi/PlanktonScope/img/`. Each folder has its own output archive, and bug #26 is now closed. Those processes communicates together using MQTT and json messages. Each message is adressed to one topic. The high level topic controls which process receives the message. The details of each topic is at the end of this commit message. Every imaging sessions has now its own folder, under the `img` root. Metadata are saved individually for every session, in a JSON file in the same directory as the pictures. The configuration is not parsed from `config.json` anymore and passed directly through MQTT messages to the concerned process. A new configuration file has been created: `hardware.json`. This file contains information related to your specific hardware configuration. You can choose to reverse the connection of the motors for example, but you can also define specific speed limits and steps number for your pump and focus stage. This will make it easier for people who wants to experiment with different kind of hardware. It's not necessary to have this file though. If it doesn't exists, the default configuration will be applied. The code is architectured around 6 modules and about 10 classes. I encourage you to have a look at the files, they're pretty straightforward to understand. There is a lot of work left around the node-red code refactoring, dashboard ui improvements, better and clearer LED messages, OLED screen integration and finer control of the segmentation process, but this is quite good for now. Here is the topic lists for MQTT and the corresponding messages. - actuator : This topic adresses the stepper control thread No publication under this topic should happen from the python process - actuator/pump : Control of the pump The message is a json object {"action":"move", "direction":"FORWARD", "volume":10, "flowrate":1} to move 10mL forward at 1mL/min action can be "move" or "stop" Receive only - actuator/focus : Control of the focus stage The message is a json object, speed is optional {"action":"move", "direction":"UP", "distance":0.26, "speed":1} to move up 10mm action can be "move" or "stop" Receive only - imager/image : This topic adresses the imaging thread Is a json object with {"action":"image","sleep":5,"volume":1,"nb_frame":200} sleep in seconds, volume in mL Can also receive a config update message: {"action":"config","config":[...]} Can also receive a camera settings message: {"action":"settings","iso":100,"shutter_speed":40} Receive only - segmenter/segment : This topic adresses the segmenter process Is a json object with {"action":"segment"} Receive only - status : This topics sends feedback to Node-Red No publication or receive at this level - status/pump : State of the pump Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/focus : State of the focus stage Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/imager : State of the imager Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Completed or 12_11_15_0.1.jpg has been imaged. Publish only - status/segmenter : Status of the segmentation - status/segmenter/name - status/segmenter/object_id - status/segmenter/metric Here is the original commit history: * Extract python main.py from flow * Fix bug in server addresses These addresses should be the loopback device instead of the network address of the device. Using the loopback address will not necessitate to update the script when the network address changes. * clean up picamera import * changes to main python and flow: update MQTT requests address to localhost (bugfix) update streaming output address to nothing update main flow to remove python script references and location * Automatically initialise imaging led on startup to off state. * Add the ability to invert outputs of the motor We added a key to config.json "hardware_config" with a subkey "stepper_reverse". If this key is present in the config file and set to 1, the output of the motors are inversed (stepper2 becomes the pump motor and stepper1 the focus motor) * move all non main script to a subfolder * add __init__.py to package * light module rewrite * json cleanup and absolute path for config file * light.py forgot to import subprocess #oups * Add command to turn the leds off * Auto formatting of main.py I've used Black with default settings, see https://github.com/psf/black * First commit of stepper.py Pump parameters still needs to be checked and tuned. * addition of hardware details in config.json * Introduce hardware.json to replace the `hardware_config` of config.json * stepper.py: calibration, typos * creates the MQTT_Client class * pump_max_speed is now in ml/min to help readability * forgot to add self to the class def * addition of threading capabilities to stepper.py (UNTESTED) * mqtt: fix topic bug * remove counter * mqtt add doc about topics * stepper.py creates an "actuator/*/state" topic * stepper.py: rename mqtt_client to pump_client * mqtt.py: add details about topics * stepper.py: rename pump_client to actuator_client * topic was not split properly and a part was lost * switch to f-strings for mqtt.py * cosmetic update * stepper.py: folder name will be planktoscope change calls * hardware.json became more straightforward * stepper.py syntax bugs * stepper.py addition of a received stop command * stepper.py: update to max travel distance * stepper.py: several typos here * rename folder * main.py: reword to reflect folder rename * main.py: remove logic that has been moved to stepper.py and mqtt.py * main.py: update to add mqtt imaging client * mqtt.py: make command and args local to class and output more verbose * make stepper.py a class * main.py: instantiate stepper class and call it * main.py: name mqtt client * update to main.json to reflect main.py changes * fix bugs around pump control * update flows to latest version from Thibault * distance can be a small value, and definitevely should be a float. * unify mqtt topics * unify mqtt output in the main flow * first logger implementation, uses loguru * mqtt: add reason to on_connect * mqtt: add on_disconnect handler * stepper: add more logger calls for debug mainly * main: add levels for logger * imager.py: first move of the imager logic * imager: time import cleanup * imager: morphocut import cleanup * imager: skimage import cleanup * imager: finishing import cleanup * imager: Class creation - WIP Also provides a fix for #26 (see line 190). * imager: threading is needed for Condition() * streamer: get the streamer server its own file * imager: creates start_camera and get the server creation out * imager: subclass multiprocessing.Process * imager: get Pipeline creation its own function * imager: cleanup of self calls * main: code removal and corresponding calls to newly created classes * imager: various formatting changes * main: management of signal shutdown * add requirements.txt * mqtt: messages are now json objects Also, addition of a flag on receiving a new message * mqtt: make message private and add logic to synchronise * stepper: creates the stepper class * stepper: use the new class * stepper: uses the new logic * stepper: add the shutdown event * stepper: add shutdown method * main: add shutdown event * imager: graceful shutdown * stepper: nicer way of checking the Eevnt * self is a required first argument for a method in a class Especially if you use said class private members! * python: various typos and small errors in import * stepper: create mqtt client during init * stepper: instanciate the mqtt client inside run Otherwise it's not accessible from inside the loop. It's a PITA, more information at https://stackoverflow.com/questions/17172878/using-pythons-multiprocessing-process-class * stepper: little bugs and typos all around * mqtt: add shutdown method * mqtt: add connect in init * stepper: fix bugs, sanitize inputs * stepper: work on delay prediction improvements * stepper: json is mean, double quote are mandatory inside * mqtt: add details about message exchanged * imager: first implementation of json messages * main.json: add new tab for RPi management + json for payloads * imager: add state_machine class * stepper: publish last will * imager: major refactor * main: make streaming server process a daemon * mqtt: insert debug statement on close * main: reorder imports * imager: make it work! Reinsert the streaming server logic in there, because there is a problem with the synchronisation part otherwise. Also, eventually, StreamingOuput() will have to be made not global Final very critical learning: it's super duper important to make sure the memory split is at least 256Meg for the GPU. Chaos ensues otherwise * main: changes to accomodate the streamer/imager fusino * imager_state_machine: insert states transition description * stepper: cleanup of code * segmenter: creation of the class * python: include segmenter changes * remove unused files * stepper: check existence of hardware.json * main.json: changes to reflect the python script evolution * remove unecessary TODOs and add some others * main: add check for config and directories * imager: update_config is implemented and we have better management of directories now * segmenter: now work recursively in all folders * flow: the configuration is now sent via mqtt * segmenter: better manage pipeline error * segmenter: declaration of archive_fn in init * imager: small bugs and typos * main: add uniqueID output * imager: add the camera settings message We can now update the ISO, shutter speed and resolution from Node-Red * package.json: update dependencies
2020-09-28 11:05:27 +02:00
"wires": [
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
[],
[],
Extraction and refactor of the python code from node-red flow The rationale for this rewrite is to improve the readability, the modularity, the reliability and the future-proofing of the main python script. All in all, this is now 124 commits that are going to be squashed and merged together, spanning more than two weeks of development and testing. Please test away this release and break things. An upgrading guide will be published in the coming days, along with a new image for people to use if they don't want to upgrade on their own. Read along if you want to know all the goodies! As a starter, the python script was extracted from the main flow, and now lives in its own files at `PlantonScope/scripts/*`. We set up the auto formatting of the code by using [Black](https://github.com/psf/black). This make the code clearer and uniform. We are using the default settings, so if you just install Black and set your editor to format on save using it, you should be good to go. The code is separated in four main processes, each with a specific set of responsibilities: - The main process controls all the others, starts everything up and cleans up on shutdown - The stepper process manages the stepper movements. It's now possible to have simultaneous movements of both motors (this closes #38 ). - The imager process controls the camera and the streaming server via a state machine. - The segmenter process manages the segmentation and its outputs. The segmentation happens recursively in all folders in `/home/pi/PlanktonScope/img/`. Each folder has its own output archive, and bug #26 is now closed. Those processes communicates together using MQTT and json messages. Each message is adressed to one topic. The high level topic controls which process receives the message. The details of each topic is at the end of this commit message. Every imaging sessions has now its own folder, under the `img` root. Metadata are saved individually for every session, in a JSON file in the same directory as the pictures. The configuration is not parsed from `config.json` anymore and passed directly through MQTT messages to the concerned process. A new configuration file has been created: `hardware.json`. This file contains information related to your specific hardware configuration. You can choose to reverse the connection of the motors for example, but you can also define specific speed limits and steps number for your pump and focus stage. This will make it easier for people who wants to experiment with different kind of hardware. It's not necessary to have this file though. If it doesn't exists, the default configuration will be applied. The code is architectured around 6 modules and about 10 classes. I encourage you to have a look at the files, they're pretty straightforward to understand. There is a lot of work left around the node-red code refactoring, dashboard ui improvements, better and clearer LED messages, OLED screen integration and finer control of the segmentation process, but this is quite good for now. Here is the topic lists for MQTT and the corresponding messages. - actuator : This topic adresses the stepper control thread No publication under this topic should happen from the python process - actuator/pump : Control of the pump The message is a json object {"action":"move", "direction":"FORWARD", "volume":10, "flowrate":1} to move 10mL forward at 1mL/min action can be "move" or "stop" Receive only - actuator/focus : Control of the focus stage The message is a json object, speed is optional {"action":"move", "direction":"UP", "distance":0.26, "speed":1} to move up 10mm action can be "move" or "stop" Receive only - imager/image : This topic adresses the imaging thread Is a json object with {"action":"image","sleep":5,"volume":1,"nb_frame":200} sleep in seconds, volume in mL Can also receive a config update message: {"action":"config","config":[...]} Can also receive a camera settings message: {"action":"settings","iso":100,"shutter_speed":40} Receive only - segmenter/segment : This topic adresses the segmenter process Is a json object with {"action":"segment"} Receive only - status : This topics sends feedback to Node-Red No publication or receive at this level - status/pump : State of the pump Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/focus : State of the focus stage Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/imager : State of the imager Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Completed or 12_11_15_0.1.jpg has been imaged. Publish only - status/segmenter : Status of the segmentation - status/segmenter/name - status/segmenter/object_id - status/segmenter/metric Here is the original commit history: * Extract python main.py from flow * Fix bug in server addresses These addresses should be the loopback device instead of the network address of the device. Using the loopback address will not necessitate to update the script when the network address changes. * clean up picamera import * changes to main python and flow: update MQTT requests address to localhost (bugfix) update streaming output address to nothing update main flow to remove python script references and location * Automatically initialise imaging led on startup to off state. * Add the ability to invert outputs of the motor We added a key to config.json "hardware_config" with a subkey "stepper_reverse". If this key is present in the config file and set to 1, the output of the motors are inversed (stepper2 becomes the pump motor and stepper1 the focus motor) * move all non main script to a subfolder * add __init__.py to package * light module rewrite * json cleanup and absolute path for config file * light.py forgot to import subprocess #oups * Add command to turn the leds off * Auto formatting of main.py I've used Black with default settings, see https://github.com/psf/black * First commit of stepper.py Pump parameters still needs to be checked and tuned. * addition of hardware details in config.json * Introduce hardware.json to replace the `hardware_config` of config.json * stepper.py: calibration, typos * creates the MQTT_Client class * pump_max_speed is now in ml/min to help readability * forgot to add self to the class def * addition of threading capabilities to stepper.py (UNTESTED) * mqtt: fix topic bug * remove counter * mqtt add doc about topics * stepper.py creates an "actuator/*/state" topic * stepper.py: rename mqtt_client to pump_client * mqtt.py: add details about topics * stepper.py: rename pump_client to actuator_client * topic was not split properly and a part was lost * switch to f-strings for mqtt.py * cosmetic update * stepper.py: folder name will be planktoscope change calls * hardware.json became more straightforward * stepper.py syntax bugs * stepper.py addition of a received stop command * stepper.py: update to max travel distance * stepper.py: several typos here * rename folder * main.py: reword to reflect folder rename * main.py: remove logic that has been moved to stepper.py and mqtt.py * main.py: update to add mqtt imaging client * mqtt.py: make command and args local to class and output more verbose * make stepper.py a class * main.py: instantiate stepper class and call it * main.py: name mqtt client * update to main.json to reflect main.py changes * fix bugs around pump control * update flows to latest version from Thibault * distance can be a small value, and definitevely should be a float. * unify mqtt topics * unify mqtt output in the main flow * first logger implementation, uses loguru * mqtt: add reason to on_connect * mqtt: add on_disconnect handler * stepper: add more logger calls for debug mainly * main: add levels for logger * imager.py: first move of the imager logic * imager: time import cleanup * imager: morphocut import cleanup * imager: skimage import cleanup * imager: finishing import cleanup * imager: Class creation - WIP Also provides a fix for #26 (see line 190). * imager: threading is needed for Condition() * streamer: get the streamer server its own file * imager: creates start_camera and get the server creation out * imager: subclass multiprocessing.Process * imager: get Pipeline creation its own function * imager: cleanup of self calls * main: code removal and corresponding calls to newly created classes * imager: various formatting changes * main: management of signal shutdown * add requirements.txt * mqtt: messages are now json objects Also, addition of a flag on receiving a new message * mqtt: make message private and add logic to synchronise * stepper: creates the stepper class * stepper: use the new class * stepper: uses the new logic * stepper: add the shutdown event * stepper: add shutdown method * main: add shutdown event * imager: graceful shutdown * stepper: nicer way of checking the Eevnt * self is a required first argument for a method in a class Especially if you use said class private members! * python: various typos and small errors in import * stepper: create mqtt client during init * stepper: instanciate the mqtt client inside run Otherwise it's not accessible from inside the loop. It's a PITA, more information at https://stackoverflow.com/questions/17172878/using-pythons-multiprocessing-process-class * stepper: little bugs and typos all around * mqtt: add shutdown method * mqtt: add connect in init * stepper: fix bugs, sanitize inputs * stepper: work on delay prediction improvements * stepper: json is mean, double quote are mandatory inside * mqtt: add details about message exchanged * imager: first implementation of json messages * main.json: add new tab for RPi management + json for payloads * imager: add state_machine class * stepper: publish last will * imager: major refactor * main: make streaming server process a daemon * mqtt: insert debug statement on close * main: reorder imports * imager: make it work! Reinsert the streaming server logic in there, because there is a problem with the synchronisation part otherwise. Also, eventually, StreamingOuput() will have to be made not global Final very critical learning: it's super duper important to make sure the memory split is at least 256Meg for the GPU. Chaos ensues otherwise * main: changes to accomodate the streamer/imager fusino * imager_state_machine: insert states transition description * stepper: cleanup of code * segmenter: creation of the class * python: include segmenter changes * remove unused files * stepper: check existence of hardware.json * main.json: changes to reflect the python script evolution * remove unecessary TODOs and add some others * main: add check for config and directories * imager: update_config is implemented and we have better management of directories now * segmenter: now work recursively in all folders * flow: the configuration is now sent via mqtt * segmenter: better manage pipeline error * segmenter: declaration of archive_fn in init * imager: small bugs and typos * main: add uniqueID output * imager: add the camera settings message We can now update the ISO, shutter speed and resolution from Node-Red * package.json: update dependencies
2020-09-28 11:05:27 +02:00
[
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"de4ba211.e1d3f"
Extraction and refactor of the python code from node-red flow The rationale for this rewrite is to improve the readability, the modularity, the reliability and the future-proofing of the main python script. All in all, this is now 124 commits that are going to be squashed and merged together, spanning more than two weeks of development and testing. Please test away this release and break things. An upgrading guide will be published in the coming days, along with a new image for people to use if they don't want to upgrade on their own. Read along if you want to know all the goodies! As a starter, the python script was extracted from the main flow, and now lives in its own files at `PlantonScope/scripts/*`. We set up the auto formatting of the code by using [Black](https://github.com/psf/black). This make the code clearer and uniform. We are using the default settings, so if you just install Black and set your editor to format on save using it, you should be good to go. The code is separated in four main processes, each with a specific set of responsibilities: - The main process controls all the others, starts everything up and cleans up on shutdown - The stepper process manages the stepper movements. It's now possible to have simultaneous movements of both motors (this closes #38 ). - The imager process controls the camera and the streaming server via a state machine. - The segmenter process manages the segmentation and its outputs. The segmentation happens recursively in all folders in `/home/pi/PlanktonScope/img/`. Each folder has its own output archive, and bug #26 is now closed. Those processes communicates together using MQTT and json messages. Each message is adressed to one topic. The high level topic controls which process receives the message. The details of each topic is at the end of this commit message. Every imaging sessions has now its own folder, under the `img` root. Metadata are saved individually for every session, in a JSON file in the same directory as the pictures. The configuration is not parsed from `config.json` anymore and passed directly through MQTT messages to the concerned process. A new configuration file has been created: `hardware.json`. This file contains information related to your specific hardware configuration. You can choose to reverse the connection of the motors for example, but you can also define specific speed limits and steps number for your pump and focus stage. This will make it easier for people who wants to experiment with different kind of hardware. It's not necessary to have this file though. If it doesn't exists, the default configuration will be applied. The code is architectured around 6 modules and about 10 classes. I encourage you to have a look at the files, they're pretty straightforward to understand. There is a lot of work left around the node-red code refactoring, dashboard ui improvements, better and clearer LED messages, OLED screen integration and finer control of the segmentation process, but this is quite good for now. Here is the topic lists for MQTT and the corresponding messages. - actuator : This topic adresses the stepper control thread No publication under this topic should happen from the python process - actuator/pump : Control of the pump The message is a json object {"action":"move", "direction":"FORWARD", "volume":10, "flowrate":1} to move 10mL forward at 1mL/min action can be "move" or "stop" Receive only - actuator/focus : Control of the focus stage The message is a json object, speed is optional {"action":"move", "direction":"UP", "distance":0.26, "speed":1} to move up 10mm action can be "move" or "stop" Receive only - imager/image : This topic adresses the imaging thread Is a json object with {"action":"image","sleep":5,"volume":1,"nb_frame":200} sleep in seconds, volume in mL Can also receive a config update message: {"action":"config","config":[...]} Can also receive a camera settings message: {"action":"settings","iso":100,"shutter_speed":40} Receive only - segmenter/segment : This topic adresses the segmenter process Is a json object with {"action":"segment"} Receive only - status : This topics sends feedback to Node-Red No publication or receive at this level - status/pump : State of the pump Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/focus : State of the focus stage Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/imager : State of the imager Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Completed or 12_11_15_0.1.jpg has been imaged. Publish only - status/segmenter : Status of the segmentation - status/segmenter/name - status/segmenter/object_id - status/segmenter/metric Here is the original commit history: * Extract python main.py from flow * Fix bug in server addresses These addresses should be the loopback device instead of the network address of the device. Using the loopback address will not necessitate to update the script when the network address changes. * clean up picamera import * changes to main python and flow: update MQTT requests address to localhost (bugfix) update streaming output address to nothing update main flow to remove python script references and location * Automatically initialise imaging led on startup to off state. * Add the ability to invert outputs of the motor We added a key to config.json "hardware_config" with a subkey "stepper_reverse". If this key is present in the config file and set to 1, the output of the motors are inversed (stepper2 becomes the pump motor and stepper1 the focus motor) * move all non main script to a subfolder * add __init__.py to package * light module rewrite * json cleanup and absolute path for config file * light.py forgot to import subprocess #oups * Add command to turn the leds off * Auto formatting of main.py I've used Black with default settings, see https://github.com/psf/black * First commit of stepper.py Pump parameters still needs to be checked and tuned. * addition of hardware details in config.json * Introduce hardware.json to replace the `hardware_config` of config.json * stepper.py: calibration, typos * creates the MQTT_Client class * pump_max_speed is now in ml/min to help readability * forgot to add self to the class def * addition of threading capabilities to stepper.py (UNTESTED) * mqtt: fix topic bug * remove counter * mqtt add doc about topics * stepper.py creates an "actuator/*/state" topic * stepper.py: rename mqtt_client to pump_client * mqtt.py: add details about topics * stepper.py: rename pump_client to actuator_client * topic was not split properly and a part was lost * switch to f-strings for mqtt.py * cosmetic update * stepper.py: folder name will be planktoscope change calls * hardware.json became more straightforward * stepper.py syntax bugs * stepper.py addition of a received stop command * stepper.py: update to max travel distance * stepper.py: several typos here * rename folder * main.py: reword to reflect folder rename * main.py: remove logic that has been moved to stepper.py and mqtt.py * main.py: update to add mqtt imaging client * mqtt.py: make command and args local to class and output more verbose * make stepper.py a class * main.py: instantiate stepper class and call it * main.py: name mqtt client * update to main.json to reflect main.py changes * fix bugs around pump control * update flows to latest version from Thibault * distance can be a small value, and definitevely should be a float. * unify mqtt topics * unify mqtt output in the main flow * first logger implementation, uses loguru * mqtt: add reason to on_connect * mqtt: add on_disconnect handler * stepper: add more logger calls for debug mainly * main: add levels for logger * imager.py: first move of the imager logic * imager: time import cleanup * imager: morphocut import cleanup * imager: skimage import cleanup * imager: finishing import cleanup * imager: Class creation - WIP Also provides a fix for #26 (see line 190). * imager: threading is needed for Condition() * streamer: get the streamer server its own file * imager: creates start_camera and get the server creation out * imager: subclass multiprocessing.Process * imager: get Pipeline creation its own function * imager: cleanup of self calls * main: code removal and corresponding calls to newly created classes * imager: various formatting changes * main: management of signal shutdown * add requirements.txt * mqtt: messages are now json objects Also, addition of a flag on receiving a new message * mqtt: make message private and add logic to synchronise * stepper: creates the stepper class * stepper: use the new class * stepper: uses the new logic * stepper: add the shutdown event * stepper: add shutdown method * main: add shutdown event * imager: graceful shutdown * stepper: nicer way of checking the Eevnt * self is a required first argument for a method in a class Especially if you use said class private members! * python: various typos and small errors in import * stepper: create mqtt client during init * stepper: instanciate the mqtt client inside run Otherwise it's not accessible from inside the loop. It's a PITA, more information at https://stackoverflow.com/questions/17172878/using-pythons-multiprocessing-process-class * stepper: little bugs and typos all around * mqtt: add shutdown method * mqtt: add connect in init * stepper: fix bugs, sanitize inputs * stepper: work on delay prediction improvements * stepper: json is mean, double quote are mandatory inside * mqtt: add details about message exchanged * imager: first implementation of json messages * main.json: add new tab for RPi management + json for payloads * imager: add state_machine class * stepper: publish last will * imager: major refactor * main: make streaming server process a daemon * mqtt: insert debug statement on close * main: reorder imports * imager: make it work! Reinsert the streaming server logic in there, because there is a problem with the synchronisation part otherwise. Also, eventually, StreamingOuput() will have to be made not global Final very critical learning: it's super duper important to make sure the memory split is at least 256Meg for the GPU. Chaos ensues otherwise * main: changes to accomodate the streamer/imager fusino * imager_state_machine: insert states transition description * stepper: cleanup of code * segmenter: creation of the class * python: include segmenter changes * remove unused files * stepper: check existence of hardware.json * main.json: changes to reflect the python script evolution * remove unecessary TODOs and add some others * main: add check for config and directories * imager: update_config is implemented and we have better management of directories now * segmenter: now work recursively in all folders * flow: the configuration is now sent via mqtt * segmenter: better manage pipeline error * segmenter: declaration of archive_fn in init * imager: small bugs and typos * main: add uniqueID output * imager: add the camera settings message We can now update the ISO, shutter speed and resolution from Node-Red * package.json: update dependencies
2020-09-28 11:05:27 +02:00
]
]
},
{
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"id": "672d89a8.4e6968",
"type": "exec",
"z": "1371dec5.76e671",
"d": true,
"command": "sudo killall -9 python3",
"addpay": true,
"append": "",
"useSpawn": "false",
"timer": "",
"oldrc": false,
"name": "Hard kill",
"x": 980,
"y": 1020,
Extraction and refactor of the python code from node-red flow The rationale for this rewrite is to improve the readability, the modularity, the reliability and the future-proofing of the main python script. All in all, this is now 124 commits that are going to be squashed and merged together, spanning more than two weeks of development and testing. Please test away this release and break things. An upgrading guide will be published in the coming days, along with a new image for people to use if they don't want to upgrade on their own. Read along if you want to know all the goodies! As a starter, the python script was extracted from the main flow, and now lives in its own files at `PlantonScope/scripts/*`. We set up the auto formatting of the code by using [Black](https://github.com/psf/black). This make the code clearer and uniform. We are using the default settings, so if you just install Black and set your editor to format on save using it, you should be good to go. The code is separated in four main processes, each with a specific set of responsibilities: - The main process controls all the others, starts everything up and cleans up on shutdown - The stepper process manages the stepper movements. It's now possible to have simultaneous movements of both motors (this closes #38 ). - The imager process controls the camera and the streaming server via a state machine. - The segmenter process manages the segmentation and its outputs. The segmentation happens recursively in all folders in `/home/pi/PlanktonScope/img/`. Each folder has its own output archive, and bug #26 is now closed. Those processes communicates together using MQTT and json messages. Each message is adressed to one topic. The high level topic controls which process receives the message. The details of each topic is at the end of this commit message. Every imaging sessions has now its own folder, under the `img` root. Metadata are saved individually for every session, in a JSON file in the same directory as the pictures. The configuration is not parsed from `config.json` anymore and passed directly through MQTT messages to the concerned process. A new configuration file has been created: `hardware.json`. This file contains information related to your specific hardware configuration. You can choose to reverse the connection of the motors for example, but you can also define specific speed limits and steps number for your pump and focus stage. This will make it easier for people who wants to experiment with different kind of hardware. It's not necessary to have this file though. If it doesn't exists, the default configuration will be applied. The code is architectured around 6 modules and about 10 classes. I encourage you to have a look at the files, they're pretty straightforward to understand. There is a lot of work left around the node-red code refactoring, dashboard ui improvements, better and clearer LED messages, OLED screen integration and finer control of the segmentation process, but this is quite good for now. Here is the topic lists for MQTT and the corresponding messages. - actuator : This topic adresses the stepper control thread No publication under this topic should happen from the python process - actuator/pump : Control of the pump The message is a json object {"action":"move", "direction":"FORWARD", "volume":10, "flowrate":1} to move 10mL forward at 1mL/min action can be "move" or "stop" Receive only - actuator/focus : Control of the focus stage The message is a json object, speed is optional {"action":"move", "direction":"UP", "distance":0.26, "speed":1} to move up 10mm action can be "move" or "stop" Receive only - imager/image : This topic adresses the imaging thread Is a json object with {"action":"image","sleep":5,"volume":1,"nb_frame":200} sleep in seconds, volume in mL Can also receive a config update message: {"action":"config","config":[...]} Can also receive a camera settings message: {"action":"settings","iso":100,"shutter_speed":40} Receive only - segmenter/segment : This topic adresses the segmenter process Is a json object with {"action":"segment"} Receive only - status : This topics sends feedback to Node-Red No publication or receive at this level - status/pump : State of the pump Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/focus : State of the focus stage Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/imager : State of the imager Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Completed or 12_11_15_0.1.jpg has been imaged. Publish only - status/segmenter : Status of the segmentation - status/segmenter/name - status/segmenter/object_id - status/segmenter/metric Here is the original commit history: * Extract python main.py from flow * Fix bug in server addresses These addresses should be the loopback device instead of the network address of the device. Using the loopback address will not necessitate to update the script when the network address changes. * clean up picamera import * changes to main python and flow: update MQTT requests address to localhost (bugfix) update streaming output address to nothing update main flow to remove python script references and location * Automatically initialise imaging led on startup to off state. * Add the ability to invert outputs of the motor We added a key to config.json "hardware_config" with a subkey "stepper_reverse". If this key is present in the config file and set to 1, the output of the motors are inversed (stepper2 becomes the pump motor and stepper1 the focus motor) * move all non main script to a subfolder * add __init__.py to package * light module rewrite * json cleanup and absolute path for config file * light.py forgot to import subprocess #oups * Add command to turn the leds off * Auto formatting of main.py I've used Black with default settings, see https://github.com/psf/black * First commit of stepper.py Pump parameters still needs to be checked and tuned. * addition of hardware details in config.json * Introduce hardware.json to replace the `hardware_config` of config.json * stepper.py: calibration, typos * creates the MQTT_Client class * pump_max_speed is now in ml/min to help readability * forgot to add self to the class def * addition of threading capabilities to stepper.py (UNTESTED) * mqtt: fix topic bug * remove counter * mqtt add doc about topics * stepper.py creates an "actuator/*/state" topic * stepper.py: rename mqtt_client to pump_client * mqtt.py: add details about topics * stepper.py: rename pump_client to actuator_client * topic was not split properly and a part was lost * switch to f-strings for mqtt.py * cosmetic update * stepper.py: folder name will be planktoscope change calls * hardware.json became more straightforward * stepper.py syntax bugs * stepper.py addition of a received stop command * stepper.py: update to max travel distance * stepper.py: several typos here * rename folder * main.py: reword to reflect folder rename * main.py: remove logic that has been moved to stepper.py and mqtt.py * main.py: update to add mqtt imaging client * mqtt.py: make command and args local to class and output more verbose * make stepper.py a class * main.py: instantiate stepper class and call it * main.py: name mqtt client * update to main.json to reflect main.py changes * fix bugs around pump control * update flows to latest version from Thibault * distance can be a small value, and definitevely should be a float. * unify mqtt topics * unify mqtt output in the main flow * first logger implementation, uses loguru * mqtt: add reason to on_connect * mqtt: add on_disconnect handler * stepper: add more logger calls for debug mainly * main: add levels for logger * imager.py: first move of the imager logic * imager: time import cleanup * imager: morphocut import cleanup * imager: skimage import cleanup * imager: finishing import cleanup * imager: Class creation - WIP Also provides a fix for #26 (see line 190). * imager: threading is needed for Condition() * streamer: get the streamer server its own file * imager: creates start_camera and get the server creation out * imager: subclass multiprocessing.Process * imager: get Pipeline creation its own function * imager: cleanup of self calls * main: code removal and corresponding calls to newly created classes * imager: various formatting changes * main: management of signal shutdown * add requirements.txt * mqtt: messages are now json objects Also, addition of a flag on receiving a new message * mqtt: make message private and add logic to synchronise * stepper: creates the stepper class * stepper: use the new class * stepper: uses the new logic * stepper: add the shutdown event * stepper: add shutdown method * main: add shutdown event * imager: graceful shutdown * stepper: nicer way of checking the Eevnt * self is a required first argument for a method in a class Especially if you use said class private members! * python: various typos and small errors in import * stepper: create mqtt client during init * stepper: instanciate the mqtt client inside run Otherwise it's not accessible from inside the loop. It's a PITA, more information at https://stackoverflow.com/questions/17172878/using-pythons-multiprocessing-process-class * stepper: little bugs and typos all around * mqtt: add shutdown method * mqtt: add connect in init * stepper: fix bugs, sanitize inputs * stepper: work on delay prediction improvements * stepper: json is mean, double quote are mandatory inside * mqtt: add details about message exchanged * imager: first implementation of json messages * main.json: add new tab for RPi management + json for payloads * imager: add state_machine class * stepper: publish last will * imager: major refactor * main: make streaming server process a daemon * mqtt: insert debug statement on close * main: reorder imports * imager: make it work! Reinsert the streaming server logic in there, because there is a problem with the synchronisation part otherwise. Also, eventually, StreamingOuput() will have to be made not global Final very critical learning: it's super duper important to make sure the memory split is at least 256Meg for the GPU. Chaos ensues otherwise * main: changes to accomodate the streamer/imager fusino * imager_state_machine: insert states transition description * stepper: cleanup of code * segmenter: creation of the class * python: include segmenter changes * remove unused files * stepper: check existence of hardware.json * main.json: changes to reflect the python script evolution * remove unecessary TODOs and add some others * main: add check for config and directories * imager: update_config is implemented and we have better management of directories now * segmenter: now work recursively in all folders * flow: the configuration is now sent via mqtt * segmenter: better manage pipeline error * segmenter: declaration of archive_fn in init * imager: small bugs and typos * main: add uniqueID output * imager: add the camera settings message We can now update the ISO, shutter speed and resolution from Node-Red * package.json: update dependencies
2020-09-28 11:05:27 +02:00
"wires": [
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
[],
[],
[]
Extraction and refactor of the python code from node-red flow The rationale for this rewrite is to improve the readability, the modularity, the reliability and the future-proofing of the main python script. All in all, this is now 124 commits that are going to be squashed and merged together, spanning more than two weeks of development and testing. Please test away this release and break things. An upgrading guide will be published in the coming days, along with a new image for people to use if they don't want to upgrade on their own. Read along if you want to know all the goodies! As a starter, the python script was extracted from the main flow, and now lives in its own files at `PlantonScope/scripts/*`. We set up the auto formatting of the code by using [Black](https://github.com/psf/black). This make the code clearer and uniform. We are using the default settings, so if you just install Black and set your editor to format on save using it, you should be good to go. The code is separated in four main processes, each with a specific set of responsibilities: - The main process controls all the others, starts everything up and cleans up on shutdown - The stepper process manages the stepper movements. It's now possible to have simultaneous movements of both motors (this closes #38 ). - The imager process controls the camera and the streaming server via a state machine. - The segmenter process manages the segmentation and its outputs. The segmentation happens recursively in all folders in `/home/pi/PlanktonScope/img/`. Each folder has its own output archive, and bug #26 is now closed. Those processes communicates together using MQTT and json messages. Each message is adressed to one topic. The high level topic controls which process receives the message. The details of each topic is at the end of this commit message. Every imaging sessions has now its own folder, under the `img` root. Metadata are saved individually for every session, in a JSON file in the same directory as the pictures. The configuration is not parsed from `config.json` anymore and passed directly through MQTT messages to the concerned process. A new configuration file has been created: `hardware.json`. This file contains information related to your specific hardware configuration. You can choose to reverse the connection of the motors for example, but you can also define specific speed limits and steps number for your pump and focus stage. This will make it easier for people who wants to experiment with different kind of hardware. It's not necessary to have this file though. If it doesn't exists, the default configuration will be applied. The code is architectured around 6 modules and about 10 classes. I encourage you to have a look at the files, they're pretty straightforward to understand. There is a lot of work left around the node-red code refactoring, dashboard ui improvements, better and clearer LED messages, OLED screen integration and finer control of the segmentation process, but this is quite good for now. Here is the topic lists for MQTT and the corresponding messages. - actuator : This topic adresses the stepper control thread No publication under this topic should happen from the python process - actuator/pump : Control of the pump The message is a json object {"action":"move", "direction":"FORWARD", "volume":10, "flowrate":1} to move 10mL forward at 1mL/min action can be "move" or "stop" Receive only - actuator/focus : Control of the focus stage The message is a json object, speed is optional {"action":"move", "direction":"UP", "distance":0.26, "speed":1} to move up 10mm action can be "move" or "stop" Receive only - imager/image : This topic adresses the imaging thread Is a json object with {"action":"image","sleep":5,"volume":1,"nb_frame":200} sleep in seconds, volume in mL Can also receive a config update message: {"action":"config","config":[...]} Can also receive a camera settings message: {"action":"settings","iso":100,"shutter_speed":40} Receive only - segmenter/segment : This topic adresses the segmenter process Is a json object with {"action":"segment"} Receive only - status : This topics sends feedback to Node-Red No publication or receive at this level - status/pump : State of the pump Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/focus : State of the focus stage Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/imager : State of the imager Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Completed or 12_11_15_0.1.jpg has been imaged. Publish only - status/segmenter : Status of the segmentation - status/segmenter/name - status/segmenter/object_id - status/segmenter/metric Here is the original commit history: * Extract python main.py from flow * Fix bug in server addresses These addresses should be the loopback device instead of the network address of the device. Using the loopback address will not necessitate to update the script when the network address changes. * clean up picamera import * changes to main python and flow: update MQTT requests address to localhost (bugfix) update streaming output address to nothing update main flow to remove python script references and location * Automatically initialise imaging led on startup to off state. * Add the ability to invert outputs of the motor We added a key to config.json "hardware_config" with a subkey "stepper_reverse". If this key is present in the config file and set to 1, the output of the motors are inversed (stepper2 becomes the pump motor and stepper1 the focus motor) * move all non main script to a subfolder * add __init__.py to package * light module rewrite * json cleanup and absolute path for config file * light.py forgot to import subprocess #oups * Add command to turn the leds off * Auto formatting of main.py I've used Black with default settings, see https://github.com/psf/black * First commit of stepper.py Pump parameters still needs to be checked and tuned. * addition of hardware details in config.json * Introduce hardware.json to replace the `hardware_config` of config.json * stepper.py: calibration, typos * creates the MQTT_Client class * pump_max_speed is now in ml/min to help readability * forgot to add self to the class def * addition of threading capabilities to stepper.py (UNTESTED) * mqtt: fix topic bug * remove counter * mqtt add doc about topics * stepper.py creates an "actuator/*/state" topic * stepper.py: rename mqtt_client to pump_client * mqtt.py: add details about topics * stepper.py: rename pump_client to actuator_client * topic was not split properly and a part was lost * switch to f-strings for mqtt.py * cosmetic update * stepper.py: folder name will be planktoscope change calls * hardware.json became more straightforward * stepper.py syntax bugs * stepper.py addition of a received stop command * stepper.py: update to max travel distance * stepper.py: several typos here * rename folder * main.py: reword to reflect folder rename * main.py: remove logic that has been moved to stepper.py and mqtt.py * main.py: update to add mqtt imaging client * mqtt.py: make command and args local to class and output more verbose * make stepper.py a class * main.py: instantiate stepper class and call it * main.py: name mqtt client * update to main.json to reflect main.py changes * fix bugs around pump control * update flows to latest version from Thibault * distance can be a small value, and definitevely should be a float. * unify mqtt topics * unify mqtt output in the main flow * first logger implementation, uses loguru * mqtt: add reason to on_connect * mqtt: add on_disconnect handler * stepper: add more logger calls for debug mainly * main: add levels for logger * imager.py: first move of the imager logic * imager: time import cleanup * imager: morphocut import cleanup * imager: skimage import cleanup * imager: finishing import cleanup * imager: Class creation - WIP Also provides a fix for #26 (see line 190). * imager: threading is needed for Condition() * streamer: get the streamer server its own file * imager: creates start_camera and get the server creation out * imager: subclass multiprocessing.Process * imager: get Pipeline creation its own function * imager: cleanup of self calls * main: code removal and corresponding calls to newly created classes * imager: various formatting changes * main: management of signal shutdown * add requirements.txt * mqtt: messages are now json objects Also, addition of a flag on receiving a new message * mqtt: make message private and add logic to synchronise * stepper: creates the stepper class * stepper: use the new class * stepper: uses the new logic * stepper: add the shutdown event * stepper: add shutdown method * main: add shutdown event * imager: graceful shutdown * stepper: nicer way of checking the Eevnt * self is a required first argument for a method in a class Especially if you use said class private members! * python: various typos and small errors in import * stepper: create mqtt client during init * stepper: instanciate the mqtt client inside run Otherwise it's not accessible from inside the loop. It's a PITA, more information at https://stackoverflow.com/questions/17172878/using-pythons-multiprocessing-process-class * stepper: little bugs and typos all around * mqtt: add shutdown method * mqtt: add connect in init * stepper: fix bugs, sanitize inputs * stepper: work on delay prediction improvements * stepper: json is mean, double quote are mandatory inside * mqtt: add details about message exchanged * imager: first implementation of json messages * main.json: add new tab for RPi management + json for payloads * imager: add state_machine class * stepper: publish last will * imager: major refactor * main: make streaming server process a daemon * mqtt: insert debug statement on close * main: reorder imports * imager: make it work! Reinsert the streaming server logic in there, because there is a problem with the synchronisation part otherwise. Also, eventually, StreamingOuput() will have to be made not global Final very critical learning: it's super duper important to make sure the memory split is at least 256Meg for the GPU. Chaos ensues otherwise * main: changes to accomodate the streamer/imager fusino * imager_state_machine: insert states transition description * stepper: cleanup of code * segmenter: creation of the class * python: include segmenter changes * remove unused files * stepper: check existence of hardware.json * main.json: changes to reflect the python script evolution * remove unecessary TODOs and add some others * main: add check for config and directories * imager: update_config is implemented and we have better management of directories now * segmenter: now work recursively in all folders * flow: the configuration is now sent via mqtt * segmenter: better manage pipeline error * segmenter: declaration of archive_fn in init * imager: small bugs and typos * main: add uniqueID output * imager: add the camera settings message We can now update the ISO, shutter speed and resolution from Node-Red * package.json: update dependencies
2020-09-28 11:05:27 +02:00
]
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
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"id": "afa9f4b.2e77988",
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"z": "1371dec5.76e671",
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"pauseType": "delay",
"timeout": "5",
"timeoutUnits": "seconds",
"rate": "1",
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"rateUnits": "second",
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"randomLast": "5",
"randomUnits": "seconds",
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"x": 460,
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Extraction and refactor of the python code from node-red flow The rationale for this rewrite is to improve the readability, the modularity, the reliability and the future-proofing of the main python script. All in all, this is now 124 commits that are going to be squashed and merged together, spanning more than two weeks of development and testing. Please test away this release and break things. An upgrading guide will be published in the coming days, along with a new image for people to use if they don't want to upgrade on their own. Read along if you want to know all the goodies! As a starter, the python script was extracted from the main flow, and now lives in its own files at `PlantonScope/scripts/*`. We set up the auto formatting of the code by using [Black](https://github.com/psf/black). This make the code clearer and uniform. We are using the default settings, so if you just install Black and set your editor to format on save using it, you should be good to go. The code is separated in four main processes, each with a specific set of responsibilities: - The main process controls all the others, starts everything up and cleans up on shutdown - The stepper process manages the stepper movements. It's now possible to have simultaneous movements of both motors (this closes #38 ). - The imager process controls the camera and the streaming server via a state machine. - The segmenter process manages the segmentation and its outputs. The segmentation happens recursively in all folders in `/home/pi/PlanktonScope/img/`. Each folder has its own output archive, and bug #26 is now closed. Those processes communicates together using MQTT and json messages. Each message is adressed to one topic. The high level topic controls which process receives the message. The details of each topic is at the end of this commit message. Every imaging sessions has now its own folder, under the `img` root. Metadata are saved individually for every session, in a JSON file in the same directory as the pictures. The configuration is not parsed from `config.json` anymore and passed directly through MQTT messages to the concerned process. A new configuration file has been created: `hardware.json`. This file contains information related to your specific hardware configuration. You can choose to reverse the connection of the motors for example, but you can also define specific speed limits and steps number for your pump and focus stage. This will make it easier for people who wants to experiment with different kind of hardware. It's not necessary to have this file though. If it doesn't exists, the default configuration will be applied. The code is architectured around 6 modules and about 10 classes. I encourage you to have a look at the files, they're pretty straightforward to understand. There is a lot of work left around the node-red code refactoring, dashboard ui improvements, better and clearer LED messages, OLED screen integration and finer control of the segmentation process, but this is quite good for now. Here is the topic lists for MQTT and the corresponding messages. - actuator : This topic adresses the stepper control thread No publication under this topic should happen from the python process - actuator/pump : Control of the pump The message is a json object {"action":"move", "direction":"FORWARD", "volume":10, "flowrate":1} to move 10mL forward at 1mL/min action can be "move" or "stop" Receive only - actuator/focus : Control of the focus stage The message is a json object, speed is optional {"action":"move", "direction":"UP", "distance":0.26, "speed":1} to move up 10mm action can be "move" or "stop" Receive only - imager/image : This topic adresses the imaging thread Is a json object with {"action":"image","sleep":5,"volume":1,"nb_frame":200} sleep in seconds, volume in mL Can also receive a config update message: {"action":"config","config":[...]} Can also receive a camera settings message: {"action":"settings","iso":100,"shutter_speed":40} Receive only - segmenter/segment : This topic adresses the segmenter process Is a json object with {"action":"segment"} Receive only - status : This topics sends feedback to Node-Red No publication or receive at this level - status/pump : State of the pump Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/focus : State of the focus stage Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/imager : State of the imager Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Completed or 12_11_15_0.1.jpg has been imaged. Publish only - status/segmenter : Status of the segmentation - status/segmenter/name - status/segmenter/object_id - status/segmenter/metric Here is the original commit history: * Extract python main.py from flow * Fix bug in server addresses These addresses should be the loopback device instead of the network address of the device. Using the loopback address will not necessitate to update the script when the network address changes. * clean up picamera import * changes to main python and flow: update MQTT requests address to localhost (bugfix) update streaming output address to nothing update main flow to remove python script references and location * Automatically initialise imaging led on startup to off state. * Add the ability to invert outputs of the motor We added a key to config.json "hardware_config" with a subkey "stepper_reverse". If this key is present in the config file and set to 1, the output of the motors are inversed (stepper2 becomes the pump motor and stepper1 the focus motor) * move all non main script to a subfolder * add __init__.py to package * light module rewrite * json cleanup and absolute path for config file * light.py forgot to import subprocess #oups * Add command to turn the leds off * Auto formatting of main.py I've used Black with default settings, see https://github.com/psf/black * First commit of stepper.py Pump parameters still needs to be checked and tuned. * addition of hardware details in config.json * Introduce hardware.json to replace the `hardware_config` of config.json * stepper.py: calibration, typos * creates the MQTT_Client class * pump_max_speed is now in ml/min to help readability * forgot to add self to the class def * addition of threading capabilities to stepper.py (UNTESTED) * mqtt: fix topic bug * remove counter * mqtt add doc about topics * stepper.py creates an "actuator/*/state" topic * stepper.py: rename mqtt_client to pump_client * mqtt.py: add details about topics * stepper.py: rename pump_client to actuator_client * topic was not split properly and a part was lost * switch to f-strings for mqtt.py * cosmetic update * stepper.py: folder name will be planktoscope change calls * hardware.json became more straightforward * stepper.py syntax bugs * stepper.py addition of a received stop command * stepper.py: update to max travel distance * stepper.py: several typos here * rename folder * main.py: reword to reflect folder rename * main.py: remove logic that has been moved to stepper.py and mqtt.py * main.py: update to add mqtt imaging client * mqtt.py: make command and args local to class and output more verbose * make stepper.py a class * main.py: instantiate stepper class and call it * main.py: name mqtt client * update to main.json to reflect main.py changes * fix bugs around pump control * update flows to latest version from Thibault * distance can be a small value, and definitevely should be a float. * unify mqtt topics * unify mqtt output in the main flow * first logger implementation, uses loguru * mqtt: add reason to on_connect * mqtt: add on_disconnect handler * stepper: add more logger calls for debug mainly * main: add levels for logger * imager.py: first move of the imager logic * imager: time import cleanup * imager: morphocut import cleanup * imager: skimage import cleanup * imager: finishing import cleanup * imager: Class creation - WIP Also provides a fix for #26 (see line 190). * imager: threading is needed for Condition() * streamer: get the streamer server its own file * imager: creates start_camera and get the server creation out * imager: subclass multiprocessing.Process * imager: get Pipeline creation its own function * imager: cleanup of self calls * main: code removal and corresponding calls to newly created classes * imager: various formatting changes * main: management of signal shutdown * add requirements.txt * mqtt: messages are now json objects Also, addition of a flag on receiving a new message * mqtt: make message private and add logic to synchronise * stepper: creates the stepper class * stepper: use the new class * stepper: uses the new logic * stepper: add the shutdown event * stepper: add shutdown method * main: add shutdown event * imager: graceful shutdown * stepper: nicer way of checking the Eevnt * self is a required first argument for a method in a class Especially if you use said class private members! * python: various typos and small errors in import * stepper: create mqtt client during init * stepper: instanciate the mqtt client inside run Otherwise it's not accessible from inside the loop. It's a PITA, more information at https://stackoverflow.com/questions/17172878/using-pythons-multiprocessing-process-class * stepper: little bugs and typos all around * mqtt: add shutdown method * mqtt: add connect in init * stepper: fix bugs, sanitize inputs * stepper: work on delay prediction improvements * stepper: json is mean, double quote are mandatory inside * mqtt: add details about message exchanged * imager: first implementation of json messages * main.json: add new tab for RPi management + json for payloads * imager: add state_machine class * stepper: publish last will * imager: major refactor * main: make streaming server process a daemon * mqtt: insert debug statement on close * main: reorder imports * imager: make it work! Reinsert the streaming server logic in there, because there is a problem with the synchronisation part otherwise. Also, eventually, StreamingOuput() will have to be made not global Final very critical learning: it's super duper important to make sure the memory split is at least 256Meg for the GPU. Chaos ensues otherwise * main: changes to accomodate the streamer/imager fusino * imager_state_machine: insert states transition description * stepper: cleanup of code * segmenter: creation of the class * python: include segmenter changes * remove unused files * stepper: check existence of hardware.json * main.json: changes to reflect the python script evolution * remove unecessary TODOs and add some others * main: add check for config and directories * imager: update_config is implemented and we have better management of directories now * segmenter: now work recursively in all folders * flow: the configuration is now sent via mqtt * segmenter: better manage pipeline error * segmenter: declaration of archive_fn in init * imager: small bugs and typos * main: add uniqueID output * imager: add the camera settings message We can now update the ISO, shutter speed and resolution from Node-Red * package.json: update dependencies
