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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
},
gallery: finishing installing thumbsup
2020-12-03 14:19:13 +01:00
{
"id": "c1660bc.e7ff7f8",
"type": "tab",
"label": "Gallery",
"disabled": false,
"info": ""
},
main update to flow
2020-11-27 11:30:57 +01:00
{
fix imager bug
2020-12-03 16:29:12 +01:00
"id": "9daf9e2b.019fc",
main update to flow
2020-11-27 11:30:57 +01:00
"type": "tab",
fix imager bug
2020-12-03 16:29:12 +01:00
"label": "Administration",
main update to flow
2020-11-27 11:30:57 +01:00
"disabled": false,
"info": ""
},
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
{
fix imager bug
2020-12-03 16:29:12 +01:00
"id": "1371dec5.76e671",
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"type": "tab",
fix imager bug
2020-12-03 16:29:12 +01:00
"label": "Settings",
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"disabled": false,
"info": ""
},
{
"id": "f21ba04.c26266",
"type": "tab",
"label": "WIFI Management",
"disabled": false,
"info": ""
},
update to main.json to fix camera bugs
2020-09-15 17:33:49 +02:00
{
main update to flow
2020-11-27 11:30:57 +01:00
"id": "9a22e67a.378818",
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"type": "tab",
main update to flow
2020-11-27 11:30:57 +01:00
"label": "MQTT Receive",
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"disabled": false,
"info": ""
update to main.json to fix camera bugs
2020-09-15 17:33:49 +02:00
},
flow: add hardware settings
2020-12-04 23:04:19 +01:00
{
"id": "1eaf21c8.f7a21e",
"type": "tab",
"label": "Hardware 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": [
{
flow: better config management
2020-12-05 00:20:44 +01:00
"x": 220,
flow: add hardware settings
2020-12-04 23:04:19 +01:00
"y": 160,
update to main.json to fix camera bugs
2020-09-15 17:33:49 +02:00
"wires": [
{
flow: better config management
2020-12-05 00:20:44 +01:00
"id": "3ad9835.08c937c"
update to main.json to fix camera bugs
2020-09-15 17:33:49 +02:00
}
]
}
],
"out": [
{
flow: better config management
2020-12-05 00:20:44 +01:00
"x": 1040,
flow: add hardware settings
2020-12-04 23:04:19 +01:00
"y": 60,
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
},
flow: add hardware settings
2020-12-04 23:04:19 +01:00
{
"id": "4ed26b8b.253504",
"type": "subflow",
"name": "Hardware config",
"info": "",
"category": "",
"in": [
{
"x": 40,
"y": 200,
"wires": [
{
"id": "53d163be.47cf24"
}
]
}
],
"out": [
{
"x": 1040,
"y": 80,
"wires": [
{
"id": "ddb4b136.fc0b78",
"port": 0
}
]
}
],
"env": [],
"color": "#DDAA99"
},
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",
main update to flow
2020-11-27 11:30:57 +01:00
"z": "",
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"name": "Preview",
"tab": "181bb236.1e94be",
"order": 1,
"disp": true,
main update to flow
2020-11-27 11:30:57 +01:00
"width": 18,
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"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",
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"z": "",
"name": "System Monitoring",
flow: icon of monitoring tab and update nginx config
2020-12-05 03:04:46 +01:00
"icon": "fa-thermometer-full",
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"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
2020-11-24 17:25:15 +01:00
"id": "4248342d.e55fac",
update to main.json to fix camera bugs
2020-09-15 17:33:49 +02:00
"type": "ui_group",
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"name": "Optic Characterization",
"tab": "181bb236.1e94be",
"order": 2,
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": 10,
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": "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
2020-11-24 17:25:15 +01:00
"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,
flow: update metadata export, cleanup net handling, add acq_imaged_volume
2020-11-29 13:26:24 +01:00
"width": 10,
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": "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",
flow: update metadata export, cleanup net handling, add acq_imaged_volume
2020-11-29 13:26:24 +01:00
"order": 3,
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"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
2020-11-24 17:25:15 +01:00
"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",
main update to flow
2020-11-27 11:30:57 +01:00
"z": "",
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
"baseColor": "#5900ce",
update to main.json to fix camera bugs
2020-09-15 17:33:49 +02:00
"baseFont": "-apple-system,BlinkMacSystemFont,Segoe UI,Roboto,Oxygen-Sans,Ubuntu,Cantarell,Helvetica Neue,sans-serif",
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
"reset": false
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"themeState": {
"base-color": {
"default": "#097479",
"value": "#097479",
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"edited": true
update to main.json to fix camera bugs
2020-09-15 17:33:49 +02:00
},
"page-titlebar-backgroundColor": {
"value": "#097479",
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"value": "#333333",
"edited": false
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"value": "#0eb8c0",
"edited": false
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"value": "#555555",
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"value": "#333333",
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"angularTheme": {
"primary": "indigo",
"accents": "blue",
"warn": "red",
"background": "grey"
Update flows.json
2020-07-14 18:27:49 +02:00
}
update to main.json to fix camera bugs
2020-09-15 17:33:49 +02:00
},
"site": {
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"name": "PlanktosScope",
update to main.json to fix camera bugs
2020-09-15 17:33:49 +02:00
"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
2020-09-15 17:33:49 +02:00
"lockMenu": "false",
"allowTempTheme": "true",
"dateFormat": "DD/MM/YYYY",
"sizes": {
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"sx": 55,
"sy": 55,
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"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
2020-07-14 18:27:49 +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
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",
Fix bugs all around
2020-11-25 16:58:32 +01:00
"z": "",
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"name": "Gallery",
flow: add new net type (decknet and hsn) and fix gallery icon
2020-12-03 14:40:45 +01:00
"icon": "fa-file-image-o",
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"order": 6,
gallery: finishing installing thumbsup
2020-12-03 14:19:13 +01:00
"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
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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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2020-12-03 14:40:45 +01:00
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2020-11-24 17:25:15 +01:00
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2020-12-03 14:40:45 +01:00
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Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
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2020-11-27 11:30:57 +01:00
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2020-11-24 17:25:15 +01:00
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2020-11-29 23:44:09 +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. 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2020-09-28 11:05:27 +02:00
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2020-10-06 17:22:25 +02:00
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Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"disp": false,
"width": "4",
"collapse": false
},
{
"id": "cef1e703.bcf3c8",
"type": "ui_group",
flow: update metadata export, cleanup net handling, add acq_imaged_volume
2020-11-29 13:26:24 +01:00
"z": "",
"name": "Sample Location",
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"tab": "737ec584.2eea2c",
"order": 2,
flow: location refactor using forms
2020-12-03 23:13:08 +01:00
"disp": false,
flow: update metadata export, cleanup net handling, add acq_imaged_volume
2020-11-29 13:26:24 +01:00
"width": "10",
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"collapse": 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
2020-11-24 17:25:15 +01:00
"id": "5517c651.b2f668",
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": "Validation",
"tab": "737ec584.2eea2c",
Flow updates
2020-10-06 17:22:25 +02:00
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Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
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main update to flow
2020-11-27 11:30:57 +01:00
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Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
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main update to flow
2020-11-27 11:30:57 +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",
"tab": "181bb236.1e94be",
main update to flow
2020-11-27 11:30:57 +01:00
"order": 5,
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 update to flow
2020-11-27 11:30:57 +01:00
"width": 10,
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"collapse": false
Flow updates
2020-10-06 17:22:25 +02:00
},
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Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"id": "7a0b4877.a5d268",
"type": "ui_group",
flow: update metadata export, cleanup net handling, add acq_imaged_volume
2020-11-29 13:26:24 +01:00
"z": "",
"name": "Navigation",
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"tab": "181bb236.1e94be",
main update to flow
2020-11-27 11:30:57 +01:00
"order": 6,
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"disp": false,
"width": "10",
"collapse": false
Flow updates
2020-10-06 17:22:25 +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": "404c301a.19c4e",
main.json: add machine name and output disable for steppers
2020-11-24 16:23:58 +01:00
"type": "ui_group",
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"name": "Fraction size",
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"disp": true,
"width": "10",
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flow: update metadata export, cleanup net handling, add acq_imaged_volume
2020-11-29 13:26:24 +01:00
"order": 3,
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"disp": true,
"width": 10,
"collapse": false
},
{
"id": "b7919ae2.c01788",
"type": "ui_group",
flow: update metadata export, cleanup net handling, add acq_imaged_volume
2020-11-29 13:26:24 +01:00
"z": "",
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"name": "Navigation",
"tab": "c9194f02.9d5e9",
"order": 6,
"disp": false,
flow: update metadata export, cleanup net handling, add acq_imaged_volume
2020-11-29 13:26:24 +01:00
"width": "10",
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"collapse": false
},
{
"id": "b5d61bc7.54fe48",
"type": "ui_group",
Fix bugs all around
2020-11-25 16:58:32 +01:00
"z": "",
"name": "Statistics",
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"tab": "c9194f02.9d5e9",
flow: update metadata export, cleanup net handling, add acq_imaged_volume
2020-11-29 13:26:24 +01:00
"order": 4,
Fix bugs all around
2020-11-25 16:58:32 +01:00
"disp": true,
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"width": "10",
"collapse": false
},
{
"id": "1be83144.4fe4bf",
"type": "ui_group",
flow: better icons
2020-12-02 21:58:22 +01:00
"z": "",
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
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flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
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main.json: add machine name and output disable for steppers
2020-11-24 16:23:58 +01:00
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flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"width": "12",
flow: better icons
2020-12-02 21:58:22 +01:00
"collapse": true
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
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"name": "Navigation",
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Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
2020-12-02 19:26:27 +01:00
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flow: better icons
2020-12-02 21:58:22 +01:00
"disp": true,
"width": 6,
main.json: add machine name and output disable for steppers
2020-11-24 16:23:58 +01:00
"collapse": false
},
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Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"id": "b5ba3f26.2e722",
"type": "ui_group",
"name": "CPU Temperature",
"tab": "d9cd733b.ab73d",
main.json: add machine name and output disable for steppers
2020-11-24 16:23:58 +01:00
"order": 2,
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"disp": true,
"width": "6",
"collapse": false
main.json: add machine name and output disable for steppers
2020-11-24 16:23:58 +01:00
},
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Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"id": "806d69c8.67fc58",
"type": "ui_group",
"name": "Memory",
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main.json: add machine name and output disable for steppers
2020-11-24 16:23:58 +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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"type": "ui_group",
"name": "Disk Usage",
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"order": 4,
"disp": true,
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"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": "8dc3722c.06efa8",
"type": "mqtt-broker",
update to main.json to fix camera bugs
2020-09-15 17:33:49 +02:00
"name": "",
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"broker": "0.0.0.0",
"port": "1883",
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"compatmode": false,
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"birthQos": "0",
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"closeQos": "0",
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"willQos": "0",
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"order": 1,
"disp": true,
flow: update metadata export, cleanup net handling, add acq_imaged_volume
2020-11-29 13:26:24 +01:00
"width": 10,
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"collapse": false
},
{
"id": "cf5d9f0e.d57e7",
"type": "ui_group",
flow: update metadata export, cleanup net handling, add acq_imaged_volume
2020-11-29 13:26:24 +01:00
"z": "",
add sample_gear_net_opening and sample_concentrated_sample_volume improve #44
2020-11-29 23:44:09 +01:00
"name": "Net Metadata",
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"tab": "737ec584.2eea2c",
"order": 3,
flow: location refactor using forms
2020-12-03 23:13:08 +01:00
"disp": false,
flow: update metadata export, cleanup net handling, add acq_imaged_volume
2020-11-29 13:26:24 +01:00
"width": "10",
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"collapse": false
},
{
"id": "ce9e278.781eed8",
"type": "ui_group",
"name": "Information",
"tab": "d9cd733b.ab73d",
add sample_gear_net_opening and sample_concentrated_sample_volume improve #44
2020-11-29 23:44:09 +01:00
"order": 5,
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"disp": true,
flow: better icons
2020-12-02 21:58:22 +01:00
"width": 6,
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"collapse": false
},
{
Fix bugs all around
2020-11-25 16:58:32 +01:00
"id": "70de8209.68416c",
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"type": "ui_group",
Fix bugs all around
2020-11-25 16:58:32 +01:00
"z": "",
"name": "Status",
"tab": "c9194f02.9d5e9",
flow: update metadata export, cleanup net handling, add acq_imaged_volume
2020-11-29 13:26:24 +01:00
"order": 5,
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"disp": true,
Fix bugs all around
2020-11-25 16:58:32 +01:00
"width": 10,
"collapse": false
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
},
{
Fix bugs all around
2020-11-25 16:58:32 +01:00
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flow: update metadata export, cleanup net handling, add acq_imaged_volume
2020-11-29 13:26:24 +01:00
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Fix bugs all around
2020-11-25 16:58:32 +01:00
"disp": true,
flow: update metadata export, cleanup net handling, add acq_imaged_volume
2020-11-29 13:26:24 +01:00
"width": 10,
Fix bugs all around
2020-11-25 16:58:32 +01:00
"collapse": false
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main update to flow
2020-11-27 11:30:57 +01:00
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Fix bugs all around
2020-11-25 16:58:32 +01:00
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add sample_gear_net_opening and sample_concentrated_sample_volume improve #44
2020-11-29 23:44:09 +01:00
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main update to flow
2020-11-27 11:30:57 +01:00
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add sample_gear_net_opening and sample_concentrated_sample_volume improve #44
2020-11-29 23:44:09 +01:00
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main update to flow
2020-11-27 11:30:57 +01:00
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add sample_gear_net_opening and sample_concentrated_sample_volume improve #44
2020-11-29 23:44:09 +01:00
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main update to flow
2020-11-27 11:30:57 +01:00
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add sample_gear_net_opening and sample_concentrated_sample_volume improve #44
2020-11-29 23:44:09 +01:00
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main update to flow
2020-11-27 11:30:57 +01:00
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add sample_gear_net_opening and sample_concentrated_sample_volume improve #44
2020-11-29 23:44:09 +01:00
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main update to flow
2020-11-27 11:30:57 +01:00
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add sleep_before, closes #48
2020-11-29 14:28:31 +01:00
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add sample_gear_net_opening and sample_concentrated_sample_volume improve #44
2020-11-29 23:44:09 +01:00
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add sleep_before, closes #48
2020-11-29 14:28:31 +01:00
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Fix bugs all around
2020-11-25 16:58:32 +01:00
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Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
2020-12-02 19:26:27 +01:00
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flow: better icons
2020-12-02 21:58:22 +01:00
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add sample_gear_net_opening and sample_concentrated_sample_volume improve #44
2020-11-29 23:44:09 +01:00
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Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
2020-12-02 19:26:27 +01:00
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flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
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Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
2020-12-02 19:26:27 +01:00
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flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
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flow: better icons
2020-12-02 21:58:22 +01:00
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Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
2020-12-02 19:26:27 +01:00
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flow: better icons
2020-12-02 21:58:22 +01:00
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flow: update name order
2020-11-30 01:52:15 +01:00
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flow: better icons
2020-12-02 21:58:22 +01:00
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flow: update name order
2020-11-30 01:52:15 +01:00
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flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
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flow: update name order
2020-11-30 01:52:15 +01:00
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flow: better icons
2020-12-02 21:58:22 +01:00
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2020-11-30 01:52:15 +01:00
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flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
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flow: update name order
2020-11-30 01:52:15 +01:00
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flow: better icons
2020-12-02 21:58:22 +01:00
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2020-11-30 01:52:15 +01:00
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flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
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flow: update name order
2020-11-30 01:52:15 +01:00
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2020-12-02 21:58:22 +01:00
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2020-11-30 01:52:15 +01:00
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flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
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flow: update name order
2020-11-30 01:52:15 +01:00
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2020-12-02 21:58:22 +01:00
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2020-11-30 01:52:15 +01:00
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flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
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flow: update name order
2020-11-30 01:52:15 +01:00
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flow: better icons
2020-12-02 21:58:22 +01:00
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flow: update name order
2020-11-30 01:52:15 +01:00
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flow: add mL to concentrated sample volume and add process_description field to metadata
2020-12-03 15:15:13 +01:00
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flow: addition of decknet flowmeter readings and better management of titles and location group activation
2020-12-04 22:24:20 +01:00
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flow: add mL to concentrated sample volume and add process_description field to metadata
2020-12-03 15:15:13 +01:00
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flow: addition of decknet flowmeter readings and better management of titles and location group activation
2020-12-04 22:24:20 +01:00
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flow: add mL to concentrated sample volume and add process_description field to metadata
2020-12-03 15:15:13 +01:00
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flow: addition of decknet flowmeter readings and better management of titles and location group activation
2020-12-04 22:24:20 +01:00
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flow: add mL to concentrated sample volume and add process_description field to metadata
2020-12-03 15:15:13 +01:00
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flow: addition of decknet flowmeter readings and better management of titles and location group activation
2020-12-04 22:24:20 +01:00
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flow: add mL to concentrated sample volume and add process_description field to metadata
2020-12-03 15:15:13 +01:00
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flow: add hardware settings
2020-12-04 23:04:19 +01:00
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Remove thumbsup and replace by simple nginx autoindex
2020-12-05 02:22:20 +01:00
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Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
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flow: better config management
2020-12-05 00:20:44 +01:00
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Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
2020-12-02 19:26:27 +01:00
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Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
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main update to flow
2020-11-27 11:30:57 +01:00
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Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
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main update to flow
2020-11-27 11:30:57 +01:00
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Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
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Fix bugs all around
2020-11-25 16:58:32 +01:00
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Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
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Fix bugs all around
2020-11-25 16:58:32 +01:00
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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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Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
2020-12-02 19:26:27 +01:00
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Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
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add sample_gear_net_opening and sample_concentrated_sample_volume improve #44
2020-11-29 23:44:09 +01:00
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Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
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Fix bugs all around
2020-11-25 16:58:32 +01:00
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Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
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Fix bugs all around
2020-11-25 16:58:32 +01:00
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Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
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Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
2020-12-02 19:26:27 +01:00
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Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
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Fix bugs all around
2020-11-25 16:58:32 +01:00
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Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
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Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
2020-12-02 19:26:27 +01:00
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Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
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Fix bugs all around
2020-11-25 16:58:32 +01:00
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Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
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Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
2020-12-02 19:26:27 +01:00
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Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
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Fix bugs all around
2020-11-25 16:58:32 +01:00
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Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
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Fix bugs all around
2020-11-25 16:58:32 +01:00
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Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
2020-12-02 19:26:27 +01:00
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Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
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Fix bugs all around
2020-11-25 16:58:32 +01:00
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Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
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Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
2020-12-02 19:26:27 +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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Update flows.json
2020-07-14 18:22:31 +02:00
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Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
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add usb backup UI
2020-12-01 21:12:29 +01:00
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Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
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Update flows.json
2020-07-14 18:22:31 +02:00
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Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
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Fix bugs all around
2020-11-25 16:58:32 +01:00
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Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
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Fix bugs all around
2020-11-25 16:58:32 +01:00
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Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
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Fix bugs all around
2020-11-25 16:58:32 +01:00
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Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
2020-12-02 19:26:27 +01:00
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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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"label": "",
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
2020-11-24 17:25:15 +01:00
"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": "",
"ymax": "",
"removeOlder": "20",
"removeOlderPoints": "",
"removeOlderUnit": "60",
"cutout": 0,
"useOneColor": false,
"colors": [
"#1f77b4",
"#aec7e8",
"#ff7f0e",
"#2ca02c",
"#98df8a",
"#d62728",
"#ff9896",
"#9467bd",
"#c5b0d5"
],
"outputs": 1,
Fix bugs all around
2020-11-25 16:58:32 +01:00
"x": 570,
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"y": 220,
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": "c7c8d192.3df27",
"type": "ui_chart",
"z": "1371dec5.76e671",
"name": "",
"group": "806d69c8.67fc58",
"order": 2,
"width": 0,
"height": 0,
"label": "",
"chartType": "line",
"legend": "false",
"xformat": "HH:mm:ss",
"interpolate": "linear",
"nodata": "",
"dot": false,
"ymin": "0",
"ymax": "100",
"removeOlder": "20",
"removeOlderPoints": "",
"removeOlderUnit": "60",
"cutout": 0,
"useOneColor": false,
"useUTC": false,
update to main.json to fix camera bugs
2020-09-15 17:33:49 +02:00
"colors": [
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"#1f77b4",
"#aec7e8",
"#ff7f0e",
"#2ca02c",
"#98df8a",
"#d62728",
"#ff9896",
"#9467bd",
"#c5b0d5"
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
"outputs": 1,
Fix bugs all around
2020-11-25 16:58:32 +01:00
"x": 570,
Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
2020-12-02 19:26:27 +01:00
"y": 300,
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"wires": [
[]
]
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": "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,
Fix bugs all around
2020-11-25 16:58:32 +01:00
"ymin": "0",
"ymax": "100",
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"removeOlder": "4",
Fix bugs all around
2020-11-25 16:58:32 +01:00
"removeOlderPoints": "200",
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"removeOlderUnit": "3600",
"cutout": 0,
"useOneColor": false,
"useUTC": false,
update to main.json to fix camera bugs
2020-09-15 17:33:49 +02:00
"colors": [
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"#1f77b4",
"#aec7e8",
"#ff7f0e",
"#2ca02c",
"#98df8a",
"#d62728",
"#ff9896",
"#9467bd",
"#c5b0d5"
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
"outputs": 1,
Fix bugs all around
2020-11-25 16:58:32 +01:00
"x": 570,
Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
2020-12-02 19:26:27 +01:00
"y": 380,
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"wires": [
[]
]
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": "1cd5b4c0.46af9b",
"type": "inject",
"z": "1371dec5.76e671",
Fix bugs all around
2020-11-25 16:58:32 +01:00
"name": "update: 15s",
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"props": [
{
Fix bugs all around
2020-11-25 16:58:32 +01:00
"p": "payload"
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
},
{
"p": "topic",
