diff --git a/README.md b/README.md index 35cebb5..97a15fa 100644 --- a/README.md +++ b/README.md @@ -1,4 +1,411 @@ -# PlanktonScope +# PlanktoScop Main Repository +The PlanktoScop is an open and affordable modular imaging platform for citizen oceanography. -Please find the documentation here : -https://planktonscope.readthedocs.io/en/latest/index.html +This GitHub is part of a community that you can find on [its website](https://www.planktonscope.org/). + +# Fast Setup + +Before going further, notice that you can download the image disk already setup without having to deal with all these command lines. +Jump here : http://planktonscope.su.domains/Images_raspberry/Raspbian_Buster_Morphocut_WiFi.img + +# Expert Setup +After getting your kit and finding the necessary components, but before assembling your kit, you should take the time to do a mockup build and setup your Raspberry. + +## Install and setup Raspbian on your Raspberry Pi + +### Computer setup +In order to make it easy to connect to the PlanktoScop, you may want to install [avahi](https://en.wikipedia.org/wiki/Avahi_%28software%29) or the [Bonjour](https://en.wikipedia.org/wiki/Bonjour_%28software%29) service on any computer you will use to access the PlanktoScop interface. This will allow you to connect to the PlantoScop using an address similar such as http://planktoscope.local instead of an IP address. + +### Download the image + +The latest Raspbian version can always be downloaded from [the Raspberry Pi Downloads page](https://www.raspberrypi.org/downloads/raspbian/). +For a first build, it's recommende to download an image of Raspbian Buster with desktop. + +#### Writing an image to the SD card + +Download the latest version of [balenaEtcher](https://www.balena.io/etcher/) and install it. + +Connect an SD card reader with the micro SD card inside. + +Open balenaEtcher and select from your hard drive the image zip file you just downloaded. + +Select the SD card you want to write your image to. + +Review your selections and click `Flash!` to begin writing data to the SD card. + +#### Prepare your Raspberry Pi +[Getting Started with your Raspberry Pi](https://projects.raspberrypi.org/en/projects/raspberry-pi-getting-started/) + +Plug the SD Card in your Raspberry Pi and connect your Pi to a screen, mouse and a keyboard. Check the connection twice before plugging the power. + +The first boot to the desktop may take up to 120 seconds. This is normal and is caused by the image expanding the filesystem to the whole SD card. DO NOT REBOOT before you reach the desktop. + +#### Finish the setup + +Make sure you have access to internet and update/upgrade your fresh Raspbian install. + +Update your Pi first. Open up a terminal, and do the following: +```sh +sudo apt update -y +sudo apt upgrade -y +sudo apt install git +``` + +You can now reboot your Pi safely. +```sh +sudo reboot now +``` + +## Raspberry Pi configuration + +### Clone this repository! + +First of all, and to ensure you have the latest documentation available locally, you should clone this repository using git. + +Simply run the following in a terminal: +```sh +git clone https://github.com/PlanktonPlanet/PlanktonScope/ +``` + +### Enable Camera/SSH/I2C in raspi-config + +You can now launch the configuration tool: +```sh +sudo raspi-config +``` + +While you're here, a wise thing to do would be to change the default password for the `pi` user. This is very warmly recommended if your PlanktoScop is connected to a shared network you do not control. Just select the first option `1 Change User Password`. + +You may also want to change the default hostname of your Raspberry. To do so, choose option `2 Network Options` then `N1 Hostname`. Choose a new hostname. We recommend using `planktoscope`. + +We need to activate a few things for the PlanktoScop to work properly. + +First, we need to activate the camera interface. Choose `5 Interfacing Options`, then `P1 Camera` and `Yes`. + +Now, you can go to `5 Interfacing Options`, then `P2 SSH`. Choose `Yes` to activate the SSH access. + +Again, select `5 Interfacing Options`, then `P4 SPI`. Choose `Yes` to enable the SPI interface. + +One more, select `5 Interfacing Options`, then `P5 I2C`. Choose `Yes` to enable the ARM I2C interface of the Raspberry. + +Finally, select `5 Interfacing Options`, then `P6 Serial`. + +This time, choose `No` to deactivate the login shell on the serial connection, but then choose `Yes` to keep the Serial port hardware enabled. + +These steps can also be done from the Raspberry Pi Configuration GUI tool that you can find in `Main Menu > Preferences`. Go to the `Interfaces` tab. Pay attention, here the Serial Port must be enabled, but the Serial Port Console must be disabled. + +Reboot your Pi safely. +```sh +sudo reboot now +``` + +## Install the needed libraries for the PlanktoScop + +Most of the following happens in a command line environment. If you are using the desktop, please start a terminal emulator. + +You can also connect to your PlanktoScop by using ssh using `ssh pi@planktoscope.local`. + +You can then run the following to make sure your Raspberry has the necessary components to install and build everything it needs and to create the necessary folders: + +```sh +sudo apt install build-essential python3 python3-pip +mkdir test libraries +``` + +### Install CircuitPython +Start by following [Adafruit's guide](https://learn.adafruit.com/circuitpython-on-raspberrypi-linux/installing-circuitpython-on-raspberry-pi). You can start at the chapter `Install Python Libraries`. + +For the record, the command are as following, however, Adafruit's page might have been updated, so please make sure this is still needed: +```sh +sudo pip3 install RPI.GPIO +sudo pip3 install adafruit-blinka +sudo pip3 install adafruit-circuitpython-motorkit +``` + +It is recommended to test this setup by creating this small script under the name `test/blinkatest.py` and running it (you can use the editor nano if you are using the terminal). +```python +#!/usr/bin/python3 +import board +import digitalio +import busio + + +print("Hello blinka!") + +# Try to great a Digital input +pin = digitalio.DigitalInOut(board.D4) +print("Digital IO ok!") + +# Try to create an I2C device +i2c = busio.I2C(board.SCL, board.SDA) +print("I2C ok!") + +# Try to create an SPI device +spi = busio.SPI(board.SCLK, board.MOSI, board.MISO) +print("SPI ok!") + +print("done!") +``` + +To run the script, just run the following: +```sh +chmod +x test/blinkatest.py +./test/blinkatest.py +``` + +The output should be similar to this: +``` +pi@planktoscope:~ $ ./test/blinkatest.py +Hello blinka! +Digital IO ok! +I2C ok! +SPI ok! +done! +``` + +### Install RPi Cam Web Interface + +You can find more information about the RPi Cam Web Interface on [eLinux' website](https://elinux.org/RPi-Cam-Web-Interface). + +To set it up, clone the code from Github and enable and run the install script with the following commands +```sh +cd ~/libraries +git clone https://github.com/silvanmelchior/RPi_Cam_Web_Interface.git +cd RPi_Cam_Web_Interface +./install.sh +``` + +Press Enter to allow default setting of the installation. Once everything is installed, press Enter to start the RPi Cam Web Interface now. + +To test the interface locally, try accessing this url from the browser in the Raspberry: http://localhost/html + +You can also try to access this page from another computer connected to the same network. + +If your computer has `avahi` or the `Bonjour` service installed and running, you can directly use this url: http://raspberrypi.local/html/ . + +If this is not the case, you first need to find the IP address of your Raspberry Pi by running the following: +```sh +sudo ip addr show | grep 'inet 1' +``` + +The web page can then be accessed at `http://[IP_ADDRESS]/html/`. + +If the interface is loading and a picture is displayed, you can stop this interface for now by simply running `./stop.sh`. + + +### Install Ultimate GPS HAT + +You can start by testing that the GPS module is working. Either install your PlanktoScop with a view of the sky, or connect the external antenna. + +Now you need to run the following: +```sh +sudo apt install gpsd gpsd-clients +stty -F /dev/serial0 raw 9600 cs8 clocal -cstopb +cat /dev/serial0 +``` + +If the GPS works, you should now see NMEA sentences scrolling: +``` +$GPGGA,000908.799,,,,,0,00,,,M,,M,,*7E +$GPGSA,A,1,,,,,,,,,,,,,,,*1E +$GPGSV,1,1,00*79 +$GPRMC,000908.799,V,,,,,0.00,0.00,060180,,,N*44 +$GPVTG,0.00,T,,M,0.00,N,0.00,K,N*32 +$GPGGA,000909.799,,,,,0,00,,,M,,M,,*7F +$GPGSA,A,1,,,,,,,,,,,,,,,*1E +$GPRMC,000909.799,V,,,,,0.00,0.00,060180,,,N*45 +$GPVTG,0.00,T,,M,0.00,N,0.00,K,N*32 +$GPGGA,000910.799,,,,,0,00,,,M,,M,,*77 +$GPGSA,A,1,,,,,,,,,,,,,,,*1E +$GPRMC,000910.799,V,,,,,0.00,0.00,060180,,,N*4D +$GPVTG,0.00,T,,M,0.00,N,0.00,K,N*32 +``` + +Until you get a GPS fix, most of the sentences are empty (see the lines starting with GPGSA and with lot of commas). + + +You can find more information in this hardware module in Adafruit documentation at [Installing Adafruit GPS HAT](https://learn.adafruit.com/adafruit-ultimate-gps-hat-for-raspberry-pi/overview) or on this page to [use Python Thread with GPS HAT](http://www.danmandle.com/blog/getting-gpsd-to-work-with-python/) + + +### Install RGB Cooling HAT +To setup the RGB Cooling HAT, you just need to clone and build the WiringPi library: +```sh +cd ~/libraries +git clone https://github.com/WiringPi/WiringPi.git +cd WiringPi +sudo ./build +gpio -v +``` + +The last command should output something similar to the following: +``` +gpio version: 2.60 +Copyright (c) 2012-2018 Gordon Henderson +This is free software with ABSOLUTELY NO WARRANTY. +For details type: gpio -warranty + +Raspberry Pi Details: + Type: Pi 4B, Revision: 01, Memory: 4096MB, Maker: Sony + * Device tree is enabled. + *--> Raspberry Pi 4 Model B Rev 1.1 + * This Raspberry Pi supports user-level GPIO access. + +``` + +You will also need to install some python modules: +```sh +sudo apt install python3-smbus i2c-tools +sudo pip3 install Adafruit-SSD1306 +``` + +More information can be found on Yahboom website, on the page [Installing RGB Cooling HAT](https://www.yahboom.net/study/RGB_Cooling_HAT). + + +### Install Node-RED + +#### Download and installation +To install Node.js, npm and Node-RED onto a Raspberry Pi, you just need to run the following command. You can review the content of this script [here](https://raw.githubusercontent.com/node-red/linux-installers/master/deb/update-nodejs-and-nodered). +```sh +bash <(curl -sL https://raw.githubusercontent.com/node-red/linux-installers/master/deb/update-nodejs-and-nodered) +``` +Type `y` at both prompts to accept the installation and its settings. + +#### Enable start on boot and launch Node-RED +To run Node-RED when the Pi is turned on or restarted, you need to enable the systemd service by running this command: +```sh +sudo systemctl enable nodered.service +``` + +You can now start Node-RED by running the following: +```sh +sudo systemctl start nodered.service +``` + +#### Check the installation +Make sure Node-RED is correctly installed by reaching the following page from the browser of your pi http://localhost:1880 or http://planktoscope.local:1880 from another computer on the same network. + +#### Install the necessary nodes +These nodes will be used by the PlanktoScop software and needs to be installed: +```sh +cd ~/.node-red/ +npm install node-red-dashboard node-red-contrib-python3-function node-red-contrib-camerapi node-red-contrib-gpsd node-red-contrib-web-worldmap node-red-contrib-interval +sudo systemctl restart nodered.service +``` + +#### Import the last GUI + +From Node-RED gui in your browser, choose the Hamburger menu top right, and then Import. You can paste the code directly from the lastest version of the GUI available [here](https://raw.githubusercontent.com/PlanktonPlanet/PlanktonScope/blob/master/flows/main.json). + +You can also download it directly: +```sh +wget -N -O ~/.node-red/flows_planktoscope.json https://raw.githubusercontent.com/PlanktonPlanet/PlanktonScope/master/flows/main.json +sudo systemctl restart nodered.service +``` + +#### More information +[Installing Node-RED on Raspberry Pi](https://nodered.org/docs/getting-started/raspberrypi) + + +### Install Mosquitto MQTT + +In order to send and receive data from Node-RED, you need to install this. Run the following: +``` +sudo apt install mosquitto mosquitto-clients + +``` + +### Install mqtt-paho + +In order to send and receive data from python, you need this library. Run the following: +``` +sudo pip3 install paho-mqtt +``` + + +### Install OpenCV + +We need to install the latest OpenCV version. Unfortunately, it is not available in the repositories. We are going to install it directly by using pip. + +First, we need to install the needed dependencies, then we will directly install opencv: +```sh +sudo apt install libgtk-3-0 libavformat58 libtiff5 libcairo2 libqt4-test libpango-1.0-0 libopenexr23 libavcodec58 libilmbase23 libatk1.0-0 libpangocairo-1.0-0 libwebp6 libqtgui4 libavutil56 libjasper1 libqtcore4 libcairo-gobject2 libswscale5 libgdk-pixbuf2.0-0 libhdf5-dev libilmbase-dev libopenexr-dev libgstreamer1.0-dev libavcodec-dev libavformat-dev libswscale-dev libwebp-dev libatlas-base-dev +sudo pip3 install "picamera[array]" +sudo pip3 install opencv-contrib-python==4.1.0.25 +``` + +You can now check that opencv is properly installed by running a python interpreter and importing the cv2 module. +```sh +pi@planktoscope:~ $ python3 +Python 3.7.3 (default, Dec 20 2019, 18:57:59) +[GCC 8.3.0] on linux +Type "help", "copyright", "credits" or "license" for more information. +>>> import cv2 +>>> cv2.__version__ +'4.1.0' +>>> quit() +``` + +If all goes well, the displayed version number should be `4.1.0`. + +More detailed information can be found on this [website](https://www.pyimagesearch.com/2019/09/16/install-opencv-4-on-raspberry-pi-4-and-raspbian-buster/). + + +### Install MorphoCut + +MorphoCut is packaged on PyPI and can be installed with pip: + +```sh +sudo apt install python3-scipy +sudo pip3 install -U git+https://github.com/morphocut/morphocut.git +``` + +To test the installation, open up once again a python interpreter and import the morphocut module: +```sh +pi@planktoscope:~ $ python3 +Python 3.7.3 (default, Dec 20 2019, 18:57:59) +[GCC 8.3.0] on linux +Type "help", "copyright", "credits" or "license" for more information. +>>> import morphocut +>>> morphocut.__version__ +'0.1.1+42.g01a051e' +>>> quit() +``` + +The MorphoCut documentation can be found [on this page](https://morphocut.readthedocs.io/en/stable/index.html). + + +## Finishing the install + +Make sure to update your Pi +``` +sudo apt update -y +sudo apt full-upgrade -y +``` + +Reboot your Pi safely +``` +sudo reboot now + +``` + +## Useful later maybe + +### Update the cloned repository + +Updates are published on Github regurlarly. Make sure to update once in a while by running this command: +```sh +cd PlanktonScope +git pull +``` + +This will pull and merge all the changes made since your last update. + +### Update node-RED interface +To update the interface and make sure you run the latest version, you need to copy the json config file from the cloned repository to the Node-RED library: +```sh +cp ~/PlanktonScope/flows/main.json ~/.node-red/flows_planktoscope.json +``` + +### Share WiFi via Ethernet + +At this link : https://www.instructables.com/id/Share-WiFi-With-Ethernet-Port-on-a-Raspberry-Pi/ diff --git a/config.txt b/config.json similarity index 100% rename from config.txt rename to config.json diff --git a/flows/flow_mqtt.json b/flows/flow_mqtt.json deleted file mode 100644 index 3619162..0000000 --- a/flows/flow_mqtt.json +++ /dev/null @@ -1,3502 +0,0 @@ -[ - { - "id": "259c8713.b50e28", - "type": "tab", - "label": "Main", - "disabled": false, - "info": "" - }, - { - "id": "6d0d6fc7.d30bb", - "type": "ui_text_input", - "z": "259c8713.b50e28", - "name": "sample_ship", - "label": "Name of the ship", - "tooltip": "", - "group": "3e1ba03d.f01d8", - "order": 3, - "width": 12, - "height": 1, - "passthru": true, - "mode": "text", - "delay": 300, - "topic": "sample_ship", - "x": 1370, - "y": 140, - "wires": [ - [ - "de9708c2.d00068" - ] - ] - }, - { - "id": "43b12fe4.c5aa3", - "type": "ui_dropdown", - "z": "259c8713.b50e28", - "name": "sample_sampling_gear", - "label": "Sampling gear", - "tooltip": "", - "place": "Select", - "group": "3e1ba03d.f01d8", - "order": 5, - "width": 0, - "height": 0, - "passthru": true, - "options": [ - { - "label": "Plankton net", - "value": "net", - "type": "str" - }, - { - "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" - } - ], - "payload": "", - "topic": "sample_sampling_gear", - "x": 1330, - "y": 220, - "wires": [ - [ - "3c6a723.145778e" - ] - ] - }, - { - "id": "458408d7.2b3b68", - "type": "ui_text_input", - "z": "259c8713.b50e28", - "name": "sample_operator", - "label": "Name of the operator", - "tooltip": "", - "group": "3e1ba03d.f01d8", - "order": 4, - "width": 12, - "height": 1, - "passthru": true, - "mode": "text", - "delay": 300, - "topic": "sample_operator", - "x": 1350, - "y": 180, - "wires": [ - [ - "a2ae6c99.188f2" - ] - ] - }, - { - "id": "a163194f.0b17c8", - "type": "ui_text_input", - "z": "259c8713.b50e28", - "name": "sample_project", - "label": "Name of the project*", - "tooltip": "", - "group": "3e1ba03d.f01d8", - "order": 1, - "width": 12, - "height": 1, - "passthru": true, - "mode": "text", - "delay": 300, - "topic": "sample_project", - "x": 1360, - "y": 60, - "wires": [ - [ - "1c2c7439.47115c" - ] - ] - }, - { - "id": "914752eb.af1b", - "type": "ui_text_input", - "z": "259c8713.b50e28", - "name": "sample_id", - "label": "ID of the station*", - "tooltip": "", - "group": "3e1ba03d.f01d8", - "order": 2, - "width": 12, - "height": 1, - "passthru": true, - "mode": "number", - "delay": 300, - "topic": "sample_id", - "x": 1370, - "y": 100, - "wires": [ - [ - "30648de6.8ebc52" - ] - ] - }, - { - "id": "8a735175.23927", - "type": "ui_date_picker", - "z": "259c8713.b50e28", - "name": "acq_date", - "label": "Date :", - "group": "52159161.72187", - "order": 2, - "width": 12, - "height": 1, - "passthru": true, - "topic": "", - "x": 1380, - "y": 1141, - "wires": [ - [ - "86aa9817.45a2e8" - ] - ] - }, - { - "id": "16d7de1c.b0c892", - "type": "ui_text_input", - "z": "259c8713.b50e28", - "name": "acq_time", - "label": "Time :", - "tooltip": "", - "group": "52159161.72187", - "order": 3, - "width": 12, - "height": 1, - "passthru": true, - "mode": "time", - "delay": 300, - "topic": "", - "x": 1380, - "y": 1181, - "wires": [ - [ - "9b1b260f.e4b338" - ] - ] - }, - { - "id": "9b1b260f.e4b338", - "type": "function", - "z": "259c8713.b50e28", - "name": "set object_time", - "func": "var time = new Date(msg.payload);\n\nvar hour = time.getUTCHours();\nif (hour<10){hour = \"0\"+hour;}\nvar minute = time.getUTCMinutes();\nif (minute<10){minute = \"0\"+minute;}\n\nvar time_UTC = \"\"+hour+minute+\"00\";\nglobal.set('object_time',time_UTC);\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 1544, - "y": 1181, - "wires": [ - [ - "829cc940.327648" - ] - ] - }, - { - "id": "86aa9817.45a2e8", - "type": "function", - "z": "259c8713.b50e28", - "name": "set object_date", - "func": "var date = new Date(msg.payload);\n\nvar year = date.getUTCFullYear();\nvar month = date.getUTCMonth()+1;\nif (month<10){month = \"0\"+month;}\nvar day = date.getUTCDate();\nif (day<10){day = \"0\"+day;}\n\nvar date_UTC = \"\"+year+month+day;\nglobal.set('object_date',date_UTC);\n\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 1544, - "y": 1141, - "wires": [ - [ - "c93577b9.a1e438" - ] - ] - }, - { - "id": "e001a28.555566", - "type": "function", - "z": "259c8713.b50e28", - "name": "get global", - "func": "msg.payload={\n \n \"generic_nb_step\":global.get(\"generic_nb_step\"),\n \"generic_flowrate\":global.get(\"generic_flowrate\"),\n \"generic_manual_volume\":global.get(\"generic_manual_volume\"),\n \"generic_sleep_before\":global.get(\"generic_sleep_before\"),\n \"generic_volume_before\":global.get(\"generic_volume_before\"),\n \"generic_path\":global.get(\"generic_path\"),\n \"generic_nb_frame\":global.get(\"generic_nb_frame\"),\n \"generic_sleep_during\":global.get(\"generic_sleep_during\"),\n \n \"sample_project\":global.get(\"sample_project\"),\n \"sample_id\":global.get(\"sample_id\"),\n \"sample_ship\":global.get(\"sample_ship\"),\n \"sample_operator\":global.get(\"sample_operator\"),\n \"sample_sampling_gear\":global.get(\"sample_sampling_gear\"),\n \n \"acq_id\":global.get(\"acq_id\"),\n \"acq_instrument\":global.get(\"acq_instrument\"),\n //\"acq_instrument_id\":global.get(\"acq_instrument_id\"),\n \"acq_celltype\":global.get(\"acq_celltype\"),\n \"acq_minimum_mesh\":global.get(\"acq_minimum_mesh\"),\n \"acq_maximum_mesh\":global.get(\"acq_maximum_mesh\"),\n \"acq_min_esd\":global.get(\"acq_min_esd\"),\n \"acq_max_esd\":global.get(\"acq_max_esd\"),\n \"acq_volume\":global.get(\"acq_volume\"),\n \"acq_magnification\":global.get(\"magnification\"),\n \"acq_fnumber_objective\":global.get(\"acq_fnumber_objective\"),\n \n \"acq_camera_name\":\"Pi Camera V2.1 - 8MP\",\n \n \"object_date\":global.get(\"object_date\"),\n \"object_time\":global.get(\"object_time\"),\n \"object_lat\":global.get(\"object_lat\"),\n \"object_lon\":global.get(\"object_lon\"),\n \"object_depth_min\":global.get(\"object_depth_min\"),\n \"object_depth_max\":global.get(\"object_depth_max\"),\n \n \"process_pixel\":global.get(\"process_pixel\"),\n \"process_id\":global.get(\"process_id\")\n \n};\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 1880, - "y": 60, - "wires": [ - [ - "76a6e6bb.a08b98" - ] - ] - }, - { - "id": "f25890f5.f2549", - "type": "file", - "z": "259c8713.b50e28", - "name": "", - "filename": "/home/pi/PlanktonScope/config.txt", - "appendNewline": true, - "createDir": true, - "overwriteFile": "true", - "encoding": "none", - "x": 2233, - "y": 60, - "wires": [ - [] - ] - }, - { - "id": "f5c1aa13.3cfbf8", - "type": "function", - "z": "259c8713.b50e28", - "name": "set optical config", - "func": "global.set(msg.topic,msg.payload);\nvar acq_fnumber_objective = String(global.get(msg.topic));\n\nswitch(acq_fnumber_objective) {\n case \"25\":\n global.set(\"magnification\",0.6);\n global.set(\"process_pixel\",1.86);\n global.set(\"sug_min\",60);\n global.set(\"sug_max\",670);\n global.set(\"sug_flowrate\",3);\n break;\n case \"16\":\n global.set(\"magnification\",0.94);\n global.set(\"process_pixel\",1.19);\n global.set(\"sug_min\",40);\n global.set(\"sug_max\",430);\n global.set(\"sug_flowrate\",2.4);\n break;\n case \"12\":\n global.set(\"magnification\",1.20);\n global.set(\"process_pixel\",0.94);\n global.set(\"sug_min\",30);\n global.set(\"sug_max\",340);\n global.set(\"sug_flowrate\",1.25);\n break;\n case \"8\":\n global.set(\"magnification\",1.78);\n global.set(\"process_pixel\",0.63);\n global.set(\"sug_min\",20);\n global.set(\"sug_max\",230);\n global.set(\"sug_flowrate\",0.42);\n break;\n case \"6\":\n global.set(\"magnification\",2.36);\n global.set(\"process_pixel\",0.48);\n global.set(\"sug_min\",15);\n global.set(\"sug_max\",170);\n global.set(\"sug_flowrate\",0.32);\n break;\n}\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 1550, - "y": 1041, - "wires": [ - [ - "72e1e23b.a8a67c" - ] - ] - }, - { - "id": "eb9181d8.25e01", - "type": "ui_dropdown", - "z": "259c8713.b50e28", - "name": "acq_fnumber_objective", - "label": "M12 Lens*", - "tooltip": "", - "place": "Select option", - "group": "52159161.72187", - "order": 7, - "width": 12, - "height": 1, - "passthru": true, - "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", - "x": 1326, - "y": 1041, - "wires": [ - [ - "f5c1aa13.3cfbf8" - ] - ] - }, - { - "id": "5aba848a.7a861c", - "type": "ui_numeric", - "z": "259c8713.b50e28", - "name": "acq_minimum_mesh", - "label": "Min fraction size (μm)", - "tooltip": "", - "group": "52159161.72187", - "order": 8, - "width": 12, - "height": 1, - "wrap": false, - "passthru": true, - "topic": "acq_minimum_mesh", - "format": "{{value}}", - "min": 0, - "max": "300", - "step": "10", - "x": 1336, - "y": 841, - "wires": [ - [ - "510bd72a.b42ea8" - ] - ] - }, - { - "id": "7cea16e.c42ace8", - "type": "ui_numeric", - "z": "259c8713.b50e28", - "name": "acq_maximum_mesh", - "label": "Max fraction size (μm)", - "tooltip": "", - "group": "52159161.72187", - "order": 9, - "width": 12, - "height": 1, - "wrap": false, - "passthru": true, - "topic": "acq_maximum_mesh", - "format": "{{value}}", - "min": "200", - "max": "2000", - "step": "100", - "x": 1336, - "y": 881, - "wires": [ - [ - "a3f18257.8a55e" - ] - ] - }, - { - "id": "6ecc9468.0271dc", - "type": "ui_text_input", - "z": "259c8713.b50e28", - "name": "acq_id", - "label": "Acquisition unique ID*", - "tooltip": "", - "group": "52159161.72187", - "order": 1, - "width": 0, - "height": 0, - "passthru": true, - "mode": "number", - "delay": 300, - "topic": "acq_id", - "x": 1386, - "y": 721, - "wires": [ - [ - "b26183bf.aa217" - ] - ] - }, - { - "id": "259fd49a.160a3c", - "type": "ui_dropdown", - "z": "259c8713.b50e28", - "name": "acq_celltype", - "label": "Thickness flowcell*", - "tooltip": "", - "place": "Select option", - "group": "52159161.72187", - "order": 6, - "width": 12, - "height": 1, - "passthru": true, - "options": [ - { - "label": "200 μm µ-Slide I Luer", - "value": 200, - "type": "num" - }, - { - "label": "400 μm µ-Slide I Luer", - "value": 400, - "type": "num" - }, - { - "label": "600 μm µ-Slide I Luer", - "value": 600, - "type": "num" - }, - { - "label": "800 μm µ-Slide I Luer", - "value": 800, - "type": "num" - } - ], - "payload": "", - "topic": "acq_celltype", - "x": 1366, - "y": 801, - "wires": [ - [ - "d96d32ec.f88b9" - ] - ] - }, - { - "id": "66a3425c.79aabc", - "type": "ui_text_input", - "z": "259c8713.b50e28", - "name": "acq_volume", - "label": "Volume to pass (ml)", - "tooltip": "", - "group": "52159161.72187", - "order": 5, - "width": 12, - "height": 1, - "passthru": true, - "mode": "number", - "delay": 300, - "topic": "acq_volume", - "x": 1366, - "y": 921, - "wires": [ - [ - "a3ec68a2.889ca8" - ] - ] - }, - { - "id": "6722bc48.d4f354", - "type": "comment", - "z": "259c8713.b50e28", - "name": "sample", - "info": "SAMPLE: a collection event\n\n sample_id [t] : unique identifier\n sample_*** [f] or [t] : other fields relative to the sample\n", - "x": 810, - "y": 60, - "wires": [] - }, - { - "id": "f93037f1.6a6238", - "type": "comment", - "z": "259c8713.b50e28", - "name": "acquisition", - "info": "ACQUISITION: metadata relative to the image acquisition\n\n acq_id [t] : unique identifier. If your acquisition differ for each sample you must have different identifier.