2020-09-28 11:05:27 +02:00
"wires": [
[
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"9998aa86.74bb"
Extraction and refactor of the python code from node-red flow The rationale for this rewrite is to improve the readability, the modularity, the reliability and the future-proofing of the main python script. All in all, this is now 124 commits that are going to be squashed and merged together, spanning more than two weeks of development and testing. Please test away this release and break things. An upgrading guide will be published in the coming days, along with a new image for people to use if they don't want to upgrade on their own. Read along if you want to know all the goodies! As a starter, the python script was extracted from the main flow, and now lives in its own files at `PlantonScope/scripts/*`. We set up the auto formatting of the code by using [Black](https://github.com/psf/black). This make the code clearer and uniform. We are using the default settings, so if you just install Black and set your editor to format on save using it, you should be good to go. The code is separated in four main processes, each with a specific set of responsibilities: - The main process controls all the others, starts everything up and cleans up on shutdown - The stepper process manages the stepper movements. It's now possible to have simultaneous movements of both motors (this closes #38 ). - The imager process controls the camera and the streaming server via a state machine. - The segmenter process manages the segmentation and its outputs. The segmentation happens recursively in all folders in `/home/pi/PlanktonScope/img/`. Each folder has its own output archive, and bug #26 is now closed. Those processes communicates together using MQTT and json messages. Each message is adressed to one topic. The high level topic controls which process receives the message. The details of each topic is at the end of this commit message. Every imaging sessions has now its own folder, under the `img` root. Metadata are saved individually for every session, in a JSON file in the same directory as the pictures. The configuration is not parsed from `config.json` anymore and passed directly through MQTT messages to the concerned process. A new configuration file has been created: `hardware.json`. This file contains information related to your specific hardware configuration. You can choose to reverse the connection of the motors for example, but you can also define specific speed limits and steps number for your pump and focus stage. This will make it easier for people who wants to experiment with different kind of hardware. It's not necessary to have this file though. If it doesn't exists, the default configuration will be applied. The code is architectured around 6 modules and about 10 classes. I encourage you to have a look at the files, they're pretty straightforward to understand. There is a lot of work left around the node-red code refactoring, dashboard ui improvements, better and clearer LED messages, OLED screen integration and finer control of the segmentation process, but this is quite good for now. Here is the topic lists for MQTT and the corresponding messages. - actuator : This topic adresses the stepper control thread No publication under this topic should happen from the python process - actuator/pump : Control of the pump The message is a json object {"action":"move", "direction":"FORWARD", "volume":10, "flowrate":1} to move 10mL forward at 1mL/min action can be "move" or "stop" Receive only - actuator/focus : Control of the focus stage The message is a json object, speed is optional {"action":"move", "direction":"UP", "distance":0.26, "speed":1} to move up 10mm action can be "move" or "stop" Receive only - imager/image : This topic adresses the imaging thread Is a json object with {"action":"image","sleep":5,"volume":1,"nb_frame":200} sleep in seconds, volume in mL Can also receive a config update message: {"action":"config","config":[...]} Can also receive a camera settings message: {"action":"settings","iso":100,"shutter_speed":40} Receive only - segmenter/segment : This topic adresses the segmenter process Is a json object with {"action":"segment"} Receive only - status : This topics sends feedback to Node-Red No publication or receive at this level - status/pump : State of the pump Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/focus : State of the focus stage Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/imager : State of the imager Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Completed or 12_11_15_0.1.jpg has been imaged. Publish only - status/segmenter : Status of the segmentation - status/segmenter/name - status/segmenter/object_id - status/segmenter/metric Here is the original commit history: * Extract python main.py from flow * Fix bug in server addresses These addresses should be the loopback device instead of the network address of the device. Using the loopback address will not necessitate to update the script when the network address changes. * clean up picamera import * changes to main python and flow: update MQTT requests address to localhost (bugfix) update streaming output address to nothing update main flow to remove python script references and location * Automatically initialise imaging led on startup to off state. * Add the ability to invert outputs of the motor We added a key to config.json "hardware_config" with a subkey "stepper_reverse". If this key is present in the config file and set to 1, the output of the motors are inversed (stepper2 becomes the pump motor and stepper1 the focus motor) * move all non main script to a subfolder * add __init__.py to package * light module rewrite * json cleanup and absolute path for config file * light.py forgot to import subprocess #oups * Add command to turn the leds off * Auto formatting of main.py I've used Black with default settings, see https://github.com/psf/black * First commit of stepper.py Pump parameters still needs to be checked and tuned. * addition of hardware details in config.json * Introduce hardware.json to replace the `hardware_config` of config.json * stepper.py: calibration, typos * creates the MQTT_Client class * pump_max_speed is now in ml/min to help readability * forgot to add self to the class def * addition of threading capabilities to stepper.py (UNTESTED) * mqtt: fix topic bug * remove counter * mqtt add doc about topics * stepper.py creates an "actuator/*/state" topic * stepper.py: rename mqtt_client to pump_client * mqtt.py: add details about topics * stepper.py: rename pump_client to actuator_client * topic was not split properly and a part was lost * switch to f-strings for mqtt.py * cosmetic update * stepper.py: folder name will be planktoscope change calls * hardware.json became more straightforward * stepper.py syntax bugs * stepper.py addition of a received stop command * stepper.py: update to max travel distance * stepper.py: several typos here * rename folder * main.py: reword to reflect folder rename * main.py: remove logic that has been moved to stepper.py and mqtt.py * main.py: update to add mqtt imaging client * mqtt.py: make command and args local to class and output more verbose * make stepper.py a class * main.py: instantiate stepper class and call it * main.py: name mqtt client * update to main.json to reflect main.py changes * fix bugs around pump control * update flows to latest version from Thibault * distance can be a small value, and definitevely should be a float. * unify mqtt topics * unify mqtt output in the main flow * first logger implementation, uses loguru * mqtt: add reason to on_connect * mqtt: add on_disconnect handler * stepper: add more logger calls for debug mainly * main: add levels for logger * imager.py: first move of the imager logic * imager: time import cleanup * imager: morphocut import cleanup * imager: skimage import cleanup * imager: finishing import cleanup * imager: Class creation - WIP Also provides a fix for #26 (see line 190). * imager: threading is needed for Condition() * streamer: get the streamer server its own file * imager: creates start_camera and get the server creation out * imager: subclass multiprocessing.Process * imager: get Pipeline creation its own function * imager: cleanup of self calls * main: code removal and corresponding calls to newly created classes * imager: various formatting changes * main: management of signal shutdown * add requirements.txt * mqtt: messages are now json objects Also, addition of a flag on receiving a new message * mqtt: make message private and add logic to synchronise * stepper: creates the stepper class * stepper: use the new class * stepper: uses the new logic * stepper: add the shutdown event * stepper: add shutdown method * main: add shutdown event * imager: graceful shutdown * stepper: nicer way of checking the Eevnt * self is a required first argument for a method in a class Especially if you use said class private members! * python: various typos and small errors in import * stepper: create mqtt client during init * stepper: instanciate the mqtt client inside run Otherwise it's not accessible from inside the loop. It's a PITA, more information at https://stackoverflow.com/questions/17172878/using-pythons-multiprocessing-process-class * stepper: little bugs and typos all around * mqtt: add shutdown method * mqtt: add connect in init * stepper: fix bugs, sanitize inputs * stepper: work on delay prediction improvements * stepper: json is mean, double quote are mandatory inside * mqtt: add details about message exchanged * imager: first implementation of json messages * main.json: add new tab for RPi management + json for payloads * imager: add state_machine class * stepper: publish last will * imager: major refactor * main: make streaming server process a daemon * mqtt: insert debug statement on close * main: reorder imports * imager: make it work! Reinsert the streaming server logic in there, because there is a problem with the synchronisation part otherwise. Also, eventually, StreamingOuput() will have to be made not global Final very critical learning: it's super duper important to make sure the memory split is at least 256Meg for the GPU. Chaos ensues otherwise * main: changes to accomodate the streamer/imager fusino * imager_state_machine: insert states transition description * stepper: cleanup of code * segmenter: creation of the class * python: include segmenter changes * remove unused files * stepper: check existence of hardware.json * main.json: changes to reflect the python script evolution * remove unecessary TODOs and add some others * main: add check for config and directories * imager: update_config is implemented and we have better management of directories now * segmenter: now work recursively in all folders * flow: the configuration is now sent via mqtt * segmenter: better manage pipeline error * segmenter: declaration of archive_fn in init * imager: small bugs and typos * main: add uniqueID output * imager: add the camera settings message We can now update the ISO, shutter speed and resolution from Node-Red * package.json: update dependencies
2020-09-28 11:05:27 +02:00
]
]
},
{
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"id": "1df370a8.6c70ff",
Extraction and refactor of the python code from node-red flow The rationale for this rewrite is to improve the readability, the modularity, the reliability and the future-proofing of the main python script. All in all, this is now 124 commits that are going to be squashed and merged together, spanning more than two weeks of development and testing. Please test away this release and break things. An upgrading guide will be published in the coming days, along with a new image for people to use if they don't want to upgrade on their own. Read along if you want to know all the goodies! As a starter, the python script was extracted from the main flow, and now lives in its own files at `PlantonScope/scripts/*`. We set up the auto formatting of the code by using [Black](https://github.com/psf/black). This make the code clearer and uniform. We are using the default settings, so if you just install Black and set your editor to format on save using it, you should be good to go. The code is separated in four main processes, each with a specific set of responsibilities: - The main process controls all the others, starts everything up and cleans up on shutdown - The stepper process manages the stepper movements. It's now possible to have simultaneous movements of both motors (this closes #38 ). - The imager process controls the camera and the streaming server via a state machine. - The segmenter process manages the segmentation and its outputs. The segmentation happens recursively in all folders in `/home/pi/PlanktonScope/img/`. Each folder has its own output archive, and bug #26 is now closed. Those processes communicates together using MQTT and json messages. Each message is adressed to one topic. The high level topic controls which process receives the message. The details of each topic is at the end of this commit message. Every imaging sessions has now its own folder, under the `img` root. Metadata are saved individually for every session, in a JSON file in the same directory as the pictures. The configuration is not parsed from `config.json` anymore and passed directly through MQTT messages to the concerned process. A new configuration file has been created: `hardware.json`. This file contains information related to your specific hardware configuration. You can choose to reverse the connection of the motors for example, but you can also define specific speed limits and steps number for your pump and focus stage. This will make it easier for people who wants to experiment with different kind of hardware. It's not necessary to have this file though. If it doesn't exists, the default configuration will be applied. The code is architectured around 6 modules and about 10 classes. I encourage you to have a look at the files, they're pretty straightforward to understand. There is a lot of work left around the node-red code refactoring, dashboard ui improvements, better and clearer LED messages, OLED screen integration and finer control of the segmentation process, but this is quite good for now. Here is the topic lists for MQTT and the corresponding messages. - actuator : This topic adresses the stepper control thread No publication under this topic should happen from the python process - actuator/pump : Control of the pump The message is a json object {"action":"move", "direction":"FORWARD", "volume":10, "flowrate":1} to move 10mL forward at 1mL/min action can be "move" or "stop" Receive only - actuator/focus : Control of the focus stage The message is a json object, speed is optional {"action":"move", "direction":"UP", "distance":0.26, "speed":1} to move up 10mm action can be "move" or "stop" Receive only - imager/image : This topic adresses the imaging thread Is a json object with {"action":"image","sleep":5,"volume":1,"nb_frame":200} sleep in seconds, volume in mL Can also receive a config update message: {"action":"config","config":[...]} Can also receive a camera settings message: {"action":"settings","iso":100,"shutter_speed":40} Receive only - segmenter/segment : This topic adresses the segmenter process Is a json object with {"action":"segment"} Receive only - status : This topics sends feedback to Node-Red No publication or receive at this level - status/pump : State of the pump Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/focus : State of the focus stage Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/imager : State of the imager Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Completed or 12_11_15_0.1.jpg has been imaged. Publish only - status/segmenter : Status of the segmentation - status/segmenter/name - status/segmenter/object_id - status/segmenter/metric Here is the original commit history: * Extract python main.py from flow * Fix bug in server addresses These addresses should be the loopback device instead of the network address of the device. Using the loopback address will not necessitate to update the script when the network address changes. * clean up picamera import * changes to main python and flow: update MQTT requests address to localhost (bugfix) update streaming output address to nothing update main flow to remove python script references and location * Automatically initialise imaging led on startup to off state. * Add the ability to invert outputs of the motor We added a key to config.json "hardware_config" with a subkey "stepper_reverse". If this key is present in the config file and set to 1, the output of the motors are inversed (stepper2 becomes the pump motor and stepper1 the focus motor) * move all non main script to a subfolder * add __init__.py to package * light module rewrite * json cleanup and absolute path for config file * light.py forgot to import subprocess #oups * Add command to turn the leds off * Auto formatting of main.py I've used Black with default settings, see https://github.com/psf/black * First commit of stepper.py Pump parameters still needs to be checked and tuned. * addition of hardware details in config.json * Introduce hardware.json to replace the `hardware_config` of config.json * stepper.py: calibration, typos * creates the MQTT_Client class * pump_max_speed is now in ml/min to help readability * forgot to add self to the class def * addition of threading capabilities to stepper.py (UNTESTED) * mqtt: fix topic bug * remove counter * mqtt add doc about topics * stepper.py creates an "actuator/*/state" topic * stepper.py: rename mqtt_client to pump_client * mqtt.py: add details about topics * stepper.py: rename pump_client to actuator_client * topic was not split properly and a part was lost * switch to f-strings for mqtt.py * cosmetic update * stepper.py: folder name will be planktoscope change calls * hardware.json became more straightforward * stepper.py syntax bugs * stepper.py addition of a received stop command * stepper.py: update to max travel distance * stepper.py: several typos here * rename folder * main.py: reword to reflect folder rename * main.py: remove logic that has been moved to stepper.py and mqtt.py * main.py: update to add mqtt imaging client * mqtt.py: make command and args local to class and output more verbose * make stepper.py a class * main.py: instantiate stepper class and call it * main.py: name mqtt client * update to main.json to reflect main.py changes * fix bugs around pump control * update flows to latest version from Thibault * distance can be a small value, and definitevely should be a float. * unify mqtt topics * unify mqtt output in the main flow * first logger implementation, uses loguru * mqtt: add reason to on_connect * mqtt: add on_disconnect handler * stepper: add more logger calls for debug mainly * main: add levels for logger * imager.py: first move of the imager logic * imager: time import cleanup * imager: morphocut import cleanup * imager: skimage import cleanup * imager: finishing import cleanup * imager: Class creation - WIP Also provides a fix for #26 (see line 190). * imager: threading is needed for Condition() * streamer: get the streamer server its own file * imager: creates start_camera and get the server creation out * imager: subclass multiprocessing.Process * imager: get Pipeline creation its own function * imager: cleanup of self calls * main: code removal and corresponding calls to newly created classes * imager: various formatting changes * main: management of signal shutdown * add requirements.txt * mqtt: messages are now json objects Also, addition of a flag on receiving a new message * mqtt: make message private and add logic to synchronise * stepper: creates the stepper class * stepper: use the new class * stepper: uses the new logic * stepper: add the shutdown event * stepper: add shutdown method * main: add shutdown event * imager: graceful shutdown * stepper: nicer way of checking the Eevnt * self is a required first argument for a method in a class Especially if you use said class private members! * python: various typos and small errors in import * stepper: create mqtt client during init * stepper: instanciate the mqtt client inside run Otherwise it's not accessible from inside the loop. It's a PITA, more information at https://stackoverflow.com/questions/17172878/using-pythons-multiprocessing-process-class * stepper: little bugs and typos all around * mqtt: add shutdown method * mqtt: add connect in init * stepper: fix bugs, sanitize inputs * stepper: work on delay prediction improvements * stepper: json is mean, double quote are mandatory inside * mqtt: add details about message exchanged * imager: first implementation of json messages * main.json: add new tab for RPi management + json for payloads * imager: add state_machine class * stepper: publish last will * imager: major refactor * main: make streaming server process a daemon * mqtt: insert debug statement on close * main: reorder imports * imager: make it work! Reinsert the streaming server logic in there, because there is a problem with the synchronisation part otherwise. Also, eventually, StreamingOuput() will have to be made not global Final very critical learning: it's super duper important to make sure the memory split is at least 256Meg for the GPU. Chaos ensues otherwise * main: changes to accomodate the streamer/imager fusino * imager_state_machine: insert states transition description * stepper: cleanup of code * segmenter: creation of the class * python: include segmenter changes * remove unused files * stepper: check existence of hardware.json * main.json: changes to reflect the python script evolution * remove unecessary TODOs and add some others * main: add check for config and directories * imager: update_config is implemented and we have better management of directories now * segmenter: now work recursively in all folders * flow: the configuration is now sent via mqtt * segmenter: better manage pipeline error * segmenter: declaration of archive_fn in init * imager: small bugs and typos * main: add uniqueID output * imager: add the camera settings message We can now update the ISO, shutter speed and resolution from Node-Red * package.json: update dependencies
2020-09-28 11:05:27 +02:00
"type": "ui_button",
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"z": "1371dec5.76e671",
"name": "Restart Python",
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Flow updates
2020-10-06 17:22:25 +02:00
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Extraction and refactor of the python code from node-red flow The rationale for this rewrite is to improve the readability, the modularity, the reliability and the future-proofing of the main python script. All in all, this is now 124 commits that are going to be squashed and merged together, spanning more than two weeks of development and testing. Please test away this release and break things. An upgrading guide will be published in the coming days, along with a new image for people to use if they don't want to upgrade on their own. Read along if you want to know all the goodies! As a starter, the python script was extracted from the main flow, and now lives in its own files at `PlantonScope/scripts/*`. We set up the auto formatting of the code by using [Black](https://github.com/psf/black). This make the code clearer and uniform. We are using the default settings, so if you just install Black and set your editor to format on save using it, you should be good to go. The code is separated in four main processes, each with a specific set of responsibilities: - The main process controls all the others, starts everything up and cleans up on shutdown - The stepper process manages the stepper movements. It's now possible to have simultaneous movements of both motors (this closes #38 ). - The imager process controls the camera and the streaming server via a state machine. - The segmenter process manages the segmentation and its outputs. The segmentation happens recursively in all folders in `/home/pi/PlanktonScope/img/`. Each folder has its own output archive, and bug #26 is now closed. Those processes communicates together using MQTT and json messages. Each message is adressed to one topic. The high level topic controls which process receives the message. The details of each topic is at the end of this commit message. Every imaging sessions has now its own folder, under the `img` root. Metadata are saved individually for every session, in a JSON file in the same directory as the pictures. The configuration is not parsed from `config.json` anymore and passed directly through MQTT messages to the concerned process. A new configuration file has been created: `hardware.json`. This file contains information related to your specific hardware configuration. You can choose to reverse the connection of the motors for example, but you can also define specific speed limits and steps number for your pump and focus stage. This will make it easier for people who wants to experiment with different kind of hardware. It's not necessary to have this file though. If it doesn't exists, the default configuration will be applied. The code is architectured around 6 modules and about 10 classes. I encourage you to have a look at the files, they're pretty straightforward to understand. There is a lot of work left around the node-red code refactoring, dashboard ui improvements, better and clearer LED messages, OLED screen integration and finer control of the segmentation process, but this is quite good for now. Here is the topic lists for MQTT and the corresponding messages. - actuator : This topic adresses the stepper control thread No publication under this topic should happen from the python process - actuator/pump : Control of the pump The message is a json object {"action":"move", "direction":"FORWARD", "volume":10, "flowrate":1} to move 10mL forward at 1mL/min action can be "move" or "stop" Receive only - actuator/focus : Control of the focus stage The message is a json object, speed is optional {"action":"move", "direction":"UP", "distance":0.26, "speed":1} to move up 10mm action can be "move" or "stop" Receive only - imager/image : This topic adresses the imaging thread Is a json object with {"action":"image","sleep":5,"volume":1,"nb_frame":200} sleep in seconds, volume in mL Can also receive a config update message: {"action":"config","config":[...]} Can also receive a camera settings message: {"action":"settings","iso":100,"shutter_speed":40} Receive only - segmenter/segment : This topic adresses the segmenter process Is a json object with {"action":"segment"} Receive only - status : This topics sends feedback to Node-Red No publication or receive at this level - status/pump : State of the pump Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/focus : State of the focus stage Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/imager : State of the imager Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Completed or 12_11_15_0.1.jpg has been imaged. Publish only - status/segmenter : Status of the segmentation - status/segmenter/name - status/segmenter/object_id - status/segmenter/metric Here is the original commit history: * Extract python main.py from flow * Fix bug in server addresses These addresses should be the loopback device instead of the network address of the device. Using the loopback address will not necessitate to update the script when the network address changes. * clean up picamera import * changes to main python and flow: update MQTT requests address to localhost (bugfix) update streaming output address to nothing update main flow to remove python script references and location * Automatically initialise imaging led on startup to off state. * Add the ability to invert outputs of the motor We added a key to config.json "hardware_config" with a subkey "stepper_reverse". If this key is present in the config file and set to 1, the output of the motors are inversed (stepper2 becomes the pump motor and stepper1 the focus motor) * move all non main script to a subfolder * add __init__.py to package * light module rewrite * json cleanup and absolute path for config file * light.py forgot to import subprocess #oups * Add command to turn the leds off * Auto formatting of main.py I've used Black with default settings, see https://github.com/psf/black * First commit of stepper.py Pump parameters still needs to be checked and tuned. * addition of hardware details in config.json * Introduce hardware.json to replace the `hardware_config` of config.json * stepper.py: calibration, typos * creates the MQTT_Client class * pump_max_speed is now in ml/min to help readability * forgot to add self to the class def * addition of threading capabilities to stepper.py (UNTESTED) * mqtt: fix topic bug * remove counter * mqtt add doc about topics * stepper.py creates an "actuator/*/state" topic * stepper.py: rename mqtt_client to pump_client * mqtt.py: add details about topics * stepper.py: rename pump_client to actuator_client * topic was not split properly and a part was lost * switch to f-strings for mqtt.py * cosmetic update * stepper.py: folder name will be planktoscope change calls * hardware.json became more straightforward * stepper.py syntax bugs * stepper.py addition of a received stop command * stepper.py: update to max travel distance * stepper.py: several typos here * rename folder * main.py: reword to reflect folder rename * main.py: remove logic that has been moved to stepper.py and mqtt.py * main.py: update to add mqtt imaging client * mqtt.py: make command and args local to class and output more verbose * make stepper.py a class * main.py: instantiate stepper class and call it * main.py: name mqtt client * update to main.json to reflect main.py changes * fix bugs around pump control * update flows to latest version from Thibault * distance can be a small value, and definitevely should be a float. * unify mqtt topics * unify mqtt output in the main flow * first logger implementation, uses loguru * mqtt: add reason to on_connect * mqtt: add on_disconnect handler * stepper: add more logger calls for debug mainly * main: add levels for logger * imager.py: first move of the imager logic * imager: time import cleanup * imager: morphocut import cleanup * imager: skimage import cleanup * imager: finishing import cleanup * imager: Class creation - WIP Also provides a fix for #26 (see line 190). * imager: threading is needed for Condition() * streamer: get the streamer server its own file * imager: creates start_camera and get the server creation out * imager: subclass multiprocessing.Process * imager: get Pipeline creation its own function * imager: cleanup of self calls * main: code removal and corresponding calls to newly created classes * imager: various formatting changes * main: management of signal shutdown * add requirements.txt * mqtt: messages are now json objects Also, addition of a flag on receiving a new message * mqtt: make message private and add logic to synchronise * stepper: creates the stepper class * stepper: use the new class * stepper: uses the new logic * stepper: add the shutdown event * stepper: add shutdown method * main: add shutdown event * imager: graceful shutdown * stepper: nicer way of checking the Eevnt * self is a required first argument for a method in a class Especially if you use said class private members! * python: various typos and small errors in import * stepper: create mqtt client during init * stepper: instanciate the mqtt client inside run Otherwise it's not accessible from inside the loop. It's a PITA, more information at https://stackoverflow.com/questions/17172878/using-pythons-multiprocessing-process-class * stepper: little bugs and typos all around * mqtt: add shutdown method * mqtt: add connect in init * stepper: fix bugs, sanitize inputs * stepper: work on delay prediction improvements * stepper: json is mean, double quote are mandatory inside * mqtt: add details about message exchanged * imager: first implementation of json messages * main.json: add new tab for RPi management + json for payloads * imager: add state_machine class * stepper: publish last will * imager: major refactor * main: make streaming server process a daemon * mqtt: insert debug statement on close * main: reorder imports * imager: make it work! Reinsert the streaming server logic in there, because there is a problem with the synchronisation part otherwise. Also, eventually, StreamingOuput() will have to be made not global Final very critical learning: it's super duper important to make sure the memory split is at least 256Meg for the GPU. Chaos ensues otherwise * main: changes to accomodate the streamer/imager fusino * imager_state_machine: insert states transition description * stepper: cleanup of code * segmenter: creation of the class * python: include segmenter changes * remove unused files * stepper: check existence of hardware.json * main.json: changes to reflect the python script evolution * remove unecessary TODOs and add some others * main: add check for config and directories * imager: update_config is implemented and we have better management of directories now * segmenter: now work recursively in all folders * flow: the configuration is now sent via mqtt * segmenter: better manage pipeline error * segmenter: declaration of archive_fn in init * imager: small bugs and typos * main: add uniqueID output * imager: add the camera settings message We can now update the ISO, shutter speed and resolution from Node-Red * package.json: update dependencies
2020-09-28 11:05:27 +02:00
"passthru": false,
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"label": "Restart Python",
Extraction and refactor of the python code from node-red flow The rationale for this rewrite is to improve the readability, the modularity, the reliability and the future-proofing of the main python script. All in all, this is now 124 commits that are going to be squashed and merged together, spanning more than two weeks of development and testing. Please test away this release and break things. An upgrading guide will be published in the coming days, along with a new image for people to use if they don't want to upgrade on their own. Read along if you want to know all the goodies! As a starter, the python script was extracted from the main flow, and now lives in its own files at `PlantonScope/scripts/*`. We set up the auto formatting of the code by using [Black](https://github.com/psf/black). This make the code clearer and uniform. We are using the default settings, so if you just install Black and set your editor to format on save using it, you should be good to go. The code is separated in four main processes, each with a specific set of responsibilities: - The main process controls all the others, starts everything up and cleans up on shutdown - The stepper process manages the stepper movements. It's now possible to have simultaneous movements of both motors (this closes #38 ). - The imager process controls the camera and the streaming server via a state machine. - The segmenter process manages the segmentation and its outputs. The segmentation happens recursively in all folders in `/home/pi/PlanktonScope/img/`. Each folder has its own output archive, and bug #26 is now closed. Those processes communicates together using MQTT and json messages. Each message is adressed to one topic. The high level topic controls which process receives the message. The details of each topic is at the end of this commit message. Every imaging sessions has now its own folder, under the `img` root. Metadata are saved individually for every session, in a JSON file in the same directory as the pictures. The configuration is not parsed from `config.json` anymore and passed directly through MQTT messages to the concerned process. A new configuration file has been created: `hardware.json`. This file contains information related to your specific hardware configuration. You can choose to reverse the connection of the motors for example, but you can also define specific speed limits and steps number for your pump and focus stage. This will make it easier for people who wants to experiment with different kind of hardware. It's not necessary to have this file though. If it doesn't exists, the default configuration will be applied. The code is architectured around 6 modules and about 10 classes. I encourage you to have a look at the files, they're pretty straightforward to understand. There is a lot of work left around the node-red code refactoring, dashboard ui improvements, better and clearer LED messages, OLED screen integration and finer control of the segmentation process, but this is quite good for now. Here is the topic lists for MQTT and the corresponding messages. - actuator : This topic adresses the stepper control thread No publication under this topic should happen from the python process - actuator/pump : Control of the pump The message is a json object {"action":"move", "direction":"FORWARD", "volume":10, "flowrate":1} to move 10mL forward at 1mL/min action can be "move" or "stop" Receive only - actuator/focus : Control of the focus stage The message is a json object, speed is optional {"action":"move", "direction":"UP", "distance":0.26, "speed":1} to move up 10mm action can be "move" or "stop" Receive only - imager/image : This topic adresses the imaging thread Is a json object with {"action":"image","sleep":5,"volume":1,"nb_frame":200} sleep in seconds, volume in mL Can also receive a config update message: {"action":"config","config":[...]} Can also receive a camera settings message: {"action":"settings","iso":100,"shutter_speed":40} Receive only - segmenter/segment : This topic adresses the segmenter process Is a json object with {"action":"segment"} Receive only - status : This topics sends feedback to Node-Red No publication or receive at this level - status/pump : State of the pump Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/focus : State of the focus stage Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/imager : State of the imager Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Completed or 12_11_15_0.1.jpg has been imaged. Publish only - status/segmenter : Status of the segmentation - status/segmenter/name - status/segmenter/object_id - status/segmenter/metric Here is the original commit history: * Extract python main.py from flow * Fix bug in server addresses These addresses should be the loopback device instead of the network address of the device. Using the loopback address will not necessitate to update the script when the network address changes. * clean up picamera import * changes to main python and flow: update MQTT requests address to localhost (bugfix) update streaming output address to nothing update main flow to remove python script references and location * Automatically initialise imaging led on startup to off state. * Add the ability to invert outputs of the motor We added a key to config.json "hardware_config" with a subkey "stepper_reverse". If this key is present in the config file and set to 1, the output of the motors are inversed (stepper2 becomes the pump motor and stepper1 the focus motor) * move all non main script to a subfolder * add __init__.py to package * light module rewrite * json cleanup and absolute path for config file * light.py forgot to import subprocess #oups * Add command to turn the leds off * Auto formatting of main.py I've used Black with default settings, see https://github.com/psf/black * First commit of stepper.py Pump parameters still needs to be checked and tuned. * addition of hardware details in config.json * Introduce hardware.json to replace the `hardware_config` of config.json * stepper.py: calibration, typos * creates the MQTT_Client class * pump_max_speed is now in ml/min to help readability * forgot to add self to the class def * addition of threading capabilities to stepper.py (UNTESTED) * mqtt: fix topic bug * remove counter * mqtt add doc about topics * stepper.py creates an "actuator/*/state" topic * stepper.py: rename mqtt_client to pump_client * mqtt.py: add details about topics * stepper.py: rename pump_client to actuator_client * topic was not split properly and a part was lost * switch to f-strings for mqtt.py * cosmetic update * stepper.py: folder name will be planktoscope change calls * hardware.json became more straightforward * stepper.py syntax bugs * stepper.py addition of a received stop command * stepper.py: update to max travel distance * stepper.py: several typos here * rename folder * main.py: reword to reflect folder rename * main.py: remove logic that has been moved to stepper.py and mqtt.py * main.py: update to add mqtt imaging client * mqtt.py: make command and args local to class and output more verbose * make stepper.py a class * main.py: instantiate stepper class and call it * main.py: name mqtt client * update to main.json to reflect main.py changes * fix bugs around pump control * update flows to latest version from Thibault * distance can be a small value, and definitevely should be a float. * unify mqtt topics * unify mqtt output in the main flow * first logger implementation, uses loguru * mqtt: add reason to on_connect * mqtt: add on_disconnect handler * stepper: add more logger calls for debug mainly * main: add levels for logger * imager.py: first move of the imager logic * imager: time import cleanup * imager: morphocut import cleanup * imager: skimage import cleanup * imager: finishing import cleanup * imager: Class creation - WIP Also provides a fix for #26 (see line 190). * imager: threading is needed for Condition() * streamer: get the streamer server its own file * imager: creates start_camera and get the server creation out * imager: subclass multiprocessing.Process * imager: get Pipeline creation its own function * imager: cleanup of self calls * main: code removal and corresponding calls to newly created classes * imager: various formatting changes * main: management of signal shutdown * add requirements.txt * mqtt: messages are now json objects Also, addition of a flag on receiving a new message * mqtt: make message private and add logic to synchronise * stepper: creates the stepper class * stepper: use the new class * stepper: uses the new logic * stepper: add the shutdown event * stepper: add shutdown method * main: add shutdown event * imager: graceful shutdown * stepper: nicer way of checking the Eevnt * self is a required first argument for a method in a class Especially if you use said class private members! * python: various typos and small errors in import * stepper: create mqtt client during init * stepper: instanciate the mqtt client inside run Otherwise it's not accessible from inside the loop. It's a PITA, more information at https://stackoverflow.com/questions/17172878/using-pythons-multiprocessing-process-class * stepper: little bugs and typos all around * mqtt: add shutdown method * mqtt: add connect in init * stepper: fix bugs, sanitize inputs * stepper: work on delay prediction improvements * stepper: json is mean, double quote are mandatory inside * mqtt: add details about message exchanged * imager: first implementation of json messages * main.json: add new tab for RPi management + json for payloads * imager: add state_machine class * stepper: publish last will * imager: major refactor * main: make streaming server process a daemon * mqtt: insert debug statement on close * main: reorder imports * imager: make it work! Reinsert the streaming server logic in there, because there is a problem with the synchronisation part otherwise. Also, eventually, StreamingOuput() will have to be made not global Final very critical learning: it's super duper important to make sure the memory split is at least 256Meg for the GPU. Chaos ensues otherwise * main: changes to accomodate the streamer/imager fusino * imager_state_machine: insert states transition description * stepper: cleanup of code * segmenter: creation of the class * python: include segmenter changes * remove unused files * stepper: check existence of hardware.json * main.json: changes to reflect the python script evolution * remove unecessary TODOs and add some others * main: add check for config and directories * imager: update_config is implemented and we have better management of directories now * segmenter: now work recursively in all folders * flow: the configuration is now sent via mqtt * segmenter: better manage pipeline error * segmenter: declaration of archive_fn in init * imager: small bugs and typos * main: add uniqueID output * imager: add the camera settings message We can now update the ISO, shutter speed and resolution from Node-Red * package.json: update dependencies
2020-09-28 11:05:27 +02:00
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Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
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Extraction and refactor of the python code from node-red flow The rationale for this rewrite is to improve the readability, the modularity, the reliability and the future-proofing of the main python script. All in all, this is now 124 commits that are going to be squashed and merged together, spanning more than two weeks of development and testing. Please test away this release and break things. An upgrading guide will be published in the coming days, along with a new image for people to use if they don't want to upgrade on their own. Read along if you want to know all the goodies! As a starter, the python script was extracted from the main flow, and now lives in its own files at `PlantonScope/scripts/*`. We set up the auto formatting of the code by using [Black](https://github.com/psf/black). This make the code clearer and uniform. We are using the default settings, so if you just install Black and set your editor to format on save using it, you should be good to go. The code is separated in four main processes, each with a specific set of responsibilities: - The main process controls all the others, starts everything up and cleans up on shutdown - The stepper process manages the stepper movements. It's now possible to have simultaneous movements of both motors (this closes #38 ). - The imager process controls the camera and the streaming server via a state machine. - The segmenter process manages the segmentation and its outputs. The segmentation happens recursively in all folders in `/home/pi/PlanktonScope/img/`. Each folder has its own output archive, and bug #26 is now closed. Those processes communicates together using MQTT and json messages. Each message is adressed to one topic. The high level topic controls which process receives the message. The details of each topic is at the end of this commit message. Every imaging sessions has now its own folder, under the `img` root. Metadata are saved individually for every session, in a JSON file in the same directory as the pictures. The configuration is not parsed from `config.json` anymore and passed directly through MQTT messages to the concerned process. A new configuration file has been created: `hardware.json`. This file contains information related to your specific hardware configuration. You can choose to reverse the connection of the motors for example, but you can also define specific speed limits and steps number for your pump and focus stage. This will make it easier for people who wants to experiment with different kind of hardware. It's not necessary to have this file though. If it doesn't exists, the default configuration will be applied. The code is architectured around 6 modules and about 10 classes. I encourage you to have a look at the files, they're pretty straightforward to understand. There is a lot of work left around the node-red code refactoring, dashboard ui improvements, better and clearer LED messages, OLED screen integration and finer control of the segmentation process, but this is quite good for now. Here is the topic lists for MQTT and the corresponding messages. - actuator : This topic adresses the stepper control thread No publication under this topic should happen from the python process - actuator/pump : Control of the pump The message is a json object {"action":"move", "direction":"FORWARD", "volume":10, "flowrate":1} to move 10mL forward at 1mL/min action can be "move" or "stop" Receive only - actuator/focus : Control of the focus stage The message is a json object, speed is optional {"action":"move", "direction":"UP", "distance":0.26, "speed":1} to move up 10mm action can be "move" or "stop" Receive only - imager/image : This topic adresses the imaging thread Is a json object with {"action":"image","sleep":5,"volume":1,"nb_frame":200} sleep in seconds, volume in mL Can also receive a config update message: {"action":"config","config":[...]} Can also receive a camera settings message: {"action":"settings","iso":100,"shutter_speed":40} Receive only - segmenter/segment : This topic adresses the segmenter process Is a json object with {"action":"segment"} Receive only - status : This topics sends feedback to Node-Red No publication or receive at this level - status/pump : State of the pump Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/focus : State of the focus stage Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/imager : State of the imager Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Completed or 12_11_15_0.1.jpg has been imaged. Publish only - status/segmenter : Status of the segmentation - status/segmenter/name - status/segmenter/object_id - status/segmenter/metric Here is the original commit history: * Extract python main.py from flow * Fix bug in server addresses These addresses should be the loopback device instead of the network address of the device. Using the loopback address will not necessitate to update the script when the network address changes. * clean up picamera import * changes to main python and flow: update MQTT requests address to localhost (bugfix) update streaming output address to nothing update main flow to remove python script references and location * Automatically initialise imaging led on startup to off state. * Add the ability to invert outputs of the motor We added a key to config.json "hardware_config" with a subkey "stepper_reverse". If this key is present in the config file and set to 1, the output of the motors are inversed (stepper2 becomes the pump motor and stepper1 the focus motor) * move all non main script to a subfolder * add __init__.py to package * light module rewrite * json cleanup and absolute path for config file * light.py forgot to import subprocess #oups * Add command to turn the leds off * Auto formatting of main.py I've used Black with default settings, see https://github.com/psf/black * First commit of stepper.py Pump parameters still needs to be checked and tuned. * addition of hardware details in config.json * Introduce hardware.json to replace the `hardware_config` of config.json * stepper.py: calibration, typos * creates the MQTT_Client class * pump_max_speed is now in ml/min to help readability * forgot to add self to the class def * addition of threading capabilities to stepper.py (UNTESTED) * mqtt: fix topic bug * remove counter * mqtt add doc about topics * stepper.py creates an "actuator/*/state" topic * stepper.py: rename mqtt_client to pump_client * mqtt.py: add details about topics * stepper.py: rename pump_client to actuator_client * topic was not split properly and a part was lost * switch to f-strings for mqtt.py * cosmetic update * stepper.py: folder name will be planktoscope change calls * hardware.json became more straightforward * stepper.py syntax bugs * stepper.py addition of a received stop command * stepper.py: update to max travel distance * stepper.py: several typos here * rename folder * main.py: reword to reflect folder rename * main.py: remove logic that has been moved to stepper.py and mqtt.py * main.py: update to add mqtt imaging client * mqtt.py: make command and args local to class and output more verbose * make stepper.py a class * main.py: instantiate stepper class and call it * main.py: name mqtt client * update to main.json to reflect main.py changes * fix bugs around pump control * update flows to latest version from Thibault * distance can be a small value, and definitevely should be a float. * unify mqtt topics * unify mqtt output in the main flow * first logger implementation, uses loguru * mqtt: add reason to on_connect * mqtt: add on_disconnect handler * stepper: add more logger calls for debug mainly * main: add levels for logger * imager.py: first move of the imager logic * imager: time import cleanup * imager: morphocut import cleanup * imager: skimage import cleanup * imager: finishing import cleanup * imager: Class creation - WIP Also provides a fix for #26 (see line 190). * imager: threading is needed for Condition() * streamer: get the streamer server its own file * imager: creates start_camera and get the server creation out * imager: subclass multiprocessing.Process * imager: get Pipeline creation its own function * imager: cleanup of self calls * main: code removal and corresponding calls to newly created classes * imager: various formatting changes * main: management of signal shutdown * add requirements.txt * mqtt: messages are now json objects Also, addition of a flag on receiving a new message * mqtt: make message private and add logic to synchronise * stepper: creates the stepper class * stepper: use the new class * stepper: uses the new logic * stepper: add the shutdown event * stepper: add shutdown method * main: add shutdown event * imager: graceful shutdown * stepper: nicer way of checking the Eevnt * self is a required first argument for a method in a class Especially if you use said class private members! * python: various typos and small errors in import * stepper: create mqtt client during init * stepper: instanciate the mqtt client inside run Otherwise it's not accessible from inside the loop. It's a PITA, more information at https://stackoverflow.com/questions/17172878/using-pythons-multiprocessing-process-class * stepper: little bugs and typos all around * mqtt: add shutdown method * mqtt: add connect in init * stepper: fix bugs, sanitize inputs * stepper: work on delay prediction improvements * stepper: json is mean, double quote are mandatory inside * mqtt: add details about message exchanged * imager: first implementation of json messages * main.json: add new tab for RPi management + json for payloads * imager: add state_machine class * stepper: publish last will * imager: major refactor * main: make streaming server process a daemon * mqtt: insert debug statement on close * main: reorder imports * imager: make it work! Reinsert the streaming server logic in there, because there is a problem with the synchronisation part otherwise. Also, eventually, StreamingOuput() will have to be made not global Final very critical learning: it's super duper important to make sure the memory split is at least 256Meg for the GPU. Chaos ensues otherwise * main: changes to accomodate the streamer/imager fusino * imager_state_machine: insert states transition description * stepper: cleanup of code * segmenter: creation of the class * python: include segmenter changes * remove unused files * stepper: check existence of hardware.json * main.json: changes to reflect the python script evolution * remove unecessary TODOs and add some others * main: add check for config and directories * imager: update_config is implemented and we have better management of directories now * segmenter: now work recursively in all folders * flow: the configuration is now sent via mqtt * segmenter: better manage pipeline error * segmenter: declaration of archive_fn in init * imager: small bugs and typos * main: add uniqueID output * imager: add the camera settings message We can now update the ISO, shutter speed and resolution from Node-Red * package.json: update dependencies
2020-09-28 11:05:27 +02:00
"wires": [
[
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"afa9f4b.2e77988",
"39edf8d2.bc92e8",