Fix bugs all around
2020-11-25 16:58:32 +01:00
"vt": "str"
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
}
],
Fix bugs all around
2020-11-25 16:58:32 +01:00
"repeat": "5",
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"crontab": "",
"once": false,
"onceDelay": "",
"topic": "",
"payload": "",
"payloadType": "date",
Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
2020-12-02 19:26:27 +01:00
"x": 100,
"y": 240,
Update flows.json
2020-07-14 18:22:31 +02:00
"wires": [
[
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"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",
add sample_gear_net_opening and sample_concentrated_sample_volume improve #44
2020-11-29 23:44:09 +01:00
"order": 3,
flow: better icons
2020-12-02 21:58:22 +01:00
"width": 1,
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"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",
flow: fan control update
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"name": "fan control",
"func": "#!/usr/bin/python\nimport smbus\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)\nif state == \"on\":\n bus.write_byte_data(DEVICE_ADDRESS, 0x08, 0x01)\n",
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"outputs": 1,
flow: fan control update
2020-11-30 11:45:34 +01:00
"x": 1110,
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"y": 40,
"wires": [
Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
2020-12-02 19:26:27 +01:00
[
"b7ab1ada.1f4158"
]
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
]
},
Update flows.json
2020-07-14 18:22:31 +02:00
{
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"id": "b7ab1ada.1f4158",
"type": "exec",
"z": "1371dec5.76e671",
"command": "i2cdetect -y 1",
"addpay": false,
"append": "",
"useSpawn": "false",
"timer": "1",
"oldrc": false,
"name": "i2c update",
Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
2020-12-02 19:26:27 +01:00
"x": 1290,
"y": 40,
Add files via upload
2020-01-08 14:32:46 +01:00
"wires": [
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
[],
[],
update to main.json to fix camera bugs
2020-09-15 17:33:49 +02:00
[]
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": "bc503fa5.f46dd",
update to main.json to fix camera bugs
2020-09-15 17:33:49 +02:00
"type": "switch",
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"z": "1371dec5.76e671",
Add files via upload
2020-01-08 14:32:46 +01:00
"name": "",
update to main.json to fix camera bugs
2020-09-15 17:33:49 +02:00
"property": "payload",
"propertyType": "msg",
"rules": [
{
"t": "gt",
add sample_gear_net_opening and sample_concentrated_sample_volume improve #44
2020-11-29 23:44:09 +01:00
"v": "40",
update to main.json to fix camera bugs
2020-09-15 17:33:49 +02:00
"vt": "num"
},
{
"t": "lte",
Flow updates
2020-10-06 17:22:25 +02:00
"v": "35",
update to main.json to fix camera bugs
2020-09-15 17:33:49 +02:00
"vt": "num"
}
],
"checkall": "true",
"repair": false,
"outputs": 2,
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"x": 570,
"y": 40,
Add files via upload
2020-01-08 14:32:46 +01:00
"wires": [
[
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"a25d6486.e1ce28"
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
"5d4f3e71.1bad4"
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": "5d4f3e71.1bad4",
update to main.json to fix camera bugs
2020-09-15 17:33:49 +02:00
"type": "change",
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"z": "1371dec5.76e671",
Fix bugs all around
2020-11-25 16:58:32 +01:00
"name": "Set OFF",
update to main.json to fix camera bugs
2020-09-15 17:33:49 +02:00
"rules": [
{
"t": "set",
"p": "payload",
"pt": "msg",
"to": "off",
"tot": "str"
}
],
"action": "",
"property": "",
"from": "",
"to": "",
"reg": false,
Fix bugs all around
2020-11-25 16:58:32 +01:00
"x": 720,
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"y": 60,
Update flows.json
2020-07-14 18:27:49 +02:00
"wires": [
[
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"8485d05.444903"
Update flows.json
2020-07-14 18:27:49 +02:00
]
]
},
{
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"id": "a25d6486.e1ce28",
"type": "change",
"z": "1371dec5.76e671",
Fix bugs all around
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"name": "Set ON",
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"rules": [
{
"t": "set",
"p": "payload",
"pt": "msg",
"to": "on",
"tot": "str"
}
],
"action": "",
"property": "",
"from": "",
"to": "",
"reg": false,
Fix bugs all around
2020-11-25 16:58:32 +01:00
"x": 720,
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"y": 20,
Update flows.json
2020-07-14 18:27:49 +02:00
"wires": [
[
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"8485d05.444903"
Update flows.json
2020-07-14 18:27:49 +02:00
]
]
},
{
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"id": "6a84252a.d52a0c",
"type": "ui_template",
"z": "bccd1f23.87219",
"group": "833bc5bb.217ba8",
"name": "Stream Pi Camera",
"order": 1,
main update to flow
2020-11-27 11:30:57 +01:00
"width": 18,
addition of white balance gain slider
2020-11-27 12:45:22 +01:00
"height": 14,
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"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
2020-07-14 18:27:49 +02:00
"wires": [
[]
]
},
{
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"id": "dc48dc42.98d18",
"type": "function",
"z": "bccd1f23.87219",
"name": "set global",
"func": "global.set(msg.topic,msg.payload);",
"outputs": 1,
"noerr": 0,
"initialize": "",
"finalize": "",
flow: better config management
2020-12-05 00:20:44 +01:00
"x": 800,
Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
2020-12-02 19:26:27 +01:00
"y": 380,
Update flows.json
2020-07-14 18:27:49 +02:00
"wires": [
[]
]
},
{
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"id": "f59a2f0d.5e9af",
"type": "ui_numeric",
"z": "baa1e3d9.cb29d",
"name": "acq_minimum_mesh",
"label": "Min fraction size (μm)",
"tooltip": "",
"group": "404c301a.19c4e",
Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
2020-12-02 19:26:27 +01:00
"order": 1,
update to main.json to fix camera bugs
2020-09-15 17:33:49 +02:00
"width": 5,
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"height": 1,
"wrap": false,
"passthru": true,
"topic": "acq_minimum_mesh",
update to main.json to fix camera bugs
2020-09-15 17:33:49 +02:00
"format": "{{value}}",
"min": 0,
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"max": "300",
"step": "10",
"x": 600,
"y": 120,
Update flows.json
2020-07-14 18:22:31 +02:00
"wires": [
[
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"fb887036.12429"
]
Update flows.json
2020-07-14 18:22:31 +02:00
]
},
{
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"id": "6008a8bb.259f08",
"type": "ui_numeric",
"z": "baa1e3d9.cb29d",
"name": "acq_maximum_mesh",
"label": "Max fraction size (μm)",
"tooltip": "",
"group": "404c301a.19c4e",
Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
2020-12-02 19:26:27 +01:00
"order": 2,
update to main.json to fix camera bugs
2020-09-15 17:33:49 +02:00
"width": 5,
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"height": 1,
"wrap": false,
"passthru": true,
"topic": "acq_maximum_mesh",
Update flows.json
2020-07-14 18:22:31 +02:00
"format": "{{value}}",
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"min": "200",
"max": "2000",
"step": "100",
"x": 600,
"y": 160,
"wires": [
[
"fb887036.12429"
]
]
Update flows.json
2020-07-14 18:22:31 +02:00
},
{
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"id": "6b34c456.83178c",
"type": "ui_text_input",
"z": "baa1e3d9.cb29d",
"name": "acq_id",
"label": "Acquisition unique ID*",
"tooltip": "",
"group": "4322c187.e73e5",
Fix bugs all around
2020-11-25 16:58:32 +01:00
"order": 1,
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"width": 5,
"height": 1,
"passthru": true,
"mode": "text",
"delay": 300,
"topic": "acq_id",
"x": 650,
Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
2020-12-02 19:26:27 +01:00
"y": 240,
Update flows.json
2020-07-14 18:22:31 +02:00
"wires": [
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
[
Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
2020-12-02 19:26:27 +01:00
"fb887036.12429"
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
]
Update flows.json
2020-07-14 18:22:31 +02:00
]
},
{
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"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
2020-09-15 17:33:49 +02:00
"height": 4,
flow: better config management
2020-12-05 00:20:44 +01:00
"format": "<md-button ng-click=\"send({payload: {tab:'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>",
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"storeOutMessages": true,
"fwdInMessages": true,
flow: better config management
2020-12-05 00:20:44 +01:00
"resendOnRefresh": false,
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"templateScope": "local",
"x": 130,
"y": 100,
Update flows.json
2020-07-14 18:22:31 +02:00
"wires": [
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
[
flow: better config management
2020-12-05 00:20:44 +01:00
"4e78af2d.90be7"
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
]
Update flows.json
2020-07-14 18:22:31 +02:00
]
},
{
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"id": "6ea6c306.f9c12c",
"type": "ui_template",
"z": "eaae323a.31b3",
"group": "ef590206.24f6",
"name": "Fluidic Acquisition",
"order": 1,
"width": 4,
"height": 4,
flow: better config management
2020-12-05 00:20:44 +01:00
"format": "<md-button ng-click=\"send({payload: {tab:'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>",
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"storeOutMessages": true,
"fwdInMessages": true,
flow: better config management
2020-12-05 00:20:44 +01:00
"resendOnRefresh": false,
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"templateScope": "local",
"x": 130,
"y": 140,
Update flows.json
2020-07-14 18:22:31 +02:00
"wires": [
[
flow: better config management
2020-12-05 00:20:44 +01:00
"4e78af2d.90be7"
Update flows.json
2020-07-14 18:22:31 +02:00
]
]
},
{
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"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
2020-09-15 17:33:49 +02:00
"height": 4,
flow: better config management
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"format": "<md-button ng-click=\"send({payload: {tab:'Segmentation'}})\" style=\"height:100%;\">\n <i class=\"fa fa-crop fa-5x\"></i>\n <div style=\"margin-top:30px;\">Segmentation</div>\n</md-button>",
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"storeOutMessages": true,
"fwdInMessages": true,
flow: better config management
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"resendOnRefresh": false,
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"templateScope": "local",
"x": 140,
"y": 180,
Update flows.json
2020-07-14 18:22:31 +02:00
"wires": [
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
[
flow: better config management
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"4e78af2d.90be7"
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
]
Update flows.json
2020-07-14 18:22:31 +02:00
]
},
{
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"id": "eaf8ee7f.96f44",
"type": "ui_template",
"z": "eaae323a.31b3",
"group": "196518b2.4d53b7",
"name": "Gallery",
"order": 1,
"width": 4,
"height": 4,
flow: better config management
2020-12-05 00:20:44 +01:00
"format": "<md-button ng-click=\"send({payload: {tab:'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>",
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"storeOutMessages": true,
"fwdInMessages": true,
Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
2020-12-02 19:26:27 +01:00
"resendOnRefresh": false,
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"templateScope": "local",
"x": 160,
"y": 220,
Update flows.json
2020-07-14 18:22:31 +02:00
"wires": [
[
flow: better config management
2020-12-05 00:20:44 +01:00
"4e78af2d.90be7"
Update flows.json
2020-07-14 18:22:31 +02:00
]
]
},
{
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"id": "811cd88c.daf528",
Update flows.json
2020-07-14 18:22:31 +02:00
"type": "ui_button",
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"z": "bccd1f23.87219",
"name": "down",
"group": "fbd92986.1028c8",
flow: addition of decknet flowmeter readings and better management of titles and location group activation
2020-12-04 22:24:20 +01:00
"order": 5,
flow: better icons
2020-12-02 21:58:22 +01:00
"width": 5,
"height": 1,
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"passthru": true,
"label": "",
"tooltip": "",
"color": "",
"bgcolor": "",
flow: better icons
2020-12-02 21:58:22 +01:00
"icon": "fa-angle-double-down fa-3x",
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"payload": "DOWN",
"payloadType": "str",
"topic": "actuator/focus",
"x": 190,
flow: better config management
2020-12-05 00:20:44 +01:00
"y": 660,
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"wires": [
[
"65ad39d.b6d4d48"
]
]
},
{
"id": "edda4df4.76de2",
"type": "ui_button",
"z": "bccd1f23.87219",
"name": "up",
"group": "fbd92986.1028c8",
Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
2020-12-02 19:26:27 +01:00
"order": 2,
flow: better icons
2020-12-02 21:58:22 +01:00
"width": 5,
"height": 1,
Add files via upload
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"passthru": false,
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"label": "",
Add files via upload
2020-01-08 14:32:46 +01:00
"tooltip": "",
update to main.json to fix camera bugs
2020-09-15 17:33:49 +02:00
"color": "",
"bgcolor": "",
flow: better icons
2020-12-02 21:58:22 +01:00
"icon": "fa-angle-double-up fa-3x",
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"payload": "UP",
Add files via upload
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"payloadType": "str",
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"topic": "actuator/focus",
"x": 190,
flow: better config management
2020-12-05 00:20:44 +01:00
"y": 620,
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"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,
Fix bugs all around
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"width": 3,
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"height": 1,
"passthru": true,
"mode": "number",
"delay": 300,
"topic": "pump_manual_volume",
Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
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"x": 510,
"y": 380,
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"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",
flow: addition of decknet flowmeter readings and better management of titles and location group activation
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"min": "0.1",
Main.json: UI upgrade
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"max": "20",
"step": "0.1",
Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
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"x": 540,
"y": 340,
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"wires": [
[
"dc48dc42.98d18"
]
]
},
{
"id": "c1b1469.9650eb8",
"type": "ui_template",
"z": "eaae323a.31b3",
"group": "777a7c33.fcd804",
flow: add hardware settings
2020-12-04 23:04:19 +01:00
"name": "System Monitoring",
Main.json: UI upgrade
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"order": 1,
"width": 4,
"height": 4,
flow: icon of monitoring tab and update nginx config
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"format": "<md-button ng-click=\"send({payload: {tab:'System Monitoring'}})\" style=\"height:100%;\">\n <i class=\"fa fa-thermometer-full fa-5x\"></i>\n <div style=\"margin-top:30px;\">System Monitoring</div>\n</md-button>",
Main.json: UI upgrade
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"storeOutMessages": true,
"fwdInMessages": true,
flow: add hardware settings
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"resendOnRefresh": false,
Main.json: UI upgrade
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"templateScope": "local",
flow: add hardware settings
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"x": 130,
Main.json: UI upgrade
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"y": 260,
"wires": [
[
flow: better config management
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"4e78af2d.90be7"
Main.json: UI upgrade
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]
]
},
{
"id": "abafd6e6.04a5f8",
"type": "ui_template",
"z": "eaae323a.31b3",
"group": "6f97e7ae.270c48",
"name": "Sample",
"order": 1,
"width": 4,
"height": 4,
flow: better config management
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"format": "<md-button ng-click=\"send({payload: {tab:'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>",
Main.json: UI upgrade
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"storeOutMessages": true,
"fwdInMessages": true,
"resendOnRefresh": false,
"templateScope": "local",
"x": 160,
"y": 60,
Add files via upload
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"wires": [
[
flow: better config management
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"4e78af2d.90be7"
Add files via upload
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]
]
},
{
Main.json: UI upgrade
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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",
flow: add wifi management, refactor settings to monitor and create administration tab
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"delay": "1000",
Main.json: UI upgrade
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"topic": "sample_ship",
main update to flow
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"x": 670,
flow: add mL to concentrated sample volume and add process_description field to metadata
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"y": 80,
Add files via upload
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"wires": [
[
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"9f501f49.45645"
Add files via upload
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]
Main.json: UI upgrade
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]
Add files via upload
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},
{
Main.json: UI upgrade
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"id": "fcfc31ae.af3af",
"type": "ui_dropdown",
"z": "b771c342.49603",
"name": "sample_sampling_gear",
flow: location refactor using forms
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"label": "Sampling gear*",
Main.json: UI upgrade
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"tooltip": "",
flow: update metadata export, cleanup net handling, add acq_imaged_volume
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"place": "Choose from list",
Main.json: UI upgrade
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"group": "3e1ba03d.f01d8",
flow: addition of decknet flowmeter readings and better management of titles and location group activation
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"order": 6,
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"width": 0,
"height": 0,
"passthru": true,
main update to flow
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"multiple": false,
Main.json: UI upgrade
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"options": [
flow: add new net type (decknet and hsn) and fix gallery icon
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{
"label": "High Speed Net",
"value": "net_hsn",
"type": "str"
},
{
"label": "Tara Decknet",
"value": "net_decknet",
"type": "str"
},
update to main.json to fix camera bugs
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{
Main.json: UI upgrade
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"label": "Plankton net",
"value": "net",
"type": "str"
update to main.json to fix camera bugs
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},
{
Main.json: UI upgrade
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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"
update to main.json to fix camera bugs
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}
],
Main.json: UI upgrade
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"payload": "",
"topic": "sample_sampling_gear",
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"x": 630,
flow: add mL to concentrated sample volume and add process_description field to metadata
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"y": 200,
Add files via upload
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"wires": [
update to main.json to fix camera bugs
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[
flow: update metadata export, cleanup net handling, add acq_imaged_volume
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"9f501f49.45645",
flow: addition of decknet flowmeter readings and better management of titles and location group activation
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"46eb1bf8.3dc5f4"
update to main.json to fix camera bugs
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]
Add files via upload
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]
},
{
Main.json: UI upgrade
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"id": "82c5fc77.59c97",
"type": "ui_text_input",
"z": "b771c342.49603",
"name": "sample_operator",
flow: location refactor using forms
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"label": "Name of the operator*",
update to main.json to fix camera bugs
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"tooltip": "",
Main.json: UI upgrade
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"group": "3e1ba03d.f01d8",
flow: addition of decknet flowmeter readings and better management of titles and location group activation
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"order": 3,
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"width": 0,
"height": 0,
"passthru": true,
"mode": "text",
flow: add wifi management, refactor settings to monitor and create administration tab
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"delay": "1000",
Main.json: UI upgrade
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"topic": "sample_operator",
Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
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"x": 650,
flow: add mL to concentrated sample volume and add process_description field to metadata
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"y": 160,
Add files via upload
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"wires": [
[
main update to flow
2020-11-27 11:30:57 +01:00
"9f501f49.45645",
"52af9ac0.60eb24"
Add files via upload
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]
]
},
{
Main.json: UI upgrade
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"id": "9c882b37.fde668",
Update flows.json
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"type": "ui_text_input",
Main.json: UI upgrade
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"z": "b771c342.49603",
"name": "sample_project",
"label": "Name of the project*",
"tooltip": "",
"group": "3e1ba03d.f01d8",
"order": 1,
Add files via upload
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"width": 0,
"height": 0,
Update flows.json
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"passthru": true,
Main.json: UI upgrade
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"mode": "text",
flow: add wifi management, refactor settings to monitor and create administration tab
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"delay": "1000",
Main.json: UI upgrade
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"topic": "sample_project",
main update to flow
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"x": 660,
flow: add mL to concentrated sample volume and add process_description field to metadata
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"y": 40,
Add files via upload
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"wires": [
Main.json: UI upgrade
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[
"9f501f49.45645"
]
Add files via upload
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]
},
{
Main.json: UI upgrade
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"id": "94eb4221.9b92c",
Update flows.json
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"type": "ui_text_input",
Main.json: UI upgrade
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"z": "b771c342.49603",
"name": "sample_id",
flow: addition of decknet flowmeter readings and better management of titles and location group activation
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"label": "Station ID*",
Update flows.json
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"tooltip": "",
Main.json: UI upgrade
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"group": "3e1ba03d.f01d8",
flow: addition of decknet flowmeter readings and better management of titles and location group activation
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"order": 4,
Update flows.json
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"width": 0,
"height": 0,
"passthru": true,
Main.json: UI upgrade
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"mode": "text",
flow: add wifi management, refactor settings to monitor and create administration tab
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"delay": "1000",
Main.json: UI upgrade
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"topic": "sample_id",
flow: add wifi management, refactor settings to monitor and create administration tab
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"x": 670,
flow: add mL to concentrated sample volume and add process_description field to metadata
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"y": 120,
Add files via upload
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"wires": [
Main.json: UI upgrade
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[
"9f501f49.45645"
]
Add files via upload
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]
},
{
Main.json: UI upgrade
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"id": "9f501f49.45645",
Add files via upload
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"type": "function",
Main.json: UI upgrade
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"z": "b771c342.49603",
"name": "set global",
main update to flow
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"func": "global.set(msg.topic,msg.payload);",
Add files via upload
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"outputs": 1,
"noerr": 0,
Flow updates
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"initialize": "",
"finalize": "",
Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
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"x": 1080,
flow: add mL to concentrated sample volume and add process_description field to metadata
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"y": 200,
Update flows.json
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"wires": [
Main.json: UI upgrade
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[]
Update flows.json
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]
},
{
Main.json: UI upgrade
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"id": "cc0ca68b.4263a8",
"type": "ui_dropdown",
"z": "baa1e3d9.cb29d",
"name": "acq_celltype",
Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
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"label": "Flowcell thickness*",
Main.json: UI upgrade
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"tooltip": "",
"place": "Select option",
Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
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"group": "4322c187.e73e5",
"order": 6,
"width": 5,
"height": 1,
Main.json: UI upgrade
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"passthru": true,
main update to flow
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"multiple": false,
Main.json: UI upgrade
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"options": [
{
"label": "200 μm µ-Slide I Luer",
"value": 200,
"type": "num"
},
add sleep_before, closes #48
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{
"label": "300 µm capillary",
"value": 300,
"type": "num"
},
Main.json: UI upgrade
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{
"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,
Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
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"y": 200,
Add files via upload
2020-01-08 14:32:46 +01:00
"wires": [
[
main update to flow
2020-11-27 11:30:57 +01:00
"fb887036.12429",
"99b11fe4.2795d"
Update flows.json
2020-07-14 18:22:31 +02:00
]
]
},
{
Main.json: UI upgrade
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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",
main update to flow
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"func": "global.set(msg.topic, msg.payload);",
Update flows.json
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"outputs": 1,
"noerr": 0,
Main.json: UI upgrade
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"initialize": "",
"finalize": "",
Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
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"x": 900,
"y": 200,
Update flows.json
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"wires": [
Main.json: UI upgrade
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[]
Update flows.json
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]
},
{
Main.json: UI upgrade
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"id": "222c851d.5d0a3a",
"type": "ui_ui_control",
"z": "b771c342.49603",
"name": "",
"events": "change",
flow: location refactor using forms
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"x": 400,
"y": 680,
Update flows.json
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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": "",
flow: location refactor using forms
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"x": 710,
"y": 800,
Update flows.json
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"wires": [
[]
]
},
{
Main.json: UI upgrade
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"id": "986d960a.c75908",
Update flows.json
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"type": "function",
Main.json: UI upgrade
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"z": "b771c342.49603",
"name": "Check form",
flow: better config management
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"func": "var sample_project= global.get(\"sample_project\");\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 object_date= global.get(\"object_date\");\nvar object_time= global.get(\"object_time\");\nif (sample_project === undefined || sample_project === \"\") {\n msg.topic = \"Missing entry :\"\n msg.payload = \"Sample project\"\n return [null, msg];\n}\n\nelse if (sample_id === undefined || sample_id === \"\") {\n msg.topic = \"Missing entry :\"\n msg.payload = \"Sample ID\"\n return [null, msg];\n}\n\nelse if (sample_operator === undefined || sample_operator === \"\") {\n msg.topic = \"Missing entry :\"\n msg.payload = \"Sample operator\"\n return [null, msg];\n}\n\nelse if (sample_sampling_gear === undefined || sample_sampling_gear === \"\") {\n msg.topic = \"Missing entry :\"\n msg.payload = \"Sample sampling gear\"\n return [null, msg];\n}\n\nelse if (object_lat === undefined || object_lat === null) {\n msg.topic = \"Missing entry :\"\n msg.payload = \"Latitude of sample\"\n return [null, msg];\n}\n\nelse if (object_lon === undefined || object_lon === null) {\n msg.topic = \"Missing entry :\"\n msg.payload = \"Longitude of sample\"\n return [null, msg];\n}\n\nelse if (object_date === undefined || object_date === \"\") {\n msg.topic = \"Missing entry :\"\n msg.payload = \"Date of sample\"\n return [null, msg];\n}\n\nelse if (object_time === undefined || object_time === \"\") {\n msg.topic = \"Missing entry :\"\n msg.payload = \"Time of sample\"\n return [null, msg];\n}\nelse if (sample_sampling_gear.startsWith(\"net\")){\n var object_lat_end = global.get(\"object_lat_end\");\n var object_lon_end = global.get(\"object_lon_end\");\n var object_date_end = global.get(\"object_date_end\");\n var object_time_end = global.get(\"object_time_end\");\n var sample_gear_net_opening = global.get(\"sample_gear_net_opening\");\n\n if (object_lat_end === undefined || object_lat_end === null) {\n msg.topic = \"Missing entry :\"\n msg.payload = \"Latitude of retrieval\"\n return [null, msg];\n }\n \n else if (object_lon_end === undefined || object_lon_end === null) {\n msg.topic = \"Missing entry :\"\n msg.payload = \"Longitude of retrieval\"\n return [null, msg];\n }\n \n else if (object_date_end === undefined || object_date_end === \"\") {\n msg.topic = \"Missing entry :\"\n msg.payload = \"Date of retrieval\"\n return [null, msg];\n }\n \n else if (object_time_end === undefined || object_time_end === \"\") {\n msg.topic = \"Missing entry :\"\n msg.payload = \"Time of retrieval\"\n return [null, msg];\n }\n \n else if (sample_gear_net_opening === undefined || sample_gear_net_opening === \"\") {\n msg.topic = \"Missing entry :\"\n msg.payload = \"Net opening dimension\"\n return [null, msg];\n }\n \n if (sample_sampling_gear == \"net_decknet\"){\n var sample_total_volume = global.get(\"sample_total_volume\");\n if (sample_total_volume === undefined || sample_total_volume === \"\") {\n msg.topic = \"Missing entry :\"\n msg.payload = \"Decknet flowmeter readings\"\n return [null, msg];\n }\n }\n}\nmsg.topic = \"config_save\"\nmsg.payload={\"tab\":\"Optic Configuration\"};\n\nreturn [msg, null];",
Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
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"outputs": 2,
Update flows.json
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"noerr": 0,
main update to flow
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"initialize": "",
"finalize": "",
flow: location refactor using forms
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"x": 410,
"y": 740,
Update flows.json
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"wires": [
[
Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
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"726a7822.cd6298",
"e2b277c1.07283"
],
[
"52f6b103.1efb6"
Update flows.json
2020-07-14 18:22:31 +02:00
]
Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
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],
"outputLabels": [
"message",
"error"
Update flows.json
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]
},
{
Main.json: UI upgrade
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"id": "18f44504.cac66b",
"type": "gpsd",
"z": "b771c342.49603",
Update flows.json
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"name": "",
Main.json: UI upgrade
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"hostname": "localhost",
"port": "2947",
"tpv": true,
"sky": false,
"info": false,
"device": false,
"gst": false,
"att": false,
flow: location refactor using forms
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"x": 230,
"y": 800,
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"wires": [
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[]
]
},
{
"id": "726a7822.cd6298",
"type": "ui_ui_control",
"z": "b771c342.49603",
"name": "",
"events": "change",
flow: location refactor using forms
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"x": 700,
"y": 720,
Main.json: UI upgrade
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"wires": [
[]
Update flows.json
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]
},
{
Main.json: UI upgrade
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"id": "6c792043.b6ff9",
"type": "ui_ui_control",
"z": "bccd1f23.87219",
"name": "",
"events": "change",
Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
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"x": 560,
flow: better config management
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"y": 1040,
Update flows.json
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"wires": [
Main.json: UI upgrade
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[]
Update flows.json
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]
},
{
Main.json: UI upgrade
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"id": "902429eb.ceacb8",
"type": "ui_toast",
"z": "bccd1f23.87219",
"position": "dialog",
"displayTime": "3",
"highlight": "",
"sendall": true,
Update flows.json
2020-07-14 18:22:31 +02:00
"outputs": 1,
Main.json: UI upgrade
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"ok": "OK",
"cancel": "",
"raw": false,
"topic": "",
"name": "",
Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
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"x": 570,
flow: better config management
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"y": 1120,
Update flows.json
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"wires": [
[]
]
},
{
Main.json: UI upgrade
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"id": "fe840e05.b46f3",
Update flows.json
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"type": "function",
Main.json: UI upgrade
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"z": "bccd1f23.87219",
"name": "Check form",
Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
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"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 return [null, msg];\n}\n\nmsg.topic = \"Change Tab\";\nmsg.payload={\"tab\":\"Fluidic Acquisition\"};\nreturn [msg, null];",
"outputs": 2,
Update flows.json
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"noerr": 0,
main update to flow
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"initialize": "",
"finalize": "",
Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
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"x": 330,
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"y": 1080,
Update flows.json
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"wires": [
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[
flow: better config management
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"6c792043.b6ff9",
"326a1d95.ca21aa"
Main.json: UI upgrade
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],
[
"902429eb.ceacb8"
]
Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
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],
"outputLabels": [
"message",
"error"
Update flows.json
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]
},
{
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"id": "5846b1d4.7971b",
Update flows.json
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"type": "ui_button",
Main.json: UI upgrade
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"z": "bccd1f23.87219",
"name": "Backward",
"group": "707d9797.c8e798",
"order": 2,
main update to flow
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"width": 2,
update to main.json to fix camera bugs
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"height": 1,
Update flows.json
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"passthru": false,
Main.json: UI upgrade
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"label": "",
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"tooltip": "",
"color": "",
Main.json: UI upgrade
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"bgcolor": "",
flow: better icons
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"icon": "fa-rotate-left fa-2x",
Main.json: UI upgrade
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"payload": "BACKWARD",
Update flows.json
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"payloadType": "str",
Main.json: UI upgrade
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"topic": "actuator/pump",
"x": 180,
"y": 220,
Update flows.json
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"wires": [
[
Main.json: UI upgrade
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"3cb96380.e575ec"
Update flows.json
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]
]
},
{
Main.json: UI upgrade
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"id": "2cab680b.baf888",
Update flows.json
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"type": "ui_button",
Main.json: UI upgrade
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"z": "bccd1f23.87219",
"name": "Forward",
"group": "707d9797.c8e798",
"order": 4,
main update to flow
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"width": 2,
update to main.json to fix camera bugs
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"height": 1,
Main.json: UI upgrade
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"passthru": true,
"label": "",
Update flows.json
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"tooltip": "",
"color": "",
Main.json: UI upgrade
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"bgcolor": "",
flow: better icons
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"icon": "fa-rotate-right fa-2x",
Main.json: UI upgrade
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"payload": "FORWARD",
Update flows.json
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"payloadType": "str",
Main.json: UI upgrade
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"topic": "actuator/pump",
"x": 180,
"y": 260,
Update flows.json
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"wires": [
[
Main.json: UI upgrade
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"3cb96380.e575ec"
Update flows.json
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]
]
},
{
Main.json: UI upgrade
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"id": "961d27e7.da65c8",
"type": "ui_switch",
"z": "bccd1f23.87219",
"name": "light_state",
"label": "Light",
"tooltip": "",
"group": "4248342d.e55fac",
"order": 1,
"width": 0,
"height": 0,
"passthru": true,
"decouple": "false",
"topic": "",
"style": "",
"onvalue": "true",
"onvalueType": "bool",
"onicon": "",
"oncolor": "",
"offvalue": "false",
"offvalueType": "bool",
"officon": "",
"offcolor": "",
"x": 280,
"y": 40,
Update flows.json
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"wires": [
[
Main.json: UI upgrade
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"cbb8afed.0a026"
Update flows.json
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]
Main.json: UI upgrade
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],
"icon": "font-awesome/fa-lightbulb-o"
Update flows.json
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},
{
Main.json: UI upgrade
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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": "",
Main.json: UI upgrade
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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,
Update flows.json
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"width": 0,
"height": 0,
"passthru": true,
Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
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"multiple": false,
Main.json: UI upgrade
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"options": [
{
"label": "f 25mm 1/2\" 5MP IR",
"value": 25,
"type": "num"
},
{
"label": "f 16mm 1/2.5\" 5MP IR",
"value": 16,
"type": "num"
},
{
"label": "f 12mm 1/2.5\" 5MP IR",
"value": 12,
"type": "num"
},
{
"label": "f 8mm 1/2.5\" 5MP IR",
"value": 8,
"type": "num"
},
{
"label": "f 6mm 1/2.5\" 5MP IR",
"value": 6,
"type": "num"
}
],
"payload": "",
"topic": "acq_fnumber_objective",
Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
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"x": 1190,
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"y": 80,
Update flows.json
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"wires": [
Main.json: UI upgrade
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[
flow: better config management
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"328cec46.09e40c"
Main.json: UI upgrade
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]
Update flows.json
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]
},
{
Main.json: UI upgrade
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"id": "9b515beb.4aea48",
"type": "ui_template",
"z": "bccd1f23.87219",
"group": "4248342d.e55fac",
"name": "Magnification",
"order": 3,
Update flows.json
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"width": 0,
"height": 0,
Main.json: UI upgrade
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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,
main update to flow
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"resendOnRefresh": false,
Main.json: UI upgrade
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"templateScope": "local",
flow: better config management
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"x": 1460,
"y": 140,
Update flows.json
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"wires": [
[]
]
},
{
Main.json: UI upgrade
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"id": "8038414a.34461",
Update flows.json
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"type": "function",
Main.json: UI upgrade
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"z": "bccd1f23.87219",
Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
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"name": "Calculate optics",
flow: fix lens bug
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"func": "var acq_fnumber_objective = String(global.get(\"acq_fnumber_objective\"));\nvar acq_camera = global.get(\"acq_camera\")\n\n// Those values needs to be recalculated, they are not good!\nif (acq_camera == \"HQ Camera\"){\n switch(acq_fnumber_objective) {\n case \"25\":\n acq_magnification= 0.6;\n process_pixel= 1.56;\n sug_min= 60;\n sug_max= 670;\n sug_flowrate= 3;\n break;\n case \"16\":\n acq_magnification= 1.6;\n process_pixel= 1;\n sug_min= 40;\n sug_max= 430;\n sug_flowrate= 2.4;\n break;\n case \"12\":\n acq_magnification= 1.20;\n process_pixel= 0.79;\n sug_min= 30;\n sug_max= 340;\n sug_flowrate= 1.25;\n break;\n case \"8\":\n acq_magnification= 1.78;\n process_pixel= 0.53;\n sug_min= 20;\n sug_max= 230;\n sug_flowrate= 0.42;\n break;\n case \"6\":\n acq_magnification= 2.36;\n process_pixel= 0.41;\n sug_min= 15;\n sug_max= 170;\n sug_flowrate= 0.32;\n break;\n }\n}\nelse if (acq_camera == \"Camera v2.1\"){\n switch(acq_fnumber_objective) {\n case \"25\":\n acq_magnification= 0.6;\n process_pixel= 1.86;\n sug_min= 60;\n sug_max= 670;\n sug_flowrate= 3;\n break;\n case \"16\":\n acq_magnification= 1.6;\n process_pixel= 0.7;\n sug_min= 40;\n sug_max= 430;\n sug_flowrate= 2.4;\n break;\n case \"12\":\n acq_magnification= 1.20;\n process_pixel= 0.94;\n sug_min= 30;\n sug_max= 340;\n sug_flowrate= 1.25;\n break;\n case \"8\":\n acq_magnification= 1.78;\n process_pixel= 0.63;\n sug_min= 20;\n sug_max= 230;\n sug_flowrate= 0.42;\n break;\n case \"6\":\n acq_magnification= 2.36;\n process_pixel= 0.48;\n sug_min= 15;\n sug_max= 170;\n sug_flowrate= 0.32;\n break;\n }\n}else {\n acq_magnification= \"ERROR\";\n process_pixel= \"ERROR\";\n sug_min= \"ERROR\";\n sug_max= \"ERROR\";\n sug_flowrate= \"ERROR\";\n}\n\nglobal.set(\"acq_magnification\",acq_magnification);\nglobal.set(\"process_pixel\",process_pixel);\n\nreturn [{payload: acq_magnification}, {payload: process_pixel}, {payload: sug_min}, {payload: sug_max}, {payload: sug_flowrate}];",
Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
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"outputs": 5,
Update flows.json
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"noerr": 0,
Main.json: UI upgrade
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"initialize": "",
"finalize": "",
flow: better config management
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"x": 1200,
"y": 180,
Update flows.json
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"wires": [
[
Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
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"9b515beb.4aea48"
],
[
"3d2360ad.e41e7"
],
[
"8e66977b.9166a8"
],
[
"26b32f2c.c64fc"
],
[]
],
"inputLabels": [
"acq_fnumber_objective"
],
"outputLabels": [
"acq_magnification",
"process_pixel",
"sug_min",
"sug_max",
"sug_flowrate"
Update flows.json
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]
},
{
Main.json: UI upgrade
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"id": "3d2360ad.e41e7",
"type": "ui_template",
"z": "bccd1f23.87219",
"group": "4248342d.e55fac",
"name": "process_pixel",
"order": 4,
"width": 0,
"height": 0,
"format": "<div>\n Pixel resolution :\n <span id=\"process_pixel\" ng-bind-html=\"msg.payload\"></span>\n μm\n</div>",
"storeOutMessages": true,
"fwdInMessages": true,
"resendOnRefresh": false,
"templateScope": "local",
flow: better config management
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"x": 1460,
"y": 180,
Update flows.json
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"wires": [
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[]
Update flows.json
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]
},
{
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"id": "8e66977b.9166a8",
"type": "ui_template",
"z": "bccd1f23.87219",
"group": "4248342d.e55fac",
"name": "min_size",
"order": 5,
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,
"templateScope": "local",
flow: better config management
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"x": 1440,
"y": 220,
Main.json: UI upgrade
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"wires": [
[]
]
Update flows.json
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},
{
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"id": "26b32f2c.c64fc",
"type": "ui_template",
"z": "bccd1f23.87219",
"group": "4248342d.e55fac",
"name": "max_size",
"order": 6,
"width": 0,
"height": 0,
"format": "<div>\n Biggest cells to explore :\n <span id=\"max_size\" ng-bind-html=\"msg.payload\"></span>\n μm\n</div>",
"storeOutMessages": true,
"fwdInMessages": true,
"templateScope": "local",
flow: better config management
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"x": 1440,
"y": 260,
Main.json: UI upgrade
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"wires": [
[]
]
},
{
"id": "bb2bb7ce.1d1458",
"type": "ui_template",
"z": "baa1e3d9.cb29d",
"group": "858a0e3c.987fe",
"name": "Stream Pi Camera",
"order": 1,
flow: update metadata export, cleanup net handling, add acq_imaged_volume
2020-11-29 13:26:24 +01:00
"width": 10,
"height": 8,
Main.json: UI upgrade
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"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,
Update flows.json
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"wires": [
[]
]
},
{
Main.json: UI upgrade
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"id": "d0c5b57d.590818",
"type": "ui_ui_control",
"z": "baa1e3d9.cb29d",
"name": "",
"events": "change",
flow: better config management
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"x": 1280,
"y": 700,
Main.json: UI upgrade
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"wires": [
[]
]
},
{
"id": "16de754c.cc969b",
"type": "ui_button",
"z": "b771c342.49603",
"name": "",
"group": "5517c651.b2f668",
"order": 1,
main update to flow
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"width": 5,
Main.json: UI upgrade
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"height": 1,
"passthru": false,
"label": "Previous",
Update flows.json
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"tooltip": "",
Main.json: UI upgrade
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"color": "#097479",
"bgcolor": "white",
"icon": "keyboard_return",
"payload": "{\"tab\":\"Home\"}",
"payloadType": "json",
"topic": "",
flow: location refactor using forms
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"x": 240,
"y": 680,
Update flows.json
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"wires": [
[
Main.json: UI upgrade
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"222c851d.5d0a3a"
Update flows.json
2020-07-14 18:22:31 +02:00
]
]
},
{
Main.json: UI upgrade
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"id": "84f3d040.5f7ea",
"type": "ui_button",
"z": "b771c342.49603",
"name": "",
"group": "5517c651.b2f668",
"order": 2,
main update to flow
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"width": 5,
Main.json: UI upgrade
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"height": 1,
"passthru": false,
"label": "Continue",
Update flows.json
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"tooltip": "",
Main.json: UI upgrade
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"color": "#097479",
"bgcolor": "white",
"icon": "keyboard_tab",
"payload": "{\"tab\":\"Home\"}",
"payloadType": "json",
"topic": "",
flow: location refactor using forms
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"x": 240,
"y": 740,
Update flows.json
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"wires": [
Main.json: UI upgrade
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[
"986d960a.c75908"
]
Update flows.json
2020-07-14 18:22:31 +02:00
]
},
{
Main.json: UI upgrade
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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": "",
Main.json: UI upgrade
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"color": "#097479",
"bgcolor": "white",
"icon": "keyboard_return",
"payload": "{\"tab\":\"Sample\"}",
"payloadType": "json",
"topic": "",
Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
2020-12-02 19:26:27 +01:00
"x": 140,
flow: better config management
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"y": 1040,
Update flows.json
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"wires": [
Main.json: UI upgrade
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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": "",
Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
2020-12-02 19:26:27 +01:00
"x": 140,
flow: better config management
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"y": 1080,
Main.json: UI upgrade
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"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": "",
flow: better config management
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"x": 1140,
"y": 700,
Main.json: UI upgrade
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"wires": [
[
"d0c5b57d.590818"
]
Update flows.json
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]
},
{
Fix bugs all around
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"id": "29be525e.0c87fe",
"type": "ui_template",
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"z": "baa1e3d9.cb29d",
Fix bugs all around
2020-11-25 16:58:32 +01:00
"group": "b5d61bc7.54fe48",
add sample_gear_net_opening and sample_concentrated_sample_volume improve #44
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"name": "Show Metadata",
"order": 9,
Fix bugs all around
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"width": 0,
"height": 0,
Remove thumbsup and replace by simple nginx autoindex
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"format": "<div>\n <table style=\"text-align: center; width:100%\">\n <tr style=\"vertical-align: top\">\n <td>\n <h2>Sample</h2>\n <p><strong>id:</strong> <span id=\"max_size\" ng-bind-html=\"msg.payload.config.sample_id\"></span></p>\n <p><strong>project:</strong> <span id=\"max_size\" ng-bind-html=\"msg.payload.config.sample_project\"></span></p>\n <p><strong>ship:</strong> <span id=\"max_size\" ng-bind-html=\"msg.payload.config.sample_ship\"></span></p>\n <p><strong>operator:</strong> <span id=\"max_size\" ng-bind-html=\"msg.payload.config.sample_operator\"></span></p>\n <p><strong>sampling gear:</strong> <span id=\"max_size\" ng-bind-html=\"msg.payload.config.sample_sampling_gear\"></span></p>\n <p><strong>concentrated volume:</strong> <span id=\"max_size\" ng-bind-html=\"msg.payload.config.sample_concentrated_sample_volume\"></span></p>\n <p><strong>gear net opening:</strong> <span id=\"max_size\" ng-bind-html=\"msg.payload.config.sample_gear_net_opening\"></span></p>\n <p><strong>total volume filtered:</strong> <span id=\"max_size\" ng-bind-html=\"msg.payload.config.sample_total_volume\"></span></p>\n </td>\n <td>\n <h2>Acquisition</h2>\n <p><strong>id:</strong> <span id=\"max_size\" ng-bind-html=\"msg.payload.config.acq_id\"></span></p>\n <p><strong>instrument:</strong> <span id=\"max_size\" ng-bind-html=\"msg.payload.config.acq_instrument\"></span></p>\n <p><strong>instrument id:</strong> <span id=\"max_size\" ng-bind-html=\"msg.payload.config.acq_instrument_id\"></span></p>\n <p><strong>camera:</strong> <span id=\"max_size\" ng-bind-html=\"msg.payload.config.acq_camera\"></span></p>\n <p><strong>celltype:</strong> <span id=\"max_size\" ng-bind-html=\"msg.payload.config.acq_celltype\"></span></p>\n <p><strong>minimum mesh:</strong> <span id=\"max_size\" ng-bind-html=\"msg.payload.config.acq_minimum_mesh\"></span></p>\n <p><strong>maximum mesh:</strong> <span id=\"max_size\" ng-bind-html=\"msg.payload.config.acq_maximum_mesh\"></span></p>\n <p><strong>min esd:</strong> <span id=\"max_size\" ng-bind-html=\"msg.payload.config.acq_min_esd\"></span></p>\n <p><strong>max esd:</strong> <span id=\"max_size\" ng-bind-html=\"msg.payload.config.acq_max_esd\"></span></p>\n <p><strong>volume:</strong> <span id=\"max_size\" ng-bind-html=\"msg.payload.config.acq_volume\"></span></p>\n <p><strong>magnification:</strong> <span id=\"max_size\" ng-bind-html=\"msg.payload.config.acq_magnification\"></span></p>\n <p><strong>fnumber objective:</strong> <span id=\"max_size\" ng-bind-html=\"msg.payload.config.acq_fnumber_objective\"></span></p>\n <p><strong>software:</strong> <span id=\"max_size\" ng-bind-html=\"msg.payload.config.acq_software\"></span></p>\n </td>\n </tr>\n <tr style=\"vertical-align: top\">\n <td>\n <h2>Object</h2>\n <p><strong>latitude:</strong> <span id=\"max_size\" ng-bind-html=\"msg.payload.config.object_lat\"></span></p>\n <p><strong>longitude:</strong> <span id=\"max_size\" ng-bind-html=\"msg.payload.config.object_lon\"></span></p>\n <p><strong>latitude end:</strong> <span id=\"max_size\" ng-bind-html=\"msg.payload.config.object_lat_end\"></span></p>\n <p><strong>longitude end:</strong> <span id=\"max_size\" ng-bind-html=\"msg.payload.config.object_lon_end\"></span></p>\n <p><strong>date:</strong> <span id=\"max_size\" ng-bind-html=\"msg.payload.config.object_date\"></span></p>\n <p><strong>time:</strong> <span id=\"max_size\" ng-bind-html=\"msg.payload.config.object_time\"></span></p>\n <p><strong>date end:</strong> <span id=\"max_size\" ng-bind-html=\"msg.payload.con
add sample_gear_net_opening and sample_concentrated_sample_volume improve #44
2020-11-29 23:44:09 +01:00
"storeOutMessages": false,
"fwdInMessages": false,
Fix bugs all around
2020-11-25 16:58:32 +01:00
"resendOnRefresh": false,
"templateScope": "local",
flow: better config management
2020-12-05 00:20:44 +01:00
"x": 1160,
"y": 420,
Update flows.json
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"wires": [
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[]
Update flows.json
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]
},
Main.json: UI upgrade
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{
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"id": "cbb8afed.0a026",
"type": "rpi-gpio out",
"z": "bccd1f23.87219",
"name": "LED Output",
"pin": "40",
"set": true,
"level": "0",
"freq": "",
"out": "out",
"x": 450,
"y": 40,
"wires": []
},
{
"id": "3cb96380.e575ec",
Update flows.json
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"type": "function",
Fix bugs all around
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"z": "bccd1f23.87219",
Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
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"name": "pump",
"func": "var 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 return [null, msg];\n}\nelse if (flowrate === undefined || flowrate === \"\" || flowrate === null) {\n msg.topic = \"Missing entry :\"\n msg.payload = \"Flowrate\";\n return [null, msg];\n}\nelse {\n msg.topic = \"actuator/pump\";\n // msg.payload is FORWARD or BACKWARD here\n msg.payload={\"action\":\"move\", \n \"direction\":msg.payload,\n \"volume\":manual_volume,\n \"flowrate\":flowrate};\n}\nreturn [msg, null];",
"outputs": 2,
Update flows.json
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"noerr": 0,
Fix bugs all around
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"initialize": "",
"finalize": "",
Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
2020-12-02 19:26:27 +01:00
"x": 370,
Fix bugs all around
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"y": 240,
Update flows.json
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"wires": [
[
Fix bugs all around
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"bdc8ce57.de1f08"
],
[
"8bcce348.efc1a"
Update flows.json
2020-07-14 18:22:31 +02:00
]
Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
2020-12-02 19:26:27 +01:00
],
"inputLabels": [
"direction"
],
"outputLabels": [
"message",
"error"
Update flows.json
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]
},
{
Fix bugs all around
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"id": "8bcce348.efc1a",
Main.json: UI upgrade
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"type": "ui_toast",
Fix bugs all around
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"z": "bccd1f23.87219",
Main.json: UI upgrade
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"position": "dialog",
"displayTime": "3",
"highlight": "",
"sendall": true,
Update flows.json
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"outputs": 1,
Main.json: UI upgrade
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"ok": "OK",
"cancel": "",
"raw": false,
"topic": "",
"name": "",
Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
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"x": 570,
"y": 240,
Main.json: UI upgrade
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"wires": [
[]
]
},
{
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"id": "bdc8ce57.de1f08",
"type": "mqtt out",
"z": "bccd1f23.87219",
"name": "",
"topic": "",
"qos": "",
"retain": "",
"broker": "8dc3722c.06efa8",
Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
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"x": 550,
"y": 180,
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"wires": []
},
Update flows.json
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{
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"id": "d71d224f.0585d8",
"type": "ui_toast",
"z": "bccd1f23.87219",
"position": "dialog",
"displayTime": "3",
"highlight": "",
"sendall": true,
"outputs": 1,
"ok": "OK",
"cancel": "",
"raw": false,
"topic": "",
"name": "",
add white balance switch
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"x": 670,
flow: better config management
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"y": 660,
Main.json: UI upgrade
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"wires": [
[]
]
},
{
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"id": "65ad39d.b6d4d48",
Update flows.json
2020-07-14 18:22:31 +02:00
"type": "function",
Fix bugs all around
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"z": "bccd1f23.87219",
Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
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"name": "focus",
"func": "var distance = global.get(\"focus_distance\");\n\nif (distance === undefined || distance === \"\" || distance === null) {\n msg.topic = \"Missing entry :\"\n msg.payload = \"Distance\";\n return [null, msg]\n}else {\n distance = global.get(\"focus_distance\");\n // msg.payload is UP or DOWN here\n msg.payload={\"action\":\"move\", \n \"direction\":msg.payload,\n \"distance\":(distance/1000)};\n}\nreturn [msg, null];",
"outputs": 2,
Update flows.json
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"noerr": 0,
Fix bugs all around
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"initialize": "",
"finalize": "",
Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
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"x": 370,
flow: better config management
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"y": 640,
Update flows.json
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"wires": [
[
Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
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"62030521.88317c"
],
[
"d71d224f.0585d8"
Update flows.json
2020-07-14 18:22:31 +02:00
]
Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
2020-12-02 19:26:27 +01:00
],
"inputLabels": [
"direction"
],