\n acq_instrument [t] : name of the instrument (UVP, ZOOSCAN, FLOWCAM, etc.)\n acq_*** [f] or [t] : other fields relative to the acquisition\n", - "x": 800, - "y": 720, - "wires": [] - }, - { - "id": "734ba3db.3f82fc", - "type": "comment", - "z": "259c8713.b50e28", - "name": "object", - "info": "OBJECT: one object to be classified, usually one organism. One object can be represented by several images. In this tsv file, there is one line per image which means the object data gets repeated on several lines.\n\n object_id [t] : unique object name (will be displayed in Ecotaxa object page)\n object_link [f] : URL of an associated website\n object_lat [f] : latitude, decimal degrees\n object_lon [f] : longitude, decimal degrees\n object_date [f] : ISO8601 YYYYMMJJ UTC\n object_time [f] : ISO8601 HHMMSS UTC\n object_depth_min [f] : minimum depth of object, meters\n object_depth_max [f] : maximum depth of object, meters\n\nAnd, for already classified objects\n\n object_annotation_date [t] : ISO8601 YYYYMMJJ UTC\n object_annotation_time [t] : ISO8601 YYYYMMJJ UTC\n object_annotation_category [t] : class of the object with optionnaly its direct parent following separated by left angle bracket without whitespace \"Cnidaria", - "storeOutMessages": true, - "fwdInMessages": true, - "templateScope": "local", - "x": 1210, - "y": 300, - "wires": [ - [] - ] - }, - { - "id": "b7d9455c.026588", - "type": "switch", - "z": "259c8713.b50e28", - "name": "", - "property": "topic", - "propertyType": "msg", - "rules": [ - { - "t": "eq", - "v": "actuator/focus", - "vt": "str" - }, - { - "t": "eq", - "v": "Missing entry :", - "vt": "str" - } - ], - "checkall": "true", - "repair": false, - "outputs": 2, - "x": 1670, - "y": 400, - "wires": [ - [ - "fdb3b132.8b341" - ], - [ - "b9d996d6.37c2f8" - ] - ] - }, - { - "id": "b9d996d6.37c2f8", - "type": "ui_toast", - "z": "259c8713.b50e28", - "position": "dialog", - "displayTime": "3", - "highlight": "", - "sendall": true, - "outputs": 1, - "ok": "OK", - "cancel": "", - "raw": false, - "topic": "", - "name": "", - "x": 1830, - "y": 420, - "wires": [ - [] - ] - }, - { - "id": "ca38a11d.0ee54", - "type": "function", - "z": "259c8713.b50e28", - "name": "init LED", - "func": "msg.payload=1;\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 240, - "y": 161, - "wires": [ - [ - "1d58e86f.a3a9e8" - ] - ] - }, - { - "id": "75701b99.c6e974", - "type": "exec", - "z": "259c8713.b50e28", - "command": "vcgencmd measure_temp | tr -d \"temp=\" | tr -d \"'C\" | tr -d \"\\n\"", - "addpay": false, - "append": "", - "useSpawn": "", - "timer": "", - "name": "RPi Temp.", - "x": 2190, - "y": 1080, - "wires": [ - [ - "aac61390.c13c6" - ], - [], - [] - ] - }, - { - "id": "1780384d.718198", - "type": "inject", - "z": "259c8713.b50e28", - "name": "", - "topic": "", - "payload": "", - "payloadType": "date", - "repeat": "10", - "crontab": "", - "once": false, - "onceDelay": "", - "x": 2030, - "y": 1080, - "wires": [ - [ - "75701b99.c6e974" - ] - ] - }, - { - "id": "aac61390.c13c6", - "type": "python3-function", - "z": "259c8713.b50e28", - "name": "fan.py", - "func": "#!/usr/bin/python\nimport smbus\nimport sys\n\ntemp = msg[\"payload\"]\n\ntemp = int(temp.split('.',1)[0])\n\nbus = smbus.SMBus(1)\n\nDEVICE_ADDRESS = 0x0d\n\nif temp < 38:\n bus.write_byte_data(DEVICE_ADDRESS, 0x08, 0x00)\n bus.write_byte_data(DEVICE_ADDRESS, 0x08, 0x00)\nif temp > 42:\n bus.write_byte_data(DEVICE_ADDRESS, 0x08, 0x01)\n bus.write_byte_data(DEVICE_ADDRESS, 0x08, 0x01)", - "outputs": 1, - "x": 2370, - "y": 1060, - "wires": [ - [] - ] - }, - { - "id": "603d5fab.08f56", - "type": "comment", - "z": "259c8713.b50e28", - "name": "save config.txt", - "info": "", - "x": 1690, - "y": 20, - "wires": [] - }, - { - "id": "72e1e23b.a8a67c", - "type": "link out", - "z": "259c8713.b50e28", - "name": "", - "links": [ - "7532db82.1dcf04", - "d473399b.081ae8" - ], - "x": 1675, - "y": 1040, - "wires": [] - }, - { - "id": "d473399b.081ae8", - "type": "link in", - "z": "259c8713.b50e28", - "name": "", - "links": [ - "72e1e23b.a8a67c", - "c93577b9.a1e438", - "829cc940.327648" - ], - "x": 1635, - "y": 100, - "wires": [ - [ - "e001a28.555566" - ] - ] - }, - { - "id": "c93577b9.a1e438", - "type": "link out", - "z": "259c8713.b50e28", - "name": "", - "links": [ - "7532db82.1dcf04", - "d473399b.081ae8" - ], - "x": 1675, - "y": 1140, - "wires": [] - }, - { - "id": "829cc940.327648", - "type": "link out", - "z": "259c8713.b50e28", - "name": "", - "links": [ - "7532db82.1dcf04", - "d473399b.081ae8" - ], - "x": 1675, - "y": 1180, - "wires": [] - }, - { - "id": "98e2e9e0.fb7418", - "type": "switch", - "z": "259c8713.b50e28", - "name": "", - "property": "topic", - "propertyType": "msg", - "rules": [ - { - "t": "eq", - "v": "actuator/pump", - "vt": "str" - }, - { - "t": "eq", - "v": "Missing entry :", - "vt": "str" - } - ], - "checkall": "true", - "repair": false, - "outputs": 2, - "x": 1670, - "y": 600, - "wires": [ - [ - "61fb057d.3c251c" - ], - [ - "46a536f0.c83138" - ] - ] - }, - { - "id": "46a536f0.c83138", - "type": "ui_toast", - "z": "259c8713.b50e28", - "position": "dialog", - "displayTime": "3", - "highlight": "", - "sendall": true, - "outputs": 1, - "ok": "OK", - "cancel": "", - "raw": false, - "topic": "", - "name": "", - "x": 1830, - "y": 620, - "wires": [ - [] - ] - }, - { - "id": "24ffcf03.2a51b", - "type": "ui_button", - "z": "259c8713.b50e28", - "name": "stop pump", - "group": "707d9797.c8e798", - "order": 5, - "width": 4, - "height": 1, - "passthru": true, - "label": "STOP PUMP", - "tooltip": "", - "color": "", - "bgcolor": "", - "icon": "", - "payload": "off", - "payloadType": "str", - "topic": "actuator/wait", - "x": 1370, - "y": 660, - "wires": [ - [ - "e2a7220a.09d43" - ] - ] - }, - { - "id": "7eb16c3b.294e54", - "type": "comment", - "z": "259c8713.b50e28", - "name": "turn ON the LED", - "info": "", - "x": 260, - "y": 121, - "wires": [] - }, - { - "id": "4f74f017.00a58", - "type": "function", - "z": "259c8713.b50e28", - "name": "focus.js", - "func": "state = global.get(\"state\");\n\nif (state == null){state=\"free\"}\n\nvar nb_step= global.get(\"nb_step\");\n\nif (nb_step === undefined || nb_step === \"\" || nb_step === null) {\n msg.topic = \"Missing entry :\"\n msg.payload = \"Number of steps\";\n \n}else {\n nb_step= global.get(\"nb_step\");\n if(msg.payload === \"UP\" & state===\"free\"){\n msg.payload=\"FORWARD \"+nb_step;\n }\n if(msg.payload === \"DOWN\" & state===\"free\"){\n msg.payload=\"BACKWARD \"+nb_step;\n }\n}\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 1520, - "y": 400, - "wires": [ - [ - "b7d9455c.026588" - ] - ], - "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": "52cc1de5.b78e84", - "type": "ui_button", - "z": "259c8713.b50e28", - "name": "stop focus", - "group": "fbd92986.1028c8", - "order": 5, - "width": 4, - "height": 1, - "passthru": true, - "label": "STOP FOCUS", - "tooltip": "", - "color": "", - "bgcolor": "", - "icon": "", - "payload": "off", - "payloadType": "str", - "topic": "actuator/wait", - "x": 1370, - "y": 460, - "wires": [ - [ - "e46763fe.7fc83" - ] - ] - }, - { - "id": "39cad6fb.1503ca", - "type": "ui_button", - "z": "259c8713.b50e28", - "name": "", - "group": "8cfadfab.327d7", - "order": 9, - "width": 11, - "height": 1, - "passthru": false, - "label": "Reboot", - "tooltip": "", - "color": "", - "bgcolor": "#AD1625", - "icon": "", - "payload": "off", - "payloadType": "str", - "topic": "reboot", - "x": 2060, - "y": 960, - "wires": [ - [ - "95b876d4.07c708", - "99d61fbe.b244b" - ] - ] - }, - { - "id": "1f53f29b.feee4d", - "type": "exec", - "z": "259c8713.b50e28", - "command": "sudo", - "addpay": true, - "append": "", - "useSpawn": "false", - "timer": "2", - "oldrc": false, - "name": "cmd", - "x": 2370, - "y": 960, - "wires": [ - [], - [], - [] - ] - }, - { - "id": "e325458b.95bff8", - "type": "ui_button", - "z": "259c8713.b50e28", - "name": "", - "group": "8cfadfab.327d7", - "order": 10, - "width": 13, - "height": 1, - "passthru": false, - "label": "Shutdown", - "tooltip": "", - "color": "", - "bgcolor": "#AD1625", - "icon": "", - "payload": "off", - "payloadType": "str", - "topic": "shutdown", - "x": 2060, - "y": 1020, - "wires": [ - [ - "95b876d4.07c708", - "99d61fbe.b244b" - ] - ] - }, - { - "id": "95b876d4.07c708", - "type": "python3-function", - "z": "259c8713.b50e28", - "name": "action", - "func": "#!/usr/bin/python\nimport smbus\nimport time\nbus = smbus.SMBus(1)\ntime.sleep(1)\n#turn off fan RGB\nbus.write_byte_data(0x0d, 0x07, 0x00)\nbus.write_byte_data(0x0d, 0x07, 0x00)\n\nmsg[\"payload\"] = str(msg[\"topic\"])+' now'\nreturn msg", - "outputs": 1, - "x": 2230, - "y": 980, - "wires": [ - [ - "d348474b.d756a8", - "1f53f29b.feee4d" - ] - ] - }, - { - "id": "d348474b.d756a8", - "type": "exec", - "z": "259c8713.b50e28", - "command": "i2cdetect -y 1", - "addpay": false, - "append": "", - "useSpawn": "false", - "timer": "1", - "oldrc": false, - "name": "i2c update", - "x": 2390, - "y": 1020, - "wires": [ - [], - [], - [] - ] - }, - { - "id": "99d61fbe.b244b", - "type": "link out", - "z": "259c8713.b50e28", - "name": "", - "links": [ - "3517d063.27073" - ], - "x": 2175, - "y": 920, - "wires": [] - }, - { - "id": "cdd1b550.da18e8", - "type": "mqtt in", - "z": "259c8713.b50e28", - "name": "", - "topic": "receiver/#", - "qos": "0", - "datatype": "auto", - "broker": "b77ffa1b.942258", - "x": 2340, - "y": 720, - "wires": [ - [ - "6920281d.dc9b48" - ] - ] - }, - { - "id": "6920281d.dc9b48", - "type": "switch", - "z": "259c8713.b50e28", - "name": "", - "property": "topic", - "propertyType": "msg", - "rules": [ - { - "t": "eq", - "v": "receiver/pump", - "vt": "str" - }, - { - "t": "eq", - "v": "receiver/focus", - "vt": "str" - } - ], - "checkall": "true", - "repair": false, - "outputs": 2, - "x": 2490, - "y": 720, - "wires": [ - [ - "2f66e917.fee586" - ], - [ - "363ee47e.ed522c" - ] - ] - }, - { - "id": "2f66e917.fee586", - "type": "switch", - "z": "259c8713.b50e28", - "name": "", - "property": "payload", - "propertyType": "msg", - "rules": [ - { - "t": "eq", - "v": "Start", - "vt": "str" - }, - { - "t": "eq", - "v": "Done", - "vt": "str" - }, - { - "t": "eq", - "v": "Interrompted", - "vt": "str" - } - ], - "checkall": "true", - "repair": false, - "outputs": 3, - "x": 2650, - "y": 640, - "wires": [ - [ - "5c0d0c35.3bcf14" - ], - [ - "cd01157d.0892d8" - ], - [ - "68e02bf4.7013e4" - ] - ] - }, - { - "id": "5c0d0c35.3bcf14", - "type": "change", - "z": "259c8713.b50e28", - "name": "", - "rules": [ - { - "t": "set", - "p": "payload", - "pt": "msg", - "to": "The pump has started", - "tot": "str" - } - ], - "action": "", - "property": "", - "from": "", - "to": "", - "reg": false, - "x": 2820, - "y": 600, - "wires": [ - [ - "61cf0388.fb10cc" - ] - ] - }, - { - "id": "cd01157d.0892d8", - "type": "change", - "z": "259c8713.b50e28", - "name": "", - "rules": [ - { - "t": "set", - "p": "payload", - "pt": "msg", - "to": "The pump has finished.", - "tot": "str" - } - ], - "action": "", - "property": "", - "from": "", - "to": "", - "reg": false, - "x": 2820, - "y": 640, - "wires": [ - [ - "61cf0388.fb10cc" - ] - ] - }, - { - "id": "68e02bf4.7013e4", - "type": "change", - "z": "259c8713.b50e28", - "name": "", - "rules": [ - { - "t": "set", - "p": "payload", - "pt": "msg", - "to": "The pump has been stopped.", - "tot": "str" - } - ], - "action": "", - "property": "", - "from": "", - "to": "", - "reg": false, - "x": 2820, - "y": 680, - "wires": [ - [ - "61cf0388.fb10cc" - ] - ] - }, - { - "id": "61cf0388.fb10cc", - "type": "debug", - "z": "259c8713.b50e28", - "name": "", - "active": true, - "tosidebar": true, - "console": false, - "tostatus": false, - "complete": "payload", - "targetType": "msg", - "x": 3030, - "y": 640, - "wires": [] - }, - { - "id": "363ee47e.ed522c", - "type": "switch", - "z": "259c8713.b50e28", - "name": "", - "property": "payload", - "propertyType": "msg", - "rules": [ - { - "t": "eq", - "v": "Start", - "vt": "str" - }, - { - "t": "eq", - "v": "Done", - "vt": "str" - }, - { - "t": "eq", - "v": "Interrompted", - "vt": "str" - } - ], - "checkall": "true", - "repair": false, - "outputs": 3, - "x": 2650, - "y": 780, - "wires": [ - [ - "c088b72f.326d98" - ], - [ - "36934381.14442c" - ], - [ - "89329cfe.c8f4" - ] - ] - }, - { - "id": "c088b72f.326d98", - "type": "change", - "z": "259c8713.b50e28", - "name": "", - "rules": [ - { - "t": "set", - "p": "payload", - "pt": "msg", - "to": "The focus has started", - "tot": "str" - } - ], - "action": "", - "property": "", - "from": "", - "to": "", - "reg": false, - "x": 2820, - "y": 740, - "wires": [ - [ - "d11ec8dd.ad71d8" - ] - ] - }, - { - "id": "36934381.14442c", - "type": "change", - "z": "259c8713.b50e28", - "name": "", - "rules": [ - { - "t": "set", - "p": "payload", - "pt": "msg", - "to": "The focus has finished.", - "tot": "str" - } - ], - "action": "", - "property": "", - "from": "", - "to": "", - "reg": false, - "x": 2820, - "y": 780, - "wires": [ - [ - "d11ec8dd.ad71d8" - ] - ] - }, - { - "id": "89329cfe.c8f4", - "type": "change", - "z": "259c8713.b50e28", - "name": "", - "rules": [ - { - "t": "set", - "p": "payload", - "pt": "msg", - "to": "The focus has been stopped.", - "tot": "str" - } - ], - "action": "", - "property": "", - "from": "", - "to": "", - "reg": false, - "x": 2820, - "y": 820, - "wires": [ - [ - "d11ec8dd.ad71d8" - ] - ] - }, - { - "id": "d11ec8dd.ad71d8", - "type": "debug", - "z": "259c8713.b50e28", - "name": "", - "active": true, - "tosidebar": true, - "console": false, - "tostatus": false, - "complete": "payload", - "targetType": "msg", - "x": 3030, - "y": 780, - "wires": [] - }, - { - "id": "fdb3b132.8b341", - "type": "mqtt out", - "z": "259c8713.b50e28", - "name": "", - "topic": "", - "qos": "", - "retain": "", - "broker": "cb2f36fe.1c7038", - "x": 1810, - "y": 380, - "wires": [] - }, - { - "id": "e46763fe.7fc83", - "type": "mqtt out", - "z": "259c8713.b50e28", - "name": "", - "topic": "", - "qos": "", - "retain": "", - "broker": "cb2f36fe.1c7038", - "x": 1510, - "y": 460, - "wires": [] - }, - { - "id": "61fb057d.3c251c", - "type": "mqtt out", - "z": "259c8713.b50e28", - "name": "", - "topic": "", - "qos": "", - "retain": "", - "broker": "cb2f36fe.1c7038", - "x": 1810, - "y": 580, - "wires": [] - }, - { - "id": "e2a7220a.09d43", - "type": "mqtt out", - "z": "259c8713.b50e28", - "name": "", - "topic": "", - "qos": "", - "retain": "", - "broker": "cb2f36fe.1c7038", - "x": 1510, - "y": 660, - "wires": [] - }, - { - "id": "577f7f72.6b68b", - "type": "ui_button", - "z": "259c8713.b50e28", - "name": "", - "group": "8cfadfab.327d7", - "order": 7, - "width": 0, - "height": 0, - "passthru": false, - "label": "Start Acquisition", - "tooltip": "", - "color": "", - "bgcolor": "", - "icon": "", - "payload": "", - "payloadType": "str", - "topic": "actuator/image", - "x": 1360, - "y": 1560, - "wires": [ - [ - "5218ba30.bbe844" - ] - ] - }, - { - "id": "d5111b87.2a64a8", - "type": "ui_text_input", - "z": "259c8713.b50e28", - "name": "generic_sleep_before", - "label": "Sleep duration before acquisition (s)", - "tooltip": "", - "group": "8cfadfab.327d7", - "order": 1, - "width": 12, - "height": 1, - "passthru": true, - "mode": "number", - "delay": 300, - "topic": "generic_sleep_before", - "x": 1340, - "y": 1360, - "wires": [ - [ - "3d141631.d548ba" - ] - ] - }, - { - "id": "3d141631.d548ba", - "type": "link out", - "z": "259c8713.b50e28", - "name": "", - "links": [ - "7532db82.1dcf04" - ], - "x": 1475, - "y": 1360, - "wires": [] - }, - { - "id": "74c89905.79d968", - "type": "ui_text_input", - "z": "259c8713.b50e28", - "name": "generic_sleep_during", - "label": "Sleep duration between acquisition (s)", - "tooltip": "", - "group": "8cfadfab.327d7", - "order": 2, - "width": 12, - "height": 1, - "passthru": true, - "mode": "number", - "delay": 300, - "topic": "generic_sleep_during", - "x": 1340, - "y": 1520, - "wires": [ - [ - "644e95b9.04b7ac" - ] - ] - }, - { - "id": "644e95b9.04b7ac", - "type": "link out", - "z": "259c8713.b50e28", - "name": "", - "links": [ - "7532db82.1dcf04" - ], - "x": 1475, - "y": 1520, - "wires": [] - }, - { - "id": "b50cf2f4.bfb84", - "type": "link out", - "z": "259c8713.b50e28", - "name": "", - "links": [ - "7532db82.1dcf04" - ], - "x": 1475, - "y": 501, - "wires": [] - }, - { - "id": "1e75fd6c.234753", - "type": "ui_slider", - "z": "259c8713.b50e28", - "name": "flowrate", - "label": "Flowrate (ml/min)*", - "tooltip": "", - "group": "707d9797.c8e798", - "order": 1, - "width": 0, - "height": 0, - "passthru": true, - "outs": "end", - "topic": "flowrate", - "min": 0, - "max": "20", - "step": "0.1", - "x": 1380, - "y": 501, - "wires": [ - [ - "b50cf2f4.bfb84" - ] - ] - }, - { - "id": "3345fc41.8341b4", - "type": "function", - "z": "259c8713.b50e28", - "name": "get generic.flowrate", - "func": "msg.payload = msg.payload.generic_flowrate;\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 1030, - "y": 501, - "wires": [ - [ - "1e75fd6c.234753" - ] - ] - }, - { - "id": "32510458.f42f9c", - "type": "link in", - "z": "259c8713.b50e28", - "name": "", - "links": [ - "b368cae7.dd66b8" - ], - "x": 895, - "y": 501, - "wires": [ - [ - "3345fc41.8341b4" - ] - ] - }, - { - "id": "3cd0a17b.0cc42e", - "type": "link out", - "z": "259c8713.b50e28", - "name": "", - "links": [ - "7532db82.1dcf04" - ], - "x": 1475, - "y": 1440, - "wires": [] - }, - { - "id": "62fea790.2840a8", - "type": "ui_text_input", - "z": "259c8713.b50e28", - "name": "generic_path", - "label": "DIrectory to store the images", - "tooltip": "", - "group": "8cfadfab.327d7", - "order": 3, - "width": 12, - "height": 1, - "passthru": true, - "mode": "text", - "delay": 300, - "topic": "generic_path", - "x": 1370, - "y": 1440, - "wires": [ - [ - "3cd0a17b.0cc42e" - ] - ] - }, - { - "id": "73e051a8.5875e", - "type": "ui_text_input", - "z": "259c8713.b50e28", - "name": "generic_volume_before", - "label": "Volume to pass before to begin", - "tooltip": "", - "group": "8cfadfab.327d7", - "order": 5, - "width": 12, - "height": 1, - "passthru": true, - "mode": "number", - "delay": 300, - "topic": "generic_volume_before", - "x": 1330, - "y": 1400, - "wires": [ - [ - "5ea01613.8cc9d8" - ] - ] - }, - { - "id": "5ea01613.8cc9d8", - "type": "link out", - "z": "259c8713.b50e28", - "name": "", - "links": [ - "7532db82.1dcf04" - ], - "x": 1475, - "y": 1400, - "wires": [] - }, - { - "id": "26549e4b.5dbf72", - "type": "ui_text_input", - "z": "259c8713.b50e28", - "name": "generic_nb_frame", - "label": "Number of frame per acquisition", - "tooltip": "", - "group": "8cfadfab.327d7", - "order": 4, - "width": 12, - "height": 1, - "passthru": true, - "mode": "number", - "delay": 300, - "topic": "generic_nb_frame", - "x": 1350, - "y": 1480, - "wires": [ - [ - "61382d0b.60c534" - ] - ] - }, - { - "id": "61382d0b.60c534", - "type": "link out", - "z": "259c8713.b50e28", - "name": "", - "links": [ - "7532db82.1dcf04" - ], - "x": 1475, - "y": 1480, - "wires": [] - }, - { - "id": "d5df5489.6523e8", - "type": "function", - "z": "259c8713.b50e28", - "name": "get generic_sleep_before", - "func": "msg.payload = msg.payload.generic_sleep_before;\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 1050, - "y": 1360, - "wires": [ - [ - "d5111b87.2a64a8" - ] - ] - }, - { - "id": "835c262e.00b468", - "type": "link in", - "z": "259c8713.b50e28", - "name": "", - "links": [ - "b368cae7.dd66b8" - ], - "x": 895, - "y": 1360, - "wires": [ - [ - "d5df5489.6523e8" - ] - ] - }, - { - "id": "9b2fe59b.be48c8", - "type": "function", - "z": "259c8713.b50e28", - "name": "get generic_volume_before", - "func": "msg.payload = msg.payload.generic_volume_before;\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 1060, - "y": 1400, - "wires": [ - [ - "73e051a8.5875e" - ] - ] - }, - { - "id": "a07dad70.7c48", - "type": "link in", - "z": "259c8713.b50e28", - "name": "", - "links": [ - "b368cae7.dd66b8" - ], - "x": 895, - "y": 1400, - "wires": [ - [ - "9b2fe59b.be48c8" - ] - ] - }, - { - "id": "54dfe4df.c6837c", - "type": "function", - "z": "259c8713.b50e28", - "name": "get generic_path", - "func": "msg.payload = msg.payload.generic_path;\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 1030, - "y": 1440, - "wires": [ - [ - "62fea790.2840a8" - ] - ] - }, - { - "id": "9fb166d6.86f908", - "type": "link in", - "z": "259c8713.b50e28", - "name": "", - "links": [ - "b368cae7.dd66b8" - ], - "x": 895, - "y": 1440, - "wires": [ - [ - "54dfe4df.c6837c" - ] - ] - }, - { - "id": "1aa409a4.7b3866", - "type": "function", - "z": "259c8713.b50e28", - "name": "get generic_nb_frame", - "func": "msg.payload = msg.payload.generic_nb_frame;\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 1040, - "y": 1480, - "wires": [ - [ - "26549e4b.5dbf72" - ] - ] - }, - { - "id": "51e769aa.92a138", - "type": "link in", - "z": "259c8713.b50e28", - "name": "", - "links": [ - "b368cae7.dd66b8" - ], - "x": 895, - "y": 1480, - "wires": [ - [ - "1aa409a4.7b3866" - ] - ] - }, - { - "id": "ce6ded0a.8ee37", - "type": "function", - "z": "259c8713.b50e28", - "name": "get generic_sleep_during", - "func": "msg.payload = msg.payload.generic_sleep_during;\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 1050, - "y": 1520, - "wires": [ - [ - "74c89905.79d968" - ] - ] - }, - { - "id": "3fa20f41.11e61", - "type": "link in", - "z": "259c8713.b50e28", - "name": "", - "links": [ - "b368cae7.dd66b8" - ], - "x": 895, - "y": 1520, - "wires": [ - [ - "ce6ded0a.8ee37" - ] - ] - }, - { - "id": "5218ba30.bbe844", - "type": "function", - "z": "259c8713.b50e28", - "name": "image.js", - "func": "state = global.get(\"state\");\n\nif (state == null){state=\"free\"}\n\nvar generic_sleep_before= global.get(\"generic_sleep_before\");\nvar generic_volume_before= global.get(\"generic_volume_before\");\nvar generic_path= global.get(\"generic_path\");\nvar generic_nb_frame= global.get(\"generic_nb_frame\");\nvar generic_sleep_during= global.get(\"generic_sleep_during\");\n\nif (generic_sleep_before === undefined || generic_sleep_before === \"\" || generic_sleep_before === null) {\n msg.topic = \"Missing entry :\"\n msg.payload = \"Duration before start the acquisition\";\n \n}else if (generic_volume_before === undefined || generic_volume_before === \"\" || generic_volume_before === null) {\n msg.topic = \"Missing entry :\"\n msg.payload = \"Volume before acquisition\";\n \n}else if (generic_path === undefined || generic_path === \"\" || generic_path === null) {\n msg.topic = \"Missing entry :\"\n msg.payload = \"Directory to store the images\";\n \n}else if (generic_nb_frame === undefined || generic_nb_frame === \"\" || generic_nb_frame === null) {\n msg.topic = \"Missing entry :\"\n msg.payload = \"Number of frames per acquisition\";\n \n}else if (generic_sleep_during === undefined || generic_sleep_during === \"\" || generic_sleep_during === null) {\n msg.topic = \"Missing entry :\"\n msg.payload = \"Duration in between each acquisition\";\n \n}else {\n generic_nb_step = 507*generic_volume_before\n msg.payload=generic_sleep_before+' '+generic_nb_step+' '+generic_path+' '+generic_nb_frame+' '+generic_sleep_during;\n}\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 1520, - "y": 1560, - "wires": [ - [ - "8142bee4.882c2" - ] - ], - "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": "8142bee4.882c2", - "type": "switch", - "z": "259c8713.b50e28", - "name": "", - "property": "topic", - "propertyType": "msg", - "rules": [ - { - "t": "eq", - "v": "actuator/image", - "vt": "str" - }, - { - "t": "eq", - "v": "Missing entry :", - "vt": "str" - } - ], - "checkall": "true", - "repair": false, - "outputs": 2, - "x": 1670, - "y": 1560, - "wires": [ - [ - "a4b8aae3.cc3ad8" - ], - [ - "54420752.4a4ab8" - ] - ] - }, - { - "id": "54420752.4a4ab8", - "type": "ui_toast", - "z": "259c8713.b50e28", - "position": "dialog", - "displayTime": "3", - "highlight": "", - 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"name": "Disk Usage", - "x": 270, - "y": 400, - "wires": [ - [ - "45e1912a.36a23", - "84ac8611.1a6ac8" - ], - [], - [] - ] - }, - { - "id": "45e1912a.36a23", - "type": "ui_gauge", - "z": "1371dec5.76e671", - "name": "", - "group": "405183bc.d8991c", - "order": 1, - "width": 0, - "height": 0, - "gtype": "gage", - "title": "Disk", - "label": "Go", - "format": "{{value}}", - "min": 0, - "max": "256", - "colors": [ - "#00b500", - "#e6e600", - "#ca3838" - ], - "seg1": "", - "seg2": "", - "x": 470, - "y": 380, - "wires": [] - }, - { - "id": "4b2b9a70.6a9af4", - "type": "ui_chart", - "z": "1371dec5.76e671", - "name": "", - "group": "3da7da8f.179606", - "order": 2, - "width": 0, - "height": 0, - "label": "", - "chartType": "line", - "legend": "false", - "xformat": "HH:mm:ss", - "interpolate": "linear", - "nodata": "", - "dot": false, - "ymin": "", - "ymax": "", - "removeOlder": "20", - "removeOlderPoints": "", - "removeOlderUnit": "60", - "cutout": 0, - "useOneColor": false, - "colors": [ - "#1f77b4", - "#aec7e8", - "#ff7f0e", - "#2ca02c", - "#98df8a", - "#d62728", - "#ff9896", - "#9467bd", - "#c5b0d5" - ], - "useOldStyle": true, - "outputs": 1, - "x": 470, - "y": 220, - "wires": [ - [] - ] - }, - { - "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": "", - "ymax": "", - "removeOlder": "20", - "removeOlderPoints": "", - "removeOlderUnit": "60", - "cutout": 0, - "useOneColor": false, - "colors": [ - "#1f77b4", - "#aec7e8", - "#ff7f0e", - "#2ca02c", - "#98df8a", - "#d62728", - "#ff9896", - "#9467bd", - "#c5b0d5" - ], - "useOldStyle": true, - "outputs": 1, - "x": 470, - "y": 320, - "wires": [ - [] - ] - }, - { - "id": "84ac8611.1a6ac8", - "type": "ui_chart", - "z": "1371dec5.76e671", - "name": "", - "group": "405183bc.d8991c", - "order": 2, - "width": 0, - "height": 0, - "label": "", - "chartType": "line", - "legend": "false", - "xformat": "HH:mm:ss", - "interpolate": "linear", - "nodata": "", - "dot": false, - "ymin": "", - "ymax": "", - "removeOlder": "4", - "removeOlderPoints": "", - "removeOlderUnit": "3600", - "cutout": 0, - "useOneColor": false, - "colors": [ - "#1f77b4", - "#aec7e8", - "#ff7f0e", - "#2ca02c", - "#98df8a", - "#d62728", - "#ff9896", - "#9467bd", - "#c5b0d5" - ], - "useOldStyle": true, - "outputs": 1, - "x": 470, - "y": 420, - "wires": [ - [] - ] - }, - { - "id": "1cd5b4c0.46af9b", - "type": "inject", - "z": "1371dec5.76e671", - "name": "", - "topic": "", - "payload": "", - "payloadType": "date", - "repeat": "60", - "crontab": "", - "once": false, - "onceDelay": "", - "x": 90, - "y": 280, - "wires": [ - [ - "3910d662.fa1f7a" - ] - ] - }, - { - "id": "96bbe41d.ee7928", - "type": "ui_switch", - "z": "1371dec5.76e671", - "name": "light_state", - "label": "Light", - "tooltip": "", - "group": "3ca00bf9.e5cac4", - "order": 2, - "width": 3, - "height": 1, - "passthru": true, - "decouple": "false", - "topic": "", - "style": "", - "onvalue": "on", - "onvalueType": "str", - "onicon": "wb_incandescent", - "oncolor": "red", - "offvalue": "off", - "offvalueType": "str", - "officon": "", - "offcolor": "blue", - "x": 1050, - "y": 140, - "wires": [ - [ - "51145654.0ce2d8" - ] - ] - }, - { - "id": "8485d05.444903", - "type": "ui_switch", - "z": "1371dec5.76e671", - "name": "fan_state", - "label": "Fan", - "tooltip": "", - "group": "3ca00bf9.e5cac4", - "order": 3, - "width": 3, - "height": 1, - "passthru": true, - "decouple": "false", - "topic": "", - "style": "", - "onvalue": "on", - "onvalueType": "str", - "onicon": "", - "oncolor": "", - "offvalue": "off", - "offvalueType": "str", - "officon": "", - "offcolor": "", - "x": 1040, - "y": 80, - "wires": [ - [ - "2549f778.4eb828" - ] - ] - }, - { - "id": "2549f778.4eb828", - "type": "python3-function", - "z": "1371dec5.76e671", - "name": "fan.py", - "func": "#!/usr/bin/python\nimport smbus\nimport sys\n\nstate = msg[\"payload\"]\n\nbus = smbus.SMBus(1)\n\nDEVICE_ADDRESS = 0x0d\n\nif state == \"off\":\n bus.write_byte_data(DEVICE_ADDRESS, 0x08, 0x00)\n bus.write_byte_data(DEVICE_ADDRESS, 0x08, 0x00)\nif state == \"on\":\n bus.write_byte_data(DEVICE_ADDRESS, 0x08, 0x01)\n bus.write_byte_data(DEVICE_ADDRESS, 0x08, 0x01)", - "outputs": 1, - "x": 1190, - "y": 80, - "wires": [ - [] - ] - }, - { - "id": "a113b518.830008", - "type": "ui_button", - "z": "1371dec5.76e671", - "name": "", - "group": "3ca00bf9.e5cac4", - "order": 4, - "width": 7, - "height": 1, - "passthru": false, - "label": "Reboot", - "tooltip": "", - "color": "", - "bgcolor": "#AD1625", - "icon": "", - "payload": "off", - "payloadType": "str", - "topic": "reboot", - "x": 720, - "y": 320, - "wires": [ - [ - "ee57d11c.ed1dd", - "d9234d01.e630d" - ] - ] - }, - { - "id": "d9a924bc.0ca078", - "type": "exec", - "z": "1371dec5.76e671", - "command": "sudo", - "addpay": true, - "append": "", - "useSpawn": "false", - "timer": "2", - "oldrc": false, - "name": "cmd", - "x": 1030, - "y": 320, - "wires": [ - [], - [], - [] - ] - }, - { - "id": "51145654.0ce2d8", - "type": "python3-function", - "z": "1371dec5.76e671", - "name": "light.py", - "func": "import RPi.GPIO as GPIO\n\nGPIO.setmode(GPIO.BCM)\nGPIO.setwarnings(False)\nGPIO.setup(21,GPIO.OUT)\n\nstate = msg[\"payload\"]\n\n \nif state == \"on\":\n GPIO.output(21,GPIO.HIGH)\nif state == \"off\":\n GPIO.output(21,GPIO.LOW)", - "outputs": 1, - "x": 1200, - "y": 140, - "wires": [ - [] - ] - }, - { - "id": "552d8bbb.cc4ca4", - "type": "ui_button", - "z": "1371dec5.76e671", - "name": "", - "group": "3ca00bf9.e5cac4", - "order": 5, - "width": 7, - "height": 1, - "passthru": false, - "label": "Shutdown", - "tooltip": "", - "color": "", - "bgcolor": "#AD1625", - "icon": "", - "payload": "off", - "payloadType": "str", - "topic": "shutdown", - "x": 720, - "y": 380, - "wires": [ - [ - "ee57d11c.ed1dd", - "d9234d01.e630d" - ] - ] - }, - { - "id": "3517d063.27073", - "type": "link in", - "z": "1371dec5.76e671", - "name": "", - "links": [ - "ec8da7a8.0eb558", - "d9234d01.e630d" - ], - "x": 895, - "y": 140, - "wires": [ - [ - "96bbe41d.ee7928", - "8485d05.444903" - ] - ] - }, - { - "id": "ee57d11c.ed1dd", - "type": "python3-function", - "z": "1371dec5.76e671", - "name": "action", - "func": "#!/usr/bin/python\nimport smbus\nimport time\nbus = smbus.SMBus(1)\ntime.sleep(1)\n#turn off fan RGB\nbus.write_byte_data(0x0d, 0x07, 0x00)\nbus.write_byte_data(0x0d, 0x07, 0x00)\n\nmsg[\"payload\"] = str(msg[\"topic\"])+' now'\nreturn msg", - "outputs": 1, - "x": 870, - "y": 340, - "wires": [ - [ - "b7ab1ada.1f4158", - "d9a924bc.0ca078" - ] - ] - }, - { - "id": "b7ab1ada.1f4158", - "type": "exec", - "z": "1371dec5.76e671", - "command": "i2cdetect -y 1", - "addpay": false, - "append": "", - "useSpawn": "false", - "timer": "1", - "oldrc": false, - "name": "i2c update", - "x": 1050, - "y": 380, - "wires": [ - [], - [], - [] - ] - }, - { - "id": "d9234d01.e630d", - "type": "link out", - "z": "1371dec5.76e671", - "name": "", - "links": [ - "3517d063.27073" - ], - "x": 835, - "y": 280, - "wires": [] - }, - { - "id": "bc503fa5.f46dd", - "type": "switch", - "z": "1371dec5.76e671", - "name": "", - "property": "payload", - "propertyType": "msg", - "rules": [ - { - "t": "gt", - "v": "45", - "vt": "num" - }, - { - "t": "lte", - "v": "38", - "vt": "num" - } - ], - "checkall": "true", - "repair": false, - "outputs": 2, - "x": 670, - "y": 80, - "wires": [ - [ - "a25d6486.e1ce28" - ], - [ - "5d4f3e71.1bad4" - ] - ] - }, - { - "id": "5d4f3e71.1bad4", - "type": "change", - "z": "1371dec5.76e671", - "name": "", - "rules": [ - { - "t": "set", - "p": "payload", - "pt": "msg", - "to": "off", - "tot": "str" - } - ], - "action": "", - "property": "", - "from": "", - "to": "", - "reg": false, - "x": 840, - "y": 100, - "wires": [ - [ - "8485d05.444903" - ] - ] - }, - { - "id": "a25d6486.e1ce28", - "type": "change", - "z": "1371dec5.76e671", - "name": "", - "rules": [ - { - "t": "set", - "p": "payload", - "pt": "msg", - "to": "on", - "tot": "str" - } - ], - "action": "", - "property": "", - "from": "", - "to": "", - "reg": false, - "x": 840, - "y": 60, - "wires": [ - [ - "8485d05.444903" - ] - ] - }, - { - "id": "37507791.4d5508", - "type": "http request", - "z": "1371dec5.76e671", - "name": "toggle timelapse", - "method": "GET", - "ret": "txt", - "paytoqs": false, - "url": "http://127.0.0.1/html/cmd_pipe.php?cmd={{{payload}}}", - "tls": "", - "persist": false, - "proxy": "", - "authType": "", - "x": 240, - "y": 780, - "wires": [ - [] - ] - }, - { - "id": "b9ff73e.19bd49", - "type": "ui_switch", - "z": "1371dec5.76e671", - "d": true, - "name": "timelapse", - "label": "toggle acquisition", - "tooltip": "", - "group": "1be83144.4fe4bf", - "order": 1, - "width": 0, - "height": 0, - "passthru": true, - "decouple": "false", - "topic": "toggle", - "style": "", - "onvalue": "tl 1", - "onvalueType": "str", - "onicon": "", - "oncolor": "", - "offvalue": "tl 0", - "offvalueType": "str", - "officon": "", - "offcolor": "", - "x": 80, - "y": 660, - "wires": [ - [ - "37507791.4d5508", - "df47f1bb.1b0bf" - ] - ] - }, - { - "id": "9a52e6b.cbbc118", - "type": "exec", - "z": "1371dec5.76e671", - "command": "ls -l /var/www/html/media | grep \"th\" | tail -1 | awk -F \" \" '{print $9}' | tr -d \"\\n\"", - "addpay": false, - "append": "", - "useSpawn": "false", - "timer": "", - "oldrc": false, - "name": "get thumbail name", - "x": 770, - "y": 720, - "wires": [ - [ - "ca6bfbdf.4a71e8" - ], - [], - [] - ] - }, - { - "id": "df47f1bb.1b0bf", - "type": "switch", - "z": "1371dec5.76e671", - "name": "", - "property": "payload", - "propertyType": "msg", - "rules": [ - { - "t": "eq", - "v": "tl 0", - "vt": "str" - }, - { - "t": "eq", - "v": "tl 1", - "vt": "str" - } - ], - "checkall": "true", - "repair": false, - "outputs": 2, - "x": 230, - "y": 660, - "wires": [ - [ - "1cf57a24.20b176" - ], - [ - "faa67658.8edf18", - "c4524676.63b608" - ] - ] - }, - { - "id": "faa67658.8edf18", - "type": "delay", - "z": "1371dec5.76e671", - "name": "", - "pauseType": "delay", - "timeout": "1", - "timeoutUnits": "seconds", - "rate": "1", - "nbRateUnits": "1", - "rateUnits": "second", - "randomFirst": "1", - "randomLast": "5", - "randomUnits": "seconds", - "drop": false, - "x": 420, - "y": 720, - "wires": [ - [ - "9a52e6b.cbbc118" - ] - ] - }, - { - "id": "ca6bfbdf.4a71e8", - "type": "ui_template", - "z": "1371dec5.76e671", - "d": true, - "group": "1be83144.4fe4bf", - "name": "", - "order": 2, - "width": 0, - "height": 0, - "format": "
\n\n\n", - "storeOutMessages": true, - "fwdInMessages": true, - "templateScope": "local", - "x": 980, - "y": 700, - "wires": [ - [] - ] - }, - { - "id": "3e73267.51682da", - "type": "exec", - "z": "1371dec5.76e671", - "command": "i2cdetect -y 1", - "addpay": false, - "append": "", - "useSpawn": "false", - "timer": "1", - "oldrc": false, - "name": "i2c update", - "x": 750, - "y": 620, - "wires": [ - [], - [], - [] - ] - }, - { - "id": "e8c9d8e.f1d5428", - "type": "python3-function", - "z": "1371dec5.76e671", - "name": "wait RGB", - "func": "import smbus\nfrom time import sleep\n\nbus = smbus.SMBus(1)\n\nbus.write_byte_data(0x0d, 0x00, 0)\nbus.write_byte_data(0x0d, 0x01, 0)\nbus.write_byte_data(0x0d, 0x02, 255)\nbus.write_byte_data(0x0d, 0x03, 0)\nbus.write_byte_data(0x0d, 0x00, 1)\nbus.write_byte_data(0x0d, 0x01, 0)\nbus.write_byte_data(0x0d, 0x02, 255)\nbus.write_byte_data(0x0d, 0x03, 0)\nbus.write_byte_data(0x0d, 0x00, 2)\nbus.write_byte_data(0x0d, 0x01, 0)\nbus.write_byte_data(0x0d, 0x02, 255)\nbus.write_byte_data(0x0d, 0x03, 0)\n \nreturn msg;", - "outputs": 1, - "x": 560, - "y": 600, - "wires": [ - [ - "3e73267.51682da" - ] - ] - }, - { - "id": "1cf57a24.20b176", - "type": "function", - "z": "1371dec5.76e671", - "name": "set free", - "func": "global.set(\"state\",\"free\");\nreturn msg", - "outputs": 1, - "noerr": 0, - "x": 420, - "y": 600, - "wires": [ - [ - "e8c9d8e.f1d5428" - ] - ] - }, - { - "id": "e3b347e3.b19f98", - "type": "python3-function", - "z": "1371dec5.76e671", - "name": "actuate RGB", - "func": "import smbus\nbus = smbus.SMBus(1)\nbus.write_byte_data(0x0d, 0x00, 0)\nbus.write_byte_data(0x0d, 0x01, 255)\nbus.write_byte_data(0x0d, 0x02, 255)\nbus.write_byte_data(0x0d, 0x03, 255)\nbus.write_byte_data(0x0d, 0x00, 1)\nbus.write_byte_data(0x0d, 0x01, 255)\nbus.write_byte_data(0x0d, 0x02, 255)\nbus.write_byte_data(0x0d, 0x03, 255)\nbus.write_byte_data(0x0d, 0x00, 2)\nbus.write_byte_data(0x0d, 0x01, 255)\nbus.write_byte_data(0x0d, 0x02, 255)\nbus.write_byte_data(0x0d, 0x03, 255)\nreturn msg;", - "outputs": 1, - "x": 570, - "y": 660, - "wires": [ - [ - "3e73267.51682da" - ] - ] - }, - { - "id": "c4524676.63b608", - "type": "function", - "z": "1371dec5.76e671", - "name": "set busy", - "func": "global.set(\"state\",\"busy\");\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 420, - "y": 660, - "wires": [ - [ - "e3b347e3.b19f98" - ] - ] - }, - { - "id": "6a84252a.d52a0c", - "type": "ui_template", - "z": "bccd1f23.87219", - "group": "833bc5bb.217ba8", - "name": "Stream Pi Camera", - "order": 1, - "width": 14, - "height": 9, - "format": "
\n", - "storeOutMessages": true, - "fwdInMessages": true, - "templateScope": "local", - "x": 110, - "y": 100, - "wires": [ - [] - ] - }, - { - "id": "dc48dc42.98d18", - "type": "function", - "z": "bccd1f23.87219", - "name": "set global", - "func": "var value = msg.payload;\nvar key = msg.topic;\n\nglobal.set(key,value);", - "outputs": 1, - "noerr": 0, - "x": 1480, - "y": 400, - "wires": [ - [] - ] - }, - { - "id": "5b043fe6.df031", - "type": "function", - "z": "bccd1f23.87219", - "name": "focus.js", - "func": "state = global.get(\"state\");\n\nif (state == null){\n state=\"free\"\n}\n\n\nvar nb_step= global.get(\"nb_step\");\n\nif (nb_step === undefined || nb_step === \"\" || nb_step === null) {\n msg.topic = \"Missing entry :\"\n msg.payload = \"Number of step\"\n}\n\nelse {\n\n if(msg.topic === \"up\" & state ===\"free\"){\n nb_step = global.get(\"nb_step\");\n msg.nb_step = nb_step;\n msg.orientation = \"up\";\n msg.rgb = {r:255, g:0, b:255}\n msg.topic = \"Focus\"\n return msg;\n }\n \n if(msg.topic === \"down\" & state ===\"free\"){\n nb_step = global.get(\"nb_step\");\n msg.nb_step = nb_step;\n msg.orientation = \"down\";\n msg.rgb = {r:255, g:0, b:255}\n msg.topic = \"Focus\"\n return msg;\n }\n}\nreturn msg;\n", - "outputs": 1, - "noerr": 0, - "x": 980, - "y": 280, - "wires": [ - [ - "e7f18662.70dcf8" - ] - ], - "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": "8c19fb64.8a1828", - "type": "python3-function", - "z": "bccd1f23.87219", - "name": "focus.py", - "func": "\nimport sys\n\nfrom adafruit_motor import stepper\nfrom adafruit_motorkit import MotorKit\nfrom time import sleep\n\nnb_step = int(msg[\"nb_step\"])\norientation = msg[\"orientation\"]\n\nkit = MotorKit()\n\nstage = kit.stepper2\n\nstage.release()\n\n#0.25mm/step\n#31um/microsteps\n\n \nif orientation == 'up':\n for i in range(nb_step):\n stage.onestep(direction=stepper.FORWARD, style=stepper.MICROSTEP)\n sleep(0.001)\n \nif orientation == 'down':\n for i in range(nb_step):\n stage.onestep(direction=stepper.BACKWARD, style=stepper.MICROSTEP)\n sleep(0.001)\n \nstage.release()\n\nmsg[\"topic\"] = \"focus\"\nmsg[\"payload\"] = \"done\"\n\nreturn msg", - "outputs": 1, - "x": 1280, - "y": 260, - "wires": [ - [ - "7b23bbd5.4483d4" - ] - ] - }, - { - "id": "21816a62.827a56", - "type": "python3-function", - "z": "bccd1f23.87219", - "name": "pump.py", - "func": "from adafruit_motor import stepper\nfrom adafruit_motorkit import MotorKit\nfrom time import sleep\n\nvolume = int(msg[\"volume\"])\norientation = str(msg[\"orientation\"])\nflowrate = float(msg[\"flowrate\"])\n\nkit = MotorKit()\n\npump_stepper = kit.stepper1\n\npump_stepper.release()\n\n \nif orientation == \"forward\":\n orientation=stepper.BACKWARD\nif orientation == \"backward\":\n orientation=stepper.FORWARD\n \nnb_step=volume*507 #if sleep(0.05) in between 2 steps\n#35000steps for 69g\n \n#nb_step=vol*460 if sleep(0) in between 2 steps\nduration=(volume*60)/flowrate\n \ndelay=(duration/nb_step)-0.005\n \nfor i in range(nb_step):\n pump_stepper.onestep(direction=orientation, style=stepper.DOUBLE)\n sleep(delay)\n \nsleep(1)\npump_stepper.release()\n\nmsg[\"topic\"] = \"pump\"\nmsg[\"payload\"] = \"done\"\n\nreturn msg", - "outputs": 1, - "x": 580, - "y": 220, - "wires": [ - [ - "90fc64b2.db5df8" - ] - ] - }, - { - "id": "7b68bdbe.e57094", - "type": "function", - "z": "bccd1f23.87219", - "name": "pump.js", - "func": "state = global.get(\"state\");\n\nif (state == null){state=\"free\"}\n\nvar manual_volume= global.get(\"manual_volume\");\nvar flowrate= global.get(\"flowrate\");\n\nif (manual_volume === undefined || manual_volume === \"\" || manual_volume === null) {\n msg.topic = \"Missing entry :\"\n msg.payload = \"Volume to pass\";\n \n}else if (flowrate === undefined || flowrate === \"\" || flowrate === null) {\n msg.topic = \"Missing entry :\"\n msg.payload = \"Flowrate\";\n \n}else {\n if(msg.topic === \"forward\" & state===\"free\"){\n volume = global.get(\"manual_volume\");\n msg.volume = volume;\n msg.orientation = \"forward\";\n msg.flowrate = global.get(\"flowrate\");\n msg.rgb = {r:0, g:255, b:255};\n msg.topic = \"Pump\"\n }\n if(msg.topic === \"backward\" & state===\"free\"){\n volume = global.get(\"manual_volume\");\n msg.volume = volume;\n msg.orientation = \"backward\";\n msg.flowrate = global.get(\"flowrate\");\n msg.rgb = {r:0, g:255, b:255};\n msg.topic = \"Pump\";\n }\n}\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 280, - "y": 240, - "wires": [ - [ - "7994feb9.fcfc9" - ] - ], - "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": "c0199136.20bd7", - "type": "link out", - "z": "bccd1f23.87219", - "name": "", - "links": [ - "a208caf.0d23338", - "d17415a3.fca5c8" - ], - "x": 1235, - "y": 220, - "wires": [] - }, - { - "id": "da53c4c2.6b17b8", - "type": "python3-function", - "z": "bccd1f23.87219", - "name": "actuate RGB", - "func": "import smbus\nfrom time import sleep\n\nbus = smbus.SMBus(1)\n\nrgb=msg['rgb']\nbus.write_byte_data(0x0d, 0x00, 0)\nbus.write_byte_data(0x0d, 0x01, rgb[\"r\"])\nbus.write_byte_data(0x0d, 0x02, rgb[\"g\"])\nbus.write_byte_data(0x0d, 0x03, rgb[\"b\"])\nbus.write_byte_data(0x0d, 0x00, 1)\nbus.write_byte_data(0x0d, 0x01, rgb[\"r\"])\nbus.write_byte_data(0x0d, 0x02, rgb[\"g\"])\nbus.write_byte_data(0x0d, 0x03, rgb[\"b\"])\nbus.write_byte_data(0x0d, 0x00, 2)\nbus.write_byte_data(0x0d, 0x01, rgb[\"r\"])\nbus.write_byte_data(0x0d, 0x02, rgb[\"g\"])\nbus.write_byte_data(0x0d, 0x03, rgb[\"b\"])\nreturn msg;", - "outputs": 1, - "x": 1490, - "y": 460, - "wires": [ - [ - "1276a75f.d8d1a9" - ] - ] - }, - { - "id": "8778c73a.ddc6e8", - "type": "exec", - "z": "bccd1f23.87219", - "command": "i2cdetect -y 1", - "addpay": false, - "append": "", - "useSpawn": "false", - "timer": "1", - "oldrc": false, - "name": "i2c update", - "x": 1830, - "y": 500, - "wires": [ - [], - [], - [] - ] - }, - { - "id": "a208caf.0d23338", - "type": "link in", - "z": "bccd1f23.87219", - "name": "", - "links": [ - "c0199136.20bd7", - "2dff3966.a5b2d6" - ], - "x": 1375, - "y": 460, - "wires": [ - [ - "da53c4c2.6b17b8" - ] - ] - }, - { - "id": "9b5cac2c.6de57", - "type": "python3-function", - "z": "bccd1f23.87219", - "name": "wait RGB", - "func": "import smbus\nfrom time import sleep\n\nbus = smbus.SMBus(1)\n\nbus.write_byte_data(0x0d, 0x00, 0)\nbus.write_byte_data(0x0d, 0x01, 0)\nbus.write_byte_data(0x0d, 0x02, 255)\nbus.write_byte_data(0x0d, 0x03, 0)\nbus.write_byte_data(0x0d, 0x00, 1)\nbus.write_byte_data(0x0d, 0x01, 0)\nbus.write_byte_data(0x0d, 0x02, 255)\nbus.write_byte_data(0x0d, 0x03, 0)\nbus.write_byte_data(0x0d, 0x00, 2)\nbus.write_byte_data(0x0d, 0x01, 0)\nbus.write_byte_data(0x0d, 0x02, 255)\nbus.write_byte_data(0x0d, 0x03, 0)\nreturn msg;", - "outputs": 1, - "x": 1480, - "y": 540, - "wires": [ - [ - "8479740e.6373c8" - ] - ] - }, - { - "id": "7b23bbd5.4483d4", - "type": "link out", - "z": "bccd1f23.87219", - "name": "", - "links": [ - "e4351408.b0b288", - "2bc762dd.1115ce", - "a50134c.ed45ac8" - ], - "x": 1395, - "y": 260, - "wires": [] - }, - { - "id": "e4351408.b0b288", - "type": "link in", - "z": "bccd1f23.87219", - "name": "", - "links": [ - "7b23bbd5.4483d4", - "90fc64b2.db5df8" - ], - "x": 1375, - "y": 540, - "wires": [ - [ - "9b5cac2c.6de57" - ] - ] - }, - { - "id": "2dff3966.a5b2d6", - "type": "link out", - "z": "bccd1f23.87219", - "name": "", - "links": [ - "a208caf.0d23338", - "d17415a3.fca5c8" - ], - "x": 535, - "y": 180, - "wires": [] - }, - { - "id": "90fc64b2.db5df8", - "type": "link out", - "z": "bccd1f23.87219", - "name": "", - "links": [ - "e4351408.b0b288", - "2bc762dd.1115ce", - "a50134c.ed45ac8" - ], - "x": 695, - "y": 220, - "wires": [] - }, - { - "id": "1276a75f.d8d1a9", - "type": "function", - "z": "bccd1f23.87219", - "name": "set busy", - "func": "global.set(\"state\",\"busy\");\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 1640, - "y": 460, - "wires": [ - [ - "8778c73a.ddc6e8" - ] - ] - }, - { - "id": "8479740e.6373c8", - "type": "function", - "z": "bccd1f23.87219", - "name": "set free", - "func": "global.set(\"state\",\"free\");\nreturn msg", - "outputs": 1, - "noerr": 0, - "x": 1640, - "y": 540, - "wires": [ - [ - "8778c73a.ddc6e8" - ] - ] - }, - { - "id": "17a53f92.824d2", - "type": "ui_template", - "z": "baa1e3d9.cb29d", - "group": "567a49a4.244cb8", - "name": "Instrument", - "order": 2, - "width": 0, - "height": 0, - "format": "
\n Instrument :\n \n PlanktonScope V2.1\n \n
", - "storeOutMessages": true, - "fwdInMessages": true, - "templateScope": "local", - "x": 150, - "y": 400, - "wires": [ - [] - ] - }, - { - "id": "d2b74a01.166498", - "type": "ui_template", - "z": "baa1e3d9.cb29d", - "group": "567a49a4.244cb8", - "name": "Software", - "order": 3, - "width": 0, - "height": 0, - "format": "
\n Software :\n \n Node-RED Dashboard V2.0\n \n
", - "storeOutMessages": true, - "fwdInMessages": true, - "templateScope": "local", - "x": 160, - "y": 440, - "wires": [ - [] - ] - }, - { - "id": "a5c019f.91d15e8", - "type": "ui_template", - "z": "baa1e3d9.cb29d", - "group": "567a49a4.244cb8", - "name": "Camera", - "order": 1, - "width": 0, - "height": 0, - "format": "
\n Camera :\n \n Pi Camera v2.1\n \n
", - "storeOutMessages": true, - "fwdInMessages": true, - "templateScope": "local", - "x": 160, - "y": 480, - "wires": [ - [] - ] - }, - { - "id": "f59a2f0d.5e9af", - "type": "ui_numeric", - "z": "baa1e3d9.cb29d", - "name": "acq_minimum_mesh", - "label": "Min fraction size (μm)", - "tooltip": "", - "group": "404c301a.19c4e", - "order": 2, - "width": 5, - "height": 1, - "wrap": false, - "passthru": true, - "topic": "acq_minimum_mesh", - "format": "{{value}}", - "min": 0, - "max": "300", - "step": "10", - "x": 120, - "y": 100, - "wires": [ - [ - "fb887036.12429" - ] - ] - }, - { - "id": "6008a8bb.259f08", - "type": "ui_numeric", - "z": "baa1e3d9.cb29d", - "name": "acq_maximum_mesh", - "label": "Max fraction size (μm)", - "tooltip": "", - "group": "404c301a.19c4e", - "order": 3, - "width": 5, - "height": 1, - "wrap": false, - "passthru": true, - "topic": "acq_maximum_mesh", - "format": "{{value}}", - "min": "200", - "max": "2000", - "step": "100", - "x": 120, - "y": 160, - "wires": [ - [ - "fb887036.12429" - ] - ] - }, - { - "id": "6b34c456.83178c", - "type": "ui_text_input", - "z": "baa1e3d9.cb29d", - "name": "acq_id", - "label": "Acquisition unique ID*", - "tooltip": "", - "group": "4322c187.e73e5", - "order": 2, - "width": 5, - "height": 1, - "passthru": true, - "mode": "text", - "delay": 300, - "topic": "acq_id", - "x": 170, - "y": 300, - "wires": [ - [ - "a39af546.4c30c8" - ] - ] - }, - { - "id": "314ebbc0.040b84", - "type": "function", - "z": "baa1e3d9.cb29d", - "name": "store generic", - "func": "global.set(\"acq_instrument\",\"PlanktonScope V2.1\");\nglobal.set(\"acq_software\",\"Node-RED Dashboard\");\nglobal.set(\"acq_camera\",\"Pi Camera V2.1\");\nglobal.set(\"acq_instrument_ID\",\"copepode\");", - "outputs": 1, - "noerr": 0, - "x": 370, - "y": 80, - "wires": [ - [] - ] - }, - { - "id": "109cf039.1ca8d", - "type": "ui_button", - "z": "baa1e3d9.cb29d", - "name": "cancel", - "group": "b7919ae2.c01788", - "order": 3, - "width": 4, - "height": 1, - "passthru": false, - "label": "Cancel Acquisition", - "tooltip": "", - "color": "#AD1625", - "bgcolor": "white", - "icon": "pause_circle_filled", - "payload": "stop", - "payloadType": "str", - "topic": "cancel", - "x": 570, - "y": 120, - "wires": [ - [ - "c339e7a4.7e7608", - "995fa523.83cba8" - ] - ] - }, - { - "id": "dae10d44.76f08", - "type": "function", - "z": "baa1e3d9.cb29d", - "name": "pump.js", - "func": "state = global.get(\"state\");\n\nif (state == null){\n state=\"free\"\n}\n\nif(state===\"free\"||state===\"canceled\"){\n volume = global.get(\"acq_volume\");\n flowrate = global.get(\"sug_flowrate\");\n duration=(((volume*60)/flowrate)-2)*1000\n global.set(\"duration\",duration);\n \n msg.volume = volume;\n msg.orientation = \"forward\";\n msg.flowrate = flowrate;\n msg.rgb = {r:0, g:255, b:255}\n msg.state = state\n \n return msg;\n \n \n}", - "outputs": 1, - "noerr": 0, - "x": 1140, - "y": 560, - "wires": [ - [ - "d3ab1a14.86b8b8", - "ff805ffc.f9134" - ] - ], - "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": "7789839d.69b48c", - "type": "ui_template", - "z": "eaae323a.31b3", - "group": "4e0cd5ea.17e59c", - "name": "Optic Configuration", - "order": 1, - "width": 4, - "height": 4, - "format": "\n \n