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Extraction and refactor of the python code from node-red flow The rationale for this rewrite is to improve the readability, the modularity, the reliability and the future-proofing of the main python script. All in all, this is now 124 commits that are going to be squashed and merged together, spanning more than two weeks of development and testing. Please test away this release and break things. An upgrading guide will be published in the coming days, along with a new image for people to use if they don't want to upgrade on their own. Read along if you want to know all the goodies! As a starter, the python script was extracted from the main flow, and now lives in its own files at `PlantonScope/scripts/*`. We set up the auto formatting of the code by using [Black](https://github.com/psf/black). This make the code clearer and uniform. We are using the default settings, so if you just install Black and set your editor to format on save using it, you should be good to go. The code is separated in four main processes, each with a specific set of responsibilities: - The main process controls all the others, starts everything up and cleans up on shutdown - The stepper process manages the stepper movements. It's now possible to have simultaneous movements of both motors (this closes #38 ). - The imager process controls the camera and the streaming server via a state machine. - The segmenter process manages the segmentation and its outputs. The segmentation happens recursively in all folders in `/home/pi/PlanktonScope/img/`. Each folder has its own output archive, and bug #26 is now closed. Those processes communicates together using MQTT and json messages. Each message is adressed to one topic. The high level topic controls which process receives the message. The details of each topic is at the end of this commit message. Every imaging sessions has now its own folder, under the `img` root. Metadata are saved individually for every session, in a JSON file in the same directory as the pictures. The configuration is not parsed from `config.json` anymore and passed directly through MQTT messages to the concerned process. A new configuration file has been created: `hardware.json`. This file contains information related to your specific hardware configuration. You can choose to reverse the connection of the motors for example, but you can also define specific speed limits and steps number for your pump and focus stage. This will make it easier for people who wants to experiment with different kind of hardware. It's not necessary to have this file though. If it doesn't exists, the default configuration will be applied. The code is architectured around 6 modules and about 10 classes. I encourage you to have a look at the files, they're pretty straightforward to understand. There is a lot of work left around the node-red code refactoring, dashboard ui improvements, better and clearer LED messages, OLED screen integration and finer control of the segmentation process, but this is quite good for now. Here is the topic lists for MQTT and the corresponding messages. - actuator : This topic adresses the stepper control thread No publication under this topic should happen from the python process - actuator/pump : Control of the pump The message is a json object {"action":"move", "direction":"FORWARD", "volume":10, "flowrate":1} to move 10mL forward at 1mL/min action can be "move" or "stop" Receive only - actuator/focus : Control of the focus stage The message is a json object, speed is optional {"action":"move", "direction":"UP", "distance":0.26, "speed":1} to move up 10mm action can be "move" or "stop" Receive only - imager/image : This topic adresses the imaging thread Is a json object with {"action":"image","sleep":5,"volume":1,"nb_frame":200} sleep in seconds, volume in mL Can also receive a config update message: {"action":"config","config":[...]} Can also receive a camera settings message: {"action":"settings","iso":100,"shutter_speed":40} Receive only - segmenter/segment : This topic adresses the segmenter process Is a json object with {"action":"segment"} Receive only - status : This topics sends feedback to Node-Red No publication or receive at this level - status/pump : State of the pump Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/focus : State of the focus stage Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/imager : State of the imager Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Completed or 12_11_15_0.1.jpg has been imaged. Publish only - status/segmenter : Status of the segmentation - status/segmenter/name - status/segmenter/object_id - status/segmenter/metric Here is the original commit history: * Extract python main.py from flow * Fix bug in server addresses These addresses should be the loopback device instead of the network address of the device. Using the loopback address will not necessitate to update the script when the network address changes. * clean up picamera import * changes to main python and flow: update MQTT requests address to localhost (bugfix) update streaming output address to nothing update main flow to remove python script references and location * Automatically initialise imaging led on startup to off state. * Add the ability to invert outputs of the motor We added a key to config.json "hardware_config" with a subkey "stepper_reverse". If this key is present in the config file and set to 1, the output of the motors are inversed (stepper2 becomes the pump motor and stepper1 the focus motor) * move all non main script to a subfolder * add __init__.py to package * light module rewrite * json cleanup and absolute path for config file * light.py forgot to import subprocess #oups * Add command to turn the leds off * Auto formatting of main.py I've used Black with default settings, see https://github.com/psf/black * First commit of stepper.py Pump parameters still needs to be checked and tuned. * addition of hardware details in config.json * Introduce hardware.json to replace the `hardware_config` of config.json * stepper.py: calibration, typos * creates the MQTT_Client class * pump_max_speed is now in ml/min to help readability * forgot to add self to the class def * addition of threading capabilities to stepper.py (UNTESTED) * mqtt: fix topic bug * remove counter * mqtt add doc about topics * stepper.py creates an "actuator/*/state" topic * stepper.py: rename mqtt_client to pump_client * mqtt.py: add details about topics * stepper.py: rename pump_client to actuator_client * topic was not split properly and a part was lost * switch to f-strings for mqtt.py * cosmetic update * stepper.py: folder name will be planktoscope change calls * hardware.json became more straightforward * stepper.py syntax bugs * stepper.py addition of a received stop command * stepper.py: update to max travel distance * stepper.py: several typos here * rename folder * main.py: reword to reflect folder rename * main.py: remove logic that has been moved to stepper.py and mqtt.py * main.py: update to add mqtt imaging client * mqtt.py: make command and args local to class and output more verbose * make stepper.py a class * main.py: instantiate stepper class and call it * main.py: name mqtt client * update to main.json to reflect main.py changes * fix bugs around pump control * update flows to latest version from Thibault * distance can be a small value, and definitevely should be a float. * unify mqtt topics * unify mqtt output in the main flow * first logger implementation, uses loguru * mqtt: add reason to on_connect * mqtt: add on_disconnect handler * stepper: add more logger calls for debug mainly * main: add levels for logger * imager.py: first move of the imager logic * imager: time import cleanup * imager: morphocut import cleanup * imager: skimage import cleanup * imager: finishing import cleanup * imager: Class creation - WIP Also provides a fix for #26 (see line 190). * imager: threading is needed for Condition() * streamer: get the streamer server its own file * imager: creates start_camera and get the server creation out * imager: subclass multiprocessing.Process * imager: get Pipeline creation its own function * imager: cleanup of self calls * main: code removal and corresponding calls to newly created classes * imager: various formatting changes * main: management of signal shutdown * add requirements.txt * mqtt: messages are now json objects Also, addition of a flag on receiving a new message * mqtt: make message private and add logic to synchronise * stepper: creates the stepper class * stepper: use the new class * stepper: uses the new logic * stepper: add the shutdown event * stepper: add shutdown method * main: add shutdown event * imager: graceful shutdown * stepper: nicer way of checking the Eevnt * self is a required first argument for a method in a class Especially if you use said class private members! * python: various typos and small errors in import * stepper: create mqtt client during init * stepper: instanciate the mqtt client inside run Otherwise it's not accessible from inside the loop. It's a PITA, more information at https://stackoverflow.com/questions/17172878/using-pythons-multiprocessing-process-class * stepper: little bugs and typos all around * mqtt: add shutdown method * mqtt: add connect in init * stepper: fix bugs, sanitize inputs * stepper: work on delay prediction improvements * stepper: json is mean, double quote are mandatory inside * mqtt: add details about message exchanged * imager: first implementation of json messages * main.json: add new tab for RPi management + json for payloads * imager: add state_machine class * stepper: publish last will * imager: major refactor * main: make streaming server process a daemon * mqtt: insert debug statement on close * main: reorder imports * imager: make it work! Reinsert the streaming server logic in there, because there is a problem with the synchronisation part otherwise. Also, eventually, StreamingOuput() will have to be made not global Final very critical learning: it's super duper important to make sure the memory split is at least 256Meg for the GPU. Chaos ensues otherwise * main: changes to accomodate the streamer/imager fusino * imager_state_machine: insert states transition description * stepper: cleanup of code * segmenter: creation of the class * python: include segmenter changes * remove unused files * stepper: check existence of hardware.json * main.json: changes to reflect the python script evolution * remove unecessary TODOs and add some others * main: add check for config and directories * imager: update_config is implemented and we have better management of directories now * segmenter: now work recursively in all folders * flow: the configuration is now sent via mqtt * segmenter: better manage pipeline error * segmenter: declaration of archive_fn in init * imager: small bugs and typos * main: add uniqueID output * imager: add the camera settings message We can now update the ISO, shutter speed and resolution from Node-Red * package.json: update dependencies
2020-09-28 11:05:27 +02:00
]
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},
{
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"id": "39edf8d2.bc92e8",
"type": "function",
"z": "1371dec5.76e671",
"name": "SIGTERM",
"func": "msg.kill = \"SIGTERM\";\nreturn msg;",
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"y": 900,
Extraction and refactor of the python code from node-red flow The rationale for this rewrite is to improve the readability, the modularity, the reliability and the future-proofing of the main python script. All in all, this is now 124 commits that are going to be squashed and merged together, spanning more than two weeks of development and testing. Please test away this release and break things. An upgrading guide will be published in the coming days, along with a new image for people to use if they don't want to upgrade on their own. Read along if you want to know all the goodies! As a starter, the python script was extracted from the main flow, and now lives in its own files at `PlantonScope/scripts/*`. We set up the auto formatting of the code by using [Black](https://github.com/psf/black). This make the code clearer and uniform. We are using the default settings, so if you just install Black and set your editor to format on save using it, you should be good to go. The code is separated in four main processes, each with a specific set of responsibilities: - The main process controls all the others, starts everything up and cleans up on shutdown - The stepper process manages the stepper movements. It's now possible to have simultaneous movements of both motors (this closes #38 ). - The imager process controls the camera and the streaming server via a state machine. - The segmenter process manages the segmentation and its outputs. The segmentation happens recursively in all folders in `/home/pi/PlanktonScope/img/`. Each folder has its own output archive, and bug #26 is now closed. Those processes communicates together using MQTT and json messages. Each message is adressed to one topic. The high level topic controls which process receives the message. The details of each topic is at the end of this commit message. Every imaging sessions has now its own folder, under the `img` root. Metadata are saved individually for every session, in a JSON file in the same directory as the pictures. The configuration is not parsed from `config.json` anymore and passed directly through MQTT messages to the concerned process. A new configuration file has been created: `hardware.json`. This file contains information related to your specific hardware configuration. You can choose to reverse the connection of the motors for example, but you can also define specific speed limits and steps number for your pump and focus stage. This will make it easier for people who wants to experiment with different kind of hardware. It's not necessary to have this file though. If it doesn't exists, the default configuration will be applied. The code is architectured around 6 modules and about 10 classes. I encourage you to have a look at the files, they're pretty straightforward to understand. There is a lot of work left around the node-red code refactoring, dashboard ui improvements, better and clearer LED messages, OLED screen integration and finer control of the segmentation process, but this is quite good for now. Here is the topic lists for MQTT and the corresponding messages. - actuator : This topic adresses the stepper control thread No publication under this topic should happen from the python process - actuator/pump : Control of the pump The message is a json object {"action":"move", "direction":"FORWARD", "volume":10, "flowrate":1} to move 10mL forward at 1mL/min action can be "move" or "stop" Receive only - actuator/focus : Control of the focus stage The message is a json object, speed is optional {"action":"move", "direction":"UP", "distance":0.26, "speed":1} to move up 10mm action can be "move" or "stop" Receive only - imager/image : This topic adresses the imaging thread Is a json object with {"action":"image","sleep":5,"volume":1,"nb_frame":200} sleep in seconds, volume in mL Can also receive a config update message: {"action":"config","config":[...]} Can also receive a camera settings message: {"action":"settings","iso":100,"shutter_speed":40} Receive only - segmenter/segment : This topic adresses the segmenter process Is a json object with {"action":"segment"} Receive only - status : This topics sends feedback to Node-Red No publication or receive at this level - status/pump : State of the pump Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/focus : State of the focus stage Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/imager : State of the imager Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Completed or 12_11_15_0.1.jpg has been imaged. Publish only - status/segmenter : Status of the segmentation - status/segmenter/name - status/segmenter/object_id - status/segmenter/metric Here is the original commit history: * Extract python main.py from flow * Fix bug in server addresses These addresses should be the loopback device instead of the network address of the device. Using the loopback address will not necessitate to update the script when the network address changes. * clean up picamera import * changes to main python and flow: update MQTT requests address to localhost (bugfix) update streaming output address to nothing update main flow to remove python script references and location * Automatically initialise imaging led on startup to off state. * Add the ability to invert outputs of the motor We added a key to config.json "hardware_config" with a subkey "stepper_reverse". If this key is present in the config file and set to 1, the output of the motors are inversed (stepper2 becomes the pump motor and stepper1 the focus motor) * move all non main script to a subfolder * add __init__.py to package * light module rewrite * json cleanup and absolute path for config file * light.py forgot to import subprocess #oups * Add command to turn the leds off * Auto formatting of main.py I've used Black with default settings, see https://github.com/psf/black * First commit of stepper.py Pump parameters still needs to be checked and tuned. * addition of hardware details in config.json * Introduce hardware.json to replace the `hardware_config` of config.json * stepper.py: calibration, typos * creates the MQTT_Client class * pump_max_speed is now in ml/min to help readability * forgot to add self to the class def * addition of threading capabilities to stepper.py (UNTESTED) * mqtt: fix topic bug * remove counter * mqtt add doc about topics * stepper.py creates an "actuator/*/state" topic * stepper.py: rename mqtt_client to pump_client * mqtt.py: add details about topics * stepper.py: rename pump_client to actuator_client * topic was not split properly and a part was lost * switch to f-strings for mqtt.py * cosmetic update * stepper.py: folder name will be planktoscope change calls * hardware.json became more straightforward * stepper.py syntax bugs * stepper.py addition of a received stop command * stepper.py: update to max travel distance * stepper.py: several typos here * rename folder * main.py: reword to reflect folder rename * main.py: remove logic that has been moved to stepper.py and mqtt.py * main.py: update to add mqtt imaging client * mqtt.py: make command and args local to class and output more verbose * make stepper.py a class * main.py: instantiate stepper class and call it * main.py: name mqtt client * update to main.json to reflect main.py changes * fix bugs around pump control * update flows to latest version from Thibault * distance can be a small value, and definitevely should be a float. * unify mqtt topics * unify mqtt output in the main flow * first logger implementation, uses loguru * mqtt: add reason to on_connect * mqtt: add on_disconnect handler * stepper: add more logger calls for debug mainly * main: add levels for logger * imager.py: first move of the imager logic * imager: time import cleanup * imager: morphocut import cleanup * imager: skimage import cleanup * imager: finishing import cleanup * imager: Class creation - WIP Also provides a fix for #26 (see line 190). * imager: threading is needed for Condition() * streamer: get the streamer server its own file * imager: creates start_camera and get the server creation out * imager: subclass multiprocessing.Process * imager: get Pipeline creation its own function * imager: cleanup of self calls * main: code removal and corresponding calls to newly created classes * imager: various formatting changes * main: management of signal shutdown * add requirements.txt * mqtt: messages are now json objects Also, addition of a flag on receiving a new message * mqtt: make message private and add logic to synchronise * stepper: creates the stepper class * stepper: use the new class * stepper: uses the new logic * stepper: add the shutdown event * stepper: add shutdown method * main: add shutdown event * imager: graceful shutdown * stepper: nicer way of checking the Eevnt * self is a required first argument for a method in a class Especially if you use said class private members! * python: various typos and small errors in import * stepper: create mqtt client during init * stepper: instanciate the mqtt client inside run Otherwise it's not accessible from inside the loop. It's a PITA, more information at https://stackoverflow.com/questions/17172878/using-pythons-multiprocessing-process-class * stepper: little bugs and typos all around * mqtt: add shutdown method * mqtt: add connect in init * stepper: fix bugs, sanitize inputs * stepper: work on delay prediction improvements * stepper: json is mean, double quote are mandatory inside * mqtt: add details about message exchanged * imager: first implementation of json messages * main.json: add new tab for RPi management + json for payloads * imager: add state_machine class * stepper: publish last will * imager: major refactor * main: make streaming server process a daemon * mqtt: insert debug statement on close * main: reorder imports * imager: make it work! Reinsert the streaming server logic in there, because there is a problem with the synchronisation part otherwise. Also, eventually, StreamingOuput() will have to be made not global Final very critical learning: it's super duper important to make sure the memory split is at least 256Meg for the GPU. Chaos ensues otherwise * main: changes to accomodate the streamer/imager fusino * imager_state_machine: insert states transition description * stepper: cleanup of code * segmenter: creation of the class * python: include segmenter changes * remove unused files * stepper: check existence of hardware.json * main.json: changes to reflect the python script evolution * remove unecessary TODOs and add some others * main: add check for config and directories * imager: update_config is implemented and we have better management of directories now * segmenter: now work recursively in all folders * flow: the configuration is now sent via mqtt * segmenter: better manage pipeline error * segmenter: declaration of archive_fn in init * imager: small bugs and typos * main: add uniqueID output * imager: add the camera settings message We can now update the ISO, shutter speed and resolution from Node-Red * package.json: update dependencies
2020-09-28 11:05:27 +02:00
"wires": [
[
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"9998aa86.74bb",
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Extraction and refactor of the python code from node-red flow The rationale for this rewrite is to improve the readability, the modularity, the reliability and the future-proofing of the main python script. All in all, this is now 124 commits that are going to be squashed and merged together, spanning more than two weeks of development and testing. Please test away this release and break things. An upgrading guide will be published in the coming days, along with a new image for people to use if they don't want to upgrade on their own. Read along if you want to know all the goodies! As a starter, the python script was extracted from the main flow, and now lives in its own files at `PlantonScope/scripts/*`. We set up the auto formatting of the code by using [Black](https://github.com/psf/black). This make the code clearer and uniform. We are using the default settings, so if you just install Black and set your editor to format on save using it, you should be good to go. The code is separated in four main processes, each with a specific set of responsibilities: - The main process controls all the others, starts everything up and cleans up on shutdown - The stepper process manages the stepper movements. It's now possible to have simultaneous movements of both motors (this closes #38 ). - The imager process controls the camera and the streaming server via a state machine. - The segmenter process manages the segmentation and its outputs. The segmentation happens recursively in all folders in `/home/pi/PlanktonScope/img/`. Each folder has its own output archive, and bug #26 is now closed. Those processes communicates together using MQTT and json messages. Each message is adressed to one topic. The high level topic controls which process receives the message. The details of each topic is at the end of this commit message. Every imaging sessions has now its own folder, under the `img` root. Metadata are saved individually for every session, in a JSON file in the same directory as the pictures. The configuration is not parsed from `config.json` anymore and passed directly through MQTT messages to the concerned process. A new configuration file has been created: `hardware.json`. This file contains information related to your specific hardware configuration. You can choose to reverse the connection of the motors for example, but you can also define specific speed limits and steps number for your pump and focus stage. This will make it easier for people who wants to experiment with different kind of hardware. It's not necessary to have this file though. If it doesn't exists, the default configuration will be applied. The code is architectured around 6 modules and about 10 classes. I encourage you to have a look at the files, they're pretty straightforward to understand. There is a lot of work left around the node-red code refactoring, dashboard ui improvements, better and clearer LED messages, OLED screen integration and finer control of the segmentation process, but this is quite good for now. Here is the topic lists for MQTT and the corresponding messages. - actuator : This topic adresses the stepper control thread No publication under this topic should happen from the python process - actuator/pump : Control of the pump The message is a json object {"action":"move", "direction":"FORWARD", "volume":10, "flowrate":1} to move 10mL forward at 1mL/min action can be "move" or "stop" Receive only - actuator/focus : Control of the focus stage The message is a json object, speed is optional {"action":"move", "direction":"UP", "distance":0.26, "speed":1} to move up 10mm action can be "move" or "stop" Receive only - imager/image : This topic adresses the imaging thread Is a json object with {"action":"image","sleep":5,"volume":1,"nb_frame":200} sleep in seconds, volume in mL Can also receive a config update message: {"action":"config","config":[...]} Can also receive a camera settings message: {"action":"settings","iso":100,"shutter_speed":40} Receive only - segmenter/segment : This topic adresses the segmenter process Is a json object with {"action":"segment"} Receive only - status : This topics sends feedback to Node-Red No publication or receive at this level - status/pump : State of the pump Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/focus : State of the focus stage Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/imager : State of the imager Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Completed or 12_11_15_0.1.jpg has been imaged. Publish only - status/segmenter : Status of the segmentation - status/segmenter/name - status/segmenter/object_id - status/segmenter/metric Here is the original commit history: * Extract python main.py from flow * Fix bug in server addresses These addresses should be the loopback device instead of the network address of the device. Using the loopback address will not necessitate to update the script when the network address changes. * clean up picamera import * changes to main python and flow: update MQTT requests address to localhost (bugfix) update streaming output address to nothing update main flow to remove python script references and location * Automatically initialise imaging led on startup to off state. * Add the ability to invert outputs of the motor We added a key to config.json "hardware_config" with a subkey "stepper_reverse". If this key is present in the config file and set to 1, the output of the motors are inversed (stepper2 becomes the pump motor and stepper1 the focus motor) * move all non main script to a subfolder * add __init__.py to package * light module rewrite * json cleanup and absolute path for config file * light.py forgot to import subprocess #oups * Add command to turn the leds off * Auto formatting of main.py I've used Black with default settings, see https://github.com/psf/black * First commit of stepper.py Pump parameters still needs to be checked and tuned. * addition of hardware details in config.json * Introduce hardware.json to replace the `hardware_config` of config.json * stepper.py: calibration, typos * creates the MQTT_Client class * pump_max_speed is now in ml/min to help readability * forgot to add self to the class def * addition of threading capabilities to stepper.py (UNTESTED) * mqtt: fix topic bug * remove counter * mqtt add doc about topics * stepper.py creates an "actuator/*/state" topic * stepper.py: rename mqtt_client to pump_client * mqtt.py: add details about topics * stepper.py: rename pump_client to actuator_client * topic was not split properly and a part was lost * switch to f-strings for mqtt.py * cosmetic update * stepper.py: folder name will be planktoscope change calls * hardware.json became more straightforward * stepper.py syntax bugs * stepper.py addition of a received stop command * stepper.py: update to max travel distance * stepper.py: several typos here * rename folder * main.py: reword to reflect folder rename * main.py: remove logic that has been moved to stepper.py and mqtt.py * main.py: update to add mqtt imaging client * mqtt.py: make command and args local to class and output more verbose * make stepper.py a class * main.py: instantiate stepper class and call it * main.py: name mqtt client * update to main.json to reflect main.py changes * fix bugs around pump control * update flows to latest version from Thibault * distance can be a small value, and definitevely should be a float. * unify mqtt topics * unify mqtt output in the main flow * first logger implementation, uses loguru * mqtt: add reason to on_connect * mqtt: add on_disconnect handler * stepper: add more logger calls for debug mainly * main: add levels for logger * imager.py: first move of the imager logic * imager: time import cleanup * imager: morphocut import cleanup * imager: skimage import cleanup * imager: finishing import cleanup * imager: Class creation - WIP Also provides a fix for #26 (see line 190). * imager: threading is needed for Condition() * streamer: get the streamer server its own file * imager: creates start_camera and get the server creation out * imager: subclass multiprocessing.Process * imager: get Pipeline creation its own function * imager: cleanup of self calls * main: code removal and corresponding calls to newly created classes * imager: various formatting changes * main: management of signal shutdown * add requirements.txt * mqtt: messages are now json objects Also, addition of a flag on receiving a new message * mqtt: make message private and add logic to synchronise * stepper: creates the stepper class * stepper: use the new class * stepper: uses the new logic * stepper: add the shutdown event * stepper: add shutdown method * main: add shutdown event * imager: graceful shutdown * stepper: nicer way of checking the Eevnt * self is a required first argument for a method in a class Especially if you use said class private members! * python: various typos and small errors in import * stepper: create mqtt client during init * stepper: instanciate the mqtt client inside run Otherwise it's not accessible from inside the loop. It's a PITA, more information at https://stackoverflow.com/questions/17172878/using-pythons-multiprocessing-process-class * stepper: little bugs and typos all around * mqtt: add shutdown method * mqtt: add connect in init * stepper: fix bugs, sanitize inputs * stepper: work on delay prediction improvements * stepper: json is mean, double quote are mandatory inside * mqtt: add details about message exchanged * imager: first implementation of json messages * main.json: add new tab for RPi management + json for payloads * imager: add state_machine class * stepper: publish last will * imager: major refactor * main: make streaming server process a daemon * mqtt: insert debug statement on close * main: reorder imports * imager: make it work! Reinsert the streaming server logic in there, because there is a problem with the synchronisation part otherwise. Also, eventually, StreamingOuput() will have to be made not global Final very critical learning: it's super duper important to make sure the memory split is at least 256Meg for the GPU. Chaos ensues otherwise * main: changes to accomodate the streamer/imager fusino * imager_state_machine: insert states transition description * stepper: cleanup of code * segmenter: creation of the class * python: include segmenter changes * remove unused files * stepper: check existence of hardware.json * main.json: changes to reflect the python script evolution * remove unecessary TODOs and add some others * main: add check for config and directories * imager: update_config is implemented and we have better management of directories now * segmenter: now work recursively in all folders * flow: the configuration is now sent via mqtt * segmenter: better manage pipeline error * segmenter: declaration of archive_fn in init * imager: small bugs and typos * main: add uniqueID output * imager: add the camera settings message We can now update the ISO, shutter speed and resolution from Node-Red * package.json: update dependencies
2020-09-28 11:05:27 +02:00
]
]
},
{
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"id": "de4ba211.e1d3f",
"type": "debug",
"z": "1371dec5.76e671",
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"active": true,
"tosidebar": true,
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"complete": "payload",
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Extraction and refactor of the python code from node-red flow The rationale for this rewrite is to improve the readability, the modularity, the reliability and the future-proofing of the main python script. All in all, this is now 124 commits that are going to be squashed and merged together, spanning more than two weeks of development and testing. Please test away this release and break things. An upgrading guide will be published in the coming days, along with a new image for people to use if they don't want to upgrade on their own. Read along if you want to know all the goodies! As a starter, the python script was extracted from the main flow, and now lives in its own files at `PlantonScope/scripts/*`. We set up the auto formatting of the code by using [Black](https://github.com/psf/black). This make the code clearer and uniform. We are using the default settings, so if you just install Black and set your editor to format on save using it, you should be good to go. The code is separated in four main processes, each with a specific set of responsibilities: - The main process controls all the others, starts everything up and cleans up on shutdown - The stepper process manages the stepper movements. It's now possible to have simultaneous movements of both motors (this closes #38 ). - The imager process controls the camera and the streaming server via a state machine. - The segmenter process manages the segmentation and its outputs. The segmentation happens recursively in all folders in `/home/pi/PlanktonScope/img/`. Each folder has its own output archive, and bug #26 is now closed. Those processes communicates together using MQTT and json messages. Each message is adressed to one topic. The high level topic controls which process receives the message. The details of each topic is at the end of this commit message. Every imaging sessions has now its own folder, under the `img` root. Metadata are saved individually for every session, in a JSON file in the same directory as the pictures. The configuration is not parsed from `config.json` anymore and passed directly through MQTT messages to the concerned process. A new configuration file has been created: `hardware.json`. This file contains information related to your specific hardware configuration. You can choose to reverse the connection of the motors for example, but you can also define specific speed limits and steps number for your pump and focus stage. This will make it easier for people who wants to experiment with different kind of hardware. It's not necessary to have this file though. If it doesn't exists, the default configuration will be applied. The code is architectured around 6 modules and about 10 classes. I encourage you to have a look at the files, they're pretty straightforward to understand. There is a lot of work left around the node-red code refactoring, dashboard ui improvements, better and clearer LED messages, OLED screen integration and finer control of the segmentation process, but this is quite good for now. Here is the topic lists for MQTT and the corresponding messages. - actuator : This topic adresses the stepper control thread No publication under this topic should happen from the python process - actuator/pump : Control of the pump The message is a json object {"action":"move", "direction":"FORWARD", "volume":10, "flowrate":1} to move 10mL forward at 1mL/min action can be "move" or "stop" Receive only - actuator/focus : Control of the focus stage The message is a json object, speed is optional {"action":"move", "direction":"UP", "distance":0.26, "speed":1} to move up 10mm action can be "move" or "stop" Receive only - imager/image : This topic adresses the imaging thread Is a json object with {"action":"image","sleep":5,"volume":1,"nb_frame":200} sleep in seconds, volume in mL Can also receive a config update message: {"action":"config","config":[...]} Can also receive a camera settings message: {"action":"settings","iso":100,"shutter_speed":40} Receive only - segmenter/segment : This topic adresses the segmenter process Is a json object with {"action":"segment"} Receive only - status : This topics sends feedback to Node-Red No publication or receive at this level - status/pump : State of the pump Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/focus : State of the focus stage Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/imager : State of the imager Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Completed or 12_11_15_0.1.jpg has been imaged. Publish only - status/segmenter : Status of the segmentation - status/segmenter/name - status/segmenter/object_id - status/segmenter/metric Here is the original commit history: * Extract python main.py from flow * Fix bug in server addresses These addresses should be the loopback device instead of the network address of the device. Using the loopback address will not necessitate to update the script when the network address changes. * clean up picamera import * changes to main python and flow: update MQTT requests address to localhost (bugfix) update streaming output address to nothing update main flow to remove python script references and location * Automatically initialise imaging led on startup to off state. * Add the ability to invert outputs of the motor We added a key to config.json "hardware_config" with a subkey "stepper_reverse". If this key is present in the config file and set to 1, the output of the motors are inversed (stepper2 becomes the pump motor and stepper1 the focus motor) * move all non main script to a subfolder * add __init__.py to package * light module rewrite * json cleanup and absolute path for config file * light.py forgot to import subprocess #oups * Add command to turn the leds off * Auto formatting of main.py I've used Black with default settings, see https://github.com/psf/black * First commit of stepper.py Pump parameters still needs to be checked and tuned. * addition of hardware details in config.json * Introduce hardware.json to replace the `hardware_config` of config.json * stepper.py: calibration, typos * creates the MQTT_Client class * pump_max_speed is now in ml/min to help readability * forgot to add self to the class def * addition of threading capabilities to stepper.py (UNTESTED) * mqtt: fix topic bug * remove counter * mqtt add doc about topics * stepper.py creates an "actuator/*/state" topic * stepper.py: rename mqtt_client to pump_client * mqtt.py: add details about topics * stepper.py: rename pump_client to actuator_client * topic was not split properly and a part was lost * switch to f-strings for mqtt.py * cosmetic update * stepper.py: folder name will be planktoscope change calls * hardware.json became more straightforward * stepper.py syntax bugs * stepper.py addition of a received stop command * stepper.py: update to max travel distance * stepper.py: several typos here * rename folder * main.py: reword to reflect folder rename * main.py: remove logic that has been moved to stepper.py and mqtt.py * main.py: update to add mqtt imaging client * mqtt.py: make command and args local to class and output more verbose * make stepper.py a class * main.py: instantiate stepper class and call it * main.py: name mqtt client * update to main.json to reflect main.py changes * fix bugs around pump control * update flows to latest version from Thibault * distance can be a small value, and definitevely should be a float. * unify mqtt topics * unify mqtt output in the main flow * first logger implementation, uses loguru * mqtt: add reason to on_connect * mqtt: add on_disconnect handler * stepper: add more logger calls for debug mainly * main: add levels for logger * imager.py: first move of the imager logic * imager: time import cleanup * imager: morphocut import cleanup * imager: skimage import cleanup * imager: finishing import cleanup * imager: Class creation - WIP Also provides a fix for #26 (see line 190). * imager: threading is needed for Condition() * streamer: get the streamer server its own file * imager: creates start_camera and get the server creation out * imager: subclass multiprocessing.Process * imager: get Pipeline creation its own function * imager: cleanup of self calls * main: code removal and corresponding calls to newly created classes * imager: various formatting changes * main: management of signal shutdown * add requirements.txt * mqtt: messages are now json objects Also, addition of a flag on receiving a new message * mqtt: make message private and add logic to synchronise * stepper: creates the stepper class * stepper: use the new class * stepper: uses the new logic * stepper: add the shutdown event * stepper: add shutdown method * main: add shutdown event * imager: graceful shutdown * stepper: nicer way of checking the Eevnt * self is a required first argument for a method in a class Especially if you use said class private members! * python: various typos and small errors in import * stepper: create mqtt client during init * stepper: instanciate the mqtt client inside run Otherwise it's not accessible from inside the loop. It's a PITA, more information at https://stackoverflow.com/questions/17172878/using-pythons-multiprocessing-process-class * stepper: little bugs and typos all around * mqtt: add shutdown method * mqtt: add connect in init * stepper: fix bugs, sanitize inputs * stepper: work on delay prediction improvements * stepper: json is mean, double quote are mandatory inside * mqtt: add details about message exchanged * imager: first implementation of json messages * main.json: add new tab for RPi management + json for payloads * imager: add state_machine class * stepper: publish last will * imager: major refactor * main: make streaming server process a daemon * mqtt: insert debug statement on close * main: reorder imports * imager: make it work! Reinsert the streaming server logic in there, because there is a problem with the synchronisation part otherwise. Also, eventually, StreamingOuput() will have to be made not global Final very critical learning: it's super duper important to make sure the memory split is at least 256Meg for the GPU. Chaos ensues otherwise * main: changes to accomodate the streamer/imager fusino * imager_state_machine: insert states transition description * stepper: cleanup of code * segmenter: creation of the class * python: include segmenter changes * remove unused files * stepper: check existence of hardware.json * main.json: changes to reflect the python script evolution * remove unecessary TODOs and add some others * main: add check for config and directories * imager: update_config is implemented and we have better management of directories now * segmenter: now work recursively in all folders * flow: the configuration is now sent via mqtt * segmenter: better manage pipeline error * segmenter: declaration of archive_fn in init * imager: small bugs and typos * main: add uniqueID output * imager: add the camera settings message We can now update the ISO, shutter speed and resolution from Node-Red * package.json: update dependencies
2020-09-28 11:05:27 +02:00
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Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"id": "7aa2e737.e16d98",
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Extraction and refactor of the python code from node-red flow The rationale for this rewrite is to improve the readability, the modularity, the reliability and the future-proofing of the main python script. All in all, this is now 124 commits that are going to be squashed and merged together, spanning more than two weeks of development and testing. Please test away this release and break things. An upgrading guide will be published in the coming days, along with a new image for people to use if they don't want to upgrade on their own. Read along if you want to know all the goodies! As a starter, the python script was extracted from the main flow, and now lives in its own files at `PlantonScope/scripts/*`. We set up the auto formatting of the code by using [Black](https://github.com/psf/black). This make the code clearer and uniform. We are using the default settings, so if you just install Black and set your editor to format on save using it, you should be good to go. The code is separated in four main processes, each with a specific set of responsibilities: - The main process controls all the others, starts everything up and cleans up on shutdown - The stepper process manages the stepper movements. It's now possible to have simultaneous movements of both motors (this closes #38 ). - The imager process controls the camera and the streaming server via a state machine. - The segmenter process manages the segmentation and its outputs. The segmentation happens recursively in all folders in `/home/pi/PlanktonScope/img/`. Each folder has its own output archive, and bug #26 is now closed. Those processes communicates together using MQTT and json messages. Each message is adressed to one topic. The high level topic controls which process receives the message. The details of each topic is at the end of this commit message. Every imaging sessions has now its own folder, under the `img` root. Metadata are saved individually for every session, in a JSON file in the same directory as the pictures. The configuration is not parsed from `config.json` anymore and passed directly through MQTT messages to the concerned process. A new configuration file has been created: `hardware.json`. This file contains information related to your specific hardware configuration. You can choose to reverse the connection of the motors for example, but you can also define specific speed limits and steps number for your pump and focus stage. This will make it easier for people who wants to experiment with different kind of hardware. It's not necessary to have this file though. If it doesn't exists, the default configuration will be applied. The code is architectured around 6 modules and about 10 classes. I encourage you to have a look at the files, they're pretty straightforward to understand. There is a lot of work left around the node-red code refactoring, dashboard ui improvements, better and clearer LED messages, OLED screen integration and finer control of the segmentation process, but this is quite good for now. Here is the topic lists for MQTT and the corresponding messages. - actuator : This topic adresses the stepper control thread No publication under this topic should happen from the python process - actuator/pump : Control of the pump The message is a json object {"action":"move", "direction":"FORWARD", "volume":10, "flowrate":1} to move 10mL forward at 1mL/min action can be "move" or "stop" Receive only - actuator/focus : Control of the focus stage The message is a json object, speed is optional {"action":"move", "direction":"UP", "distance":0.26, "speed":1} to move up 10mm action can be "move" or "stop" Receive only - imager/image : This topic adresses the imaging thread Is a json object with {"action":"image","sleep":5,"volume":1,"nb_frame":200} sleep in seconds, volume in mL Can also receive a config update message: {"action":"config","config":[...]} Can also receive a camera settings message: {"action":"settings","iso":100,"shutter_speed":40} Receive only - segmenter/segment : This topic adresses the segmenter process Is a json object with {"action":"segment"} Receive only - status : This topics sends feedback to Node-Red No publication or receive at this level - status/pump : State of the pump Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/focus : State of the focus stage Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/imager : State of the imager Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Completed or 12_11_15_0.1.jpg has been imaged. Publish only - status/segmenter : Status of the segmentation - status/segmenter/name - status/segmenter/object_id - status/segmenter/metric Here is the original commit history: * Extract python main.py from flow * Fix bug in server addresses These addresses should be the loopback device instead of the network address of the device. Using the loopback address will not necessitate to update the script when the network address changes. * clean up picamera import * changes to main python and flow: update MQTT requests address to localhost (bugfix) update streaming output address to nothing update main flow to remove python script references and location * Automatically initialise imaging led on startup to off state. * Add the ability to invert outputs of the motor We added a key to config.json "hardware_config" with a subkey "stepper_reverse". If this key is present in the config file and set to 1, the output of the motors are inversed (stepper2 becomes the pump motor and stepper1 the focus motor) * move all non main script to a subfolder * add __init__.py to package * light module rewrite * json cleanup and absolute path for config file * light.py forgot to import subprocess #oups * Add command to turn the leds off * Auto formatting of main.py I've used Black with default settings, see https://github.com/psf/black * First commit of stepper.py Pump parameters still needs to be checked and tuned. * addition of hardware details in config.json * Introduce hardware.json to replace the `hardware_config` of config.json * stepper.py: calibration, typos * creates the MQTT_Client class * pump_max_speed is now in ml/min to help readability * forgot to add self to the class def * addition of threading capabilities to stepper.py (UNTESTED) * mqtt: fix topic bug * remove counter * mqtt add doc about topics * stepper.py creates an "actuator/*/state" topic * stepper.py: rename mqtt_client to pump_client * mqtt.py: add details about topics * stepper.py: rename pump_client to actuator_client * topic was not split properly and a part was lost * switch to f-strings for mqtt.py * cosmetic update * stepper.py: folder name will be planktoscope change calls * hardware.json became more straightforward * stepper.py syntax bugs * stepper.py addition of a received stop command * stepper.py: update to max travel distance * stepper.py: several typos here * rename folder * main.py: reword to reflect folder rename * main.py: remove logic that has been moved to stepper.py and mqtt.py * main.py: update to add mqtt imaging client * mqtt.py: make command and args local to class and output more verbose * make stepper.py a class * main.py: instantiate stepper class and call it * main.py: name mqtt client * update to main.json to reflect main.py changes * fix bugs around pump control * update flows to latest version from Thibault * distance can be a small value, and definitevely should be a float. * unify mqtt topics * unify mqtt output in the main flow * first logger implementation, uses loguru * mqtt: add reason to on_connect * mqtt: add on_disconnect handler * stepper: add more logger calls for debug mainly * main: add levels for logger * imager.py: first move of the imager logic * imager: time import cleanup * imager: morphocut import cleanup * imager: skimage import cleanup * imager: finishing import cleanup * imager: Class creation - WIP Also provides a fix for #26 (see line 190). * imager: threading is needed for Condition() * streamer: get the streamer server its own file * imager: creates start_camera and get the server creation out * imager: subclass multiprocessing.Process * imager: get Pipeline creation its own function * imager: cleanup of self calls * main: code removal and corresponding calls to newly created classes * imager: various formatting changes * main: management of signal shutdown * add requirements.txt * mqtt: messages are now json objects Also, addition of a flag on receiving a new message * mqtt: make message private and add logic to synchronise * stepper: creates the stepper class * stepper: use the new class * stepper: uses the new logic * stepper: add the shutdown event * stepper: add shutdown method * main: add shutdown event * imager: graceful shutdown * stepper: nicer way of checking the Eevnt * self is a required first argument for a method in a class Especially if you use said class private members! * python: various typos and small errors in import * stepper: create mqtt client during init * stepper: instanciate the mqtt client inside run Otherwise it's not accessible from inside the loop. It's a PITA, more information at https://stackoverflow.com/questions/17172878/using-pythons-multiprocessing-process-class * stepper: little bugs and typos all around * mqtt: add shutdown method * mqtt: add connect in init * stepper: fix bugs, sanitize inputs * stepper: work on delay prediction improvements * stepper: json is mean, double quote are mandatory inside * mqtt: add details about message exchanged * imager: first implementation of json messages * main.json: add new tab for RPi management + json for payloads * imager: add state_machine class * stepper: publish last will * imager: major refactor * main: make streaming server process a daemon * mqtt: insert debug statement on close * main: reorder imports * imager: make it work! Reinsert the streaming server logic in there, because there is a problem with the synchronisation part otherwise. Also, eventually, StreamingOuput() will have to be made not global Final very critical learning: it's super duper important to make sure the memory split is at least 256Meg for the GPU. Chaos ensues otherwise * main: changes to accomodate the streamer/imager fusino * imager_state_machine: insert states transition description * stepper: cleanup of code * segmenter: creation of the class * python: include segmenter changes * remove unused files * stepper: check existence of hardware.json * main.json: changes to reflect the python script evolution * remove unecessary TODOs and add some others * main: add check for config and directories * imager: update_config is implemented and we have better management of directories now * segmenter: now work recursively in all folders * flow: the configuration is now sent via mqtt * segmenter: better manage pipeline error * segmenter: declaration of archive_fn in init * imager: small bugs and typos * main: add uniqueID output * imager: add the camera settings message We can now update the ISO, shutter speed and resolution from Node-Red * package.json: update dependencies
2020-09-28 11:05:27 +02:00
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Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
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Extraction and refactor of the python code from node-red flow The rationale for this rewrite is to improve the readability, the modularity, the reliability and the future-proofing of the main python script. All in all, this is now 124 commits that are going to be squashed and merged together, spanning more than two weeks of development and testing. Please test away this release and break things. An upgrading guide will be published in the coming days, along with a new image for people to use if they don't want to upgrade on their own. Read along if you want to know all the goodies! As a starter, the python script was extracted from the main flow, and now lives in its own files at `PlantonScope/scripts/*`. We set up the auto formatting of the code by using [Black](https://github.com/psf/black). This make the code clearer and uniform. We are using the default settings, so if you just install Black and set your editor to format on save using it, you should be good to go. The code is separated in four main processes, each with a specific set of responsibilities: - The main process controls all the others, starts everything up and cleans up on shutdown - The stepper process manages the stepper movements. It's now possible to have simultaneous movements of both motors (this closes #38 ). - The imager process controls the camera and the streaming server via a state machine. - The segmenter process manages the segmentation and its outputs. The segmentation happens recursively in all folders in `/home/pi/PlanktonScope/img/`. Each folder has its own output archive, and bug #26 is now closed. Those processes communicates together using MQTT and json messages. Each message is adressed to one topic. The high level topic controls which process receives the message. The details of each topic is at the end of this commit message. Every imaging sessions has now its own folder, under the `img` root. Metadata are saved individually for every session, in a JSON file in the same directory as the pictures. The configuration is not parsed from `config.json` anymore and passed directly through MQTT messages to the concerned process. A new configuration file has been created: `hardware.json`. This file contains information related to your specific hardware configuration. You can choose to reverse the connection of the motors for example, but you can also define specific speed limits and steps number for your pump and focus stage. This will make it easier for people who wants to experiment with different kind of hardware. It's not necessary to have this file though. If it doesn't exists, the default configuration will be applied. The code is architectured around 6 modules and about 10 classes. I encourage you to have a look at the files, they're pretty straightforward to understand. There is a lot of work left around the node-red code refactoring, dashboard ui improvements, better and clearer LED messages, OLED screen integration and finer control of the segmentation process, but this is quite good for now. Here is the topic lists for MQTT and the corresponding messages. - actuator : This topic adresses the stepper control thread No publication under this topic should happen from the python process - actuator/pump : Control of the pump The message is a json object {"action":"move", "direction":"FORWARD", "volume":10, "flowrate":1} to move 10mL forward at 1mL/min action can be "move" or "stop" Receive only - actuator/focus : Control of the focus stage The message is a json object, speed is optional {"action":"move", "direction":"UP", "distance":0.26, "speed":1} to move up 10mm action can be "move" or "stop" Receive only - imager/image : This topic adresses the imaging thread Is a json object with {"action":"image","sleep":5,"volume":1,"nb_frame":200} sleep in seconds, volume in mL Can also receive a config update message: {"action":"config","config":[...]} Can also receive a camera settings message: {"action":"settings","iso":100,"shutter_speed":40} Receive only - segmenter/segment : This topic adresses the segmenter process Is a json object with {"action":"segment"} Receive only - status : This topics sends feedback to Node-Red No publication or receive at this level - status/pump : State of the pump Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/focus : State of the focus stage Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/imager : State of the imager Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Completed or 12_11_15_0.1.jpg has been imaged. Publish only - status/segmenter : Status of the segmentation - status/segmenter/name - status/segmenter/object_id - status/segmenter/metric Here is the original commit history: * Extract python main.py from flow * Fix bug in server addresses These addresses should be the loopback device instead of the network address of the device. Using the loopback address will not necessitate to update the script when the network address changes. * clean up picamera import * changes to main python and flow: update MQTT requests address to localhost (bugfix) update streaming output address to nothing update main flow to remove python script references and location * Automatically initialise imaging led on startup to off state. * Add the ability to invert outputs of the motor We added a key to config.json "hardware_config" with a subkey "stepper_reverse". If this key is present in the config file and set to 1, the output of the motors are inversed (stepper2 becomes the pump motor and stepper1 the focus motor) * move all non main script to a subfolder * add __init__.py to package * light module rewrite * json cleanup and absolute path for config file * light.py forgot to import subprocess #oups * Add command to turn the leds off * Auto formatting of main.py I've used Black with default settings, see https://github.com/psf/black * First commit of stepper.py Pump parameters still needs to be checked and tuned. * addition of hardware details in config.json * Introduce hardware.json to replace the `hardware_config` of config.json * stepper.py: calibration, typos * creates the MQTT_Client class * pump_max_speed is now in ml/min to help readability * forgot to add self to the class def * addition of threading capabilities to stepper.py (UNTESTED) * mqtt: fix topic bug * remove counter * mqtt add doc about topics * stepper.py creates an "actuator/*/state" topic * stepper.py: rename mqtt_client to pump_client * mqtt.py: add details about topics * stepper.py: rename pump_client to actuator_client * topic was not split properly and a part was lost * switch to f-strings for mqtt.py * cosmetic update * stepper.py: folder name will be planktoscope change calls * hardware.json became more straightforward * stepper.py syntax bugs * stepper.py addition of a received stop command * stepper.py: update to max travel distance * stepper.py: several typos here * rename folder * main.py: reword to reflect folder rename * main.py: remove logic that has been moved to stepper.py and mqtt.py * main.py: update to add mqtt imaging client * mqtt.py: make command and args local to class and output more verbose * make stepper.py a class * main.py: instantiate stepper class and call it * main.py: name mqtt client * update to main.json to reflect main.py changes * fix bugs around pump control * update flows to latest version from Thibault * distance can be a small value, and definitevely should be a float. * unify mqtt topics * unify mqtt output in the main flow * first logger implementation, uses loguru * mqtt: add reason to on_connect * mqtt: add on_disconnect handler * stepper: add more logger calls for debug mainly * main: add levels for logger * imager.py: first move of the imager logic * imager: time import cleanup * imager: morphocut import cleanup * imager: skimage import cleanup * imager: finishing import cleanup * imager: Class creation - WIP Also provides a fix for #26 (see line 190). * imager: threading is needed for Condition() * streamer: get the streamer server its own file * imager: creates start_camera and get the server creation out * imager: subclass multiprocessing.Process * imager: get Pipeline creation its own function * imager: cleanup of self calls * main: code removal and corresponding calls to newly created classes * imager: various formatting changes * main: management of signal shutdown * add requirements.txt * mqtt: messages are now json objects Also, addition of a flag on receiving a new message * mqtt: make message private and add logic to synchronise * stepper: creates the stepper class * stepper: use the new class * stepper: uses the new logic * stepper: add the shutdown event * stepper: add shutdown method * main: add shutdown event * imager: graceful shutdown * stepper: nicer way of checking the Eevnt * self is a required first argument for a method in a class Especially if you use said class private members! * python: various typos and small errors in import * stepper: create mqtt client during init * stepper: instanciate the mqtt client inside run Otherwise it's not accessible from inside the loop. It's a PITA, more information at https://stackoverflow.com/questions/17172878/using-pythons-multiprocessing-process-class * stepper: little bugs and typos all around * mqtt: add shutdown method * mqtt: add connect in init * stepper: fix bugs, sanitize inputs * stepper: work on delay prediction improvements * stepper: json is mean, double quote are mandatory inside * mqtt: add details about message exchanged * imager: first implementation of json messages * main.json: add new tab for RPi management + json for payloads * imager: add state_machine class * stepper: publish last will * imager: major refactor * main: make streaming server process a daemon * mqtt: insert debug statement on close * main: reorder imports * imager: make it work! Reinsert the streaming server logic in there, because there is a problem with the synchronisation part otherwise. Also, eventually, StreamingOuput() will have to be made not global Final very critical learning: it's super duper important to make sure the memory split is at least 256Meg for the GPU. Chaos ensues otherwise * main: changes to accomodate the streamer/imager fusino * imager_state_machine: insert states transition description * stepper: cleanup of code * segmenter: creation of the class * python: include segmenter changes * remove unused files * stepper: check existence of hardware.json * main.json: changes to reflect the python script evolution * remove unecessary TODOs and add some others * main: add check for config and directories * imager: update_config is implemented and we have better management of directories now * segmenter: now work recursively in all folders * flow: the configuration is now sent via mqtt * segmenter: better manage pipeline error * segmenter: declaration of archive_fn in init * imager: small bugs and typos * main: add uniqueID output * imager: add the camera settings message We can now update the ISO, shutter speed and resolution from Node-Red * package.json: update dependencies