"outputLabels": [
"message",
"error"
Update flows.json
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]
},
{
Fix bugs all around
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"id": "1962d999.4a97e6",
"type": "ui_button",
"z": "bccd1f23.87219",
"name": "stop focus",
"group": "fbd92986.1028c8",
flow: addition of decknet flowmeter readings and better management of titles and location group activation
2020-12-04 22:24:20 +01:00
"order": 6,
Fix bugs all around
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"width": 0,
"height": 0,
"passthru": true,
flow: better icons
2020-12-02 21:58:22 +01:00
"label": " STOP FOCUS",
Fix bugs all around
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"tooltip": "",
"color": "",
"bgcolor": "#AD1625",
flow: better icons
2020-12-02 21:58:22 +01:00
"icon": "fa-pause fa-2x",
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"payload": "{\"action\":\"stop\"}",
"payloadType": "json",
"topic": "actuator/focus",
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"x": 170,
flow: better config management
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"y": 500,
Main.json: UI upgrade
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"wires": [
[
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"62030521.88317c"
Main.json: UI upgrade
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]
]
},
{
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"id": "62030521.88317c",
"type": "mqtt out",
"z": "bccd1f23.87219",
Main.json: UI upgrade
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"name": "",
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"topic": "",
"qos": "",
"retain": "",
"broker": "8dc3722c.06efa8",
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"x": 650,
flow: better config management
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"y": 580,
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"wires": []
},
Update flows.json
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{
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"id": "3bd43039.bc5fb8",
"type": "ui_button",
"z": "bccd1f23.87219",
"name": "",
"group": "fbd92986.1028c8",
Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
2020-12-02 19:26:27 +01:00
"order": 1,
flow: better icons
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"width": 5,
"height": 1,
Fix bugs all around
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"passthru": false,
"label": "UP 1mm",
"tooltip": "",
"color": "",
"bgcolor": "",
flow: better icons
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"icon": "fa-angle-up fa-3x",
Fix bugs all around
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"payload": "{\"action\":\"move\",\"direction\":\"UP\",\"distance\":1}",
"payloadType": "json",
"topic": "actuator/focus",
"x": 180,
flow: better config management
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"y": 540,
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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",
"name": "",
"group": "fbd92986.1028c8",
flow: addition of decknet flowmeter readings and better management of titles and location group activation
2020-12-04 22:24:20 +01:00
"order": 4,
flow: better icons
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"width": 5,
"height": 1,
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"passthru": false,
"label": "DOWN 1mm",
"tooltip": "",
"color": "",
"bgcolor": "",
flow: better icons
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"icon": "fa-angle-down fa-3x",
Fix bugs all around
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"payload": "{\"action\":\"move\",\"direction\":\"DOWN\",\"distance\":1}",
"payloadType": "json",
"topic": "actuator/focus",
"x": 170,
flow: better config management
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"y": 580,
Update flows.json
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"wires": [
[
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"62030521.88317c"
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]
]
},
{
Fix bugs all around
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"id": "69d4ea6c.4c1e2c",
"type": "ui_slider",
"z": "bccd1f23.87219",
"name": "focus_distance",
Remove thumbsup and replace by simple nginx autoindex
2020-12-05 02:22:20 +01:00
"label": "Focus Distance",
Fix bugs all around
2020-11-25 16:58:32 +01:00
"tooltip": "in µm",
"group": "fbd92986.1028c8",
flow: addition of decknet flowmeter readings and better management of titles and location group activation
2020-12-04 22:24:20 +01:00
"order": 3,
Fix bugs all around
2020-11-25 16:58:32 +01:00
"width": 0,
"height": 0,
"passthru": true,
"outs": "end",
"topic": "focus_distance",
"min": "25",
"max": "2000",
"step": "25",
flow: addition of decknet flowmeter readings and better management of titles and location group activation
2020-12-04 22:24:20 +01:00
"x": 540,
"y": 420,
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"wires": [
[
flow: addition of decknet flowmeter readings and better management of titles and location group activation
2020-12-04 22:24:20 +01:00
"dc48dc42.98d18"
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
]
]
},
{
Fix bugs all around
2020-11-25 16:58:32 +01:00
"id": "71f55a58.d7eaf4",
"type": "inject",
"z": "bccd1f23.87219",
"name": "Default: 500µm",
"props": [
{
"p": "payload"
}
],
"repeat": "",
"crontab": "",
"once": true,
flow: addition of decknet flowmeter readings and better management of titles and location group activation
2020-12-04 22:24:20 +01:00
"onceDelay": "0.5",
Fix bugs all around
2020-11-25 16:58:32 +01:00
"topic": "",
"payload": "500",
"payloadType": "num",
"x": 120,
flow: addition of decknet flowmeter readings and better management of titles and location group activation
2020-12-04 22:24:20 +01:00
"y": 420,
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"wires": [
[
Fix bugs all around
2020-11-25 16:58:32 +01:00
"69d4ea6c.4c1e2c"
]
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
]
},
{
Fix bugs all around
2020-11-25 16:58:32 +01:00
"id": "9a1d0e7c.2d5a1",
"type": "inject",
"z": "bccd1f23.87219",
"name": "Default: OFF",
"props": [
{
"p": "payload"
}
],
"repeat": "",
"crontab": "",
"once": true,
"onceDelay": 0.1,
"topic": "",
"payload": "false",
"payloadType": "bool",
"x": 110,
"y": 40,
Update flows.json
2020-07-14 18:22:31 +02:00
"wires": [
[
Fix bugs all around
2020-11-25 16:58:32 +01:00
"961d27e7.da65c8"
Update flows.json
2020-07-14 18:22:31 +02:00
]
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
]
Update flows.json
2020-07-14 18:22:31 +02:00
},
{
Fix bugs all around
2020-11-25 16:58:32 +01:00
"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.",
main update to flow
2020-11-27 11:30:57 +01:00
"group": "8c38a81e.9897a8",
"order": 2,
Fix bugs all around
2020-11-25 16:58:32 +01:00
"width": 0,
"height": 0,
"passthru": true,
"outs": "end",
"topic": "imager/image",
"min": "100",
"max": "800",
"step": "20",
"x": 360,
flow: better config management
2020-12-05 00:20:44 +01:00
"y": 720,
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"wires": [
Fix bugs all around
2020-11-25 16:58:32 +01:00
[
"bb090334.1e21a8"
]
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
]
},
{
Fix bugs all around
2020-11-25 16:58:32 +01:00
"id": "bb090334.1e21a8",
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"type": "function",
Fix bugs all around
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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",
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"outputs": 1,
"noerr": 0,
Fix bugs all around
2020-11-25 16:58:32 +01:00
"initialize": "",
"finalize": "",
"x": 520,
flow: better config management
2020-12-05 00:20:44 +01:00
"y": 720,
Update flows.json
2020-07-14 18:22:31 +02:00
"wires": [
[
Fix bugs all around
2020-11-25 16:58:32 +01:00
"16aa0238.209276",
"8ea9dc9a.c7d87"
Update flows.json
2020-07-14 18:22:31 +02:00
]
]
},
{
Fix bugs all around
2020-11-25 16:58:32 +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": "",
flow: better config management
2020-12-05 00:20:44 +01:00
"x": 740,
"y": 720,
Update flows.json
2020-07-14 18:22:31 +02:00
"wires": [
[
Fix bugs all around
2020-11-25 16:58:32 +01:00
"845e06e1.0d812"
Update flows.json
2020-07-14 18:22:31 +02:00
]
]
},
{
Fix bugs all around
2020-11-25 16:58:32 +01:00
"id": "5765a825.a595c8",
"type": "ui_slider",
"z": "bccd1f23.87219",
"name": "Shutter speed slider",
"label": "Shutter Speed",
addition of white balance gain slider
2020-11-27 12:45:22 +01:00
"tooltip": "In microseconds, up to 1000µs, 1µs by default",
main update to flow
2020-11-27 11:30:57 +01:00
"group": "8c38a81e.9897a8",
"order": 1,
Fix bugs all around
2020-11-25 16:58:32 +01:00
"width": 0,
"height": 0,
"passthru": true,
"outs": "end",
"topic": "imager/image",
addition of white balance gain slider
2020-11-27 12:45:22 +01:00
"min": "1",
"max": "1000",
"step": "1",
Fix bugs all around
2020-11-25 16:58:32 +01:00
"x": 390,
flow: better config management
2020-12-05 00:20:44 +01:00
"y": 800,
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"wires": [
Fix bugs all around
2020-11-25 16:58:32 +01:00
[
"c38509b.fb08af8"
]
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
]
},
{
Fix bugs all around
2020-11-25 16:58:32 +01:00
"id": "c38509b.fb08af8",
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"type": "function",
Fix bugs all around
2020-11-25 16:58:32 +01:00
"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;",
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"outputs": 1,
"noerr": 0,
Fix bugs all around
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"initialize": "",
"finalize": "",
flow: better config management
2020-12-05 00:20:44 +01:00
"x": 740,
"y": 800,
Update flows.json
2020-07-14 18:22:31 +02:00
"wires": [
[
Fix bugs all around
2020-11-25 16:58:32 +01:00
"845e06e1.0d812"
Update flows.json
2020-07-14 18:22:31 +02:00
]
]
},
{
Fix bugs all around
2020-11-25 16:58:32 +01:00
"id": "845e06e1.0d812",
"type": "mqtt out",
"z": "bccd1f23.87219",
Update flows.json
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"name": "",
Fix bugs all around
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"topic": "",
"qos": "",
"retain": "",
"broker": "8dc3722c.06efa8",
add white balance switch
2020-11-27 18:39:09 +01:00
"x": 1010,
flow: better config management
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"y": 840,
Fix bugs all around
2020-11-25 16:58:32 +01:00
"wires": []
},
{
"id": "2350e507.d4e302",
"type": "inject",
"z": "bccd1f23.87219",
addition of white balance gain slider
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"name": "Default: 1µs",
Fix bugs all around
2020-11-25 16:58:32 +01:00
"props": [
{
"p": "payload"
}
],
"repeat": "",
"crontab": "",
"once": true,
"onceDelay": "1",
"topic": "",
addition of white balance gain slider
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"payload": "1",
Fix bugs all around
2020-11-25 16:58:32 +01:00
"payloadType": "num",
"x": 110,
flow: better config management
2020-12-05 00:20:44 +01:00
"y": 800,
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"wires": [
Fix bugs all around
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[
"5765a825.a595c8"
]
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
]
},
{
Fix bugs all around
2020-11-25 16:58:32 +01:00
"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",
Remove thumbsup and replace by simple nginx autoindex
2020-12-05 02:22:20 +01:00
"x": 130,
flow: better config management
2020-12-05 00:20:44 +01:00
"y": 720,
Update flows.json
2020-07-14 18:22:31 +02:00
"wires": [
Fix bugs all around
2020-11-25 16:58:32 +01:00
[
"16aa0238.209276"
]
Update flows.json
2020-07-14 18:22:31 +02:00
]
},
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
{
Fix bugs all around
2020-11-25 16:58:32 +01:00
"id": "f782a471.447748",
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"type": "inject",
Fix bugs all around
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"z": "bccd1f23.87219",
"name": "Default: 5mL/min",
"props": [
{
"p": "payload"
}
],
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"repeat": "",
"crontab": "",
Fix bugs all around
2020-11-25 16:58:32 +01:00
"once": true,
flow: addition of decknet flowmeter readings and better management of titles and location group activation
2020-12-04 22:24:20 +01:00
"onceDelay": "0.5",
Update flows.json
2020-07-14 18:22:31 +02:00
"topic": "",
Fix bugs all around
2020-11-25 16:58:32 +01:00
"payload": "5",
"payloadType": "num",
"x": 130,
Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
2020-12-02 19:26:27 +01:00
"y": 340,
Update flows.json
2020-07-14 18:22:31 +02:00
"wires": [
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
[
Fix bugs all around
2020-11-25 16:58:32 +01:00
"34c81624.df1cea"
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
]
Update flows.json
2020-07-14 18:22:31 +02:00
]
},
{
Fix bugs all around
2020-11-25 16:58:32 +01:00
"id": "73b8252a.5ca754",
"type": "inject",
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"z": "bccd1f23.87219",
Fix bugs all around
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"name": "Default: 2mL",
"props": [
{
"p": "payload"
}
],
"repeat": "",
"crontab": "",
"once": true,
flow: addition of decknet flowmeter readings and better management of titles and location group activation
2020-12-04 22:24:20 +01:00
"onceDelay": "0.5",
Fix bugs all around
2020-11-25 16:58:32 +01:00
"topic": "",
"payload": "2",
"payloadType": "num",
"x": 110,
Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
2020-12-02 19:26:27 +01:00
"y": 380,
Update flows.json
2020-07-14 18:22:31 +02:00
"wires": [
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
[
Fix bugs all around
2020-11-25 16:58:32 +01:00
"68962547.34a67c"
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
]
Update flows.json
2020-07-14 18:22:31 +02:00
]
},
{
Fix bugs all around
2020-11-25 16:58:32 +01:00
"id": "8ec68b82.17e3d8",
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"type": "ui_button",
Fix bugs all around
2020-11-25 16:58:32 +01:00
"z": "cb95299c.2817c8",
"name": "Start segmentation",
"group": "abeb6dad.635a2",
flow: update metadata export, cleanup net handling, add acq_imaged_volume
2020-11-29 13:26:24 +01:00
"order": 2,
"width": 5,
Fix bugs all around
2020-11-25 16:58:32 +01:00
"height": 1,
"passthru": false,
"label": "Start segmentation",
"tooltip": "",
"color": "",
"bgcolor": "",
"icon": "",
"payload": "{\"action\":\"segment\"}",
"payloadType": "json",
"topic": "segmenter/segment",
"x": 370,
flow: update metadata export, cleanup net handling, add acq_imaged_volume
2020-11-29 13:26:24 +01:00
"y": 300,
Update flows.json
2020-07-14 18:22:31 +02:00
"wires": [
[
Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
2020-12-02 19:26:27 +01:00
"33c28dc1.238002"
Update flows.json
2020-07-14 18:22:31 +02:00
]
]
},
{
Fix bugs all around
2020-11-25 16:58:32 +01:00
"id": "27be7971.b3fbce",
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"type": "ui_button",
Fix bugs all around
2020-11-25 16:58:32 +01:00
"z": "cb95299c.2817c8",
"name": "Stop segmentation",
"group": "abeb6dad.635a2",
flow: update metadata export, cleanup net handling, add acq_imaged_volume
2020-11-29 13:26:24 +01:00
"order": 3,
"width": 5,
Fix bugs all around
2020-11-25 16:58:32 +01:00
"height": 1,
"passthru": true,
"label": "Stop segmentation",
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"tooltip": "",
"color": "",
Fix bugs all around
2020-11-25 16:58:32 +01:00
"bgcolor": "#AD1625",
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"icon": "",
Fix bugs all around
2020-11-25 16:58:32 +01:00
"payload": "{\"action\":\"stop\"}",
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"payloadType": "json",
Fix bugs all around
2020-11-25 16:58:32 +01:00
"topic": "segmenter/segment",
"x": 370,
flow: update metadata export, cleanup net handling, add acq_imaged_volume
2020-11-29 13:26:24 +01:00
"y": 340,
Update flows.json
2020-07-14 18:22:31 +02:00
"wires": [
[
Fix bugs all around
2020-11-25 16:58:32 +01:00
"16f3cef4.0acac9"
Update flows.json
2020-07-14 18:22:31 +02:00
]
]
},
{
Fix bugs all around
2020-11-25 16:58:32 +01:00
"id": "16f3cef4.0acac9",
"type": "mqtt out",
"z": "cb95299c.2817c8",
Update flows.json
2020-07-14 18:22:31 +02:00
"name": "",
Fix bugs all around
2020-11-25 16:58:32 +01:00
"topic": "",
"qos": "",
"retain": "",
"broker": "8dc3722c.06efa8",
Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
2020-12-02 19:26:27 +01:00
"x": 810,
"y": 340,
Fix bugs all around
2020-11-25 16:58:32 +01:00
"wires": []
},
{
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"id": "569154a.b53182c",
"type": "inject",
Fix bugs all around
2020-11-25 16:58:32 +01:00
"z": "1371dec5.76e671",
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"name": "once",
"props": [
{
"p": "payload"
}
],
"repeat": "",
"crontab": "",
"once": true,
"onceDelay": "",
"topic": "",
"payload": "start",
"payloadType": "str",
"x": 130,
"y": 580,
"wires": [
[
"452af41c.43940c",
"b3c21aa9.8c06c"
]
]
},
{
"id": "4b489713.ccde5",
"type": "ui_button",
"z": "baa1e3d9.cb29d",
"name": "",
"group": "4322c187.e73e5",
"order": 12,
"width": 5,
Fix bugs all around
2020-11-25 16:58:32 +01:00
"height": 1,
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"passthru": false,
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"label": "Start Acquisition",
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"tooltip": "",
"color": "",
"bgcolor": "",
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"icon": "camera",
Fix bugs all around
2020-11-25 16:58:32 +01:00
"payload": "",
"payloadType": "str",
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"topic": "imager/image",
flow: better config management
2020-12-05 00:20:44 +01:00
"x": 420,
"y": 500,
Update flows.json
2020-07-14 18:22:31 +02:00
"wires": [
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
[
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"c9f510c0.7d1328"
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
]
Update flows.json
2020-07-14 18:22:31 +02:00
]
},
{
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"id": "c9f510c0.7d1328",
"type": "function",
"z": "baa1e3d9.cb29d",
"name": "Image control",
"func": "// Reset the number of images taken\nglobal.set('img_counter', 0);\n\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 imaging_pump_volume = global.get(\"imaging_pump_volume\");\nvar acq_id = global.get(\"acq_id\");\nvar nb_frame = global.get(\"nb_frame\");\nvar pump_direction = global.get(\"pump_direction\");\nvar sleep_before = global.get(\"sleep_before\");\n\nif (acq_celltype === undefined || acq_celltype === \"\") {\n msg.topic = \"Missing entry :\";\n msg.payload = \"Type of the flowcell\";\n return [null, msg];\n} else if (acq_minimum_mesh === undefined || acq_minimum_mesh === \"\") {\n msg.topic = \"Missing entry :\";\n msg.payload = \"Lower fraction size\";\n return [null, msg];\n} else if (acq_maximum_mesh === undefined || acq_maximum_mesh === \"\") {\n msg.topic = \"Missing entry :\";\n msg.payload = \"Upper fraction size\";\n return [null, msg];\n} else if (imaging_pump_volume === undefined || imaging_pump_volume === \"\" || imaging_pump_volume === null) {\n msg.topic = \"Missing entry :\";\n msg.payload = \"Volume inbetween images\";\n return [null, msg];\n} else if (acq_id === undefined || acq_id === \"\") {\n msg.topic = \"Missing entry :\";\n msg.payload = \"Acquisition ID\";\n return [null, msg];\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 return [null, msg];\n} else if (pump_direction === undefined || pump_direction === \"\" || pump_direction === null) {\n msg.topic = \"Missing entry :\";\n msg.payload = \"Pump direction\";\n return [null, msg];\n} else if (sleep_before === undefined || sleep_before === \"\" || pump_direction === null) {\n msg.topic = \"Missing entry :\";\n msg.payload = \"Delay before image\";\n return [null, msg];\n}\nmsg.payload = {\n \"action\": \"image\",\n \"sleep\": sleep_before,\n \"pump_direction\": pump_direction,\n \"volume\": imaging_pump_volume,\n \"nb_frame\": nb_frame,\n}\n\nreturn [msg, null];",
"outputs": 2,
"noerr": 0,
"initialize": "",
"finalize": "",
flow: better config management
2020-12-05 00:20:44 +01:00
"x": 640,
"y": 500,
Update flows.json
2020-07-14 18:22:31 +02:00
"wires": [
[
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"52ea7d01.711034",
flow: better config management
2020-12-05 00:20:44 +01:00
"40c12463.a1f84c",
"a4abb1ae.2ae418"
Fix bugs all around
2020-11-25 16:58:32 +01:00
],
[
"20e0a8c8.edbeb"
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
]
Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
2020-12-02 19:26:27 +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
},
{
Fix bugs all around
2020-11-25 16:58:32 +01:00
"id": "20e0a8c8.edbeb",
"type": "ui_toast",
"z": "baa1e3d9.cb29d",
"position": "dialog",
"displayTime": "3",
"highlight": "",
"sendall": true,
"outputs": 1,
"ok": "OK",
"cancel": "",
"raw": false,
"topic": "",
"name": "",
flow: better config management
2020-12-05 00:20:44 +01:00
"x": 890,
"y": 580,
Fix bugs all around
2020-11-25 16:58:32 +01:00
"wires": [
[]
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},
{
"id": "c3e50240.82aa58",
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"type": "mqtt out",
Fix bugs all around
2020-11-25 16:58:32 +01:00
"z": "baa1e3d9.cb29d",
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"name": "",
"topic": "",
"qos": "",
"retain": "",
"broker": "8dc3722c.06efa8",
flow: better config management
2020-12-05 00:20:44 +01:00
"x": 1130,
"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": []
},
{
Fix bugs all around
2020-11-25 16:58:32 +01:00
"id": "3a4450b1.4459a8",
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"type": "ui_button",
Fix bugs all around
2020-11-25 16:58:32 +01:00
"z": "baa1e3d9.cb29d",
"name": "Stop Acquisition",
"group": "4322c187.e73e5",
Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
2020-12-02 19:26:27 +01:00
"order": 11,
Fix bugs all around
2020-11-25 16:58:32 +01:00
"width": 5,
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"height": 1,
Fix bugs all around
2020-11-25 16:58:32 +01:00
"passthru": true,
"label": "STOP ACQUISITION",
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"tooltip": "",
"color": "",
Fix bugs all around
2020-11-25 16:58:32 +01:00
"bgcolor": "#AD1625",
"icon": "cancel",
"payload": "{\"action\":\"stop\"}",
"payloadType": "json",
"topic": "imager/image",
flow: better config management
2020-12-05 00:20:44 +01:00
"x": 420,
"y": 540,
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": [
[
Fix bugs all around
2020-11-25 16:58:32 +01:00
"d74210ef.edc15"
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
]
]
},
{
Fix bugs all around
2020-11-25 16:58:32 +01:00
"id": "d74210ef.edc15",
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"z": "baa1e3d9.cb29d",
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"broker": "8dc3722c.06efa8",
flow: better config management
2020-12-05 00:20:44 +01:00
"x": 610,
"y": 540,
Fix bugs all around
2020-11-25 16:58:32 +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
},
{
Fix bugs all around
2020-11-25 16:58:32 +01:00
"id": "bb62da8a.ebc328",
"type": "ui_switch",
"z": "baa1e3d9.cb29d",
"name": "Pump direction",
"label": "Pump direction",
"tooltip": "BACKWARD / FORWARD",
"group": "4322c187.e73e5",
Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
2020-12-02 19:26:27 +01:00
"order": 9,
Fix bugs all around
2020-11-25 16:58:32 +01:00
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"decouple": "false",
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"onvalue": "FORWARD",
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"oncolor": "",
"offvalue": "BACKWARD",
"offvalueType": "str",
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flow: better config management
2020-12-05 00:20:44 +01:00
"x": 420,
"y": 580,
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 update to flow
2020-11-27 11:30:57 +01:00
"6b2239f3.41fa3"
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
]
]
},
{
Fix bugs all around
2020-11-25 16:58:32 +01:00
"id": "52ea7d01.711034",
"type": "function",
"z": "baa1e3d9.cb29d",
"name": "Encapsulate config",
flow: better config management
2020-12-05 00:20:44 +01:00
"func": "msg.payload = {\n\t\"action\": \"update_config\",\n\t\"config\": {\n \t\"description\": {\n \t\t\"sample_project\": \"Project's name\",\n \t\t\"sample_id\": \"Sample ID\",\n \t\t\"sample_uuid\": \"Sample UUID (Autogenerated)\",\n \t\t\"sample_ship\": \"Ship's name\",\n \t\t\"sample_operator\": \"Operator's name\",\n \t\t\"sample_sampling_gear\": \"Sampling gear used\",\n \t\t\"sample_concentrated_sample_volume\": \"Volume of concentrated sample, in mL\",\n \t\t\"sample_total_volume\": \"Total volume filtered by the net used, in L\",\n \t\t\"acq_id\": \"Acquisition ID\",\n \t\t\"acq_uuid\": \"Acquisition UUID (Autogenerated)\",\n \t\t\"acq_instrument\": \"Instrument type\",\n \t\t\"acq_instrument_id\": \"Instrument ID\",\n \t\t\"acq_celltype\": \"Flow cell dimension thickness, in µm\",\n \t\t\"acq_minimum_mesh\": \"Minimum filtration mesh size, in µm\",\n \t\t\"acq_maximum_mesh\": \"Maximum filtration mesh size, in µm\",\n \t\t\"acq_min_esd\": \"\",\n \t\t\"acq_max_esd\": \"\",\n \t\t\"acq_volume\": \"Imaged volume, in mL\",\n \t\t\"acq_magnification\": \"Optical magnification\",\n \t\t\"acq_fnumber_objective\": \"Focal length of the objective, in mm\",\n \t\t\"acq_camera_name\": \"Name of the camera used\",\n \t\t\"acq_nb_frame\": \"Number of picture taken\",\n \"acq_local_datetime\": \"Instrument local datetime\",\n \"acq_camera_resolution\": \"Resolution of the images\",\n \"acq_camera_iso\": \"ISO Number of the images\",\n \"acq_camera_shutter_speed\": \"Shutter speed of the images, in µs\",\n \"acq_software\": \"Software version number\",\n \t\t\"object_date\": \"Sample collection date (or beginning if using a net)\",\n \t\t\"object_time\": \"Sample collection time (or beginning if using a net)\",\n \t\t\"object_lat\": \"Sample collection latitude (or beginning if using a net)\",\n \t\t\"object_lon\": \"Sample collection longitude (or beginning if using a net)\",\n \t\t\"object_depth_min\": \"Sample collection minimal depth, in m\",\n \t\t\"object_depth_max\": \"Sample collection maximum depth, in m\",\n \t\t\"process_pixel\": \"Pixel imaging resolution, in µm/pixel\",\n \t\t\"process_id\": \"Segmentation ID\",\n \t\t\"process_uuid\": \"Segmentation UUID (Autogenerated)\",\n \t\t\"sample_gear_net_opening\": \"Sample mouth opening dimension, in mm\",\n \t\t\"object_date_end\": \"Sample end collection date when using a net\",\n \t\t\"object_time_end\": \"Sample end collection time when using a net\",\n \t\t\"object_lat_end\": \"Sample end collection latitude when using a net\",\n \t\t\"object_lon_end\": \"Sample end collection longitude when using a net\",\n \t},\n\t\t\"sample_project\": global.get(\"sample_project\"),\n\t\t\"sample_id\": global.get(\"sample_id\"),\n\t\t\"sample_ship\": global.get(\"sample_ship\"),\n\t\t\"sample_operator\": global.get(\"sample_operator\"),\n\t\t\"sample_sampling_gear\": global.get(\"sample_sampling_gear\"),\n\t\t\"sample_concentrated_sample_volume\": global.get(\"sample_concentrated_sample_volume\"),\n\n\t\t\"acq_id\": global.get(\"acq_id\"),\n\t\t\"acq_instrument\": global.get(\"acq_instrument\"),\n\t\t\"acq_instrument_id\": global.get(\"acq_instrument_id\"),\n\t\t\"acq_celltype\": global.get(\"acq_celltype\"),\n\t\t\"acq_minimum_mesh\": global.get(\"acq_minimum_mesh\"),\n\t\t\"acq_maximum_mesh\": global.get(\"acq_maximum_mesh\"),\n\t\t\"acq_min_esd\": global.get(\"acq_min_esd\"),\n\t\t\"acq_max_esd\": global.get(\"acq_max_esd\"),\n\t\t\"acq_volume\": global.get(\"acq_volume\"),\n\t\t\"acq_magnification\": global.get(\"magnification\"),\n\t\t\"acq_fnumber_objective\": global.get(\"acq_fnumber_objective\"),\n\t\t\"acq_camera\": global.get(\"acq_camera\"),\n\t\t\"acq_nb_frame\": global.get(\"nb_frame\"),\n\t\t\"acq_software\": global.get(\"acq_software\"),\n\n\t\t\"object_date\": global.get(\"object_date\"),\n\t\t\"object_time\": global.get(\"object_time\"),\n\t\t\"object_lat\": global.get(\"object
Fix bugs all around
2020-11-25 16:58:32 +01:00
"outputs": 1,
"noerr": 0,
"initialize": "",
"finalize": "",
flow: better config management
2020-12-05 00:20:44 +01:00
"x": 870,
"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": [
Fix bugs all around
2020-11-25 16:58:32 +01:00
[
add sleep_before, closes #48
2020-11-29 14:28:31 +01:00
"c3e50240.82aa58",
"29be525e.0c87fe"
Fix bugs all around
2020-11-25 16:58:32 +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
},
{
Fix bugs all around
2020-11-25 16:58:32 +01:00
"id": "40c12463.a1f84c",
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"type": "delay",
Fix bugs all around
2020-11-25 16:58:32 +01:00
"z": "baa1e3d9.cb29d",
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"name": "",
"pauseType": "delay",
Fix bugs all around
2020-11-25 16:58:32 +01:00
"timeout": "1",
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"timeoutUnits": "seconds",
"rate": "1",
"nbRateUnits": "1",
"rateUnits": "second",
"randomFirst": "1",
"randomLast": "5",
"randomUnits": "seconds",
"drop": false,
flow: better config management
2020-12-05 00:20:44 +01:00
"x": 900,
"y": 500,
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": [
[
Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
2020-12-02 19:26:27 +01:00
"c3e50240.82aa58"
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
]
]
},
{
Fix bugs all around
2020-11-25 16:58:32 +01:00
"id": "4d1b02cb.83b51c",
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",
Fix bugs all around
2020-11-25 16:58:32 +01:00
"z": "baa1e3d9.cb29d",
"name": "",
"group": "4322c187.e73e5",
Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
2020-12-02 19:26:27 +01:00
"order": 10,
Fix bugs all around
2020-11-25 16:58:32 +01:00
"width": 5,
Flow updates
2020-10-06 17:22:25 +02:00
"height": 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
"passthru": false,
Fix bugs all around
2020-11-25 16:58:32 +01:00
"label": "Update config",
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
"tooltip": "",
"color": "",
Fix bugs all around
2020-11-25 16:58:32 +01:00
"bgcolor": "",
flow: better icons
2020-12-02 21:58:22 +01:00
"icon": "save",
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"payload": "",
"payloadType": "str",
Fix bugs all around
2020-11-25 16:58:32 +01:00
"topic": "imager/image",
flow: better config management
2020-12-05 00:20:44 +01:00
"x": 420,
"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": [
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flow: better config management
2020-12-05 00:20:44 +01:00
"52ea7d01.711034"
Fix bugs all around
2020-11-25 16:58:32 +01:00
]
]
},
{
"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,
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"x": 350,
"y": 620,
Fix bugs all around
2020-11-25 16:58:32 +01:00
"wires": [
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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
]
]
},
{
Fix bugs all around
2020-11-25 16:58:32 +01:00
"id": "4828d2f4.7c712c",
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"type": "function",
"z": "1371dec5.76e671",
Fix bugs all around
2020-11-25 16:58:32 +01:00
"name": "set global",
main update to flow
2020-11-27 11:30:57 +01:00
"func": "global.set(msg.topic,msg.payload);\n",
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"outputs": 1,
"noerr": 0,
"initialize": "",
"finalize": "",
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"x": 580,
"y": 640,
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": [
Fix bugs all around
2020-11-25 16:58:32 +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
]
},
Fix bugs all around
2020-11-25 16:58:32 +01:00
{
"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": "",
flow: better config management
2020-12-05 00:20:44 +01:00
"x": 310,
flow: add mL to concentrated sample volume and add process_description field to metadata
2020-12-03 15:15:13 +01:00
"y": 40,
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"wires": [
[
Fix bugs all around
2020-11-25 16:58:32 +01:00
"9c882b37.fde668"
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
},
{
Fix bugs all around
2020-11-25 16:58:32 +01:00