Optic Configuration
\n", - "storeOutMessages": true, - "fwdInMessages": true, - "templateScope": "local", - "x": 130, - "y": 100, - "wires": [ - [ - "2a65c3ec.49a6bc" - ] - ] - }, - { - "id": "6ea6c306.f9c12c", - "type": "ui_template", - "z": "eaae323a.31b3", - "group": "ef590206.24f6", - "name": "Fluidic Acquisition", - "order": 1, - "width": 4, - "height": 4, - "format": "\n \n
Fluidic Acquisition
\n", - "storeOutMessages": true, - "fwdInMessages": true, - "templateScope": "local", - "x": 130, - "y": 140, - "wires": [ - [ - "2a65c3ec.49a6bc" - ] - ] - }, - { - "id": "bb9eb153.9e36c", - "type": "ui_template", - "z": "eaae323a.31b3", - "group": "ae8f6620.073358", - "name": "Segmentation", - "order": 1, - "width": 4, - "height": 4, - "format": "\n \n
Segmentation
\n", - "storeOutMessages": true, - "fwdInMessages": true, - "templateScope": "local", - "x": 140, - "y": 180, - "wires": [ - [ - "2a65c3ec.49a6bc" - ] - ] - }, - { - "id": "eaf8ee7f.96f44", - "type": "ui_template", - "z": "eaae323a.31b3", - "group": "196518b2.4d53b7", - "name": "Gallery", - "order": 1, - "width": 4, - "height": 4, - "format": "\n \n
Gallery
\n", - "storeOutMessages": true, - "fwdInMessages": true, - "templateScope": "local", - "x": 160, - "y": 220, - "wires": [ - [ - "2a65c3ec.49a6bc" - ] - ] - }, - { - "id": "f37444ff.d17068", - "type": "ui_text_input", - "z": "bccd1f23.87219", - "name": "nb_step", - "label": "Number of step(s)", - "tooltip": "", - "group": "fbd92986.1028c8", - "order": 2, - "width": 0, - "height": 0, - "passthru": true, - "mode": "number", - "delay": 300, - "topic": "nb_step", - "x": 820, - "y": 340, - "wires": [ - [ - "2f51f4e2.4dcaec" - ] - ] - }, - { - "id": "811cd88c.daf528", - "type": "ui_button", - "z": "bccd1f23.87219", - "name": "down", - "group": "fbd92986.1028c8", - "order": 3, - "width": 0, - "height": 0, - "passthru": true, - "label": "", - "tooltip": "", - "color": "", - "bgcolor": "", - "icon": "arrow_downward", - "payload": "down", - "payloadType": "str", - "topic": "down", - "x": 830, - "y": 300, - "wires": [ - [ - "5b043fe6.df031" - ] - ] - }, - { - "id": "edda4df4.76de2", - "type": "ui_button", - "z": "bccd1f23.87219", - "name": "up", - "group": "fbd92986.1028c8", - "order": 1, - "width": 0, - "height": 0, - "passthru": false, - "label": "", - "tooltip": "", - "color": "", - "bgcolor": "", - "icon": "arrow_upwards", - "payload": "up", - "payloadType": "str", - "topic": "up", - "x": 830, - "y": 260, - "wires": [ - [ - "5b043fe6.df031" - ] - ] - }, - { - "id": "bb667f4c.06e44", - "type": "link out", - "z": "bccd1f23.87219", - "name": "", - "links": [ - "e4892a16.664bf8" - ], - "x": 235, - "y": 300, - "wires": [] - }, - { - "id": "e4892a16.664bf8", - "type": "link in", - "z": "bccd1f23.87219", - "name": "", - "links": [ - "bb667f4c.06e44", - "2f51f4e2.4dcaec", - "4a0baa98.618744" - ], - "x": 1375, - "y": 400, - "wires": [ - [ - "dc48dc42.98d18" - ] - ] - }, - { - "id": "2f51f4e2.4dcaec", - "type": "link out", - "z": "bccd1f23.87219", - "name": "", - "links": [ - "e4892a16.664bf8" - ], - "x": 975, - "y": 340, - "wires": [] - }, - { - "id": "68962547.34a67c", - "type": "ui_text_input", - "z": "bccd1f23.87219", - "name": "manual_volume", - "label": "Volume to pass (ml)", - "tooltip": "", - "group": "707d9797.c8e798", - "order": 3, - "width": 4, - "height": 1, - "passthru": true, - "mode": "number", - "delay": 300, - "topic": "manual_volume", - "x": 100, - "y": 340, - "wires": [ - [ - "4a0baa98.618744" - ] - ] - }, - { - "id": "4a0baa98.618744", - "type": "link out", - "z": "bccd1f23.87219", - "name": "", - "links": [ - "e4892a16.664bf8" - ], - "x": 235, - "y": 340, - "wires": [] - }, - { - "id": "34c81624.df1cea", - "type": "ui_slider", - "z": "bccd1f23.87219", - "name": "flowrate", - "label": "Flowrate (ml/min)*", - "tooltip": "", - "group": "707d9797.c8e798", - "order": 1, - "width": 0, - "height": 0, - "passthru": true, - "outs": "end", - "topic": "flowrate", - "min": 0, - "max": "20", - "step": "0.1", - "x": 120, - "y": 300, - "wires": [ - [ - "bb667f4c.06e44" - ] - ] - }, - { - "id": "c1b1469.9650eb8", - "type": "ui_template", - "z": "eaae323a.31b3", - "group": "777a7c33.fcd804", - "name": "Settings", - "order": 1, - "width": 4, - "height": 4, - "format": "\n \n
Settings
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Sample
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"wires": [ - [ - "3dba84a2.0de1bc" - ] - ] - }, - { - "id": "207fbdbb.2fe2a2", - "type": "ui_text_input", - "z": "b771c342.49603", - "name": "", - "label": "Time :", - "tooltip": "", - "group": "cef1e703.bcf3c8", - "order": 3, - "width": 7, - "height": 1, - "passthru": true, - "mode": "time", - "delay": 300, - "topic": "", - "x": 210, - "y": 380, - "wires": [ - [ - "61f9d7df.83ffe8" - ] - ] - }, - { - "id": "61f9d7df.83ffe8", - "type": "function", - "z": "b771c342.49603", - "name": "set time global", - "func": "var dt = new Date(msg.payload);\nglobal.set('sample_hour',dt.getHours()-1);\nglobal.set('sample_min',dt.getMinutes());", - "outputs": 1, - "noerr": 0, - "x": 420, - "y": 380, - "wires": [ - [] - ] - }, - { - "id": "3dba84a2.0de1bc", - "type": "function", - "z": "b771c342.49603", - "name": "set date global", - "func": "var dt = new Date(msg.payload);\n\nglobal.set('sample_month',dt.getMonth() + 1);\nglobal.set('sample_day',dt.getDate());\nglobal.set('sample_year',dt.getFullYear());\n", - 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"payloadType": "str", - "topic": "backward", - "x": 120, - "y": 220, - "wires": [ - [ - "7b68bdbe.e57094" - ] - ] - }, - { - "id": "2cab680b.baf888", - "type": "ui_button", - "z": "bccd1f23.87219", - "name": "foward", - "group": "707d9797.c8e798", - "order": 4, - "width": 5, - "height": 1, - "passthru": true, - "label": "", - "tooltip": "", - "color": "", - "bgcolor": "", - "icon": "arrow_forward", - "payload": "forward", - "payloadType": "str", - "topic": "forward", - "x": 130, - "y": 260, - "wires": [ - [ - "7b68bdbe.e57094" - ] - ] - }, - { - "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": "1", - "onvalueType": "num", - "onicon": "", - "oncolor": "", - "offvalue": "0", - "offvalueType": "num", - "officon": "", - "offcolor": "", - "x": 90, - "y": 40, - "wires": [ - [ - "cbb8afed.0a026" - ] - ], - "icon": "font-awesome/fa-lightbulb-o" - }, - { - "id": "cc966678.da8d08", - "type": "ui_dropdown", - "z": "bccd1f23.87219", - "name": "acq_fnumber_objective", - "label": "M12 Lens*", - "tooltip": "", - "place": "Select option", - "group": "4248342d.e55fac", - "order": 2, - "width": 0, - "height": 0, - "passthru": true, - "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", - "x": 870, - "y": 40, - "wires": [ - [ - "8038414a.34461" - ] - ] - }, - { - "id": "9b515beb.4aea48", - "type": "ui_template", - "z": "bccd1f23.87219", - "group": "4248342d.e55fac", - 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\n Biggest cells to explore :\n \n μm\n
", - "storeOutMessages": true, - "fwdInMessages": true, - "templateScope": "local", - "x": 1420, - "y": 160, - "wires": [ - [] - ] - }, - { - "id": "ad87820f.b1d1e", - "type": "function", - "z": "bccd1f23.87219", - "name": "get magnification", - "func": "var magnification = global.get(\"magnification\");\nmsg.payload = magnification;\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 1250, - "y": 40, - "wires": [ - [ - "9b515beb.4aea48" - ] - ] - }, - { - "id": "d68a52ee.82e8e", - "type": "function", - "z": "bccd1f23.87219", - "name": "get process_pixel", - "func": "var process_pixel = global.get(\"process_pixel\");\nmsg.payload = process_pixel;\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 1250, - "y": 80, - "wires": [ - [ - "3d2360ad.e41e7" - ] - ] - }, - { - "id": "238f26b1.e2089a", - "type": "function", - "z": "bccd1f23.87219", - "name": "get sug_min", - "func": "var sug_min = global.get(\"sug_min\");\nmsg.payload = sug_min;\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 1230, - "y": 120, - "wires": [ - [ - "8e66977b.9166a8" - ] - ] - }, - { - "id": "6e0f6d36.a6b854", - "type": "function", - "z": "bccd1f23.87219", - "name": "get sug_max", - "func": "var sug_max = global.get(\"sug_max\");\nmsg.payload = sug_max;\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 1230, - "y": 160, - "wires": [ - [ - "26b32f2c.c64fc" - ] - ] - }, - { - "id": "bb2bb7ce.1d1458", - "type": "ui_template", - "z": "baa1e3d9.cb29d", - "group": "858a0e3c.987fe", - "name": "Stream Pi Camera", - "order": 1, - "width": 14, - "height": 11, - "format": "
", - "storeOutMessages": true, - "fwdInMessages": true, - "templateScope": "local", - "x": 590, - "y": 40, - "wires": [ - [] - ] - }, - { - "id": "d0c5b57d.590818", - "type": "ui_ui_control", - "z": "baa1e3d9.cb29d", - "name": "", - "events": "change", - "x": 700, - "y": 80, - "wires": [ - [] - ] - }, - { - "id": "2fb129de.024a06", - "type": "ui_toast", - "z": "baa1e3d9.cb29d", - "position": "dialog", - "displayTime": "3", - "highlight": "", - "sendall": true, - "outputs": 1, - "ok": "OK", - "cancel": "", - "raw": false, - "topic": "", - "name": "", - "x": 650, - "y": 540, - "wires": [ - [] - ] - }, - { - "id": "61b4993e.1f3fb8", - "type": "function", - "z": "baa1e3d9.cb29d", - "name": "Check form", - "func": "var acq_celltype= global.get(\"acq_celltype\");\nvar acq_minimum_mesh= global.get(\"acq_minimum_mesh\");\nvar acq_maximum_mesh= global.get(\"acq_maximum_mesh\");\nvar acq_volume= global.get(\"acq_volume\");\nvar acq_id= global.get(\"acq_id\");\n\nif (acq_celltype === undefined || acq_celltype === \"\") {\n msg.topic = \"Missing entry :\"\n msg.payload = \"Type of the flowcell\"\n}\nelse if (acq_minimum_mesh === undefined || acq_minimum_mesh === \"\") {\n msg.topic = \"Missing entry :\"\n msg.payload = \"Lower fraction size\"\n}\nelse if (acq_maximum_mesh === undefined || acq_maximum_mesh === \"\") {\n msg.topic = \"Missing entry :\"\n msg.payload = \"Upper fraction size\"\n}\nelse if (acq_volume === undefined || acq_volume === \"\") {\n msg.topic = \"Missing entry :\"\n msg.payload = \"Volume to image\"\n}\nelse if (acq_id === undefined || acq_id === \"\") {\n msg.topic = \"Missing entry :\"\n msg.payload = \"Acquisition ID\"\n}\nelse {\n msg.topic = \"Start\";\n}\nreturn msg;\n", - "outputs": 1, - "noerr": 0, - "x": 730, - "y": 280, - "wires": [ - [ - "9e7bd689.f9c278" - ] - ] - }, - { - "id": "9e7bd689.f9c278", - "type": "switch", - "z": "baa1e3d9.cb29d", - "name": "", - "property": "topic", - "propertyType": "msg", - "rules": [ - { - "t": "eq", - "v": "Start", - "vt": "str" - }, - { - "t": "eq", - "v": "Missing entry :", - "vt": "str" - } - ], - "checkall": "true", - "repair": false, - "outputs": 2, - "x": 870, - "y": 280, - "wires": [ - [ - "f7fa6acf.f6ed28" - ], - [ - "2fb129de.024a06" - ] - ] - }, - { - "id": "16de754c.cc969b", - "type": "ui_button", - "z": "b771c342.49603", - "name": "", - "group": "5517c651.b2f668", - "order": 1, - "width": 12, - "height": 1, - "passthru": false, - "label": "Previous", - "tooltip": "", - "color": "#097479", - "bgcolor": "white", - "icon": "keyboard_return", - "payload": "{\"tab\":\"Home\"}", - "payloadType": "json", - "topic": "", - "x": 220, - "y": 480, - "wires": [ - [ - "222c851d.5d0a3a" - ] - ] - }, - { - "id": "84f3d040.5f7ea", - "type": "ui_button", - "z": "b771c342.49603", - "name": "", - "group": "5517c651.b2f668", - "order": 2, - "width": 12, - "height": 1, - "passthru": false, - "label": "Continue", - "tooltip": "", - "color": "#097479", - "bgcolor": "white", - "icon": "keyboard_tab", - "payload": "{\"tab\":\"Home\"}", - "payloadType": "json", - "topic": "", - "x": 220, - "y": 540, - "wires": [ - [ - "986d960a.c75908" - ] - ] - }, - { - "id": "f61aaed5.1e64", - "type": "ui_button", - "z": "bccd1f23.87219", - "name": "", - "group": "7a0b4877.a5d268", - "order": 1, - "width": 5, - "height": 1, - "passthru": false, - "label": "Previous", - "tooltip": "", - "color": "#097479", - "bgcolor": "white", - "icon": "keyboard_return", - "payload": "{\"tab\":\"Sample\"}", - "payloadType": "json", - "topic": "", - "x": 360, - "y": 520, - "wires": [ - [ - "6c792043.b6ff9" - ] - ] - }, - { - "id": "9ba6ec0a.22c96", - "type": "ui_button", - "z": "bccd1f23.87219", - "name": "", - "group": "7a0b4877.a5d268", - "order": 2, - "width": 5, - "height": 1, - "passthru": false, - "label": "Continue", - "tooltip": "", - "color": "#097479", - "bgcolor": "white", - "icon": "keyboard_tab", - "payload": "{\"tab\":\"Home\"}", - "payloadType": "json", - "topic": "", - "x": 360, - "y": 580, - "wires": [ - [ - "fe840e05.b46f3" - ] - ] - }, - { - "id": "c72f8fae.23bd4", - "type": "ui_button", - "z": "baa1e3d9.cb29d", - "name": "", - "group": "b7919ae2.c01788", - "order": 2, - "width": 5, - "height": 1, - "passthru": false, - "label": "Previous", - "tooltip": "", - "color": "#097479", - "bgcolor": "white", - "icon": "keyboard_return", - "payload": "{\"tab\":\"Optic Configuration\"}", - "payloadType": "json", - "topic": "", - "x": 560, - "y": 80, - "wires": [ - [ - "d0c5b57d.590818" - ] - ] - }, - { - "id": "cf48a0b9.7f208", - "type": "ui_button", - "z": "baa1e3d9.cb29d", - "name": "", - "group": "b7919ae2.c01788", - "order": 5, - "width": 0, - "height": 0, - "passthru": false, - "label": "Start", - "tooltip": "", - "color": "#097479", - "bgcolor": "white", - "icon": "keyboard_tab", - "payload": "{\"tab\":\"Home\"}", - "payloadType": "json", - "topic": "", - "x": 570, - "y": 280, - "wires": [ - [ - "61b4993e.1f3fb8" - ] - ] - }, - { - "id": "389bef3.d94c61", - "type": "ui_text_input", - "z": "baa1e3d9.cb29d", - "name": "acq_volume", - "label": "Volume to pass (ml)", - "tooltip": "", - "group": "4322c187.e73e5", - "order": 1, - "width": 5, - "height": 1, - "passthru": true, - "mode": "number", - "delay": 300, - "topic": "acq_volume", - "x": 150, - "y": 220, - "wires": [ - [ - "fb887036.12429" - ] - ] - }, - { - "id": "a39af546.4c30c8", - "type": "function", - "z": "baa1e3d9.cb29d", - "name": "set global join", - "func": "var value = msg.payload.split(' ').join('_');\nvar key = msg.topic;\n\nglobal.set(key,value);", - "outputs": 1, - "noerr": 0, - "x": 380, - "y": 280, - "wires": [ - [] - ] - }, - { - "id": "75b738f0.cea208", - "type": "ui_toast", - "z": "bccd1f23.87219", - "position": "dialog", - "displayTime": "3", - "highlight": "", - "sendall": true, - "outputs": 1, - "ok": "OK", - "cancel": "", - "raw": false, - "topic": "", - "name": "", - "x": 1290, - "y": 320, - "wires": [ - [] - ] - }, - { - "id": "e7f18662.70dcf8", - "type": "switch", - "z": "bccd1f23.87219", - "name": "", - "property": "topic", - "propertyType": "msg", - "rules": [ - { - "t": "eq", - "v": "Focus", - "vt": "str" - }, - { - "t": "eq", - "v": "Missing entry :", - "vt": "str" - } - ], - "checkall": "true", - "repair": false, - "outputs": 2, - "x": 1130, - "y": 280, - "wires": [ - [ - "c0199136.20bd7", - "8c19fb64.8a1828" - ], - [ - "75b738f0.cea208" - ] - ] - }, - { - "id": "c2aeba5f.a2ac98", - "type": "ui_toast", - "z": "bccd1f23.87219", - "position": "dialog", - "displayTime": "3", - "highlight": "", - "sendall": true, - "outputs": 1, - "ok": "OK", - "cancel": "", - "raw": false, - "topic": "", - "name": "", - "x": 590, - "y": 280, - "wires": [ - [] - ] - }, - { - "id": "7994feb9.fcfc9", - "type": "switch", - "z": "bccd1f23.87219", - "name": "", - "property": "topic", - "propertyType": "msg", - "rules": [ - { - "t": "eq", - "v": "Pump", - "vt": "str" - }, - { - "t": "eq", - "v": "Missing entry :", - "vt": "str" - } - ], - "checkall": "true", - "repair": false, - "outputs": 2, - "x": 430, - "y": 240, - "wires": [ - [ - "21816a62.827a56", - "2dff3966.a5b2d6" - ], - [ - "c2aeba5f.a2ac98" - ] - ] - }, - { - "id": "201ad81d.4a6d78", - "type": "http request", - "z": "baa1e3d9.cb29d", - "name": "Start timelapse", - "method": "GET", - "ret": "txt", - "paytoqs": false, - "url": "http://127.0.0.1/html/cmd_pipe.php?cmd=tl%201", - "tls": "", - "persist": false, - "proxy": "", - "authType": "", - "x": 980, - "y": 800, - "wires": [ - [] - ] - }, - { - "id": "c339e7a4.7e7608", - "type": "http request", - "z": "baa1e3d9.cb29d", - "name": "Stop timelapse", - "method": "GET", - "ret": "txt", - "paytoqs": false, - "url": "http://127.0.0.1/html/cmd_pipe.php?cmd=tl%200", - "tls": "", - "persist": false, - "proxy": "", - "authType": "", - "x": 720, - "y": 120, - "wires": [ - [ - "eaab9f19.c68ba" - ] - ] - }, - { - "id": "b4d324de.a2bd28", - "type": "ui_worldmap", - "z": "b771c342.49603", - "group": "cef1e703.bcf3c8", - "order": 6, - "width": 0, - "height": 0, - "name": "", - "lat": "1.5", - "lon": "1.5", - "zoom": "4", - "layer": "OSM grey", - "cluster": "1", - "maxage": "", - "usermenu": "hide", - "layers": "hide", - "panit": "false", - "panlock": "false", - "zoomlock": "false", - "hiderightclick": "true", - "coords": "deg", - "showgrid": "false", - "path": "/worldmap", - "x": 780, - "y": 400, - "wires": [] - }, - { - "id": "cf3e1477.25af68", - "type": "function", - "z": "b771c342.49603", - "name": "set point", - "func": "var sample_id= global.get(\"sample_id\");\nvar object_lat= global.get(\"object_lat\");\nvar object_lon= global.get(\"object_lon\");\n\nif (sample_id === undefined || sample_id === \"\") {\n msg.topic = \"Missing entry :\"\n msg.payload = \"Sample ID\"\n}\nelse if (object_lat === undefined || object_lat === null) {\n msg.topic = \"Missing entry :\"\n msg.payload = \"Sample latitude\"\n}\n\nelse if (object_lon === undefined || object_lon === null) {\n msg.topic = \"Missing entry :\"\n msg.payload = \"Sample longitude\"\n}\n\nelse {\n msg.topic = \"Place\"\n msg.payload={\"name\":sample_id, \"lat\":object_lat, \"lon\":object_lon}\n}\nreturn msg;\n", - "outputs": 1, - "noerr": 0, - "x": 360, - "y": 440, - "wires": [ - [ - "105e9b1b.725865" - ] - ] - }, - { - "id": "d7a44df2.0fb29", - "type": "ui_button", - "z": "b771c342.49603", - "name": "", - "group": "cef1e703.bcf3c8", - "order": 5, - "width": 5, - "height": 1, - "passthru": false, - "label": "Place", - "tooltip": "", - "color": "#333333", - "bgcolor": "white", - "icon": "", - "payload": "", - "payloadType": "str", - "topic": "", - "x": 210, - "y": 440, - "wires": [ - [ - "cf3e1477.25af68" - ] - ] - }, - { - "id": "105e9b1b.725865", - "type": "switch", - "z": "b771c342.49603", - "name": "", - "property": "topic", - "propertyType": "msg", - "rules": [ - { - "t": "eq", - "v": "Place", - "vt": "str" - }, - { - "t": "eq", - "v": "Missing entry :", - "vt": "str" - } - ], - "checkall": "true", - "repair": false, - "outputs": 2, - "x": 550, - "y": 440, - "wires": [ - [ - "b4d324de.a2bd28" - ], - [ - "10c9c12a.feae6f" - ] - ] - }, - { - "id": "10c9c12a.feae6f", - "type": "ui_toast", - "z": "b771c342.49603", - "position": "dialog", - "displayTime": "3", - "highlight": "", - "sendall": true, - "outputs": 1, - "ok": "OK", - "cancel": "", - "raw": false, - "topic": "", - "name": "", - "x": 790, - "y": 460, - "wires": [ - [] - ] - }, - { - "id": "32f57168.89cbae", - "type": "comment", - "z": "baa1e3d9.cb29d", - "name": "generic info", - "info": "", - "x": 150, - "y": 360, - "wires": [] - }, - { - "id": "44094d9d.62c6c4", - "type": "exec", - "z": "baa1e3d9.cb29d", - "command": "i2cdetect -y 1", - "addpay": false, - "append": "", - "useSpawn": "false", - "timer": "1", - "oldrc": false, - "name": "i2c update", - "x": 1170, - "y": 120, - "wires": [ - [], - [], - [] - ] - }, - { - "id": "eaab9f19.c68ba", - "type": "python3-function", - "z": "baa1e3d9.cb29d", - "name": "wait RGB", - "func": "import smbus\nfrom time import sleep\n\nbus = smbus.SMBus(1)\n\nbus.write_byte_data(0x0d, 0x00, 0)\nbus.write_byte_data(0x0d, 0x01, 0)\nbus.write_byte_data(0x0d, 0x02, 255)\nbus.write_byte_data(0x0d, 0x03, 0)\nbus.write_byte_data(0x0d, 0x00, 1)\nbus.write_byte_data(0x0d, 0x01, 0)\nbus.write_byte_data(0x0d, 0x02, 255)\nbus.write_byte_data(0x0d, 0x03, 0)\nbus.write_byte_data(0x0d, 0x00, 2)\nbus.write_byte_data(0x0d, 0x01, 0)\nbus.write_byte_data(0x0d, 0x02, 255)\nbus.write_byte_data(0x0d, 0x03, 0)\nreturn msg;", - "outputs": 1, - "x": 880, - "y": 120, - "wires": [ - [ - "154d5ce1.81ed03" - ] - ] - }, - { - "id": "154d5ce1.81ed03", - "type": "function", - "z": "baa1e3d9.cb29d", - "name": "set free", - "func": "global.set(\"state\",\"free\");\nreturn msg", - "outputs": 1, - "noerr": 0, - "x": 1020, - "y": 120, - "wires": [ - [ - "44094d9d.62c6c4" - ] - ] - }, - { - "id": "f07dec1d.147ce", - "type": "ui_text_input", - "z": "baa1e3d9.cb29d", - "name": "comment", - "label": "Comment", - "tooltip": "", - "group": "b7919ae2.c01788", - "order": 1, - "width": 0, - "height": 0, - "passthru": true, - "mode": "text", - "delay": 300, - "topic": "comment", - "x": 160, - "y": 260, - "wires": [ - [ - "fb887036.12429" - ] - ] - }, - { - "id": "8bd55b54.8e3938", - "type": "file", - "z": "baa1e3d9.cb29d", - "name": "logs.json", - "filename": "/var/www/logs.json", - "appendNewline": false, - "createDir": false, - "overwriteFile": "false", - "encoding": "none", - "x": 2000, - "y": 1340, - "wires": [ - [ - "20a2d27e.7ccafe" - ] - ] - }, - { - "id": "99fd2803.0843a8", - "type": "function", - "z": "baa1e3d9.cb29d", - "name": "get global", - "func": "msg.payload = {\n \"comment\":global.get(\"comment\"),\n \"sample_project\":global.get(\"sample_project\"),\n \"sample_ship\":global.get(\"sample_ship\"),\n \"sample_operator\":global.get(\"sample_operator\"),\n \"sample_id\":global.get(\"sample_id\"),\n \"sample_sampling_gear\":global.get(\"sample_sampling_gear\"),\n \n \"sample_hour\":global.get(\"sample_hour\"),\n \"sample_minute\":global.get(\"sample_minute\"),\n \"sample_day\":global.get(\"sample_day\"),\n \"sample_month\":global.get(\"sample_month\"),\n \"sample_year\":global.get(\"sample_year\"),\n \n \"object_lat\":global.get(\"object_lat\"),\n \"object_lon\":global.get(\"object_lon\"),\n \n \"acq_id\":global.get(\"acq_id\"),\n \"acq_fnumber_objective\":global.get(\"acq_fnumber_objective\"),\n \"acq_celltype\":global.get(\"acq_celltype\"),\n \"acq_maximum_mesh\":global.get(\"acq_maximum_mesh\"),\n \"acq_minimum_mesh\":global.get(\"acq_minimum_mesh\"),\n \"process_pixel\":global.get(\"process_pixel\"),\n \n \"acq_camera\":global.get(\"acq_camera\"),\n \"acq_instrument\":global.get(\"acq_instrument\"),\n \"acq_software\":global.get(\"acq_software\"),\n \"acq_instrument_ID\":global.get(\"acq_instrument_ID\"),\n \"acq_volume\":global.get(\"acq_volume\"),\n \"acq_flowrate\":global.get(\"sug_flowrate\")\n }\n\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 1820, - "y": 1340, - "wires": [ - [ - "8bd55b54.8e3938" - ] - ] - }, - { - "id": "ae692178.d44d1", - "type": "python3-function", - "z": "baa1e3d9.cb29d", - "name": "pump.py", - "func": "from adafruit_motor import stepper\nfrom adafruit_motorkit import MotorKit\nfrom time import sleep\n\nkit = MotorKit()\npump_stepper = kit.stepper1\npump_stepper.release()\n\nstate = str(msg[\"state\"])\nvolume = int(msg[\"volume\"])\norientation = str(msg[\"orientation\"])\nflowrate = float(msg[\"flowrate\"])\n\n\nif(state==\"free\"):\n #35000steps will pass 69ml if sleep(0.05) in between 2 steps\n #1ml is about 35000/69=507steps\n nb_step=volume*507 \n #nb_step=vol*460 if sleep(0) in between 2 steps\n \n duration=(volume*60)/flowrate\n \n delay=(duration/nb_step)-0.005\n \nif(state==\"canceled\"):\n nb_step=0\n \nfor i in range(nb_step):\n pump_stepper.onestep(direction=stepper.BACKWARD, style=stepper.DOUBLE)\n sleep(delay)\n \nsleep(1)\npump_stepper.release()\n\nmsg[\"topic\"] = \"pump\"\nmsg[\"payload\"] = \"done\"\n\nreturn msg", - "outputs": 1, - "x": 1240, - "y": 1260, - "wires": [ - [ - "783209c7.51c5a8" - ] - ] - }, - { - "id": "a3fd6b29.2ef5f8", - "type": "function", - "z": "baa1e3d9.cb29d", - "name": "pump.js", - "func": "state = global.get(\"state\");\n\nif (state == null){\n state=\"free\"\n}\n\nif(state===\"free\"||state===\"canceled\"){\n volume = global.get(\"acq_volume\");\n flowrate = global.get(\"sug_flowrate\");\n duration=(((volume*60)/flowrate)-2)*1000\n global.set(\"duration\",duration);\n \n msg.volume = volume;\n msg.orientation = \"forward\";\n msg.flowrate = flowrate;\n msg.rgb = {r:0, g:255, b:255}\n msg.state = state\n \n return msg;\n \n \n}", - "outputs": 1, - "noerr": 0, - "x": 1040, - "y": 1360, - "wires": [ - [ - "ae692178.d44d1", - "e0f9efda.fa4ce" - ] - ], - "info": "### Focusing\n##### focus.py `nb_step` `orientation`\n\n- `nb_step` : **integer** (from 1 to 100000) - number of step to perform by the stage (about 31um/step)\n- `orientation` : **string** - orientation