2020-09-28 11:05:27 +02:00
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Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
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Extraction and refactor of the python code from node-red flow The rationale for this rewrite is to improve the readability, the modularity, the reliability and the future-proofing of the main python script. All in all, this is now 124 commits that are going to be squashed and merged together, spanning more than two weeks of development and testing. Please test away this release and break things. An upgrading guide will be published in the coming days, along with a new image for people to use if they don't want to upgrade on their own. Read along if you want to know all the goodies! As a starter, the python script was extracted from the main flow, and now lives in its own files at `PlantonScope/scripts/*`. We set up the auto formatting of the code by using [Black](https://github.com/psf/black). This make the code clearer and uniform. We are using the default settings, so if you just install Black and set your editor to format on save using it, you should be good to go. The code is separated in four main processes, each with a specific set of responsibilities: - The main process controls all the others, starts everything up and cleans up on shutdown - The stepper process manages the stepper movements. It's now possible to have simultaneous movements of both motors (this closes #38 ). - The imager process controls the camera and the streaming server via a state machine. - The segmenter process manages the segmentation and its outputs. The segmentation happens recursively in all folders in `/home/pi/PlanktonScope/img/`. Each folder has its own output archive, and bug #26 is now closed. Those processes communicates together using MQTT and json messages. Each message is adressed to one topic. The high level topic controls which process receives the message. The details of each topic is at the end of this commit message. Every imaging sessions has now its own folder, under the `img` root. Metadata are saved individually for every session, in a JSON file in the same directory as the pictures. The configuration is not parsed from `config.json` anymore and passed directly through MQTT messages to the concerned process. A new configuration file has been created: `hardware.json`. This file contains information related to your specific hardware configuration. You can choose to reverse the connection of the motors for example, but you can also define specific speed limits and steps number for your pump and focus stage. This will make it easier for people who wants to experiment with different kind of hardware. It's not necessary to have this file though. If it doesn't exists, the default configuration will be applied. The code is architectured around 6 modules and about 10 classes. I encourage you to have a look at the files, they're pretty straightforward to understand. There is a lot of work left around the node-red code refactoring, dashboard ui improvements, better and clearer LED messages, OLED screen integration and finer control of the segmentation process, but this is quite good for now. Here is the topic lists for MQTT and the corresponding messages. - actuator : This topic adresses the stepper control thread No publication under this topic should happen from the python process - actuator/pump : Control of the pump The message is a json object {"action":"move", "direction":"FORWARD", "volume":10, "flowrate":1} to move 10mL forward at 1mL/min action can be "move" or "stop" Receive only - actuator/focus : Control of the focus stage The message is a json object, speed is optional {"action":"move", "direction":"UP", "distance":0.26, "speed":1} to move up 10mm action can be "move" or "stop" Receive only - imager/image : This topic adresses the imaging thread Is a json object with {"action":"image","sleep":5,"volume":1,"nb_frame":200} sleep in seconds, volume in mL Can also receive a config update message: {"action":"config","config":[...]} Can also receive a camera settings message: {"action":"settings","iso":100,"shutter_speed":40} Receive only - segmenter/segment : This topic adresses the segmenter process Is a json object with {"action":"segment"} Receive only - status : This topics sends feedback to Node-Red No publication or receive at this level - status/pump : State of the pump Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/focus : State of the focus stage Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/imager : State of the imager Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Completed or 12_11_15_0.1.jpg has been imaged. Publish only - status/segmenter : Status of the segmentation - status/segmenter/name - status/segmenter/object_id - status/segmenter/metric Here is the original commit history: * Extract python main.py from flow * Fix bug in server addresses These addresses should be the loopback device instead of the network address of the device. Using the loopback address will not necessitate to update the script when the network address changes. * clean up picamera import * changes to main python and flow: update MQTT requests address to localhost (bugfix) update streaming output address to nothing update main flow to remove python script references and location * Automatically initialise imaging led on startup to off state. * Add the ability to invert outputs of the motor We added a key to config.json "hardware_config" with a subkey "stepper_reverse". If this key is present in the config file and set to 1, the output of the motors are inversed (stepper2 becomes the pump motor and stepper1 the focus motor) * move all non main script to a subfolder * add __init__.py to package * light module rewrite * json cleanup and absolute path for config file * light.py forgot to import subprocess #oups * Add command to turn the leds off * Auto formatting of main.py I've used Black with default settings, see https://github.com/psf/black * First commit of stepper.py Pump parameters still needs to be checked and tuned. * addition of hardware details in config.json * Introduce hardware.json to replace the `hardware_config` of config.json * stepper.py: calibration, typos * creates the MQTT_Client class * pump_max_speed is now in ml/min to help readability * forgot to add self to the class def * addition of threading capabilities to stepper.py (UNTESTED) * mqtt: fix topic bug * remove counter * mqtt add doc about topics * stepper.py creates an "actuator/*/state" topic * stepper.py: rename mqtt_client to pump_client * mqtt.py: add details about topics * stepper.py: rename pump_client to actuator_client * topic was not split properly and a part was lost * switch to f-strings for mqtt.py * cosmetic update * stepper.py: folder name will be planktoscope change calls * hardware.json became more straightforward * stepper.py syntax bugs * stepper.py addition of a received stop command * stepper.py: update to max travel distance * stepper.py: several typos here * rename folder * main.py: reword to reflect folder rename * main.py: remove logic that has been moved to stepper.py and mqtt.py * main.py: update to add mqtt imaging client * mqtt.py: make command and args local to class and output more verbose * make stepper.py a class * main.py: instantiate stepper class and call it * main.py: name mqtt client * update to main.json to reflect main.py changes * fix bugs around pump control * update flows to latest version from Thibault * distance can be a small value, and definitevely should be a float. * unify mqtt topics * unify mqtt output in the main flow * first logger implementation, uses loguru * mqtt: add reason to on_connect * mqtt: add on_disconnect handler * stepper: add more logger calls for debug mainly * main: add levels for logger * imager.py: first move of the imager logic * imager: time import cleanup * imager: morphocut import cleanup * imager: skimage import cleanup * imager: finishing import cleanup * imager: Class creation - WIP Also provides a fix for #26 (see line 190). * imager: threading is needed for Condition() * streamer: get the streamer server its own file * imager: creates start_camera and get the server creation out * imager: subclass multiprocessing.Process * imager: get Pipeline creation its own function * imager: cleanup of self calls * main: code removal and corresponding calls to newly created classes * imager: various formatting changes * main: management of signal shutdown * add requirements.txt * mqtt: messages are now json objects Also, addition of a flag on receiving a new message * mqtt: make message private and add logic to synchronise * stepper: creates the stepper class * stepper: use the new class * stepper: uses the new logic * stepper: add the shutdown event * stepper: add shutdown method * main: add shutdown event * imager: graceful shutdown * stepper: nicer way of checking the Eevnt * self is a required first argument for a method in a class Especially if you use said class private members! * python: various typos and small errors in import * stepper: create mqtt client during init * stepper: instanciate the mqtt client inside run Otherwise it's not accessible from inside the loop. It's a PITA, more information at https://stackoverflow.com/questions/17172878/using-pythons-multiprocessing-process-class * stepper: little bugs and typos all around * mqtt: add shutdown method * mqtt: add connect in init * stepper: fix bugs, sanitize inputs * stepper: work on delay prediction improvements * stepper: json is mean, double quote are mandatory inside * mqtt: add details about message exchanged * imager: first implementation of json messages * main.json: add new tab for RPi management + json for payloads * imager: add state_machine class * stepper: publish last will * imager: major refactor * main: make streaming server process a daemon * mqtt: insert debug statement on close * main: reorder imports * imager: make it work! Reinsert the streaming server logic in there, because there is a problem with the synchronisation part otherwise. Also, eventually, StreamingOuput() will have to be made not global Final very critical learning: it's super duper important to make sure the memory split is at least 256Meg for the GPU. Chaos ensues otherwise * main: changes to accomodate the streamer/imager fusino * imager_state_machine: insert states transition description * stepper: cleanup of code * segmenter: creation of the class * python: include segmenter changes * remove unused files * stepper: check existence of hardware.json * main.json: changes to reflect the python script evolution * remove unecessary TODOs and add some others * main: add check for config and directories * imager: update_config is implemented and we have better management of directories now * segmenter: now work recursively in all folders * flow: the configuration is now sent via mqtt * segmenter: better manage pipeline error * segmenter: declaration of archive_fn in init * imager: small bugs and typos * main: add uniqueID output * imager: add the camera settings message We can now update the ISO, shutter speed and resolution from Node-Red * package.json: update dependencies
2020-09-28 11:05:27 +02:00
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Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"id": "35ea3cf0.a398ac",
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Extraction and refactor of the python code from node-red flow The rationale for this rewrite is to improve the readability, the modularity, the reliability and the future-proofing of the main python script. All in all, this is now 124 commits that are going to be squashed and merged together, spanning more than two weeks of development and testing. Please test away this release and break things. An upgrading guide will be published in the coming days, along with a new image for people to use if they don't want to upgrade on their own. Read along if you want to know all the goodies! As a starter, the python script was extracted from the main flow, and now lives in its own files at `PlantonScope/scripts/*`. We set up the auto formatting of the code by using [Black](https://github.com/psf/black). This make the code clearer and uniform. We are using the default settings, so if you just install Black and set your editor to format on save using it, you should be good to go. The code is separated in four main processes, each with a specific set of responsibilities: - The main process controls all the others, starts everything up and cleans up on shutdown - The stepper process manages the stepper movements. It's now possible to have simultaneous movements of both motors (this closes #38 ). - The imager process controls the camera and the streaming server via a state machine. - The segmenter process manages the segmentation and its outputs. The segmentation happens recursively in all folders in `/home/pi/PlanktonScope/img/`. Each folder has its own output archive, and bug #26 is now closed. Those processes communicates together using MQTT and json messages. Each message is adressed to one topic. The high level topic controls which process receives the message. The details of each topic is at the end of this commit message. Every imaging sessions has now its own folder, under the `img` root. Metadata are saved individually for every session, in a JSON file in the same directory as the pictures. The configuration is not parsed from `config.json` anymore and passed directly through MQTT messages to the concerned process. A new configuration file has been created: `hardware.json`. This file contains information related to your specific hardware configuration. You can choose to reverse the connection of the motors for example, but you can also define specific speed limits and steps number for your pump and focus stage. This will make it easier for people who wants to experiment with different kind of hardware. It's not necessary to have this file though. If it doesn't exists, the default configuration will be applied. The code is architectured around 6 modules and about 10 classes. I encourage you to have a look at the files, they're pretty straightforward to understand. There is a lot of work left around the node-red code refactoring, dashboard ui improvements, better and clearer LED messages, OLED screen integration and finer control of the segmentation process, but this is quite good for now. Here is the topic lists for MQTT and the corresponding messages. - actuator : This topic adresses the stepper control thread No publication under this topic should happen from the python process - actuator/pump : Control of the pump The message is a json object {"action":"move", "direction":"FORWARD", "volume":10, "flowrate":1} to move 10mL forward at 1mL/min action can be "move" or "stop" Receive only - actuator/focus : Control of the focus stage The message is a json object, speed is optional {"action":"move", "direction":"UP", "distance":0.26, "speed":1} to move up 10mm action can be "move" or "stop" Receive only - imager/image : This topic adresses the imaging thread Is a json object with {"action":"image","sleep":5,"volume":1,"nb_frame":200} sleep in seconds, volume in mL Can also receive a config update message: {"action":"config","config":[...]} Can also receive a camera settings message: {"action":"settings","iso":100,"shutter_speed":40} Receive only - segmenter/segment : This topic adresses the segmenter process Is a json object with {"action":"segment"} Receive only - status : This topics sends feedback to Node-Red No publication or receive at this level - status/pump : State of the pump Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/focus : State of the focus stage Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/imager : State of the imager Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Completed or 12_11_15_0.1.jpg has been imaged. Publish only - status/segmenter : Status of the segmentation - status/segmenter/name - status/segmenter/object_id - status/segmenter/metric Here is the original commit history: * Extract python main.py from flow * Fix bug in server addresses These addresses should be the loopback device instead of the network address of the device. Using the loopback address will not necessitate to update the script when the network address changes. * clean up picamera import * changes to main python and flow: update MQTT requests address to localhost (bugfix) update streaming output address to nothing update main flow to remove python script references and location * Automatically initialise imaging led on startup to off state. * Add the ability to invert outputs of the motor We added a key to config.json "hardware_config" with a subkey "stepper_reverse". If this key is present in the config file and set to 1, the output of the motors are inversed (stepper2 becomes the pump motor and stepper1 the focus motor) * move all non main script to a subfolder * add __init__.py to package * light module rewrite * json cleanup and absolute path for config file * light.py forgot to import subprocess #oups * Add command to turn the leds off * Auto formatting of main.py I've used Black with default settings, see https://github.com/psf/black * First commit of stepper.py Pump parameters still needs to be checked and tuned. * addition of hardware details in config.json * Introduce hardware.json to replace the `hardware_config` of config.json * stepper.py: calibration, typos * creates the MQTT_Client class * pump_max_speed is now in ml/min to help readability * forgot to add self to the class def * addition of threading capabilities to stepper.py (UNTESTED) * mqtt: fix topic bug * remove counter * mqtt add doc about topics * stepper.py creates an "actuator/*/state" topic * stepper.py: rename mqtt_client to pump_client * mqtt.py: add details about topics * stepper.py: rename pump_client to actuator_client * topic was not split properly and a part was lost * switch to f-strings for mqtt.py * cosmetic update * stepper.py: folder name will be planktoscope change calls * hardware.json became more straightforward * stepper.py syntax bugs * stepper.py addition of a received stop command * stepper.py: update to max travel distance * stepper.py: several typos here * rename folder * main.py: reword to reflect folder rename * main.py: remove logic that has been moved to stepper.py and mqtt.py * main.py: update to add mqtt imaging client * mqtt.py: make command and args local to class and output more verbose * make stepper.py a class * main.py: instantiate stepper class and call it * main.py: name mqtt client * update to main.json to reflect main.py changes * fix bugs around pump control * update flows to latest version from Thibault * distance can be a small value, and definitevely should be a float. * unify mqtt topics * unify mqtt output in the main flow * first logger implementation, uses loguru * mqtt: add reason to on_connect * mqtt: add on_disconnect handler * stepper: add more logger calls for debug mainly * main: add levels for logger * imager.py: first move of the imager logic * imager: time import cleanup * imager: morphocut import cleanup * imager: skimage import cleanup * imager: finishing import cleanup * imager: Class creation - WIP Also provides a fix for #26 (see line 190). * imager: threading is needed for Condition() * streamer: get the streamer server its own file * imager: creates start_camera and get the server creation out * imager: subclass multiprocessing.Process * imager: get Pipeline creation its own function * imager: cleanup of self calls * main: code removal and corresponding calls to newly created classes * imager: various formatting changes * main: management of signal shutdown * add requirements.txt * mqtt: messages are now json objects Also, addition of a flag on receiving a new message * mqtt: make message private and add logic to synchronise * stepper: creates the stepper class * stepper: use the new class * stepper: uses the new logic * stepper: add the shutdown event * stepper: add shutdown method * main: add shutdown event * imager: graceful shutdown * stepper: nicer way of checking the Eevnt * self is a required first argument for a method in a class Especially if you use said class private members! * python: various typos and small errors in import * stepper: create mqtt client during init * stepper: instanciate the mqtt client inside run Otherwise it's not accessible from inside the loop. It's a PITA, more information at https://stackoverflow.com/questions/17172878/using-pythons-multiprocessing-process-class * stepper: little bugs and typos all around * mqtt: add shutdown method * mqtt: add connect in init * stepper: fix bugs, sanitize inputs * stepper: work on delay prediction improvements * stepper: json is mean, double quote are mandatory inside * mqtt: add details about message exchanged * imager: first implementation of json messages * main.json: add new tab for RPi management + json for payloads * imager: add state_machine class * stepper: publish last will * imager: major refactor * main: make streaming server process a daemon * mqtt: insert debug statement on close * main: reorder imports * imager: make it work! Reinsert the streaming server logic in there, because there is a problem with the synchronisation part otherwise. Also, eventually, StreamingOuput() will have to be made not global Final very critical learning: it's super duper important to make sure the memory split is at least 256Meg for the GPU. Chaos ensues otherwise * main: changes to accomodate the streamer/imager fusino * imager_state_machine: insert states transition description * stepper: cleanup of code * segmenter: creation of the class * python: include segmenter changes * remove unused files * stepper: check existence of hardware.json * main.json: changes to reflect the python script evolution * remove unecessary TODOs and add some others * main: add check for config and directories * imager: update_config is implemented and we have better management of directories now * segmenter: now work recursively in all folders * flow: the configuration is now sent via mqtt * segmenter: better manage pipeline error * segmenter: declaration of archive_fn in init * imager: small bugs and typos * main: add uniqueID output * imager: add the camera settings message We can now update the ISO, shutter speed and resolution from Node-Red * package.json: update dependencies
2020-09-28 11:05:27 +02:00
"wires": [
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
[],
[],
[]
Extraction and refactor of the python code from node-red flow The rationale for this rewrite is to improve the readability, the modularity, the reliability and the future-proofing of the main python script. All in all, this is now 124 commits that are going to be squashed and merged together, spanning more than two weeks of development and testing. Please test away this release and break things. An upgrading guide will be published in the coming days, along with a new image for people to use if they don't want to upgrade on their own. Read along if you want to know all the goodies! As a starter, the python script was extracted from the main flow, and now lives in its own files at `PlantonScope/scripts/*`. We set up the auto formatting of the code by using [Black](https://github.com/psf/black). This make the code clearer and uniform. We are using the default settings, so if you just install Black and set your editor to format on save using it, you should be good to go. The code is separated in four main processes, each with a specific set of responsibilities: - The main process controls all the others, starts everything up and cleans up on shutdown - The stepper process manages the stepper movements. It's now possible to have simultaneous movements of both motors (this closes #38 ). - The imager process controls the camera and the streaming server via a state machine. - The segmenter process manages the segmentation and its outputs. The segmentation happens recursively in all folders in `/home/pi/PlanktonScope/img/`. Each folder has its own output archive, and bug #26 is now closed. Those processes communicates together using MQTT and json messages. Each message is adressed to one topic. The high level topic controls which process receives the message. The details of each topic is at the end of this commit message. Every imaging sessions has now its own folder, under the `img` root. Metadata are saved individually for every session, in a JSON file in the same directory as the pictures. The configuration is not parsed from `config.json` anymore and passed directly through MQTT messages to the concerned process. A new configuration file has been created: `hardware.json`. This file contains information related to your specific hardware configuration. You can choose to reverse the connection of the motors for example, but you can also define specific speed limits and steps number for your pump and focus stage. This will make it easier for people who wants to experiment with different kind of hardware. It's not necessary to have this file though. If it doesn't exists, the default configuration will be applied. The code is architectured around 6 modules and about 10 classes. I encourage you to have a look at the files, they're pretty straightforward to understand. There is a lot of work left around the node-red code refactoring, dashboard ui improvements, better and clearer LED messages, OLED screen integration and finer control of the segmentation process, but this is quite good for now. Here is the topic lists for MQTT and the corresponding messages. - actuator : This topic adresses the stepper control thread No publication under this topic should happen from the python process - actuator/pump : Control of the pump The message is a json object {"action":"move", "direction":"FORWARD", "volume":10, "flowrate":1} to move 10mL forward at 1mL/min action can be "move" or "stop" Receive only - actuator/focus : Control of the focus stage The message is a json object, speed is optional {"action":"move", "direction":"UP", "distance":0.26, "speed":1} to move up 10mm action can be "move" or "stop" Receive only - imager/image : This topic adresses the imaging thread Is a json object with {"action":"image","sleep":5,"volume":1,"nb_frame":200} sleep in seconds, volume in mL Can also receive a config update message: {"action":"config","config":[...]} Can also receive a camera settings message: {"action":"settings","iso":100,"shutter_speed":40} Receive only - segmenter/segment : This topic adresses the segmenter process Is a json object with {"action":"segment"} Receive only - status : This topics sends feedback to Node-Red No publication or receive at this level - status/pump : State of the pump Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/focus : State of the focus stage Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/imager : State of the imager Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Completed or 12_11_15_0.1.jpg has been imaged. Publish only - status/segmenter : Status of the segmentation - status/segmenter/name - status/segmenter/object_id - status/segmenter/metric Here is the original commit history: * Extract python main.py from flow * Fix bug in server addresses These addresses should be the loopback device instead of the network address of the device. Using the loopback address will not necessitate to update the script when the network address changes. * clean up picamera import * changes to main python and flow: update MQTT requests address to localhost (bugfix) update streaming output address to nothing update main flow to remove python script references and location * Automatically initialise imaging led on startup to off state. * Add the ability to invert outputs of the motor We added a key to config.json "hardware_config" with a subkey "stepper_reverse". If this key is present in the config file and set to 1, the output of the motors are inversed (stepper2 becomes the pump motor and stepper1 the focus motor) * move all non main script to a subfolder * add __init__.py to package * light module rewrite * json cleanup and absolute path for config file * light.py forgot to import subprocess #oups * Add command to turn the leds off * Auto formatting of main.py I've used Black with default settings, see https://github.com/psf/black * First commit of stepper.py Pump parameters still needs to be checked and tuned. * addition of hardware details in config.json * Introduce hardware.json to replace the `hardware_config` of config.json * stepper.py: calibration, typos * creates the MQTT_Client class * pump_max_speed is now in ml/min to help readability * forgot to add self to the class def * addition of threading capabilities to stepper.py (UNTESTED) * mqtt: fix topic bug * remove counter * mqtt add doc about topics * stepper.py creates an "actuator/*/state" topic * stepper.py: rename mqtt_client to pump_client * mqtt.py: add details about topics * stepper.py: rename pump_client to actuator_client * topic was not split properly and a part was lost * switch to f-strings for mqtt.py * cosmetic update * stepper.py: folder name will be planktoscope change calls * hardware.json became more straightforward * stepper.py syntax bugs * stepper.py addition of a received stop command * stepper.py: update to max travel distance * stepper.py: several typos here * rename folder * main.py: reword to reflect folder rename * main.py: remove logic that has been moved to stepper.py and mqtt.py * main.py: update to add mqtt imaging client * mqtt.py: make command and args local to class and output more verbose * make stepper.py a class * main.py: instantiate stepper class and call it * main.py: name mqtt client * update to main.json to reflect main.py changes * fix bugs around pump control * update flows to latest version from Thibault * distance can be a small value, and definitevely should be a float. * unify mqtt topics * unify mqtt output in the main flow * first logger implementation, uses loguru * mqtt: add reason to on_connect * mqtt: add on_disconnect handler * stepper: add more logger calls for debug mainly * main: add levels for logger * imager.py: first move of the imager logic * imager: time import cleanup * imager: morphocut import cleanup * imager: skimage import cleanup * imager: finishing import cleanup * imager: Class creation - WIP Also provides a fix for #26 (see line 190). * imager: threading is needed for Condition() * streamer: get the streamer server its own file * imager: creates start_camera and get the server creation out * imager: subclass multiprocessing.Process * imager: get Pipeline creation its own function * imager: cleanup of self calls * main: code removal and corresponding calls to newly created classes * imager: various formatting changes * main: management of signal shutdown * add requirements.txt * mqtt: messages are now json objects Also, addition of a flag on receiving a new message * mqtt: make message private and add logic to synchronise * stepper: creates the stepper class * stepper: use the new class * stepper: uses the new logic * stepper: add the shutdown event * stepper: add shutdown method * main: add shutdown event * imager: graceful shutdown * stepper: nicer way of checking the Eevnt * self is a required first argument for a method in a class Especially if you use said class private members! * python: various typos and small errors in import * stepper: create mqtt client during init * stepper: instanciate the mqtt client inside run Otherwise it's not accessible from inside the loop. It's a PITA, more information at https://stackoverflow.com/questions/17172878/using-pythons-multiprocessing-process-class * stepper: little bugs and typos all around * mqtt: add shutdown method * mqtt: add connect in init * stepper: fix bugs, sanitize inputs * stepper: work on delay prediction improvements * stepper: json is mean, double quote are mandatory inside * mqtt: add details about message exchanged * imager: first implementation of json messages * main.json: add new tab for RPi management + json for payloads * imager: add state_machine class * stepper: publish last will * imager: major refactor * main: make streaming server process a daemon * mqtt: insert debug statement on close * main: reorder imports * imager: make it work! Reinsert the streaming server logic in there, because there is a problem with the synchronisation part otherwise. Also, eventually, StreamingOuput() will have to be made not global Final very critical learning: it's super duper important to make sure the memory split is at least 256Meg for the GPU. Chaos ensues otherwise * main: changes to accomodate the streamer/imager fusino * imager_state_machine: insert states transition description * stepper: cleanup of code * segmenter: creation of the class * python: include segmenter changes * remove unused files * stepper: check existence of hardware.json * main.json: changes to reflect the python script evolution * remove unecessary TODOs and add some others * main: add check for config and directories * imager: update_config is implemented and we have better management of directories now * segmenter: now work recursively in all folders * flow: the configuration is now sent via mqtt * segmenter: better manage pipeline error * segmenter: declaration of archive_fn in init * imager: small bugs and typos * main: add uniqueID output * imager: add the camera settings message We can now update the ISO, shutter speed and resolution from Node-Red * package.json: update dependencies
2020-09-28 11:05:27 +02:00
]
},
{
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"id": "a776b9fc.d542e8",
"type": "delay",
"z": "1371dec5.76e671",
"d": true,
"name": "",
"pauseType": "delay",
"timeout": "4",
"timeoutUnits": "seconds",
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Extraction and refactor of the python code from node-red flow The rationale for this rewrite is to improve the readability, the modularity, the reliability and the future-proofing of the main python script. All in all, this is now 124 commits that are going to be squashed and merged together, spanning more than two weeks of development and testing. Please test away this release and break things. An upgrading guide will be published in the coming days, along with a new image for people to use if they don't want to upgrade on their own. Read along if you want to know all the goodies! As a starter, the python script was extracted from the main flow, and now lives in its own files at `PlantonScope/scripts/*`. We set up the auto formatting of the code by using [Black](https://github.com/psf/black). This make the code clearer and uniform. We are using the default settings, so if you just install Black and set your editor to format on save using it, you should be good to go. The code is separated in four main processes, each with a specific set of responsibilities: - The main process controls all the others, starts everything up and cleans up on shutdown - The stepper process manages the stepper movements. It's now possible to have simultaneous movements of both motors (this closes #38 ). - The imager process controls the camera and the streaming server via a state machine. - The segmenter process manages the segmentation and its outputs. The segmentation happens recursively in all folders in `/home/pi/PlanktonScope/img/`. Each folder has its own output archive, and bug #26 is now closed. Those processes communicates together using MQTT and json messages. Each message is adressed to one topic. The high level topic controls which process receives the message. The details of each topic is at the end of this commit message. Every imaging sessions has now its own folder, under the `img` root. Metadata are saved individually for every session, in a JSON file in the same directory as the pictures. The configuration is not parsed from `config.json` anymore and passed directly through MQTT messages to the concerned process. A new configuration file has been created: `hardware.json`. This file contains information related to your specific hardware configuration. You can choose to reverse the connection of the motors for example, but you can also define specific speed limits and steps number for your pump and focus stage. This will make it easier for people who wants to experiment with different kind of hardware. It's not necessary to have this file though. If it doesn't exists, the default configuration will be applied. The code is architectured around 6 modules and about 10 classes. I encourage you to have a look at the files, they're pretty straightforward to understand. There is a lot of work left around the node-red code refactoring, dashboard ui improvements, better and clearer LED messages, OLED screen integration and finer control of the segmentation process, but this is quite good for now. Here is the topic lists for MQTT and the corresponding messages. - actuator : This topic adresses the stepper control thread No publication under this topic should happen from the python process - actuator/pump : Control of the pump The message is a json object {"action":"move", "direction":"FORWARD", "volume":10, "flowrate":1} to move 10mL forward at 1mL/min action can be "move" or "stop" Receive only - actuator/focus : Control of the focus stage The message is a json object, speed is optional {"action":"move", "direction":"UP", "distance":0.26, "speed":1} to move up 10mm action can be "move" or "stop" Receive only - imager/image : This topic adresses the imaging thread Is a json object with {"action":"image","sleep":5,"volume":1,"nb_frame":200} sleep in seconds, volume in mL Can also receive a config update message: {"action":"config","config":[...]} Can also receive a camera settings message: {"action":"settings","iso":100,"shutter_speed":40} Receive only - segmenter/segment : This topic adresses the segmenter process Is a json object with {"action":"segment"} Receive only - status : This topics sends feedback to Node-Red No publication or receive at this level - status/pump : State of the pump Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/focus : State of the focus stage Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/imager : State of the imager Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Completed or 12_11_15_0.1.jpg has been imaged. Publish only - status/segmenter : Status of the segmentation - status/segmenter/name - status/segmenter/object_id - status/segmenter/metric Here is the original commit history: * Extract python main.py from flow * Fix bug in server addresses These addresses should be the loopback device instead of the network address of the device. Using the loopback address will not necessitate to update the script when the network address changes. * clean up picamera import * changes to main python and flow: update MQTT requests address to localhost (bugfix) update streaming output address to nothing update main flow to remove python script references and location * Automatically initialise imaging led on startup to off state. * Add the ability to invert outputs of the motor We added a key to config.json "hardware_config" with a subkey "stepper_reverse". If this key is present in the config file and set to 1, the output of the motors are inversed (stepper2 becomes the pump motor and stepper1 the focus motor) * move all non main script to a subfolder * add __init__.py to package * light module rewrite * json cleanup and absolute path for config file * light.py forgot to import subprocess #oups * Add command to turn the leds off * Auto formatting of main.py I've used Black with default settings, see https://github.com/psf/black * First commit of stepper.py Pump parameters still needs to be checked and tuned. * addition of hardware details in config.json * Introduce hardware.json to replace the `hardware_config` of config.json * stepper.py: calibration, typos * creates the MQTT_Client class * pump_max_speed is now in ml/min to help readability * forgot to add self to the class def * addition of threading capabilities to stepper.py (UNTESTED) * mqtt: fix topic bug * remove counter * mqtt add doc about topics * stepper.py creates an "actuator/*/state" topic * stepper.py: rename mqtt_client to pump_client * mqtt.py: add details about topics * stepper.py: rename pump_client to actuator_client * topic was not split properly and a part was lost * switch to f-strings for mqtt.py * cosmetic update * stepper.py: folder name will be planktoscope change calls * hardware.json became more straightforward * stepper.py syntax bugs * stepper.py addition of a received stop command * stepper.py: update to max travel distance * stepper.py: several typos here * rename folder * main.py: reword to reflect folder rename * main.py: remove logic that has been moved to stepper.py and mqtt.py * main.py: update to add mqtt imaging client * mqtt.py: make command and args local to class and output more verbose * make stepper.py a class * main.py: instantiate stepper class and call it * main.py: name mqtt client * update to main.json to reflect main.py changes * fix bugs around pump control * update flows to latest version from Thibault * distance can be a small value, and definitevely should be a float. * unify mqtt topics * unify mqtt output in the main flow * first logger implementation, uses loguru * mqtt: add reason to on_connect * mqtt: add on_disconnect handler * stepper: add more logger calls for debug mainly * main: add levels for logger * imager.py: first move of the imager logic * imager: time import cleanup * imager: morphocut import cleanup * imager: skimage import cleanup * imager: finishing import cleanup * imager: Class creation - WIP Also provides a fix for #26 (see line 190). * imager: threading is needed for Condition() * streamer: get the streamer server its own file * imager: creates start_camera and get the server creation out * imager: subclass multiprocessing.Process * imager: get Pipeline creation its own function * imager: cleanup of self calls * main: code removal and corresponding calls to newly created classes * imager: various formatting changes * main: management of signal shutdown * add requirements.txt * mqtt: messages are now json objects Also, addition of a flag on receiving a new message * mqtt: make message private and add logic to synchronise * stepper: creates the stepper class * stepper: use the new class * stepper: uses the new logic * stepper: add the shutdown event * stepper: add shutdown method * main: add shutdown event * imager: graceful shutdown * stepper: nicer way of checking the Eevnt * self is a required first argument for a method in a class Especially if you use said class private members! * python: various typos and small errors in import * stepper: create mqtt client during init * stepper: instanciate the mqtt client inside run Otherwise it's not accessible from inside the loop. It's a PITA, more information at https://stackoverflow.com/questions/17172878/using-pythons-multiprocessing-process-class * stepper: little bugs and typos all around * mqtt: add shutdown method * mqtt: add connect in init * stepper: fix bugs, sanitize inputs * stepper: work on delay prediction improvements * stepper: json is mean, double quote are mandatory inside * mqtt: add details about message exchanged * imager: first implementation of json messages * main.json: add new tab for RPi management + json for payloads * imager: add state_machine class * stepper: publish last will * imager: major refactor * main: make streaming server process a daemon * mqtt: insert debug statement on close * main: reorder imports * imager: make it work! Reinsert the streaming server logic in there, because there is a problem with the synchronisation part otherwise. Also, eventually, StreamingOuput() will have to be made not global Final very critical learning: it's super duper important to make sure the memory split is at least 256Meg for the GPU. Chaos ensues otherwise * main: changes to accomodate the streamer/imager fusino * imager_state_machine: insert states transition description * stepper: cleanup of code * segmenter: creation of the class * python: include segmenter changes * remove unused files * stepper: check existence of hardware.json * main.json: changes to reflect the python script evolution * remove unecessary TODOs and add some others * main: add check for config and directories * imager: update_config is implemented and we have better management of directories now * segmenter: now work recursively in all folders * flow: the configuration is now sent via mqtt * segmenter: better manage pipeline error * segmenter: declaration of archive_fn in init * imager: small bugs and typos * main: add uniqueID output * imager: add the camera settings message We can now update the ISO, shutter speed and resolution from Node-Red * package.json: update dependencies
2020-09-28 11:05:27 +02:00
"wires": [
[
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"672d89a8.4e6968"
Extraction and refactor of the python code from node-red flow The rationale for this rewrite is to improve the readability, the modularity, the reliability and the future-proofing of the main python script. All in all, this is now 124 commits that are going to be squashed and merged together, spanning more than two weeks of development and testing. Please test away this release and break things. An upgrading guide will be published in the coming days, along with a new image for people to use if they don't want to upgrade on their own. Read along if you want to know all the goodies! As a starter, the python script was extracted from the main flow, and now lives in its own files at `PlantonScope/scripts/*`. We set up the auto formatting of the code by using [Black](https://github.com/psf/black). This make the code clearer and uniform. We are using the default settings, so if you just install Black and set your editor to format on save using it, you should be good to go. The code is separated in four main processes, each with a specific set of responsibilities: - The main process controls all the others, starts everything up and cleans up on shutdown - The stepper process manages the stepper movements. It's now possible to have simultaneous movements of both motors (this closes #38 ). - The imager process controls the camera and the streaming server via a state machine. - The segmenter process manages the segmentation and its outputs. The segmentation happens recursively in all folders in `/home/pi/PlanktonScope/img/`. Each folder has its own output archive, and bug #26 is now closed. Those processes communicates together using MQTT and json messages. Each message is adressed to one topic. The high level topic controls which process receives the message. The details of each topic is at the end of this commit message. Every imaging sessions has now its own folder, under the `img` root. Metadata are saved individually for every session, in a JSON file in the same directory as the pictures. The configuration is not parsed from `config.json` anymore and passed directly through MQTT messages to the concerned process. A new configuration file has been created: `hardware.json`. This file contains information related to your specific hardware configuration. You can choose to reverse the connection of the motors for example, but you can also define specific speed limits and steps number for your pump and focus stage. This will make it easier for people who wants to experiment with different kind of hardware. It's not necessary to have this file though. If it doesn't exists, the default configuration will be applied. The code is architectured around 6 modules and about 10 classes. I encourage you to have a look at the files, they're pretty straightforward to understand. There is a lot of work left around the node-red code refactoring, dashboard ui improvements, better and clearer LED messages, OLED screen integration and finer control of the segmentation process, but this is quite good for now. Here is the topic lists for MQTT and the corresponding messages. - actuator : This topic adresses the stepper control thread No publication under this topic should happen from the python process - actuator/pump : Control of the pump The message is a json object {"action":"move", "direction":"FORWARD", "volume":10, "flowrate":1} to move 10mL forward at 1mL/min action can be "move" or "stop" Receive only - actuator/focus : Control of the focus stage The message is a json object, speed is optional {"action":"move", "direction":"UP", "distance":0.26, "speed":1} to move up 10mm action can be "move" or "stop" Receive only - imager/image : This topic adresses the imaging thread Is a json object with {"action":"image","sleep":5,"volume":1,"nb_frame":200} sleep in seconds, volume in mL Can also receive a config update message: {"action":"config","config":[...]} Can also receive a camera settings message: {"action":"settings","iso":100,"shutter_speed":40} Receive only - segmenter/segment : This topic adresses the segmenter process Is a json object with {"action":"segment"} Receive only - status : This topics sends feedback to Node-Red No publication or receive at this level - status/pump : State of the pump Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/focus : State of the focus stage Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/imager : State of the imager Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Completed or 12_11_15_0.1.jpg has been imaged. Publish only - status/segmenter : Status of the segmentation - status/segmenter/name - status/segmenter/object_id - status/segmenter/metric Here is the original commit history: * Extract python main.py from flow * Fix bug in server addresses These addresses should be the loopback device instead of the network address of the device. Using the loopback address will not necessitate to update the script when the network address changes. * clean up picamera import * changes to main python and flow: update MQTT requests address to localhost (bugfix) update streaming output address to nothing update main flow to remove python script references and location * Automatically initialise imaging led on startup to off state. * Add the ability to invert outputs of the motor We added a key to config.json "hardware_config" with a subkey "stepper_reverse". If this key is present in the config file and set to 1, the output of the motors are inversed (stepper2 becomes the pump motor and stepper1 the focus motor) * move all non main script to a subfolder * add __init__.py to package * light module rewrite * json cleanup and absolute path for config file * light.py forgot to import subprocess #oups * Add command to turn the leds off * Auto formatting of main.py I've used Black with default settings, see https://github.com/psf/black * First commit of stepper.py Pump parameters still needs to be checked and tuned. * addition of hardware details in config.json * Introduce hardware.json to replace the `hardware_config` of config.json * stepper.py: calibration, typos * creates the MQTT_Client class * pump_max_speed is now in ml/min to help readability * forgot to add self to the class def * addition of threading capabilities to stepper.py (UNTESTED) * mqtt: fix topic bug * remove counter * mqtt add doc about topics * stepper.py creates an "actuator/*/state" topic * stepper.py: rename mqtt_client to pump_client * mqtt.py: add details about topics * stepper.py: rename pump_client to actuator_client * topic was not split properly and a part was lost * switch to f-strings for mqtt.py * cosmetic update * stepper.py: folder name will be planktoscope change calls * hardware.json became more straightforward * stepper.py syntax bugs * stepper.py addition of a received stop command * stepper.py: update to max travel distance * stepper.py: several typos here * rename folder * main.py: reword to reflect folder rename * main.py: remove logic that has been moved to stepper.py and mqtt.py * main.py: update to add mqtt imaging client * mqtt.py: make command and args local to class and output more verbose * make stepper.py a class * main.py: instantiate stepper class and call it * main.py: name mqtt client * update to main.json to reflect main.py changes * fix bugs around pump control * update flows to latest version from Thibault * distance can be a small value, and definitevely should be a float. * unify mqtt topics * unify mqtt output in the main flow * first logger implementation, uses loguru * mqtt: add reason to on_connect * mqtt: add on_disconnect handler * stepper: add more logger calls for debug mainly * main: add levels for logger * imager.py: first move of the imager logic * imager: time import cleanup * imager: morphocut import cleanup * imager: skimage import cleanup * imager: finishing import cleanup * imager: Class creation - WIP Also provides a fix for #26 (see line 190). * imager: threading is needed for Condition() * streamer: get the streamer server its own file * imager: creates start_camera and get the server creation out * imager: subclass multiprocessing.Process * imager: get Pipeline creation its own function * imager: cleanup of self calls * main: code removal and corresponding calls to newly created classes * imager: various formatting changes * main: management of signal shutdown * add requirements.txt * mqtt: messages are now json objects Also, addition of a flag on receiving a new message * mqtt: make message private and add logic to synchronise * stepper: creates the stepper class * stepper: use the new class * stepper: uses the new logic * stepper: add the shutdown event * stepper: add shutdown method * main: add shutdown event * imager: graceful shutdown * stepper: nicer way of checking the Eevnt * self is a required first argument for a method in a class Especially if you use said class private members! * python: various typos and small errors in import * stepper: create mqtt client during init * stepper: instanciate the mqtt client inside run Otherwise it's not accessible from inside the loop. It's a PITA, more information at https://stackoverflow.com/questions/17172878/using-pythons-multiprocessing-process-class * stepper: little bugs and typos all around * mqtt: add shutdown method * mqtt: add connect in init * stepper: fix bugs, sanitize inputs * stepper: work on delay prediction improvements * stepper: json is mean, double quote are mandatory inside * mqtt: add details about message exchanged * imager: first implementation of json messages * main.json: add new tab for RPi management + json for payloads * imager: add state_machine class * stepper: publish last will * imager: major refactor * main: make streaming server process a daemon * mqtt: insert debug statement on close * main: reorder imports * imager: make it work! Reinsert the streaming server logic in there, because there is a problem with the synchronisation part otherwise. Also, eventually, StreamingOuput() will have to be made not global Final very critical learning: it's super duper important to make sure the memory split is at least 256Meg for the GPU. Chaos ensues otherwise * main: changes to accomodate the streamer/imager fusino * imager_state_machine: insert states transition description * stepper: cleanup of code * segmenter: creation of the class * python: include segmenter changes * remove unused files * stepper: check existence of hardware.json * main.json: changes to reflect the python script evolution * remove unecessary TODOs and add some others * main: add check for config and directories * imager: update_config is implemented and we have better management of directories now * segmenter: now work recursively in all folders * flow: the configuration is now sent via mqtt * segmenter: better manage pipeline error * segmenter: declaration of archive_fn in init * imager: small bugs and typos * main: add uniqueID output * imager: add the camera settings message We can now update the ISO, shutter speed and resolution from Node-Red * package.json: update dependencies
2020-09-28 11:05:27 +02:00
]
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},
{
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"id": "569154a.b53182c",
"type": "inject",
"z": "1371dec5.76e671",
"name": "once",
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Extraction and refactor of the python code from node-red flow The rationale for this rewrite is to improve the readability, the modularity, the reliability and the future-proofing of the main python script. All in all, this is now 124 commits that are going to be squashed and merged together, spanning more than two weeks of development and testing. Please test away this release and break things. An upgrading guide will be published in the coming days, along with a new image for people to use if they don't want to upgrade on their own. Read along if you want to know all the goodies! As a starter, the python script was extracted from the main flow, and now lives in its own files at `PlantonScope/scripts/*`. We set up the auto formatting of the code by using [Black](https://github.com/psf/black). This make the code clearer and uniform. We are using the default settings, so if you just install Black and set your editor to format on save using it, you should be good to go. The code is separated in four main processes, each with a specific set of responsibilities: - The main process controls all the others, starts everything up and cleans up on shutdown - The stepper process manages the stepper movements. It's now possible to have simultaneous movements of both motors (this closes #38 ). - The imager process controls the camera and the streaming server via a state machine. - The segmenter process manages the segmentation and its outputs. The segmentation happens recursively in all folders in `/home/pi/PlanktonScope/img/`. Each folder has its own output archive, and bug #26 is now closed. Those processes communicates together using MQTT and json messages. Each message is adressed to one topic. The high level topic controls which process receives the message. The details of each topic is at the end of this commit message. Every imaging sessions has now its own folder, under the `img` root. Metadata are saved individually for every session, in a JSON file in the same directory as the pictures. The configuration is not parsed from `config.json` anymore and passed directly through MQTT messages to the concerned process. A new configuration file has been created: `hardware.json`. This file contains information related to your specific hardware configuration. You can choose to reverse the connection of the motors for example, but you can also define specific speed limits and steps number for your pump and focus stage. This will make it easier for people who wants to experiment with different kind of hardware. It's not necessary to have this file though. If it doesn't exists, the default configuration will be applied. The code is architectured around 6 modules and about 10 classes. I encourage you to have a look at the files, they're pretty straightforward to understand. There is a lot of work left around the node-red code refactoring, dashboard ui improvements, better and clearer LED messages, OLED screen integration and finer control of the segmentation process, but this is quite good for now. Here is the topic lists for MQTT and the corresponding messages. - actuator : This topic adresses the stepper control thread No publication under this topic should happen from the python process - actuator/pump : Control of the pump The message is a json object {"action":"move", "direction":"FORWARD", "volume":10, "flowrate":1} to move 10mL forward at 1mL/min action can be "move" or "stop" Receive only - actuator/focus : Control of the focus stage The message is a json object, speed is optional {"action":"move", "direction":"UP", "distance":0.26, "speed":1} to move up 10mm action can be "move" or "stop" Receive only - imager/image : This topic adresses the imaging thread Is a json object with {"action":"image","sleep":5,"volume":1,"nb_frame":200} sleep in seconds, volume in mL Can also receive a config update message: {"action":"config","config":[...]} Can also receive a camera settings message: {"action":"settings","iso":100,"shutter_speed":40} Receive only - segmenter/segment : This topic adresses the segmenter process Is a json object with {"action":"segment"} Receive only - status : This topics sends feedback to Node-Red No publication or receive at this level - status/pump : State of the pump Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/focus : State of the focus stage Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/imager : State of the imager Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Completed or 12_11_15_0.1.jpg has been imaged. Publish only - status/segmenter : Status of the segmentation - status/segmenter/name - status/segmenter/object_id - status/segmenter/metric Here is the original commit history: * Extract python main.py from flow * Fix bug in server addresses These addresses should be the loopback device instead of the network address of the device. Using the loopback address will not necessitate to update the script when the network address changes. * clean up picamera import * changes to main python and flow: update MQTT requests address to localhost (bugfix) update streaming output address to nothing update main flow to remove python script references and location * Automatically initialise imaging led on startup to off state. * Add the ability to invert outputs of the motor We added a key to config.json "hardware_config" with a subkey "stepper_reverse". If this key is present in the config file and set to 1, the output of the motors are inversed (stepper2 becomes the pump motor and stepper1 the focus motor) * move all non main script to a subfolder * add __init__.py to package * light module rewrite * json cleanup and absolute path for config file * light.py forgot to import subprocess #oups * Add command to turn the leds off * Auto formatting of main.py I've used Black with default settings, see https://github.com/psf/black * First commit of stepper.py Pump parameters still needs to be checked and tuned. * addition of hardware details in config.json * Introduce hardware.json to replace the `hardware_config` of config.json * stepper.py: calibration, typos * creates the MQTT_Client class * pump_max_speed is now in ml/min to help readability * forgot to add self to the class def * addition of threading capabilities to stepper.py (UNTESTED) * mqtt: fix topic bug * remove counter * mqtt add doc about topics * stepper.py creates an "actuator/*/state" topic * stepper.py: rename mqtt_client to pump_client * mqtt.py: add details about topics * stepper.py: rename pump_client to actuator_client * topic was not split properly and a part was lost * switch to f-strings for mqtt.py * cosmetic update * stepper.py: folder name will be planktoscope change calls * hardware.json became more straightforward * stepper.py syntax bugs * stepper.py addition of a received stop command * stepper.py: update to max travel distance * stepper.py: several typos here * rename folder * main.py: reword to reflect folder rename * main.py: remove logic that has been moved to stepper.py and mqtt.py * main.py: update to add mqtt imaging client * mqtt.py: make command and args local to class and output more verbose * make stepper.py a class * main.py: instantiate stepper class and call it * main.py: name mqtt client * update to main.json to reflect main.py changes * fix bugs around pump control * update flows to latest version from Thibault * distance can be a small value, and definitevely should be a float. * unify mqtt topics * unify mqtt output in the main flow * first logger implementation, uses loguru * mqtt: add reason to on_connect * mqtt: add on_disconnect handler * stepper: add more logger calls for debug mainly * main: add levels for logger * imager.py: first move of the imager logic * imager: time import cleanup * imager: morphocut import cleanup * imager: skimage import cleanup * imager: finishing import cleanup * imager: Class creation - WIP Also provides a fix for #26 (see line 190). * imager: threading is needed for Condition() * streamer: get the streamer server its own file * imager: creates start_camera and get the server creation out * imager: subclass multiprocessing.Process * imager: get Pipeline creation its own function * imager: cleanup of self calls * main: code removal and corresponding calls to newly created classes * imager: various formatting changes * main: management of signal shutdown * add requirements.txt * mqtt: messages are now json objects Also, addition of a flag on receiving a new message * mqtt: make message private and add logic to synchronise * stepper: creates the stepper class * stepper: use the new class * stepper: uses the new logic * stepper: add the shutdown event * stepper: add shutdown method * main: add shutdown event * imager: graceful shutdown * stepper: nicer way of checking the Eevnt * self is a required first argument for a method in a class Especially if you use said class private members! * python: various typos and small errors in import * stepper: create mqtt client during init * stepper: instanciate the mqtt client inside run Otherwise it's not accessible from inside the loop. It's a PITA, more information at https://stackoverflow.com/questions/17172878/using-pythons-multiprocessing-process-class * stepper: little bugs and typos all around * mqtt: add shutdown method * mqtt: add connect in init * stepper: fix bugs, sanitize inputs * stepper: work on delay prediction improvements * stepper: json is mean, double quote are mandatory inside * mqtt: add details about message exchanged * imager: first implementation of json messages * main.json: add new tab for RPi management + json for payloads * imager: add state_machine class * stepper: publish last will * imager: major refactor * main: make streaming server process a daemon * mqtt: insert debug statement on close * main: reorder imports * imager: make it work! Reinsert the streaming server logic in there, because there is a problem with the synchronisation part otherwise. Also, eventually, StreamingOuput() will have to be made not global Final very critical learning: it's super duper important to make sure the memory split is at least 256Meg for the GPU. Chaos ensues otherwise * main: changes to accomodate the streamer/imager fusino * imager_state_machine: insert states transition description * stepper: cleanup of code * segmenter: creation of the class * python: include segmenter changes * remove unused files * stepper: check existence of hardware.json * main.json: changes to reflect the python script evolution * remove unecessary TODOs and add some others * main: add check for config and directories * imager: update_config is implemented and we have better management of directories now * segmenter: now work recursively in all folders * flow: the configuration is now sent via mqtt * segmenter: better manage pipeline error * segmenter: declaration of archive_fn in init * imager: small bugs and typos * main: add uniqueID output * imager: add the camera settings message We can now update the ISO, shutter speed and resolution from Node-Red * package.json: update dependencies