"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,
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flow: better config management
2020-12-05 00:20:44 +01:00
"x": 310,
flow: add mL to concentrated sample volume and add process_description field to metadata
2020-12-03 15:15:13 +01:00
"y": 80,
Fix bugs all around
2020-11-25 16:58:32 +01:00
"wires": [
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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
},
{
Fix bugs all around
2020-11-25 16:58:32 +01:00
"id": "45911c98.2bd83c",
"type": "function",
"z": "b771c342.49603",
"name": "get sample_id",
"func": "msg.payload = msg.payload.sample_id;\nreturn msg;",
"outputs": 1,
"noerr": 0,
"initialize": "",
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flow: better config management
2020-12-05 00:20:44 +01:00
"x": 300,
flow: add mL to concentrated sample volume and add process_description field to metadata
2020-12-03 15:15:13 +01:00
"y": 120,
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": [
Fix bugs all around
2020-11-25 16:58:32 +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
]
},
{
Fix bugs all around
2020-11-25 16:58:32 +01:00
"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": "",
flow: better config management
2020-12-05 00:20:44 +01:00
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flow: add mL to concentrated sample volume and add process_description field to metadata
2020-12-03 15:15:13 +01:00
"y": 160,
Fix bugs all around
2020-11-25 16:58:32 +01:00
"wires": [
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flow: add mL to concentrated sample volume and add process_description field to metadata
2020-12-03 15:15:13 +01:00
"func": "if (msg.payload.sample_sampling_gear === null){\n msg.payload = \"net\";\n}\nelse\n{\n msg.payload = msg.payload.sample_sampling_gear;\n}\nreturn msg;",
Fix bugs all around
2020-11-25 16:58:32 +01:00
"outputs": 1,
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flow: add mL to concentrated sample volume and add process_description field to metadata
2020-12-03 15:15:13 +01:00
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flow: better config management
2020-12-05 00:20:44 +01:00
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flow: add mL to concentrated sample volume and add process_description field to metadata
2020-12-03 15:15:13 +01:00
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Fix bugs all around
2020-11-25 16:58:32 +01:00
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Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"name": "",
Fix bugs all around
2020-11-25 16:58:32 +01:00
"filename": "/home/pi/PlanktonScope/config.json",
"format": "utf8",
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flow: add hardware settings
2020-12-04 23:04:19 +01:00
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Fix bugs all around
2020-11-25 16:58:32 +01:00
"wires": [
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"info": "# PlanktonScope Help\nThis Node will read the content of the file named **config.txt** containing all the input placeholders.\n"
},
{
"id": "15ceb135.6628bf",
"type": "json",
"z": "1c24ad9c.bebec2",
"name": "config.json",
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flow: better config management
2020-12-05 00:20:44 +01:00
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flow: add hardware settings
2020-12-04 23:04:19 +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": [
[
Fix bugs all around
2020-11-25 16:58:32 +01:00
"ad541674.4791c8"
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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Fix bugs all around
2020-11-25 16:58:32 +01:00
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2020-11-24 17:25:15 +01:00
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Fix bugs all around
2020-11-25 16:58:32 +01:00
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2020-11-24 17:25:15 +01:00
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Fix bugs all around
2020-11-25 16:58:32 +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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Fix bugs all around
2020-11-25 16:58:32 +01:00
"7205d267.36adcc"
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
]
]
},
{
Fix bugs all around
2020-11-25 16:58:32 +01:00
"id": "ad541674.4791c8",
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",
Fix bugs all around
2020-11-25 16:58:32 +01:00
"z": "1c24ad9c.bebec2",
"name": "Global Set",
flow: better config management
2020-12-05 00:20:44 +01:00
"func": "global.set(\"config_keys\", Object.keys(msg.payload));\n\nfor (const key in msg.payload) {\n global.set(key, msg.payload[key]);\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": "",
flow: better config management
2020-12-05 00:20:44 +01:00
"x": 910,
flow: add hardware settings
2020-12-04 23:04:19 +01:00
"y": 60,
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": [
Fix bugs all around
2020-11-25 16:58:32 +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
},
{
Fix bugs all around
2020-11-25 16:58:32 +01:00
"id": "3e9a33c.141384c",
"type": "inject",
"z": "1c24ad9c.bebec2",
"name": "Load config",
"props": [
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
{
Fix bugs all around
2020-11-25 16:58:32 +01:00
"p": "topic",
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"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
}
],
Fix bugs all around
2020-11-25 16:58:32 +01:00
"repeat": "",
"crontab": "",
"once": true,
"onceDelay": 0.1,
"topic": "",
flow: better config management
2020-12-05 00:20:44 +01:00
"x": 210,
flow: add hardware settings
2020-12-04 23:04:19 +01:00
"y": 60,
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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Fix bugs all around
2020-11-25 16:58:32 +01:00
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flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
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Fix bugs all around
2020-11-25 16:58:32 +01:00
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Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
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retrieve camera name
2020-11-27 18:57:43 +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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Fix bugs all around
2020-11-25 16:58:32 +01:00
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Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
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Fix bugs all around
2020-11-25 16:58:32 +01:00
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flow: better config management
2020-12-05 00:20:44 +01:00
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flow: add mL to concentrated sample volume and add process_description field to metadata
2020-12-03 15:15:13 +01:00
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Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
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Fix bugs all around
2020-11-25 16:58:32 +01:00
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flow: better config management
2020-12-05 00:20:44 +01:00
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Fix bugs all around
2020-11-25 16:58:32 +01:00
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Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
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Fix bugs all around
2020-11-25 16:58:32 +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
"name": "",
main update to flow
2020-11-27 11:30:57 +01:00
"env": [],
flow: location refactor using forms
2020-12-03 23:13:08 +01:00
"x": 690,
"y": 760,
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"wires": [
Fix bugs all around
2020-11-25 16:58:32 +01:00
[]
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
]
Flow updates
2020-10-06 17:22:25 +02:00
},
{
Fix bugs all around
2020-11-25 16:58:32 +01:00
"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",
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"x": 310,
"y": 540,
Flow updates
2020-10-06 17:22:25 +02:00
"wires": [
[
update: final update to flow
2020-11-27 12:50:35 +01:00
"3e64877a.9684b"
Fix bugs all around
2020-11-25 16:58:32 +01:00
],
[],
[]
Flow updates
2020-10-06 17:22:25 +02:00
]
},
{
Fix bugs all around
2020-11-25 16:58:32 +01:00
"id": "3e64877a.9684b",
"type": "function",
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"z": "1371dec5.76e671",
main update to flow
2020-11-27 11:30:57 +01:00
"name": "store version",
Fix bugs all around
2020-11-25 16:58:32 +01:00
"func": "msg.payload = \"PlanktoScope v2.2-\"+msg.payload.trim()\n\nglobal.set(\"acq_software\",msg.payload);\n\nreturn msg\n",
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"outputs": 1,
Fix bugs all around
2020-11-25 16:58:32 +01:00
"noerr": 0,
"initialize": "",
"finalize": "",
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"x": 590,
"y": 520,
Flow updates
2020-10-06 17:22:25 +02:00
"wires": [
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
[
Fix bugs all around
2020-11-25 16:58:32 +01:00
"8343fa69.49339"
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
{
Fix bugs all around
2020-11-25 16:58:32 +01:00
"id": "68fa1227.dbdd5c",
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"type": "function",
Fix bugs all around
2020-11-25 16:58:32 +01:00
"z": "bccd1f23.87219",
"name": "get acq_fnumber_objective",
flow: typo in acq_fnumber
2020-12-03 17:34:38 +01:00
"func": "msg.payload = msg.payload.acq_fnumber_objective;\n\nglobal.set(\"acq_fnumber_objective\",msg.payload);\n\nreturn msg;",
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"outputs": 1,
"noerr": 0,
"initialize": "",
"finalize": "",
Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
2020-12-02 19:26:27 +01:00
"x": 920,
flow: better config management
2020-12-05 00:20:44 +01:00
"y": 80,
Flow updates
2020-10-06 17:22:25 +02:00
"wires": [
Fix bugs all around
2020-11-25 16:58:32 +01:00
[
"cc966678.da8d08"
]
Flow updates
2020-10-06 17:22:25 +02:00
]
},
{
Fix bugs all around
2020-11-25 16:58:32 +01:00
"id": "1c45ea1c.80234e",
"type": "subflow:1c24ad9c.bebec2",
"z": "bccd1f23.87219",
"name": "",
flow: better config management
2020-12-05 00:20:44 +01:00
"x": 710,
"y": 80,
Fix bugs all around
2020-11-25 16:58:32 +01:00
"wires": [
[
"68fa1227.dbdd5c"
]
]
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
},
{
Fix bugs all around
2020-11-25 16:58:32 +01:00
"id": "5921d0d0.a3d568",
"type": "subflow:1c24ad9c.bebec2",
"z": "baa1e3d9.cb29d",
"name": "",
Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
2020-12-02 19:26:27 +01:00
"env": [],
Fix bugs all around
2020-11-25 16:58:32 +01:00
"x": 90,
Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
2020-12-02 19:26:27 +01:00
"y": 180,
Flow updates
2020-10-06 17:22:25 +02:00
"wires": [
[
Fix bugs all around
2020-11-25 16:58:32 +01:00
"f3658d30.b8448",
"d3ca8847.4d1ae",
"5e3dec55.881074",
"de2c90cf.b73b08"
Flow updates
2020-10-06 17:22:25 +02:00
]
]
},
{
Fix bugs all around
2020-11-25 16:58:32 +01:00
"id": "f3658d30.b8448",
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"type": "function",
Fix bugs all around
2020-11-25 16:58:32 +01:00
"z": "baa1e3d9.cb29d",
"name": "get acq_id",
"func": "msg.payload = msg.payload.acq_id;\nreturn msg;",
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"outputs": 1,
"noerr": 0,
"initialize": "",
"finalize": "",
flow: fan control update
2020-11-30 11:45:34 +01:00
"x": 310,
Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
2020-12-02 19:26:27 +01:00
"y": 240,
Flow updates
2020-10-06 17:22:25 +02:00
"wires": [
[
Fix bugs all around
2020-11-25 16:58:32 +01:00
"6b34c456.83178c"
Flow updates
2020-10-06 17:22:25 +02:00
]
]
},
{
Fix bugs all around
2020-11-25 16:58:32 +01:00
"id": "de2c90cf.b73b08",
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"type": "function",
Fix bugs all around
2020-11-25 16:58:32 +01:00
"z": "baa1e3d9.cb29d",
"name": "get acq_celltype",
"func": "msg.payload = msg.payload.acq_celltype;\nreturn msg;",
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"outputs": 1,
"noerr": 0,
Fix bugs all around
2020-11-25 16:58:32 +01:00
"x": 320,
Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
2020-12-02 19:26:27 +01:00
"y": 200,
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"wires": [
[
Fix bugs all around
2020-11-25 16:58:32 +01:00
"cc0ca68b.4263a8"
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
]
]
Flow updates
2020-10-06 17:22:25 +02:00
},
{
Fix bugs all around
2020-11-25 16:58:32 +01:00
"id": "5e3dec55.881074",
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"type": "function",
Fix bugs all around
2020-11-25 16:58:32 +01:00
"z": "baa1e3d9.cb29d",
"name": "get acq_minimum_mesh",
"func": "msg.payload = msg.payload.acq_minimum_mesh;\nreturn msg;",
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"outputs": 1,
"noerr": 0,
Fix bugs all around
2020-11-25 16:58:32 +01:00
"x": 350,
"y": 120,
Flow updates
2020-10-06 17:22:25 +02:00
"wires": [
[
Fix bugs all around
2020-11-25 16:58:32 +01:00
"f59a2f0d.5e9af"
Flow updates
2020-10-06 17:22:25 +02:00
]
]
},
{
Fix bugs all around
2020-11-25 16:58:32 +01:00
"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,
Flow updates
2020-10-06 17:22:25 +02:00
"wires": [
[
Fix bugs all around
2020-11-25 16:58:32 +01:00
"6008a8bb.259f08"
Flow updates
2020-10-06 17:22:25 +02:00
]
]
},
{
Fix bugs all around
2020-11-25 16:58:32 +01:00
"id": "bdc6718a.dd5d48",
"type": "ui_text",
"z": "1371dec5.76e671",
"group": "ce9e278.781eed8",
flow: update name order
2020-11-30 01:52:15 +01:00
"order": 2,
Fix bugs all around
2020-11-25 16:58:32 +01:00
"width": 0,
"height": 0,
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"name": "",
Fix bugs all around
2020-11-25 16:58:32 +01:00
"label": "Instrument Type",
"format": "{{msg.payload.acq_instrument}}",
"layout": "row-spread",
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"x": 840,
"y": 560,
Fix bugs all around
2020-11-25 16:58:32 +01:00
"wires": []
},
{
"id": "a400a97e.e333a8",
"type": "ui_text",
"z": "1371dec5.76e671",
"group": "ce9e278.781eed8",
add sample_gear_net_opening and sample_concentrated_sample_volume improve #44
2020-11-29 23:44:09 +01:00
"order": 1,
Fix bugs all around
2020-11-25 16:58:32 +01:00
"width": 0,
"height": 0,
"name": "",
"label": "Instrument Name",
"format": "{{msg.payload}}",
"layout": "row-spread",
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"x": 610,
"y": 600,
Fix bugs all around
2020-11-25 16:58:32 +01:00
"wires": []
},
{
"id": "8343fa69.49339",
"type": "ui_text",
"z": "1371dec5.76e671",
"group": "ce9e278.781eed8",
add sample_gear_net_opening and sample_concentrated_sample_volume improve #44
2020-11-29 23:44:09 +01:00
"order": 3,
Fix bugs all around
2020-11-25 16:58:32 +01:00
"width": 0,
"height": 0,
"name": "",
"label": "Software version",
"format": "{{msg.payload}}",
"layout": "row-spread",
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"x": 840,
"y": 520,
Fix bugs all around
2020-11-25 16:58:32 +01:00
"wires": []
},
{
"id": "f783aefd.c3bfd8",
"type": "ui_text",
"z": "1371dec5.76e671",
"group": "ce9e278.781eed8",
flow: update name order
2020-11-30 01:52:15 +01:00
"order": 4,
Fix bugs all around
2020-11-25 16:58:32 +01:00
"width": 0,
"height": 0,
"name": "",
"label": "Camera Name",
add larger gain control range (up to 8.0)
2020-11-28 22:25:59 +01:00
"format": "{{msg.payload}}",
Fix bugs all around
2020-11-25 16:58:32 +01:00
"layout": "row-spread",
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"x": 1020,
"y": 620,
Fix bugs all around
2020-11-25 16:58:32 +01:00
"wires": []
},
Flow updates
2020-10-06 17:22:25 +02:00
{
Fix bugs all around
2020-11-25 16:58:32 +01:00
"id": "906d9fea.4bab48",
"type": "status",
"z": "b771c342.49603",
"d": true,
"name": "GPS Status",
"scope": [],
flow: location refactor using forms
2020-12-03 23:13:08 +01:00
"x": 250,
"y": 880,
Flow updates
2020-10-06 17:22:25 +02:00
"wires": [
[
Fix bugs all around
2020-11-25 16:58:32 +01:00
"7116e906.9f50f"
Flow updates
2020-10-06 17:22:25 +02:00
]
]
},
{
Fix bugs all around
2020-11-25 16:58:32 +01:00
"id": "7116e906.9f50f",
"type": "ui_text",
"z": "b771c342.49603",
"d": true,
flow: addition of decknet flowmeter readings and better management of titles and location group activation
2020-12-04 22:24:20 +01:00
"group": "3e1ba03d.f01d8",
"order": 15,
"width": 2,
Fix bugs all around
2020-11-25 16:58:32 +01:00
"height": 1,
"name": "GPS Status Display",
"label": "GPS Status:",
"format": "{{msg.status.text}}",
"layout": "row-left",
flow: location refactor using forms
2020-12-03 23:13:08 +01:00
"x": 750,
"y": 880,
Fix bugs all around
2020-11-25 16:58:32 +01:00
"wires": []
},
Flow updates
2020-10-06 17:22:25 +02:00
{
Fix bugs all around
2020-11-25 16:58:32 +01:00
"id": "48879182.6fd718",
Flow updates
2020-10-06 17:22:25 +02:00
"type": "inject",
Fix bugs all around
2020-11-25 16:58:32 +01:00
"z": "baa1e3d9.cb29d",
Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
2020-12-02 19:26:27 +01:00
"name": "Default: 100",
Flow updates
2020-10-06 17:22:25 +02:00
"props": [
Fix bugs all around
2020-11-25 16:58:32 +01:00
{
"p": "payload"
Flow updates
2020-10-06 17:22:25 +02:00
}
],
"repeat": "",
"crontab": "",
"once": true,
"onceDelay": 0.1,
"topic": "",
Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
2020-12-02 19:26:27 +01:00
"payload": "100",
Fix bugs all around
2020-11-25 16:58:32 +01:00
"payloadType": "num",
"x": 310,
Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
2020-12-02 19:26:27 +01:00
"y": 280,
Flow updates
2020-10-06 17:22:25 +02:00
"wires": [
[
main update to flow
2020-11-27 11:30:57 +01:00
"51b4d0df.d70a88"
Flow updates
2020-10-06 17:22:25 +02:00
]
]
},
main update to flow
2020-11-27 11:30:57 +01:00
{
"id": "6451f991.aaac1",
"type": "ui_button",
"z": "bccd1f23.87219",
"name": "stop pump",
"group": "707d9797.c8e798",
flow: better icons
2020-12-02 21:58:22 +01:00
"order": 5,
"width": 3,
main update to flow
2020-11-27 11:30:57 +01:00
"height": 1,
"passthru": true,
flow: better icons
2020-12-02 21:58:22 +01:00
"label": " STOP PUMP",
main update to flow
2020-11-27 11:30:57 +01:00
"tooltip": "",
"color": "",
"bgcolor": "#AD1625",
flow: better icons
2020-12-02 21:58:22 +01:00
"icon": "fa-pause fa-2x",
main update to flow
2020-11-27 11:30:57 +01:00
"payload": "{\"action\":\"stop\"}",
"payloadType": "json",
"topic": "actuator/pump",
"x": 170,
"y": 180,
Flow updates
2020-10-06 17:22:25 +02:00
"wires": [
[
add white balance switch
2020-11-27 18:39:09 +01:00
"bdc8ce57.de1f08"
Flow updates
2020-10-06 17:22:25 +02:00
]
]
},
main update to flow
2020-11-27 11:30:57 +01:00
{
"id": "b402f719.55bc98",
"type": "inject",
"z": "baa1e3d9.cb29d",
"name": "Default: FORWARD",
"props": [
Fix bugs all around
2020-11-25 16:58:32 +01:00
{
main update to flow
2020-11-27 11:30:57 +01:00
"p": "payload"
Fix bugs all around
2020-11-25 16:58:32 +01:00
},
{
main update to flow
2020-11-27 11:30:57 +01:00
"p": "topic",
"vt": "str"
Fix bugs all around
2020-11-25 16:58:32 +01:00
}
],
main update to flow
2020-11-27 11:30:57 +01:00
"repeat": "",
"crontab": "",
"once": true,
"onceDelay": 0.1,
"topic": "pump_direction",
"payload": "FORWARD",
"payloadType": "str",
flow: better config management
2020-12-05 00:20:44 +01:00
"x": 180,
"y": 580,
Flow updates
2020-10-06 17:22:25 +02:00
"wires": [
[
main update to flow
2020-11-27 11:30:57 +01:00
"bb62da8a.ebc328"
Flow updates
2020-10-06 17:22:25 +02:00
]
]
},
{
Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
2020-12-02 19:26:27 +01:00
"id": "6b2239f3.41fa3",
Fix bugs all around
2020-11-25 16:58:32 +01:00
"type": "function",
Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
2020-12-02 19:26:27 +01:00
"z": "baa1e3d9.cb29d",
"name": "set global",
"func": "global.set(msg.topic, msg.payload);",
Fix bugs all around
2020-11-25 16:58:32 +01:00
"outputs": 1,
"noerr": 0,
"initialize": "",
"finalize": "",
flow: better config management
2020-12-05 00:20:44 +01:00
"x": 620,
"y": 580,
main update to flow
2020-11-27 11:30:57 +01:00
"wires": [
[]
]
},
{
"id": "51b4d0df.d70a88",
"type": "ui_text_input",
"z": "baa1e3d9.cb29d",
"name": "nb_frame",
"label": "Number of images to acquire",
"tooltip": "",
"group": "4322c187.e73e5",
Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
2020-12-02 19:26:27 +01:00
"order": 2,
"width": 5,
"height": 1,
main update to flow
2020-11-27 11:30:57 +01:00
"passthru": true,
"mode": "number",
"delay": 300,
"topic": "nb_frame",
"x": 640,
Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
2020-12-02 19:26:27 +01:00
"y": 280,
main update to flow
2020-11-27 11:30:57 +01:00
"wires": [
[
"fb887036.12429",
Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
2020-12-02 19:26:27 +01:00
"67091ac0.8f9f6c",
"99b11fe4.2795d"
main update to flow
2020-11-27 11:30:57 +01:00
]
]
},
{
"id": "9c7f7fc9.c8d3a",
"type": "ui_text_input",
"z": "b771c342.49603",
"name": "object_depth_max",
flow: addition of decknet flowmeter readings and better management of titles and location group activation
2020-12-04 22:24:20 +01:00
"label": "Max sampling depth (m)",
flow: location refactor using forms
2020-12-03 23:13:08 +01:00
"tooltip": "in m",
main update to flow
2020-11-27 11:30:57 +01:00
"group": "3e1ba03d.f01d8",
flow: addition of decknet flowmeter readings and better management of titles and location group activation
2020-12-04 22:24:20 +01:00
"order": 12,
main update to flow
2020-11-27 11:30:57 +01:00
"width": 5,
"height": 1,
"passthru": true,
"mode": "number",
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"delay": "1000",
main update to flow
2020-11-27 11:30:57 +01:00
"topic": "object_depth_max",
"x": 650,
flow: better config management
2020-12-05 00:20:44 +01:00
"y": 240,
main update to flow
2020-11-27 11:30:57 +01:00
"wires": [
[
"9f501f49.45645"
]
]
},
{
"id": "317eeeb7.8d3042",
"type": "ui_text_input",
"z": "b771c342.49603",
"name": "object_depth_min",
flow: addition of decknet flowmeter readings and better management of titles and location group activation
2020-12-04 22:24:20 +01:00
"label": "Min sampling depth (m)",
flow: location refactor using forms
2020-12-03 23:13:08 +01:00
"tooltip": "in m",
main update to flow
2020-11-27 11:30:57 +01:00
"group": "3e1ba03d.f01d8",
flow: addition of decknet flowmeter readings and better management of titles and location group activation
2020-12-04 22:24:20 +01:00
"order": 11,
main update to flow
2020-11-27 11:30:57 +01:00
"width": 5,
"height": 1,
"passthru": true,
"mode": "number",
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"delay": "1000",
main update to flow
2020-11-27 11:30:57 +01:00
"topic": "object_depth_min",
"x": 650,
flow: better config management
2020-12-05 00:20:44 +01:00
"y": 280,
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 update to flow
2020-11-27 11:30:57 +01:00
"9f501f49.45645"
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 update to flow
2020-11-27 11:30:57 +01:00
"id": "999065ca.27edb8",
Fix bugs all around
2020-11-25 16:58:32 +01:00
"type": "switch",
main update to flow
2020-11-27 11:30:57 +01:00
"z": "baa1e3d9.cb29d",
"name": "topic filter",
Fix bugs all around
2020-11-25 16:58:32 +01:00
"property": "topic",
"propertyType": "msg",
"rules": [
{
"t": "eq",
main update to flow
2020-11-27 11:30:57 +01:00
"v": "status/pump",
Fix bugs all around
2020-11-25 16:58:32 +01:00
"vt": "str"
},
{
"t": "eq",
main update to flow
2020-11-27 11:30:57 +01:00
"v": "status/focus",
Fix bugs all around
2020-11-25 16:58:32 +01:00
"vt": "str"
},
{
"t": "eq",
main update to flow
2020-11-27 11:30:57 +01:00
"v": "status/imager",
Fix bugs all around
2020-11-25 16:58:32 +01:00
"vt": "str"
}
],
"checkall": "true",
"repair": false,
main update to flow
2020-11-27 11:30:57 +01:00
"outputs": 3,
flow: better config management
2020-12-05 00:20:44 +01:00
"x": 320,
"y": 840,
Flow updates
2020-10-06 17:22:25 +02:00
"wires": [
[
main update to flow
2020-11-27 11:30:57 +01:00
"a46a1e7f.88a92",
"6742014e.1bb238"
Fix bugs all around
2020-11-25 16:58:32 +01:00
],
[
main update to flow
2020-11-27 11:30:57 +01:00
"c516d9ea.f7f6e",
"6742014e.1bb238"
Fix bugs all around
2020-11-25 16:58:32 +01:00
],
[
retrieve camera name
2020-11-27 18:57:43 +01:00
"307c851e.fb0f7a",
"2b9d6988.d84836"
Flow updates
2020-10-06 17:22:25 +02:00
]
]
},
{
main update to flow
2020-11-27 11:30:57 +01:00
"id": "2b009bd7.c07004",
"type": "ui_text",
"z": "baa1e3d9.cb29d",
"group": "70de8209.68416c",
"order": 3,
"width": 10,
Fix bugs all around
2020-11-25 16:58:32 +01:00
"height": 2,
main update to flow
2020-11-27 11:30:57 +01:00
"name": "imager",
"label": "Imager status:",
"format": "{{msg.payload.status}}",
"layout": "col-center",
flow: better config management
2020-12-05 00:20:44 +01:00
"x": 770,
"y": 780,
main update to flow
2020-11-27 11:30:57 +01:00
"wires": []
},
{
"id": "c516d9ea.f7f6e",
"type": "ui_text",
"z": "baa1e3d9.cb29d",
"group": "70de8209.68416c",
"order": 1,
"width": 5,
"height": 1,
"name": "focus",
"label": "Focus status:",
"format": "{{msg.payload.status}}",
"layout": "col-center",
flow: better config management
2020-12-05 00:20:44 +01:00
"x": 770,
"y": 740,
main update to flow
2020-11-27 11:30:57 +01:00
"wires": []
},
{
"id": "a46a1e7f.88a92",
"type": "ui_text",
"z": "baa1e3d9.cb29d",
"group": "70de8209.68416c",
"order": 2,
"width": 5,
"height": 1,
"name": "pump",
"label": "Pump status:",
"format": "{{msg.payload.status}}",
"layout": "col-center",
flow: better config management
2020-12-05 00:20:44 +01:00
"x": 770,
"y": 700,
main update to flow
2020-11-27 11:30:57 +01:00
"wires": []
},
{
"id": "bb628f8d.98f108",
"type": "link in",
"z": "baa1e3d9.cb29d",
"name": "Status for fluidic module",
"links": [
"58f2e0f.4e8b12"
Fix bugs all around
2020-11-25 16:58:32 +01:00
],
flow: better config management
2020-12-05 00:20:44 +01:00
"x": 175,
"y": 840,
Flow updates
2020-10-06 17:22:25 +02:00
"wires": [
main update to flow
2020-11-27 11:30:57 +01:00
[
"999065ca.27edb8"
]
]
},
{
"id": "1fdf77b5.24e4e",
"type": "mqtt in",
"z": "9a22e67a.378818",
"name": "",
"topic": "status/#",
"qos": "0",
"datatype": "json",
"broker": "8dc3722c.06efa8",
"x": 290,
"y": 340,
"wires": [
[
"fa73983d.318188"
]
]
},
{
"id": "4a1e9e3e.27506",
"type": "switch",
"z": "9a22e67a.378818",
"name": "Filter segmenter out",
"property": "topic",
"propertyType": "msg",
"rules": [
{
"t": "else"
},
{
"t": "cont",
"v": "status/segmenter",
"vt": "str"
}
],
"checkall": "true",
"repair": false,
"outputs": 2,
"x": 620,
"y": 340,
"wires": [
[
"58f2e0f.4e8b12"
],
[
"dcf5bd45.16a8d"
]
]
},
{
"id": "fa73983d.318188",
"type": "json",
"z": "9a22e67a.378818",
"name": "",
"property": "payload",
"action": "obj",
"pretty": true,
"x": 430,
"y": 340,
"wires": [
[
"4a1e9e3e.27506"
]
]
},
{
"id": "58f2e0f.4e8b12",
"type": "link out",
"z": "9a22e67a.378818",
"name": "Fluidic module status",
"links": [
"bb628f8d.98f108"
],
"x": 795,
"y": 320,
"wires": []
},
{
"id": "307c851e.fb0f7a",
"type": "switch",
"z": "baa1e3d9.cb29d",
"name": "Imaging state",
"property": "payload",
"propertyType": "msg",
"rules": [
{
"t": "jsonata_exp",
"v": "$contains(msg.payload.status, \"jpg\")\t",
"vt": "jsonata"
},
{
"t": "else"
}
],
"checkall": "false",
"repair": false,
"outputs": 2,
flow: better config management
2020-12-05 00:20:44 +01:00
"x": 550,
"y": 940,
main update to flow
2020-11-27 11:30:57 +01:00
"wires": [
[
"db8e3dde.44efb8"
],
[
"6742014e.1bb238"
]
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
]
},
{
main update to flow
2020-11-27 11:30:57 +01:00
"id": "db8e3dde.44efb8",
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"type": "function",
main update to flow
2020-11-27 11:30:57 +01:00
"z": "baa1e3d9.cb29d",
"name": "img_counter.js",
"func": "img_counter=global.get('img_counter')\nimg_counter=img_counter+1\nglobal.set('img_counter',img_counter)\nmsg.payload = img_counter\nreturn msg;",
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"outputs": 1,
"noerr": 0,
"initialize": "",
"finalize": "",
flow: better config management
2020-12-05 00:20:44 +01:00
"x": 800,
"y": 980,
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"wires": [
Fix bugs all around
2020-11-25 16:58:32 +01:00
[
main update to flow
2020-11-27 11:30:57 +01:00
"39812a27.6cb10e"
Fix bugs all around
2020-11-25 16:58:32 +01:00
]
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
]
},
{
main update to flow
2020-11-27 11:30:57 +01:00
"id": "59164d65.e7993c",
Fix bugs all around
2020-11-25 16:58:32 +01:00
"type": "ui_toast",
main update to flow
2020-11-27 11:30:57 +01:00
"z": "baa1e3d9.cb29d",
Fix bugs all around
2020-11-25 16:58:32 +01:00
"position": "top right",
"displayTime": "5",
"highlight": "",
"sendall": true,
"outputs": 0,
"ok": "OK",
"cancel": "",
"raw": false,
"topic": "",
"name": "",
flow: better config management
2020-12-05 00:20:44 +01:00
"x": 1260,
"y": 880,
Fix bugs all around
2020-11-25 16:58:32 +01:00
"wires": []
main.json: add machine name and output disable for steppers
2020-11-24 16:23:58 +01:00
},
{
main update to flow
2020-11-27 11:30:57 +01:00
"id": "8c7348aa.1962e8",
Fix bugs all around
2020-11-25 16:58:32 +01:00
"type": "template",
main update to flow
2020-11-27 11:30:57 +01:00
"z": "baa1e3d9.cb29d",
Fix bugs all around
2020-11-25 16:58:32 +01:00
"name": "Create sentence",
"field": "payload",
"fieldType": "msg",
"format": "handlebars",
"syntax": "mustache",
"template": "The {{topic}} is {{payload.status}}",
"output": "str",
flow: better config management
2020-12-05 00:20:44 +01:00
"x": 1060,
"y": 880,
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"wires": [
[
main update to flow
2020-11-27 11:30:57 +01:00
"59164d65.e7993c"
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
]
]
main.json: add machine name and output disable for steppers
2020-11-24 16:23:58 +01:00
},
{
main update to flow
2020-11-27 11:30:57 +01:00
"id": "6742014e.1bb238",
Fix bugs all around
2020-11-25 16:58:32 +01:00
"type": "change",
main update to flow
2020-11-27 11:30:57 +01:00
"z": "baa1e3d9.cb29d",
Fix bugs all around
2020-11-25 16:58:32 +01:00
"name": "Remove high-level topic",
"rules": [
{
"t": "change",
"p": "topic",
"pt": "msg",
"from": "status/",
"fromt": "str",
"to": "",
"tot": "str"
}
],
"action": "",
"property": "",
"from": "",
"to": "",
"reg": false,
flow: better config management
2020-12-05 00:20:44 +01:00
"x": 830,
"y": 880,
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"wires": [
[
main update to flow
2020-11-27 11:30:57 +01:00
"8c7348aa.1962e8"
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
]
]
main.json: add machine name and output disable for steppers
2020-11-24 16:23:58 +01:00
},
Fix bugs all around
2020-11-25 16:58:32 +01:00
{
main update to flow
2020-11-27 11:30:57 +01:00
"id": "1a2e721a.f5e876",
Fix bugs all around
2020-11-25 16:58:32 +01:00
"type": "ui_gauge",
main update to flow
2020-11-27 11:30:57 +01:00
"z": "baa1e3d9.cb29d",
add sample_gear_net_opening and sample_concentrated_sample_volume improve #44
2020-11-29 23:44:09 +01:00
"name": "progress donut",
Fix bugs all around
2020-11-25 16:58:32 +01:00
"group": "b5d61bc7.54fe48",
add sample_gear_net_opening and sample_concentrated_sample_volume improve #44
2020-11-29 23:44:09 +01:00
"order": 3,
"width": 6,
Fix bugs all around
2020-11-25 16:58:32 +01:00
"height": 3,
"gtype": "donut",
add sample_gear_net_opening and sample_concentrated_sample_volume improve #44
2020-11-29 23:44:09 +01:00
"title": "",
Fix bugs all around
2020-11-25 16:58:32 +01:00
"label": "%",
"format": "{{value}}",
"min": 0,
"max": "100",
"colors": [
"#ffa83f",
"#e6ff02",
"#00dfe9"
],
"seg1": "50",
"seg2": "75",
flow: better config management
2020-12-05 00:20:44 +01:00
"x": 1260,
"y": 980,
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"wires": []
},
{
main update to flow
2020-11-27 11:30:57 +01:00
"id": "39812a27.6cb10e",
Fix bugs all around
2020-11-25 16:58:32 +01:00
"type": "function",
main update to flow
2020-11-27 11:30:57 +01:00
"z": "baa1e3d9.cb29d",
Fix bugs all around
2020-11-25 16:58:32 +01:00
"name": "percent image",
main update to flow
2020-11-27 11:30:57 +01:00
"func": "msg.payload = (100 * msg.payload/global.get('nb_frame')).toFixed(2)\nreturn msg;",
Fix bugs all around
2020-11-25 16:58:32 +01:00
"outputs": 1,
"noerr": 0,
"initialize": "",
"finalize": "",
flow: better config management
2020-12-05 00:20:44 +01:00
"x": 1040,
"y": 980,
Fix bugs all around