of the focus either `up` or `down`\n\nExample:\n\n python3.7 $HOME/PlanktonScope/scripts/focus.py 650 up\n" - }, - { - "id": "e0f9efda.fa4ce", - "type": "python3-function", - "z": "baa1e3d9.cb29d", - "name": "actuate RGB", - "func": "import smbus\nfrom time import sleep\n\nbus = smbus.SMBus(1)\n\nrgb=msg['rgb']\nbus.write_byte_data(0x0d, 0x00, 0)\nbus.write_byte_data(0x0d, 0x01, rgb[\"r\"])\nbus.write_byte_data(0x0d, 0x02, rgb[\"g\"])\nbus.write_byte_data(0x0d, 0x03, rgb[\"b\"])\nbus.write_byte_data(0x0d, 0x00, 1)\nbus.write_byte_data(0x0d, 0x01, rgb[\"r\"])\nbus.write_byte_data(0x0d, 0x02, rgb[\"g\"])\nbus.write_byte_data(0x0d, 0x03, rgb[\"b\"])\nbus.write_byte_data(0x0d, 0x00, 2)\nbus.write_byte_data(0x0d, 0x01, rgb[\"r\"])\nbus.write_byte_data(0x0d, 0x02, rgb[\"g\"])\nbus.write_byte_data(0x0d, 0x03, rgb[\"b\"])\nreturn msg;", - "outputs": 1, - "x": 1250, - "y": 1200, - "wires": [ - [ - "3b498e72.6e6292" - ] - ] - }, - { - "id": "7baf5071.dc3b2", - "type": "exec", - "z": "baa1e3d9.cb29d", - "command": "i2cdetect -y 1", - "addpay": false, - "append": "", - "useSpawn": "false", - "timer": "1", - "oldrc": false, - "name": "i2c update", - "x": 1570, - "y": 1200, - "wires": [ - [], - [], - [] - ] - }, - { - "id": "783209c7.51c5a8", - "type": "link out", - "z": "baa1e3d9.cb29d", - "name": "", - "links": [ - "e1354861.0bb648", - "2bc762dd.1115ce", - "a50134c.ed45ac8", - "f0ef065a.362028" - ], - "x": 1335, - "y": 1260, - "wires": [] - }, - { - "id": "3b498e72.6e6292", - "type": "function", - "z": "baa1e3d9.cb29d", - "name": "set busy", - "func": "global.set(\"state\",\"busy\");\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 1420, - "y": 1200, - "wires": [ - [ - "7baf5071.dc3b2" - ] - ] - }, - { - "id": "cd56bb1c.8ce378", - "type": "ui_toast", - "z": "baa1e3d9.cb29d", - "position": "dialog", - "displayTime": "3", - "highlight": "", - "sendall": true, - "outputs": 1, - "ok": "OK", - "cancel": "", - "raw": false, - "topic": "", - "name": "", - "x": 1010, - "y": 1200, - "wires": [ - [] - ] - }, - { - "id": "c82e467c.99e208", - "type": "switch", - "z": "baa1e3d9.cb29d", - "name": "", - "property": "topic", - "propertyType": "msg", - "rules": [ - { - "t": "eq", - "v": "Missing entry :", - "vt": "str" - }, - { - "t": "eq", - "v": "Start", - "vt": "str" - } - ], - "checkall": "true", - "repair": false, - "outputs": 2, - "x": 850, - "y": 1220, - "wires": [ - [ - "cd56bb1c.8ce378" - ], - [ - "a3fd6b29.2ef5f8", - "a642fc0b.b6dd7" - ] - ] - }, - { - "id": "c6bd5987.c48f78", - "type": "http request", - "z": "baa1e3d9.cb29d", - "name": "Start timelapse", - "method": "GET", - "ret": "txt", - "paytoqs": false, - "url": "http://127.0.0.1/html/cmd_pipe.php?cmd=tl%201", - "tls": "", - "persist": false, - "proxy": "", - "authType": "", - "x": 1100, - "y": 1600, - "wires": [ - [] - ] - }, - { - "id": "8c15fd05.81b5", - "type": "function", - "z": "baa1e3d9.cb29d", - "name": "get duration acquisition", - "func": "msg.delay = global.get(\"duration\");\n\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 1290, - "y": 1360, - "wires": [ - [ - "2ff9c0cb.7288b", - "34929df1.bfe602" - ] - ] - }, - { - "id": "2ff9c0cb.7288b", - "type": "delay", - "z": "baa1e3d9.cb29d", - "name": "wait duration", - "pauseType": "delayv", - "timeout": "1", - "timeoutUnits": "seconds", - "rate": "1", - "nbRateUnits": "1", - "rateUnits": "second", - "randomFirst": "1", - "randomLast": "5", - "randomUnits": "seconds", - "drop": false, - "x": 1510, - "y": 1360, - "wires": [ - [ - "99fd2803.0843a8", - "3475ecd5.6655f4", - "8f991d2e.6e8f3", - "e6a12f33.c7768" - ] - ] - }, - { - "id": "a642fc0b.b6dd7", - "type": "delay", - "z": "baa1e3d9.cb29d", - "name": "", - "pauseType": "delay", - "timeout": "500", - "timeoutUnits": "milliseconds", - "rate": "1", - "nbRateUnits": "1", - "rateUnits": "second", - "randomFirst": "1", - "randomLast": "5", - "randomUnits": "seconds", - "drop": false, - "x": 810, - "y": 1540, - "wires": [ - [ - "c6bd5987.c48f78", - "8c15fd05.81b5" - ] - ] - }, - { - "id": "6aaa3bc6.b7dda4", - "type": "ui_gauge", - "z": "baa1e3d9.cb29d", - "name": "", - "group": "b5d61bc7.54fe48", - "order": 1, - "width": 10, - "height": 2, - "gtype": "donut", - "title": "", - "label": "%", - "format": "{{value}}", - "min": 0, - "max": "100", - "colors": [ - "#ffffff", - "#ffffff", - "#097479" - ], - "seg1": "", - "seg2": "", - "x": 2250, - "y": 1500, - "wires": [] - }, - { - "id": "34929df1.bfe602", - "type": "trigger", - "z": "baa1e3d9.cb29d", - "op1": "1", - "op2": "0", - "op1type": "str", - "op2type": "str", - "duration": "-1", - "extend": false, - "units": "s", - "reset": "done", - "bytopic": "all", - "name": "", - "x": 1960, - "y": 1600, - "wires": [ - [ - "e98903d2.f35c1" - ] - ] - }, - { - "id": "3475ecd5.6655f4", - "type": "function", - "z": "baa1e3d9.cb29d", - "name": "stop", - "func": "global.set(\"time_to_wait\",0);\nmsg.payload=\"done\";\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 1810, - "y": 1500, - "wires": [ - [ - "34929df1.bfe602", - "6aaa3bc6.b7dda4" - ] - ] - }, - { - "id": "e98903d2.f35c1", - "type": "function", - "z": "baa1e3d9.cb29d", - "name": "pulse", - "func": "var time_to_wait= global.get(\"time_to_wait\");\n\nif (time_to_wait === undefined || time_to_wait === \"\"|| time_to_wait == NaN) {\n time_to_wait=0\n global.set(\"time_to_wait\",time_to_wait);\n}else {\n time_to_wait++;\n global.set(\"time_to_wait\",time_to_wait);\n duration=global.get(\"duration\")/1000;\n percent=(100* time_to_wait/duration).toFixed(0)\n msg.payload=percent;\n return msg;\n \n}", - "outputs": 1, - "noerr": 0, - "x": 2110, - "y": 1600, - "wires": [ - [ - "6aaa3bc6.b7dda4" - ] - ] - }, - { - "id": "f0ef065a.362028", - "type": "link in", - "z": "baa1e3d9.cb29d", - "name": "", - "links": [ - "a61d4164.135dd", - "783209c7.51c5a8", - "260e60f3.878ad", - "c5ee25c5.3c1848" - ], - "x": 1635, - "y": 1560, - "wires": [ - [ - "3475ecd5.6655f4" - ] - ] - }, - { - "id": "8f991d2e.6e8f3", - "type": "exec", - "z": "baa1e3d9.cb29d", - "command": "ls -l /var/www/html/media | grep \"th\" | tail -1 | awk -F \" \" '{print $9}' | awk -F \"_\" '{print $1\"_\"$2}'| tr -d \"\\n\"", - "addpay": false, - "append": "", - "useSpawn": "false", - "timer": "", - "oldrc": false, - "name": "get thumbail name", - "x": 1850, - "y": 1280, - "wires": [ - [ - "9dcdbf1f.4aa21" - ], - [], - [] - ] - }, - { - "id": "e6a12f33.c7768", - "type": "function", - "z": "baa1e3d9.cb29d", - "name": "mkdir", - "func": "acq_id=global.get(\"acq_id\")\nmsg.payload=\"/var/www/\"+acq_id\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 1770, - "y": 1140, - "wires": [ - [ - "43c69256.b9633c" - ] - ] - }, - { - "id": "43c69256.b9633c", - "type": "exec", - "z": "baa1e3d9.cb29d", - "command": "mkdir", - "addpay": true, - "append": "", - "useSpawn": "false", - "timer": "", - "oldrc": false, - "name": "mkdir acq_id", - "x": 1910, - "y": 1140, - "wires": [ - [], - [], - [] - ] - }, - { - "id": "517f13e8.e0793c", - "type": "function", - "z": "baa1e3d9.cb29d", - "name": "move", - "func": "file_prefix=msg.payload;\nacq_id=global.get(\"acq_id\")\nmsg.payload=\"/var/www/html/media/\"+file_prefix+\"* /var/www/\"+acq_id+\"/\";\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 2330, - "y": 1240, - "wires": [ - [ - "83a1d49e.a29a48" - ] - ] - }, - { - "id": "9dcdbf1f.4aa21", - "type": "delay", - "z": "baa1e3d9.cb29d", - "name": "", - "pauseType": "delay", - "timeout": "200", - "timeoutUnits": "milliseconds", - "rate": "1", - "nbRateUnits": "1", - "rateUnits": "second", - "randomFirst": "1", - "randomLast": "5", - "randomUnits": "seconds", - "drop": false, - "x": 2090, - "y": 1260, - "wires": [ - [ - "517f13e8.e0793c" - ] - ] - }, - { - "id": "83a1d49e.a29a48", - "type": "exec", - "z": "baa1e3d9.cb29d", - "command": "mv", - "addpay": true, - "append": "", - "useSpawn": "false", - "timer": "", - "oldrc": false, - "name": "", - "x": 2480, - "y": 1260, - "wires": [ - [], - [], - [] - ] - }, - { - "id": "20a2d27e.7ccafe", - "type": "function", - "z": "baa1e3d9.cb29d", - "name": "move", - "func": "file_prefix=msg.payload;\nacq_id=global.get(\"acq_id\")\nmsg.payload=\"/var/www/logs.json /var/www/\"+acq_id+\"/\";\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 2330, - "y": 1320, - "wires": [ - [ - "87cff57.f6d3708" - ] - ] - }, - { - "id": "87cff57.f6d3708", - "type": "exec", - "z": "baa1e3d9.cb29d", - "command": "mv", - "addpay": true, - "append": "", - "useSpawn": "false", - "timer": "", - "oldrc": false, - "name": "", - "x": 2480, - "y": 1340, - "wires": [ - [], - [], - [] - ] - }, - { - "id": "d91229e3.bf0f18", - "type": "while-loop", - "z": "baa1e3d9.cb29d", - "name": "", - "condi": "global.get(\"job\")===\"run\"", - "x": 1330, - "y": 200, - "wires": [ - [ - "427871db.b4902", - "a61b71c3.afaf" - ], - [ - "427871db.b4902", - "a61b71c3.afaf" - ] - ] - }, - { - "id": "217ff214.a25c2e", - "type": "function", - "z": "baa1e3d9.cb29d", - "name": "Run", - "func": "global.set(\"job\",\"run\")\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 1030, - "y": 220, - "wires": [ - [ - "d91229e3.bf0f18" - ] - ] - }, - { - "id": "995fa523.83cba8", - "type": "function", - "z": "baa1e3d9.cb29d", - "name": "Stop", - "func": "global.set(\"job\",\"stop\")\nmsg.payload=\"stop\"\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 1030, - "y": 180, - "wires": [ - [ - "d91229e3.bf0f18" - ] - ] - }, - { - "id": "d3ab1a14.86b8b8", - "type": "python3-function", - "z": "baa1e3d9.cb29d", - "name": "pump.py", - "func": "from adafruit_motor import stepper\nfrom adafruit_motorkit import MotorKit\nfrom time import sleep\n\nkit = MotorKit()\npump_stepper = kit.stepper1\npump_stepper.release()\n\nstate = str(msg[\"state\"])\nvolume = int(msg[\"volume\"])\norientation = str(msg[\"orientation\"])\nflowrate = float(msg[\"flowrate\"])\n\n\nif(state==\"free\"):\n #35000steps will pass 69ml if sleep(0.05) in between 2 steps\n #1ml is about 35000/69=507steps\n nb_step=volume*507 \n #nb_step=vol*460 if sleep(0) in between 2 steps\n \n duration=(volume*60)/flowrate\n \n delay=(duration/nb_step)-0.005\n \nif(state==\"canceled\"):\n nb_step=0\n \nfor i in range(nb_step):\n pump_stepper.onestep(direction=stepper.BACKWARD, style=stepper.DOUBLE)\n sleep(delay)\n \nsleep(1)\npump_stepper.release()\n\nmsg[\"topic\"] = \"pump\"\nmsg[\"payload\"] = \"done\"\n\nreturn msg", - "outputs": 1, - "x": 1380, - "y": 520, - "wires": [ - [ - "444587e4.dc23a8" - ] - ] - }, - { - "id": "ff805ffc.f9134", - "type": "python3-function", - "z": "baa1e3d9.cb29d", - "name": "actuate RGB", - "func": "import smbus\nfrom time import sleep\n\nbus = smbus.SMBus(1)\n\nrgb=msg['rgb']\nbus.write_byte_data(0x0d, 0x00, 0)\nbus.write_byte_data(0x0d, 0x01, rgb[\"r\"])\nbus.write_byte_data(0x0d, 0x02, rgb[\"g\"])\nbus.write_byte_data(0x0d, 0x03, rgb[\"b\"])\nbus.write_byte_data(0x0d, 0x00, 1)\nbus.write_byte_data(0x0d, 0x01, rgb[\"r\"])\nbus.write_byte_data(0x0d, 0x02, rgb[\"g\"])\nbus.write_byte_data(0x0d, 0x03, rgb[\"b\"])\nbus.write_byte_data(0x0d, 0x00, 2)\nbus.write_byte_data(0x0d, 0x01, rgb[\"r\"])\nbus.write_byte_data(0x0d, 0x02, rgb[\"g\"])\nbus.write_byte_data(0x0d, 0x03, rgb[\"b\"])\nreturn msg;", - "outputs": 1, - "x": 1390, - "y": 460, - "wires": [ - [ - "a27b3163.19c31" - ] - ] - }, - { - "id": "444587e4.dc23a8", - "type": "link out", - "z": "baa1e3d9.cb29d", - "name": "", - "links": [ - "e1354861.0bb648", - "2bc762dd.1115ce", - "a50134c.ed45ac8", - "17d09d70.b50223" - ], - "x": 1475, - "y": 520, - "wires": [] - }, - { - "id": "a27b3163.19c31", - "type": "function", - "z": "baa1e3d9.cb29d", - "name": "set busy", - "func": "global.set(\"state\",\"busy\");\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 1560, - "y": 460, - "wires": [ - [] - ] - }, - { - "id": "7c974057.4d3f", - "type": "function", - "z": "baa1e3d9.cb29d", - "name": "get duration acquisition", - "func": "msg.delay = global.get(\"duration\");\n\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 1430, - "y": 620, - "wires": [ - [] - ] - }, - { - "id": "482c8e09.a77df", - "type": "python3-function", - "z": "baa1e3d9.cb29d", - "name": "pump.py", - "func": "from adafruit_motor import stepper\nfrom adafruit_motorkit import MotorKit\nfrom time import sleep\n\nkit = MotorKit()\npump_stepper = kit.stepper1\n\npump_stepper.onestep(direction=stepper.BACKWARD, style=stepper.SIMPLE)\nsleep(0.1)", - "outputs": 1, - "x": 1820, - "y": 280, - "wires": [ - [] - ] - }, - { - "id": "427871db.b4902", - "type": "debug", - "z": "baa1e3d9.cb29d", - "name": "", - "active": true, - "tosidebar": true, - "console": false, - "tostatus": false, - "complete": "false", - "x": 1850, - "y": 220, - "wires": [] - }, - { - "id": "a61b71c3.afaf", - "type": "trigger", - "z": "baa1e3d9.cb29d", - "op1": "1", - "op2": "0", - "op1type": "str", - "op2type": "str", - "duration": "-250", - "extend": false, - "units": "ms", - "reset": "stop", - "bytopic": "all", - "name": "", - "x": 1620, - "y": 280, - "wires": [ - [ - "482c8e09.a77df" - ] - ] - }, - { - "id": "f7fa6acf.f6ed28", - "type": "function", - "z": "baa1e3d9.cb29d", - "name": "pump.js", - "func": "state = global.get(\"state\");\n\nif (state == null){\n state=\"free\"\n}\n\nif(state===\"free\"||state===\"canceled\"){\n volume = global.get(\"acq_volume\");\n flowrate = global.get(\"sug_flowrate\");\n duration=(((volume*60)/flowrate)-2)*1000\n global.set(\"duration\",duration);\n \n msg.volume = volume;\n msg.orientation = \"forward\";\n msg.flowrate = flowrate;\n msg.rgb = {r:0, g:255, b:255}\n msg.state = state\n \n return msg;\n \n \n}", - "outputs": 1, - "noerr": 0, - "x": 1100, - "y": 340, - "wires": [ - [ - "dd817ccf.04ec" - ] - ], - "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": "dd817ccf.04ec", - "type": "python3-function", - "z": "baa1e3d9.cb29d", - "name": "pump.py", - "func": "from adafruit_motor import stepper\nfrom adafruit_motorkit import MotorKit\nfrom time import sleep\n\nkit = MotorKit()\npump_stepper = kit.stepper1\npump_stepper.release()\n\nstate = str(msg[\"state\"])\nvolume = int(msg[\"volume\"])\nflowrate = float(msg[\"flowrate\"])\n\n\nif(state==\"free\"):\n #35000steps will pass 69ml if sleep(0.05) in between 2 steps\n #1ml is about 35000/69=507steps\n nb_step=volume*507 \n #nb_step=vol*460 if sleep(0) in between 2 steps\n \n duration=(volume*60)/flowrate\n \n delay=(duration/nb_step)-0.005\n \nif(state==\"canceled\"):\n nb_step=0\n \nfor i in range(nb_step):\n pump_stepper.onestep(direction=stepper.BACKWARD, style=stepper.DOUBLE)\n sleep(delay)\n \nsleep(1)\npump_stepper.release()\n\nmsg[\"topic\"] = \"pump\"\nmsg[\"payload\"] = \"done\"\n\nreturn msg", - "outputs": 1, - "x": 1280, - "y": 340, - "wires": [ - [] - ] - }, - { - "id": "7a5b8294.92ad3c", - "type": "ui_button", - "z": "baa1e3d9.cb29d", - "name": "", - "group": "b7919ae2.c01788", - "order": 4, - "width": 5, - "height": 1, - "passthru": false, - "label": "Show", - "tooltip": "", - "color": "#097479", - "bgcolor": "white", - "icon": "keyboard_tab", - "payload": "", - "payloadType": "str", - "topic": "", - "x": 470, - "y": 380, - "wires": [ - [ - "e2919164.70927" - ] - ] - }, - { - "id": "29be525e.0c87fe", - "type": "ui_template", - "z": "baa1e3d9.cb29d", - "group": "b5d61bc7.54fe48", - "name": "show global", - "order": 2, - "width": 0, - "height": 0, - "format": "
\n \n
", - "storeOutMessages": true, - "fwdInMessages": true, - "templateScope": "local", - "x": 750, - "y": 380, - "wires": [ - [] - ] - }, - { - "id": "e2919164.70927", - "type": "function", - "z": "baa1e3d9.cb29d", - "name": "get global", - "func": "msg.payload = {\n \"comment\":global.get(\"comment\"),\n \"sample_project\":global.get(\"sample_project\"),\n \"sample_ship\":global.get(\"sample_ship\"),\n \"sample_operator\":global.get(\"sample_operator\"),\n \"sample_id\":global.get(\"sample_id\"),\n \"sample_sampling_gear\":global.get(\"sample_sampling_gear\"),\n \n \"sample_hour\":global.get(\"sample_hour\"),\n \"sample_minute\":global.get(\"sample_minute\"),\n \"sample_day\":global.get(\"sample_day\"),\n \"sample_month\":global.get(\"sample_month\"),\n \"sample_year\":global.get(\"sample_year\"),\n \n \"object_lat\":global.get(\"object_lat\"),\n \"object_lon\":global.get(\"object_lon\"),\n \n \"acq_id\":global.get(\"acq_id\"),\n \"acq_fnumber_objective\":global.get(\"acq_fnumber_objective\"),\n \"acq_celltype\":global.get(\"acq_celltype\"),\n \"acq_maximum_mesh\":global.get(\"acq_maximum_mesh\"),\n \"acq_minimum_mesh\":global.get(\"acq_minimum_mesh\"),\n \"process_pixel\":global.get(\"process_pixel\"),\n \n \"acq_camera\":global.get(\"acq_camera\"),\n \"acq_instrument\":global.get(\"acq_instrument\"),\n \"acq_software\":global.get(\"acq_software\"),\n \"acq_instrument_ID\":global.get(\"acq_instrument_ID\"),\n \"acq_volume\":global.get(\"acq_volume\"),\n \"acq_flowrate\":global.get(\"sug_flowrate\")\n }\n\nreturn msg;", - 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"edited": false - }, - "base-font": { - "value": "-apple-system,BlinkMacSystemFont,Segoe UI,Roboto,Oxygen-Sans,Ubuntu,Cantarell,Helvetica Neue,sans-serif" - } - }, - "angularTheme": { - "primary": "indigo", - "accents": "blue", - "warn": "red", - "background": "grey" - } - }, - "site": { - "name": "Node-RED Dashboard", - "hideToolbar": "false", - "allowSwipe": "false", - "lockMenu": "false", - "allowTempTheme": "true", - "dateFormat": "DD/MM/YYYY", - "sizes": { - "sx": 48, - "sy": 48, - "gx": 6, - "gy": 6, - "cx": 6, - "cy": 6, - "px": 0, - "py": 0 - } - } - }, - { - "id": "c18fae15.516ce", - "type": "ui_tab", - "z": "", - "name": "Home", - "icon": "dashboard", - "order": 1, - "disabled": false, - "hidden": false - }, - { - "id": "29a78fc9.b034c", - "type": "ui_group", - "z": "", - "name": "Static Observation", - "tab": "c18fae15.516ce", - "order": 1, - "disp": false, - "width": "12", - "collapse": false - }, - { - "id": "10d36e29.c78b42", - "type": "ui_group", - "z": "", - "name": "Fluidic Acquisition", - 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"type": "ui_tab", - "z": "", - "name": "Dashboard Control", - "icon": "dashboard", - "order": 5, - "disabled": false, - "hidden": false - }, - { - "id": "498d73e3.d1c94c", - "type": "ui_group", - "name": "Group 1", - "tab": "98e9fd1a.1bbe5", - "order": 1, - "disp": true, - "width": 6 - }, - { - "id": "72fe0cc7.df9fd4", - "type": "ui_group", - "name": "Group 1", - "tab": "2e62c9a8.c191f6", - "order": 1, - "disp": true, - "width": 6 - }, - { - "id": "54c8e6e0.223fc8", - "type": "ui_group", - "name": "Group 1", - "tab": "609b39b5.d91f28", - "order": 1, - "disp": true, - "width": 6 - }, - { - "id": "5841eafd.95e5e4", - "type": "ui_group", - "name": "Group 1", - "tab": "b253b89c.1c4458", - "order": 1, - "disp": true, - "width": 6 - }, - { - "id": "df3ac001.1d82a", - "type": "ui_button", - "z": "7f885510.6173fc", - "name": "", - "group": "29a78fc9.b034c", - "order": 1, - "width": 12, - "height": 6, - "passthru": false, - "label": "Static Observation", - "tooltip": "", - "color": "", - "bgcolor": "", - 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] - ] - }, - { - "id": "47a9f575.dc2c8c", - "type": "ui_button", - "z": "7f885510.6173fc", - "name": "", - "group": "edb89598.853498", - "order": 1, - "width": 12, - "height": 6, - "passthru": false, - "label": "Dashboard Control", - "tooltip": "", - "color": "", - "bgcolor": "", - "icon": "", - "payload": "", - "payloadType": "str", - "topic": "Dashboard Control", - "x": 270, - "y": 380, - "wires": [ - [ - "82696634.821678" - ] - ] - }, - { - "id": "c0f2a501.1677c8", - "type": "ui_ui_control", - "z": "7f885510.6173fc", - "name": "", - "events": "change", - "x": 540, - "y": 260, - "wires": [ - [] - ] - }, - { - "id": "c52be0d9.e6412", - "type": "ui_button", - "z": "55a31f5b.d4ec5", - "name": "", - "group": "498d73e3.d1c94c", - "order": 0, - "width": 0, - "height": 0, - "passthru": false, - "label": "Home", - "tooltip": "", - "color": "", - "bgcolor": "", - "icon": "", - "payload": "", - "payloadType": "str", - "topic": "Home", - "x": 70, - "y": 40, - "wires": [ - [ - "66e609a2.2d57d8" - ] - ] - }, - { - "id": "82696634.821678", - "type": "function", - "z": "7f885510.6173fc", - "name": "swtich tab", - "func": "\nmsg.payload={\"tab\":msg.topic};\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 400, - "y": 260, - "wires": [ - [ - "c0f2a501.1677c8" - ] - ] - }, - { - "id": "8059df68.0963c", - "type": "ui_ui_control", - "z": "55a31f5b.d4ec5", - "name": "", - "events": "change", - "x": 380, - "y": 40, - "wires": [ - [] - ] - }, - { - "id": "66e609a2.2d57d8", - "type": "function", - "z": "55a31f5b.d4ec5", - "name": "change tab", - "func": "\nmsg.payload={\"tab\":msg.topic};\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 220, - "y": 40, - "wires": [ - [ - "8059df68.0963c" - ] - ] - }, - { - "id": "f8c2a4c7.928f88", - "type": "ui_button", - "z": "c04dcc2a.47862", - "name": "", - "group": "72fe0cc7.df9fd4", - "order": 0, - "width": 0, - "height": 0, - "passthru": false, - "label": "Home", - "tooltip": "", - "color": "", - "bgcolor": "", - "icon": "", - "payload": "", - "payloadType": "str", - "topic": "Home", - "x": 70, - "y": 40, - "wires": [ - [ - "6715b713.0ea1e8" - ] - ] - }, - { - "id": "16edbf14.c67bb1", - "type": "ui_ui_control", - "z": "c04dcc2a.47862", - "name": "", - "events": "change", - "x": 380, - "y": 40, - "wires": [ - [] - ] - }, - { - "id": "6715b713.0ea1e8", - "type": "function", - "z": "c04dcc2a.47862", - "name": "change tab", - "func": "\nmsg.payload={\"tab\":msg.topic};\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 220, - "y": 40, - "wires": [ - [ - "16edbf14.c67bb1" - ] - ] - }, - { - "id": "e46b58fd.671568", - "type": "ui_button", - "z": "300f077.33624f8", - "name": "", - "group": "54c8e6e0.223fc8", - "order": 0, - "width": 0, - "height": 0, - "passthru": false, - "label": "Home", - "tooltip": "", - "color": "", - "bgcolor": "", - "icon": "", - "payload": "", - "payloadType": "str", - "topic": "Home", - "x": 70, - "y": 40, - "wires": [ - [ - "5c885d69.f82f74" - ] - ] - }, - { - "id": "c492a6c.3ff6558", - "type": "ui_ui_control", - "z": "300f077.33624f8", - "name": "", - "events": "change", - "x": 380, - "y": 40, - "wires": [ - [] - ] - }, - { - "id": "5c885d69.f82f74", - "type": "function", - "z": "300f077.33624f8", - "name": "change tab", - "func": "\nmsg.payload={\"tab\":msg.topic};\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 220, - "y": 40, - "wires": [ - [ - "c492a6c.3ff6558" - ] - ] - }, - { - "id": "cb7440f4.3efff", - "type": "ui_button", - "z": "121f01ae.4c4abe", - "name": "", - "group": "5841eafd.95e5e4", - "order": 0, - "width": 0, - "height": 0, - "passthru": false, - "label": "Home", - "tooltip": "", - "color": "", - "bgcolor": "", - "icon": "", - "payload": "", - "payloadType": "str", - "topic": "Home", - "x": 70, - "y": 40, - "wires": [ - [ - "b0b1ec9.5371e1" - ] - ] - }, - { - "id": "a4505700.60eb18", - "type": "ui_ui_control", - "z": "121f01ae.4c4abe", - "name": "", - "events": "change", - "x": 380, - "y": 40, - "wires": [ - [] - ] - }, - { - "id": "b0b1ec9.5371e1", - "type": "function", - "z": "121f01ae.4c4abe", - "name": "change tab", - "func": "\nmsg.payload={\"tab\":msg.topic};\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 220, - "y": 40, - "wires": [ - [ - "a4505700.60eb18" - ] - ] - } -] diff --git a/flows/flows_planktonscope.json b/flows/flows_planktonscope.json deleted file mode 100644 index f7cec23..0000000 --- a/flows/flows_planktonscope.json +++ /dev/null @@ -1,1747 +0,0 @@ -[ - { - "id": "7f885510.6173fc", - "type": "tab", - "label": "Flow 1", - "disabled": false, - "info": "" - }, - { - "id": "955fdac.f54f328", - "type": "ui_text_input", - "z": "7f885510.6173fc", - "name": "sample_ship", - "label": "Name of the ship", - "tooltip": "", - "group": "c627ea8d.f886e8", - "order": 2, - "width": 0, - "height": 0, - "passthru": true, - "mode": "text", - "delay": 300, - "topic": "sample_ship", - "x": 170, - "y": 100, - "wires": [ - [ - "3dd9a121.e386de" - ] - ] - }, - { - "id": "dfb29406.d68148", - "type": "ui_dropdown", - "z": "7f885510.6173fc", - "name": "sample_sampling_gear", - "label": "Sampling gear", - "tooltip": "", - "place": "Select", - "group": "c627ea8d.f886e8", - "order": 5, - "width": 0, - "height": 0, - "passthru": true, - "options": [ - { - "label": "Plankton net", - "value": "net", - "type": "str" - }, - { - "label": "Niskin bottle 12L", - "value": "niskin_12L", - "type": "str" - }, - { - "label": "Niskin bottle 24L", - "value": "niskin_24L", - "type": "str" - } - ], - "payload": "", - "topic": "sample_sampling_gear", - "x": 130, - "y": 220, - "wires": [ - [ - "8861710f.55b92" - ] - ] - }, - { - "id": "bfce92c6.5f66a", - "type": "ui_text_input", - "z": "7f885510.6173fc", - "name": "sample_operator", - "label": "Name of the operator", - "tooltip": "", - "group": "c627ea8d.f886e8", - "order": 4, - "width": 0, - "height": 0, - "passthru": true, - "mode": "text", - "delay": 300, - "topic": "sample_operator", - "x": 150, - "y": 180, - "wires": [ - [ - "3dd9a121.e386de" - ] - ] - }, - { - "id": "bae9c122.3612f", - "type": "ui_text_input", - "z": "7f885510.6173fc", - "name": "sample_project", - "label": "Name of the project*", - "tooltip": "", - "group": "c627ea8d.f886e8", - "order": 1, - "width": 0, - "height": 0, - "passthru": true, - "mode": "text", - "delay": 300, - "topic": "sample_project", - "x": 160, - "y": 40, - "wires": [ - [ - "3dd9a121.e386de", - "a8cb0c6e.7220d" - ] - ] - }, - { - "id": "eb39c21c.a3fec", - "type": "ui_text_input", - "z": "7f885510.6173fc", - "name": "object_lat", - "label": "Lattitude (decimal degrees)", - "tooltip": "", - "group": "106f0e1b.6478a2", - "order": 7, - "width": 0, - "height": 0, - "passthru": true, - "mode": "number", - "delay": 300, - "topic": "object_lat", - "x": 1020, - "y": 320, - "wires": [ - [ - "c650b922.6adef8" - ] - ] - }, - { - "id": "404b41a5.ae3d5", - "type": "ui_text_input", - "z": "7f885510.6173fc", - "name": "object_lon", - "label": "Longitude (decimal degrees)", - "tooltip": "", - "group": "106f0e1b.6478a2", - "order": 8, - "width": 0, - "height": 0, - "passthru": true, - "mode": "number", - "delay": 300, - "topic": "object_lon", - "x": 1010, - "y": 360, - "wires": [ - [ - "c650b922.6adef8" - ] - ] - }, - { - "id": "d90c72f2.cf1ca", - "type": "ui_text_input", - "z": "7f885510.6173fc", - "name": "sample_id", - "label": "Name of the station*", - "tooltip": "", - "group": "c627ea8d.f886e8", - "order": 3, - "width": 0, - "height": 0, - "passthru": true, - "mode": "text", - "delay": 300, - "topic": "sample_id", - "x": 170, - "y": 140, - "wires": [ - [ - "3dd9a121.e386de" - ] - ] - }, - { - "id": "3300f426.cc515c", - "type": "ui_dropdown", - "z": "7f885510.6173fc", - "name": "acq_fnumber_objective", - "label": "M12 Lens*", - "tooltip": "", - "place": "Select option", - "group": "832434ce.ebe498", - "order": 1, - "width": 0, - "height": 0, - "passthru": true, - "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", - "x": 1030, - "y": 40, - "wires": [ - [ - "de455648.b432f8" - ] - ] - }, - { - "id": "72d57e31.59234", - "type": "ui_template", - "z": "7f885510.6173fc", - "group": "832434ce.ebe498", - "name": "Magnification", - "order": 2, - "width": 0, - "height": 0, - "format": "