2020-09-28 11:05:27 +02:00
"wires": [
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Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
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Extraction and refactor of the python code from node-red flow The rationale for this rewrite is to improve the readability, the modularity, the reliability and the future-proofing of the main python script. All in all, this is now 124 commits that are going to be squashed and merged together, spanning more than two weeks of development and testing. Please test away this release and break things. An upgrading guide will be published in the coming days, along with a new image for people to use if they don't want to upgrade on their own. Read along if you want to know all the goodies! As a starter, the python script was extracted from the main flow, and now lives in its own files at `PlantonScope/scripts/*`. We set up the auto formatting of the code by using [Black](https://github.com/psf/black). This make the code clearer and uniform. We are using the default settings, so if you just install Black and set your editor to format on save using it, you should be good to go. The code is separated in four main processes, each with a specific set of responsibilities: - The main process controls all the others, starts everything up and cleans up on shutdown - The stepper process manages the stepper movements. It's now possible to have simultaneous movements of both motors (this closes #38 ). - The imager process controls the camera and the streaming server via a state machine. - The segmenter process manages the segmentation and its outputs. The segmentation happens recursively in all folders in `/home/pi/PlanktonScope/img/`. Each folder has its own output archive, and bug #26 is now closed. Those processes communicates together using MQTT and json messages. Each message is adressed to one topic. The high level topic controls which process receives the message. The details of each topic is at the end of this commit message. Every imaging sessions has now its own folder, under the `img` root. Metadata are saved individually for every session, in a JSON file in the same directory as the pictures. The configuration is not parsed from `config.json` anymore and passed directly through MQTT messages to the concerned process. A new configuration file has been created: `hardware.json`. This file contains information related to your specific hardware configuration. You can choose to reverse the connection of the motors for example, but you can also define specific speed limits and steps number for your pump and focus stage. This will make it easier for people who wants to experiment with different kind of hardware. It's not necessary to have this file though. If it doesn't exists, the default configuration will be applied. The code is architectured around 6 modules and about 10 classes. I encourage you to have a look at the files, they're pretty straightforward to understand. There is a lot of work left around the node-red code refactoring, dashboard ui improvements, better and clearer LED messages, OLED screen integration and finer control of the segmentation process, but this is quite good for now. Here is the topic lists for MQTT and the corresponding messages. - actuator : This topic adresses the stepper control thread No publication under this topic should happen from the python process - actuator/pump : Control of the pump The message is a json object {"action":"move", "direction":"FORWARD", "volume":10, "flowrate":1} to move 10mL forward at 1mL/min action can be "move" or "stop" Receive only - actuator/focus : Control of the focus stage The message is a json object, speed is optional {"action":"move", "direction":"UP", "distance":0.26, "speed":1} to move up 10mm action can be "move" or "stop" Receive only - imager/image : This topic adresses the imaging thread Is a json object with {"action":"image","sleep":5,"volume":1,"nb_frame":200} sleep in seconds, volume in mL Can also receive a config update message: {"action":"config","config":[...]} Can also receive a camera settings message: {"action":"settings","iso":100,"shutter_speed":40} Receive only - segmenter/segment : This topic adresses the segmenter process Is a json object with {"action":"segment"} Receive only - status : This topics sends feedback to Node-Red No publication or receive at this level - status/pump : State of the pump Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/focus : State of the focus stage Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/imager : State of the imager Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Completed or 12_11_15_0.1.jpg has been imaged. Publish only - status/segmenter : Status of the segmentation - status/segmenter/name - status/segmenter/object_id - status/segmenter/metric Here is the original commit history: * Extract python main.py from flow * Fix bug in server addresses These addresses should be the loopback device instead of the network address of the device. Using the loopback address will not necessitate to update the script when the network address changes. * clean up picamera import * changes to main python and flow: update MQTT requests address to localhost (bugfix) update streaming output address to nothing update main flow to remove python script references and location * Automatically initialise imaging led on startup to off state. * Add the ability to invert outputs of the motor We added a key to config.json "hardware_config" with a subkey "stepper_reverse". If this key is present in the config file and set to 1, the output of the motors are inversed (stepper2 becomes the pump motor and stepper1 the focus motor) * move all non main script to a subfolder * add __init__.py to package * light module rewrite * json cleanup and absolute path for config file * light.py forgot to import subprocess #oups * Add command to turn the leds off * Auto formatting of main.py I've used Black with default settings, see https://github.com/psf/black * First commit of stepper.py Pump parameters still needs to be checked and tuned. * addition of hardware details in config.json * Introduce hardware.json to replace the `hardware_config` of config.json * stepper.py: calibration, typos * creates the MQTT_Client class * pump_max_speed is now in ml/min to help readability * forgot to add self to the class def * addition of threading capabilities to stepper.py (UNTESTED) * mqtt: fix topic bug * remove counter * mqtt add doc about topics * stepper.py creates an "actuator/*/state" topic * stepper.py: rename mqtt_client to pump_client * mqtt.py: add details about topics * stepper.py: rename pump_client to actuator_client * topic was not split properly and a part was lost * switch to f-strings for mqtt.py * cosmetic update * stepper.py: folder name will be planktoscope change calls * hardware.json became more straightforward * stepper.py syntax bugs * stepper.py addition of a received stop command * stepper.py: update to max travel distance * stepper.py: several typos here * rename folder * main.py: reword to reflect folder rename * main.py: remove logic that has been moved to stepper.py and mqtt.py * main.py: update to add mqtt imaging client * mqtt.py: make command and args local to class and output more verbose * make stepper.py a class * main.py: instantiate stepper class and call it * main.py: name mqtt client * update to main.json to reflect main.py changes * fix bugs around pump control * update flows to latest version from Thibault * distance can be a small value, and definitevely should be a float. * unify mqtt topics * unify mqtt output in the main flow * first logger implementation, uses loguru * mqtt: add reason to on_connect * mqtt: add on_disconnect handler * stepper: add more logger calls for debug mainly * main: add levels for logger * imager.py: first move of the imager logic * imager: time import cleanup * imager: morphocut import cleanup * imager: skimage import cleanup * imager: finishing import cleanup * imager: Class creation - WIP Also provides a fix for #26 (see line 190). * imager: threading is needed for Condition() * streamer: get the streamer server its own file * imager: creates start_camera and get the server creation out * imager: subclass multiprocessing.Process * imager: get Pipeline creation its own function * imager: cleanup of self calls * main: code removal and corresponding calls to newly created classes * imager: various formatting changes * main: management of signal shutdown * add requirements.txt * mqtt: messages are now json objects Also, addition of a flag on receiving a new message * mqtt: make message private and add logic to synchronise * stepper: creates the stepper class * stepper: use the new class * stepper: uses the new logic * stepper: add the shutdown event * stepper: add shutdown method * main: add shutdown event * imager: graceful shutdown * stepper: nicer way of checking the Eevnt * self is a required first argument for a method in a class Especially if you use said class private members! * python: various typos and small errors in import * stepper: create mqtt client during init * stepper: instanciate the mqtt client inside run Otherwise it's not accessible from inside the loop. It's a PITA, more information at https://stackoverflow.com/questions/17172878/using-pythons-multiprocessing-process-class * stepper: little bugs and typos all around * mqtt: add shutdown method * mqtt: add connect in init * stepper: fix bugs, sanitize inputs * stepper: work on delay prediction improvements * stepper: json is mean, double quote are mandatory inside * mqtt: add details about message exchanged * imager: first implementation of json messages * main.json: add new tab for RPi management + json for payloads * imager: add state_machine class * stepper: publish last will * imager: major refactor * main: make streaming server process a daemon * mqtt: insert debug statement on close * main: reorder imports * imager: make it work! Reinsert the streaming server logic in there, because there is a problem with the synchronisation part otherwise. Also, eventually, StreamingOuput() will have to be made not global Final very critical learning: it's super duper important to make sure the memory split is at least 256Meg for the GPU. Chaos ensues otherwise * main: changes to accomodate the streamer/imager fusino * imager_state_machine: insert states transition description * stepper: cleanup of code * segmenter: creation of the class * python: include segmenter changes * remove unused files * stepper: check existence of hardware.json * main.json: changes to reflect the python script evolution * remove unecessary TODOs and add some others * main: add check for config and directories * imager: update_config is implemented and we have better management of directories now * segmenter: now work recursively in all folders * flow: the configuration is now sent via mqtt * segmenter: better manage pipeline error * segmenter: declaration of archive_fn in init * imager: small bugs and typos * main: add uniqueID output * imager: add the camera settings message We can now update the ISO, shutter speed and resolution from Node-Red * package.json: update dependencies
2020-09-28 11:05:27 +02:00
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Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"id": "3829adc.ccc87d2",
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"z": "1371dec5.76e671",
"command": "sudo killall -15 raspimjpeg",
"addpay": true,
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"useSpawn": "false",
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"oldrc": false,
"name": "Raspimjpeg soft kill",
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"order": 1,
Extraction and refactor of the python code from node-red flow The rationale for this rewrite is to improve the readability, the modularity, the reliability and the future-proofing of the main python script. All in all, this is now 124 commits that are going to be squashed and merged together, spanning more than two weeks of development and testing. Please test away this release and break things. An upgrading guide will be published in the coming days, along with a new image for people to use if they don't want to upgrade on their own. Read along if you want to know all the goodies! As a starter, the python script was extracted from the main flow, and now lives in its own files at `PlantonScope/scripts/*`. We set up the auto formatting of the code by using [Black](https://github.com/psf/black). This make the code clearer and uniform. We are using the default settings, so if you just install Black and set your editor to format on save using it, you should be good to go. The code is separated in four main processes, each with a specific set of responsibilities: - The main process controls all the others, starts everything up and cleans up on shutdown - The stepper process manages the stepper movements. It's now possible to have simultaneous movements of both motors (this closes #38 ). - The imager process controls the camera and the streaming server via a state machine. - The segmenter process manages the segmentation and its outputs. The segmentation happens recursively in all folders in `/home/pi/PlanktonScope/img/`. Each folder has its own output archive, and bug #26 is now closed. Those processes communicates together using MQTT and json messages. Each message is adressed to one topic. The high level topic controls which process receives the message. The details of each topic is at the end of this commit message. Every imaging sessions has now its own folder, under the `img` root. Metadata are saved individually for every session, in a JSON file in the same directory as the pictures. The configuration is not parsed from `config.json` anymore and passed directly through MQTT messages to the concerned process. A new configuration file has been created: `hardware.json`. This file contains information related to your specific hardware configuration. You can choose to reverse the connection of the motors for example, but you can also define specific speed limits and steps number for your pump and focus stage. This will make it easier for people who wants to experiment with different kind of hardware. It's not necessary to have this file though. If it doesn't exists, the default configuration will be applied. The code is architectured around 6 modules and about 10 classes. I encourage you to have a look at the files, they're pretty straightforward to understand. There is a lot of work left around the node-red code refactoring, dashboard ui improvements, better and clearer LED messages, OLED screen integration and finer control of the segmentation process, but this is quite good for now. Here is the topic lists for MQTT and the corresponding messages. - actuator : This topic adresses the stepper control thread No publication under this topic should happen from the python process - actuator/pump : Control of the pump The message is a json object {"action":"move", "direction":"FORWARD", "volume":10, "flowrate":1} to move 10mL forward at 1mL/min action can be "move" or "stop" Receive only - actuator/focus : Control of the focus stage The message is a json object, speed is optional {"action":"move", "direction":"UP", "distance":0.26, "speed":1} to move up 10mm action can be "move" or "stop" Receive only - imager/image : This topic adresses the imaging thread Is a json object with {"action":"image","sleep":5,"volume":1,"nb_frame":200} sleep in seconds, volume in mL Can also receive a config update message: {"action":"config","config":[...]} Can also receive a camera settings message: {"action":"settings","iso":100,"shutter_speed":40} Receive only - segmenter/segment : This topic adresses the segmenter process Is a json object with {"action":"segment"} Receive only - status : This topics sends feedback to Node-Red No publication or receive at this level - status/pump : State of the pump Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/focus : State of the focus stage Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/imager : State of the imager Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Completed or 12_11_15_0.1.jpg has been imaged. Publish only - status/segmenter : Status of the segmentation - status/segmenter/name - status/segmenter/object_id - status/segmenter/metric Here is the original commit history: * Extract python main.py from flow * Fix bug in server addresses These addresses should be the loopback device instead of the network address of the device. Using the loopback address will not necessitate to update the script when the network address changes. * clean up picamera import * changes to main python and flow: update MQTT requests address to localhost (bugfix) update streaming output address to nothing update main flow to remove python script references and location * Automatically initialise imaging led on startup to off state. * Add the ability to invert outputs of the motor We added a key to config.json "hardware_config" with a subkey "stepper_reverse". If this key is present in the config file and set to 1, the output of the motors are inversed (stepper2 becomes the pump motor and stepper1 the focus motor) * move all non main script to a subfolder * add __init__.py to package * light module rewrite * json cleanup and absolute path for config file * light.py forgot to import subprocess #oups * Add command to turn the leds off * Auto formatting of main.py I've used Black with default settings, see https://github.com/psf/black * First commit of stepper.py Pump parameters still needs to be checked and tuned. * addition of hardware details in config.json * Introduce hardware.json to replace the `hardware_config` of config.json * stepper.py: calibration, typos * creates the MQTT_Client class * pump_max_speed is now in ml/min to help readability * forgot to add self to the class def * addition of threading capabilities to stepper.py (UNTESTED) * mqtt: fix topic bug * remove counter * mqtt add doc about topics * stepper.py creates an "actuator/*/state" topic * stepper.py: rename mqtt_client to pump_client * mqtt.py: add details about topics * stepper.py: rename pump_client to actuator_client * topic was not split properly and a part was lost * switch to f-strings for mqtt.py * cosmetic update * stepper.py: folder name will be planktoscope change calls * hardware.json became more straightforward * stepper.py syntax bugs * stepper.py addition of a received stop command * stepper.py: update to max travel distance * stepper.py: several typos here * rename folder * main.py: reword to reflect folder rename * main.py: remove logic that has been moved to stepper.py and mqtt.py * main.py: update to add mqtt imaging client * mqtt.py: make command and args local to class and output more verbose * make stepper.py a class * main.py: instantiate stepper class and call it * main.py: name mqtt client * update to main.json to reflect main.py changes * fix bugs around pump control * update flows to latest version from Thibault * distance can be a small value, and definitevely should be a float. * unify mqtt topics * unify mqtt output in the main flow * first logger implementation, uses loguru * mqtt: add reason to on_connect * mqtt: add on_disconnect handler * stepper: add more logger calls for debug mainly * main: add levels for logger * imager.py: first move of the imager logic * imager: time import cleanup * imager: morphocut import cleanup * imager: skimage import cleanup * imager: finishing import cleanup * imager: Class creation - WIP Also provides a fix for #26 (see line 190). * imager: threading is needed for Condition() * streamer: get the streamer server its own file * imager: creates start_camera and get the server creation out * imager: subclass multiprocessing.Process * imager: get Pipeline creation its own function * imager: cleanup of self calls * main: code removal and corresponding calls to newly created classes * imager: various formatting changes * main: management of signal shutdown * add requirements.txt * mqtt: messages are now json objects Also, addition of a flag on receiving a new message * mqtt: make message private and add logic to synchronise * stepper: creates the stepper class * stepper: use the new class * stepper: uses the new logic * stepper: add the shutdown event * stepper: add shutdown method * main: add shutdown event * imager: graceful shutdown * stepper: nicer way of checking the Eevnt * self is a required first argument for a method in a class Especially if you use said class private members! * python: various typos and small errors in import * stepper: create mqtt client during init * stepper: instanciate the mqtt client inside run Otherwise it's not accessible from inside the loop. It's a PITA, more information at https://stackoverflow.com/questions/17172878/using-pythons-multiprocessing-process-class * stepper: little bugs and typos all around * mqtt: add shutdown method * mqtt: add connect in init * stepper: fix bugs, sanitize inputs * stepper: work on delay prediction improvements * stepper: json is mean, double quote are mandatory inside * mqtt: add details about message exchanged * imager: first implementation of json messages * main.json: add new tab for RPi management + json for payloads * imager: add state_machine class * stepper: publish last will * imager: major refactor * main: make streaming server process a daemon * mqtt: insert debug statement on close * main: reorder imports * imager: make it work! Reinsert the streaming server logic in there, because there is a problem with the synchronisation part otherwise. Also, eventually, StreamingOuput() will have to be made not global Final very critical learning: it's super duper important to make sure the memory split is at least 256Meg for the GPU. Chaos ensues otherwise * main: changes to accomodate the streamer/imager fusino * imager_state_machine: insert states transition description * stepper: cleanup of code * segmenter: creation of the class * python: include segmenter changes * remove unused files * stepper: check existence of hardware.json * main.json: changes to reflect the python script evolution * remove unecessary TODOs and add some others * main: add check for config and directories * imager: update_config is implemented and we have better management of directories now * segmenter: now work recursively in all folders * flow: the configuration is now sent via mqtt * segmenter: better manage pipeline error * segmenter: declaration of archive_fn in init * imager: small bugs and typos * main: add uniqueID output * imager: add the camera settings message We can now update the ISO, shutter speed and resolution from Node-Red * package.json: update dependencies
2020-09-28 11:05:27 +02:00
"width": 0,
"height": 0,
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"format": "<div><center>If you want to update to the latest code version of Node-Red and Python, please click here.\n<br>\nPlease note that all your changes are going to be saved with git stash but are not going to be restored!</center></div>",
"storeOutMessages": true,
"fwdInMessages": true,
"resendOnRefresh": true,
"templateScope": "local",
"x": 100,
"y": 460,
"wires": [
[]
]
},
{
"id": "4b489713.ccde5",
"type": "ui_button",
"z": "baa1e3d9.cb29d",
"name": "",
"group": "4322c187.e73e5",
"order": 9,
"width": 5,
"height": 1,
"passthru": false,
"label": "Start Acquisition",
"tooltip": "",
"color": "",
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Extraction and refactor of the python code from node-red flow The rationale for this rewrite is to improve the readability, the modularity, the reliability and the future-proofing of the main python script. All in all, this is now 124 commits that are going to be squashed and merged together, spanning more than two weeks of development and testing. Please test away this release and break things. An upgrading guide will be published in the coming days, along with a new image for people to use if they don't want to upgrade on their own. Read along if you want to know all the goodies! As a starter, the python script was extracted from the main flow, and now lives in its own files at `PlantonScope/scripts/*`. We set up the auto formatting of the code by using [Black](https://github.com/psf/black). This make the code clearer and uniform. We are using the default settings, so if you just install Black and set your editor to format on save using it, you should be good to go. The code is separated in four main processes, each with a specific set of responsibilities: - The main process controls all the others, starts everything up and cleans up on shutdown - The stepper process manages the stepper movements. It's now possible to have simultaneous movements of both motors (this closes #38 ). - The imager process controls the camera and the streaming server via a state machine. - The segmenter process manages the segmentation and its outputs. The segmentation happens recursively in all folders in `/home/pi/PlanktonScope/img/`. Each folder has its own output archive, and bug #26 is now closed. Those processes communicates together using MQTT and json messages. Each message is adressed to one topic. The high level topic controls which process receives the message. The details of each topic is at the end of this commit message. Every imaging sessions has now its own folder, under the `img` root. Metadata are saved individually for every session, in a JSON file in the same directory as the pictures. The configuration is not parsed from `config.json` anymore and passed directly through MQTT messages to the concerned process. A new configuration file has been created: `hardware.json`. This file contains information related to your specific hardware configuration. You can choose to reverse the connection of the motors for example, but you can also define specific speed limits and steps number for your pump and focus stage. This will make it easier for people who wants to experiment with different kind of hardware. It's not necessary to have this file though. If it doesn't exists, the default configuration will be applied. The code is architectured around 6 modules and about 10 classes. I encourage you to have a look at the files, they're pretty straightforward to understand. There is a lot of work left around the node-red code refactoring, dashboard ui improvements, better and clearer LED messages, OLED screen integration and finer control of the segmentation process, but this is quite good for now. Here is the topic lists for MQTT and the corresponding messages. - actuator : This topic adresses the stepper control thread No publication under this topic should happen from the python process - actuator/pump : Control of the pump The message is a json object {"action":"move", "direction":"FORWARD", "volume":10, "flowrate":1} to move 10mL forward at 1mL/min action can be "move" or "stop" Receive only - actuator/focus : Control of the focus stage The message is a json object, speed is optional {"action":"move", "direction":"UP", "distance":0.26, "speed":1} to move up 10mm action can be "move" or "stop" Receive only - imager/image : This topic adresses the imaging thread Is a json object with {"action":"image","sleep":5,"volume":1,"nb_frame":200} sleep in seconds, volume in mL Can also receive a config update message: {"action":"config","config":[...]} Can also receive a camera settings message: {"action":"settings","iso":100,"shutter_speed":40} Receive only - segmenter/segment : This topic adresses the segmenter process Is a json object with {"action":"segment"} Receive only - status : This topics sends feedback to Node-Red No publication or receive at this level - status/pump : State of the pump Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/focus : State of the focus stage Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/imager : State of the imager Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Completed or 12_11_15_0.1.jpg has been imaged. Publish only - status/segmenter : Status of the segmentation - status/segmenter/name - status/segmenter/object_id - status/segmenter/metric Here is the original commit history: * Extract python main.py from flow * Fix bug in server addresses These addresses should be the loopback device instead of the network address of the device. Using the loopback address will not necessitate to update the script when the network address changes. * clean up picamera import * changes to main python and flow: update MQTT requests address to localhost (bugfix) update streaming output address to nothing update main flow to remove python script references and location * Automatically initialise imaging led on startup to off state. * Add the ability to invert outputs of the motor We added a key to config.json "hardware_config" with a subkey "stepper_reverse". If this key is present in the config file and set to 1, the output of the motors are inversed (stepper2 becomes the pump motor and stepper1 the focus motor) * move all non main script to a subfolder * add __init__.py to package * light module rewrite * json cleanup and absolute path for config file * light.py forgot to import subprocess #oups * Add command to turn the leds off * Auto formatting of main.py I've used Black with default settings, see https://github.com/psf/black * First commit of stepper.py Pump parameters still needs to be checked and tuned. * addition of hardware details in config.json * Introduce hardware.json to replace the `hardware_config` of config.json * stepper.py: calibration, typos * creates the MQTT_Client class * pump_max_speed is now in ml/min to help readability * forgot to add self to the class def * addition of threading capabilities to stepper.py (UNTESTED) * mqtt: fix topic bug * remove counter * mqtt add doc about topics * stepper.py creates an "actuator/*/state" topic * stepper.py: rename mqtt_client to pump_client * mqtt.py: add details about topics * stepper.py: rename pump_client to actuator_client * topic was not split properly and a part was lost * switch to f-strings for mqtt.py * cosmetic update * stepper.py: folder name will be planktoscope change calls * hardware.json became more straightforward * stepper.py syntax bugs * stepper.py addition of a received stop command * stepper.py: update to max travel distance * stepper.py: several typos here * rename folder * main.py: reword to reflect folder rename * main.py: remove logic that has been moved to stepper.py and mqtt.py * main.py: update to add mqtt imaging client * mqtt.py: make command and args local to class and output more verbose * make stepper.py a class * main.py: instantiate stepper class and call it * main.py: name mqtt client * update to main.json to reflect main.py changes * fix bugs around pump control * update flows to latest version from Thibault * distance can be a small value, and definitevely should be a float. * unify mqtt topics * unify mqtt output in the main flow * first logger implementation, uses loguru * mqtt: add reason to on_connect * mqtt: add on_disconnect handler * stepper: add more logger calls for debug mainly * main: add levels for logger * imager.py: first move of the imager logic * imager: time import cleanup * imager: morphocut import cleanup * imager: skimage import cleanup * imager: finishing import cleanup * imager: Class creation - WIP Also provides a fix for #26 (see line 190). * imager: threading is needed for Condition() * streamer: get the streamer server its own file * imager: creates start_camera and get the server creation out * imager: subclass multiprocessing.Process * imager: get Pipeline creation its own function * imager: cleanup of self calls * main: code removal and corresponding calls to newly created classes * imager: various formatting changes * main: management of signal shutdown * add requirements.txt * mqtt: messages are now json objects Also, addition of a flag on receiving a new message * mqtt: make message private and add logic to synchronise * stepper: creates the stepper class * stepper: use the new class * stepper: uses the new logic * stepper: add the shutdown event * stepper: add shutdown method * main: add shutdown event * imager: graceful shutdown * stepper: nicer way of checking the Eevnt * self is a required first argument for a method in a class Especially if you use said class private members! * python: various typos and small errors in import * stepper: create mqtt client during init * stepper: instanciate the mqtt client inside run Otherwise it's not accessible from inside the loop. It's a PITA, more information at https://stackoverflow.com/questions/17172878/using-pythons-multiprocessing-process-class * stepper: little bugs and typos all around * mqtt: add shutdown method * mqtt: add connect in init * stepper: fix bugs, sanitize inputs * stepper: work on delay prediction improvements * stepper: json is mean, double quote are mandatory inside * mqtt: add details about message exchanged * imager: first implementation of json messages * main.json: add new tab for RPi management + json for payloads * imager: add state_machine class * stepper: publish last will * imager: major refactor * main: make streaming server process a daemon * mqtt: insert debug statement on close * main: reorder imports * imager: make it work! Reinsert the streaming server logic in there, because there is a problem with the synchronisation part otherwise. Also, eventually, StreamingOuput() will have to be made not global Final very critical learning: it's super duper important to make sure the memory split is at least 256Meg for the GPU. Chaos ensues otherwise * main: changes to accomodate the streamer/imager fusino * imager_state_machine: insert states transition description * stepper: cleanup of code * segmenter: creation of the class * python: include segmenter changes * remove unused files * stepper: check existence of hardware.json * main.json: changes to reflect the python script evolution * remove unecessary TODOs and add some others * main: add check for config and directories * imager: update_config is implemented and we have better management of directories now * segmenter: now work recursively in all folders * flow: the configuration is now sent via mqtt * segmenter: better manage pipeline error * segmenter: declaration of archive_fn in init * imager: small bugs and typos * main: add uniqueID output * imager: add the camera settings message We can now update the ISO, shutter speed and resolution from Node-Red * package.json: update dependencies
2020-09-28 11:05:27 +02:00
"topic": "imager/image",
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"x": 520,
"y": 460,
Extraction and refactor of the python code from node-red flow The rationale for this rewrite is to improve the readability, the modularity, the reliability and the future-proofing of the main python script. All in all, this is now 124 commits that are going to be squashed and merged together, spanning more than two weeks of development and testing. Please test away this release and break things. An upgrading guide will be published in the coming days, along with a new image for people to use if they don't want to upgrade on their own. Read along if you want to know all the goodies! As a starter, the python script was extracted from the main flow, and now lives in its own files at `PlantonScope/scripts/*`. We set up the auto formatting of the code by using [Black](https://github.com/psf/black). This make the code clearer and uniform. We are using the default settings, so if you just install Black and set your editor to format on save using it, you should be good to go. The code is separated in four main processes, each with a specific set of responsibilities: - The main process controls all the others, starts everything up and cleans up on shutdown - The stepper process manages the stepper movements. It's now possible to have simultaneous movements of both motors (this closes #38 ). - The imager process controls the camera and the streaming server via a state machine. - The segmenter process manages the segmentation and its outputs. The segmentation happens recursively in all folders in `/home/pi/PlanktonScope/img/`. Each folder has its own output archive, and bug #26 is now closed. Those processes communicates together using MQTT and json messages. Each message is adressed to one topic. The high level topic controls which process receives the message. The details of each topic is at the end of this commit message. Every imaging sessions has now its own folder, under the `img` root. Metadata are saved individually for every session, in a JSON file in the same directory as the pictures. The configuration is not parsed from `config.json` anymore and passed directly through MQTT messages to the concerned process. A new configuration file has been created: `hardware.json`. This file contains information related to your specific hardware configuration. You can choose to reverse the connection of the motors for example, but you can also define specific speed limits and steps number for your pump and focus stage. This will make it easier for people who wants to experiment with different kind of hardware. It's not necessary to have this file though. If it doesn't exists, the default configuration will be applied. The code is architectured around 6 modules and about 10 classes. I encourage you to have a look at the files, they're pretty straightforward to understand. There is a lot of work left around the node-red code refactoring, dashboard ui improvements, better and clearer LED messages, OLED screen integration and finer control of the segmentation process, but this is quite good for now. Here is the topic lists for MQTT and the corresponding messages. - actuator : This topic adresses the stepper control thread No publication under this topic should happen from the python process - actuator/pump : Control of the pump The message is a json object {"action":"move", "direction":"FORWARD", "volume":10, "flowrate":1} to move 10mL forward at 1mL/min action can be "move" or "stop" Receive only - actuator/focus : Control of the focus stage The message is a json object, speed is optional {"action":"move", "direction":"UP", "distance":0.26, "speed":1} to move up 10mm action can be "move" or "stop" Receive only - imager/image : This topic adresses the imaging thread Is a json object with {"action":"image","sleep":5,"volume":1,"nb_frame":200} sleep in seconds, volume in mL Can also receive a config update message: {"action":"config","config":[...]} Can also receive a camera settings message: {"action":"settings","iso":100,"shutter_speed":40} Receive only - segmenter/segment : This topic adresses the segmenter process Is a json object with {"action":"segment"} Receive only - status : This topics sends feedback to Node-Red No publication or receive at this level - status/pump : State of the pump Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/focus : State of the focus stage Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/imager : State of the imager Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Completed or 12_11_15_0.1.jpg has been imaged. Publish only - status/segmenter : Status of the segmentation - status/segmenter/name - status/segmenter/object_id - status/segmenter/metric Here is the original commit history: * Extract python main.py from flow * Fix bug in server addresses These addresses should be the loopback device instead of the network address of the device. Using the loopback address will not necessitate to update the script when the network address changes. * clean up picamera import * changes to main python and flow: update MQTT requests address to localhost (bugfix) update streaming output address to nothing update main flow to remove python script references and location * Automatically initialise imaging led on startup to off state. * Add the ability to invert outputs of the motor We added a key to config.json "hardware_config" with a subkey "stepper_reverse". If this key is present in the config file and set to 1, the output of the motors are inversed (stepper2 becomes the pump motor and stepper1 the focus motor) * move all non main script to a subfolder * add __init__.py to package * light module rewrite * json cleanup and absolute path for config file * light.py forgot to import subprocess #oups * Add command to turn the leds off * Auto formatting of main.py I've used Black with default settings, see https://github.com/psf/black * First commit of stepper.py Pump parameters still needs to be checked and tuned. * addition of hardware details in config.json * Introduce hardware.json to replace the `hardware_config` of config.json * stepper.py: calibration, typos * creates the MQTT_Client class * pump_max_speed is now in ml/min to help readability * forgot to add self to the class def * addition of threading capabilities to stepper.py (UNTESTED) * mqtt: fix topic bug * remove counter * mqtt add doc about topics * stepper.py creates an "actuator/*/state" topic * stepper.py: rename mqtt_client to pump_client * mqtt.py: add details about topics * stepper.py: rename pump_client to actuator_client * topic was not split properly and a part was lost * switch to f-strings for mqtt.py * cosmetic update * stepper.py: folder name will be planktoscope change calls * hardware.json became more straightforward * stepper.py syntax bugs * stepper.py addition of a received stop command * stepper.py: update to max travel distance * stepper.py: several typos here * rename folder * main.py: reword to reflect folder rename * main.py: remove logic that has been moved to stepper.py and mqtt.py * main.py: update to add mqtt imaging client * mqtt.py: make command and args local to class and output more verbose * make stepper.py a class * main.py: instantiate stepper class and call it * main.py: name mqtt client * update to main.json to reflect main.py changes * fix bugs around pump control * update flows to latest version from Thibault * distance can be a small value, and definitevely should be a float. * unify mqtt topics * unify mqtt output in the main flow * first logger implementation, uses loguru * mqtt: add reason to on_connect * mqtt: add on_disconnect handler * stepper: add more logger calls for debug mainly * main: add levels for logger * imager.py: first move of the imager logic * imager: time import cleanup * imager: morphocut import cleanup * imager: skimage import cleanup * imager: finishing import cleanup * imager: Class creation - WIP Also provides a fix for #26 (see line 190). * imager: threading is needed for Condition() * streamer: get the streamer server its own file * imager: creates start_camera and get the server creation out * imager: subclass multiprocessing.Process * imager: get Pipeline creation its own function * imager: cleanup of self calls * main: code removal and corresponding calls to newly created classes * imager: various formatting changes * main: management of signal shutdown * add requirements.txt * mqtt: messages are now json objects Also, addition of a flag on receiving a new message * mqtt: make message private and add logic to synchronise * stepper: creates the stepper class * stepper: use the new class * stepper: uses the new logic * stepper: add the shutdown event * stepper: add shutdown method * main: add shutdown event * imager: graceful shutdown * stepper: nicer way of checking the Eevnt * self is a required first argument for a method in a class Especially if you use said class private members! * python: various typos and small errors in import * stepper: create mqtt client during init * stepper: instanciate the mqtt client inside run Otherwise it's not accessible from inside the loop. It's a PITA, more information at https://stackoverflow.com/questions/17172878/using-pythons-multiprocessing-process-class * stepper: little bugs and typos all around * mqtt: add shutdown method * mqtt: add connect in init * stepper: fix bugs, sanitize inputs * stepper: work on delay prediction improvements * stepper: json is mean, double quote are mandatory inside * mqtt: add details about message exchanged * imager: first implementation of json messages * main.json: add new tab for RPi management + json for payloads * imager: add state_machine class * stepper: publish last will * imager: major refactor * main: make streaming server process a daemon * mqtt: insert debug statement on close * main: reorder imports * imager: make it work! Reinsert the streaming server logic in there, because there is a problem with the synchronisation part otherwise. Also, eventually, StreamingOuput() will have to be made not global Final very critical learning: it's super duper important to make sure the memory split is at least 256Meg for the GPU. Chaos ensues otherwise * main: changes to accomodate the streamer/imager fusino * imager_state_machine: insert states transition description * stepper: cleanup of code * segmenter: creation of the class * python: include segmenter changes * remove unused files * stepper: check existence of hardware.json * main.json: changes to reflect the python script evolution * remove unecessary TODOs and add some others * main: add check for config and directories * imager: update_config is implemented and we have better management of directories now * segmenter: now work recursively in all folders * flow: the configuration is now sent via mqtt * segmenter: better manage pipeline error * segmenter: declaration of archive_fn in init * imager: small bugs and typos * main: add uniqueID output * imager: add the camera settings message We can now update the ISO, shutter speed and resolution from Node-Red * package.json: update dependencies
2020-09-28 11:05:27 +02:00
"wires": [
[
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"52ea7d01.711034",
"40c12463.a1f84c"
Extraction and refactor of the python code from node-red flow The rationale for this rewrite is to improve the readability, the modularity, the reliability and the future-proofing of the main python script. All in all, this is now 124 commits that are going to be squashed and merged together, spanning more than two weeks of development and testing. Please test away this release and break things. An upgrading guide will be published in the coming days, along with a new image for people to use if they don't want to upgrade on their own. Read along if you want to know all the goodies! As a starter, the python script was extracted from the main flow, and now lives in its own files at `PlantonScope/scripts/*`. We set up the auto formatting of the code by using [Black](https://github.com/psf/black). This make the code clearer and uniform. We are using the default settings, so if you just install Black and set your editor to format on save using it, you should be good to go. The code is separated in four main processes, each with a specific set of responsibilities: - The main process controls all the others, starts everything up and cleans up on shutdown - The stepper process manages the stepper movements. It's now possible to have simultaneous movements of both motors (this closes #38 ). - The imager process controls the camera and the streaming server via a state machine. - The segmenter process manages the segmentation and its outputs. The segmentation happens recursively in all folders in `/home/pi/PlanktonScope/img/`. Each folder has its own output archive, and bug #26 is now closed. Those processes communicates together using MQTT and json messages. Each message is adressed to one topic. The high level topic controls which process receives the message. The details of each topic is at the end of this commit message. Every imaging sessions has now its own folder, under the `img` root. Metadata are saved individually for every session, in a JSON file in the same directory as the pictures. The configuration is not parsed from `config.json` anymore and passed directly through MQTT messages to the concerned process. A new configuration file has been created: `hardware.json`. This file contains information related to your specific hardware configuration. You can choose to reverse the connection of the motors for example, but you can also define specific speed limits and steps number for your pump and focus stage. This will make it easier for people who wants to experiment with different kind of hardware. It's not necessary to have this file though. If it doesn't exists, the default configuration will be applied. The code is architectured around 6 modules and about 10 classes. I encourage you to have a look at the files, they're pretty straightforward to understand. There is a lot of work left around the node-red code refactoring, dashboard ui improvements, better and clearer LED messages, OLED screen integration and finer control of the segmentation process, but this is quite good for now. Here is the topic lists for MQTT and the corresponding messages. - actuator : This topic adresses the stepper control thread No publication under this topic should happen from the python process - actuator/pump : Control of the pump The message is a json object {"action":"move", "direction":"FORWARD", "volume":10, "flowrate":1} to move 10mL forward at 1mL/min action can be "move" or "stop" Receive only - actuator/focus : Control of the focus stage The message is a json object, speed is optional {"action":"move", "direction":"UP", "distance":0.26, "speed":1} to move up 10mm action can be "move" or "stop" Receive only - imager/image : This topic adresses the imaging thread Is a json object with {"action":"image","sleep":5,"volume":1,"nb_frame":200} sleep in seconds, volume in mL Can also receive a config update message: {"action":"config","config":[...]} Can also receive a camera settings message: {"action":"settings","iso":100,"shutter_speed":40} Receive only - segmenter/segment : This topic adresses the segmenter process Is a json object with {"action":"segment"} Receive only - status : This topics sends feedback to Node-Red No publication or receive at this level - status/pump : State of the pump Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/focus : State of the focus stage Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/imager : State of the imager Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Completed or 12_11_15_0.1.jpg has been imaged. Publish only - status/segmenter : Status of the segmentation - status/segmenter/name - status/segmenter/object_id - status/segmenter/metric Here is the original commit history: * Extract python main.py from flow * Fix bug in server addresses These addresses should be the loopback device instead of the network address of the device. Using the loopback address will not necessitate to update the script when the network address changes. * clean up picamera import * changes to main python and flow: update MQTT requests address to localhost (bugfix) update streaming output address to nothing update main flow to remove python script references and location * Automatically initialise imaging led on startup to off state. * Add the ability to invert outputs of the motor We added a key to config.json "hardware_config" with a subkey "stepper_reverse". If this key is present in the config file and set to 1, the output of the motors are inversed (stepper2 becomes the pump motor and stepper1 the focus motor) * move all non main script to a subfolder * add __init__.py to package * light module rewrite * json cleanup and absolute path for config file * light.py forgot to import subprocess #oups * Add command to turn the leds off * Auto formatting of main.py I've used Black with default settings, see https://github.com/psf/black * First commit of stepper.py Pump parameters still needs to be checked and tuned. * addition of hardware details in config.json * Introduce hardware.json to replace the `hardware_config` of config.json * stepper.py: calibration, typos * creates the MQTT_Client class * pump_max_speed is now in ml/min to help readability * forgot to add self to the class def * addition of threading capabilities to stepper.py (UNTESTED) * mqtt: fix topic bug * remove counter * mqtt add doc about topics * stepper.py creates an "actuator/*/state" topic * stepper.py: rename mqtt_client to pump_client * mqtt.py: add details about topics * stepper.py: rename pump_client to actuator_client * topic was not split properly and a part was lost * switch to f-strings for mqtt.py * cosmetic update * stepper.py: folder name will be planktoscope change calls * hardware.json became more straightforward * stepper.py syntax bugs * stepper.py addition of a received stop command * stepper.py: update to max travel distance * stepper.py: several typos here * rename folder * main.py: reword to reflect folder rename * main.py: remove logic that has been moved to stepper.py and mqtt.py * main.py: update to add mqtt imaging client * mqtt.py: make command and args local to class and output more verbose * make stepper.py a class * main.py: instantiate stepper class and call it * main.py: name mqtt client * update to main.json to reflect main.py changes * fix bugs around pump control * update flows to latest version from Thibault * distance can be a small value, and definitevely should be a float. * unify mqtt topics * unify mqtt output in the main flow * first logger implementation, uses loguru * mqtt: add reason to on_connect * mqtt: add on_disconnect handler * stepper: add more logger calls for debug mainly * main: add levels for logger * imager.py: first move of the imager logic * imager: time import cleanup * imager: morphocut import cleanup * imager: skimage import cleanup * imager: finishing import cleanup * imager: Class creation - WIP Also provides a fix for #26 (see line 190). * imager: threading is needed for Condition() * streamer: get the streamer server its own file * imager: creates start_camera and get the server creation out * imager: subclass multiprocessing.Process * imager: get Pipeline creation its own function * imager: cleanup of self calls * main: code removal and corresponding calls to newly created classes * imager: various formatting changes * main: management of signal shutdown * add requirements.txt * mqtt: messages are now json objects Also, addition of a flag on receiving a new message * mqtt: make message private and add logic to synchronise * stepper: creates the stepper class * stepper: use the new class * stepper: uses the new logic * stepper: add the shutdown event * stepper: add shutdown method * main: add shutdown event * imager: graceful shutdown * stepper: nicer way of checking the Eevnt * self is a required first argument for a method in a class Especially if you use said class private members! * python: various typos and small errors in import * stepper: create mqtt client during init * stepper: instanciate the mqtt client inside run Otherwise it's not accessible from inside the loop. It's a PITA, more information at https://stackoverflow.com/questions/17172878/using-pythons-multiprocessing-process-class * stepper: little bugs and typos all around * mqtt: add shutdown method * mqtt: add connect in init * stepper: fix bugs, sanitize inputs * stepper: work on delay prediction improvements * stepper: json is mean, double quote are mandatory inside * mqtt: add details about message exchanged * imager: first implementation of json messages * main.json: add new tab for RPi management + json for payloads * imager: add state_machine class * stepper: publish last will * imager: major refactor * main: make streaming server process a daemon * mqtt: insert debug statement on close * main: reorder imports * imager: make it work! Reinsert the streaming server logic in there, because there is a problem with the synchronisation part otherwise. Also, eventually, StreamingOuput() will have to be made not global Final very critical learning: it's super duper important to make sure the memory split is at least 256Meg for the GPU. Chaos ensues otherwise * main: changes to accomodate the streamer/imager fusino * imager_state_machine: insert states transition description * stepper: cleanup of code * segmenter: creation of the class * python: include segmenter changes * remove unused files * stepper: check existence of hardware.json * main.json: changes to reflect the python script evolution * remove unecessary TODOs and add some others * main: add check for config and directories * imager: update_config is implemented and we have better management of directories now * segmenter: now work recursively in all folders * flow: the configuration is now sent via mqtt * segmenter: better manage pipeline error * segmenter: declaration of archive_fn in init * imager: small bugs and typos * main: add uniqueID output * imager: add the camera settings message We can now update the ISO, shutter speed and resolution from Node-Red * package.json: update dependencies
2020-09-28 11:05:27 +02:00
]
]
},
{
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"id": "c9f510c0.7d1328",