2020-11-25 16:58:32 +01:00
"wires": [
[
main update to flow
2020-11-27 11:30:57 +01:00
"1a2e721a.f5e876"
Fix bugs all around
2020-11-25 16:58:32 +01:00
]
]
},
main.json: add machine name and output disable for steppers
2020-11-24 16:23:58 +01:00
{
main update to flow
2020-11-27 11:30:57 +01:00
"id": "8f3788f6.ddcf98",
Fix bugs all around
2020-11-25 16:58:32 +01:00
"type": "function",
main update to flow
2020-11-27 11:30:57 +01:00
"z": "cb95299c.2817c8",
"name": "obj_counter.js",
"func": "obj_counter=global.get('obj_counter')\nobj_counter=obj_counter+1\nglobal.set('obj_counter',obj_counter)\nmsg.payload = obj_counter\nreturn msg;",
Fix bugs all around
2020-11-25 16:58:32 +01:00
"outputs": 1,
"noerr": 0,
"initialize": "",
"finalize": "",
main update to flow
2020-11-27 11:30:57 +01:00
"x": 820,
"y": 840,
main.json: add machine name and output disable for steppers
2020-11-24 16:23:58 +01:00
"wires": [
[
main update to flow
2020-11-27 11:30:57 +01:00
"9d53dbe2.dbffe8",
"fa3b7929.ac7da8"
]
]
},
{
"id": "aa38dbbc.cf0a9",
"type": "switch",
"z": "cb95299c.2817c8",
"name": "Segmenter",
"property": "topic",
"propertyType": "msg",
"rules": [
{
"t": "eq",
"v": "status/segmenter",
"vt": "str"
},
{
"t": "eq",
"v": "status/segmenter/name",
"vt": "str"
},
{
"t": "eq",
"v": "status/segmenter/object_id",
"vt": "str"
},
{
"t": "eq",
"v": "status/segmenter/metric",
"vt": "str"
}
],
"checkall": "true",
"repair": false,
"outputs": 4,
"x": 490,
"y": 740,
"wires": [
[
"b9a23b91.93638",
"6919465f.332e5"
],
[
"49af3d24.1799e4"
],
[
"8f3788f6.ddcf98"
],
[
"50ce901f.b5034"
]
]
},
{
"id": "9d53dbe2.dbffe8",
"type": "ui_chart",
"z": "cb95299c.2817c8",
flow: update metadata export, cleanup net handling, add acq_imaged_volume
2020-11-29 13:26:24 +01:00
"name": "counter graph",
main update to flow
2020-11-27 11:30:57 +01:00
"group": "46be9c86.dea684",
flow: update metadata export, cleanup net handling, add acq_imaged_volume
2020-11-29 13:26:24 +01:00
"order": 6,
"width": 10,
main update to flow
2020-11-27 11:30:57 +01:00
"height": 2,
flow: update metadata export, cleanup net handling, add acq_imaged_volume
2020-11-29 13:26:24 +01:00
"label": "",
main update to flow
2020-11-27 11:30:57 +01:00
"chartType": "horizontalBar",
"legend": "false",
"xformat": "HH:mm:ss",
"interpolate": "linear",
"nodata": "Objects count will be shown here once the segmentation is started",
"dot": false,
"ymin": "",
"ymax": "",
"removeOlder": 1,
"removeOlderPoints": "",
"removeOlderUnit": "3600",
"cutout": 0,
"useOneColor": true,
"useUTC": false,
"colors": [
"#1f77b4",
"#aec7e8",
"#ff7f0e",
"#2ca02c",
"#98df8a",
"#d62728",
"#ff9896",
"#9467bd",
"#c5b0d5"
],
"outputs": 1,
flow: update metadata export, cleanup net handling, add acq_imaged_volume
2020-11-29 13:26:24 +01:00
"x": 1340,
main update to flow
2020-11-27 11:30:57 +01:00
"y": 840,
"wires": [
[]
]
},
{
"id": "50ce901f.b5034",
"type": "function",
"z": "cb95299c.2817c8",
"name": "ex : area",
"func": "msg.payload=msg.payload.object_area\nmsg.topic=\"area\"\n\nreturn msg;",
"outputs": 1,
"noerr": 0,
"initialize": "",
"finalize": "",
"x": 800,
flow: update metadata export, cleanup net handling, add acq_imaged_volume
2020-11-29 13:26:24 +01:00
"y": 920,
main update to flow
2020-11-27 11:30:57 +01:00
"wires": [
[
"458cd82e.03d258"
]
]
},
{
"id": "a4f0f0d1.3aca88",
"type": "ui_toast",
"z": "cb95299c.2817c8",
"position": "top right",
"displayTime": "5",
"highlight": "",
"sendall": true,
"outputs": 0,
"ok": "OK",
"cancel": "",
"raw": false,
"topic": "",
"name": "",
"x": 1340,
"y": 680,
"wires": []
},
{
"id": "458cd82e.03d258",
"type": "ui_chart",
"z": "cb95299c.2817c8",
"name": "Area chart",
"group": "46be9c86.dea684",
"order": 9,
flow: update metadata export, cleanup net handling, add acq_imaged_volume
2020-11-29 13:26:24 +01:00
"width": 10,
"height": 6,
"label": "",
main update to flow
2020-11-27 11:30:57 +01:00
"chartType": "line",
"legend": "false",
"xformat": "HH:mm:ss",
"interpolate": "linear",
"nodata": "Objects area will be shown here once the segmentation is started",
"dot": true,
"ymin": "",
"ymax": "",
"removeOlder": 1,
"removeOlderPoints": "1000",
"removeOlderUnit": "3600",
"cutout": 0,
"useOneColor": false,
"useUTC": true,
"colors": [
"#1f77b4",
"#aec7e8",
"#ff7f0e",
"#2ca02c",
"#98df8a",
"#d62728",
"#ff9896",
"#9467bd",
"#c5b0d5"
],
"outputs": 1,
flow: update metadata export, cleanup net handling, add acq_imaged_volume
2020-11-29 13:26:24 +01:00
"x": 1320,
"y": 920,
main update to flow
2020-11-27 11:30:57 +01:00
"wires": [
[]
]
},
{
"id": "49af3d24.1799e4",
"type": "debug",
"z": "cb95299c.2817c8",
"name": "segmentation name",
"active": true,
"tosidebar": true,
"console": false,
"tostatus": false,
"complete": "true",
"targetType": "full",
"statusVal": "",
"statusType": "auto",
Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
2020-12-02 19:26:27 +01:00
"x": 840,
main update to flow
2020-11-27 11:30:57 +01:00
"y": 760,
"wires": []
},
{
"id": "7088a5be.0c79a4",
"type": "template",
"z": "cb95299c.2817c8",
"name": "Create sentence",
"field": "payload",
"fieldType": "msg",
"format": "handlebars",
"syntax": "mustache",
"template": "The {{topic}} is {{payload.status}}",
"output": "str",
"x": 1100,
"y": 680,
"wires": [
[
"a4f0f0d1.3aca88"
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
},
{
main update to flow
2020-11-27 11:30:57 +01:00
"id": "b9a23b91.93638",
Fix bugs all around
2020-11-25 16:58:32 +01:00
"type": "change",
main update to flow
2020-11-27 11:30:57 +01:00
"z": "cb95299c.2817c8",
"name": "Remove high-level topic",
Fix bugs all around
2020-11-25 16:58:32 +01:00
"rules": [
{
main update to flow
2020-11-27 11:30:57 +01:00
"t": "change",
"p": "topic",
"pt": "msg",
"from": "status/",
"fromt": "str",
"to": "",
"tot": "str"
Fix bugs all around
2020-11-25 16:58:32 +01:00
}
],
"action": "",
"property": "",
"from": "",
"to": "",
"reg": false,
main update to flow
2020-11-27 11:30:57 +01:00
"x": 850,
"y": 680,
Main.json: UI upgrade
2020-11-24 17:25:15 +01:00
"wires": [
main update to flow
2020-11-27 11:30:57 +01:00
[
"7088a5be.0c79a4"
]
]
},
{
"id": "6919465f.332e5",
"type": "ui_text",
"z": "cb95299c.2817c8",
"group": "46be9c86.dea684",
"order": 1,
flow: update metadata export, cleanup net handling, add acq_imaged_volume
2020-11-29 13:26:24 +01:00
"width": 10,
main update to flow
2020-11-27 11:30:57 +01:00
"height": 1,
"name": "segmenter",
"label": "Segmenter status:",
"format": "{{msg.payload.status}}",
flow: update metadata export, cleanup net handling, add acq_imaged_volume
2020-11-29 13:26:24 +01:00
"layout": "row-spread",
main update to flow
2020-11-27 11:30:57 +01:00
"x": 810,
"y": 720,
"wires": []
},
{
"id": "fa3b7929.ac7da8",
"type": "ui_text",
"z": "cb95299c.2817c8",
"group": "46be9c86.dea684",
flow: update metadata export, cleanup net handling, add acq_imaged_volume
2020-11-29 13:26:24 +01:00
"order": 4,
main update to flow
2020-11-27 11:30:57 +01:00
"width": 4,
"height": 1,
flow: update metadata export, cleanup net handling, add acq_imaged_volume
2020-11-29 13:26:24 +01:00
"name": "counter",
"label": "",
main update to flow
2020-11-27 11:30:57 +01:00
"format": "{{msg.payload}}",
"layout": "col-center",
"x": 1320,
"y": 800,
"wires": []
},
{
"id": "640ece83.88cab",
"type": "inject",
"z": "cb95299c.2817c8",
"name": "Init graphs",
"props": [
{
"p": "payload"
},
{
"p": "topic",
"vt": "str"
}
],
"repeat": "",
"crontab": "",
"once": true,
"onceDelay": 0.1,
"topic": "",
"payload": "0",
"payloadType": "num",
"x": 810,
"y": 800,
"wires": [
[
"cd10a556.6a9a08"
]
]
},
{
"id": "cd10a556.6a9a08",
"type": "function",
"z": "cb95299c.2817c8",
"name": "obj_counter init",
"func": "obj_counter=0\nglobal.set('obj_counter',obj_counter)\nmsg.payload = obj_counter\nreturn msg;",
"outputs": 1,
"noerr": 0,
"initialize": "",
"finalize": "",
"x": 1000,
"y": 800,
"wires": [
[
"fa3b7929.ac7da8"
]
]
},
{
"id": "25867454.a8e334",
"type": "link in",
"z": "cb95299c.2817c8",
"name": "Segmenter module status",
"links": [
"dcf5bd45.16a8d"
],
"x": 295,
"y": 740,
"wires": [
[
"aa38dbbc.cf0a9"
]
]
},
{
"id": "dcf5bd45.16a8d",
"type": "link out",
"z": "9a22e67a.378818",
"name": "Segmenter module status",
"links": [
"25867454.a8e334"
],
"x": 795,
"y": 360,
"wires": []
},
{
"id": "52af9ac0.60eb24",
"type": "link out",
"z": "b771c342.49603",
"name": "Sample Operator",
"links": [
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"c1d4934c.9bb628",
"35eb925e.5f8016"
main update to flow
2020-11-27 11:30:57 +01:00
],
"x": 815,
flow: add mL to concentrated sample volume and add process_description field to metadata
2020-12-03 15:15:13 +01:00
"y": 160,
main update to flow
2020-11-27 11:30:57 +01:00
"wires": []
},
{
"id": "9bd72495.a8a098",
"type": "ui_text",
"z": "baa1e3d9.cb29d",
"group": "4322c187.e73e5",
Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
2020-12-02 19:26:27 +01:00
"order": 5,
main update to flow
2020-11-27 11:30:57 +01:00
"width": 5,
"height": 1,
Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
2020-12-02 19:26:27 +01:00
"name": "Total imaged volume",
"label": "Total imaged volume",
main update to flow
2020-11-27 11:30:57 +01:00
"format": "{{msg.payload}}",
Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
2020-12-02 19:26:27 +01:00
"layout": "col-center",
"x": 1180,
"y": 240,
main update to flow
2020-11-27 11:30:57 +01:00
"wires": []
},
{
"id": "99b11fe4.2795d",
"type": "function",
"z": "baa1e3d9.cb29d",
flow: update metadata export, cleanup net handling, add acq_imaged_volume
2020-11-29 13:26:24 +01:00
"name": "imaged volume calc",
Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
2020-12-02 19:26:27 +01:00
"func": "camera = global.get(\"acq_camera\");\ncell = global.get(\"acq_celltype\");\nnb_frame = global.get(\"nb_frame\");\n\nif (camera == \"HQ Camera\"){\n volume = nb_frame * (4.15*3.14*cell/1000) / 1000;\n}\nelse if (camera == \"Camera v2.1\"){\n volume = nb_frame * (2.31*1.74*cell/1000) / 1000;\n}\nelse{\n msg.payload = \"The camera is not known to this system\";\n return msg;\n}\n\nglobal.set(\"acq_imaged_volume\", volume.toFixed(4))\n\nmsg.payload = volume.toFixed(2) + \" mL\"\nreturn msg;",
main update to flow
2020-11-27 11:30:57 +01:00
"outputs": 1,
"noerr": 0,
"initialize": "",
"finalize": "",
Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
2020-12-02 19:26:27 +01:00
"x": 940,
"y": 240,
main update to flow
2020-11-27 11:30:57 +01:00
"wires": [
[
"9bd72495.a8a098"
]
],
"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": "8e16aa2f.e40398",
"type": "ui_text",
"z": "baa1e3d9.cb29d",
"group": "4322c187.e73e5",
Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
2020-12-02 19:26:27 +01:00
"order": 7,
main update to flow
2020-11-27 11:30:57 +01:00
"width": 5,
"height": 1,
Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
2020-12-02 19:26:27 +01:00
"name": "Total pumped volume",
"label": "Total pumped volume",
main update to flow
2020-11-27 11:30:57 +01:00
"format": "{{msg.payload}}",
Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
2020-12-02 19:26:27 +01:00
"layout": "col-center",
"x": 1180,
main update to flow
2020-11-27 11:30:57 +01:00
"y": 300,
"wires": []
},
{
"id": "67091ac0.8f9f6c",
"type": "function",
"z": "baa1e3d9.cb29d",
Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
2020-12-02 19:26:27 +01:00
"name": "acq_volume calc",
"func": "var imaging_pump_volume = global.get(\"imaging_pump_volume\");\nvar nb_frame = global.get(\"nb_frame\");\n\nvar acq_volume = (Number(nb_frame)*Number(imaging_pump_volume)).toFixed(2)\nglobal.set(\"acq_volume\", acq_volume)\n\nmsg.payload = acq_volume + \" mL\"\nreturn msg;",
main update to flow
2020-11-27 11:30:57 +01:00
"outputs": 1,
"noerr": 0,
"initialize": "",
"finalize": "",
Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
2020-12-02 19:26:27 +01:00
"x": 930,
main update to flow
2020-11-27 11:30:57 +01:00
"y": 300,
"wires": [
[
retrieve camera name
2020-11-27 18:57:43 +01:00
"8e16aa2f.e40398"
main update to flow
2020-11-27 11:30:57 +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"
},
addition of white balance gain slider
2020-11-27 12:45:22 +01:00
{
"id": "43737d43.eb0e9c",
"type": "ui_slider",
"z": "bccd1f23.87219",
"name": "WB Red slider",
"label": "WB: Red",
add larger gain control range (up to 8.0)
2020-11-28 22:25:59 +01:00
"tooltip": "from 1.0 to 8.0",
addition of white balance gain slider
2020-11-27 12:45:22 +01:00
"group": "8c38a81e.9897a8",
add larger gain control range (up to 8.0)
2020-11-28 22:25:59 +01:00
"order": 4,
"width": 8,
addition of white balance gain slider
2020-11-27 12:45:22 +01:00
"height": 1,
"passthru": true,
"outs": "end",
flow: better config management
2020-12-05 00:20:44 +01:00
"topic": "wb_red_gain",
addition of white balance gain slider
2020-11-27 12:45:22 +01:00
"min": "1.0",
add larger gain control range (up to 8.0)
2020-11-28 22:25:59 +01:00
"max": "8.0",
addition of white balance gain slider
2020-11-27 12:45:22 +01:00
"step": "0.01",
flow: better config management
2020-12-05 00:20:44 +01:00
"x": 500,
"y": 880,
addition of white balance gain slider
2020-11-27 12:45:22 +01:00
"wires": [
[
flow: better config management
2020-12-05 00:20:44 +01:00
"5e147425.7666ec",
"56835fa1.2fe538"
addition of white balance gain slider
2020-11-27 12:45:22 +01:00
]
]
},
{
"id": "5e147425.7666ec",
"type": "function",
"z": "bccd1f23.87219",
"name": "Encapsulate settings",
flow: better config management
2020-12-05 00:20:44 +01:00
"func": "if (msg.topic == \"wb_red_gain\"){\n msg.payload = {\n \"action\":\"settings\", \n \"settings\":{\"white_balance_gain\":{\n \"red\":Math.round(msg.payload*100)\n }\n }\n }\n}\nif (msg.topic == \"wb_blue_gain\"){\n msg.payload = {\n \"action\":\"settings\", \n \"settings\":{\"white_balance_gain\":{\n \"blue\":Math.round(msg.payload*100)\n }\n }\n }\n}\nmsg.topic = \"imager/image\"\nreturn msg;",
addition of white balance gain slider
2020-11-27 12:45:22 +01:00
"outputs": 1,
"noerr": 0,
"initialize": "",
"finalize": "",
flow: better config management
2020-12-05 00:20:44 +01:00
"x": 740,
"y": 880,
addition of white balance gain slider
2020-11-27 12:45:22 +01:00
"wires": [
[
add white balance switch
2020-11-27 18:39:09 +01:00
"845e06e1.0d812"
addition of white balance gain slider
2020-11-27 12:45:22 +01:00
]
]
},
{
flow: better config management
2020-12-05 00:20:44 +01:00
"id": "7b699798.3d568",
"type": "ui_slider",
"z": "bccd1f23.87219",
"name": "WB Blue slider",
"label": "WB: Blue",
"tooltip": "from 1.0 to 8.0",
"group": "8c38a81e.9897a8",
"order": 5,
"width": 8,
"height": 1,
"passthru": true,
"outs": "end",
"topic": "wb_blue_gain",
"min": "1.0",
"max": "8.0",
"step": "0.01",
"x": 500,
"y": 920,
"wires": [
[
"5e147425.7666ec",
"56835fa1.2fe538"
]
]
},
{
"id": "daedda1b.9805b8",
addition of white balance gain slider
2020-11-27 12:45:22 +01:00
"type": "function",
"z": "bccd1f23.87219",
"name": "Encapsulate settings",
flow: better config management
2020-12-05 00:20:44 +01:00
"func": "msg.payload = {\n \"action\":\"settings\", \n \"settings\":{\"white_balance\":msg.payload}\n}\nmsg.topic = \"imager/image\"\nreturn msg;",
addition of white balance gain slider
2020-11-27 12:45:22 +01:00
"outputs": 1,
"noerr": 0,
"initialize": "",
"finalize": "",
flow: better config management
2020-12-05 00:20:44 +01:00
"x": 740,
"y": 960,
addition of white balance gain slider
2020-11-27 12:45:22 +01:00
"wires": [
[
add white balance switch
2020-11-27 18:39:09 +01:00
"845e06e1.0d812"
addition of white balance gain slider
2020-11-27 12:45:22 +01:00
]
]
},
{
flow: better config management
2020-12-05 00:20:44 +01:00
"id": "82722a3c.846b3",
addition of white balance gain slider
2020-11-27 12:45:22 +01:00
"type": "inject",
"z": "bccd1f23.87219",
flow: better config management
2020-12-05 00:20:44 +01:00
"name": "Default: OFF",
add white balance switch
2020-11-27 18:39:09 +01:00
"props": [
{
"p": "payload"
}
],
"repeat": "",
"crontab": "",
"once": true,
"onceDelay": "1",
"topic": "",
"payload": "false",
"payloadType": "bool",
"x": 110,
flow: better config management
2020-12-05 00:20:44 +01:00
"y": 960,
add white balance switch
2020-11-27 18:39:09 +01:00
"wires": [
[
"60e44330.50bdec"
]
]
},
{
"id": "60e44330.50bdec",
"type": "ui_switch",
"z": "bccd1f23.87219",
"name": "AWB",
"label": "Auto White Balance",
"tooltip": "",
"group": "8c38a81e.9897a8",
add larger gain control range (up to 8.0)
2020-11-28 22:25:59 +01:00
"order": 3,
"width": 2,
"height": 2,
add white balance switch
2020-11-27 18:39:09 +01:00
"passthru": true,
"decouple": "false",
"topic": "imager/image",
"style": "",
"onvalue": "auto",
"onvalueType": "str",
"onicon": "",
"oncolor": "",
"offvalue": "off",
"offvalueType": "str",
"officon": "",
"offcolor": "",
flow: better config management
2020-12-05 00:20:44 +01:00
"x": 510,
"y": 960,
add white balance switch
2020-11-27 18:39:09 +01:00
"wires": [
[
"daedda1b.9805b8"
]
]
retrieve camera name
2020-11-27 18:57:43 +01:00
},
{
"id": "2b9d6988.d84836",
"type": "switch",
"z": "baa1e3d9.cb29d",
"name": "",
"property": "payload",
"propertyType": "msg",
"rules": [
{
"t": "hask",
"v": "status",
"vt": "str"
},
{
"t": "hask",
"v": "camera_name",
"vt": "str"
}
],
"checkall": "true",
"repair": false,
"outputs": 2,
flow: better config management
2020-12-05 00:20:44 +01:00
"x": 650,
"y": 800,
retrieve camera name
2020-11-27 18:57:43 +01:00
"wires": [
[
"2b009bd7.c07004"
],
[
"3bbb756a.84190a"
]
]
},
{
"id": "3bbb756a.84190a",
"type": "function",
"z": "baa1e3d9.cb29d",
"name": "set camera name",
add larger gain control range (up to 8.0)
2020-11-28 22:25:59 +01:00
"func": "global.set(\"acq_camera\", msg.payload.camera_name);\n\nmsg.payload = msg.payload.camera_name;\n\nreturn msg;",
retrieve camera name
2020-11-27 18:57:43 +01:00
"outputs": 1,
"noerr": 0,
"initialize": "",
"finalize": "",
flow: better config management
2020-12-05 00:20:44 +01:00
"x": 810,
"y": 820,
retrieve camera name
2020-11-27 18:57:43 +01:00
"wires": [
[
"559a8085.1d6b9"
]
]
},
{
"id": "559a8085.1d6b9",
"type": "link out",
"z": "baa1e3d9.cb29d",
"name": "Camera Name",
"links": [
flox fix imaged volume initialisation
2020-11-29 18:57:18 +01:00
"30067f35.532f2",
Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
2020-12-02 19:26:27 +01:00
"572a6daa.6004c4",
"cfc783d7.d6ceb"
retrieve camera name
2020-11-27 18:57:43 +01:00
],
flow: better config management
2020-12-05 00:20:44 +01:00
"x": 965,
"y": 820,
retrieve camera name
2020-11-27 18:57:43 +01:00
"wires": []
},
{
"id": "30067f35.532f2",
"type": "link in",
"z": "1371dec5.76e671",
"name": "Camera Name",
"links": [
"559a8085.1d6b9"
],
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"x": 875,
"y": 620,
retrieve camera name
2020-11-27 18:57:43 +01:00
"wires": [
[
"f783aefd.c3bfd8"
]
]
add larger gain control range (up to 8.0)
2020-11-28 22:25:59 +01:00
},
{
"id": "11b51f8f.acd308",
"type": "python3-function",
"z": "1371dec5.76e671",
add sample_gear_net_opening and sample_concentrated_sample_volume improve #44
2020-11-29 23:44:09 +01:00
"d": true,
change default fan
2020-11-29 19:07:29 +01:00
"name": "fan temperature",
add sample_gear_net_opening and sample_concentrated_sample_volume improve #44
2020-11-29 23:44:09 +01:00
"func": "import smbus\nbus = smbus.SMBus(1)\n\naddr = 0x0d\nfan_reg = 0x08\n\ntemp = float( msg[\"payload\"])\n\n# 0x01 full speed, 0x02: 20% speed, ..., 0x09: 90% speed\n\nif temp < 38:\n bus.write_byte_data(addr, fan_reg, 0x00)\nelif temp < 43:\n bus.write_byte_data(addr, fan_reg, 0x02)\nelif temp < 46:\n bus.write_byte_data(addr, fan_reg, 0x04)\nelif temp < 48:\n bus.write_byte_data(addr, fan_reg, 0x06)\nelif temp < 52:\n bus.write_byte_data(addr, fan_reg, 0x08)\nelse:\n bus.write_byte_data(addr, fan_reg, 0x01)\n\nreturn msg",
add larger gain control range (up to 8.0)
2020-11-28 22:25:59 +01:00
"outputs": 1,
Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
2020-12-02 19:26:27 +01:00
"x": 1520,
"y": 40,
add larger gain control range (up to 8.0)
2020-11-28 22:25:59 +01:00
"wires": [
[]
]
flow: update metadata export, cleanup net handling, add acq_imaged_volume
2020-11-29 13:26:24 +01:00
},
{
"id": "cbb123ab.fd3428",
"type": "ui_ui_control",
"z": "b771c342.49603",
"name": "",
"events": "change",
flow: addition of decknet flowmeter readings and better management of titles and location group activation
2020-12-04 22:24:20 +01:00
"x": 1280,
flow: better config management
2020-12-05 00:20:44 +01:00
"y": 260,
flow: update metadata export, cleanup net handling, add acq_imaged_volume
2020-11-29 13:26:24 +01:00
"wires": [
[]
]
},
{
flow: location refactor using forms
2020-12-03 23:13:08 +01:00
"id": "c8749cbb.55254",
"type": "function",
"z": "cb95299c.2817c8",
"name": "set global",
"func": "global.set(msg.topic, msg.payload);",
"outputs": 1,
"noerr": 0,
"initialize": "",
"finalize": "",
"x": 560,
"y": 200,
flow: update metadata export, cleanup net handling, add acq_imaged_volume
2020-11-29 13:26:24 +01:00
"wires": [
flow: location refactor using forms
2020-12-03 23:13:08 +01:00
[]
flow: update metadata export, cleanup net handling, add acq_imaged_volume
2020-11-29 13:26:24 +01:00
]
},
{
"id": "d43c3ed9.e6cb1",
"type": "ui_template",
"z": "cb95299c.2817c8",
"group": "46be9c86.dea684",
"name": "Object counts",
"order": 2,
"width": 0,
"height": 0,
"format": "<div><center><h2>Object counts</h2></center></div>",
"storeOutMessages": true,
"fwdInMessages": true,
"resendOnRefresh": true,
"templateScope": "local",
"x": 1340,
"y": 760,
"wires": [
[]
]
},
{
"id": "857e90c1.cd25b",
"type": "ui_template",
"z": "cb95299c.2817c8",
"group": "46be9c86.dea684",
"name": "Area chart",
"order": 8,
"width": 0,
"height": 0,
"format": "<div><center><h2>Area chart</h2></center></div>",
"storeOutMessages": true,
"fwdInMessages": true,
"resendOnRefresh": true,
"templateScope": "local",
"x": 1320,
"y": 880,
"wires": [
[]
]
add sleep_before, closes #48
2020-11-29 14:28:31 +01:00
},
{
"id": "a8bf2334.279c",
"type": "inject",
"z": "baa1e3d9.cb29d",
"name": "Default: 0.5",
"props": [
{
"p": "payload"
}
],
"repeat": "",
"crontab": "",
"once": true,
"onceDelay": 0.1,
"topic": "",
"payload": "0.5",
"payloadType": "num",
"x": 310,
"y": 80,
"wires": [
[
"49ea1123.ee1768"
]
]
},
{
"id": "49ea1123.ee1768",
"type": "ui_numeric",
"z": "baa1e3d9.cb29d",
"name": "sleep_before",
"label": "Delay to stabilize image (s)",
"tooltip": "Happens before every capture",
"group": "4322c187.e73e5",
Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
2020-12-02 19:26:27 +01:00
"order": 4,
add sleep_before, closes #48
2020-11-29 14:28:31 +01:00
"width": 5,
Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
2020-12-02 19:26:27 +01:00
"height": 1,
add sleep_before, closes #48
2020-11-29 14:28:31 +01:00
"wrap": false,
"passthru": true,
"topic": "sleep_before",
"format": "{{value}}",
"min": "0.1",
"max": "5",
"step": "0.1",
"x": 630,
"y": 80,
"wires": [
[
"fb887036.12429"
]
]
flox fix imaged volume initialisation
2020-11-29 18:57:18 +01:00
},
{
"id": "2911fbc6.d28c24",
"type": "ui_template",
"z": "c1660bc.e7ff7f8",
"group": "c0ebfc57.42527",
"name": "Image browser",
"order": 1,
"width": 24,
"height": 24,
add sample_gear_net_opening and sample_concentrated_sample_volume improve #44
2020-11-29 23:44:09 +01:00
"format": "<div>\n <center>\n <object data=\"http://planktoscope.local:80/\" width=\"1400px\" height=\"1100px\"></object>\n </center>\n</div>",
flox fix imaged volume initialisation
2020-11-29 18:57:18 +01:00
"storeOutMessages": true,
"fwdInMessages": true,
"resendOnRefresh": false,
"templateScope": "local",
Remove thumbsup and replace by simple nginx autoindex
2020-12-05 02:22:20 +01:00
"x": 440,
"y": 140,
flox fix imaged volume initialisation
2020-11-29 18:57:18 +01:00
"wires": [
[]
]
},
{
"id": "572a6daa.6004c4",
"type": "link in",
"z": "baa1e3d9.cb29d",
"name": "",
"links": [
"559a8085.1d6b9"
],
Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
2020-12-02 19:26:27 +01:00
"x": 795,
flox fix imaged volume initialisation
2020-11-29 18:57:18 +01:00
"y": 260,
"wires": [
[
"99b11fe4.2795d"
]
]
add sample_gear_net_opening and sample_concentrated_sample_volume improve #44
2020-11-29 23:44:09 +01:00
},
{
"id": "642ff403.1ed91c",
"type": "ui_text_input",
"z": "b771c342.49603",
"name": "sample_concentrated_sample_volume",
flow: add mL to concentrated sample volume and add process_description field to metadata
2020-12-03 15:15:13 +01:00
"label": "Concentrated sample volume (mL)",
"tooltip": "Volume extracted from the net (in mL)",
add sample_gear_net_opening and sample_concentrated_sample_volume improve #44
2020-11-29 23:44:09 +01:00
"group": "3e1ba03d.f01d8",
flow: addition of decknet flowmeter readings and better management of titles and location group activation
2020-12-04 22:24:20 +01:00
"order": 13,
add sample_gear_net_opening and sample_concentrated_sample_volume improve #44
2020-11-29 23:44:09 +01:00
"width": 5,
"height": 1,
"passthru": true,
"mode": "number",
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"delay": "1000",
add sample_gear_net_opening and sample_concentrated_sample_volume improve #44
2020-11-29 23:44:09 +01:00
"topic": "sample_concentrated_sample_volume",
"x": 590,
flow: better config management
2020-12-05 00:20:44 +01:00
"y": 360,
add sample_gear_net_opening and sample_concentrated_sample_volume improve #44
2020-11-29 23:44:09 +01:00
"wires": [
[
"9f501f49.45645"
]
]
},
{
"id": "e967b844.46aa48",
"type": "ui_text_input",
"z": "b771c342.49603",
"name": "sample_gear_net_opening",
flow: addition of decknet flowmeter readings and better management of titles and location group activation
2020-12-04 22:24:20 +01:00
"label": "Net opening dimension (mm)",
"tooltip": "Size of the net mouth opening (in mm)",
"group": "cf5d9f0e.d57e7",
"order": 3,
add sample_gear_net_opening and sample_concentrated_sample_volume improve #44
2020-11-29 23:44:09 +01:00
"width": 10,
"height": 1,
"passthru": true,
"mode": "number",
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"delay": "1000",
add sample_gear_net_opening and sample_concentrated_sample_volume improve #44
2020-11-29 23:44:09 +01:00
"topic": "sample_gear_net_opening",
"x": 620,
flow: better config management
2020-12-05 00:20:44 +01:00
"y": 320,
add sample_gear_net_opening and sample_concentrated_sample_volume improve #44
2020-11-29 23:44:09 +01:00
"wires": [
[
"9f501f49.45645"
]
]
},
{
"id": "8032ea50.1b57f",
"type": "ui_template",
"z": "baa1e3d9.cb29d",
"group": "b5d61bc7.54fe48",
"name": "progress header",
"order": 1,
"width": 0,
"height": 0,
"format": "<center><h2>Capture progress</h2></center>",
"storeOutMessages": false,
"fwdInMessages": false,
"resendOnRefresh": false,
"templateScope": "local",
flow: better config management
2020-12-05 00:20:44 +01:00
"x": 1270,
"y": 940,
add sample_gear_net_opening and sample_concentrated_sample_volume improve #44
2020-11-29 23:44:09 +01:00
"wires": [
[]
]
add usb backup UI
2020-12-01 21:12:29 +01:00
},
{
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"id": "eaf74a43.fa27d",
"type": "switch",
add usb backup UI
2020-12-01 21:12:29 +01:00
"z": "1371dec5.76e671",
"name": "",
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"property": "payload",
"propertyType": "msg",
"rules": [
add usb backup UI
2020-12-01 21:12:29 +01:00
{
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"t": "gte",
"v": "90",
"vt": "num"
add usb backup UI
2020-12-01 21:12:29 +01:00
}
],
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"checkall": "true",
"repair": false,
"outputs": 1,
"x": 490,
"y": 420,
add usb backup UI
2020-12-01 21:12:29 +01:00
"wires": [
[
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"24df077a.cb252"
add usb backup UI
2020-12-01 21:12:29 +01:00
]
]
},
{
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"id": "46d5e78b.15f998",
"type": "ui_toast",
add usb backup UI
2020-12-01 21:12:29 +01:00
"z": "1371dec5.76e671",
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"position": "dialog",
"displayTime": "10",
"highlight": "",
"sendall": true,
"outputs": 1,
"ok": "OK",
"cancel": "",
"raw": false,
add usb backup UI
2020-12-01 21:12:29 +01:00
"topic": "",
"name": "",
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"x": 790,
"y": 420,
add usb backup UI
2020-12-01 21:12:29 +01:00
"wires": [
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
[]
add usb backup UI
2020-12-01 21:12:29 +01:00
]
},
{
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"id": "24df077a.cb252",
add usb backup UI
2020-12-01 21:12:29 +01:00
"type": "change",
"z": "1371dec5.76e671",
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"name": "full disk msg",
add usb backup UI
2020-12-01 21:12:29 +01:00
"rules": [
{
"t": "set",
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"p": "payload",
add usb backup UI
2020-12-01 21:12:29 +01:00
"pt": "msg",
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"to": "\"Your drive has reached 90% capacity, you should do a backup to an external drive and a purge.\"",
"tot": "str"
add usb backup UI
2020-12-01 21:12:29 +01:00
}
],
"action": "",
"property": "",
"from": "",
"to": "",
"reg": false,
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"x": 630,
"y": 420,
add usb backup UI
2020-12-01 21:12:29 +01:00
"wires": [
[
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"46d5e78b.15f998"
add usb backup UI
2020-12-01 21:12:29 +01:00
]
]
},
{
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"id": "df1ea904.cd261",
"type": "ui_slider",
"z": "baa1e3d9.cb29d",
"name": "imaging_pump_volume",
"label": "Pumped volume (mL)",
"tooltip": "inbetween frames",
"group": "4322c187.e73e5",
add usb backup UI
2020-12-01 21:12:29 +01:00
"order": 3,
"width": 0,
"height": 0,
"passthru": false,
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"outs": "end",
"topic": "imaging_pump_volume",
"min": "0.01",
"max": "1",
"step": "0.01",
"x": 590,
"y": 320,
add usb backup UI
2020-12-01 21:12:29 +01:00
"wires": [
[
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"fb887036.12429",
"67091ac0.8f9f6c"
]
add usb backup UI
2020-12-01 21:12:29 +01:00
]
},
{
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"id": "a4abb1ae.2ae418",
"type": "subflow:1c24ad9c.bebec2",
"z": "baa1e3d9.cb29d",
"name": "",
"env": [],
flow: better config management
2020-12-05 00:20:44 +01:00
"x": 890,
"y": 540,
add usb backup UI
2020-12-01 21:12:29 +01:00
"wires": [
[]
]
},
{
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"id": "cfc783d7.d6ceb",
"type": "link in",
"z": "bccd1f23.87219",
"name": "Camera Name",
"links": [
"559a8085.1d6b9"
],
flow: better config management
2020-12-05 00:20:44 +01:00
"x": 1035,
"y": 200,
add usb backup UI
2020-12-01 21:12:29 +01:00
"wires": [
[
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"8038414a.34461"
add usb backup UI
2020-12-01 21:12:29 +01:00
]
]
},
{
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"id": "db44a49e.960558",
"type": "ui_dropdown",
"z": "b771c342.49603",
flow: addition of decknet flowmeter readings and better management of titles and location group activation
2020-12-04 22:24:20 +01:00
"name": "coordinates_type",
"label": "",
"tooltip": "Format of GPS coordinates",
"place": "",
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"group": "3e1ba03d.f01d8",
flow: addition of decknet flowmeter readings and better management of titles and location group activation
2020-12-04 22:24:20 +01:00
"order": 8,
"width": 8,
"height": 1,
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"passthru": true,
"multiple": false,
"options": [
add usb backup UI
2020-12-01 21:12:29 +01:00
{
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"label": "DD.DDDD° N (45.543° N)",
"value": "dd",
"type": "str"
add usb backup UI
2020-12-01 21:12:29 +01:00
},
{
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"label": "DD°MM.MMMM'N (45°54.534' N)",
"value": "ddm",
"type": "str"
add usb backup UI
2020-12-01 21:12:29 +01:00
}
],
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"payload": "",
"topic": "coordinates_type",
flow: location refactor using forms
2020-12-03 23:13:08 +01:00
"x": 650,
flow: addition of decknet flowmeter readings and better management of titles and location group activation
2020-12-04 22:24:20 +01:00
"y": 440,
add usb backup UI
2020-12-01 21:12:29 +01:00
"wires": [
[
flow: location refactor using forms
2020-12-03 23:13:08 +01:00
"6d281807.b003a"
add usb backup UI
2020-12-01 21:12:29 +01:00
]
]
},
{
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"id": "c0ce5626.b6c5",