\n Magnification : X\n \n \n
", - "storeOutMessages": true, - "fwdInMessages": true, - "templateScope": "local", - "x": 1590, - "y": 40, - "wires": [ - [] - ] - }, - { - "id": "98a4bc0a.f3304", - "type": "ui_template", - "z": "7f885510.6173fc", - "group": "77a6994b.e3efb8", - "name": "Instrument", - "order": 1, - "width": 0, - "height": 0, - "format": "
\n Instrument :\n \n PlanktonScope V2.1\n \n
", - "storeOutMessages": true, - "fwdInMessages": true, - "templateScope": "local", - "x": 170, - "y": 480, - "wires": [ - [] - ] - }, - { - "id": "53b3cb43.2acf04", - "type": "ui_template", - "z": "7f885510.6173fc", - "group": "77a6994b.e3efb8", - "name": "Software", - "order": 2, - "width": 0, - "height": 0, - "format": "
\n Software :\n \n Node-RED Dashboard\n \n
", - "storeOutMessages": true, - "fwdInMessages": true, - "templateScope": "local", - "x": 180, - "y": 520, - "wires": [ - [] - ] - }, - { - "id": "1a0a45f1.2cd7da", - "type": "ui_template", - "z": "7f885510.6173fc", - "group": "77a6994b.e3efb8", - "name": "Camera", - "order": 3, - "width": 0, - "height": 0, - "format": "
\n Camera :\n \n Pi Camera v2.1\n \n
", - "storeOutMessages": true, - "fwdInMessages": true, - "templateScope": "local", - "x": 180, - "y": 560, - "wires": [ - [] - ] - }, - { - "id": "de455648.b432f8", - "type": "function", - "z": "7f885510.6173fc", - "name": "calculate", - "func": "global.set(msg.topic,msg.payload);\nvar acq_fnumber_objective = String(global.get(msg.topic));\n\nswitch(acq_fnumber_objective) {\n case \"25\":\n global.set(\"magnification\",0.6);\n global.set(\"process_pixel\",1.86);\n global.set(\"sug_min\",60);\n global.set(\"sug_max\",670);\n global.set(\"sug_flowrate\",3);\n break;\n case \"16\":\n global.set(\"magnification\",0.94);\n global.set(\"process_pixel\",1.19);\n global.set(\"sug_min\",40);\n global.set(\"sug_max\",430);\n global.set(\"sug_flowrate\",2.4);\n break;\n case \"12\":\n global.set(\"magnification\",1.20);\n global.set(\"process_pixel\",0.94);\n global.set(\"sug_min\",30);\n global.set(\"sug_max\",340);\n global.set(\"sug_flowrate\",1.25);\n break;\n case \"8\":\n global.set(\"magnification\",1.78);\n global.set(\"process_pixel\",0.63);\n global.set(\"sug_min\",20);\n global.set(\"sug_max\",230);\n global.set(\"sug_flowrate\",0.42);\n break;\n case \"6\":\n global.set(\"magnification\",2.36);\n global.set(\"process_pixel\",0.48);\n global.set(\"sug_min\",15);\n global.set(\"sug_max\",170);\n global.set(\"sug_flowrate\",0.32);\n break;\n}\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 1220, - "y": 40, - "wires": [ - [ - "c83fc403.8ba2d8", - "48d9cc9c.852214", - "44969aec.4e87e4", - "a1201a.dc3f8fe8", - "89b9399b.9389a8" - ] - ] - }, - { - "id": "f3aa18d.65f0de8", - "type": "ui_dropdown", - "z": "7f885510.6173fc", - "name": "acq_celltype", - "label": "Thickness flowcell*", - "tooltip": "", - "place": "Select option", - "group": "a72a9ec6.bb144", - "order": 1, - "width": 0, - "height": 0, - "passthru": true, - "options": [ - { - "label": "200 μm µ-Slide I Luer", - "value": 200, - "type": "num" - }, - { - "label": "400 μm µ-Slide I Luer", - "value": 400, - "type": "num" - }, - { - "label": "600 μm µ-Slide I Luer", - "value": 600, - "type": "num" - }, - { - "label": "800 μm µ-Slide I Luer", - "value": 800, - "type": "num" - } - ], - "payload": "", - "topic": "acq_celltype", - "x": 170, - "y": 280, - "wires": [ - [ - "8861710f.55b92" - ] - ] - }, - { - "id": "45568fe8.67759", - "type": "ui_numeric", - "z": "7f885510.6173fc", - "name": "acq_minimum_mesh", - "label": "Min fraction size (μm)", - "tooltip": "", - "group": "a72a9ec6.bb144", - "order": 2, - "width": 0, - "height": 0, - "wrap": false, - "passthru": true, - "topic": "acq_minimum_mesh", - "format": "{{value}}", - "min": 0, - "max": "300", - "step": "10", - "x": 140, - "y": 320, - "wires": [ - [ - "8861710f.55b92" - ] - ] - }, - { - "id": "918b69e2.7e6e88", - "type": "ui_numeric", - "z": "7f885510.6173fc", - "name": "acq_maximum_mesh", - "label": "Max fraction size (μm)", - "tooltip": "", - "group": "a72a9ec6.bb144", - "order": 3, - "width": 0, - "height": 0, - "wrap": false, - "passthru": true, - "topic": "acq_maximum_mesh", - "format": "{{value}}", - "min": "200", - "max": "2000", - "step": "100", - "x": 140, - "y": 360, - "wires": [ - [ - "8861710f.55b92" - ] - ] - }, - { - "id": "86d762dc.47911", - "type": "ui_switch", - "z": "7f885510.6173fc", - "name": "light_state", - "label": "Light", - "tooltip": "", - "group": "c62ffbd3.787ef8", - "order": 1, - "width": 2, - "height": 1, - "passthru": true, - "decouple": "false", - "topic": "", - "style": "", - "onvalue": "true", - "onvalueType": "bool", - "onicon": "", - "oncolor": "", - "offvalue": "false", - "offvalueType": "bool", - "officon": "", - "offcolor": "", - "x": 510, - "y": 160, - "wires": [ - [ - "b5a366b4.cb6918" - ] - ] - }, - { - "id": "b5a366b4.cb6918", - "type": "exec", - "z": "7f885510.6173fc", - "command": "python3.7 $HOME/PlanktonScope/scripts/light.py", - "addpay": true, - "append": "", - "useSpawn": "false", - "timer": "", - "oldrc": false, - "name": "light.py", - "x": 820, - "y": 160, - "wires": [ - [], - [], - [] - ], - "icon": "node-red/light.svg" - }, - { - "id": "5ea28a70.42ae14", - "type": "ui_button", - "z": "7f885510.6173fc", - "name": "up", - "group": "c62ffbd3.787ef8", - "order": 3, - "width": 1, - "height": 1, - "passthru": false, - "label": "", - "tooltip": "", - "color": "", - "bgcolor": "", - "icon": "arrow_upwards", - "payload": "up", - "payloadType": "str", - "topic": "up", - "x": 530, - "y": 280, - "wires": [ - [ - "523fdeaa.50c6c" - ] - ] - }, - { - "id": "27f16831.dde938", - "type": "ui_button", - "z": "7f885510.6173fc", - "name": "down", - "group": "c62ffbd3.787ef8", - "order": 5, - "width": 1, - "height": 1, - "passthru": true, - "label": "", - "tooltip": "", - "color": "", - "bgcolor": "", - "icon": "arrow_downward", - "payload": "down", - "payloadType": "str", - "topic": "down", - "x": 530, - "y": 360, - "wires": [ - [ - "523fdeaa.50c6c" - ] - ] - }, - { - "id": "b110542b.5de4f8", - "type": "ui_button", - "z": "7f885510.6173fc", - "name": "kill_focus", - "group": "c62ffbd3.787ef8", - "order": 6, - "width": 2, - "height": 1, - "passthru": false, - "label": "Cancel focus", - "tooltip": "", - "color": "#AD1625", - "bgcolor": "#333333", - "icon": "pause", - "payload": "", - "payloadType": "str", - "topic": "", - "x": 520, - "y": 400, - "wires": [ - [ - "d9dea2bc.47097" - ] - ] - }, - { - "id": "523fdeaa.50c6c", - "type": "function", - "z": "7f885510.6173fc", - "name": "focus", - "func": "if(msg.topic === \"nb_step\"){\n nb_step = msg.payload;\n global.set(\"nb_step\",nb_step);\n}\nif(msg.topic === \"up\"){\n\n nb_step = global.get(\"nb_step\");\n\n orientation = \"up\";\n\n msg.payload = String(nb_step).concat(' ', orientation);\n return msg;\n}\nif(msg.topic === \"down\"){\n \n nb_step = global.get(\"nb_step\");\n\n orientation = \"down\";\n msg.payload = String(nb_step).concat(' ', orientation);\n\n return msg;\n}\n\n", - "outputs": 1, - "noerr": 0, - "x": 670, - "y": 320, - "wires": [ - [ - "ada728bd.8e7818" - ] - ], - "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": "ada728bd.8e7818", - "type": "exec", - "z": "7f885510.6173fc", - "command": "python3.7 $HOME/PlanktonScope/scripts/focus.py", - "addpay": true, - "append": "", - "useSpawn": "false", - "timer": "", - "oldrc": false, - "name": "focus.py", - "x": 820, - "y": 320, - "wires": [ - [], - [], - [] - ], - "icon": "node-red/sort.svg" - }, - { - "id": "d9dea2bc.47097", - "type": "exec", - "z": "7f885510.6173fc", - "command": "bash $HOME/PlanktonScope/scripts/killer.sh focus.py && bash $HOME/PlanktonScope/scripts/killer.sh focus.py", - "addpay": false, - "append": "", - "useSpawn": "false", - "timer": "", - "oldrc": false, - "name": "Kill Focus", - "x": 820, - "y": 400, - "wires": [ - [], - [], - [] - ], - "icon": "font-awesome/fa-stop" - }, - { - "id": "2d0f6720.0f92f8", - "type": "ui_template", - "z": "7f885510.6173fc", - "group": "832434ce.ebe498", - "name": "Pi Camera settings", - "order": 7, - "width": 0, - "height": 0, - "format": "\n", - "storeOutMessages": true, - "fwdInMessages": true, - "templateScope": "local", - "x": 1010, - "y": 100, - "wires": [ - [] - ] - }, - { - "id": "9599b953.529c28", - "type": "ui_template", - "z": "7f885510.6173fc", - "group": "832434ce.ebe498", - "name": "process_pixel", - "order": 3, - "width": 0, - "height": 0, - "format": "
\n Pixel resolution :\n \n μm\n
", - "storeOutMessages": true, - "fwdInMessages": true, - "templateScope": "local", - "x": 1600, - "y": 80, - "wires": [ - [] - ] - }, - { - "id": "612e2b9b.ed1684", - "type": "ui_template", - "z": "7f885510.6173fc", - "group": "832434ce.ebe498", - "name": "min_size", - "order": 4, - "width": 0, - "height": 0, - "format": "
\n Smallest cells to explore :\n \n μm\n
", - "storeOutMessages": true, - "fwdInMessages": true, - "templateScope": "local", - "x": 1580, - "y": 120, - "wires": [ - [] - ] - }, - { - "id": "f84ab57a.556df8", - "type": "ui_template", - "z": "7f885510.6173fc", - "group": "832434ce.ebe498", - "name": "max_size", - "order": 5, - "width": 0, - "height": 0, - "format": "
\n Biggest cells to explore :\n \n μm\n
", - "storeOutMessages": true, - "fwdInMessages": true, - "templateScope": "local", - "x": 1580, - "y": 160, - "wires": [ - [] - ] - }, - { - "id": "45f53656.d631e8", - "type": "ui_template", - "z": "7f885510.6173fc", - "group": "832434ce.ebe498", - "name": "flowrate", - "order": 6, - "width": 0, - "height": 0, - "format": "
\n Suggested flowrate :\n \n ml/min\n
", - "storeOutMessages": true, - "fwdInMessages": true, - "templateScope": "local", - "x": 1580, - "y": 200, - "wires": [ - [] - ] - }, - { - "id": "53ec5f97.7567c", - "type": "ui_template", - "z": "7f885510.6173fc", - "group": "3d740a07.4674e6", - "name": "Stream Pi Camera", - "order": 1, - "width": 0, - "height": 0, - "format": "
", - "storeOutMessages": true, - "fwdInMessages": true, - "templateScope": "local", - "x": 570, - "y": 40, - "wires": [ - [] - ] - }, - { - "id": "c84f1718.4af6b8", - "type": "ui_switch", - "z": "7f885510.6173fc", - "name": "fan_state", - "label": "Fan", - "tooltip": "", - "group": "c62ffbd3.787ef8", - "order": 2, - "width": 2, - "height": 1, - "passthru": true, - "decouple": "false", - "topic": "", - "style": "", - "onvalue": "true", - "onvalueType": "bool", - "onicon": "", - "oncolor": "", - "offvalue": "false", - "offvalueType": "bool", - "officon": "", - "offcolor": "", - "x": 520, - "y": 220, - "wires": [ - [ - "dec2b84a.6faa18" - ] - ] - }, - { - "id": "dec2b84a.6faa18", - "type": "exec", - "z": "7f885510.6173fc", - "command": "python3.7 $HOME/PlanktonScope/scripts/fan.py", - "addpay": true, - "append": "", - "useSpawn": "false", - "timer": "", - "oldrc": false, - "name": "fan.py", - "x": 810, - "y": 220, - "wires": [ - [], - [], - [] - ], - "icon": "font-awesome/fa-spinner" - }, - { - "id": "477dc1bd.c3de8", - "type": "ui_text_input", - "z": "7f885510.6173fc", - "name": "acq_id", - "label": "Acquisition unique ID*", - "tooltip": "", - "group": "a61f7be8.af6418", - "order": 1, - "width": 4, - "height": 1, - "passthru": true, - "mode": "text", - "delay": 300, - "topic": "acq_id", - "x": 530, - "y": 680, - "wires": [ - [ - "263878b3.e0a478" - ] - ] - }, - { - "id": "3dd9a121.e386de", - "type": "function", - "z": "7f885510.6173fc", - "name": "set global", - "func": "var value = msg.payload.split(' ').join('_');\nvar key = msg.topic;\n\nglobal.set(key,value);", - "outputs": 1, - "noerr": 0, - "x": 340, - "y": 40, - "wires": [ - [] - ] - }, - { - "id": "c83fc403.8ba2d8", - "type": "function", - "z": "7f885510.6173fc", - "name": "get magnification", - "func": "var magnification = global.get(\"magnification\");\nmsg.payload = magnification;\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 1410, - "y": 40, - "wires": [ - [ - "72d57e31.59234" - ] - ] - }, - { - "id": "48d9cc9c.852214", - "type": "function", - "z": "7f885510.6173fc", - "name": "get process_pixel", - "func": "var process_pixel = global.get(\"process_pixel\");\nmsg.payload = process_pixel;\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 1410, - "y": 80, - "wires": [ - [ - "9599b953.529c28" - ] - ] - }, - { - "id": "44969aec.4e87e4", - "type": "function", - "z": "7f885510.6173fc", - "name": "get sug_min", - "func": "var sug_min = global.get(\"sug_min\");\nmsg.payload = sug_min;\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 1390, - "y": 120, - "wires": [ - [ - "612e2b9b.ed1684" - ] - ] - }, - { - "id": "a1201a.dc3f8fe8", - "type": "function", - "z": "7f885510.6173fc", - "name": "get sug_max", - "func": "var sug_max = global.get(\"sug_max\");\nmsg.payload = sug_max;\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 1390, - "y": 160, - "wires": [ - [ - "f84ab57a.556df8" - ] - ] - }, - { - "id": "89b9399b.9389a8", - "type": "function", - "z": "7f885510.6173fc", - "name": "get flowrate", - "func": "var sug_flowrate = global.get(\"sug_flowrate\");\nmsg.payload = sug_flowrate\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 1390, - "y": 200, - "wires": [ - [ - "45f53656.d631e8" - ] - ] - }, - { - "id": "c650b922.6adef8", - "type": "function", - "z": "7f885510.6173fc", - "name": "set global", - "func": "var value = msg.payload;\nvar key = msg.topic;\n\nglobal.set(key,value);", - "outputs": 1, - "noerr": 0, - "x": 1180, - "y": 320, - "wires": [ - [] - ] - }, - { - "id": "e4c54d5a.19ff3", - "type": "ui_numeric", - "z": "7f885510.6173fc", - "name": "sample_year", - "label": "/", - "tooltip": "", - "group": "106f0e1b.6478a2", - "order": 3, - "width": 2, - "height": 1, - "wrap": false, - "passthru": true, - "topic": "sample_year", - "format": "{{value}}", - "min": "19", - "max": "50", - "step": 1, - "x": 1010, - "y": 480, - "wires": [ - [ - "c650b922.6adef8" - ] - ] - }, - { - "id": "b45db708.cedec8", - "type": "ui_numeric", - "z": "7f885510.6173fc", - "name": "sample_month", - "label": "/", - "tooltip": "", - "group": "106f0e1b.6478a2", - "order": 2, - "width": 2, - "height": 1, - "wrap": false, - "passthru": true, - "topic": "sample_month", - "format": "{{value}}", - "min": "1", - "max": "12", - "step": 1, - "x": 1000, - "y": 440, - "wires": [ - [ - "c650b922.6adef8" - ] - ] - }, - { - "id": "6351d257.6d7f1c", - "type": "ui_numeric", - "z": "7f885510.6173fc", - "name": "sample_day", - "label": "Date*", - "tooltip": "", - "group": "106f0e1b.6478a2", - "order": 1, - "width": 3, - "height": 1, - "wrap": false, - "passthru": true, - "topic": "sample_day", - "format": "{{value}}", - "min": "1", - "max": "31", - "step": 1, - "x": 1010, - "y": 400, - "wires": [ - [ - "c650b922.6adef8" - ] - ] - }, - { - "id": "9ee03294.39987", - "type": "ui_numeric", - "z": "7f885510.6173fc", - "name": "sample_hour", - "label": "Time*", - "tooltip": "", - "group": "106f0e1b.6478a2", - "order": 4, - "width": 5, - "height": 1, - "wrap": false, - "passthru": true, - "topic": "sample_hour", - "format": "{{value}}", - "min": "0", - "max": "24", - "step": 1, - "x": 1010, - "y": 520, - "wires": [ - [ - "c650b922.6adef8" - ] - ] - }, - { - "id": "5bd11314.ae6e4c", - "type": "ui_numeric", - "z": "7f885510.6173fc", - "name": "sample_minute", - "label": ":", - "tooltip": "", - "group": "106f0e1b.6478a2", - "order": 5, - "width": 2, - "height": 1, - "wrap": false, - "passthru": true, - "topic": "sample_minute", - "format": "{{value}}", - "min": "0", - "max": "59", - "step": 1, - "x": 1000, - "y": 560, - "wires": [ - [ - "c650b922.6adef8" - ] - ] - }, - { - "id": "8861710f.55b92", - "type": "function", - "z": "7f885510.6173fc", - "name": "set global", - "func": "var value = msg.payload;\nvar key = msg.topic;\n\nglobal.set(key,value);", - "outputs": 1, - "noerr": 0, - "x": 340, - "y": 280, - "wires": [ - [] - ] - }, - { - "id": "a8cb0c6e.7220d", - "type": "function", - "z": "7f885510.6173fc", - "name": "store generic", - "func": "global.set(\"acq_instrument\",\"PlanktonScope V2.1\");\nglobal.set(\"acq_software\",\"Node-RED Dashboard\");\nglobal.set(\"acq_camera\",\"Pi Camera V2.1\");\nglobal.set(\"acq_instrument_ID\",\"Odezenne\");", - "outputs": 1, - "noerr": 0, - "x": 350, - "y": 420, - "wires": [ - [] - ] - }, - { - "id": "263878b3.e0a478", - "type": "function", - "z": "7f885510.6173fc", - "name": "set global", - "func": "var value = msg.payload;\nvar key = msg.topic;\n\nglobal.set(key,value);", - "outputs": 1, - "noerr": 0, - "x": 680, - "y": 660, - "wires": [ - [] - ] - }, - { - "id": "4b3ea5bd.03248c", - "type": "ui_button", - "z": "7f885510.6173fc", - "name": "backward", - "group": "c62ffbd3.787ef8", - "order": 7, - "width": 3, - "height": 1, - "passthru": false, - "label": "Backward", - "tooltip": "", - "color": "", - "bgcolor": "", - "icon": "arrow_back", - "payload": "backward", - "payloadType": "str", - "topic": "backward", - "x": 520, - "y": 460, - "wires": [ - [ - "84fd85fd.426878" - ] - ] - }, - { - "id": "cfe9783a.286438", - "type": "ui_button", - "z": "7f885510.6173fc", - "name": "foward", - "group": "c62ffbd3.787ef8", - "order": 9, - "width": 3, - "height": 1, - "passthru": true, - "label": "Forward", - "tooltip": "", - "color": "", - "bgcolor": "", - "icon": "arrow_forward", - "payload": "foward", - "payloadType": "str", - "topic": "foward", - "x": 530, - "y": 540, - "wires": [ - [ - "84fd85fd.426878" - ] - ] - }, - { - "id": "83d75b6b.6afa28", - "type": "ui_button", - "z": "7f885510.6173fc", - "name": "kill_pump", - "group": "c62ffbd3.787ef8", - "order": 10, - "width": 2, - "height": 1, - "passthru": false, - "label": "Cancel pump", - "tooltip": "", - "color": "#AD1625", - "bgcolor": "#333333", - "icon": "pause", - "payload": "", - "payloadType": "str", - "topic": "", - "x": 520, - "y": 580, - "wires": [ - [ - "8fc930df.c7ae6" - ] - ] - }, - { - "id": "84fd85fd.426878", - "type": "function", - "z": "7f885510.6173fc", - "name": "pump", - "func": "if(msg.topic === \"volume\"){\n volume = msg.payload;\n global.set(\"volume\",volume);\n}\nif(msg.topic === \"foward\"){\n\n volume = global.get(\"volume\");\n flowrate = global.get(\"flowrate\");\n\n action = \" foward\";\n\n msg.payload = String(volume).concat(' ',flowrate, action);\n return msg;\n}\nif(msg.topic === \"backward\"){\n \n volume = global.get(\"volume\");\n flowrate = global.get(\"flowrate\");\n\n action = \" backward\";\n msg.payload = String(volume).concat(' ',flowrate, action);\n\n return msg;\n}\n\n", - "outputs": 1, - "noerr": 0, - "x": 670, - "y": 500, - "wires": [ - [ - "649f7ec8.06a84" - ] - ], - "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": "649f7ec8.06a84", - "type": "exec", - "z": "7f885510.6173fc", - "command": "python3.7 $HOME/PlanktonScope/scripts/pump.py", - "addpay": true, - "append": "", - "useSpawn": "false", - "timer": "", - "oldrc": false, - "name": "pump.py", - "x": 820, - "y": 500, - "wires": [ - [], - [], - [] - ], - "icon": "font-awesome/fa-rotate-left" - }, - { - "id": "8fc930df.c7ae6", - "type": "exec", - "z": "7f885510.6173fc", - "command": "bash $HOME/PlanktonScope/scripts/killer.sh pump.py && bash $HOME/PlanktonScope/scripts/killer.sh pump.py", - "addpay": false, - "append": "", - "useSpawn": "false", - "timer": "", - "oldrc": false, - "name": "Kill Pump", - "x": 820, - "y": 580, - "wires": [ - [], - [], - [] - ], - "icon": "font-awesome/fa-stop" - }, - { - "id": "6bf10b4c.c83c84", - "type": "ui_button", - "z": "7f885510.6173fc", - "name": "start", - "group": "a61f7be8.af6418", - "order": 2, - "width": 4, - "height": 1, - "passthru": false, - "label": "Start Acquisition", - "tooltip": "", - "color": "", - "bgcolor": "", - "icon": "play_circle_fill", - "payload": "", - "payloadType": "str", - "topic": "start", - "x": 530, - "y": 760, - "wires": [ - [ - "3fe055c2.6ab7da", - "82c90711.145108", - "e1dbc623.8df898", - "5a95f150.76ab3" - ] - ] - }, - { - "id": "2c9498e7.bf0c38", - "type": "ui_button", - "z": "7f885510.6173fc", - "name": "cancel", - "group": "a61f7be8.af6418", - "order": 3, - "width": 4, - "height": 1, - "passthru": false, - "label": "Cancel Acquisition", - "tooltip": "", - "color": "#AD1625", - "bgcolor": "#333333", - "icon": "pause_circle_filled", - "payload": "", - "payloadType": "str", - "topic": "cancel", - "x": 530, - "y": 980, - "wires": [ - [ - "f2acb5e0.c2c898", - "2bfa509a.9fc06", - "a2a07a68.274a78", - "4cd6d848.672778" - ] - ] - }, - { - "id": "b0fda998.f0ad48", - "type": "file", - "z": "7f885510.6173fc", - "name": "logs.json", - "filename": "/var/www/logs.json", - "appendNewline": true, - "createDir": false, - "overwriteFile": "false", - "encoding": "none", - "x": 820, - "y": 760, - "wires": [ - [] - ] - }, - { - "id": "3fe055c2.6ab7da", - "type": "function", - "z": "7f885510.6173fc", - "name": "get global", - "func": "msg.payload = {\n \"sample\":{\n \"sample_project\":global.get(\"sample_project\"),\n \"sample_ship\":global.get(\"sample_ship\"),\n \"sample_operator\":global.get(\"sample_operator\"),\n \"sample_id\":global.get(\"sample_id\"),\n \"sample_sampling_gear\":global.get(\"sample_sampling_gear\"),\n \"sample_hour\":global.get(\"sample_hour\"),\n \"sample_minute\":global.get(\"sample_minute\"),\n \"sample_day\":global.get(\"sample_day\"),\n \"sample_month\":global.get(\"sample_month\"),\n \"sample_year\":global.get(\"sample_year\")\n },\n \"object\":{\n \"object_lat\":global.get(\"object_lat\"),\n \"object_lon\":global.get(\"object_lon\")\n },\n \"acquisition\":{\n \"acq_id\":global.get(\"acq_id\"),\n \"acq_fnumber_objective\":global.get(\"acq_fnumber_objective\"),\n \"acq_celltype\":global.get(\"acq_celltype\"),\n \"acq_maximum_mesh\":global.get(\"acq_maximum_mesh\"),\n \"acq_minimum_mesh\":global.get(\"acq_minimum_mesh\"),\n \"process_pixel\":global.get(\"process_pixel\"),\n \"acq_camera\":global.get(\"acq_camera\"),\n \"acq_instrument\":global.get(\"acq_instrument\"),\n \"acq_software\":global.get(\"acq_software\"),\n \"acq_instrument_ID\":global.get(\"acq_instrument_ID\")\n },\n \"process\":{\n \"process_pixel\":global.get(\"process_pixel\")\n }\n}\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 680, - "y": 760, - "wires": [ - [ - "b0fda998.f0ad48" - ] - ] - }, - { - "id": "f2acb5e0.c2c898", - "type": "exec", - "z": "7f885510.6173fc", - "command": "sed -ie '$d' /home/pi/PlanktonScope/logs.json", - "addpay": false, - "append": "", - "useSpawn": "false", - "timer": "", - "oldrc": false, - "name": "Remove last log", - "x": 700, - "y": 1000, - "wires": [ - [], - [], - [] - ], - "icon": "font-awesome/fa-close" - }, - { - "id": "2bfa509a.9fc06", - "type": "link out", - "z": "7f885510.6173fc", - "name": "cancel_pump", - "links": [ - "eadbf812.3ea798" - ], - "x": 635, - "y": 940, - "wires": [] - }, - { - "id": "eadbf812.3ea798", - "type": "link in", - "z": "7f885510.6173fc", - "name": "", - "links": [ - "2bfa509a.9fc06" - ], - "x": 715, - "y": 600, - "wires": [ - [ - "8fc930df.c7ae6" - ] - ] - }, - { - "id": "217d8bc.8fb7374", - "type": "ui_template", - "z": "7f885510.6173fc", - "group": "79767bcc.30bb94", - "name": "Instructions", - "order": 1, - "width": 0, - "height": 0, - "format": "