Extraction and refactor of the python code from node-red flow The rationale for this rewrite is to improve the readability, the modularity, the reliability and the future-proofing of the main python script. All in all, this is now 124 commits that are going to be squashed and merged together, spanning more than two weeks of development and testing. Please test away this release and break things. An upgrading guide will be published in the coming days, along with a new image for people to use if they don't want to upgrade on their own. Read along if you want to know all the goodies! As a starter, the python script was extracted from the main flow, and now lives in its own files at `PlantonScope/scripts/*`. We set up the auto formatting of the code by using [Black](https://github.com/psf/black). This make the code clearer and uniform. We are using the default settings, so if you just install Black and set your editor to format on save using it, you should be good to go. The code is separated in four main processes, each with a specific set of responsibilities: - The main process controls all the others, starts everything up and cleans up on shutdown - The stepper process manages the stepper movements. It's now possible to have simultaneous movements of both motors (this closes #38 ). - The imager process controls the camera and the streaming server via a state machine. - The segmenter process manages the segmentation and its outputs. The segmentation happens recursively in all folders in `/home/pi/PlanktonScope/img/`. Each folder has its own output archive, and bug #26 is now closed. Those processes communicates together using MQTT and json messages. Each message is adressed to one topic. The high level topic controls which process receives the message. The details of each topic is at the end of this commit message. Every imaging sessions has now its own folder, under the `img` root. Metadata are saved individually for every session, in a JSON file in the same directory as the pictures. The configuration is not parsed from `config.json` anymore and passed directly through MQTT messages to the concerned process. A new configuration file has been created: `hardware.json`. This file contains information related to your specific hardware configuration. You can choose to reverse the connection of the motors for example, but you can also define specific speed limits and steps number for your pump and focus stage. This will make it easier for people who wants to experiment with different kind of hardware. It's not necessary to have this file though. If it doesn't exists, the default configuration will be applied. The code is architectured around 6 modules and about 10 classes. I encourage you to have a look at the files, they're pretty straightforward to understand. There is a lot of work left around the node-red code refactoring, dashboard ui improvements, better and clearer LED messages, OLED screen integration and finer control of the segmentation process, but this is quite good for now. Here is the topic lists for MQTT and the corresponding messages. - actuator : This topic adresses the stepper control thread No publication under this topic should happen from the python process - actuator/pump : Control of the pump The message is a json object {"action":"move", "direction":"FORWARD", "volume":10, "flowrate":1} to move 10mL forward at 1mL/min action can be "move" or "stop" Receive only - actuator/focus : Control of the focus stage The message is a json object, speed is optional {"action":"move", "direction":"UP", "distance":0.26, "speed":1} to move up 10mm action can be "move" or "stop" Receive only - imager/image : This topic adresses the imaging thread Is a json object with {"action":"image","sleep":5,"volume":1,"nb_frame":200} sleep in seconds, volume in mL Can also receive a config update message: {"action":"config","config":[...]} Can also receive a camera settings message: {"action":"settings","iso":100,"shutter_speed":40} Receive only - segmenter/segment : This topic adresses the segmenter process Is a json object with {"action":"segment"} Receive only - status : This topics sends feedback to Node-Red No publication or receive at this level - status/pump : State of the pump Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/focus : State of the focus stage Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/imager : State of the imager Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Completed or 12_11_15_0.1.jpg has been imaged. Publish only - status/segmenter : Status of the segmentation - status/segmenter/name - status/segmenter/object_id - status/segmenter/metric Here is the original commit history: * Extract python main.py from flow * Fix bug in server addresses These addresses should be the loopback device instead of the network address of the device. Using the loopback address will not necessitate to update the script when the network address changes. * clean up picamera import * changes to main python and flow: update MQTT requests address to localhost (bugfix) update streaming output address to nothing update main flow to remove python script references and location * Automatically initialise imaging led on startup to off state. * Add the ability to invert outputs of the motor We added a key to config.json "hardware_config" with a subkey "stepper_reverse". If this key is present in the config file and set to 1, the output of the motors are inversed (stepper2 becomes the pump motor and stepper1 the focus motor) * move all non main script to a subfolder * add __init__.py to package * light module rewrite * json cleanup and absolute path for config file * light.py forgot to import subprocess #oups * Add command to turn the leds off * Auto formatting of main.py I've used Black with default settings, see https://github.com/psf/black * First commit of stepper.py Pump parameters still needs to be checked and tuned. * addition of hardware details in config.json * Introduce hardware.json to replace the `hardware_config` of config.json * stepper.py: calibration, typos * creates the MQTT_Client class * pump_max_speed is now in ml/min to help readability * forgot to add self to the class def * addition of threading capabilities to stepper.py (UNTESTED) * mqtt: fix topic bug * remove counter * mqtt add doc about topics * stepper.py creates an "actuator/*/state" topic * stepper.py: rename mqtt_client to pump_client * mqtt.py: add details about topics * stepper.py: rename pump_client to actuator_client * topic was not split properly and a part was lost * switch to f-strings for mqtt.py * cosmetic update * stepper.py: folder name will be planktoscope change calls * hardware.json became more straightforward * stepper.py syntax bugs * stepper.py addition of a received stop command * stepper.py: update to max travel distance * stepper.py: several typos here * rename folder * main.py: reword to reflect folder rename * main.py: remove logic that has been moved to stepper.py and mqtt.py * main.py: update to add mqtt imaging client * mqtt.py: make command and args local to class and output more verbose * make stepper.py a class * main.py: instantiate stepper class and call it * main.py: name mqtt client * update to main.json to reflect main.py changes * fix bugs around pump control * update flows to latest version from Thibault * distance can be a small value, and definitevely should be a float. * unify mqtt topics * unify mqtt output in the main flow * first logger implementation, uses loguru * mqtt: add reason to on_connect * mqtt: add on_disconnect handler * stepper: add more logger calls for debug mainly * main: add levels for logger * imager.py: first move of the imager logic * imager: time import cleanup * imager: morphocut import cleanup * imager: skimage import cleanup * imager: finishing import cleanup * imager: Class creation - WIP Also provides a fix for #26 (see line 190). * imager: threading is needed for Condition() * streamer: get the streamer server its own file * imager: creates start_camera and get the server creation out * imager: subclass multiprocessing.Process * imager: get Pipeline creation its own function * imager: cleanup of self calls * main: code removal and corresponding calls to newly created classes * imager: various formatting changes * main: management of signal shutdown * add requirements.txt * mqtt: messages are now json objects Also, addition of a flag on receiving a new message * mqtt: make message private and add logic to synchronise * stepper: creates the stepper class * stepper: use the new class * stepper: uses the new logic * stepper: add the shutdown event * stepper: add shutdown method * main: add shutdown event * imager: graceful shutdown * stepper: nicer way of checking the Eevnt * self is a required first argument for a method in a class Especially if you use said class private members! * python: various typos and small errors in import * stepper: create mqtt client during init * stepper: instanciate the mqtt client inside run Otherwise it's not accessible from inside the loop. It's a PITA, more information at https://stackoverflow.com/questions/17172878/using-pythons-multiprocessing-process-class * stepper: little bugs and typos all around * mqtt: add shutdown method * mqtt: add connect in init * stepper: fix bugs, sanitize inputs * stepper: work on delay prediction improvements * stepper: json is mean, double quote are mandatory inside * mqtt: add details about message exchanged * imager: first implementation of json messages * main.json: add new tab for RPi management + json for payloads * imager: add state_machine class * stepper: publish last will * imager: major refactor * main: make streaming server process a daemon * mqtt: insert debug statement on close * main: reorder imports * imager: make it work! Reinsert the streaming server logic in there, because there is a problem with the synchronisation part otherwise. Also, eventually, StreamingOuput() will have to be made not global Final very critical learning: it's super duper important to make sure the memory split is at least 256Meg for the GPU. Chaos ensues otherwise * main: changes to accomodate the streamer/imager fusino * imager_state_machine: insert states transition description * stepper: cleanup of code * segmenter: creation of the class * python: include segmenter changes * remove unused files * stepper: check existence of hardware.json * main.json: changes to reflect the python script evolution * remove unecessary TODOs and add some others * main: add check for config and directories * imager: update_config is implemented and we have better management of directories now * segmenter: now work recursively in all folders * flow: the configuration is now sent via mqtt * segmenter: better manage pipeline error * segmenter: declaration of archive_fn in init * imager: small bugs and typos * main: add uniqueID output * imager: add the camera settings message We can now update the ISO, shutter speed and resolution from Node-Red * package.json: update dependencies
2020-09-28 11:05:27 +02:00
"type": "function",
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"z": "baa1e3d9.cb29d",
"name": "image.js",
"func": "state = global.get(\"state\");\nglobal.set('img_counter',0);\nglobal.set('obj_counter',0);\nif (state === null){state=\"free\"}\n\nvar sleep_before= global.get(\"custom_sleep_before\");\nvar nb_step= global.get(\"custom_nb_step\");\nvar nb_frame= global.get(\"custom_nb_frame\");\nvar acq_celltype= global.get(\"acq_celltype\");\nvar acq_minimum_mesh= global.get(\"acq_minimum_mesh\");\nvar acq_maximum_mesh= global.get(\"acq_maximum_mesh\");\nvar acq_volume= global.get(\"acq_volume\");\nvar acq_id= global.get(\"acq_id\");\n\nif (acq_celltype === undefined || acq_celltype === \"\") {\n msg.topic = \"Missing entry :\"\n msg.payload = \"Type of the flowcell\"\n}\nelse if (acq_minimum_mesh === undefined || acq_minimum_mesh === \"\") {\n msg.topic = \"Missing entry :\"\n msg.payload = \"Lower fraction size\"\n}\nelse if (acq_maximum_mesh === undefined || acq_maximum_mesh === \"\") {\n msg.topic = \"Missing entry :\"\n msg.payload = \"Upper fraction size\"\n}\nelse if (acq_volume === undefined || acq_volume === \"\") {\n msg.topic = \"Missing entry :\"\n msg.payload = \"Volume to image\"\n}\nelse if (acq_id === undefined || acq_id === \"\") {\n msg.topic = \"Missing entry :\"\n msg.payload = \"Acquisition ID\"\n}\nelse if (sleep_before === undefined || sleep_before === \"\" || sleep_before === null) {\n msg.topic = \"Missing entry :\";\n msg.payload = \"Duration before the acquisition\";\n \n}else if (nb_step === undefined || nb_step === \"\" || nb_step === null) {\n msg.topic = \"Missing entry :\";\n msg.payload = \"Number of step in between two frames\";\n \n}else if (nb_frame === undefined || nb_frame === \"\" || nb_frame === null) {\n msg.topic = \"Missing entry :\";\n msg.payload = \"Number of image to save\";\n \n}else {\n msg.payload={\"action\":\"image\", \n \"sleep\":sleep_before,\n \"volume\":nb_step,\n \"nb_frame\":nb_frame,\n }\n}\n\nreturn msg;",
Extraction and refactor of the python code from node-red flow The rationale for this rewrite is to improve the readability, the modularity, the reliability and the future-proofing of the main python script. All in all, this is now 124 commits that are going to be squashed and merged together, spanning more than two weeks of development and testing. Please test away this release and break things. An upgrading guide will be published in the coming days, along with a new image for people to use if they don't want to upgrade on their own. Read along if you want to know all the goodies! As a starter, the python script was extracted from the main flow, and now lives in its own files at `PlantonScope/scripts/*`. We set up the auto formatting of the code by using [Black](https://github.com/psf/black). This make the code clearer and uniform. We are using the default settings, so if you just install Black and set your editor to format on save using it, you should be good to go. The code is separated in four main processes, each with a specific set of responsibilities: - The main process controls all the others, starts everything up and cleans up on shutdown - The stepper process manages the stepper movements. It's now possible to have simultaneous movements of both motors (this closes #38 ). - The imager process controls the camera and the streaming server via a state machine. - The segmenter process manages the segmentation and its outputs. The segmentation happens recursively in all folders in `/home/pi/PlanktonScope/img/`. Each folder has its own output archive, and bug #26 is now closed. Those processes communicates together using MQTT and json messages. Each message is adressed to one topic. The high level topic controls which process receives the message. The details of each topic is at the end of this commit message. Every imaging sessions has now its own folder, under the `img` root. Metadata are saved individually for every session, in a JSON file in the same directory as the pictures. The configuration is not parsed from `config.json` anymore and passed directly through MQTT messages to the concerned process. A new configuration file has been created: `hardware.json`. This file contains information related to your specific hardware configuration. You can choose to reverse the connection of the motors for example, but you can also define specific speed limits and steps number for your pump and focus stage. This will make it easier for people who wants to experiment with different kind of hardware. It's not necessary to have this file though. If it doesn't exists, the default configuration will be applied. The code is architectured around 6 modules and about 10 classes. I encourage you to have a look at the files, they're pretty straightforward to understand. There is a lot of work left around the node-red code refactoring, dashboard ui improvements, better and clearer LED messages, OLED screen integration and finer control of the segmentation process, but this is quite good for now. Here is the topic lists for MQTT and the corresponding messages. - actuator : This topic adresses the stepper control thread No publication under this topic should happen from the python process - actuator/pump : Control of the pump The message is a json object {"action":"move", "direction":"FORWARD", "volume":10, "flowrate":1} to move 10mL forward at 1mL/min action can be "move" or "stop" Receive only - actuator/focus : Control of the focus stage The message is a json object, speed is optional {"action":"move", "direction":"UP", "distance":0.26, "speed":1} to move up 10mm action can be "move" or "stop" Receive only - imager/image : This topic adresses the imaging thread Is a json object with {"action":"image","sleep":5,"volume":1,"nb_frame":200} sleep in seconds, volume in mL Can also receive a config update message: {"action":"config","config":[...]} Can also receive a camera settings message: {"action":"settings","iso":100,"shutter_speed":40} Receive only - segmenter/segment : This topic adresses the segmenter process Is a json object with {"action":"segment"} Receive only - status : This topics sends feedback to Node-Red No publication or receive at this level - status/pump : State of the pump Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/focus : State of the focus stage Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/imager : State of the imager Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Completed or 12_11_15_0.1.jpg has been imaged. Publish only - status/segmenter : Status of the segmentation - status/segmenter/name - status/segmenter/object_id - status/segmenter/metric Here is the original commit history: * Extract python main.py from flow * Fix bug in server addresses These addresses should be the loopback device instead of the network address of the device. Using the loopback address will not necessitate to update the script when the network address changes. * clean up picamera import * changes to main python and flow: update MQTT requests address to localhost (bugfix) update streaming output address to nothing update main flow to remove python script references and location * Automatically initialise imaging led on startup to off state. * Add the ability to invert outputs of the motor We added a key to config.json "hardware_config" with a subkey "stepper_reverse". If this key is present in the config file and set to 1, the output of the motors are inversed (stepper2 becomes the pump motor and stepper1 the focus motor) * move all non main script to a subfolder * add __init__.py to package * light module rewrite * json cleanup and absolute path for config file * light.py forgot to import subprocess #oups * Add command to turn the leds off * Auto formatting of main.py I've used Black with default settings, see https://github.com/psf/black * First commit of stepper.py Pump parameters still needs to be checked and tuned. * addition of hardware details in config.json * Introduce hardware.json to replace the `hardware_config` of config.json * stepper.py: calibration, typos * creates the MQTT_Client class * pump_max_speed is now in ml/min to help readability * forgot to add self to the class def * addition of threading capabilities to stepper.py (UNTESTED) * mqtt: fix topic bug * remove counter * mqtt add doc about topics * stepper.py creates an "actuator/*/state" topic * stepper.py: rename mqtt_client to pump_client * mqtt.py: add details about topics * stepper.py: rename pump_client to actuator_client * topic was not split properly and a part was lost * switch to f-strings for mqtt.py * cosmetic update * stepper.py: folder name will be planktoscope change calls * hardware.json became more straightforward * stepper.py syntax bugs * stepper.py addition of a received stop command * stepper.py: update to max travel distance * stepper.py: several typos here * rename folder * main.py: reword to reflect folder rename * main.py: remove logic that has been moved to stepper.py and mqtt.py * main.py: update to add mqtt imaging client * mqtt.py: make command and args local to class and output more verbose * make stepper.py a class * main.py: instantiate stepper class and call it * main.py: name mqtt client * update to main.json to reflect main.py changes * fix bugs around pump control * update flows to latest version from Thibault * distance can be a small value, and definitevely should be a float. * unify mqtt topics * unify mqtt output in the main flow * first logger implementation, uses loguru * mqtt: add reason to on_connect * mqtt: add on_disconnect handler * stepper: add more logger calls for debug mainly * main: add levels for logger * imager.py: first move of the imager logic * imager: time import cleanup * imager: morphocut import cleanup * imager: skimage import cleanup * imager: finishing import cleanup * imager: Class creation - WIP Also provides a fix for #26 (see line 190). * imager: threading is needed for Condition() * streamer: get the streamer server its own file * imager: creates start_camera and get the server creation out * imager: subclass multiprocessing.Process * imager: get Pipeline creation its own function * imager: cleanup of self calls * main: code removal and corresponding calls to newly created classes * imager: various formatting changes * main: management of signal shutdown * add requirements.txt * mqtt: messages are now json objects Also, addition of a flag on receiving a new message * mqtt: make message private and add logic to synchronise * stepper: creates the stepper class * stepper: use the new class * stepper: uses the new logic * stepper: add the shutdown event * stepper: add shutdown method * main: add shutdown event * imager: graceful shutdown * stepper: nicer way of checking the Eevnt * self is a required first argument for a method in a class Especially if you use said class private members! * python: various typos and small errors in import * stepper: create mqtt client during init * stepper: instanciate the mqtt client inside run Otherwise it's not accessible from inside the loop. It's a PITA, more information at https://stackoverflow.com/questions/17172878/using-pythons-multiprocessing-process-class * stepper: little bugs and typos all around * mqtt: add shutdown method * mqtt: add connect in init * stepper: fix bugs, sanitize inputs * stepper: work on delay prediction improvements * stepper: json is mean, double quote are mandatory inside * mqtt: add details about message exchanged * imager: first implementation of json messages * main.json: add new tab for RPi management + json for payloads * imager: add state_machine class * stepper: publish last will * imager: major refactor * main: make streaming server process a daemon * mqtt: insert debug statement on close * main: reorder imports * imager: make it work! Reinsert the streaming server logic in there, because there is a problem with the synchronisation part otherwise. Also, eventually, StreamingOuput() will have to be made not global Final very critical learning: it's super duper important to make sure the memory split is at least 256Meg for the GPU. Chaos ensues otherwise * main: changes to accomodate the streamer/imager fusino * imager_state_machine: insert states transition description * stepper: cleanup of code * segmenter: creation of the class * python: include segmenter changes * remove unused files * stepper: check existence of hardware.json * main.json: changes to reflect the python script evolution * remove unecessary TODOs and add some others * main: add check for config and directories * imager: update_config is implemented and we have better management of directories now * segmenter: now work recursively in all folders * flow: the configuration is now sent via mqtt * segmenter: better manage pipeline error * segmenter: declaration of archive_fn in init * imager: small bugs and typos * main: add uniqueID output * imager: add the camera settings message We can now update the ISO, shutter speed and resolution from Node-Red * package.json: update dependencies
2020-09-28 11:05:27 +02:00
"outputs": 1,
"noerr": 0,
"initialize": "",
"finalize": "",
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"x": 880,
"y": 460,
Extraction and refactor of the python code from node-red flow The rationale for this rewrite is to improve the readability, the modularity, the reliability and the future-proofing of the main python script. All in all, this is now 124 commits that are going to be squashed and merged together, spanning more than two weeks of development and testing. Please test away this release and break things. An upgrading guide will be published in the coming days, along with a new image for people to use if they don't want to upgrade on their own. Read along if you want to know all the goodies! As a starter, the python script was extracted from the main flow, and now lives in its own files at `PlantonScope/scripts/*`. We set up the auto formatting of the code by using [Black](https://github.com/psf/black). This make the code clearer and uniform. We are using the default settings, so if you just install Black and set your editor to format on save using it, you should be good to go. The code is separated in four main processes, each with a specific set of responsibilities: - The main process controls all the others, starts everything up and cleans up on shutdown - The stepper process manages the stepper movements. It's now possible to have simultaneous movements of both motors (this closes #38 ). - The imager process controls the camera and the streaming server via a state machine. - The segmenter process manages the segmentation and its outputs. The segmentation happens recursively in all folders in `/home/pi/PlanktonScope/img/`. Each folder has its own output archive, and bug #26 is now closed. Those processes communicates together using MQTT and json messages. Each message is adressed to one topic. The high level topic controls which process receives the message. The details of each topic is at the end of this commit message. Every imaging sessions has now its own folder, under the `img` root. Metadata are saved individually for every session, in a JSON file in the same directory as the pictures. The configuration is not parsed from `config.json` anymore and passed directly through MQTT messages to the concerned process. A new configuration file has been created: `hardware.json`. This file contains information related to your specific hardware configuration. You can choose to reverse the connection of the motors for example, but you can also define specific speed limits and steps number for your pump and focus stage. This will make it easier for people who wants to experiment with different kind of hardware. It's not necessary to have this file though. If it doesn't exists, the default configuration will be applied. The code is architectured around 6 modules and about 10 classes. I encourage you to have a look at the files, they're pretty straightforward to understand. There is a lot of work left around the node-red code refactoring, dashboard ui improvements, better and clearer LED messages, OLED screen integration and finer control of the segmentation process, but this is quite good for now. Here is the topic lists for MQTT and the corresponding messages. - actuator : This topic adresses the stepper control thread No publication under this topic should happen from the python process - actuator/pump : Control of the pump The message is a json object {"action":"move", "direction":"FORWARD", "volume":10, "flowrate":1} to move 10mL forward at 1mL/min action can be "move" or "stop" Receive only - actuator/focus : Control of the focus stage The message is a json object, speed is optional {"action":"move", "direction":"UP", "distance":0.26, "speed":1} to move up 10mm action can be "move" or "stop" Receive only - imager/image : This topic adresses the imaging thread Is a json object with {"action":"image","sleep":5,"volume":1,"nb_frame":200} sleep in seconds, volume in mL Can also receive a config update message: {"action":"config","config":[...]} Can also receive a camera settings message: {"action":"settings","iso":100,"shutter_speed":40} Receive only - segmenter/segment : This topic adresses the segmenter process Is a json object with {"action":"segment"} Receive only - status : This topics sends feedback to Node-Red No publication or receive at this level - status/pump : State of the pump Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/focus : State of the focus stage Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/imager : State of the imager Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Completed or 12_11_15_0.1.jpg has been imaged. Publish only - status/segmenter : Status of the segmentation - status/segmenter/name - status/segmenter/object_id - status/segmenter/metric Here is the original commit history: * Extract python main.py from flow * Fix bug in server addresses These addresses should be the loopback device instead of the network address of the device. Using the loopback address will not necessitate to update the script when the network address changes. * clean up picamera import * changes to main python and flow: update MQTT requests address to localhost (bugfix) update streaming output address to nothing update main flow to remove python script references and location * Automatically initialise imaging led on startup to off state. * Add the ability to invert outputs of the motor We added a key to config.json "hardware_config" with a subkey "stepper_reverse". If this key is present in the config file and set to 1, the output of the motors are inversed (stepper2 becomes the pump motor and stepper1 the focus motor) * move all non main script to a subfolder * add __init__.py to package * light module rewrite * json cleanup and absolute path for config file * light.py forgot to import subprocess #oups * Add command to turn the leds off * Auto formatting of main.py I've used Black with default settings, see https://github.com/psf/black * First commit of stepper.py Pump parameters still needs to be checked and tuned. * addition of hardware details in config.json * Introduce hardware.json to replace the `hardware_config` of config.json * stepper.py: calibration, typos * creates the MQTT_Client class * pump_max_speed is now in ml/min to help readability * forgot to add self to the class def * addition of threading capabilities to stepper.py (UNTESTED) * mqtt: fix topic bug * remove counter * mqtt add doc about topics * stepper.py creates an "actuator/*/state" topic * stepper.py: rename mqtt_client to pump_client * mqtt.py: add details about topics * stepper.py: rename pump_client to actuator_client * topic was not split properly and a part was lost * switch to f-strings for mqtt.py * cosmetic update * stepper.py: folder name will be planktoscope change calls * hardware.json became more straightforward * stepper.py syntax bugs * stepper.py addition of a received stop command * stepper.py: update to max travel distance * stepper.py: several typos here * rename folder * main.py: reword to reflect folder rename * main.py: remove logic that has been moved to stepper.py and mqtt.py * main.py: update to add mqtt imaging client * mqtt.py: make command and args local to class and output more verbose * make stepper.py a class * main.py: instantiate stepper class and call it * main.py: name mqtt client * update to main.json to reflect main.py changes * fix bugs around pump control * update flows to latest version from Thibault * distance can be a small value, and definitevely should be a float. * unify mqtt topics * unify mqtt output in the main flow * first logger implementation, uses loguru * mqtt: add reason to on_connect * mqtt: add on_disconnect handler * stepper: add more logger calls for debug mainly * main: add levels for logger * imager.py: first move of the imager logic * imager: time import cleanup * imager: morphocut import cleanup * imager: skimage import cleanup * imager: finishing import cleanup * imager: Class creation - WIP Also provides a fix for #26 (see line 190). * imager: threading is needed for Condition() * streamer: get the streamer server its own file * imager: creates start_camera and get the server creation out * imager: subclass multiprocessing.Process * imager: get Pipeline creation its own function * imager: cleanup of self calls * main: code removal and corresponding calls to newly created classes * imager: various formatting changes * main: management of signal shutdown * add requirements.txt * mqtt: messages are now json objects Also, addition of a flag on receiving a new message * mqtt: make message private and add logic to synchronise * stepper: creates the stepper class * stepper: use the new class * stepper: uses the new logic * stepper: add the shutdown event * stepper: add shutdown method * main: add shutdown event * imager: graceful shutdown * stepper: nicer way of checking the Eevnt * self is a required first argument for a method in a class Especially if you use said class private members! * python: various typos and small errors in import * stepper: create mqtt client during init * stepper: instanciate the mqtt client inside run Otherwise it's not accessible from inside the loop. It's a PITA, more information at https://stackoverflow.com/questions/17172878/using-pythons-multiprocessing-process-class * stepper: little bugs and typos all around * mqtt: add shutdown method * mqtt: add connect in init * stepper: fix bugs, sanitize inputs * stepper: work on delay prediction improvements * stepper: json is mean, double quote are mandatory inside * mqtt: add details about message exchanged * imager: first implementation of json messages * main.json: add new tab for RPi management + json for payloads * imager: add state_machine class * stepper: publish last will * imager: major refactor * main: make streaming server process a daemon * mqtt: insert debug statement on close * main: reorder imports * imager: make it work! Reinsert the streaming server logic in there, because there is a problem with the synchronisation part otherwise. Also, eventually, StreamingOuput() will have to be made not global Final very critical learning: it's super duper important to make sure the memory split is at least 256Meg for the GPU. Chaos ensues otherwise * main: changes to accomodate the streamer/imager fusino * imager_state_machine: insert states transition description * stepper: cleanup of code * segmenter: creation of the class * python: include segmenter changes * remove unused files * stepper: check existence of hardware.json * main.json: changes to reflect the python script evolution * remove unecessary TODOs and add some others * main: add check for config and directories * imager: update_config is implemented and we have better management of directories now * segmenter: now work recursively in all folders * flow: the configuration is now sent via mqtt * segmenter: better manage pipeline error * segmenter: declaration of archive_fn in init * imager: small bugs and typos * main: add uniqueID output * imager: add the camera settings message We can now update the ISO, shutter speed and resolution from Node-Red * package.json: update dependencies
2020-09-28 11:05:27 +02:00
"wires": [
[
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"d6ebaa2.ea21d58"
Extraction and refactor of the python code from node-red flow The rationale for this rewrite is to improve the readability, the modularity, the reliability and the future-proofing of the main python script. All in all, this is now 124 commits that are going to be squashed and merged together, spanning more than two weeks of development and testing. Please test away this release and break things. An upgrading guide will be published in the coming days, along with a new image for people to use if they don't want to upgrade on their own. Read along if you want to know all the goodies! As a starter, the python script was extracted from the main flow, and now lives in its own files at `PlantonScope/scripts/*`. We set up the auto formatting of the code by using [Black](https://github.com/psf/black). This make the code clearer and uniform. We are using the default settings, so if you just install Black and set your editor to format on save using it, you should be good to go. The code is separated in four main processes, each with a specific set of responsibilities: - The main process controls all the others, starts everything up and cleans up on shutdown - The stepper process manages the stepper movements. It's now possible to have simultaneous movements of both motors (this closes #38 ). - The imager process controls the camera and the streaming server via a state machine. - The segmenter process manages the segmentation and its outputs. The segmentation happens recursively in all folders in `/home/pi/PlanktonScope/img/`. Each folder has its own output archive, and bug #26 is now closed. Those processes communicates together using MQTT and json messages. Each message is adressed to one topic. The high level topic controls which process receives the message. The details of each topic is at the end of this commit message. Every imaging sessions has now its own folder, under the `img` root. Metadata are saved individually for every session, in a JSON file in the same directory as the pictures. The configuration is not parsed from `config.json` anymore and passed directly through MQTT messages to the concerned process. A new configuration file has been created: `hardware.json`. This file contains information related to your specific hardware configuration. You can choose to reverse the connection of the motors for example, but you can also define specific speed limits and steps number for your pump and focus stage. This will make it easier for people who wants to experiment with different kind of hardware. It's not necessary to have this file though. If it doesn't exists, the default configuration will be applied. The code is architectured around 6 modules and about 10 classes. I encourage you to have a look at the files, they're pretty straightforward to understand. There is a lot of work left around the node-red code refactoring, dashboard ui improvements, better and clearer LED messages, OLED screen integration and finer control of the segmentation process, but this is quite good for now. Here is the topic lists for MQTT and the corresponding messages. - actuator : This topic adresses the stepper control thread No publication under this topic should happen from the python process - actuator/pump : Control of the pump The message is a json object {"action":"move", "direction":"FORWARD", "volume":10, "flowrate":1} to move 10mL forward at 1mL/min action can be "move" or "stop" Receive only - actuator/focus : Control of the focus stage The message is a json object, speed is optional {"action":"move", "direction":"UP", "distance":0.26, "speed":1} to move up 10mm action can be "move" or "stop" Receive only - imager/image : This topic adresses the imaging thread Is a json object with {"action":"image","sleep":5,"volume":1,"nb_frame":200} sleep in seconds, volume in mL Can also receive a config update message: {"action":"config","config":[...]} Can also receive a camera settings message: {"action":"settings","iso":100,"shutter_speed":40} Receive only - segmenter/segment : This topic adresses the segmenter process Is a json object with {"action":"segment"} Receive only - status : This topics sends feedback to Node-Red No publication or receive at this level - status/pump : State of the pump Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/focus : State of the focus stage Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/imager : State of the imager Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Completed or 12_11_15_0.1.jpg has been imaged. Publish only - status/segmenter : Status of the segmentation - status/segmenter/name - status/segmenter/object_id - status/segmenter/metric Here is the original commit history: * Extract python main.py from flow * Fix bug in server addresses These addresses should be the loopback device instead of the network address of the device. Using the loopback address will not necessitate to update the script when the network address changes. * clean up picamera import * changes to main python and flow: update MQTT requests address to localhost (bugfix) update streaming output address to nothing update main flow to remove python script references and location * Automatically initialise imaging led on startup to off state. * Add the ability to invert outputs of the motor We added a key to config.json "hardware_config" with a subkey "stepper_reverse". If this key is present in the config file and set to 1, the output of the motors are inversed (stepper2 becomes the pump motor and stepper1 the focus motor) * move all non main script to a subfolder * add __init__.py to package * light module rewrite * json cleanup and absolute path for config file * light.py forgot to import subprocess #oups * Add command to turn the leds off * Auto formatting of main.py I've used Black with default settings, see https://github.com/psf/black * First commit of stepper.py Pump parameters still needs to be checked and tuned. * addition of hardware details in config.json * Introduce hardware.json to replace the `hardware_config` of config.json * stepper.py: calibration, typos * creates the MQTT_Client class * pump_max_speed is now in ml/min to help readability * forgot to add self to the class def * addition of threading capabilities to stepper.py (UNTESTED) * mqtt: fix topic bug * remove counter * mqtt add doc about topics * stepper.py creates an "actuator/*/state" topic * stepper.py: rename mqtt_client to pump_client * mqtt.py: add details about topics * stepper.py: rename pump_client to actuator_client * topic was not split properly and a part was lost * switch to f-strings for mqtt.py * cosmetic update * stepper.py: folder name will be planktoscope change calls * hardware.json became more straightforward * stepper.py syntax bugs * stepper.py addition of a received stop command * stepper.py: update to max travel distance * stepper.py: several typos here * rename folder * main.py: reword to reflect folder rename * main.py: remove logic that has been moved to stepper.py and mqtt.py * main.py: update to add mqtt imaging client * mqtt.py: make command and args local to class and output more verbose * make stepper.py a class * main.py: instantiate stepper class and call it * main.py: name mqtt client * update to main.json to reflect main.py changes * fix bugs around pump control * update flows to latest version from Thibault * distance can be a small value, and definitevely should be a float. * unify mqtt topics * unify mqtt output in the main flow * first logger implementation, uses loguru * mqtt: add reason to on_connect * mqtt: add on_disconnect handler * stepper: add more logger calls for debug mainly * main: add levels for logger * imager.py: first move of the imager logic * imager: time import cleanup * imager: morphocut import cleanup * imager: skimage import cleanup * imager: finishing import cleanup * imager: Class creation - WIP Also provides a fix for #26 (see line 190). * imager: threading is needed for Condition() * streamer: get the streamer server its own file * imager: creates start_camera and get the server creation out * imager: subclass multiprocessing.Process * imager: get Pipeline creation its own function * imager: cleanup of self calls * main: code removal and corresponding calls to newly created classes * imager: various formatting changes * main: management of signal shutdown * add requirements.txt * mqtt: messages are now json objects Also, addition of a flag on receiving a new message * mqtt: make message private and add logic to synchronise * stepper: creates the stepper class * stepper: use the new class * stepper: uses the new logic * stepper: add the shutdown event * stepper: add shutdown method * main: add shutdown event * imager: graceful shutdown * stepper: nicer way of checking the Eevnt * self is a required first argument for a method in a class Especially if you use said class private members! * python: various typos and small errors in import * stepper: create mqtt client during init * stepper: instanciate the mqtt client inside run Otherwise it's not accessible from inside the loop. It's a PITA, more information at https://stackoverflow.com/questions/17172878/using-pythons-multiprocessing-process-class * stepper: little bugs and typos all around * mqtt: add shutdown method * mqtt: add connect in init * stepper: fix bugs, sanitize inputs * stepper: work on delay prediction improvements * stepper: json is mean, double quote are mandatory inside * mqtt: add details about message exchanged * imager: first implementation of json messages * main.json: add new tab for RPi management + json for payloads * imager: add state_machine class * stepper: publish last will * imager: major refactor * main: make streaming server process a daemon * mqtt: insert debug statement on close * main: reorder imports * imager: make it work! Reinsert the streaming server logic in there, because there is a problem with the synchronisation part otherwise. Also, eventually, StreamingOuput() will have to be made not global Final very critical learning: it's super duper important to make sure the memory split is at least 256Meg for the GPU. Chaos ensues otherwise * main: changes to accomodate the streamer/imager fusino * imager_state_machine: insert states transition description * stepper: cleanup of code * segmenter: creation of the class * python: include segmenter changes * remove unused files * stepper: check existence of hardware.json * main.json: changes to reflect the python script evolution * remove unecessary TODOs and add some others * main: add check for config and directories * imager: update_config is implemented and we have better management of directories now * segmenter: now work recursively in all folders * flow: the configuration is now sent via mqtt * segmenter: better manage pipeline error * segmenter: declaration of archive_fn in init * imager: small bugs and typos * main: add uniqueID output * imager: add the camera settings message We can now update the ISO, shutter speed and resolution from Node-Red * package.json: update dependencies
2020-09-28 11:05:27 +02:00
]
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
],
"info": "### Focusing\n##### focus.py `nb_step` `orientation`\n\n- `nb_step` : **integer** (from 1 to 100000) - number of step to perform by the stage (about 31um/step)\n- `orientation` : **string** - orientation of the focus either `up` or `down`\n\nExample:\n\n python3.7 $HOME/PlanktonScope/scripts/focus.py 650 up\n"
Extraction and refactor of the python code from node-red flow The rationale for this rewrite is to improve the readability, the modularity, the reliability and the future-proofing of the main python script. All in all, this is now 124 commits that are going to be squashed and merged together, spanning more than two weeks of development and testing. Please test away this release and break things. An upgrading guide will be published in the coming days, along with a new image for people to use if they don't want to upgrade on their own. Read along if you want to know all the goodies! As a starter, the python script was extracted from the main flow, and now lives in its own files at `PlantonScope/scripts/*`. We set up the auto formatting of the code by using [Black](https://github.com/psf/black). This make the code clearer and uniform. We are using the default settings, so if you just install Black and set your editor to format on save using it, you should be good to go. The code is separated in four main processes, each with a specific set of responsibilities: - The main process controls all the others, starts everything up and cleans up on shutdown - The stepper process manages the stepper movements. It's now possible to have simultaneous movements of both motors (this closes #38 ). - The imager process controls the camera and the streaming server via a state machine. - The segmenter process manages the segmentation and its outputs. The segmentation happens recursively in all folders in `/home/pi/PlanktonScope/img/`. Each folder has its own output archive, and bug #26 is now closed. Those processes communicates together using MQTT and json messages. Each message is adressed to one topic. The high level topic controls which process receives the message. The details of each topic is at the end of this commit message. Every imaging sessions has now its own folder, under the `img` root. Metadata are saved individually for every session, in a JSON file in the same directory as the pictures. The configuration is not parsed from `config.json` anymore and passed directly through MQTT messages to the concerned process. A new configuration file has been created: `hardware.json`. This file contains information related to your specific hardware configuration. You can choose to reverse the connection of the motors for example, but you can also define specific speed limits and steps number for your pump and focus stage. This will make it easier for people who wants to experiment with different kind of hardware. It's not necessary to have this file though. If it doesn't exists, the default configuration will be applied. The code is architectured around 6 modules and about 10 classes. I encourage you to have a look at the files, they're pretty straightforward to understand. There is a lot of work left around the node-red code refactoring, dashboard ui improvements, better and clearer LED messages, OLED screen integration and finer control of the segmentation process, but this is quite good for now. Here is the topic lists for MQTT and the corresponding messages. - actuator : This topic adresses the stepper control thread No publication under this topic should happen from the python process - actuator/pump : Control of the pump The message is a json object {"action":"move", "direction":"FORWARD", "volume":10, "flowrate":1} to move 10mL forward at 1mL/min action can be "move" or "stop" Receive only - actuator/focus : Control of the focus stage The message is a json object, speed is optional {"action":"move", "direction":"UP", "distance":0.26, "speed":1} to move up 10mm action can be "move" or "stop" Receive only - imager/image : This topic adresses the imaging thread Is a json object with {"action":"image","sleep":5,"volume":1,"nb_frame":200} sleep in seconds, volume in mL Can also receive a config update message: {"action":"config","config":[...]} Can also receive a camera settings message: {"action":"settings","iso":100,"shutter_speed":40} Receive only - segmenter/segment : This topic adresses the segmenter process Is a json object with {"action":"segment"} Receive only - status : This topics sends feedback to Node-Red No publication or receive at this level - status/pump : State of the pump Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/focus : State of the focus stage Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/imager : State of the imager Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Completed or 12_11_15_0.1.jpg has been imaged. Publish only - status/segmenter : Status of the segmentation - status/segmenter/name - status/segmenter/object_id - status/segmenter/metric Here is the original commit history: * Extract python main.py from flow * Fix bug in server addresses These addresses should be the loopback device instead of the network address of the device. Using the loopback address will not necessitate to update the script when the network address changes. * clean up picamera import * changes to main python and flow: update MQTT requests address to localhost (bugfix) update streaming output address to nothing update main flow to remove python script references and location * Automatically initialise imaging led on startup to off state. * Add the ability to invert outputs of the motor We added a key to config.json "hardware_config" with a subkey "stepper_reverse". If this key is present in the config file and set to 1, the output of the motors are inversed (stepper2 becomes the pump motor and stepper1 the focus motor) * move all non main script to a subfolder * add __init__.py to package * light module rewrite * json cleanup and absolute path for config file * light.py forgot to import subprocess #oups * Add command to turn the leds off * Auto formatting of main.py I've used Black with default settings, see https://github.com/psf/black * First commit of stepper.py Pump parameters still needs to be checked and tuned. * addition of hardware details in config.json * Introduce hardware.json to replace the `hardware_config` of config.json * stepper.py: calibration, typos * creates the MQTT_Client class * pump_max_speed is now in ml/min to help readability * forgot to add self to the class def * addition of threading capabilities to stepper.py (UNTESTED) * mqtt: fix topic bug * remove counter * mqtt add doc about topics * stepper.py creates an "actuator/*/state" topic * stepper.py: rename mqtt_client to pump_client * mqtt.py: add details about topics * stepper.py: rename pump_client to actuator_client * topic was not split properly and a part was lost * switch to f-strings for mqtt.py * cosmetic update * stepper.py: folder name will be planktoscope change calls * hardware.json became more straightforward * stepper.py syntax bugs * stepper.py addition of a received stop command * stepper.py: update to max travel distance * stepper.py: several typos here * rename folder * main.py: reword to reflect folder rename * main.py: remove logic that has been moved to stepper.py and mqtt.py * main.py: update to add mqtt imaging client * mqtt.py: make command and args local to class and output more verbose * make stepper.py a class * main.py: instantiate stepper class and call it * main.py: name mqtt client * update to main.json to reflect main.py changes * fix bugs around pump control * update flows to latest version from Thibault * distance can be a small value, and definitevely should be a float. * unify mqtt topics * unify mqtt output in the main flow * first logger implementation, uses loguru * mqtt: add reason to on_connect * mqtt: add on_disconnect handler * stepper: add more logger calls for debug mainly * main: add levels for logger * imager.py: first move of the imager logic * imager: time import cleanup * imager: morphocut import cleanup * imager: skimage import cleanup * imager: finishing import cleanup * imager: Class creation - WIP Also provides a fix for #26 (see line 190). * imager: threading is needed for Condition() * streamer: get the streamer server its own file * imager: creates start_camera and get the server creation out * imager: subclass multiprocessing.Process * imager: get Pipeline creation its own function * imager: cleanup of self calls * main: code removal and corresponding calls to newly created classes * imager: various formatting changes * main: management of signal shutdown * add requirements.txt * mqtt: messages are now json objects Also, addition of a flag on receiving a new message * mqtt: make message private and add logic to synchronise * stepper: creates the stepper class * stepper: use the new class * stepper: uses the new logic * stepper: add the shutdown event * stepper: add shutdown method * main: add shutdown event * imager: graceful shutdown * stepper: nicer way of checking the Eevnt * self is a required first argument for a method in a class Especially if you use said class private members! * python: various typos and small errors in import * stepper: create mqtt client during init * stepper: instanciate the mqtt client inside run Otherwise it's not accessible from inside the loop. It's a PITA, more information at https://stackoverflow.com/questions/17172878/using-pythons-multiprocessing-process-class * stepper: little bugs and typos all around * mqtt: add shutdown method * mqtt: add connect in init * stepper: fix bugs, sanitize inputs * stepper: work on delay prediction improvements * stepper: json is mean, double quote are mandatory inside * mqtt: add details about message exchanged * imager: first implementation of json messages * main.json: add new tab for RPi management + json for payloads * imager: add state_machine class * stepper: publish last will * imager: major refactor * main: make streaming server process a daemon * mqtt: insert debug statement on close * main: reorder imports * imager: make it work! Reinsert the streaming server logic in there, because there is a problem with the synchronisation part otherwise. Also, eventually, StreamingOuput() will have to be made not global Final very critical learning: it's super duper important to make sure the memory split is at least 256Meg for the GPU. Chaos ensues otherwise * main: changes to accomodate the streamer/imager fusino * imager_state_machine: insert states transition description * stepper: cleanup of code * segmenter: creation of the class * python: include segmenter changes * remove unused files * stepper: check existence of hardware.json * main.json: changes to reflect the python script evolution * remove unecessary TODOs and add some others * main: add check for config and directories * imager: update_config is implemented and we have better management of directories now * segmenter: now work recursively in all folders * flow: the configuration is now sent via mqtt * segmenter: better manage pipeline error * segmenter: declaration of archive_fn in init * imager: small bugs and typos * main: add uniqueID output * imager: add the camera settings message We can now update the ISO, shutter speed and resolution from Node-Red * package.json: update dependencies
2020-09-28 11:05:27 +02:00
},
{
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"id": "d6ebaa2.ea21d58",
"type": "switch",
"z": "baa1e3d9.cb29d",
Extraction and refactor of the python code from node-red flow The rationale for this rewrite is to improve the readability, the modularity, the reliability and the future-proofing of the main python script. All in all, this is now 124 commits that are going to be squashed and merged together, spanning more than two weeks of development and testing. Please test away this release and break things. An upgrading guide will be published in the coming days, along with a new image for people to use if they don't want to upgrade on their own. Read along if you want to know all the goodies! As a starter, the python script was extracted from the main flow, and now lives in its own files at `PlantonScope/scripts/*`. We set up the auto formatting of the code by using [Black](https://github.com/psf/black). This make the code clearer and uniform. We are using the default settings, so if you just install Black and set your editor to format on save using it, you should be good to go. The code is separated in four main processes, each with a specific set of responsibilities: - The main process controls all the others, starts everything up and cleans up on shutdown - The stepper process manages the stepper movements. It's now possible to have simultaneous movements of both motors (this closes #38 ). - The imager process controls the camera and the streaming server via a state machine. - The segmenter process manages the segmentation and its outputs. The segmentation happens recursively in all folders in `/home/pi/PlanktonScope/img/`. Each folder has its own output archive, and bug #26 is now closed. Those processes communicates together using MQTT and json messages. Each message is adressed to one topic. The high level topic controls which process receives the message. The details of each topic is at the end of this commit message. Every imaging sessions has now its own folder, under the `img` root. Metadata are saved individually for every session, in a JSON file in the same directory as the pictures. The configuration is not parsed from `config.json` anymore and passed directly through MQTT messages to the concerned process. A new configuration file has been created: `hardware.json`. This file contains information related to your specific hardware configuration. You can choose to reverse the connection of the motors for example, but you can also define specific speed limits and steps number for your pump and focus stage. This will make it easier for people who wants to experiment with different kind of hardware. It's not necessary to have this file though. If it doesn't exists, the default configuration will be applied. The code is architectured around 6 modules and about 10 classes. I encourage you to have a look at the files, they're pretty straightforward to understand. There is a lot of work left around the node-red code refactoring, dashboard ui improvements, better and clearer LED messages, OLED screen integration and finer control of the segmentation process, but this is quite good for now. Here is the topic lists for MQTT and the corresponding messages. - actuator : This topic adresses the stepper control thread No publication under this topic should happen from the python process - actuator/pump : Control of the pump The message is a json object {"action":"move", "direction":"FORWARD", "volume":10, "flowrate":1} to move 10mL forward at 1mL/min action can be "move" or "stop" Receive only - actuator/focus : Control of the focus stage The message is a json object, speed is optional {"action":"move", "direction":"UP", "distance":0.26, "speed":1} to move up 10mm action can be "move" or "stop" Receive only - imager/image : This topic adresses the imaging thread Is a json object with {"action":"image","sleep":5,"volume":1,"nb_frame":200} sleep in seconds, volume in mL Can also receive a config update message: {"action":"config","config":[...]} Can also receive a camera settings message: {"action":"settings","iso":100,"shutter_speed":40} Receive only - segmenter/segment : This topic adresses the segmenter process Is a json object with {"action":"segment"} Receive only - status : This topics sends feedback to Node-Red No publication or receive at this level - status/pump : State of the pump Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/focus : State of the focus stage Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/imager : State of the imager Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Completed or 12_11_15_0.1.jpg has been imaged. Publish only - status/segmenter : Status of the segmentation - status/segmenter/name - status/segmenter/object_id - status/segmenter/metric Here is the original commit history: * Extract python main.py from flow * Fix bug in server addresses These addresses should be the loopback device instead of the network address of the device. Using the loopback address will not necessitate to update the script when the network address changes. * clean up picamera import * changes to main python and flow: update MQTT requests address to localhost (bugfix) update streaming output address to nothing update main flow to remove python script references and location * Automatically initialise imaging led on startup to off state. * Add the ability to invert outputs of the motor We added a key to config.json "hardware_config" with a subkey "stepper_reverse". If this key is present in the config file and set to 1, the output of the motors are inversed (stepper2 becomes the pump motor and stepper1 the focus motor) * move all non main script to a subfolder * add __init__.py to package * light module rewrite * json cleanup and absolute path for config file * light.py forgot to import subprocess #oups * Add command to turn the leds off * Auto formatting of main.py I've used Black with default settings, see https://github.com/psf/black * First commit of stepper.py Pump parameters still needs to be checked and tuned. * addition of hardware details in config.json * Introduce hardware.json to replace the `hardware_config` of config.json * stepper.py: calibration, typos * creates the MQTT_Client class * pump_max_speed is now in ml/min to help readability * forgot to add self to the class def * addition of threading capabilities to stepper.py (UNTESTED) * mqtt: fix topic bug * remove counter * mqtt add doc about topics * stepper.py creates an "actuator/*/state" topic * stepper.py: rename mqtt_client to pump_client * mqtt.py: add details about topics * stepper.py: rename pump_client to actuator_client * topic was not split properly and a part was lost * switch to f-strings for mqtt.py * cosmetic update * stepper.py: folder name will be planktoscope change calls * hardware.json became more straightforward * stepper.py syntax bugs * stepper.py addition of a received stop command * stepper.py: update to max travel distance * stepper.py: several typos here * rename folder * main.py: reword to reflect folder rename * main.py: remove logic that has been moved to stepper.py and mqtt.py * main.py: update to add mqtt imaging client * mqtt.py: make command and args local to class and output more verbose * make stepper.py a class * main.py: instantiate stepper class and call it * main.py: name mqtt client * update to main.json to reflect main.py changes * fix bugs around pump control * update flows to latest version from Thibault * distance can be a small value, and definitevely should be a float. * unify mqtt topics * unify mqtt output in the main flow * first logger implementation, uses loguru * mqtt: add reason to on_connect * mqtt: add on_disconnect handler * stepper: add more logger calls for debug mainly * main: add levels for logger * imager.py: first move of the imager logic * imager: time import cleanup * imager: morphocut import cleanup * imager: skimage import cleanup * imager: finishing import cleanup * imager: Class creation - WIP Also provides a fix for #26 (see line 190). * imager: threading is needed for Condition() * streamer: get the streamer server its own file * imager: creates start_camera and get the server creation out * imager: subclass multiprocessing.Process * imager: get Pipeline creation its own function * imager: cleanup of self calls * main: code removal and corresponding calls to newly created classes * imager: various formatting changes * main: management of signal shutdown * add requirements.txt * mqtt: messages are now json objects Also, addition of a flag on receiving a new message * mqtt: make message private and add logic to synchronise * stepper: creates the stepper class * stepper: use the new class * stepper: uses the new logic * stepper: add the shutdown event * stepper: add shutdown method * main: add shutdown event * imager: graceful shutdown * stepper: nicer way of checking the Eevnt * self is a required first argument for a method in a class Especially if you use said class private members! * python: various typos and small errors in import * stepper: create mqtt client during init * stepper: instanciate the mqtt client inside run Otherwise it's not accessible from inside the loop. It's a PITA, more information at https://stackoverflow.com/questions/17172878/using-pythons-multiprocessing-process-class * stepper: little bugs and typos all around * mqtt: add shutdown method * mqtt: add connect in init * stepper: fix bugs, sanitize inputs * stepper: work on delay prediction improvements * stepper: json is mean, double quote are mandatory inside * mqtt: add details about message exchanged * imager: first implementation of json messages * main.json: add new tab for RPi management + json for payloads * imager: add state_machine class * stepper: publish last will * imager: major refactor * main: make streaming server process a daemon * mqtt: insert debug statement on close * main: reorder imports * imager: make it work! Reinsert the streaming server logic in there, because there is a problem with the synchronisation part otherwise. Also, eventually, StreamingOuput() will have to be made not global Final very critical learning: it's super duper important to make sure the memory split is at least 256Meg for the GPU. Chaos ensues otherwise * main: changes to accomodate the streamer/imager fusino * imager_state_machine: insert states transition description * stepper: cleanup of code * segmenter: creation of the class * python: include segmenter changes * remove unused files * stepper: check existence of hardware.json * main.json: changes to reflect the python script evolution * remove unecessary TODOs and add some others * main: add check for config and directories * imager: update_config is implemented and we have better management of directories now * segmenter: now work recursively in all folders * flow: the configuration is now sent via mqtt * segmenter: better manage pipeline error * segmenter: declaration of archive_fn in init * imager: small bugs and typos * main: add uniqueID output * imager: add the camera settings message We can now update the ISO, shutter speed and resolution from Node-Red * package.json: update dependencies