add usb backup UI
2020-12-01 21:12:29 +01:00
"type": "ui_toast",
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"z": "b771c342.49603",
add usb backup UI
2020-12-01 21:12:29 +01:00
"position": "dialog",
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"displayTime": "3",
add usb backup UI
2020-12-01 21:12:29 +01:00
"highlight": "",
"sendall": true,
"outputs": 1,
"ok": "OK",
"cancel": "",
"raw": false,
"topic": "",
"name": "",
flow: addition of decknet flowmeter readings and better management of titles and location group activation
2020-12-04 22:24:20 +01:00
"x": 1070,
flow: location refactor using forms
2020-12-03 23:13:08 +01:00
"y": 540,
add usb backup UI
2020-12-01 21:12:29 +01:00
"wires": [
[]
]
},
{
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"id": "fc20cd7e.afaab8",
"type": "inject",
"z": "b771c342.49603",
"name": "Default: dd",
"props": [
{
"p": "payload"
},
{
"p": "topic",
"vt": "str"
}
],
"repeat": "",
"crontab": "",
"once": true,
"onceDelay": 0.1,
"topic": "coordinates_type",
"payload": "dd",
"payloadType": "str",
flow: location refactor using forms
2020-12-03 23:13:08 +01:00
"x": 450,
flow: addition of decknet flowmeter readings and better management of titles and location group activation
2020-12-04 22:24:20 +01:00
"y": 440,
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"wires": [
[
"db44a49e.960558"
]
]
},
{
"id": "33c28dc1.238002",
add usb backup UI
2020-12-01 21:12:29 +01:00
"type": "function",
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"z": "cb95299c.2817c8",
"name": "reset obj_counter",
"func": "global.set('obj_counter', 0);\n\nreturn msg;global.set('img_counter', 0);\nglobal.set('obj_counter', 0);\n",
add usb backup UI
2020-12-01 21:12:29 +01:00
"outputs": 1,
"noerr": 0,
"initialize": "",
"finalize": "",
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"x": 590,
"y": 300,
add usb backup UI
2020-12-01 21:12:29 +01:00
"wires": [
[
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"16f3cef4.0acac9"
add usb backup UI
2020-12-01 21:12:29 +01:00
]
]
},
{
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"id": "b9bf06d6.26c518",
"type": "exec",
"z": "f21ba04.c26266",
"command": "sudo iwlist wlan0 scan | grep ESSID | sed 's/ESSID://g;s/\"//g;s/^ *//;s/ *$//'",
"addpay": false,
"append": "",
"useSpawn": "false",
"timer": "",
"oldrc": false,
"name": "scan",
"x": 450,
"y": 80,
add usb backup UI
2020-12-01 21:12:29 +01:00
"wires": [
[
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"9642cb31.663b4"
],
[],
[]
add usb backup UI
2020-12-01 21:12:29 +01:00
]
},
{
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"id": "9642cb31.663b4",
"type": "function",
"z": "f21ba04.c26266",
"name": "parseOptions",
"func": "var ssids = msg.payload.split('\\n').filter(s => !!s)\n\nssids = [...new Set(ssids)];\n\nmsg.options = ssids\nmsg.payload = null\n\nreturn msg;",
add usb backup UI
2020-12-01 21:12:29 +01:00
"outputs": 1,
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"noerr": 0,
"x": 640,
"y": 80,
add usb backup UI
2020-12-01 21:12:29 +01:00
"wires": [
[
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"dbc0d44.5361b28"
add usb backup UI
2020-12-01 21:12:29 +01:00
]
]
},
{
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"id": "3db572cd.cf972e",
"type": "inject",
"z": "f21ba04.c26266",
"name": "once",
"props": [
{
"p": "payload"
},
{
"p": "topic",
"vt": "str"
}
],
"repeat": "",
"crontab": "",
"once": true,
"onceDelay": 0.1,
add usb backup UI
2020-12-01 21:12:29 +01:00
"topic": "",
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"payload": "",
"payloadType": "date",
"x": 270,
"y": 180,
"wires": [
[
"b9bf06d6.26c518",
"4c0400c.69a1e8",
"448b4c37.be50bc"
]
]
},
{
"id": "dbc0d44.5361b28",
"type": "ui_dropdown",
"z": "f21ba04.c26266",
add usb backup UI
2020-12-01 21:12:29 +01:00
"name": "",
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"label": "Wifi",
"tooltip": "",
"place": "Select a WIFI",
"group": "9e409235.73cd7",
"order": 2,
"width": 0,
"height": 0,
"passthru": false,
"multiple": false,
"options": [],
"payload": "",
"topic": "",
"x": 830,
"y": 80,
"wires": [
[
"cdfa9013.b91278"
]
]
add usb backup UI
2020-12-01 21:12:29 +01:00
},
{
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"id": "2bf338e3.966468",
"type": "ui_button",
"z": "f21ba04.c26266",
add usb backup UI
2020-12-01 21:12:29 +01:00
"name": "",
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"group": "9e409235.73cd7",
"order": 1,
"width": 0,
"height": 0,
"passthru": false,
"label": "Scan",
"tooltip": "",
"color": "",
"bgcolor": "",
"icon": "fa-wifi fa-2x",
"payload": "true",
"payloadType": "bool",
"topic": "",
"x": 270,
"y": 40,
"wires": [
[
"b9bf06d6.26c518"
]
]
},
{
"id": "63b885ac.46f384",
"type": "switch",
"z": "f21ba04.c26266",
"name": "ifWifi",
"property": "name",
add usb backup UI
2020-12-01 21:12:29 +01:00
"propertyType": "msg",
"rules": [
{
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"t": "eq",
"v": "Wifi",
add usb backup UI
2020-12-01 21:12:29 +01:00
"vt": "str"
}
],
"checkall": "true",
"repair": false,
"outputs": 1,
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"x": 271,
"y": 80,
add usb backup UI
2020-12-01 21:12:29 +01:00
"wires": [
[
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"b9bf06d6.26c518",
"4c0400c.69a1e8",
"448b4c37.be50bc"
add usb backup UI
2020-12-01 21:12:29 +01:00
]
]
},
{
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"id": "4c0400c.69a1e8",
add usb backup UI
2020-12-01 21:12:29 +01:00
"type": "exec",
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"z": "f21ba04.c26266",
"command": "ifconfig wlan0",
add usb backup UI
2020-12-01 21:12:29 +01:00
"addpay": false,
"append": "",
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"useSpawn": "false",
add usb backup UI
2020-12-01 21:12:29 +01:00
"timer": "",
"oldrc": false,
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"name": "getInfo",
"x": 460,
"y": 180,
add usb backup UI
2020-12-01 21:12:29 +01:00
"wires": [
[
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"bcb20e39.00cea8"
add usb backup UI
2020-12-01 21:12:29 +01:00
],
[],
[]
]
},
{
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"id": "bcb20e39.00cea8",
"type": "function",
"z": "f21ba04.c26266",
"name": "parseInfo",
"func": "var ip = msg.payload.match(/inet ([0-9\\.]+)/)[1]\nvar mask = msg.payload.match(/netmask ([0-9\\.]+)/)[1]\nvar broadcast = msg.payload.match(/broadcast ([0-9\\.]+)/)[1]\n\n\nnode.send({topic: 'ip', payload: ip})\nnode.send({topic: 'mask', payload: mask})\nnode.send({topic: 'broadcast', payload: broadcast})",
"outputs": 1,
"noerr": 0,
"x": 640,
"y": 180,
"wires": [
[
"b10ebb83.8214a8"
]
]
},
{
"id": "b10ebb83.8214a8",
add usb backup UI
2020-12-01 21:12:29 +01:00
"type": "switch",
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"z": "f21ba04.c26266",
add usb backup UI
2020-12-01 21:12:29 +01:00
"name": "",
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"property": "topic",
add usb backup UI
2020-12-01 21:12:29 +01:00
"propertyType": "msg",
"rules": [
{
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"t": "eq",
"v": "ip",
"vt": "str"
},
{
"t": "eq",
"v": "mask",
"vt": "str"
},
{
"t": "eq",
"v": "broadcast",
"vt": "str"
add usb backup UI
2020-12-01 21:12:29 +01:00
}
],
"checkall": "true",
"repair": false,
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"outputs": 3,
"x": 810,
"y": 181,
add usb backup UI
2020-12-01 21:12:29 +01:00
"wires": [
[
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"d71c8185.800fd"
],
[
"67d052ba.99ff24"
],
[
"dc305a26.b33fc"
add usb backup UI
2020-12-01 21:12:29 +01:00
]
]
},
{
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"id": "d71c8185.800fd",
"type": "ui_text",
"z": "f21ba04.c26266",
"group": "919923a3.d10868",
"order": 2,
"width": 0,
"height": 0,
add usb backup UI
2020-12-01 21:12:29 +01:00
"name": "",
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"label": "IP",
"format": "{{msg.payload || '---'}}",
"layout": "row-spread",
"x": 990,
"y": 141,
"wires": []
add usb backup UI
2020-12-01 21:12:29 +01:00
},
{
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"id": "67d052ba.99ff24",
"type": "ui_text",
"z": "f21ba04.c26266",
"group": "919923a3.d10868",
"order": 3,
"width": 0,
"height": 0,
"name": "",
"label": "Netmask",
"format": "{{msg.payload || '---'}}",
"layout": "row-spread",
"x": 1000,
"y": 181,
"wires": []
Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
2020-12-02 19:26:27 +01:00
},
{
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"id": "dc305a26.b33fc",
"type": "ui_text",
"z": "f21ba04.c26266",
"group": "919923a3.d10868",
"order": 4,
Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
2020-12-02 19:26:27 +01:00
"width": 0,
"height": 0,
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"name": "",
"label": "Broadcast",
"format": "{{msg.payload || '---'}}",
"layout": "row-spread",
"x": 1010,
"y": 220,
"wires": []
Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
2020-12-02 19:26:27 +01:00
},
{
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"id": "94b2e8fc.aa20e",
"type": "ui_form",
"z": "f21ba04.c26266",
Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
2020-12-02 19:26:27 +01:00
"name": "",
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"label": "Update",
"group": "9e409235.73cd7",
"order": 3,
"width": 0,
"height": 0,
"options": [
{
"label": "SSID",
"value": "ssid",
"type": "text",
"required": true,
"rows": null
},
{
"label": "Password",
"value": "password",
"type": "password",
"required": true,
"rows": null
}
],
"formValue": {
"ssid": "",
"password": ""
},
"payload": "",
"submit": "UPDATE",
"cancel": "RESET",
"topic": "",
"x": 1160,
"y": 80,
Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
2020-12-02 19:26:27 +01:00
"wires": [
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
[
"d59021e3.1b63e8"
]
Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
2020-12-02 19:26:27 +01:00
]
},
{
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"id": "cdfa9013.b91278",
Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
2020-12-02 19:26:27 +01:00
"type": "function",
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"z": "f21ba04.c26266",
"name": "insert ssid",
"func": "\nmsg.payload = {ssid: msg.payload}\n\nreturn msg;",
Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
2020-12-02 19:26:27 +01:00
"outputs": 1,
"noerr": 0,
"initialize": "",
"finalize": "",
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"x": 990,
"y": 80,
Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
2020-12-02 19:26:27 +01:00
"wires": [
[
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"94b2e8fc.aa20e"
Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
2020-12-02 19:26:27 +01:00
]
]
},
{
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"id": "448b4c37.be50bc",
"type": "exec",
"z": "f21ba04.c26266",
"command": "iwgetid",
"addpay": false,
"append": "",
"useSpawn": "false",
"timer": "",
"oldrc": false,
"name": "getCurrentSSID",
"x": 480,
"y": 260,
Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
2020-12-02 19:26:27 +01:00
"wires": [
[
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"151819d4.0dbe56"
],
[],
[]
]
},
{
"id": "c8a5ae48.ef1308",
"type": "ui_text",
"z": "f21ba04.c26266",
"group": "919923a3.d10868",
"order": 1,
"width": 0,
"height": 0,
"name": "",
"label": "SSID",
"format": "{{msg.payload || '---'}}",
"layout": "row-spread",
"x": 990,
"y": 260,
"wires": []
},
{
"id": "151819d4.0dbe56",
"type": "function",
"z": "f21ba04.c26266",
"name": "parseInfo",
"func": "var ssid = msg.payload.match(/ESSID:\"([^\"]+)\"/)[1]\n\n\nnode.send({topic: 'ssid', payload: ssid})\n",
"outputs": 1,
"noerr": 0,
"x": 720,
"y": 260,
"wires": [
[
"c8a5ae48.ef1308"
]
]
},
{
"id": "ff059f3f.9c0f28",
"type": "ui_ui_control",
"z": "f21ba04.c26266",
"name": "onTab",
"events": "all",
"x": 130,
"y": 80,
"wires": [
[
"63b885ac.46f384"
]
]
},
{
"id": "167d7bd0.679ce4",
"type": "function",
"z": "f21ba04.c26266",
"name": "update contry code",
"func": "var template = `sudo sed -i \\\"s/^country.*/country=\"${msg.payload}\"/\\\" /home/pi/wpa_supplicant.conf`\n// sudo tee /etc/wpa_supplicant/wpa_supplicant.conf <<EOF\n//ctrl_interface=DIR=/var/run/wpa_supplicant GROUP=netdev\n//update_config=1\n//country=IT\nmsg.payload = template\n\nreturn msg;",
"outputs": 1,
"noerr": 0,
"initialize": "",
"finalize": "",
"x": 630,
"y": 400,
"wires": [
[
fix WiFi bug
2020-12-04 21:25:07 +01:00
"9d30f7b5.aac88"
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
]
]
},
{
"id": "9d30f7b5.aac88",
"type": "exec",
"z": "f21ba04.c26266",
"command": "",
"addpay": true,
"append": "",
"useSpawn": "false",
"timer": "",
"oldrc": false,
"name": "updateConf",
"x": 890,
"y": 400,
"wires": [
fix WiFi bug
2020-12-04 21:25:07 +01:00
[],
[],
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
[]
]
},
{
"id": "deb8c14e.ff1fd",
"type": "ui_button",
"z": "f21ba04.c26266",
"name": "",
"group": "9e409235.73cd7",
"order": 6,
"width": 0,
"height": 0,
"passthru": false,
"label": "Change Country Code",
"tooltip": "",
"color": "",
"bgcolor": "",
"icon": "",
"payload": "country_code",
"payloadType": "flow",
"topic": "",
"x": 400,
"y": 400,
"wires": [
[
"167d7bd0.679ce4"
]
]
},
{
"id": "6d4ce391.04abf4",
"type": "ui_text_input",
"z": "f21ba04.c26266",
"name": "country_code",
"label": "Country Code",
"tooltip": "ISO/IEC alpha2 country code",
"group": "9e409235.73cd7",
"order": 5,
"width": 0,
"height": 0,
"passthru": true,
"mode": "text",
"delay": "500",
"topic": "country_code",
"x": 420,
"y": 360,
"wires": [
[
"3f60469d.620aea"
]
]
},
{
"id": "3f60469d.620aea",
"type": "change",
"z": "f21ba04.c26266",
"name": "",
"rules": [
{
"t": "set",
"p": "country_code",
"pt": "flow",
"to": "payload",
"tot": "msg"
}
],
"action": "",
"property": "",
"from": "",
"to": "",
"reg": false,
"x": 640,
"y": 360,
"wires": [
[]
]
},
{
"id": "4f02c726.de69b8",
"type": "ui_button",
"z": "9daf9e2b.019fc",
"name": "",
"group": "1be83144.4fe4bf",
"order": 10,
"width": 2,
"height": 1,
"passthru": false,
"label": "Reboot",
"tooltip": "",
"color": "",
"bgcolor": "#AD1625",
"icon": "fa-repeat fa-2x",
"payload": "reboot",
"payloadType": "str",
"topic": "reboot",
"x": 400,
"y": 420,
"wires": [
[
"4af9112d.87767"
]
]
},
{
"id": "611a8b1c.a829b4",
"type": "exec",
"z": "9daf9e2b.019fc",
"command": "sudo",
"addpay": true,
"append": "now",
"useSpawn": "false",
"timer": "2",
"oldrc": false,
"name": "cmd",
"x": 870,
"y": 460,
"wires": [
[],
[],
[]
]
},
{
"id": "bc76c4d6.a7ad28",
"type": "ui_button",
"z": "9daf9e2b.019fc",
"name": "",
"group": "1be83144.4fe4bf",
"order": 8,
"width": 2,
"height": 1,
"passthru": false,
"label": "Shutdown",
"tooltip": "",
"color": "",
"bgcolor": "#AD1625",
"icon": "fa-power-off fa-2x",
"payload": "shutdown",
"payloadType": "str",
"topic": "shutdown",
"x": 390,
"y": 500,
"wires": [
[
"4af9112d.87767"
]
]
},
{
"id": "4af9112d.87767",
"type": "python3-function",
"z": "9daf9e2b.019fc",
"name": "action",
"func": "#!/usr/bin/python\nimport smbus\n\nbus = smbus.SMBus(1)\n#turn off LED\nbus.write_byte_data(0x0d, 0x07, 0x00)\n#turn off Fan\nbus.write_byte_data(0x0d, 0x08, 0x00)\n\n#msg[\"payload\"] = str(msg[\"topic\"])+' now'\nreturn msg",
"outputs": 1,
"x": 690,
"y": 460,
"wires": [
[
"611a8b1c.a829b4"
]
]
},
{
"id": "fa914867.0a0658",
"type": "exec",
"z": "9daf9e2b.019fc",
"command": "python3 -u /home/pi/PlanktonScope/scripts/main.py",
"addpay": false,
"append": "",
"useSpawn": "true",
"timer": "",
"oldrc": false,
"name": "",
"x": 1100,
"y": 340,
"wires": [
[],
[
"8b511c2b.9c24c8"
],
[]
]
},
{
"id": "1575db82.742854",
"type": "delay",
"z": "9daf9e2b.019fc",
"name": "",
"pauseType": "delay",
"timeout": "5",
"timeoutUnits": "seconds",
"rate": "1",
"nbRateUnits": "1",
"rateUnits": "second",
"randomFirst": "1",
"randomLast": "5",
"randomUnits": "seconds",
"drop": false,
"x": 700,
"y": 340,
"wires": [
[
"fa914867.0a0658"
]
]
},
{
"id": "466eb611.4da048",
"type": "ui_button",
"z": "9daf9e2b.019fc",
"name": "Restart Python",
"group": "1be83144.4fe4bf",
"order": 6,
"width": 4,
"height": 1,
"passthru": true,
"label": "Restart Python",
"tooltip": "",
"color": "",
"bgcolor": "#AD1625",
"icon": "fa-refresh fa-2x",
"payload": "",
"payloadType": "str",
"topic": "",
"x": 380,
"y": 340,
"wires": [
[
"1575db82.742854",
"bd5cceef.b17ad",
"ed7503f3.d95a48"
]
]
},
{
"id": "ed7503f3.d95a48",
"type": "exec",
"z": "9daf9e2b.019fc",
"command": "sudo killall -15 python3",
"addpay": false,
"append": "",
"useSpawn": "false",
"timer": "",
"oldrc": false,
"name": "Python soft kill",
"x": 720,
"y": 400,
"wires": [
[],
[],
[]
]
},
{
"id": "bd5cceef.b17ad",
"type": "exec",
"z": "9daf9e2b.019fc",
"command": "sudo killall -15 raspimjpeg",
"addpay": false,
"append": "",
"useSpawn": "false",
"timer": "",
"oldrc": false,
"name": "Raspimjpeg soft kill",
"x": 730,
"y": 280,
"wires": [
[],
[],
[]
]
},
{
"id": "d12008a0.47be4",
"type": "ui_template",
"z": "9daf9e2b.019fc",
"group": "a7d64879.38298",
"name": "Log table",
"order": 1,
"width": 12,
"height": 10,
"format": "<script type=\"text/javascript\">\n function selectElementContents(el) {\n var body = document.body, range, sel;\n if (document.createRange && window.getSelection) {\n range = document.createRange();\n sel = window.getSelection();\n sel.removeAllRanges();\n try {\n range.selectNodeContents(el);\n sel.addRange(range);\n } catch (e) {\n range.selectNode(el);\n sel.addRange(range);\n }\n document.execCommand(\"copy\");\n sel.removeAllRanges();\n\n } else if (body.createTextRange) {\n range = body.createTextRange();\n range.moveToElementText(el);\n range.select();\n range.execCommand(\"Copy\");\n }\n }\n</script>\n\n<md-button onclick=\"selectElementContents( document.getElementById('log_table') );\">\n <i class=\"fa fa-copy fa-1x\"></i> Copy Log\n</md-button>\n\n<table id=\"log_table\" style=\"font-family: mono;font-size: 5px;\">\n <tr ng-repeat=\"row in msg.payload\">\n <td>{{row}}</td>\n </tr>\n</table>\n\n",
"storeOutMessages": false,
"fwdInMessages": false,
"resendOnRefresh": false,
"templateScope": "local",
"x": 1660,
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"wires": [
[]
]
},
{
"id": "8b511c2b.9c24c8",
"type": "function",
"z": "9daf9e2b.019fc",
"name": "Log array",
flow: set log to flow context
2020-12-05 03:10:25 +01:00
"func": "var log = flow.get(\"python_log\")||[];\n\nlog = log.concat(msg.payload.trim().split('\\n'));\n\nwhile (log.length > 500){\n log.shift();\n}\n\nflow.set(\"python_log\", log);\n\nmsg.payload = log;\nreturn msg;",
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"outputs": 1,
"noerr": 0,
"initialize": "",
"finalize": "",
"x": 1480,
flow: better config management
2020-12-05 00:20:44 +01:00
"y": 300,
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"wires": [
[
"d12008a0.47be4"
]
]
},
{
"id": "7a1dedf.1c63094",
"type": "ui_button",
"z": "9daf9e2b.019fc",
"name": "",
"group": "a7d64879.38298",
"order": 2,
"width": 0,
"height": 0,
"passthru": false,
"label": "Clear Log",
"tooltip": "",
"color": "",
"bgcolor": "",
"icon": "fa-eraser",
"payload": "",
"payloadType": "str",
"topic": "",
"x": 1320,
"y": 460,
"wires": [
[
"73500be7.9ab7c4"
]
]
},
{
"id": "9187bf97.9922b8",
"type": "catch",
"z": "9daf9e2b.019fc",
"name": "Catch Errors",
"scope": null,
"uncaught": false,
"x": 1070,
flow: better config management
2020-12-05 00:20:44 +01:00
"y": 400,
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"wires": [
[
"f9a871d5.a73828"
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},
{
"id": "f9a871d5.a73828",
"type": "function",
"z": "9daf9e2b.019fc",
"name": "Get error",
"func": "msg.payload = \"Node Red Error: \" + msg.error + \" created by the message \" + msg.payload;\nreturn msg;",
"outputs": 1,
"noerr": 0,
"initialize": "",
"finalize": "",
"x": 1240,
flow: better config management
2020-12-05 00:20:44 +01:00
"y": 400,
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"wires": [
[
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},
{
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"name": "Clear log",
flow: set log to flow context
2020-12-05 03:10:25 +01:00
"func": "flow.set(\"python_log\", []);\n\nmsg.payload = [];\nreturn msg;",
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"outputs": 1,
"noerr": 0,
"initialize": "",
"finalize": "",
"x": 1480,
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"wires": [
[
"d12008a0.47be4"
]
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},
{
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"name": "once",
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{
"p": "payload"
}
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"repeat": "",
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"onceDelay": "",
"topic": "",
"payload": "start",
"payloadType": "str",
"x": 130,
"y": 340,
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[
"466eb611.4da048"
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},
{
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"name": "",
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"order": 1,
"width": 4,
"height": 1,
"passthru": false,
"label": "Home",
"tooltip": "",
"color": "",
"bgcolor": "",
"icon": "home",
"payload": "{\"tab\":\"Home\"}",
"payloadType": "json",
"topic": "",
"x": 430,
"y": 740,
"wires": [
[
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},
{
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"name": "",
"events": "change",
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"y": 740,
"wires": [
[]
]
},
{
"id": "43cf8ff7.75231",
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"set": true,
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"freq": "",
"out": "out",
"x": 420,
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"wires": []
},
{
"id": "4bca8a25.15be3c",
"type": "rpi-gpio out",
"z": "9daf9e2b.019fc",
"name": "Focus Enable",
"pin": "32",
"set": true,
"level": "1",
"freq": "",
"out": "out",
"x": 420,
"y": 120,
"wires": []
},
{
"id": "50f9b5b.a84bccc",
"type": "inject",
"z": "9daf9e2b.019fc",
"name": "Default: ON",
"props": [
{
"p": "payload"
}
],
"repeat": "",
"crontab": "",
"once": true,
"onceDelay": "0.01",
"topic": "",
"payload": "true",
"payloadType": "bool",
"x": 150,
"y": 100,
"wires": [
[
"43cf8ff7.75231",
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},
{
"id": "8bd1f3dc.9affe8",
"type": "exec",
"z": "9daf9e2b.019fc",
"command": "",
"addpay": true,
"append": "",
"useSpawn": "false",
"timer": "1",
"oldrc": false,
"name": "git user.name",
"x": 1400,
"y": 60,
"wires": [
[],
[],
[]
]
},
{
"id": "b40d1f65.39e14",
"type": "template",
"z": "9daf9e2b.019fc",
"name": "git config",
"field": "payload",
"fieldType": "msg",
"format": "handlebars",
"syntax": "mustache",
"template": "git config --global --replace-all user.name \"{{payload}}\"",
"output": "str",
"x": 1220,
"y": 60,
"wires": [
[
"8bd1f3dc.9affe8"
]
]
},
{
"id": "35eb925e.5f8016",
"type": "link in",
"z": "9daf9e2b.019fc",
"name": "Git config",
"links": [
flow: addition of decknet flowmeter readings and better management of titles and location group activation
2020-12-04 22:24:20 +01:00
"52af9ac0.60eb24",
"3caed565.fad25a"
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
],
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},
{
"id": "4e5183bd.e77bac",
"type": "exec",
"z": "9daf9e2b.019fc",
"command": "",
"addpay": true,
"append": "",
"useSpawn": "false",
"timer": "1",
"oldrc": false,
"name": "git user.email",
"x": 1390,
"y": 140,
"wires": [
[],
[],
[]
]
},
{
"id": "6d7dd372.3b7814",
"type": "template",
"z": "9daf9e2b.019fc",
"name": "git config",
"field": "payload",
"fieldType": "msg",
"format": "handlebars",
"syntax": "mustache",
"template": "git config --global --replace-all user.email \"{{payload}}\"",
"output": "str",
"x": 1220,
"y": 140,
"wires": [
[
"4e5183bd.e77bac"
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]
},
{
"id": "e564e9ad.7c312",
"type": "ui_button",
"z": "9daf9e2b.019fc",
"name": "Update",
"group": "1be83144.4fe4bf",
"order": 3,
"width": 6,
"height": 1,
"passthru": false,
"label": "Update",
"tooltip": "",
"color": "",
"bgcolor": "",
"icon": "mi-system_update",
"payload": "",
"payloadType": "str",
"topic": "update",
"x": 400,
"y": 220,
"wires": [
[
"2d2ef1fd.40e6e6"
]
]
},
{
"id": "2d2ef1fd.40e6e6",
"type": "exec",
"z": "9daf9e2b.019fc",
"command": "bash /home/pi/PlanktonScope/scripts/bash/update.sh",
"addpay": false,
"append": "",
"useSpawn": "true",
"timer": "",
"oldrc": false,
"name": "Update",
"x": 700,
"y": 220,
"wires": [
[
flow: add update output to log
2020-12-03 13:23:25 +01:00
"64f61762.68c788",
"8b511c2b.9c24c8"
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
],
gallery: finishing installing thumbsup
2020-12-03 14:19:13 +01:00
[
"64f61762.68c788",
"8b511c2b.9c24c8"
],
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
[]
]
},
{
"id": "8f08c4eb.db74b8",
"type": "ui_template",
"z": "9daf9e2b.019fc",
"group": "1be83144.4fe4bf",
"name": "Update message",
"order": 1,
"width": 12,
"height": 2,
"format": "<div><center>If you want to update to the latest code version of Node-Red and Python, please click here.\nWe are trying to save your configuration changes with git stash and restore them afterwards, but clearly, things may break!\nIf you have made changes to the flow, you will lose them. Please commit those changes from Node-Red interface, from the Project History tab.</center></div>",
"storeOutMessages": true,
"fwdInMessages": true,
"resendOnRefresh": true,
"templateScope": "local",
"x": 390,
"y": 180,
"wires": [
[]
]
},
{
"id": "64f61762.68c788",
"type": "ui_toast",
"z": "9daf9e2b.019fc",
"position": "dialog",
"displayTime": "10",
"highlight": "",
"sendall": true,
"outputs": 1,
"ok": "OK",
"cancel": "",
"raw": false,
"topic": "",
"name": "Update notif",
"x": 970,
flow: better config management
2020-12-05 00:20:44 +01:00
"y": 200,
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"wires": [
[]
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},
{
"id": "d59021e3.1b63e8",
"type": "function",
"z": "f21ba04.c26266",
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"noerr": 0,
"initialize": "",
"finalize": "",
"x": 1330,
"y": 80,
"wires": [
[
"64a1f2f2.3de8b4"
Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
2020-12-02 19:26:27 +01:00
]
]
},
{
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"id": "64a1f2f2.3de8b4",
"type": "exec",
"z": "f21ba04.c26266",
"command": "",
"addpay": true,
"append": "",
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"timer": "",
"oldrc": false,
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"x": 1520,
"y": 80,
"wires": [
[
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[]
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},
{
"id": "6868b4c4.65987c",
"type": "exec",
"z": "f21ba04.c26266",
fix WiFi bug
2020-12-04 21:25:07 +01:00
"command": "sudo /usr/bin/autohotspotN >/dev/null",
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"addpay": false,
"append": "",
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"timer": "",
"oldrc": false,
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[
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[]
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{
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"type": "function",
"z": "f21ba04.c26266",
"name": "showMessage",
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"noerr": 0,
"initialize": "",
"finalize": "",
flow: better config management
2020-12-05 00:20:44 +01:00
"x": 1440,
"y": 180,
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"wires": [
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]
},
{
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"type": "ui_toast",
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"highlight": "",
"sendall": true,
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"ok": "OK",
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"raw": false,
"topic": "",
"name": "",
flow: better config management
2020-12-05 00:20:44 +01:00
"x": 1670,
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flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"wires": []
},
{
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Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
2020-12-02 19:26:27 +01:00
"type": "ui_dropdown",
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"z": "1371dec5.76e671",
Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
2020-12-02 19:26:27 +01:00
"name": "",
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"label": "",
Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
2020-12-02 19:26:27 +01:00
"tooltip": "",
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"place": "Choose USB device",
"group": "52d1b77.28369c8",
"order": 2,
Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
2020-12-02 19:26:27 +01:00
"width": 0,
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flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"passthru": false,
Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
2020-12-02 19:26:27 +01:00
"multiple": false,
"options": [
{
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"label": "",
"value": "No Drive Detected",
Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
2020-12-02 19:26:27 +01:00
"type": "str"
}
],
"payload": "",
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"topic": "device_path",
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Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
2020-12-02 19:26:27 +01:00
"wires": [
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flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"d1b9fed3.f3ead8"
Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
2020-12-02 19:26:27 +01:00
]
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},
{
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"id": "fe29acc2.c25d18",
"type": "ui_button",
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"name": "Detect drive",
"group": "52d1b77.28369c8",
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"width": 0,
"height": 0,
"passthru": false,
"label": "Detect drive",
"tooltip": "",
"color": "",
"bgcolor": "",
"icon": "fa-usb fa-2x",
"payload": "",
"payloadType": "str",
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"x": 150,
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Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
2020-12-02 19:26:27 +01:00
"wires": [
[
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"4c00cd96.6b2f6c"
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{
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[
"2dc1e43d.cd3d64"
Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
2020-12-02 19:26:27 +01:00
],
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
[],
[]
]
},
{
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"pretty": false,
"x": 490,
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"wires": [
Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
2020-12-02 19:26:27 +01:00
[
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"6b730649.09351"
Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
2020-12-02 19:26:27 +01:00
]
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
]
},
{
"id": "6b730649.09351",
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"z": "1371dec5.76e671",
"name": "",
"rules": [
{
"t": "set",
"p": "options",
"pt": "msg",
"to": "[payload.blockdevices.children[mountpoint=null].name]",
"tot": "jsonata"
}
Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
2020-12-02 19:26:27 +01:00
],
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"action": "",
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"from": "",
"to": "",
"reg": false,
"x": 660,
"y": 820,
"wires": [
[
"f30bf784.90d58"
]
Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
2020-12-02 19:26:27 +01:00
]
},
{
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"id": "1ece8d8e.1008e2",
"type": "ui_button",
"z": "1371dec5.76e671",
"name": "Backup to USB",
"group": "52d1b77.28369c8",
"order": 3,
"width": 0,
"height": 0,
"passthru": false,
"label": "Backup to USB",
"tooltip": "",
"color": "",
"bgcolor": "",
"icon": "archive",
"payload": "",
"payloadType": "str",
Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
2020-12-02 19:26:27 +01:00
"topic": "",
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"x": 160,