In case you forget dude but it's important to read this whenever you are not sure before clicking on any buttons.

\n
\n

Focusing :

\n

To focus, you need to specify a value for the number of steps. Then, you can click once but wait while the stage is moving.

\n

To cancel a focusing, click once on CANCEL FOCUS.

\n
\n

Pumping manually :

\n

To focus, you need to specify a value for the volume. Then, you can click once in order to pump manually a defined volume in a certain direction.

\n

To cancel a pumping event, click once on CANCEL PUMP.

\n

Do not run an acquisition if you are using the pump manually.

\n
\n

Start Acquisition :

\n

Taking images will requires few inputs :

\n
    \n
  1. Name of the project
    2. \n
  2. Name of the station
    3. \n
  3. Acquisition ID
    4. \n
  4. Volume
    5. \n
  5. M12 Lens
    6. \n
\n

If any of the previous settings are missing, it's going to be a real mess and delete previous acquisition. So check twice here !!

\n

The other inputs are always welcome ;)

\n
\n

Cancel Acquisition :

\n

I made this button CANCEL ACQUISITION to cancel an acquisition which maybe be fucked.

\n

Image you click it, it's going to delete the folder in which you save this acquisition, meaning execute :

\n

 

\nrm -r  /var/www/Name_of_the_project/Name_of_the_station/Acquisition_ID\n

 

\n

So if you made a great acquisition, then run a new one with the same input for Acquisition ID and finally click on this button, you are going to delete them both.

\n

Don't use it if you don't need it and please never click twice because the pi might burn.