2020-09-28 11:05:27 +02:00
"name": "",
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"property": "topic",
"propertyType": "msg",
"rules": [
Extraction and refactor of the python code from node-red flow The rationale for this rewrite is to improve the readability, the modularity, the reliability and the future-proofing of the main python script. All in all, this is now 124 commits that are going to be squashed and merged together, spanning more than two weeks of development and testing. Please test away this release and break things. An upgrading guide will be published in the coming days, along with a new image for people to use if they don't want to upgrade on their own. Read along if you want to know all the goodies! As a starter, the python script was extracted from the main flow, and now lives in its own files at `PlantonScope/scripts/*`. We set up the auto formatting of the code by using [Black](https://github.com/psf/black). This make the code clearer and uniform. We are using the default settings, so if you just install Black and set your editor to format on save using it, you should be good to go. The code is separated in four main processes, each with a specific set of responsibilities: - The main process controls all the others, starts everything up and cleans up on shutdown - The stepper process manages the stepper movements. It's now possible to have simultaneous movements of both motors (this closes #38 ). - The imager process controls the camera and the streaming server via a state machine. - The segmenter process manages the segmentation and its outputs. The segmentation happens recursively in all folders in `/home/pi/PlanktonScope/img/`. Each folder has its own output archive, and bug #26 is now closed. Those processes communicates together using MQTT and json messages. Each message is adressed to one topic. The high level topic controls which process receives the message. The details of each topic is at the end of this commit message. Every imaging sessions has now its own folder, under the `img` root. Metadata are saved individually for every session, in a JSON file in the same directory as the pictures. The configuration is not parsed from `config.json` anymore and passed directly through MQTT messages to the concerned process. A new configuration file has been created: `hardware.json`. This file contains information related to your specific hardware configuration. You can choose to reverse the connection of the motors for example, but you can also define specific speed limits and steps number for your pump and focus stage. This will make it easier for people who wants to experiment with different kind of hardware. It's not necessary to have this file though. If it doesn't exists, the default configuration will be applied. The code is architectured around 6 modules and about 10 classes. I encourage you to have a look at the files, they're pretty straightforward to understand. There is a lot of work left around the node-red code refactoring, dashboard ui improvements, better and clearer LED messages, OLED screen integration and finer control of the segmentation process, but this is quite good for now. Here is the topic lists for MQTT and the corresponding messages. - actuator : This topic adresses the stepper control thread No publication under this topic should happen from the python process - actuator/pump : Control of the pump The message is a json object {"action":"move", "direction":"FORWARD", "volume":10, "flowrate":1} to move 10mL forward at 1mL/min action can be "move" or "stop" Receive only - actuator/focus : Control of the focus stage The message is a json object, speed is optional {"action":"move", "direction":"UP", "distance":0.26, "speed":1} to move up 10mm action can be "move" or "stop" Receive only - imager/image : This topic adresses the imaging thread Is a json object with {"action":"image","sleep":5,"volume":1,"nb_frame":200} sleep in seconds, volume in mL Can also receive a config update message: {"action":"config","config":[...]} Can also receive a camera settings message: {"action":"settings","iso":100,"shutter_speed":40} Receive only - segmenter/segment : This topic adresses the segmenter process Is a json object with {"action":"segment"} Receive only - status : This topics sends feedback to Node-Red No publication or receive at this level - status/pump : State of the pump Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/focus : State of the focus stage Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/imager : State of the imager Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Completed or 12_11_15_0.1.jpg has been imaged. Publish only - status/segmenter : Status of the segmentation - status/segmenter/name - status/segmenter/object_id - status/segmenter/metric Here is the original commit history: * Extract python main.py from flow * Fix bug in server addresses These addresses should be the loopback device instead of the network address of the device. Using the loopback address will not necessitate to update the script when the network address changes. * clean up picamera import * changes to main python and flow: update MQTT requests address to localhost (bugfix) update streaming output address to nothing update main flow to remove python script references and location * Automatically initialise imaging led on startup to off state. * Add the ability to invert outputs of the motor We added a key to config.json "hardware_config" with a subkey "stepper_reverse". If this key is present in the config file and set to 1, the output of the motors are inversed (stepper2 becomes the pump motor and stepper1 the focus motor) * move all non main script to a subfolder * add __init__.py to package * light module rewrite * json cleanup and absolute path for config file * light.py forgot to import subprocess #oups * Add command to turn the leds off * Auto formatting of main.py I've used Black with default settings, see https://github.com/psf/black * First commit of stepper.py Pump parameters still needs to be checked and tuned. * addition of hardware details in config.json * Introduce hardware.json to replace the `hardware_config` of config.json * stepper.py: calibration, typos * creates the MQTT_Client class * pump_max_speed is now in ml/min to help readability * forgot to add self to the class def * addition of threading capabilities to stepper.py (UNTESTED) * mqtt: fix topic bug * remove counter * mqtt add doc about topics * stepper.py creates an "actuator/*/state" topic * stepper.py: rename mqtt_client to pump_client * mqtt.py: add details about topics * stepper.py: rename pump_client to actuator_client * topic was not split properly and a part was lost * switch to f-strings for mqtt.py * cosmetic update * stepper.py: folder name will be planktoscope change calls * hardware.json became more straightforward * stepper.py syntax bugs * stepper.py addition of a received stop command * stepper.py: update to max travel distance * stepper.py: several typos here * rename folder * main.py: reword to reflect folder rename * main.py: remove logic that has been moved to stepper.py and mqtt.py * main.py: update to add mqtt imaging client * mqtt.py: make command and args local to class and output more verbose * make stepper.py a class * main.py: instantiate stepper class and call it * main.py: name mqtt client * update to main.json to reflect main.py changes * fix bugs around pump control * update flows to latest version from Thibault * distance can be a small value, and definitevely should be a float. * unify mqtt topics * unify mqtt output in the main flow * first logger implementation, uses loguru * mqtt: add reason to on_connect * mqtt: add on_disconnect handler * stepper: add more logger calls for debug mainly * main: add levels for logger * imager.py: first move of the imager logic * imager: time import cleanup * imager: morphocut import cleanup * imager: skimage import cleanup * imager: finishing import cleanup * imager: Class creation - WIP Also provides a fix for #26 (see line 190). * imager: threading is needed for Condition() * streamer: get the streamer server its own file * imager: creates start_camera and get the server creation out * imager: subclass multiprocessing.Process * imager: get Pipeline creation its own function * imager: cleanup of self calls * main: code removal and corresponding calls to newly created classes * imager: various formatting changes * main: management of signal shutdown * add requirements.txt * mqtt: messages are now json objects Also, addition of a flag on receiving a new message * mqtt: make message private and add logic to synchronise * stepper: creates the stepper class * stepper: use the new class * stepper: uses the new logic * stepper: add the shutdown event * stepper: add shutdown method * main: add shutdown event * imager: graceful shutdown * stepper: nicer way of checking the Eevnt * self is a required first argument for a method in a class Especially if you use said class private members! * python: various typos and small errors in import * stepper: create mqtt client during init * stepper: instanciate the mqtt client inside run Otherwise it's not accessible from inside the loop. It's a PITA, more information at https://stackoverflow.com/questions/17172878/using-pythons-multiprocessing-process-class * stepper: little bugs and typos all around * mqtt: add shutdown method * mqtt: add connect in init * stepper: fix bugs, sanitize inputs * stepper: work on delay prediction improvements * stepper: json is mean, double quote are mandatory inside * mqtt: add details about message exchanged * imager: first implementation of json messages * main.json: add new tab for RPi management + json for payloads * imager: add state_machine class * stepper: publish last will * imager: major refactor * main: make streaming server process a daemon * mqtt: insert debug statement on close * main: reorder imports * imager: make it work! Reinsert the streaming server logic in there, because there is a problem with the synchronisation part otherwise. Also, eventually, StreamingOuput() will have to be made not global Final very critical learning: it's super duper important to make sure the memory split is at least 256Meg for the GPU. Chaos ensues otherwise * main: changes to accomodate the streamer/imager fusino * imager_state_machine: insert states transition description * stepper: cleanup of code * segmenter: creation of the class * python: include segmenter changes * remove unused files * stepper: check existence of hardware.json * main.json: changes to reflect the python script evolution * remove unecessary TODOs and add some others * main: add check for config and directories * imager: update_config is implemented and we have better management of directories now * segmenter: now work recursively in all folders * flow: the configuration is now sent via mqtt * segmenter: better manage pipeline error * segmenter: declaration of archive_fn in init * imager: small bugs and typos * main: add uniqueID output * imager: add the camera settings message We can now update the ISO, shutter speed and resolution from Node-Red * package.json: update dependencies
2020-09-28 11:05:27 +02:00
{
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"t": "eq",
"v": "imager/image",
"vt": "str"
},
{
"t": "eq",
"v": "Missing entry :",
"vt": "str"
Extraction and refactor of the python code from node-red flow The rationale for this rewrite is to improve the readability, the modularity, the reliability and the future-proofing of the main python script. All in all, this is now 124 commits that are going to be squashed and merged together, spanning more than two weeks of development and testing. Please test away this release and break things. An upgrading guide will be published in the coming days, along with a new image for people to use if they don't want to upgrade on their own. Read along if you want to know all the goodies! As a starter, the python script was extracted from the main flow, and now lives in its own files at `PlantonScope/scripts/*`. We set up the auto formatting of the code by using [Black](https://github.com/psf/black). This make the code clearer and uniform. We are using the default settings, so if you just install Black and set your editor to format on save using it, you should be good to go. The code is separated in four main processes, each with a specific set of responsibilities: - The main process controls all the others, starts everything up and cleans up on shutdown - The stepper process manages the stepper movements. It's now possible to have simultaneous movements of both motors (this closes #38 ). - The imager process controls the camera and the streaming server via a state machine. - The segmenter process manages the segmentation and its outputs. The segmentation happens recursively in all folders in `/home/pi/PlanktonScope/img/`. Each folder has its own output archive, and bug #26 is now closed. Those processes communicates together using MQTT and json messages. Each message is adressed to one topic. The high level topic controls which process receives the message. The details of each topic is at the end of this commit message. Every imaging sessions has now its own folder, under the `img` root. Metadata are saved individually for every session, in a JSON file in the same directory as the pictures. The configuration is not parsed from `config.json` anymore and passed directly through MQTT messages to the concerned process. A new configuration file has been created: `hardware.json`. This file contains information related to your specific hardware configuration. You can choose to reverse the connection of the motors for example, but you can also define specific speed limits and steps number for your pump and focus stage. This will make it easier for people who wants to experiment with different kind of hardware. It's not necessary to have this file though. If it doesn't exists, the default configuration will be applied. The code is architectured around 6 modules and about 10 classes. I encourage you to have a look at the files, they're pretty straightforward to understand. There is a lot of work left around the node-red code refactoring, dashboard ui improvements, better and clearer LED messages, OLED screen integration and finer control of the segmentation process, but this is quite good for now. Here is the topic lists for MQTT and the corresponding messages. - actuator : This topic adresses the stepper control thread No publication under this topic should happen from the python process - actuator/pump : Control of the pump The message is a json object {"action":"move", "direction":"FORWARD", "volume":10, "flowrate":1} to move 10mL forward at 1mL/min action can be "move" or "stop" Receive only - actuator/focus : Control of the focus stage The message is a json object, speed is optional {"action":"move", "direction":"UP", "distance":0.26, "speed":1} to move up 10mm action can be "move" or "stop" Receive only - imager/image : This topic adresses the imaging thread Is a json object with {"action":"image","sleep":5,"volume":1,"nb_frame":200} sleep in seconds, volume in mL Can also receive a config update message: {"action":"config","config":[...]} Can also receive a camera settings message: {"action":"settings","iso":100,"shutter_speed":40} Receive only - segmenter/segment : This topic adresses the segmenter process Is a json object with {"action":"segment"} Receive only - status : This topics sends feedback to Node-Red No publication or receive at this level - status/pump : State of the pump Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/focus : State of the focus stage Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/imager : State of the imager Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Completed or 12_11_15_0.1.jpg has been imaged. Publish only - status/segmenter : Status of the segmentation - status/segmenter/name - status/segmenter/object_id - status/segmenter/metric Here is the original commit history: * Extract python main.py from flow * Fix bug in server addresses These addresses should be the loopback device instead of the network address of the device. Using the loopback address will not necessitate to update the script when the network address changes. * clean up picamera import * changes to main python and flow: update MQTT requests address to localhost (bugfix) update streaming output address to nothing update main flow to remove python script references and location * Automatically initialise imaging led on startup to off state. * Add the ability to invert outputs of the motor We added a key to config.json "hardware_config" with a subkey "stepper_reverse". If this key is present in the config file and set to 1, the output of the motors are inversed (stepper2 becomes the pump motor and stepper1 the focus motor) * move all non main script to a subfolder * add __init__.py to package * light module rewrite * json cleanup and absolute path for config file * light.py forgot to import subprocess #oups * Add command to turn the leds off * Auto formatting of main.py I've used Black with default settings, see https://github.com/psf/black * First commit of stepper.py Pump parameters still needs to be checked and tuned. * addition of hardware details in config.json * Introduce hardware.json to replace the `hardware_config` of config.json * stepper.py: calibration, typos * creates the MQTT_Client class * pump_max_speed is now in ml/min to help readability * forgot to add self to the class def * addition of threading capabilities to stepper.py (UNTESTED) * mqtt: fix topic bug * remove counter * mqtt add doc about topics * stepper.py creates an "actuator/*/state" topic * stepper.py: rename mqtt_client to pump_client * mqtt.py: add details about topics * stepper.py: rename pump_client to actuator_client * topic was not split properly and a part was lost * switch to f-strings for mqtt.py * cosmetic update * stepper.py: folder name will be planktoscope change calls * hardware.json became more straightforward * stepper.py syntax bugs * stepper.py addition of a received stop command * stepper.py: update to max travel distance * stepper.py: several typos here * rename folder * main.py: reword to reflect folder rename * main.py: remove logic that has been moved to stepper.py and mqtt.py * main.py: update to add mqtt imaging client * mqtt.py: make command and args local to class and output more verbose * make stepper.py a class * main.py: instantiate stepper class and call it * main.py: name mqtt client * update to main.json to reflect main.py changes * fix bugs around pump control * update flows to latest version from Thibault * distance can be a small value, and definitevely should be a float. * unify mqtt topics * unify mqtt output in the main flow * first logger implementation, uses loguru * mqtt: add reason to on_connect * mqtt: add on_disconnect handler * stepper: add more logger calls for debug mainly * main: add levels for logger * imager.py: first move of the imager logic * imager: time import cleanup * imager: morphocut import cleanup * imager: skimage import cleanup * imager: finishing import cleanup * imager: Class creation - WIP Also provides a fix for #26 (see line 190). * imager: threading is needed for Condition() * streamer: get the streamer server its own file * imager: creates start_camera and get the server creation out * imager: subclass multiprocessing.Process * imager: get Pipeline creation its own function * imager: cleanup of self calls * main: code removal and corresponding calls to newly created classes * imager: various formatting changes * main: management of signal shutdown * add requirements.txt * mqtt: messages are now json objects Also, addition of a flag on receiving a new message * mqtt: make message private and add logic to synchronise * stepper: creates the stepper class * stepper: use the new class * stepper: uses the new logic * stepper: add the shutdown event * stepper: add shutdown method * main: add shutdown event * imager: graceful shutdown * stepper: nicer way of checking the Eevnt * self is a required first argument for a method in a class Especially if you use said class private members! * python: various typos and small errors in import * stepper: create mqtt client during init * stepper: instanciate the mqtt client inside run Otherwise it's not accessible from inside the loop. It's a PITA, more information at https://stackoverflow.com/questions/17172878/using-pythons-multiprocessing-process-class * stepper: little bugs and typos all around * mqtt: add shutdown method * mqtt: add connect in init * stepper: fix bugs, sanitize inputs * stepper: work on delay prediction improvements * stepper: json is mean, double quote are mandatory inside * mqtt: add details about message exchanged * imager: first implementation of json messages * main.json: add new tab for RPi management + json for payloads * imager: add state_machine class * stepper: publish last will * imager: major refactor * main: make streaming server process a daemon * mqtt: insert debug statement on close * main: reorder imports * imager: make it work! Reinsert the streaming server logic in there, because there is a problem with the synchronisation part otherwise. Also, eventually, StreamingOuput() will have to be made not global Final very critical learning: it's super duper important to make sure the memory split is at least 256Meg for the GPU. Chaos ensues otherwise * main: changes to accomodate the streamer/imager fusino * imager_state_machine: insert states transition description * stepper: cleanup of code * segmenter: creation of the class * python: include segmenter changes * remove unused files * stepper: check existence of hardware.json * main.json: changes to reflect the python script evolution * remove unecessary TODOs and add some others * main: add check for config and directories * imager: update_config is implemented and we have better management of directories now * segmenter: now work recursively in all folders * flow: the configuration is now sent via mqtt * segmenter: better manage pipeline error * segmenter: declaration of archive_fn in init * imager: small bugs and typos * main: add uniqueID output * imager: add the camera settings message We can now update the ISO, shutter speed and resolution from Node-Red * package.json: update dependencies
2020-09-28 11:05:27 +02:00
}
],
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"checkall": "true",
"repair": false,
"outputs": 2,
"x": 1030,
"y": 460,
Extraction and refactor of the python code from node-red flow The rationale for this rewrite is to improve the readability, the modularity, the reliability and the future-proofing of the main python script. All in all, this is now 124 commits that are going to be squashed and merged together, spanning more than two weeks of development and testing. Please test away this release and break things. An upgrading guide will be published in the coming days, along with a new image for people to use if they don't want to upgrade on their own. Read along if you want to know all the goodies! As a starter, the python script was extracted from the main flow, and now lives in its own files at `PlantonScope/scripts/*`. We set up the auto formatting of the code by using [Black](https://github.com/psf/black). This make the code clearer and uniform. We are using the default settings, so if you just install Black and set your editor to format on save using it, you should be good to go. The code is separated in four main processes, each with a specific set of responsibilities: - The main process controls all the others, starts everything up and cleans up on shutdown - The stepper process manages the stepper movements. It's now possible to have simultaneous movements of both motors (this closes #38 ). - The imager process controls the camera and the streaming server via a state machine. - The segmenter process manages the segmentation and its outputs. The segmentation happens recursively in all folders in `/home/pi/PlanktonScope/img/`. Each folder has its own output archive, and bug #26 is now closed. Those processes communicates together using MQTT and json messages. Each message is adressed to one topic. The high level topic controls which process receives the message. The details of each topic is at the end of this commit message. Every imaging sessions has now its own folder, under the `img` root. Metadata are saved individually for every session, in a JSON file in the same directory as the pictures. The configuration is not parsed from `config.json` anymore and passed directly through MQTT messages to the concerned process. A new configuration file has been created: `hardware.json`. This file contains information related to your specific hardware configuration. You can choose to reverse the connection of the motors for example, but you can also define specific speed limits and steps number for your pump and focus stage. This will make it easier for people who wants to experiment with different kind of hardware. It's not necessary to have this file though. If it doesn't exists, the default configuration will be applied. The code is architectured around 6 modules and about 10 classes. I encourage you to have a look at the files, they're pretty straightforward to understand. There is a lot of work left around the node-red code refactoring, dashboard ui improvements, better and clearer LED messages, OLED screen integration and finer control of the segmentation process, but this is quite good for now. Here is the topic lists for MQTT and the corresponding messages. - actuator : This topic adresses the stepper control thread No publication under this topic should happen from the python process - actuator/pump : Control of the pump The message is a json object {"action":"move", "direction":"FORWARD", "volume":10, "flowrate":1} to move 10mL forward at 1mL/min action can be "move" or "stop" Receive only - actuator/focus : Control of the focus stage The message is a json object, speed is optional {"action":"move", "direction":"UP", "distance":0.26, "speed":1} to move up 10mm action can be "move" or "stop" Receive only - imager/image : This topic adresses the imaging thread Is a json object with {"action":"image","sleep":5,"volume":1,"nb_frame":200} sleep in seconds, volume in mL Can also receive a config update message: {"action":"config","config":[...]} Can also receive a camera settings message: {"action":"settings","iso":100,"shutter_speed":40} Receive only - segmenter/segment : This topic adresses the segmenter process Is a json object with {"action":"segment"} Receive only - status : This topics sends feedback to Node-Red No publication or receive at this level - status/pump : State of the pump Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/focus : State of the focus stage Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/imager : State of the imager Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Completed or 12_11_15_0.1.jpg has been imaged. Publish only - status/segmenter : Status of the segmentation - status/segmenter/name - status/segmenter/object_id - status/segmenter/metric Here is the original commit history: * Extract python main.py from flow * Fix bug in server addresses These addresses should be the loopback device instead of the network address of the device. Using the loopback address will not necessitate to update the script when the network address changes. * clean up picamera import * changes to main python and flow: update MQTT requests address to localhost (bugfix) update streaming output address to nothing update main flow to remove python script references and location * Automatically initialise imaging led on startup to off state. * Add the ability to invert outputs of the motor We added a key to config.json "hardware_config" with a subkey "stepper_reverse". If this key is present in the config file and set to 1, the output of the motors are inversed (stepper2 becomes the pump motor and stepper1 the focus motor) * move all non main script to a subfolder * add __init__.py to package * light module rewrite * json cleanup and absolute path for config file * light.py forgot to import subprocess #oups * Add command to turn the leds off * Auto formatting of main.py I've used Black with default settings, see https://github.com/psf/black * First commit of stepper.py Pump parameters still needs to be checked and tuned. * addition of hardware details in config.json * Introduce hardware.json to replace the `hardware_config` of config.json * stepper.py: calibration, typos * creates the MQTT_Client class * pump_max_speed is now in ml/min to help readability * forgot to add self to the class def * addition of threading capabilities to stepper.py (UNTESTED) * mqtt: fix topic bug * remove counter * mqtt add doc about topics * stepper.py creates an "actuator/*/state" topic * stepper.py: rename mqtt_client to pump_client * mqtt.py: add details about topics * stepper.py: rename pump_client to actuator_client * topic was not split properly and a part was lost * switch to f-strings for mqtt.py * cosmetic update * stepper.py: folder name will be planktoscope change calls * hardware.json became more straightforward * stepper.py syntax bugs * stepper.py addition of a received stop command * stepper.py: update to max travel distance * stepper.py: several typos here * rename folder * main.py: reword to reflect folder rename * main.py: remove logic that has been moved to stepper.py and mqtt.py * main.py: update to add mqtt imaging client * mqtt.py: make command and args local to class and output more verbose * make stepper.py a class * main.py: instantiate stepper class and call it * main.py: name mqtt client * update to main.json to reflect main.py changes * fix bugs around pump control * update flows to latest version from Thibault * distance can be a small value, and definitevely should be a float. * unify mqtt topics * unify mqtt output in the main flow * first logger implementation, uses loguru * mqtt: add reason to on_connect * mqtt: add on_disconnect handler * stepper: add more logger calls for debug mainly * main: add levels for logger * imager.py: first move of the imager logic * imager: time import cleanup * imager: morphocut import cleanup * imager: skimage import cleanup * imager: finishing import cleanup * imager: Class creation - WIP Also provides a fix for #26 (see line 190). * imager: threading is needed for Condition() * streamer: get the streamer server its own file * imager: creates start_camera and get the server creation out * imager: subclass multiprocessing.Process * imager: get Pipeline creation its own function * imager: cleanup of self calls * main: code removal and corresponding calls to newly created classes * imager: various formatting changes * main: management of signal shutdown * add requirements.txt * mqtt: messages are now json objects Also, addition of a flag on receiving a new message * mqtt: make message private and add logic to synchronise * stepper: creates the stepper class * stepper: use the new class * stepper: uses the new logic * stepper: add the shutdown event * stepper: add shutdown method * main: add shutdown event * imager: graceful shutdown * stepper: nicer way of checking the Eevnt * self is a required first argument for a method in a class Especially if you use said class private members! * python: various typos and small errors in import * stepper: create mqtt client during init * stepper: instanciate the mqtt client inside run Otherwise it's not accessible from inside the loop. It's a PITA, more information at https://stackoverflow.com/questions/17172878/using-pythons-multiprocessing-process-class * stepper: little bugs and typos all around * mqtt: add shutdown method * mqtt: add connect in init * stepper: fix bugs, sanitize inputs * stepper: work on delay prediction improvements * stepper: json is mean, double quote are mandatory inside * mqtt: add details about message exchanged * imager: first implementation of json messages * main.json: add new tab for RPi management + json for payloads * imager: add state_machine class * stepper: publish last will * imager: major refactor * main: make streaming server process a daemon * mqtt: insert debug statement on close * main: reorder imports * imager: make it work! Reinsert the streaming server logic in there, because there is a problem with the synchronisation part otherwise. Also, eventually, StreamingOuput() will have to be made not global Final very critical learning: it's super duper important to make sure the memory split is at least 256Meg for the GPU. Chaos ensues otherwise * main: changes to accomodate the streamer/imager fusino * imager_state_machine: insert states transition description * stepper: cleanup of code * segmenter: creation of the class * python: include segmenter changes * remove unused files * stepper: check existence of hardware.json * main.json: changes to reflect the python script evolution * remove unecessary TODOs and add some others * main: add check for config and directories * imager: update_config is implemented and we have better management of directories now * segmenter: now work recursively in all folders * flow: the configuration is now sent via mqtt * segmenter: better manage pipeline error * segmenter: declaration of archive_fn in init * imager: small bugs and typos * main: add uniqueID output * imager: add the camera settings message We can now update the ISO, shutter speed and resolution from Node-Red * package.json: update dependencies
2020-09-28 11:05:27 +02:00
"wires": [
[
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"c3e50240.82aa58"
],
[
"20e0a8c8.edbeb"
Extraction and refactor of the python code from node-red flow The rationale for this rewrite is to improve the readability, the modularity, the reliability and the future-proofing of the main python script. All in all, this is now 124 commits that are going to be squashed and merged together, spanning more than two weeks of development and testing. Please test away this release and break things. An upgrading guide will be published in the coming days, along with a new image for people to use if they don't want to upgrade on their own. Read along if you want to know all the goodies! As a starter, the python script was extracted from the main flow, and now lives in its own files at `PlantonScope/scripts/*`. We set up the auto formatting of the code by using [Black](https://github.com/psf/black). This make the code clearer and uniform. We are using the default settings, so if you just install Black and set your editor to format on save using it, you should be good to go. The code is separated in four main processes, each with a specific set of responsibilities: - The main process controls all the others, starts everything up and cleans up on shutdown - The stepper process manages the stepper movements. It's now possible to have simultaneous movements of both motors (this closes #38 ). - The imager process controls the camera and the streaming server via a state machine. - The segmenter process manages the segmentation and its outputs. The segmentation happens recursively in all folders in `/home/pi/PlanktonScope/img/`. Each folder has its own output archive, and bug #26 is now closed. Those processes communicates together using MQTT and json messages. Each message is adressed to one topic. The high level topic controls which process receives the message. The details of each topic is at the end of this commit message. Every imaging sessions has now its own folder, under the `img` root. Metadata are saved individually for every session, in a JSON file in the same directory as the pictures. The configuration is not parsed from `config.json` anymore and passed directly through MQTT messages to the concerned process. A new configuration file has been created: `hardware.json`. This file contains information related to your specific hardware configuration. You can choose to reverse the connection of the motors for example, but you can also define specific speed limits and steps number for your pump and focus stage. This will make it easier for people who wants to experiment with different kind of hardware. It's not necessary to have this file though. If it doesn't exists, the default configuration will be applied. The code is architectured around 6 modules and about 10 classes. I encourage you to have a look at the files, they're pretty straightforward to understand. There is a lot of work left around the node-red code refactoring, dashboard ui improvements, better and clearer LED messages, OLED screen integration and finer control of the segmentation process, but this is quite good for now. Here is the topic lists for MQTT and the corresponding messages. - actuator : This topic adresses the stepper control thread No publication under this topic should happen from the python process - actuator/pump : Control of the pump The message is a json object {"action":"move", "direction":"FORWARD", "volume":10, "flowrate":1} to move 10mL forward at 1mL/min action can be "move" or "stop" Receive only - actuator/focus : Control of the focus stage The message is a json object, speed is optional {"action":"move", "direction":"UP", "distance":0.26, "speed":1} to move up 10mm action can be "move" or "stop" Receive only - imager/image : This topic adresses the imaging thread Is a json object with {"action":"image","sleep":5,"volume":1,"nb_frame":200} sleep in seconds, volume in mL Can also receive a config update message: {"action":"config","config":[...]} Can also receive a camera settings message: {"action":"settings","iso":100,"shutter_speed":40} Receive only - segmenter/segment : This topic adresses the segmenter process Is a json object with {"action":"segment"} Receive only - status : This topics sends feedback to Node-Red No publication or receive at this level - status/pump : State of the pump Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/focus : State of the focus stage Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/imager : State of the imager Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Completed or 12_11_15_0.1.jpg has been imaged. Publish only - status/segmenter : Status of the segmentation - status/segmenter/name - status/segmenter/object_id - status/segmenter/metric Here is the original commit history: * Extract python main.py from flow * Fix bug in server addresses These addresses should be the loopback device instead of the network address of the device. Using the loopback address will not necessitate to update the script when the network address changes. * clean up picamera import * changes to main python and flow: update MQTT requests address to localhost (bugfix) update streaming output address to nothing update main flow to remove python script references and location * Automatically initialise imaging led on startup to off state. * Add the ability to invert outputs of the motor We added a key to config.json "hardware_config" with a subkey "stepper_reverse". If this key is present in the config file and set to 1, the output of the motors are inversed (stepper2 becomes the pump motor and stepper1 the focus motor) * move all non main script to a subfolder * add __init__.py to package * light module rewrite * json cleanup and absolute path for config file * light.py forgot to import subprocess #oups * Add command to turn the leds off * Auto formatting of main.py I've used Black with default settings, see https://github.com/psf/black * First commit of stepper.py Pump parameters still needs to be checked and tuned. * addition of hardware details in config.json * Introduce hardware.json to replace the `hardware_config` of config.json * stepper.py: calibration, typos * creates the MQTT_Client class * pump_max_speed is now in ml/min to help readability * forgot to add self to the class def * addition of threading capabilities to stepper.py (UNTESTED) * mqtt: fix topic bug * remove counter * mqtt add doc about topics * stepper.py creates an "actuator/*/state" topic * stepper.py: rename mqtt_client to pump_client * mqtt.py: add details about topics * stepper.py: rename pump_client to actuator_client * topic was not split properly and a part was lost * switch to f-strings for mqtt.py * cosmetic update * stepper.py: folder name will be planktoscope change calls * hardware.json became more straightforward * stepper.py syntax bugs * stepper.py addition of a received stop command * stepper.py: update to max travel distance * stepper.py: several typos here * rename folder * main.py: reword to reflect folder rename * main.py: remove logic that has been moved to stepper.py and mqtt.py * main.py: update to add mqtt imaging client * mqtt.py: make command and args local to class and output more verbose * make stepper.py a class * main.py: instantiate stepper class and call it * main.py: name mqtt client * update to main.json to reflect main.py changes * fix bugs around pump control * update flows to latest version from Thibault * distance can be a small value, and definitevely should be a float. * unify mqtt topics * unify mqtt output in the main flow * first logger implementation, uses loguru * mqtt: add reason to on_connect * mqtt: add on_disconnect handler * stepper: add more logger calls for debug mainly * main: add levels for logger * imager.py: first move of the imager logic * imager: time import cleanup * imager: morphocut import cleanup * imager: skimage import cleanup * imager: finishing import cleanup * imager: Class creation - WIP Also provides a fix for #26 (see line 190). * imager: threading is needed for Condition() * streamer: get the streamer server its own file * imager: creates start_camera and get the server creation out * imager: subclass multiprocessing.Process * imager: get Pipeline creation its own function * imager: cleanup of self calls * main: code removal and corresponding calls to newly created classes * imager: various formatting changes * main: management of signal shutdown * add requirements.txt * mqtt: messages are now json objects Also, addition of a flag on receiving a new message * mqtt: make message private and add logic to synchronise * stepper: creates the stepper class * stepper: use the new class * stepper: uses the new logic * stepper: add the shutdown event * stepper: add shutdown method * main: add shutdown event * imager: graceful shutdown * stepper: nicer way of checking the Eevnt * self is a required first argument for a method in a class Especially if you use said class private members! * python: various typos and small errors in import * stepper: create mqtt client during init * stepper: instanciate the mqtt client inside run Otherwise it's not accessible from inside the loop. It's a PITA, more information at https://stackoverflow.com/questions/17172878/using-pythons-multiprocessing-process-class * stepper: little bugs and typos all around * mqtt: add shutdown method * mqtt: add connect in init * stepper: fix bugs, sanitize inputs * stepper: work on delay prediction improvements * stepper: json is mean, double quote are mandatory inside * mqtt: add details about message exchanged * imager: first implementation of json messages * main.json: add new tab for RPi management + json for payloads * imager: add state_machine class * stepper: publish last will * imager: major refactor * main: make streaming server process a daemon * mqtt: insert debug statement on close * main: reorder imports * imager: make it work! Reinsert the streaming server logic in there, because there is a problem with the synchronisation part otherwise. Also, eventually, StreamingOuput() will have to be made not global Final very critical learning: it's super duper important to make sure the memory split is at least 256Meg for the GPU. Chaos ensues otherwise * main: changes to accomodate the streamer/imager fusino * imager_state_machine: insert states transition description * stepper: cleanup of code * segmenter: creation of the class * python: include segmenter changes * remove unused files * stepper: check existence of hardware.json * main.json: changes to reflect the python script evolution * remove unecessary TODOs and add some others * main: add check for config and directories * imager: update_config is implemented and we have better management of directories now * segmenter: now work recursively in all folders * flow: the configuration is now sent via mqtt * segmenter: better manage pipeline error * segmenter: declaration of archive_fn in init * imager: small bugs and typos * main: add uniqueID output * imager: add the camera settings message We can now update the ISO, shutter speed and resolution from Node-Red * package.json: update dependencies
2020-09-28 11:05:27 +02:00
]
]
},
{
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
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Extraction and refactor of the python code from node-red flow The rationale for this rewrite is to improve the readability, the modularity, the reliability and the future-proofing of the main python script. All in all, this is now 124 commits that are going to be squashed and merged together, spanning more than two weeks of development and testing. Please test away this release and break things. An upgrading guide will be published in the coming days, along with a new image for people to use if they don't want to upgrade on their own. Read along if you want to know all the goodies! As a starter, the python script was extracted from the main flow, and now lives in its own files at `PlantonScope/scripts/*`. We set up the auto formatting of the code by using [Black](https://github.com/psf/black). This make the code clearer and uniform. We are using the default settings, so if you just install Black and set your editor to format on save using it, you should be good to go. The code is separated in four main processes, each with a specific set of responsibilities: - The main process controls all the others, starts everything up and cleans up on shutdown - The stepper process manages the stepper movements. It's now possible to have simultaneous movements of both motors (this closes #38 ). - The imager process controls the camera and the streaming server via a state machine. - The segmenter process manages the segmentation and its outputs. The segmentation happens recursively in all folders in `/home/pi/PlanktonScope/img/`. Each folder has its own output archive, and bug #26 is now closed. Those processes communicates together using MQTT and json messages. Each message is adressed to one topic. The high level topic controls which process receives the message. The details of each topic is at the end of this commit message. Every imaging sessions has now its own folder, under the `img` root. Metadata are saved individually for every session, in a JSON file in the same directory as the pictures. The configuration is not parsed from `config.json` anymore and passed directly through MQTT messages to the concerned process. A new configuration file has been created: `hardware.json`. This file contains information related to your specific hardware configuration. You can choose to reverse the connection of the motors for example, but you can also define specific speed limits and steps number for your pump and focus stage. This will make it easier for people who wants to experiment with different kind of hardware. It's not necessary to have this file though. If it doesn't exists, the default configuration will be applied. The code is architectured around 6 modules and about 10 classes. I encourage you to have a look at the files, they're pretty straightforward to understand. There is a lot of work left around the node-red code refactoring, dashboard ui improvements, better and clearer LED messages, OLED screen integration and finer control of the segmentation process, but this is quite good for now. Here is the topic lists for MQTT and the corresponding messages. - actuator : This topic adresses the stepper control thread No publication under this topic should happen from the python process - actuator/pump : Control of the pump The message is a json object {"action":"move", "direction":"FORWARD", "volume":10, "flowrate":1} to move 10mL forward at 1mL/min action can be "move" or "stop" Receive only - actuator/focus : Control of the focus stage The message is a json object, speed is optional {"action":"move", "direction":"UP", "distance":0.26, "speed":1} to move up 10mm action can be "move" or "stop" Receive only - imager/image : This topic adresses the imaging thread Is a json object with {"action":"image","sleep":5,"volume":1,"nb_frame":200} sleep in seconds, volume in mL Can also receive a config update message: {"action":"config","config":[...]} Can also receive a camera settings message: {"action":"settings","iso":100,"shutter_speed":40} Receive only - segmenter/segment : This topic adresses the segmenter process Is a json object with {"action":"segment"} Receive only - status : This topics sends feedback to Node-Red No publication or receive at this level - status/pump : State of the pump Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/focus : State of the focus stage Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/imager : State of the imager Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Completed or 12_11_15_0.1.jpg has been imaged. Publish only - status/segmenter : Status of the segmentation - status/segmenter/name - status/segmenter/object_id - status/segmenter/metric Here is the original commit history: * Extract python main.py from flow * Fix bug in server addresses These addresses should be the loopback device instead of the network address of the device. Using the loopback address will not necessitate to update the script when the network address changes. * clean up picamera import * changes to main python and flow: update MQTT requests address to localhost (bugfix) update streaming output address to nothing update main flow to remove python script references and location * Automatically initialise imaging led on startup to off state. * Add the ability to invert outputs of the motor We added a key to config.json "hardware_config" with a subkey "stepper_reverse". If this key is present in the config file and set to 1, the output of the motors are inversed (stepper2 becomes the pump motor and stepper1 the focus motor) * move all non main script to a subfolder * add __init__.py to package * light module rewrite * json cleanup and absolute path for config file * light.py forgot to import subprocess #oups * Add command to turn the leds off * Auto formatting of main.py I've used Black with default settings, see https://github.com/psf/black * First commit of stepper.py Pump parameters still needs to be checked and tuned. * addition of hardware details in config.json * Introduce hardware.json to replace the `hardware_config` of config.json * stepper.py: calibration, typos * creates the MQTT_Client class * pump_max_speed is now in ml/min to help readability * forgot to add self to the class def * addition of threading capabilities to stepper.py (UNTESTED) * mqtt: fix topic bug * remove counter * mqtt add doc about topics * stepper.py creates an "actuator/*/state" topic * stepper.py: rename mqtt_client to pump_client * mqtt.py: add details about topics * stepper.py: rename pump_client to actuator_client * topic was not split properly and a part was lost * switch to f-strings for mqtt.py * cosmetic update * stepper.py: folder name will be planktoscope change calls * hardware.json became more straightforward * stepper.py syntax bugs * stepper.py addition of a received stop command * stepper.py: update to max travel distance * stepper.py: several typos here * rename folder * main.py: reword to reflect folder rename * main.py: remove logic that has been moved to stepper.py and mqtt.py * main.py: update to add mqtt imaging client * mqtt.py: make command and args local to class and output more verbose * make stepper.py a class * main.py: instantiate stepper class and call it * main.py: name mqtt client * update to main.json to reflect main.py changes * fix bugs around pump control * update flows to latest version from Thibault * distance can be a small value, and definitevely should be a float. * unify mqtt topics * unify mqtt output in the main flow * first logger implementation, uses loguru * mqtt: add reason to on_connect * mqtt: add on_disconnect handler * stepper: add more logger calls for debug mainly * main: add levels for logger * imager.py: first move of the imager logic * imager: time import cleanup * imager: morphocut import cleanup * imager: skimage import cleanup * imager: finishing import cleanup * imager: Class creation - WIP Also provides a fix for #26 (see line 190). * imager: threading is needed for Condition() * streamer: get the streamer server its own file * imager: creates start_camera and get the server creation out * imager: subclass multiprocessing.Process * imager: get Pipeline creation its own function * imager: cleanup of self calls * main: code removal and corresponding calls to newly created classes * imager: various formatting changes * main: management of signal shutdown * add requirements.txt * mqtt: messages are now json objects Also, addition of a flag on receiving a new message * mqtt: make message private and add logic to synchronise * stepper: creates the stepper class * stepper: use the new class * stepper: uses the new logic * stepper: add the shutdown event * stepper: add shutdown method * main: add shutdown event * imager: graceful shutdown * stepper: nicer way of checking the Eevnt * self is a required first argument for a method in a class Especially if you use said class private members! * python: various typos and small errors in import * stepper: create mqtt client during init * stepper: instanciate the mqtt client inside run Otherwise it's not accessible from inside the loop. It's a PITA, more information at https://stackoverflow.com/questions/17172878/using-pythons-multiprocessing-process-class * stepper: little bugs and typos all around * mqtt: add shutdown method * mqtt: add connect in init * stepper: fix bugs, sanitize inputs * stepper: work on delay prediction improvements * stepper: json is mean, double quote are mandatory inside * mqtt: add details about message exchanged * imager: first implementation of json messages * main.json: add new tab for RPi management + json for payloads * imager: add state_machine class * stepper: publish last will * imager: major refactor * main: make streaming server process a daemon * mqtt: insert debug statement on close * main: reorder imports * imager: make it work! Reinsert the streaming server logic in there, because there is a problem with the synchronisation part otherwise. Also, eventually, StreamingOuput() will have to be made not global Final very critical learning: it's super duper important to make sure the memory split is at least 256Meg for the GPU. Chaos ensues otherwise * main: changes to accomodate the streamer/imager fusino * imager_state_machine: insert states transition description * stepper: cleanup of code * segmenter: creation of the class * python: include segmenter changes * remove unused files * stepper: check existence of hardware.json * main.json: changes to reflect the python script evolution * remove unecessary TODOs and add some others * main: add check for config and directories * imager: update_config is implemented and we have better management of directories now * segmenter: now work recursively in all folders * flow: the configuration is now sent via mqtt * segmenter: better manage pipeline error * segmenter: declaration of archive_fn in init * imager: small bugs and typos * main: add uniqueID output * imager: add the camera settings message We can now update the ISO, shutter speed and resolution from Node-Red * package.json: update dependencies
2020-09-28 11:05:27 +02:00
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Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