"y": 900,
Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
2020-12-02 19:26:27 +01:00
"wires": [
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
[
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]
Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
2020-12-02 19:26:27 +01:00
]
},
{
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"id": "d1b9fed3.f3ead8",
Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
2020-12-02 19:26:27 +01:00
"type": "function",
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"z": "1371dec5.76e671",
Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
2020-12-02 19:26:27 +01:00
"name": "set local",
"func": "flow.set(msg.topic,msg.payload);",
"outputs": 1,
"noerr": 0,
"initialize": "",
"finalize": "",
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"x": 1000,
"y": 820,
Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
2020-12-02 19:26:27 +01:00
"wires": [
[]
]
},
{
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"id": "6b2fed77.883c0c",
"type": "function",
"z": "1371dec5.76e671",
"name": "get device_path",
"func": "msg.payload = flow.get(\"device_path\");\nreturn msg",
"outputs": 1,
"noerr": 0,
"initialize": "",
"finalize": "",
"x": 360,
"y": 900,
"wires": [
[
"df4d4d6a.24787"
]
]
},
{
"id": "c74fe76.bcba718",
"type": "exec",
"z": "1371dec5.76e671",
"command": "sudo /home/pi/PlanktonScope/scripts/bash/usb_backup.sh",
"addpay": true,
"append": "",
"useSpawn": "true",
"timer": "",
"oldrc": false,
"name": "usb_backup.sh",
"x": 700,
"y": 920,
"wires": [
[
"72f5e8d4.40fcb8"
],
[],
[
"a2c36500.6d376"
]
]
},
{
"id": "df4d4d6a.24787",
"type": "switch",
"z": "1371dec5.76e671",
"name": "",
"property": "payload",
"propertyType": "msg",
"rules": [
Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
2020-12-02 19:26:27 +01:00
{
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"t": "eq",
"v": "No Drive Detected",
"vt": "str"
Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
2020-12-02 19:26:27 +01:00
},
{
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"t": "else"
Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
2020-12-02 19:26:27 +01:00
}
],
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"checkall": "false",
"repair": false,
"outputs": 2,
"x": 530,
"y": 900,
Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
2020-12-02 19:26:27 +01:00
"wires": [
[
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"9a577caa.1535a"
],
[
"c74fe76.bcba718"
Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
2020-12-02 19:26:27 +01:00
]
]
},
{
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"id": "9a577caa.1535a",
"type": "ui_toast",
"z": "1371dec5.76e671",
"position": "dialog",
"displayTime": "5",
"highlight": "",
"sendall": true,
Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
2020-12-02 19:26:27 +01:00
"outputs": 1,
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"ok": "OK",
"cancel": "",
"raw": false,
"topic": "",
"name": "",
"x": 690,
"y": 880,
Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
2020-12-02 19:26:27 +01:00
"wires": [
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
[]
Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
2020-12-02 19:26:27 +01:00
]
},
{
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"id": "72f5e8d4.40fcb8",
"type": "ui_toast",
Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
2020-12-02 19:26:27 +01:00
"z": "1371dec5.76e671",
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"position": "top right",
"displayTime": "5",
"highlight": "",
"sendall": true,
"outputs": 0,
"ok": "OK",
"cancel": "",
"raw": false,
"topic": "",
"name": "",
"x": 910,
"y": 900,
"wires": []
},
{
"id": "81a48376.27a66",
"type": "ui_toast",
"z": "1371dec5.76e671",
"position": "dialog",
"displayTime": "5",
"highlight": "",
"sendall": true,
"outputs": 1,
"ok": "OK",
"cancel": "",
"raw": false,
"topic": "",
"name": "",
"x": 1070,
Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
2020-12-02 19:26:27 +01:00
"y": 940,
"wires": [
[]
]
},
{
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"id": "a2c36500.6d376",
Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
2020-12-02 19:26:27 +01:00
"type": "function",
"z": "1371dec5.76e671",
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"name": "error message",
"func": "switch (msg.payload.code){\ncase 0:\n msg.payload = \"All files successfully copied, you can remove your usb drive!\";\n break;\ncase 1:\n msg.payload = \"There was an error!\";\n break;\ncase 2:\n msg.payload = \"Error: your device is already mounted\"\n break;\ncase 3:\n msg.payload = \"Error while mounting the device\"\n break;\ncase 4:\n msg.payload = \"Error: some files were corrupted during the copy!\"\n break;\n}\nreturn msg;",
Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
2020-12-02 19:26:27 +01:00
"outputs": 1,
"noerr": 0,
"initialize": "",
"finalize": "",
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"x": 900,
Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
2020-12-02 19:26:27 +01:00
"y": 940,
"wires": [
[
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"81a48376.27a66"
Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
2020-12-02 19:26:27 +01:00
]
]
},
{
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"id": "dde0025c.3df9f",
Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
2020-12-02 19:26:27 +01:00
"type": "ui_button",
"z": "1371dec5.76e671",
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"name": "Purge local",
"group": "52d1b77.28369c8",
"order": 4,
Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
2020-12-02 19:26:27 +01:00
"width": 0,
"height": 0,
"passthru": false,
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"label": "Purge local data",
Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
2020-12-02 19:26:27 +01:00
"tooltip": "",
"color": "",
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"bgcolor": "#AD1625",
"icon": "delete_forever",
"payload": "THIS IS GOING TO WIPE ALL THE LOCAL DATA. MAKE SURE YOU DID A BACKUP TO AN USB DRIVE BEFOREHAND.",
Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
2020-12-02 19:26:27 +01:00
"payloadType": "str",
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"topic": "BE EXTRA CAREFUL",
"x": 150,
"y": 980,
Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
2020-12-02 19:26:27 +01:00
"wires": [
[
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"ba72704a.8a38a"
Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
2020-12-02 19:26:27 +01:00
]
]
},
{
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"id": "ba72704a.8a38a",
"type": "ui_toast",
Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
2020-12-02 19:26:27 +01:00
"z": "1371dec5.76e671",
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"position": "dialog",
"displayTime": "5",
"highlight": "",
"sendall": true,
"outputs": 1,
"ok": "GO BACK",
"cancel": "YES I'M SURE, I WANT TO PURGE THE DATA",
"raw": false,
"topic": "",
"name": "",
"x": 370,
Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
2020-12-02 19:26:27 +01:00
"y": 980,
"wires": [
[
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"d80e6307.3aaf8"
Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
2020-12-02 19:26:27 +01:00
]
]
},
{
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"id": "b57cc390.f055c8",
"type": "ui_toast",
Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
2020-12-02 19:26:27 +01:00
"z": "1371dec5.76e671",
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"position": "top right",
"displayTime": "5",
"highlight": "",
"sendall": true,
"outputs": 0,
"ok": "OK",
"cancel": "",
"raw": false,
"topic": "",
"name": "",
"x": 870,
"y": 980,
"wires": []
},
{
"id": "d80e6307.3aaf8",
"type": "switch",
"z": "1371dec5.76e671",
"name": "",
"property": "payload",
"propertyType": "msg",
"rules": [
{
"t": "cont",
"v": "YES I'M SURE",
"vt": "str"
}
],
"checkall": "true",
"repair": false,
Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
2020-12-02 19:26:27 +01:00
"outputs": 1,
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"x": 530,
Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
2020-12-02 19:26:27 +01:00
"y": 980,
"wires": [
[
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"4a8cb5d4.52e4bc"
Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
2020-12-02 19:26:27 +01:00
]
]
},
{
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"id": "4a8cb5d4.52e4bc",
"type": "exec",
Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
2020-12-02 19:26:27 +01:00
"z": "1371dec5.76e671",
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"command": "rm -R /home/pi/data/*",
"addpay": false,
"append": "",
"useSpawn": "true",
"timer": "",
"oldrc": false,
"name": "rm data",
"x": 680,
"y": 980,
Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
2020-12-02 19:26:27 +01:00
"wires": [
[
flow: add wifi management, refactor settings to monitor and create administration tab
2020-12-03 11:42:00 +01:00
"b57cc390.f055c8"
],
[],
[]
Flow: addition of log output, refactoring of GPS coordinates handling, refactoring of datetime management
2020-12-02 19:26:27 +01:00
]
imager bug if object_date is not set
2020-12-03 16:45:01 +01:00
},
{
"id": "2dc762df.08cd7e",
"type": "inject",
"z": "baa1e3d9.cb29d",
"name": "Default: 0.01",
"props": [
{
"p": "payload"
}
],
"repeat": "",
"crontab": "",
"once": true,
"onceDelay": 0.1,
"topic": "",
"payload": "0.05",
"payloadType": "num",
"x": 310,
"y": 320,
"wires": [
[
"df1ea904.cd261"
]
]
flow: location refactor using forms
2020-12-03 23:13:08 +01:00
},
{
"id": "c33f1124.af6688",
"type": "ui_form",
"z": "b771c342.49603",
"name": "sample_location",
"label": "Sample Location",
"group": "cef1e703.bcf3c8",
"order": 1,
"width": 0,
"height": 0,
"options": [
{
"label": "Latitude",
"value": "object_lat",
"type": "text",
"required": true,
"rows": null
},
{
"label": "Longitude",
"value": "object_lon",
"type": "text",
"required": true,
"rows": null
},
{
"label": "Date (DD/MM/YYYY)",
"value": "object_date",
"type": "text",
"required": true,
"rows": null
},
{
"label": "Time (15:00)",
"value": "object_time",
"type": "text",
"required": true,
"rows": null
}
],
"formValue": {
"object_lat": "",
"object_lon": "",
"object_date": "",
"object_time": ""
},
"payload": "",
"submit": "Validate",
"cancel": "Reset",
"topic": "sample_location",
"x": 660,
"y": 500,
"wires": [
[
"14658615.47c862"
]
]
},
{
"id": "358908cd.416ab",
"type": "ui_form",
"z": "b771c342.49603",
"name": "net_throw_location",
"label": "Net Throw Location",
"group": "cf5d9f0e.d57e7",
flow: addition of decknet flowmeter readings and better management of titles and location group activation
2020-12-04 22:24:20 +01:00
"order": 1,
flow: location refactor using forms
2020-12-03 23:13:08 +01:00
"width": 0,
"height": 0,
"options": [
{
"label": "Latitude",
"value": "object_lat",
"type": "text",
"required": true,
"rows": null
},
{
"label": "Longitude",
"value": "object_lon",
"type": "text",
"required": true,
"rows": null
},
{
"label": "Date (DD/MM/YYYY)",
"value": "object_date",
"type": "text",
"required": true,
"rows": null
},
{
"label": "Time (15:00)",
"value": "object_time",
"type": "text",
"required": true,
"rows": null
}
],
"formValue": {
"object_lat": "",
"object_lon": "",
"object_date": "",
"object_time": ""
},
"payload": "",
"submit": "Validate",
"cancel": "Reset",
"topic": "net_throw_location",
"x": 650,
"y": 540,
"wires": [
[
"14658615.47c862"
]
]
},
{
"id": "56d40584.eff4e4",
"type": "ui_form",
"z": "b771c342.49603",
"name": "net_retrieval_location",
"label": "Net Retrieval Location",
"group": "cf5d9f0e.d57e7",
flow: addition of decknet flowmeter readings and better management of titles and location group activation
2020-12-04 22:24:20 +01:00
"order": 2,
flow: location refactor using forms
2020-12-03 23:13:08 +01:00
"width": 0,
"height": 0,
"options": [
{
"label": "Latitude",
"value": "object_lat_end",
"type": "text",
"required": true,
"rows": null
},
{
"label": "Longitude",
"value": "object_lon_end",
"type": "text",
"required": true,
"rows": null
},
{
"label": "Date (DD/MM/YYYY)",
"value": "object_date_end",
"type": "text",
"required": true,
"rows": null
},
{
"label": "Time (15:00)",
"value": "object_time_end",
"type": "text",
"required": true,
"rows": null
}
],
"formValue": {
"object_lat_end": "",
"object_lon_end": "",
"object_date_end": "",
"object_time_end": ""
},
"payload": "",
"submit": "Validate",
"cancel": "Reset",
"topic": "net_retrieval_location",
"x": 640,
"y": 580,
"wires": [
[
"14658615.47c862"
]
]
},
{
"id": "14658615.47c862",
"type": "function",
"z": "b771c342.49603",
"name": "Validate Form",
"func": "function ConvertDDMMToDD(input) {\n // Input Format 36°57.4439' N, 110°4.2100' W\n // From https://stackoverflow.com/questions/1140189/converting-latitude-and-longitude-to-decimal-values\n var parts = input.split(/[^\\d\\w]+/)\n var dd = Number(parts[0]) + (Number(parts[1]) + Number(parts[2])/10000)/60\n return dd.toFixed(6) + parts[3]\n}\n\nfunction ValidateCoordinates(input, lat){\n // Input Format 36.574439° N, 110.42100° W\n var direction = input.match(/[NSEW]/)\n var position = input.match(/[\\+\\-\\d\\.]+/)\n var error = {}\n \n if (direction === null){\n error.topic = \"Error with the \"\n error.payload = \"You need to explicitely enter N/S/E/W\"\n return [null, error]\n }\n \n // Test that position is only made of digits!\n if(/^[\\+\\-]/.test(position)){\n error.topic = \"Error with the \"\n error.payload = \"Use of +/- sign is inconsistent with N/S/E/W letter! Please only use N/S/E/W!\"\n return [null, error]\n }\n \n var dd = Number(position)\n if (lat){\n // Check latitude\n if (direction == \"S\" || direction == \"N\") {\n if (dd>90.0){\n error.topic = \"Error with the \"\n error.payload = \"Latitude is more than 90°\"\n return [null, error]\n }\n }\n if (direction == \"W\" || direction == \"E\") {\n error.topic = \"Error with the \"\n error.payload = \"This is not a Latitude!\"\n return [null, error]\n }\n }\n else{\n // Check longitude\n if (direction == \"W\" || direction == \"E\") {\n if (dd>180.0){\n error.topic = \"Error with the \"\n error.payload = \"Longitude is more than 180°\"\n return [null, error]\n }\n }\n if (direction == \"N\" || direction == \"S\") {\n error.topic = \"Error with the \"\n error.payload = \"This is not a Longitude!\"\n return [null, error]\n }\n }\n \n if (direction == \"S\" || direction == \"W\") {\n dd = dd * -1\n } // Don't do anything for N or E\n return [dd.toFixed(4), null]\n\n}\nvar ret\n\nif (msg.topic == \"net_retrieval_location\"){\n if (flow.get(\"coordinates_type\") == \"ddm\"){\n msg.payload.object_lat_end = ConvertDDMMToDD(msg.payload.object_lat_end)\n msg.payload.object_lon_end = ConvertDDMMToDD(msg.payload.object_lon_end)\n }\n ret = ValidateCoordinates(msg.payload.object_lat_end, true);\n if (ret[1] !== null){\n msg.topic = ret[1].topic + \" Latitude\"\n msg.payload = ret[1].payload\n return msg\n }\n global.set(\"object_lat_end\", ret[0])\n ret = ValidateCoordinates(msg.payload.object_lon_end, false)\n if (ret[1] !== null){\n msg.topic = ret[1].topic + \" Longitude\"\n msg.payload = ret[1].payload\n return msg\n }\n global.set(\"object_lon_end\", ret[0]);\n \n var date = new Date(msg.payload.object_date_end)\n global.set(\"object_date_end\", date.toISOString().split('T')[0].replace(/-/gi, ''))\n\n var time = msg.payload.object_time_end.replace(/\\D/g, \"\") // remove non-digit characters\n if (time.length<5) time += \"00\"\n global.set(\"object_time_end\", time)\n}\nelse{\n if (flow.get(\"coordinates_type\") == \"ddm\"){\n msg.payload.object_lat = ConvertDDMMToDD(msg.payload.object_lat)\n msg.payload.object_lon = ConvertDDMMToDD(msg.payload.object_lon)\n }\n ret = ValidateCoordinates(msg.payload.object_lat, true);\n if (ret[1] !== null){\n msg.topic = ret[1].topic + \" Latitude\";\n msg.payload = ret[1].payload\n return msg\n }\n global.set(\"object_lat\", ret[0]);\n ret = ValidateCoordinates(msg.payload.object_lon, false);\n if (ret[1] !== null){\n msg.topic = ret[1].topic + \" Longitude\"\n msg.payload = ret[1].payload\n return msg\n }\n global.set(\"object_
"outputs": 1,
"noerr": 0,
"initialize": "",
"finalize": "",
flow: addition of decknet flowmeter readings and better management of titles and location group activation
2020-12-04 22:24:20 +01:00
"x": 880,
flow: location refactor using forms
2020-12-03 23:13:08 +01:00
"y": 540,
"wires": [
[
"c0ce5626.b6c5"
]
],
"inputLabels": [
"location"
],
"outputLabels": [
"checked location"
]
},
{
"id": "6d281807.b003a",
"type": "change",
"z": "b771c342.49603",
"name": "",
"rules": [
{
"t": "set",
"p": "coordinates_type",
"pt": "flow",
"to": "payload",
"tot": "msg"
}
],
"action": "",
"property": "",
"from": "",
"to": "",
"reg": false,
"x": 890,
flow: addition of decknet flowmeter readings and better management of titles and location group activation
2020-12-04 22:24:20 +01:00
"y": 440,
"wires": [
[]
]
},
{
"id": "7a40646c.9fa6bc",
"type": "ui_template",
"z": "b771c342.49603",
"group": "3e1ba03d.f01d8",
"name": "Coordinates format header",
"order": 7,
"width": 2,
"height": 1,
"format": "<div>Coordinates format*</div>",
"storeOutMessages": true,
"fwdInMessages": true,
"resendOnRefresh": true,
"templateScope": "local",
"x": 620,
flow: location refactor using forms
2020-12-03 23:13:08 +01:00
"y": 400,
"wires": [
[]
]
flow: addition of decknet flowmeter readings and better management of titles and location group activation
2020-12-04 22:24:20 +01:00
},
{
"id": "296c73f.78ff10c",
"type": "delay",
"z": "b771c342.49603",
"name": "",
"pauseType": "delay",
"timeout": "1",
"timeoutUnits": "seconds",
"rate": "1",
"nbRateUnits": "1",
"rateUnits": "second",
"randomFirst": "1",
"randomLast": "2",
"randomUnits": "milliseconds",
"drop": false,
flow: better config management
2020-12-05 00:20:44 +01:00
"x": 140,
flow: addition of decknet flowmeter readings and better management of titles and location group activation
2020-12-04 22:24:20 +01:00
"y": 200,
"wires": [
[
"a3272681.f271c8"
]
]
},
{
"id": "46eb1bf8.3dc5f4",
"type": "function",
"z": "b771c342.49603",
"name": "Net check",
"func": "var decknet = {}\nvar activation_msg = {}\n\nif (msg.payload.startsWith(\"net_decknet\")){\n decknet.enabled = true;\n}\nelse {\n decknet.enabled = false;\n}\n\nif (msg.payload.startsWith(\"net\")){\n activation_msg.payload = {\"group\":{\"show\":[\"Sample_Net_Metadata\"],\"hide\":[\"Sample_Sample_Location\"]}};\n}\nelse{\n activation_msg.payload = {\"group\":{\"hide\":[\"Sample_Net_Metadata\"],\"show\":[\"Sample_Sample_Location\"]}};\n}\n\n\nreturn [decknet, activation_msg];",
"outputs": 2,
"noerr": 0,
"initialize": "",
"finalize": "",
"x": 1080,
flow: better config management
2020-12-05 00:20:44 +01:00
"y": 240,
flow: addition of decknet flowmeter readings and better management of titles and location group activation
2020-12-04 22:24:20 +01:00
"wires": [
[
"516375fd.2ed61c",
"470e382a.25691",
"fbe32ac8.ff6a38"
],
[
"cbb123ab.fd3428"
]
],
"outputLabels": [
"decknet activation",
"group display control"
]
},
{
"id": "516375fd.2ed61c",
"type": "ui_text_input",
"z": "b771c342.49603",
"name": "sample_total_volume_start",
"label": "Decknet flowmeter start",
"tooltip": "",
"group": "cf5d9f0e.d57e7",
"order": 5,
"width": 5,
"height": 1,
"passthru": true,
"mode": "text",
"delay": 300,
"topic": "sample_total_volume_start",
"x": 1340,
flow: better config management
2020-12-05 00:20:44 +01:00
"y": 180,
flow: addition of decknet flowmeter readings and better management of titles and location group activation
2020-12-04 22:24:20 +01:00
"wires": [
[
"c23967d8.8d088"
]
]
},
{
"id": "470e382a.25691",
"type": "ui_text_input",
"z": "b771c342.49603",
"name": "sample_total_volume_end",
"label": "Decknet flowmeter end",
"tooltip": "",
"group": "cf5d9f0e.d57e7",
"order": 6,
"width": 5,
"height": 1,
"passthru": true,
"mode": "text",
"delay": 300,
"topic": "sample_total_volume_end",
"x": 1340,
flow: better config management
2020-12-05 00:20:44 +01:00
"y": 220,
flow: addition of decknet flowmeter readings and better management of titles and location group activation
2020-12-04 22:24:20 +01:00
"wires": [
[
"c23967d8.8d088"
]
]
},
{
"id": "c23967d8.8d088",
"type": "function",
"z": "b771c342.49603",
"name": "Store sample_total_volume",
"func": "if (msg.topic == \"sample_total_volume_start\"){\n context.set(\"sample_total_volume_start\", msg.payload);\n}\nif (msg.topic == \"sample_total_volume_end\"){\n context.set(\"sample_total_volume_end\", msg.payload);\n}\nif (context.keys().length == 2){\n sample_total_volume = context.get(\"sample_total_volume_end\") - context.get(\"sample_total_volume_start\");\n global.set(\"sample_total_volume\", sample_total_volume);\n}\n\n",
"outputs": 2,
"noerr": 0,
"initialize": "",
"finalize": "",
"x": 1640,
flow: better config management
2020-12-05 00:20:44 +01:00
"y": 200,
flow: addition of decknet flowmeter readings and better management of titles and location group activation
2020-12-04 22:24:20 +01:00
"wires": [
[],
[]
],
"outputLabels": [
"decknet activation",
"group display control"
]
},
{
"id": "fbe32ac8.ff6a38",
"type": "ui_template",
"z": "b771c342.49603",
"group": "cf5d9f0e.d57e7",
"name": "Decknet flowmeter read",
"order": 4,
"width": 10,
"height": 1,
"format": "<div style=\"line-height: 100%;\">\n <p class=\"formlabel\" style=\"font-size: larger;\">Decknet flowmeter readings</p>\n <p style=\"font-size: smaller;\">Those values are used to calculate <font style=\"font-family: mono;\">sample_total_volume</font>.</p>\n</div>\n",
"storeOutMessages": true,
"fwdInMessages": true,
"resendOnRefresh": true,
"templateScope": "local",
"x": 1330,
flow: better config management
2020-12-05 00:20:44 +01:00
"y": 140,
flow: addition of decknet flowmeter readings and better management of titles and location group activation
2020-12-04 22:24:20 +01:00
"wires": [
[]
]
flow: add hardware settings
2020-12-04 23:04:19 +01:00
},
{
"id": "1f63860d.5f5efa",
"type": "file in",
"z": "4ed26b8b.253504",
"name": "",
"filename": "/home/pi/PlanktonScope/hardware.json",
"format": "utf8",
"chunk": false,
"sendError": false,
"encoding": "none",
"x": 380,
"y": 80,
"wires": [
[
"8c1fda48.d7d828"
]
],
"info": "# PlanktonScope Help\nThis Node will read the content of the file named **config.txt** containing all the input placeholders.\n"
},
{
"id": "8c1fda48.d7d828",
"type": "json",
"z": "4ed26b8b.253504",
"name": "Parse JSON",
"property": "payload",
"action": "",
"pretty": false,
"x": 650,
"y": 80,
"wires": [
[
"ddb4b136.fc0b78"
]
]
},
{
"id": "82099021.9ceb08",
"type": "file",
"z": "4ed26b8b.253504",
"name": "",
flow: better config management
2020-12-05 00:20:44 +01:00
"filename": "/home/pi/PlanktonScope/hardware.json",
flow: add hardware settings
2020-12-04 23:04:19 +01:00
"appendNewline": true,
"createDir": true,
"overwriteFile": "true",
"encoding": "none",
flow: better config management
2020-12-05 00:20:44 +01:00
"x": 780,
flow: add hardware settings
2020-12-04 23:04:19 +01:00
"y": 200,
"wires": [
[]
]
},
{
"id": "bb0a8725.a1849",
"type": "json",
"z": "4ed26b8b.253504",
"name": "Create JSON",
"property": "payload",
"action": "str",
"pretty": true,
"x": 500,
"y": 200,
"wires": [
[
"82099021.9ceb08"
]
]
},
{
"id": "f748d952.4b6bc8",
"type": "inject",
"z": "4ed26b8b.253504",
"name": "Load config",
"props": [
{
"p": "topic",
"vt": "str"
}
],
"repeat": "",
"crontab": "",
"once": true,
"onceDelay": 0.1,
"topic": "",
"x": 110,
"y": 80,
"wires": [
[
"1f63860d.5f5efa"
]
]
},
{
"id": "ddb4b136.fc0b78",
"type": "change",
"z": "4ed26b8b.253504",
"name": "",
"rules": [
{
"t": "set",
"p": "hardware_conf",
"pt": "global",
"to": "payload",
"tot": "msg"
}
],
"action": "",
"property": "",
"from": "",
"to": "",
"reg": false,
"x": 870,
"y": 80,
"wires": [
[]
]
},
{
"id": "44efaeb3.59bf6",
"type": "subflow:4ed26b8b.253504",
"z": "1eaf21c8.f7a21e",
"name": "",
"env": [],
"x": 100,
"y": 180,
"wires": [
[
"e10f5e55.00b828",
"c534fd26.13741",
"54ba7f16.709ad8"
]
]
},
{
"id": "e10f5e55.00b828",
"type": "change",
"z": "1eaf21c8.f7a21e",
"name": "Get stepper_type",
"rules": [
{
"t": "set",
"p": "payload",
"pt": "msg",
"to": "payload.stepper_type",
"tot": "msg"
}
],
"action": "",
"property": "",
"from": "",
"to": "",
"reg": false,
"x": 330,
"y": 140,
"wires": [
[
"dee52a36.2af72"
]
]
},
{
"id": "dee52a36.2af72",
"type": "ui_dropdown",
"z": "1eaf21c8.f7a21e",
"name": "stepper_type",
"label": "",
"tooltip": "",
"place": "",
"group": "6be36295.0ab324",
"order": 3,
"width": 3,
"height": 1,
"passthru": false,
"multiple": false,
"options": [
{
"label": "",
"value": "adafruit",
"type": "str"
},
{
"label": "",
"value": "waveshare",
"type": "str"
}
],
"payload": "",
"topic": "stepper_type",
"x": 610,
"y": 140,
"wires": [
[
"2068e7f.f4efb18",
"8e3b3d3c.955148"
]
]
},
{
"id": "e41870d7.300eb8",
"type": "link out",
"z": "1eaf21c8.f7a21e",
"name": "Stepper_type change",
"links": [
"45a7b5aa.2ed20c"
],
"x": 955,
"y": 160,
"wires": []
},
{
"id": "2068e7f.f4efb18",
"type": "delay",
"z": "1eaf21c8.f7a21e",
"name": "",
"pauseType": "delay",
"timeout": "1",
"timeoutUnits": "seconds",
"rate": "1",
"nbRateUnits": "1",
"rateUnits": "second",
"randomFirst": "1",
"randomLast": "5",
"randomUnits": "seconds",
"drop": false,
"x": 820,
"y": 160,
"wires": [
[
"e41870d7.300eb8"
]
]
},
{
"id": "45a7b5aa.2ed20c",
"type": "link in",
"z": "9daf9e2b.019fc",
"name": "Python restart",
"links": [
"e41870d7.300eb8"
],
"x": 155,
"y": 300,
"wires": [
[
"466eb611.4da048"
]
]
},
{
"id": "53d163be.47cf24",
"type": "function",
"z": "4ed26b8b.253504",
"name": "Update and retrieve hardware_conf",
"func": "// change global\nhardware_conf = global.get(\"hardware_conf\");\nif (msg.topic !== null){\n hardware_conf[msg.topic] = msg.payload;\n global.set(\"hardware_conf\", hardware_conf);\n}\n\nreturn {\"payload\": hardware_conf};",
"outputs": 1,
"noerr": 0,
"initialize": "",
"finalize": "",
"x": 240,
"y": 200,
"wires": [
[
"bb0a8725.a1849"
]
]
},
{
"id": "8e3b3d3c.955148",
"type": "subflow:4ed26b8b.253504",
"z": "1eaf21c8.f7a21e",
"name": "",
"env": [],
"x": 840,
"y": 200,
"wires": [
[]
]
},
{
"id": "c534fd26.13741",
"type": "change",
"z": "1eaf21c8.f7a21e",
"name": "Get stepper_reverse",
"rules": [
{
"t": "set",
"p": "payload",
"pt": "msg",
"to": "payload.stepper_reverse",
"tot": "msg"
}
],
"action": "",
"property": "",
"from": "",
"to": "",
"reg": false,
"x": 340,
"y": 180,
"wires": [
[
"cd1987c7.027f58"
]
]
},
{
"id": "cd1987c7.027f58",
"type": "ui_switch",
"z": "1eaf21c8.f7a21e",
"name": "stepper_reverse",
"label": "Invert stepper output",
"tooltip": "Stepper 1 is controlled by output 1 or the other way around",
"group": "6be36295.0ab324",
"order": 4,
"width": 0,
"height": 0,
"passthru": false,
"decouple": "false",
"topic": "stepper_reverse",
"style": "",
"onvalue": "true",
"onvalueType": "bool",
"onicon": "",
"oncolor": "",
"offvalue": "false",
"offvalueType": "bool",
"officon": "",
"offcolor": "",
"x": 600,
"y": 180,
"wires": [
[
"8e3b3d3c.955148",
"2068e7f.f4efb18"
]
]
},
{
"id": "54ba7f16.709ad8",
"type": "change",
"z": "1eaf21c8.f7a21e",
"name": "Get pump_steps_per_ml",
"rules": [
{
"t": "set",
"p": "payload",
"pt": "msg",
"to": "payload.pump_steps_per_ml",
"tot": "msg"
}
],
"action": "",
"property": "",
"from": "",
"to": "",
"reg": false,
"x": 350,
"y": 220,
"wires": [
[
"ee58b91c.396108"
]
]
},
{
"id": "ee58b91c.396108",
"type": "ui_text_input",
"z": "1eaf21c8.f7a21e",
"name": "pump_steps_per_ml",
"label": "Pump: steps per mL",
"tooltip": "",
"group": "6be36295.0ab324",
"order": 5,
"width": 0,
"height": 0,
"passthru": false,
"mode": "number",
"delay": "2000",
"topic": "pump_steps_per_ml",
"x": 580,
"y": 220,
"wires": [
[
"2068e7f.f4efb18",
"8e3b3d3c.955148"
]
]
},
{
"id": "be888117.5cd67",
"type": "ui_template",
"z": "1eaf21c8.f7a21e",
"group": "6be36295.0ab324",
"name": "Stepper controller type header",
"order": 2,
"width": 3,
"height": 1,
"format": "<div>Stepper controller type</div>",
"storeOutMessages": true,
"fwdInMessages": true,
"resendOnRefresh": true,
"templateScope": "local",
"x": 550,
"y": 100,
"wires": [
[]
]
},
{
"id": "7534dfd9.8cf3e8",
"type": "ui_template",
"z": "1eaf21c8.f7a21e",
"group": "6be36295.0ab324",
"name": "Information",
"order": 1,
"width": 6,
"height": 3,
"format": "<div style=\"text-align: center;\">\n <p>Changing one of these values will make the python back-end to restart.</p>\n <p><strong style=\"font-size: large;\">If you are not sure, you probably should not be touching anything here!</strong></p>\n</div>",
"storeOutMessages": true,
"fwdInMessages": true,
"resendOnRefresh": true,
"templateScope": "local",
"x": 610,
"y": 60,
"wires": [
[]
]
flow: better config management
2020-12-05 00:20:44 +01:00
},
{
"id": "c3cdf9e.1d27308",
"type": "subflow:4ed26b8b.253504",
"z": "bccd1f23.87219",
"name": "",
"env": [],
Remove thumbsup and replace by simple nginx autoindex
2020-12-05 02:22:20 +01:00
"x": 100,
flow: better config management
2020-12-05 00:20:44 +01:00
"y": 900,
"wires": [
[
"6be64480.7e7e24",
"6d49d161.13628"
]
]
},
{
"id": "6be64480.7e7e24",
"type": "change",
"z": "bccd1f23.87219",
"name": "Get wb_red_gain",
"rules": [
{
"t": "set",
"p": "payload",
"pt": "msg",
"to": "payload.wb_red_gain",
"tot": "msg"
}
],
"action": "",
"property": "",
"from": "",
"to": "",
"reg": false,
"x": 290,
"y": 880,
"wires": [
[
"43737d43.eb0e9c"
]
]
},
{
"id": "6d49d161.13628",
"type": "change",
"z": "bccd1f23.87219",
"name": "Get wb_blue_gain",
"rules": [
{
"t": "set",
"p": "payload",
"pt": "msg",
"to": "payload.wb_blue_gain",
"tot": "msg"
}
],
"action": "",
"property": "",
"from": "",
"to": "",
"reg": false,
"x": 290,
"y": 920,
"wires": [
[
"7b699798.3d568"
]
]
},
{
"id": "56835fa1.2fe538",
"type": "subflow:4ed26b8b.253504",
"z": "bccd1f23.87219",
"name": "",
"env": [],
"x": 720,
"y": 920,
"wires": [
[]
]
},
{
"id": "3ad9835.08c937c",
"type": "function",
"z": "1c24ad9c.bebec2",
"name": "get config payload",
"func": "keys = global.get(\"config_keys\")\n\nvar payload = {}\n\nkeys.forEach(function(item, index, array) {\n payload[item] = global.get(item);\n})\n\nreturn {\"payload\": payload};",
"outputs": 1,
"noerr": 0,
"initialize": "",
"finalize": "",
"x": 410,
"y": 160,
"wires": [
[
"2e6ddf51.c0dba"
]
]
},
{
"id": "f408a273.4fb538",
"type": "function",
"z": "b771c342.49603",
"name": "get sample_gear_net_opening",
"func": "if (msg.payload.sample_gear_net_opening === null){\n msg.payload = 0;\n}\nelse\n{\n msg.payload = msg.payload.sample_gear_net_opening;\n}\nreturn msg;",
"outputs": 1,
"noerr": 0,
"initialize": "",
"finalize": "",
"x": 350,
"y": 320,
"wires": [
[
"e967b844.46aa48"
]
]
},
{
"id": "fa12f9f8.00cfa8",
"type": "subflow:1c24ad9c.bebec2",
"z": "cb95299c.2817c8",
"name": "",
"env": [],
"x": 210,
"y": 200,
"wires": [
[
"3b72d11c.86e9e6"
]
]
},
{
"id": "3b72d11c.86e9e6",
"type": "function",
"z": "cb95299c.2817c8",
"name": "get process_id",
"func": "msg.payload = msg.payload.process_id;\nmsg.topic = \"process_id\";\nreturn msg;",
"outputs": 1,
"noerr": 0,
"initialize": "",
"finalize": "",
"x": 380,
"y": 200,
"wires": [
[
"c8749cbb.55254"
]
]
},
{
"id": "8dff1648.82e42",
"type": "function",
"z": "b771c342.49603",
"name": "get object_depth_max",
"func": "if (msg.payload.object_depth_max === null){\n msg.payload = 0;\n}\nelse\n{\n msg.payload = msg.payload.object_depth_max;\n}\nreturn msg;",
"outputs": 1,
"noerr": 0,
"initialize": "",
"finalize": "",
"x": 320,
"y": 240,
"wires": [
[
"9c7f7fc9.c8d3a"
]
]
},
{
"id": "9f04c5ec.75f3d8",
"type": "function",
"z": "b771c342.49603",
"name": "get object_depth_min",
"func": "if (msg.payload.object_depth_min === null){\n msg.payload = 0;\n}\nelse\n{\n msg.payload = msg.payload.object_depth_min;\n}\nreturn msg;",
"outputs": 1,
"noerr": 0,
"initialize": "",
"finalize": "",
"x": 320,
"y": 280,
"wires": [
[
"317eeeb7.8d3042"
]
]
},
{
"id": "326a1d95.ca21aa",
"type": "subflow:1c24ad9c.bebec2",
"z": "bccd1f23.87219",
"name": "",
"x": 550,
"y": 1080,
"wires": [
[]
]
},
{
"id": "328cec46.09e40c",
"type": "change",
"z": "bccd1f23.87219",
"name": "",
"rules": [
{
"t": "set",
"p": "acq_fnumber_objective",
"pt": "global",
"to": "payload",
"tot": "msg"
}
],
"action": "",
"property": "",
"from": "",
"to": "",
"reg": false,
"x": 920,
"y": 160,
"wires": [
[
"8038414a.34461"
]
]
Add files via upload
2020-01-08 14:32:46 +01:00
}
Fix bugs all around
2020-11-25 16:58:32 +01:00
]
Reference in a new issue Copy permalink