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Extraction and refactor of the python code from node-red flow The rationale for this rewrite is to improve the readability, the modularity, the reliability and the future-proofing of the main python script. All in all, this is now 124 commits that are going to be squashed and merged together, spanning more than two weeks of development and testing. Please test away this release and break things. An upgrading guide will be published in the coming days, along with a new image for people to use if they don't want to upgrade on their own. Read along if you want to know all the goodies! As a starter, the python script was extracted from the main flow, and now lives in its own files at `PlantonScope/scripts/*`. We set up the auto formatting of the code by using [Black](https://github.com/psf/black). This make the code clearer and uniform. We are using the default settings, so if you just install Black and set your editor to format on save using it, you should be good to go. The code is separated in four main processes, each with a specific set of responsibilities: - The main process controls all the others, starts everything up and cleans up on shutdown - The stepper process manages the stepper movements. It's now possible to have simultaneous movements of both motors (this closes #38 ). - The imager process controls the camera and the streaming server via a state machine. - The segmenter process manages the segmentation and its outputs. The segmentation happens recursively in all folders in `/home/pi/PlanktonScope/img/`. Each folder has its own output archive, and bug #26 is now closed. Those processes communicates together using MQTT and json messages. Each message is adressed to one topic. The high level topic controls which process receives the message. The details of each topic is at the end of this commit message. Every imaging sessions has now its own folder, under the `img` root. Metadata are saved individually for every session, in a JSON file in the same directory as the pictures. The configuration is not parsed from `config.json` anymore and passed directly through MQTT messages to the concerned process. A new configuration file has been created: `hardware.json`. This file contains information related to your specific hardware configuration. You can choose to reverse the connection of the motors for example, but you can also define specific speed limits and steps number for your pump and focus stage. This will make it easier for people who wants to experiment with different kind of hardware. It's not necessary to have this file though. If it doesn't exists, the default configuration will be applied. The code is architectured around 6 modules and about 10 classes. I encourage you to have a look at the files, they're pretty straightforward to understand. There is a lot of work left around the node-red code refactoring, dashboard ui improvements, better and clearer LED messages, OLED screen integration and finer control of the segmentation process, but this is quite good for now. Here is the topic lists for MQTT and the corresponding messages. - actuator : This topic adresses the stepper control thread No publication under this topic should happen from the python process - actuator/pump : Control of the pump The message is a json object {"action":"move", "direction":"FORWARD", "volume":10, "flowrate":1} to move 10mL forward at 1mL/min action can be "move" or "stop" Receive only - actuator/focus : Control of the focus stage The message is a json object, speed is optional {"action":"move", "direction":"UP", "distance":0.26, "speed":1} to move up 10mm action can be "move" or "stop" Receive only - imager/image : This topic adresses the imaging thread Is a json object with {"action":"image","sleep":5,"volume":1,"nb_frame":200} sleep in seconds, volume in mL Can also receive a config update message: {"action":"config","config":[...]} Can also receive a camera settings message: {"action":"settings","iso":100,"shutter_speed":40} Receive only - segmenter/segment : This topic adresses the segmenter process Is a json object with {"action":"segment"} Receive only - status : This topics sends feedback to Node-Red No publication or receive at this level - status/pump : State of the pump Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/focus : State of the focus stage Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/imager : State of the imager Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Completed or 12_11_15_0.1.jpg has been imaged. Publish only - status/segmenter : Status of the segmentation - status/segmenter/name - status/segmenter/object_id - status/segmenter/metric Here is the original commit history: * Extract python main.py from flow * Fix bug in server addresses These addresses should be the loopback device instead of the network address of the device. Using the loopback address will not necessitate to update the script when the network address changes. * clean up picamera import * changes to main python and flow: update MQTT requests address to localhost (bugfix) update streaming output address to nothing update main flow to remove python script references and location * Automatically initialise imaging led on startup to off state. * Add the ability to invert outputs of the motor We added a key to config.json "hardware_config" with a subkey "stepper_reverse". If this key is present in the config file and set to 1, the output of the motors are inversed (stepper2 becomes the pump motor and stepper1 the focus motor) * move all non main script to a subfolder * add __init__.py to package * light module rewrite * json cleanup and absolute path for config file * light.py forgot to import subprocess #oups * Add command to turn the leds off * Auto formatting of main.py I've used Black with default settings, see https://github.com/psf/black * First commit of stepper.py Pump parameters still needs to be checked and tuned. * addition of hardware details in config.json * Introduce hardware.json to replace the `hardware_config` of config.json * stepper.py: calibration, typos * creates the MQTT_Client class * pump_max_speed is now in ml/min to help readability * forgot to add self to the class def * addition of threading capabilities to stepper.py (UNTESTED) * mqtt: fix topic bug * remove counter * mqtt add doc about topics * stepper.py creates an "actuator/*/state" topic * stepper.py: rename mqtt_client to pump_client * mqtt.py: add details about topics * stepper.py: rename pump_client to actuator_client * topic was not split properly and a part was lost * switch to f-strings for mqtt.py * cosmetic update * stepper.py: folder name will be planktoscope change calls * hardware.json became more straightforward * stepper.py syntax bugs * stepper.py addition of a received stop command * stepper.py: update to max travel distance * stepper.py: several typos here * rename folder * main.py: reword to reflect folder rename * main.py: remove logic that has been moved to stepper.py and mqtt.py * main.py: update to add mqtt imaging client * mqtt.py: make command and args local to class and output more verbose * make stepper.py a class * main.py: instantiate stepper class and call it * main.py: name mqtt client * update to main.json to reflect main.py changes * fix bugs around pump control * update flows to latest version from Thibault * distance can be a small value, and definitevely should be a float. * unify mqtt topics * unify mqtt output in the main flow * first logger implementation, uses loguru * mqtt: add reason to on_connect * mqtt: add on_disconnect handler * stepper: add more logger calls for debug mainly * main: add levels for logger * imager.py: first move of the imager logic * imager: time import cleanup * imager: morphocut import cleanup * imager: skimage import cleanup * imager: finishing import cleanup * imager: Class creation - WIP Also provides a fix for #26 (see line 190). * imager: threading is needed for Condition() * streamer: get the streamer server its own file * imager: creates start_camera and get the server creation out * imager: subclass multiprocessing.Process * imager: get Pipeline creation its own function * imager: cleanup of self calls * main: code removal and corresponding calls to newly created classes * imager: various formatting changes * main: management of signal shutdown * add requirements.txt * mqtt: messages are now json objects Also, addition of a flag on receiving a new message * mqtt: make message private and add logic to synchronise * stepper: creates the stepper class * stepper: use the new class * stepper: uses the new logic * stepper: add the shutdown event * stepper: add shutdown method * main: add shutdown event * imager: graceful shutdown * stepper: nicer way of checking the Eevnt * self is a required first argument for a method in a class Especially if you use said class private members! * python: various typos and small errors in import * stepper: create mqtt client during init * stepper: instanciate the mqtt client inside run Otherwise it's not accessible from inside the loop. It's a PITA, more information at https://stackoverflow.com/questions/17172878/using-pythons-multiprocessing-process-class * stepper: little bugs and typos all around * mqtt: add shutdown method * mqtt: add connect in init * stepper: fix bugs, sanitize inputs * stepper: work on delay prediction improvements * stepper: json is mean, double quote are mandatory inside * mqtt: add details about message exchanged * imager: first implementation of json messages * main.json: add new tab for RPi management + json for payloads * imager: add state_machine class * stepper: publish last will * imager: major refactor * main: make streaming server process a daemon * mqtt: insert debug statement on close * main: reorder imports * imager: make it work! Reinsert the streaming server logic in there, because there is a problem with the synchronisation part otherwise. Also, eventually, StreamingOuput() will have to be made not global Final very critical learning: it's super duper important to make sure the memory split is at least 256Meg for the GPU. Chaos ensues otherwise * main: changes to accomodate the streamer/imager fusino * imager_state_machine: insert states transition description * stepper: cleanup of code * segmenter: creation of the class * python: include segmenter changes * remove unused files * stepper: check existence of hardware.json * main.json: changes to reflect the python script evolution * remove unecessary TODOs and add some others * main: add check for config and directories * imager: update_config is implemented and we have better management of directories now * segmenter: now work recursively in all folders * flow: the configuration is now sent via mqtt * segmenter: better manage pipeline error * segmenter: declaration of archive_fn in init * imager: small bugs and typos * main: add uniqueID output * imager: add the camera settings message We can now update the ISO, shutter speed and resolution from Node-Red * package.json: update dependencies
2020-09-28 11:05:27 +02:00
"wires": [
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Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
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Extraction and refactor of the python code from node-red flow The rationale for this rewrite is to improve the readability, the modularity, the reliability and the future-proofing of the main python script. All in all, this is now 124 commits that are going to be squashed and merged together, spanning more than two weeks of development and testing. Please test away this release and break things. An upgrading guide will be published in the coming days, along with a new image for people to use if they don't want to upgrade on their own. Read along if you want to know all the goodies! As a starter, the python script was extracted from the main flow, and now lives in its own files at `PlantonScope/scripts/*`. We set up the auto formatting of the code by using [Black](https://github.com/psf/black). This make the code clearer and uniform. We are using the default settings, so if you just install Black and set your editor to format on save using it, you should be good to go. The code is separated in four main processes, each with a specific set of responsibilities: - The main process controls all the others, starts everything up and cleans up on shutdown - The stepper process manages the stepper movements. It's now possible to have simultaneous movements of both motors (this closes #38 ). - The imager process controls the camera and the streaming server via a state machine. - The segmenter process manages the segmentation and its outputs. The segmentation happens recursively in all folders in `/home/pi/PlanktonScope/img/`. Each folder has its own output archive, and bug #26 is now closed. Those processes communicates together using MQTT and json messages. Each message is adressed to one topic. The high level topic controls which process receives the message. The details of each topic is at the end of this commit message. Every imaging sessions has now its own folder, under the `img` root. Metadata are saved individually for every session, in a JSON file in the same directory as the pictures. The configuration is not parsed from `config.json` anymore and passed directly through MQTT messages to the concerned process. A new configuration file has been created: `hardware.json`. This file contains information related to your specific hardware configuration. You can choose to reverse the connection of the motors for example, but you can also define specific speed limits and steps number for your pump and focus stage. This will make it easier for people who wants to experiment with different kind of hardware. It's not necessary to have this file though. If it doesn't exists, the default configuration will be applied. The code is architectured around 6 modules and about 10 classes. I encourage you to have a look at the files, they're pretty straightforward to understand. There is a lot of work left around the node-red code refactoring, dashboard ui improvements, better and clearer LED messages, OLED screen integration and finer control of the segmentation process, but this is quite good for now. Here is the topic lists for MQTT and the corresponding messages. - actuator : This topic adresses the stepper control thread No publication under this topic should happen from the python process - actuator/pump : Control of the pump The message is a json object {"action":"move", "direction":"FORWARD", "volume":10, "flowrate":1} to move 10mL forward at 1mL/min action can be "move" or "stop" Receive only - actuator/focus : Control of the focus stage The message is a json object, speed is optional {"action":"move", "direction":"UP", "distance":0.26, "speed":1} to move up 10mm action can be "move" or "stop" Receive only - imager/image : This topic adresses the imaging thread Is a json object with {"action":"image","sleep":5,"volume":1,"nb_frame":200} sleep in seconds, volume in mL Can also receive a config update message: {"action":"config","config":[...]} Can also receive a camera settings message: {"action":"settings","iso":100,"shutter_speed":40} Receive only - segmenter/segment : This topic adresses the segmenter process Is a json object with {"action":"segment"} Receive only - status : This topics sends feedback to Node-Red No publication or receive at this level - status/pump : State of the pump Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/focus : State of the focus stage Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/imager : State of the imager Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Completed or 12_11_15_0.1.jpg has been imaged. Publish only - status/segmenter : Status of the segmentation - status/segmenter/name - status/segmenter/object_id - status/segmenter/metric Here is the original commit history: * Extract python main.py from flow * Fix bug in server addresses These addresses should be the loopback device instead of the network address of the device. Using the loopback address will not necessitate to update the script when the network address changes. * clean up picamera import * changes to main python and flow: update MQTT requests address to localhost (bugfix) update streaming output address to nothing update main flow to remove python script references and location * Automatically initialise imaging led on startup to off state. * Add the ability to invert outputs of the motor We added a key to config.json "hardware_config" with a subkey "stepper_reverse". If this key is present in the config file and set to 1, the output of the motors are inversed (stepper2 becomes the pump motor and stepper1 the focus motor) * move all non main script to a subfolder * add __init__.py to package * light module rewrite * json cleanup and absolute path for config file * light.py forgot to import subprocess #oups * Add command to turn the leds off * Auto formatting of main.py I've used Black with default settings, see https://github.com/psf/black * First commit of stepper.py Pump parameters still needs to be checked and tuned. * addition of hardware details in config.json * Introduce hardware.json to replace the `hardware_config` of config.json * stepper.py: calibration, typos * creates the MQTT_Client class * pump_max_speed is now in ml/min to help readability * forgot to add self to the class def * addition of threading capabilities to stepper.py (UNTESTED) * mqtt: fix topic bug * remove counter * mqtt add doc about topics * stepper.py creates an "actuator/*/state" topic * stepper.py: rename mqtt_client to pump_client * mqtt.py: add details about topics * stepper.py: rename pump_client to actuator_client * topic was not split properly and a part was lost * switch to f-strings for mqtt.py * cosmetic update * stepper.py: folder name will be planktoscope change calls * hardware.json became more straightforward * stepper.py syntax bugs * stepper.py addition of a received stop command * stepper.py: update to max travel distance * stepper.py: several typos here * rename folder * main.py: reword to reflect folder rename * main.py: remove logic that has been moved to stepper.py and mqtt.py * main.py: update to add mqtt imaging client * mqtt.py: make command and args local to class and output more verbose * make stepper.py a class * main.py: instantiate stepper class and call it * main.py: name mqtt client * update to main.json to reflect main.py changes * fix bugs around pump control * update flows to latest version from Thibault * distance can be a small value, and definitevely should be a float. * unify mqtt topics * unify mqtt output in the main flow * first logger implementation, uses loguru * mqtt: add reason to on_connect * mqtt: add on_disconnect handler * stepper: add more logger calls for debug mainly * main: add levels for logger * imager.py: first move of the imager logic * imager: time import cleanup * imager: morphocut import cleanup * imager: skimage import cleanup * imager: finishing import cleanup * imager: Class creation - WIP Also provides a fix for #26 (see line 190). * imager: threading is needed for Condition() * streamer: get the streamer server its own file * imager: creates start_camera and get the server creation out * imager: subclass multiprocessing.Process * imager: get Pipeline creation its own function * imager: cleanup of self calls * main: code removal and corresponding calls to newly created classes * imager: various formatting changes * main: management of signal shutdown * add requirements.txt * mqtt: messages are now json objects Also, addition of a flag on receiving a new message * mqtt: make message private and add logic to synchronise * stepper: creates the stepper class * stepper: use the new class * stepper: uses the new logic * stepper: add the shutdown event * stepper: add shutdown method * main: add shutdown event * imager: graceful shutdown * stepper: nicer way of checking the Eevnt * self is a required first argument for a method in a class Especially if you use said class private members! * python: various typos and small errors in import * stepper: create mqtt client during init * stepper: instanciate the mqtt client inside run Otherwise it's not accessible from inside the loop. It's a PITA, more information at https://stackoverflow.com/questions/17172878/using-pythons-multiprocessing-process-class * stepper: little bugs and typos all around * mqtt: add shutdown method * mqtt: add connect in init * stepper: fix bugs, sanitize inputs * stepper: work on delay prediction improvements * stepper: json is mean, double quote are mandatory inside * mqtt: add details about message exchanged * imager: first implementation of json messages * main.json: add new tab for RPi management + json for payloads * imager: add state_machine class * stepper: publish last will * imager: major refactor * main: make streaming server process a daemon * mqtt: insert debug statement on close * main: reorder imports * imager: make it work! Reinsert the streaming server logic in there, because there is a problem with the synchronisation part otherwise. Also, eventually, StreamingOuput() will have to be made not global Final very critical learning: it's super duper important to make sure the memory split is at least 256Meg for the GPU. Chaos ensues otherwise * main: changes to accomodate the streamer/imager fusino * imager_state_machine: insert states transition description * stepper: cleanup of code * segmenter: creation of the class * python: include segmenter changes * remove unused files * stepper: check existence of hardware.json * main.json: changes to reflect the python script evolution * remove unecessary TODOs and add some others * main: add check for config and directories * imager: update_config is implemented and we have better management of directories now * segmenter: now work recursively in all folders * flow: the configuration is now sent via mqtt * segmenter: better manage pipeline error * segmenter: declaration of archive_fn in init * imager: small bugs and typos * main: add uniqueID output * imager: add the camera settings message We can now update the ISO, shutter speed and resolution from Node-Red * package.json: update dependencies
2020-09-28 11:05:27 +02:00
]
]
},
{
Main.json: UI upgrade
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"id": "d74210ef.edc15",
"type": "mqtt out",
"z": "baa1e3d9.cb29d",
Extraction and refactor of the python code from node-red flow The rationale for this rewrite is to improve the readability, the modularity, the reliability and the future-proofing of the main python script. All in all, this is now 124 commits that are going to be squashed and merged together, spanning more than two weeks of development and testing. Please test away this release and break things. An upgrading guide will be published in the coming days, along with a new image for people to use if they don't want to upgrade on their own. Read along if you want to know all the goodies! As a starter, the python script was extracted from the main flow, and now lives in its own files at `PlantonScope/scripts/*`. We set up the auto formatting of the code by using [Black](https://github.com/psf/black). This make the code clearer and uniform. We are using the default settings, so if you just install Black and set your editor to format on save using it, you should be good to go. The code is separated in four main processes, each with a specific set of responsibilities: - The main process controls all the others, starts everything up and cleans up on shutdown - The stepper process manages the stepper movements. It's now possible to have simultaneous movements of both motors (this closes #38 ). - The imager process controls the camera and the streaming server via a state machine. - The segmenter process manages the segmentation and its outputs. The segmentation happens recursively in all folders in `/home/pi/PlanktonScope/img/`. Each folder has its own output archive, and bug #26 is now closed. Those processes communicates together using MQTT and json messages. Each message is adressed to one topic. The high level topic controls which process receives the message. The details of each topic is at the end of this commit message. Every imaging sessions has now its own folder, under the `img` root. Metadata are saved individually for every session, in a JSON file in the same directory as the pictures. The configuration is not parsed from `config.json` anymore and passed directly through MQTT messages to the concerned process. A new configuration file has been created: `hardware.json`. This file contains information related to your specific hardware configuration. You can choose to reverse the connection of the motors for example, but you can also define specific speed limits and steps number for your pump and focus stage. This will make it easier for people who wants to experiment with different kind of hardware. It's not necessary to have this file though. If it doesn't exists, the default configuration will be applied. The code is architectured around 6 modules and about 10 classes. I encourage you to have a look at the files, they're pretty straightforward to understand. There is a lot of work left around the node-red code refactoring, dashboard ui improvements, better and clearer LED messages, OLED screen integration and finer control of the segmentation process, but this is quite good for now. Here is the topic lists for MQTT and the corresponding messages. - actuator : This topic adresses the stepper control thread No publication under this topic should happen from the python process - actuator/pump : Control of the pump The message is a json object {"action":"move", "direction":"FORWARD", "volume":10, "flowrate":1} to move 10mL forward at 1mL/min action can be "move" or "stop" Receive only - actuator/focus : Control of the focus stage The message is a json object, speed is optional {"action":"move", "direction":"UP", "distance":0.26, "speed":1} to move up 10mm action can be "move" or "stop" Receive only - imager/image : This topic adresses the imaging thread Is a json object with {"action":"image","sleep":5,"volume":1,"nb_frame":200} sleep in seconds, volume in mL Can also receive a config update message: {"action":"config","config":[...]} Can also receive a camera settings message: {"action":"settings","iso":100,"shutter_speed":40} Receive only - segmenter/segment : This topic adresses the segmenter process Is a json object with {"action":"segment"} Receive only - status : This topics sends feedback to Node-Red No publication or receive at this level - status/pump : State of the pump Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/focus : State of the focus stage Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Done, Interrupted Publish only - status/imager : State of the imager Is a json object with {"status":"Start", "time_left":25} Status is one of Started, Ready, Completed or 12_11_15_0.1.jpg has been imaged. Publish only - status/segmenter : Status of the segmentation - status/segmenter/name - status/segmenter/object_id - status/segmenter/metric Here is the original commit history: * Extract python main.py from flow * Fix bug in server addresses These addresses should be the loopback device instead of the network address of the device. Using the loopback address will not necessitate to update the script when the network address changes. * clean up picamera import * changes to main python and flow: update MQTT requests address to localhost (bugfix) update streaming output address to nothing update main flow to remove python script references and location * Automatically initialise imaging led on startup to off state. * Add the ability to invert outputs of the motor We added a key to config.json "hardware_config" with a subkey "stepper_reverse". If this key is present in the config file and set to 1, the output of the motors are inversed (stepper2 becomes the pump motor and stepper1 the focus motor) * move all non main script to a subfolder * add __init__.py to package * light module rewrite * json cleanup and absolute path for config file * light.py forgot to import subprocess #oups * Add command to turn the leds off * Auto formatting of main.py I've used Black with default settings, see https://github.com/psf/black * First commit of stepper.py Pump parameters still needs to be checked and tuned. * addition of hardware details in config.json * Introduce hardware.json to replace the `hardware_config` of config.json * stepper.py: calibration, typos * creates the MQTT_Client class * pump_max_speed is now in ml/min to help readability * forgot to add self to the class def * addition of threading capabilities to stepper.py (UNTESTED) * mqtt: fix topic bug * remove counter * mqtt add doc about topics * stepper.py creates an "actuator/*/state" topic * stepper.py: rename mqtt_client to pump_client * mqtt.py: add details about topics * stepper.py: rename pump_client to actuator_client * topic was not split properly and a part was lost * switch to f-strings for mqtt.py * cosmetic update * stepper.py: folder name will be planktoscope change calls * hardware.json became more straightforward * stepper.py syntax bugs * stepper.py addition of a received stop command * stepper.py: update to max travel distance * stepper.py: several typos here * rename folder * main.py: reword to reflect folder rename * main.py: remove logic that has been moved to stepper.py and mqtt.py * main.py: update to add mqtt imaging client * mqtt.py: make command and args local to class and output more verbose * make stepper.py a class * main.py: instantiate stepper class and call it * main.py: name mqtt client * update to main.json to reflect main.py changes * fix bugs around pump control * update flows to latest version from Thibault * distance can be a small value, and definitevely should be a float. * unify mqtt topics * unify mqtt output in the main flow * first logger implementation, uses loguru * mqtt: add reason to on_connect * mqtt: add on_disconnect handler * stepper: add more logger calls for debug mainly * main: add levels for logger * imager.py: first move of the imager logic * imager: time import cleanup * imager: morphocut import cleanup * imager: skimage import cleanup * imager: finishing import cleanup * imager: Class creation - WIP Also provides a fix for #26 (see line 190). * imager: threading is needed for Condition() * streamer: get the streamer server its own file * imager: creates start_camera and get the server creation out * imager: subclass multiprocessing.Process * imager: get Pipeline creation its own function * imager: cleanup of self calls * main: code removal and corresponding calls to newly created classes * imager: various formatting changes * main: management of signal shutdown * add requirements.txt * mqtt: messages are now json objects Also, addition of a flag on receiving a new message * mqtt: make message private and add logic to synchronise * stepper: creates the stepper class * stepper: use the new class * stepper: uses the new logic * stepper: add the shutdown event * stepper: add shutdown method * main: add shutdown event * imager: graceful shutdown * stepper: nicer way of checking the Eevnt * self is a required first argument for a method in a class Especially if you use said class private members! * python: various typos and small errors in import * stepper: create mqtt client during init * stepper: instanciate the mqtt client inside run Otherwise it's not accessible from inside the loop. It's a PITA, more information at https://stackoverflow.com/questions/17172878/using-pythons-multiprocessing-process-class * stepper: little bugs and typos all around * mqtt: add shutdown method * mqtt: add connect in init * stepper: fix bugs, sanitize inputs * stepper: work on delay prediction improvements * stepper: json is mean, double quote are mandatory inside * mqtt: add details about message exchanged * imager: first implementation of json messages * main.json: add new tab for RPi management + json for payloads * imager: add state_machine class * stepper: publish last will * imager: major refactor * main: make streaming server process a daemon * mqtt: insert debug statement on close * main: reorder imports * imager: make it work! Reinsert the streaming server logic in there, because there is a problem with the synchronisation part otherwise. Also, eventually, StreamingOuput() will have to be made not global Final very critical learning: it's super duper important to make sure the memory split is at least 256Meg for the GPU. Chaos ensues otherwise * main: changes to accomodate the streamer/imager fusino * imager_state_machine: insert states transition description * stepper: cleanup of code * segmenter: creation of the class * python: include segmenter changes * remove unused files * stepper: check existence of hardware.json * main.json: changes to reflect the python script evolution * remove unecessary TODOs and add some others * main: add check for config and directories * imager: update_config is implemented and we have better management of directories now * segmenter: now work recursively in all folders * flow: the configuration is now sent via mqtt * segmenter: better manage pipeline error * segmenter: declaration of archive_fn in init * imager: small bugs and typos * main: add uniqueID output * imager: add the camera settings message We can now update the ISO, shutter speed and resolution from Node-Red * package.json: update dependencies
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"name": "",
Main.json: UI upgrade
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"topic": "",
"qos": "",
"retain": "",
"broker": "8dc3722c.06efa8",
"x": 710,
"y": 500,
Flow updates
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"wires": []
},
{
"id": "bb62da8a.ebc328",
"type": "ui_switch",
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"z": "baa1e3d9.cb29d",
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"name": "",
"label": "Pump FORWARD/BACKWARD",
"tooltip": "",
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"group": "4322c187.e73e5",
"order": 4,
"width": 3,
"height": 1,
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"passthru": true,
"decouple": "false",
"topic": "",
"style": "",
"onvalue": "FORWARD",
"onvalueType": "str",
"onicon": "",
"oncolor": "",
"offvalue": "BACKWARD",
"offvalueType": "str",
"officon": "",
"offcolor": "",
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"x": 470,
"y": 540,
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"wires": [
[]
]
},
{
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"id": "52ea7d01.711034",
"type": "function",
"z": "baa1e3d9.cb29d",
"name": "Encapsulate config",
"func": "msg.payload = {\n \"action\":\"update_config\", \n \"config\":{\n \"sample_project\":global.get(\"sample_project\"),\n \"sample_id\":global.get(\"sample_id\"),\n \"sample_ship\":global.get(\"sample_ship\"),\n \"sample_operator\":global.get(\"sample_operator\"),\n \"sample_sampling_gear\":global.get(\"sample_sampling_gear\"),\n \n \"acq_id\":global.get(\"acq_id\"),\n \"acq_instrument\":global.get(\"acq_instrument\"),\n //\"acq_instrument_id\":global.get(\"acq_instrument_id\"),\n \"acq_celltype\":global.get(\"acq_celltype\"),\n \"acq_minimum_mesh\":global.get(\"acq_minimum_mesh\"),\n \"acq_maximum_mesh\":global.get(\"acq_maximum_mesh\"),\n \"acq_min_esd\":global.get(\"acq_min_esd\"),\n \"acq_max_esd\":global.get(\"acq_max_esd\"),\n \"acq_volume\":global.get(\"acq_volume\"),\n \"acq_magnification\":global.get(\"magnification\"),\n \"acq_fnumber_objective\":global.get(\"acq_fnumber_objective\"),\n \"acq_camera_name\":\"Pi Camera V2.1 - 8MP\",\n \"acq_nb_frame\":global.get(\"custom_nb_frame\"),\n\n \"object_date\":global.get(\"object_date\"),\n \"object_time\":global.get(\"object_time\"),\n \"object_lat\":global.get(\"object_lat\"),\n \"object_lon\":global.get(\"object_lon\"),\n \"object_depth_min\":global.get(\"object_depth_min\"),\n \"object_depth_max\":global.get(\"object_depth_max\"),\n \n \"process_pixel\":global.get(\"process_pixel\"),\n \"process_id\":global.get(\"process_id\")\n }\n};\nreturn msg;",
"outputs": 1,
"noerr": 0,
"initialize": "",
"finalize": "",
"x": 750,
"y": 420,
Flow updates
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"wires": [
[
Main.json: UI upgrade
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"c3e50240.82aa58"
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]
]
},
{
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"id": "40c12463.a1f84c",
"type": "delay",
"z": "baa1e3d9.cb29d",
"name": "",
"pauseType": "delay",
"timeout": "1",
"timeoutUnits": "seconds",
"rate": "1",
"nbRateUnits": "1",
"rateUnits": "second",
"randomFirst": "1",
"randomLast": "5",
"randomUnits": "seconds",
"drop": false,
"x": 720,
"y": 460,
"wires": [
[
"c9f510c0.7d1328"
]
]
Flow updates
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},
{
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"id": "4d1b02cb.83b51c",
"type": "ui_button",
"z": "baa1e3d9.cb29d",
Flow updates
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"name": "",
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"group": "4322c187.e73e5",
"order": 6,
"width": 6,
"height": 1,
"passthru": false,
"label": "Update config",
"tooltip": "",
"color": "",
"bgcolor": "",
"icon": "",
"payload": "",
"payloadType": "str",
"topic": "imager/image",
"x": 520,
"y": 420,
Flow updates
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"wires": [
[
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"52ea7d01.711034",
"e2919164.70927"
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]
]
},
{
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"id": "452af41c.43940c",
"type": "python3-function",
"z": "1371dec5.76e671",
"name": "Get MachineName",
"func": "import sys\nsys.path.append('/home/pi/PlanktonScope/scripts')\nimport planktoscope.uuidName\n\nmsg['payload'] = planktoscope.uuidName.machineName(machine=planktoscope.uuidName.getSerial())\nmsg['topic'] = \"acq_instrument_id\";\nreturn msg",
"outputs": 1,
"x": 490,
"y": 760,
Flow updates
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"wires": [
Main.json: UI upgrade
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[
"4828d2f4.7c712c",
"e2f39a35.f57298",
"a400a97e.e333a8"
]
Flow updates
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]
},
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{
"id": "4828d2f4.7c712c",
"type": "function",
"z": "1371dec5.76e671",
"name": "set global",
"func": "global.set(msg.topic,msg.payload);\nreturn msg;",
"outputs": 1,
"noerr": 0,
"initialize": "",
"finalize": "",
"x": 780,
"y": 800,
Flow updates
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"wires": [
[]
]
},
{
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"id": "2200e2ae.0d183e",
"type": "rpi-gpio out",
"z": "1371dec5.76e671",
"name": "Pump Enable",
"pin": "7",
"set": true,
"level": "1",
"freq": "",
"out": "out",
"x": 470,
"y": 600,
Flow updates
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"wires": []
},
{
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"id": "592c4dac.b8a9dc",
"type": "rpi-gpio out",
"z": "1371dec5.76e671",
"name": "Focus Enable",
"pin": "32",
"set": true,
"level": "1",
"freq": "",
"out": "out",
"x": 480,
"y": 640,
"wires": []
},
{
"id": "d027a6bf.7049e8",
"type": "function",
"z": "b771c342.49603",
"name": "get sample_projet",
"func": "msg.payload = msg.payload.sample_project;\nreturn msg;",
"outputs": 1,
"noerr": 0,
"initialize": "",
"finalize": "",
"x": 350,
"y": 300,
Flow updates
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"wires": [
[
Main.json: UI upgrade
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"9c882b37.fde668"
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]
]
},
{
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"id": "5a811caf.0f3144",
"type": "function",
"z": "b771c342.49603",
"name": "get sample_ship",
"func": "msg.payload = msg.payload.sample_ship;\nreturn msg;",
"outputs": 1,
"noerr": 0,
"initialize": "",
"finalize": "",
"x": 340,
"y": 340,
Flow updates
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"wires": [
[
Main.json: UI upgrade
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"4557d689.a4fa88"
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]
]
},
{
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"id": "45911c98.2bd83c",
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"type": "function",
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"z": "b771c342.49603",
"name": "get sample_id",
"func": "msg.payload = msg.payload.sample_id;\nreturn msg;",
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"outputs": 1,
"noerr": 0,
"initialize": "",
"finalize": "",
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"x": 340,
"y": 380,
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"wires": [
[
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"94eb4221.9b92c"
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]
]
},
{
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"id": "1e09a4ab.72996b",
"type": "function",
"z": "b771c342.49603",
"name": "get sample_operator",
"func": "msg.payload = msg.payload.sample_operator;\nreturn msg;",
"outputs": 1,
"noerr": 0,
"initialize": "",
"finalize": "",
"x": 360,
"y": 420,
"wires": [
[
"82c5fc77.59c97"
]
]
Flow updates
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},
{
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"id": "a3272681.f271c8",
"type": "function",
"z": "b771c342.49603",
"name": "get sample_sampling_gear",
"func": "msg.payload = msg.payload.sample_sampling_gear;\nreturn msg;",
"outputs": 1,
"noerr": 0,
"x": 380,
"y": 460,
Flow updates
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"wires": [
[
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"fcfc31ae.af3af"
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]
]
},
{
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"id": "6465bdd5.15eb8c",
"type": "file in",
"z": "1c24ad9c.bebec2",
"name": "",
"filename": "/home/pi/PlanktonScope/config.json",
"format": "utf8",
"chunk": false,
"sendError": false,
"encoding": "none",
"x": 660,
"y": 300,
"wires": [
[
"15ceb135.6628bf"
]
],
"info": "# PlanktonScope Help\nThis Node will read the content of the file named **config.txt** containing all the input placeholders.\n"
Flow updates
2020-10-06 17:22:25 +02:00
},
{
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"id": "15ceb135.6628bf",
"type": "json",
"z": "1c24ad9c.bebec2",
"name": "config.json",
"property": "payload",
"action": "",
"pretty": false,
"x": 910,
"y": 300,
Flow updates
2020-10-06 17:22:25 +02:00
"wires": [
[
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"ad541674.4791c8"
Flow updates
2020-10-06 17:22:25 +02:00
]
]
},
{
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"id": "b584292a.24b08",
Flow updates
2020-10-06 17:22:25 +02:00
"type": "function",
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"z": "1c24ad9c.bebec2",
"name": "get global",
"func": "msg.payload={\n \n \"sample_project\":global.get(\"sample_project\"),\n \"sample_id\":global.get(\"sample_id\"),\n \"sample_ship\":global.get(\"sample_ship\"),\n \"sample_operator\":global.get(\"sample_operator\"),\n \"sample_sampling_gear\":global.get(\"sample_sampling_gear\"),\n \n \n \"acq_id\":global.get(\"acq_id\"),\n \"acq_instrument\":global.get(\"acq_instrument\"),\n \"acq_instrument_id\":global.get(\"machine_name\"),\n \"acq_celltype\":global.get(\"acq_celltype\"),\n \"acq_minimum_mesh\":global.get(\"acq_minimum_mesh\"),\n \"acq_maximum_mesh\":global.get(\"acq_maximum_mesh\"),\n \"acq_min_esd\":global.get(\"acq_min_esd\"),\n \"acq_max_esd\":global.get(\"acq_max_esd\"),\n \"acq_volume\":global.get(\"acq_volume\"),\n \"acq_magnification\":global.get(\"magnification\"),\n \"acq_fnumber_objective\":global.get(\"acq_fnumber_objective\"),\n \"acq_camera\":global.get(\"camera_name\"),\n\n \"custom_nb_frame\":global.get(\"custom_nb_frame\"),\n \"custom_nb_step\":global.get(\"custom_nb_step\"),\n \"custom_segmentation\":global.get(\"custom_segmentation\"),\n \"custom_sleep_before\":global.get(\"custom_sleep_before\"),\n \"focus_nb_step\":global.get(\"focus_nb_step\"),\n \"pump_flowrate\":global.get(\"pump_flowrate\"),\n \"pump_manual_volume\":global.get(\"pump_manual_volume\"),\n};\nreturn msg;",
Flow updates
2020-10-06 17:22:25 +02:00
"outputs": 1,
"noerr": 0,
"initialize": "",
"finalize": "",
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"x": 560,
"y": 860,
Flow updates
2020-10-06 17:22:25 +02:00
"wires": [
[
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"2e6ddf51.c0dba"
Flow updates
2020-10-06 17:22:25 +02:00
]
]
},
{
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"id": "7205d267.36adcc",
"type": "file",
"z": "1c24ad9c.bebec2",
"name": "",
"filename": "/home/pi/PlanktonScope/config.json",
"appendNewline": true,
"createDir": true,
"overwriteFile": "true",
"encoding": "none",
"x": 970,
"y": 860,
Flow updates
2020-10-06 17:22:25 +02:00
"wires": [
[]
]
},
{
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"id": "2e6ddf51.c0dba",
"type": "json",
"z": "1c24ad9c.bebec2",
"name": "config.json",
"property": "payload",
"action": "str",
"pretty": true,
"x": 720,
"y": 860,
Flow updates
2020-10-06 17:22:25 +02:00
"wires": [
[
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"7205d267.36adcc"
Flow updates
2020-10-06 17:22:25 +02:00
]
]
},
{
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"id": "ad541674.4791c8",
"type": "function",
"z": "1c24ad9c.bebec2",
"name": "Global Set",
"func": "for (const key in msg.payload) {\n global.set(key, msg.payload[key]);\n}\n\nreturn msg;",
"outputs": 1,
"noerr": 0,
"initialize": "",
"finalize": "",
"x": 1090,
"y": 300,
Flow updates
2020-10-06 17:22:25 +02:00
"wires": [
[]
]
},
{
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"id": "3e9a33c.141384c",
Flow updates
2020-10-06 17:22:25 +02:00
"type": "inject",
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"z": "1c24ad9c.bebec2",
"name": "Load config",
Flow updates
2020-10-06 17:22:25 +02:00
"props": [
{
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"p": "topic",
"vt": "str"
Flow updates
2020-10-06 17:22:25 +02:00
}
],
"repeat": "",
"crontab": "",
"once": true,
"onceDelay": 0.1,
"topic": "",
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"x": 410,
"y": 300,
Flow updates
2020-10-06 17:22:25 +02:00
"wires": [
[
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"6465bdd5.15eb8c"
Flow updates
2020-10-06 17:22:25 +02:00
]
]
},
{
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"id": "e2f39a35.f57298",
"type": "subflow:1c24ad9c.bebec2",
"z": "1371dec5.76e671",
"name": "",
"env": [],
"x": 770,
"y": 720,
Flow updates
2020-10-06 17:22:25 +02:00
"wires": [
[
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"bdc6718a.dd5d48",
"f783aefd.c3bfd8"
Flow updates
2020-10-06 17:22:25 +02:00
]
]
},
{
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"id": "a6907a38.f6611",
"type": "subflow:1c24ad9c.bebec2",
"z": "b771c342.49603",
Flow updates
2020-10-06 17:22:25 +02:00
"name": "",
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"env": [],
"x": 90,
"y": 380,
Flow updates
2020-10-06 17:22:25 +02:00
"wires": [
[
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"d027a6bf.7049e8",
"5a811caf.0f3144",
"45911c98.2bd83c",
"1e09a4ab.72996b",
"a3272681.f271c8"
Flow updates
2020-10-06 17:22:25 +02:00
]
]
},
{
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"id": "e2b277c1.07283",
"type": "subflow:1c24ad9c.bebec2",
"z": "b771c342.49603",
Flow updates
2020-10-06 17:22:25 +02:00
"name": "",
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"x": 830,
"y": 1080,
Flow updates
2020-10-06 17:22:25 +02:00
"wires": [
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
[]
Flow updates
2020-10-06 17:22:25 +02:00
]
},
{
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"id": "3cea1f2.20525e",
"type": "ui_text_input",
"z": "b771c342.49603",
"name": "object_lat_end",
"label": "Latitude of retrieval",
"tooltip": "",
"group": "cf5d9f0e.d57e7",
Flow updates
2020-10-06 17:22:25 +02:00
"order": 1,
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"width": 12,
Flow updates
2020-10-06 17:22:25 +02:00
"height": 1,
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"passthru": true,
"mode": "number",
"delay": 300,
"topic": "object_lat_end",
"x": 640,
"y": 700,
Flow updates
2020-10-06 17:22:25 +02:00
"wires": [
[
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"9f501f49.45645"
Flow updates
2020-10-06 17:22:25 +02:00
]
]
},
{
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"id": "661818e.5a31368",
"type": "ui_text_input",
"z": "b771c342.49603",
"name": "object_lon_end",
"label": "Longitude of retrieval",
Flow updates
2020-10-06 17:22:25 +02:00
"tooltip": "",
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"group": "cf5d9f0e.d57e7",
"order": 2,
"width": 12,
"height": 1,
"passthru": true,
"mode": "number",
"delay": 300,
"topic": "object_lon_end",
"x": 640,
"y": 740,
Flow updates
2020-10-06 17:22:25 +02:00
"wires": [
[
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"9f501f49.45645"
Flow updates
2020-10-06 17:22:25 +02:00
]
]
},
{
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"id": "f9d71e4b.2940a",
"type": "ui_date_picker",
"z": "b771c342.49603",
"name": "object_date_end",
"label": "Date",
"group": "cf5d9f0e.d57e7",
Flow updates
2020-10-06 17:22:25 +02:00
"order": 3,
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"width": 12,
Flow updates
2020-10-06 17:22:25 +02:00
"height": 1,
"passthru": true,
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"topic": "object_date_end",
"x": 640,
"y": 780,
Flow updates
2020-10-06 17:22:25 +02:00
"wires": [
flow: add link between text field and slider for focus movement
2020-10-19 11:27:40 +02:00
[
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"29f2b365.4327ec"
flow: add link between text field and slider for focus movement
2020-10-19 11:27:40 +02:00
]
Flow updates
2020-10-06 17:22:25 +02:00
]
},
{
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"id": "2a514f3b.97a6b",
"type": "ui_text_input",
"z": "b771c342.49603",
"name": "object_time_end",
"label": "Time :",
Flow updates
2020-10-06 17:22:25 +02:00
"tooltip": "",
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"group": "cf5d9f0e.d57e7",
"order": 4,
"width": 12,
Flow updates
2020-10-06 17:22:25 +02:00
"height": 1,
"passthru": true,
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"mode": "time",
"delay": 300,
"topic": "object_time_end",
"x": 640,
"y": 820,
Flow updates
2020-10-06 17:22:25 +02:00
"wires": [
[
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"1a945afa.d60aad"
Flow updates
2020-10-06 17:22:25 +02:00
]
]
},
{
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"id": "1a945afa.d60aad",
Flow updates
2020-10-06 17:22:25 +02:00
"type": "function",
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"z": "b771c342.49603",
"name": "set time global",
"func": "var date = new Date(global.get(msg.topic));\n// From https://stackoverflow.com/a/53752557/2108279\n\n\n// attempt to parse string as time. return js date object\nstring = msg.payload\n\nvar am = null;\n\n// check if \"apm\" or \"pm\" explicitly specified, otherwise null\nif (string.toLowerCase().includes(\"p\")) am = false;\nelse if (string.toLowerCase().includes(\"a\")) am = true;\n\nstring = string.replace(/\\D/g, \"\"); // remove non-digit characters\nstring = string.substring(0, 4); // take only first 4 digits\nif (string.length === 3) string = \"0\" + string; // consider eg \"030\" as \"0030\"\nstring = string.replace(/^00/, \"24\"); // add 24 hours to preserve eg \"0012\" as \"00:12\" instead of \"12:00\", since will be converted to integer\n\nvar time = parseInt(string); // convert to integer\n// default time if all else fails\nvar hours = 12,\nminutes = 0;\n\n// if able to parse as int\nif (Number.isInteger(time)) {\n// treat eg \"4\" as \"4:00pm\" (or \"4:00am\" if \"am\" explicitly specified)\nif (time >= 0 && time <= 12) {\n hours = time;\n minutes = 0;\n // if \"am\" or \"pm\" not specified, establish from number\n if (am === null) {\n if (hours >= 1 && hours <= 12) am = false;\n else am = true;\n }\n}\n// treat eg \"20\" as \"8:00pm\"\nelse if (time >= 13 && time <= 99) {\n hours = time % 24;\n minutes = 0;\n // if \"am\" or \"pm\" not specified, force \"am\"\n if (am === null) am = true;\n}\n// treat eg \"52:95\" as 52 hours 95 minutes \nelse if (time >= 100) {\n hours = Math.floor(time / 100); // take first two digits as hour\n minutes = time % 100; // take last two digits as minute\n // if \"am\" or \"pm\" not specified, establish from number\n if (am === null) {\n if (hours >= 1 && hours <= 12) am = false;\n else am = true;\n }\n}\n\n// add 12 hours if \"pm\"\nif (am === false && hours !== 12) hours += 12;\n// sub 12 hours if \"12:00am\" (midnight), making \"00:00\"\nif (am === true && hours === 12) hours = 0;\n\n// keep hours within 24 and minutes within 60\n// eg 52 hours 95 minutes becomes 4 hours 35 minutes\nhours = hours % 24;\nminutes = minutes % 60;\n}\n\n// convert to js date object\ndate.setHours(hours);\ndate.setMinutes(minutes);\ndate.setSeconds(0);\n\nglobal.set(msg.topic,date.toISOString().split('T')[1].split('.')[0].replace(/:/gi, ''));",
Flow updates
2020-10-06 17:22:25 +02:00
"outputs": 1,
"noerr": 0,
"initialize": "",
"finalize": "",
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"x": 980,
"y": 740,
Flow updates
2020-10-06 17:22:25 +02:00
"wires": [
[]
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
]
},
{
"id": "29f2b365.4327ec",
"type": "function",
"z": "b771c342.49603",
"name": "set date global",
"func": "var date = new Date(msg.payload);\n\nglobal.set(msg.topic,date.toISOString().split('T')[0].replace(/-/gi, ''));",
"outputs": 1,
"noerr": 0,
"initialize": "",
"finalize": "",
"x": 980,
"y": 700,
"wires": [
[]
]
},
{
"id": "b3c21aa9.8c06c",
"type": "exec",
"z": "1371dec5.76e671",
"command": "git --git-dir /home/pi/PlanktonScope/.git/ rev-parse --short master",
"addpay": false,
"append": "",
"useSpawn": "false",
"timer": "",
"oldrc": false,
"name": "git rev",
"x": 450,
flow: fix display bugs around the segmentation
2020-10-21 00:36:24 +02:00
"y": 700,
ui: add counter fields and fields initialize at 0
2020-10-16 08:03:23 +02:00
"wires": [
[
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"3e64877a.9684b",
"1bdd7f07.616f69"
],
[],
[]
flow: fix display bugs around the segmentation
2020-10-21 00:36:24 +02:00
]
},
{
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"id": "3e64877a.9684b",
flow: fix display bugs around the segmentation
2020-10-21 00:36:24 +02:00
"type": "function",
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"z": "1371dec5.76e671",
"name": "store git rev",
"func": "msg.payload = \"PlanktoScope v2.2-\"+msg.payload\n\nglobal.set(\"acq_software\",msg.payload);\n\nreturn msg\n",
flow: fix display bugs around the segmentation
2020-10-21 00:36:24 +02:00
"outputs": 1,
"noerr": 0,
"initialize": "",
"finalize": "",
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"x": 790,
flow: fix display bugs around the segmentation
2020-10-21 00:36:24 +02:00
"y": 640,
"wires": [
[
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"8343fa69.49339"
flow: fix display bugs around the segmentation
2020-10-21 00:36:24 +02:00
]
]
},
{
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"id": "68fa1227.dbdd5c",
flow: fix display bugs around the segmentation
2020-10-21 00:36:24 +02:00
"type": "function",
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"z": "bccd1f23.87219",
"name": "get acq_fnumber_objective",
"func": "msg.payload = msg.payload.acq_fnumber_objective;\nreturn msg;",
flow: fix display bugs around the segmentation
2020-10-21 00:36:24 +02:00
"outputs": 1,
"noerr": 0,
"initialize": "",
"finalize": "",
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"x": 820,
"y": 100,
flow: fix display bugs around the segmentation
2020-10-21 00:36:24 +02:00
"wires": [
[
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"cc966678.da8d08"
ui: add counter fields and fields initialize at 0
2020-10-16 08:03:23 +02:00
]
]
main.json: add machine name and output disable for steppers
2020-11-24 16:23:58 +01:00
},
{
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"id": "1c45ea1c.80234e",
"type": "subflow:1c24ad9c.bebec2",
"z": "bccd1f23.87219",
"name": "",
"x": 600,
"y": 100,
"wires": [
[
"68fa1227.dbdd5c"
]
]
main.json: add machine name and output disable for steppers
2020-11-24 16:23:58 +01:00
},
{
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"id": "5921d0d0.a3d568",
"type": "subflow:1c24ad9c.bebec2",
"z": "baa1e3d9.cb29d",
"name": "",
"x": 80,
"y": 120,
"wires": [
[
"f3658d30.b8448",
"1f133196.96564e",
"d3ca8847.4d1ae",
"5e3dec55.881074",
"de2c90cf.b73b08"
]
]
main.json: add machine name and output disable for steppers
2020-11-24 16:23:58 +01:00
},
{
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"id": "f3658d30.b8448",
"type": "function",
"z": "baa1e3d9.cb29d",
"name": "get acq_id",
"func": "msg.payload = msg.payload.acq_id+1;\nreturn msg;",
"outputs": 1,
"noerr": 0,
"x": 310,
main.json: add machine name and output disable for steppers
2020-11-24 16:23:58 +01:00
"y": 240,
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"wires": [
[
"6b34c456.83178c"
]
]
main.json: add machine name and output disable for steppers
2020-11-24 16:23:58 +01:00
},
{
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"id": "5acd51d4.4ab13",
main.json: add machine name and output disable for steppers
2020-11-24 16:23:58 +01:00
"type": "function",
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"z": "baa1e3d9.cb29d",
"name": "get acq_instrument",
"func": "msg.payload = msg.payload.acq_instrument;\nreturn msg;",
main.json: add machine name and output disable for steppers
2020-11-24 16:23:58 +01:00
"outputs": 1,
"noerr": 0,
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"x": 370,
"y": 780,
main.json: add machine name and output disable for steppers
2020-11-24 16:23:58 +01:00
"wires": [
[]
]
},
{
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"id": "de2c90cf.b73b08",
"type": "function",
"z": "baa1e3d9.cb29d",
"name": "get acq_celltype",
"func": "msg.payload = msg.payload.acq_celltype;\nreturn msg;",
"outputs": 1,
"noerr": 0,
"x": 320,
"y": 80,
"wires": [
[
"cc0ca68b.4263a8"
]
]
},
{
"id": "5e3dec55.881074",
"type": "function",
"z": "baa1e3d9.cb29d",
"name": "get acq_minimum_mesh",
"func": "msg.payload = msg.payload.acq_minimum_mesh;\nreturn msg;",
main.json: add machine name and output disable for steppers
2020-11-24 16:23:58 +01:00
"outputs": 1,
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"noerr": 0,
main.json: add machine name and output disable for steppers
2020-11-24 16:23:58 +01:00
"x": 350,
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"y": 120,
main.json: add machine name and output disable for steppers
2020-11-24 16:23:58 +01:00
"wires": [
[
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"f59a2f0d.5e9af"
main.json: add machine name and output disable for steppers
2020-11-24 16:23:58 +01:00
]
]
},
{
Main.json: UI upgrade
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"id": "d3ca8847.4d1ae",
"type": "function",
"z": "baa1e3d9.cb29d",
"name": "get acq_maximum_mesh",
"func": "msg.payload = msg.payload.acq_maximum_mesh;\nreturn msg;",
"outputs": 1,
"noerr": 0,
"x": 350,
"y": 160,
main.json: add machine name and output disable for steppers
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"wires": [
Main.json: UI upgrade
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[
"6008a8bb.259f08"
]
main.json: add machine name and output disable for steppers
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]
},
{
Main.json: UI upgrade
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"id": "1f133196.96564e",
"type": "function",
"z": "baa1e3d9.cb29d",
"name": "get acq_volume",
"func": "msg.payload = msg.payload.acq_volume;\nreturn msg;",
"outputs": 1,
"noerr": 0,
"x": 320,
"y": 200,
main.json: add machine name and output disable for steppers
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"wires": [
[
Main.json: UI upgrade
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"389bef3.d94c61"
main.json: add machine name and output disable for steppers
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]
]
},
{
Main.json: UI upgrade
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"id": "bdc6718a.dd5d48",
"type": "ui_text",
"z": "1371dec5.76e671",
"group": "ce9e278.781eed8",
"order": 3,
"width": 0,
"height": 0,
"name": "",
"label": "Instrument Type",
"format": "{{msg.payload.acq_instrument}}",
"layout": "row-spread",
"x": 1040,
"y": 700,
"wires": []
},
{
"id": "a400a97e.e333a8",
"type": "ui_text",
"z": "1371dec5.76e671",
"group": "ce9e278.781eed8",
"order": 0,
"width": 0,
"height": 0,
"name": "",
"label": "Instrument Name",
"format": "{{msg.payload}}",
"layout": "row-spread",
"x": 810,
"y": 760,
"wires": []
},
{
"id": "8343fa69.49339",
"type": "ui_text",
"z": "1371dec5.76e671",
"group": "ce9e278.781eed8",
"order": 1,
"width": 0,
"height": 0,
"name": "",
"label": "Software version",
"format": "{{msg.payload}}",
"layout": "row-spread",
"x": 1040,
"y": 640,
"wires": []
},
{
"id": "f783aefd.c3bfd8",
"type": "ui_text",
"z": "1371dec5.76e671",
"group": "ce9e278.781eed8",
"order": 0,
"width": 0,
"height": 0,
"name": "",
"label": "Camera Name",
"format": "{{msg.payload.acq_camera}}",
"layout": "row-spread",
"x": 1040,
"y": 740,
"wires": []
},
{
"id": "1bdd7f07.616f69",
"type": "debug",
"z": "1371dec5.76e671",
"name": "",
"active": true,
"tosidebar": true,
"console": false,
"tostatus": false,
"complete": "false",
"statusVal": "",
"statusType": "auto",
"x": 790,
"y": 680,
"wires": []
},
{
"id": "a0e2d78c.a587e",
main.json: add machine name and output disable for steppers
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"type": "inject",
Main.json: UI upgrade
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"z": "1371dec5.76e671",
"name": "ON",
main.json: add machine name and output disable for steppers
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"props": [
{
"p": "payload"
}
],
Main.json: UI upgrade
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"repeat": "60",
main.json: add machine name and output disable for steppers
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"crontab": "",
"once": true,
Main.json: UI upgrade
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"onceDelay": "",
main.json: add machine name and output disable for steppers
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"topic": "",
Main.json: UI upgrade
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"payload": "true",
"payloadType": "bool",
"x": 130,
"y": 620,
main.json: add machine name and output disable for steppers
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"wires": [
[
Main.json: UI upgrade
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"2200e2ae.0d183e",
"592c4dac.b8a9dc"
main.json: add machine name and output disable for steppers
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]
]
},
{
Main.json: UI upgrade
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"id": "906d9fea.4bab48",
"type": "status",
"z": "b771c342.49603",
"d": true,
"name": "GPS Status",
"scope": [],
"x": 310,
"y": 1320,
main.json: add machine name and output disable for steppers
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"wires": [
[
Main.json: UI upgrade
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"7116e906.9f50f"
main.json: add machine name and output disable for steppers
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]
]
Main.json: UI upgrade
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},
{
"id": "7116e906.9f50f",
"type": "ui_text",
"z": "b771c342.49603",
"d": true,
"group": "cf5d9f0e.d57e7",
"order": 5,
"width": 6,
"height": 1,
"name": "GPS Status Display",
"label": "GPS Status:",
"format": "{{msg.status.text}}",
"layout": "row-left",
"x": 810,
"y": 1320,
"wires": []
},
{
"id": "3269f55f.05d0d2",
"type": "function",
"z": "b771c342.49603",
"name": "Convert DD to DMS",
"func": "function ConvertDDToDMS(D, lng){\n // from https://stackoverflow.com/a/5786281/2108279\n return {\n dir : D<0?lng?'W':'S':lng?'E':'N',\n deg : 0|(D<0?D=-D:D),\n min : 0|D%1*60,\n sec :(0|D*60%1*6000)/100\n };\n}\n\nmsg.payload = {\n \"lat\":ConvertDDToDMS(msg.payload.lat, false),\n \"lon\":ConvertDDToDMS(msg.payload.lon, true)\n};\nreturn msg;",
"outputs": 1,
"noerr": 0,
"initialize": "",
"finalize": "",
"x": 550,
"y": 1240,
"wires": [
[]
]
Add files via upload
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}
config: update default and flow update bug
2020-11-24 17:26:10 +01:00
]
Reference in a new issue Copy permalink