\n
\n

ssh :

\n

To access the inside of the pi, you can use ssh from from terminal once your are connected to the WiFi by typing this command : ssh -Y planktonscope@192.168.4.1

\n

 

\n

The Password is : raspberry

\n
\n

Data :

\n

In order to access your acquisitions, you can either click on this link or get to the directory via ssh : /var/www/

\n
\n

In order to access the script via ssh, you can get to the directory : /home/pi/PlanktonScope/

\n", - "storeOutMessages": true, - "fwdInMessages": true, - "templateScope": "local", - "x": 570, - "y": 1180, - "wires": [ - [] - ] - }, - { - "id": "82c90711.145108", - "type": "function", - "z": "7f885510.6173fc", - "name": "image", - "func": "var sample_project= global.get(\"sample_project\");\nvar sample_id= global.get(\"sample_id\");\nvar acq_id= global.get(\"acq_id\");\nvar volume= global.get(\"volume\");\nvar flowrate= global.get(\"flowrate\");\nmsg.payload = \"/var/www/\"+sample_project+\"/\"+sample_id+\"/\"+acq_id+\" \"+volume+\" \"+flowrate\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 670, - "y": 800, - "wires": [ - [ - "38c8440d.d0139c" - ] - ] - }, - { - "id": "1e9ae141.a0729f", - "type": "exec", - "z": "7f885510.6173fc", - "command": "python3.7 $HOME/PlanktonScope/scripts/image.py", - "addpay": true, - "append": "", - "useSpawn": "false", - "timer": "", - "oldrc": false, - "name": "image.py", - "x": 960, - "y": 800, - "wires": [ - [], - [], - [] - ], - "icon": "font-awesome/fa-file-image-o" - }, - { - "id": "7d2d5235.35f5ec", - "type": "exec", - "z": "7f885510.6173fc", - "command": "bash /home/pi/PlanktonScope/scripts/kill_image.sh", - "addpay": true, - "append": "", - "useSpawn": "false", - "timer": "", - "oldrc": false, - "name": "Kill Image", - "x": 840, - "y": 1060, - "wires": [ - [], - [], - [] - ] - }, - { - "id": "a2a07a68.274a78", - "type": "function", - "z": "7f885510.6173fc", - "name": "get global", - "func": "var in_path= global.get(\"in_path\");\nvar sample_project= global.get(\"sample_project\");\nvar sample_id= global.get(\"sample_id\");\nvar acq_id= global.get(\"acq_id\");\nmsg.payload = \"/var/www/\"+sample_project+\"/\"+sample_id+\"/\"+acq_id\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 680, - "y": 1060, - "wires": [ - [ - "7d2d5235.35f5ec" - ] - ] - }, - { - "id": "e1dbc623.8df898", - "type": "exec", - "z": "7f885510.6173fc", - "command": "bash /home/pi/RPi_Cam_Web_Interface/stop.sh", - "addpay": false, - "append": "", - "useSpawn": "false", - "timer": "", - "oldrc": false, - "name": "Stop RPi Web Interface", - "x": 730, - "y": 860, - "wires": [ - [], - [], - [] - ] - }, - { - "id": "597635eb.72154c", - "type": "exec", - "z": "7f885510.6173fc", - "command": "bash /home/pi/RPi_Cam_Web_Interface/start.sh", - "addpay": false, - "append": "", - "useSpawn": "false", - "timer": "", - "oldrc": false, - "name": "Start RPi Web Interface", - "x": 890, - "y": 1120, - "wires": [ - [], - [], - [] - ] - }, - { - "id": "4cd6d848.672778", - "type": "delay", - "z": "7f885510.6173fc", - "name": "", - "pauseType": "delay", - "timeout": "2", - "timeoutUnits": "seconds", - "rate": "1", - "nbRateUnits": "1", - "rateUnits": "second", - "randomFirst": "1", - "randomLast": "5", - "randomUnits": "seconds", - "drop": false, - "x": 680, - "y": 1120, - "wires": [ - [ - "597635eb.72154c" - ] - ] - }, - { - "id": "38c8440d.d0139c", - "type": "delay", - "z": "7f885510.6173fc", - "name": "", - "pauseType": "delay", - "timeout": "2", - "timeoutUnits": "seconds", - "rate": "1", - "nbRateUnits": "1", - "rateUnits": "second", - "randomFirst": "1", - "randomLast": "5", - "randomUnits": "seconds", - "drop": false, - "x": 820, - "y": 800, - "wires": [ - [ - "1e9ae141.a0729f" - ] - ] - }, - { - "id": "5a95f150.76ab3", - "type": "link out", - "z": "7f885510.6173fc", - "name": "start_pump", - "links": [ - "5da0773a.700338" - ], - "x": 635, - "y": 720, - "wires": [] - }, - { - "id": "5da0773a.700338", - "type": "link in", - "z": "7f885510.6173fc", - "name": "", - "links": [ - "5a95f150.76ab3" - ], - "x": 715, - "y": 540, - "wires": [ - [ - "649f7ec8.06a84" - ] - ] - }, - { - "id": "4b817fa7.d0d14", - "type": "ui_numeric", - "z": "7f885510.6173fc", - "name": "flowrate", - "label": "Flowrate (ml/min)*", - "tooltip": "", - "group": "a72a9ec6.bb144", - "order": 4, - "width": 0, - "height": 0, - "wrap": false, - "passthru": true, - "topic": "flowrate", - "format": "{{value}}", - "min": "0.3", - "max": "20", - "step": "0.1", - "x": 180, - "y": 400, - "wires": [ - [ - "8861710f.55b92" - ] - ] - }, - { - "id": "42d9d2cb.9d3f84", - "type": "ui_numeric", - "z": "7f885510.6173fc", - "name": "nb_step", - "label": "nb step (30μm/step)", - "tooltip": "", - "group": "c62ffbd3.787ef8", - "order": 4, - "width": 4, - "height": 1, - "wrap": false, - "passthru": true, - "topic": "nb_step", - "format": "{{value}}", - "min": "1", - "max": "5000", - "step": 1, - "x": 520, - "y": 320, - "wires": [ - [ - "523fdeaa.50c6c" - ] - ] - }, - { - "id": "4287fe47.26a63", - "type": "ui_numeric", - "z": "7f885510.6173fc", - "name": "volume", - "label": "Volume (ml)*", - "tooltip": "", - "group": "c62ffbd3.787ef8", - "order": 8, - "width": 4, - "height": 1, - "wrap": false, - "passthru": true, - "topic": "volume", - "format": "{{value}}", - "min": "1", - "max": "5000", - "step": 1, - "x": 520, - "y": 500, - "wires": [ - [ - "84fd85fd.426878" - ] - ] - }, - { - "id": "c627ea8d.f886e8", - "type": "ui_group", - "z": "", - "name": "Sample", - "tab": "6b01f851.598028", - "order": 1, - "disp": true, - "width": 6, - "collapse": false - }, - { - "id": "106f0e1b.6478a2", - "type": "ui_group", - "z": "", - "name": "Spatio Temporal", - "tab": "6b01f851.598028", - "order": 6, - "disp": true, - "width": 7, - "collapse": false - }, - { - "id": "832434ce.ebe498", - "type": "ui_group", - "z": "", - "name": "Optic Settings", - "tab": "6b01f851.598028", - "order": 3, - "disp": true, - "width": "7", - "collapse": false - }, - { - "id": "77a6994b.e3efb8", - "type": "ui_group", - "z": "", - "name": "Generic info", - "tab": "6b01f851.598028", - "order": 7, - "disp": true, - "width": 6, - "collapse": false - }, - { - "id": "a72a9ec6.bb144", - "type": "ui_group", - "z": "", - "name": "Fluidic settings", - "tab": "6b01f851.598028", - "order": 4, - "disp": true, - "width": 6, - "collapse": false - }, - { - "id": "c62ffbd3.787ef8", - "type": "ui_group", - "z": "", - "name": "Controller", - "tab": "6b01f851.598028", - "order": 5, - "disp": true, - "width": "12", - "collapse": false - }, - { - "id": "3d740a07.4674e6", - "type": "ui_group", - "z": "", - "name": "Preview", - "tab": "6b01f851.598028", - "order": 2, - "disp": true, - "width": 12, - "collapse": false - }, - { - "id": "a61f7be8.af6418", - "type": "ui_group", - "z": "", - "name": "Acquisition", - "tab": "6b01f851.598028", - "order": 8, - "disp": true, - "width": 12, - "collapse": false - }, - { - "id": "79767bcc.30bb94", - "type": "ui_group", - "z": "", - "name": "Reminder", - "tab": "6b01f851.598028", - "order": 9, - "disp": true, - "width": 27, - "collapse": false - }, - { - "id": "6b01f851.598028", - "type": "ui_tab", - "z": "", - "name": "PlanktonScope GUI v2.1", - "icon": "date_range", - "order": 1, - "disabled": false, - "hidden": false - } -] diff --git a/flows/flow_chaetoceros.json b/flows/main.json similarity index 55% rename from flows/flow_chaetoceros.json rename to flows/main.json index 17282c3..4106b23 100644 --- a/flows/flow_chaetoceros.json +++ b/flows/main.json @@ -1,475 +1,6 @@ [ { - "id": "259c8713.b50e28", - "type": "tab", - "label": "Main", - "disabled": false, - "info": "" - }, - { - "id": "173a6e6b.e5ca6a", - "type": "subflow", - "name": "sample metadata", - "info": "", - "category": "", - "in": [ - { - "x": 40, - "y": 40, - "wires": [ - { - "id": "2582798f.eddcc6" - }, - { - "id": "1d28205b.58a37" - }, - { - "id": "1590a418.9166dc" - }, - { - "id": "d96f9fa3.d4cfc" - }, - { - "id": "784e2f78.9b96f" - } - ] - } - ], - "out": [ - { - "x": 840, - "y": 40, - "wires": [ - { - "id": "a163194f.0b17c8", - "port": 0 - }, - { - "id": "914752eb.af1b", - "port": 0 - }, - { - "id": "6d0d6fc7.d30bb", - "port": 0 - }, - { - "id": "458408d7.2b3b68", - "port": 0 - }, - { - "id": "43b12fe4.c5aa3", - "port": 0 - } - ] - } - ], - "env": [], - "color": "#DDAA99" - }, - { - "id": "ae90e3e.7d9fba", - "type": "subflow", - "name": "Focus actuation", - "info": "", - "category": "", - "in": [ - { - "x": 40, - "y": 40, - "wires": [ - { - "id": "81a7627c.bac92" - } - ] - } - ], - "out": [ - { - "x": 800, - "y": 200, - "wires": [ - { - "id": "5f4a72d1.9f6adc", - "port": 0 - } - ] - } - ], - "env": [], - "color": "#A6BBCF", - "icon": "node-red/sort.svg" - }, - { - "id": "407d8cdb.3cb7cc", - "type": "subflow", - "name": "Pump actuation", - "info": "", - "category": "", - "in": [ - { - "x": 40, - "y": 40, - "wires": [ - { - "id": "d9a85435.ced5e" - }, - { - "id": "f859eeef.c59ed" - } - ] - } - ], - "out": [ - { - "x": 700, - "y": 40, - "wires": [ - { - "id": "59b05f7f.9e83f8", - "port": 0 - }, - { - "id": "309468bc.ac83f8", - "port": 0 - } - ] - } - ], - "env": [], - "color": "#A6BBCF", - "icon": "font-awesome/fa-recycle" - }, - { - "id": "bdd6e33e.5db3b8", - "type": "subflow", - "name": "acquisition metadata", - "info": "", - "category": "", - "in": [ - { - "x": 50, - "y": 30, - "wires": [ - { - "id": "47459dcd.81b594" - }, - { - "id": "eec199a3.a5a768" - }, - { - "id": "2d278f0a.1a97a" - }, - { 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"env": [], - "color": "#F3B567", - "icon": "node-red/bridge.svg" - }, - { - "id": "4475ba6c.45604c", - "type": "subflow", - "name": "process metadata", - "info": "", - "category": "", - "in": [ - { - "x": 40, - "y": 80, - "wires": [ - { - "id": "d899c841.e6c178" - } - ] - } - ], - "out": [ - { - "x": 700, - "y": 80, - "wires": [ - { - "id": "23e45d82.a01f82", - "port": 0 - } - ] - } - ], - "env": [], - "color": "#DDAA99" - }, - { - "id": "b73d5eb8.60ef3", - "type": "subflow", - "name": "Valves actuation", - "info": "", - "category": "", - "in": [ - { - "x": 40, - "y": 40, - "wires": [ - { - "id": "3808d004.94ea28" - }, - { - "id": "69799a39.13803c" - }, - { - "id": "f7cc1192.5a51e8" - }, - { - "id": "10ce45f6.3036ca" - }, - { - "id": "70dfb6bb.9319" - }, - { - "id": "a0b53585.93216" - } - ] - } - ], - "out": [ - { - "x": 680, - "y": 40, - "wires": [ - { - "id": "c14cf94.1413e88", - "port": 0 - }, - { - "id": "7a0b6294.e887c4", - "port": 0 - }, - { - "id": "8729ec5c.cf4ab8", - "port": 0 - }, - { - "id": "d7b55d02.e41f1", - "port": 0 - }, - { - "id": "27bbe0f0.05b2c", - "port": 0 - }, - { - "id": "b31fd152.a5489", - "port": 0 - } - ] - } - ], - "env": [], - "color": "#A6BBCF", - "icon": "node-red-contrib-camerapi/photo.png" - }, - { - "id": "1b486ba8.f8c41c", - "type": "subflow", - "name": "Datetime update", - "info": "", - "category": "", - "in": [ - { - "x": 140, - "y": 80, - "wires": [ - { - "id": "48033b32.2bca94" - } - ] - } - ], - "out": [], - "env": [], - "color": "#DDAA99", - "icon": "font-awesome/fa-clock-o" - }, - { - "id": "66c23d37.f72cdc", - "type": "subflow", - "name": "MQQT Cmds", - "info": "", - "category": "", - "in": [ - { - "x": 40, - "y": 20, - "wires": [ - { - "id": "ca843dd8.d1c62" - } - ] - } - ], - "out": [], - "env": [], - "color": "#DDAA99" - }, - { - "id": "8d959937.18735", + "id": "97600dff.93378", "type": "subflow", "name": "Acquisition actuation", "info": "", @@ -480,1076 +11,1174 @@ "color": "#A6BBCF" }, { - "id": "cc8bc4eb.651868", - "type": "ui_base", - "theme": { - "name": "theme-dark", - "lightTheme": { - "default": "#0094CE", - "baseColor": "#5900ce", - "baseFont": "-apple-system,BlinkMacSystemFont,Segoe UI,Roboto,Oxygen-Sans,Ubuntu,Cantarell,Helvetica Neue,sans-serif", - "edited": true, - "reset": false - }, - "darkTheme": { - "default": "#097479", - "baseColor": "#059276", - "baseFont": "-apple-system,BlinkMacSystemFont,Segoe UI,Roboto,Oxygen-Sans,Ubuntu,Cantarell,Helvetica Neue,sans-serif", - "edited": true, - "reset": false - }, - "customTheme": { - "name": "Untitled Theme 1", - "default": "#4B7930", - "baseColor": "#4B7930", - "baseFont": "-apple-system,BlinkMacSystemFont,Segoe UI,Roboto,Oxygen-Sans,Ubuntu,Cantarell,Helvetica Neue,sans-serif" - }, - "themeState": { - "base-color": { - "default": "#097479", - "value": "#059276", - "edited": true - }, - "page-titlebar-backgroundColor": { - "value": "#059276", - "edited": false - }, - "page-backgroundColor": { - "value": "#111111", - "edited": false - }, - "page-sidebar-backgroundColor": { - "value": "#ffffff", - "edited": false - }, - "group-textColor": { - "value": "#08dcb2", - "edited": false - }, - "group-borderColor": { - "value": "#555555", - "edited": false - }, - "group-backgroundColor": { - "value": "#333333", - "edited": false - }, - "widget-textColor": { - "value": "#eeeeee", - "edited": false - }, - "widget-backgroundColor": { - "value": "#059276", - "edited": false - }, - "widget-borderColor": { - "value": "#333333", - "edited": false - }, - "base-font": { - "value": "-apple-system,BlinkMacSystemFont,Segoe UI,Roboto,Oxygen-Sans,Ubuntu,Cantarell,Helvetica Neue,sans-serif" - } - }, - "angularTheme": { - "primary": "indigo", - "accents": "blue", - "warn": "red", - "background": "grey" - } - }, - "site": { - "name": "Node-RED Dashboard", - "hideToolbar": "false", - "allowSwipe": "false", - "lockMenu": "true", - "allowTempTheme": "true", - "dateFormat": "DD/MM/YYYY", - "sizes": { - "sx": 56, - "sy": 56, - "gx": 5, - "gy": 5, - "cx": 5, - "cy": 5, - "px": 5, - "py": 5 - } - } - }, - { - "id": "737ec584.2eea2c", - "type": "ui_tab", - "z": "", - "name": "GUI", - "icon": "fa-eyedropper", - "order": 2, - "disabled": false, - "hidden": false - }, - { - "id": "3e1ba03d.f01d8", - "type": "ui_group", - "z": "", - "name": "Sample metadata", - "tab": "737ec584.2eea2c", - "order": 2, - "disp": true, - "width": "24", - "collapse": false - }, - { - "id": "cef1e703.bcf3c8", - "type": "ui_group", - "z": "", - "name": "Object metadata", - "tab": "737ec584.2eea2c", - "order": 6, - "disp": true, - "width": "24", - "collapse": false - }, - { - "id": "fbd92986.1028c8", - "type": "ui_group", - "z": "", - "name": "Focus actuation", - "tab": "737ec584.2eea2c", - "order": 4, - "disp": true, - "width": "24", - "collapse": false - }, - { - "id": "707d9797.c8e798", - "type": "ui_group", - "z": "", - "name": "Pump actuation", - "tab": "737ec584.2eea2c", - "order": 5, - "disp": true, - "width": "24", - "collapse": false - }, - { - "id": "52159161.72187", - "type": "ui_group", - "z": "", - "name": "Acquisition metadata", - "tab": "737ec584.2eea2c", - "order": 7, - "disp": true, - "width": "24", - "collapse": false - }, - { - "id": "8cfadfab.327d7", - "type": "ui_group", - "z": "", - "name": "MQTT Plots", - "tab": "737ec584.2eea2c", - "order": 11, - "disp": true, - "width": "24", - "collapse": false - }, - { - "id": "b77ffa1b.942258", - "type": "mqtt-broker", - "z": "", + "id": "604c996b.1a8428", + "type": "ui_button", + "z": "97600dff.93378", "name": "", - "broker": "127.0.0.1", - "port": "1883", - "clientid": "test", - "usetls": false, - "compatmode": false, - "keepalive": "60", - "cleansession": true, - "birthTopic": "", - "birthQos": "0", - "birthPayload": "", - "closeTopic": "", - "closeQos": "0", - "closePayload": "", - "willTopic": "", - "willQos": "0", - "willPayload": "" - }, - { - "id": "cb2f36fe.1c7038", - "type": "mqtt-broker", - "z": "", - "name": "", - "broker": "0.0.0.0", - "port": "1883", - "clientid": "Client_node", - "usetls": false, - "compatmode": false, - "keepalive": "60", - "cleansession": true, - "birthTopic": "", - "birthQos": "0", - "birthPayload": "", - "closeTopic": "", - "closeQos": "0", - "closePayload": "", - "willTopic": "", - "willQos": "0", - "willPayload": "" - }, - { - "id": "c6a276ac.3eb74", - "type": "ui_group", - "z": "", - "name": "Commands", - "tab": "737ec584.2eea2c", - "order": 12, - "disp": true, - "width": 24, - "collapse": false - }, - { - "id": "f5194cae.c84688", - "type": "ui_group", - "z": "", - "name": "Streaming camera", - "tab": "737ec584.2eea2c", - "order": 3, - "disp": true, - "width": 24, - "collapse": false - }, - { - "id": "b1321ea9.cfcf28", - "type": "ui_group", - "z": "", - "name": "Process metadata", - "tab": "737ec584.2eea2c", - "order": 8, - "disp": true, - "width": 24, - "collapse": false - }, - { - "id": "f41d0ecb.8be06", - "type": "ui_group", - "z": "", - "name": "Valve actuation", - "tab": "737ec584.2eea2c", - "order": 9, - "disp": true, - "width": "24", - "collapse": false - }, - { - "id": "9214d59d.e7b52", - "type": "ui_group", - "z": "", - "name": "Datetime", - "tab": "737ec584.2eea2c", + "group": "cdb72118.692578", "order": 1, - "disp": true, - "width": "24", - "collapse": false + "width": 0, + "height": 0, + "passthru": false, + "label": "Start Acquisition", + "tooltip": "", + "color": "", + "bgcolor": "", + "icon": "", + "payload": "", + "payloadType": "str", + "topic": "actuator/image", + "x": 200, + "y": 100, + "wires": [ + [ + "b854ad48.5869e8" + ] + ] }, { - "id": "d170ac9c.3b4828", + "id": "b854ad48.5869e8", + "type": "function", + "z": "97600dff.93378", + "name": "image.js", + "func": "state = global.get(\"state\");\nglobal.set('img_counter',0)\nglobal.set('obj_counter',0)\nif (state == null){state=\"free\"}\n\nvar sleep_before= global.get(\"custom_sleep_before\");\nvar nb_step= global.get(\"custom_nb_step\");\nvar nb_frame= global.get(\"custom_nb_frame\");\nvar segmentation= global.get(\"custom_segmentation\");\n\nif (sleep_before === undefined || sleep_before === \"\" || sleep_before === null) {\n msg.topic = \"Missing entry :\"\n msg.payload = \"Duration before the acquisition\";\n \n}else if (nb_step === undefined || nb_step === \"\" || nb_step === null) {\n msg.topic = \"Missing entry :\"\n msg.payload = \"Number of step in between two frames\";\n \n}else if (nb_frame === undefined || nb_frame === \"\" || nb_frame === null) {\n msg.topic = \"Missing entry :\"\n msg.payload = \"Number of image to save\";\n \n}else if (segmentation === undefined || segmentation === \"\" || segmentation === null) {\n msg.topic = \"Missing entry :\"\n msg.payload = \"Realize or not the segmentation\";\n \n}else {\n nb_frame=nb_frame-1\n \n msg.payload=sleep_before+' '+nb_step+' '+nb_frame+' '+segmentation;\n}\nreturn msg;", + "outputs": 1, + "noerr": 0, + "x": 360, + "y": 100, + "wires": [ + [ + "84505b75.883a48" + ] + ], + "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": "84505b75.883a48", + "type": "switch", + "z": "97600dff.93378", + "name": "", + "property": "topic", + "propertyType": "msg", + "rules": [ + { + "t": "eq", + "v": "actuator/image", + "vt": "str" + }, + { + "t": "eq", + "v": "Missing entry :", + "vt": "str" + } + ], + "checkall": "true", + "repair": false, + "outputs": 2, + "x": 510, + "y": 100, + "wires": [ + [ + "715a8f15.dc211" + ], + [ + "3173806b.bb0c7" + ] + ] + }, + { + "id": "3173806b.bb0c7", + "type": "ui_toast", + "z": "97600dff.93378", + "position": "dialog", + "displayTime": "3", + "highlight": "", + "sendall": true, + "outputs": 1, + "ok": "OK", + "cancel": "", + "raw": false, + "topic": "", + "name": "", + "x": 690, + "y": 120, + "wires": [ + [] + ] + }, + { + "id": "715a8f15.dc211", + "type": "mqtt out", + "z": "97600dff.93378", + "name": "", + "topic": "", + "qos": "", + "retain": "", + "broker": "e8ab36cc.74d77", + "x": 670, + "y": 80, + "wires": [] + }, + { + "id": "ed689faa.3a3e08", + "type": "ui_button", + "z": "97600dff.93378", + "name": "Stop Acquisition", + "group": "cdb72118.692578", + "order": 2, + "width": 0, + "height": 0, + "passthru": true, + "label": "STOP ACQUISITION", + "tooltip": "", + "color": "", + "bgcolor": "#AD1625", + "icon": "", + "payload": "off", + "payloadType": "str", + "topic": "actuator/wait", + "x": 200, + "y": 140, + "wires": [ + [ + "f6bd3440.60d5a" + ] + ] + }, + { + "id": "f6bd3440.60d5a", + "type": "mqtt out", + "z": "97600dff.93378", + "name": "", + "topic": "", + "qos": "", + "retain": "", + "broker": "e8ab36cc.74d77", + "x": 350, + "y": 140, + "wires": [] + }, + { + "id": "3b827bf5.c7bc64", + "type": "mqtt out", + "z": "97600dff.93378", + "name": "", + "topic": "", + "qos": "", + "retain": "", + "broker": "e8ab36cc.74d77", + "x": 350, + "y": 180, + "wires": [] + }, + { + "id": "cdb72118.692578", "type": "ui_group", "z": "", "name": "Acquisition actuation", - "tab": "737ec584.2eea2c", + "tab": "2b97fe34.a699fa", "order": 10, "disp": true, "width": 24, "collapse": false }, { - "id": "5b1410c.f92017", - "type": "ui_spacer", - "name": "spacer", - "group": "8cfadfab.327d7", - "order": 3, - "width": 1, - "height": 1 - }, - { - "id": "26072b87.02a7a4", - "type": "ui_spacer", - "name": "spacer", - "group": "8cfadfab.327d7", - "order": 4, - "width": 1, - "height": 1 - }, - { - "id": "a8c8abef.b19ea", - "type": "ui_spacer", - "name": "spacer", - "group": "8cfadfab.327d7", - "order": 6, - "width": 1, - "height": 1 - }, - { - "id": "41550c87.dbb054", - "type": "ui_spacer", - "name": "spacer", - "group": "8cfadfab.327d7", - "order": 7, - "width": 1, - "height": 1 - }, - { - "id": "6d0d6fc7.d30bb", - "type": "ui_text_input", - "z": "173a6e6b.e5ca6a", - "name": "sample_ship", - "label": "Name of the ship", - "tooltip": "", - "group": "3e1ba03d.f01d8", - "order": 2, - "width": 0, - "height": 0, - "passthru": true, - "mode": "text", - "delay": 300, - "topic": "sample_ship", - "x": 590, - "y": 120, - "wires": [ - [] - ] - }, - { - "id": "43b12fe4.c5aa3", - "type": "ui_dropdown", - "z": "173a6e6b.e5ca6a", - "name": "sample_sampling_gear", - "label": "Sampling gear", - "tooltip": "", - "place": "Select", - "group": "3e1ba03d.f01d8", - "order": 4, - "width": 0, - "height": 0, - "passthru": true, - "options": [ + "id": "e8320d42.9a3ad8", + "type": "subflow", + "name": "MQQT Cmds", + "info": "", + "category": "", + "in": [ { - "label": "Plankton net", - "value": "net", - "type": "str" - }, - { - "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" + "x": 40, + "y": 40, + "wires": [ + { + "id": "cf9e02a2.3feff" + }, + { + "id": "18da28e6.7b000f" + } + ] } ], - "payload": "", - "topic": "sample_sampling_gear", - "x": 550, - "y": 200, - "wires": [ - [] - ] + "out": [], + "env": [], + "color": "#DDAA99" }, { - "id": "458408d7.2b3b68", - "type": "ui_text_input", - "z": "173a6e6b.e5ca6a", - "name": "sample_operator", - "label": "Name of the operator", - "tooltip": "", - "group": "3e1ba03d.f01d8", - "order": 3, - "width": 0, - "height": 0, - "passthru": true, - "mode": "text", - "delay": 300, - "topic": "sample_operator", - "x": 570, - "y": 160, - "wires": [ - [] - ] - }, - { - "id": "a163194f.0b17c8", - "type": "ui_text_input", - "z": "173a6e6b.e5ca6a", - "name": "sample_project", - "label": "Name of the project*", - "tooltip": "", - "group": "3e1ba03d.f01d8", - "order": 1, - "width": 0, - "height": 0, - "passthru": true, - "mode": "text", - "delay": 300, - "topic": "sample_project", - "x": 580, - "y": 40, - "wires": [ - [] - ] - }, - { - "id": "914752eb.af1b", - "type": "ui_text_input", - "z": "173a6e6b.e5ca6a", - "name": "sample_id", - "label": "ID of the station*", - "tooltip": "", - "group": "3e1ba03d.f01d8", - "order": 5, - "width": 0, - "height": 0, - "passthru": true, - "mode": "number", - "delay": 300, - "topic": "sample_id", - "x": 590, - "y": 80, - "wires": [ - [] - ] - }, - { - "id": "e001a28.555566", - "type": "function", - "z": "259c8713.b50e28", - "name": "get global", - "func": "msg.payload={\n \n \"duration_bef_cycle\":global.get(\"duration_bef_cycle\"),\n \"duration_flush\":global.get(\"duration_flush\"),\n \"nb_img\":global.get(\"nb_img\"),\n \"duration_bef_seq\":global.get(\"duration_bef_seq\"),\n \"duration_bef_img\":global.get(\"duration_bef_img\"),\n \"duration_between\":global.get(\"duration_between\"),\n \n \"sample_project\":global.get(\"sample_project\"),\n \"sample_id\":global.get(\"sample_id\"),\n \"sample_ship\":global.get(\"sample_ship\"),\n \"sample_operator\":global.get(\"sample_operator\"),\n \"sample_sampling_gear\":global.get(\"sample_sampling_gear\"),\n \n \"acq_id\":global.get(\"acq_id\"),\n \"acq_instrument\":global.get(\"acq_instrument\"),\n //\"acq_instrument_id\":global.get(\"acq_instrument_id\"),\n \"acq_celltype\":global.get(\"acq_celltype\"),\n \"acq_minimum_mesh\":global.get(\"acq_minimum_mesh\"),\n \"acq_maximum_mesh\":global.get(\"acq_maximum_mesh\"),\n \"acq_min_esd\":global.get(\"acq_min_esd\"),\n \"acq_max_esd\":global.get(\"acq_max_esd\"),\n \"acq_volume\":global.get(\"acq_volume\"),\n \"acq_magnification\":global.get(\"magnification\"),\n \"acq_fnumber_objective\":global.get(\"acq_fnumber_objective\"),\n \n \"acq_camera_name\":\"Pi Camera V2.1 - 8MP\",\n \n \"object_date\":global.get(\"object_date\"),\n \"object_time\":global.get(\"object_time\"),\n \"object_lat\":global.get(\"object_lat\"),\n \"object_lon\":global.get(\"object_lon\"),\n \"object_depth_min\":global.get(\"object_depth_min\"),\n \"object_depth_max\":global.get(\"object_depth_max\"),\n \n \"process_pixel\":global.get(\"process_pixel\"),\n \"process_id\":global.get(\"process_id\")\n \n};\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 1180, - "y": 100, + "id": "a7301ba5.d56d48", + "type": "exec", + "z": "e8320d42.9a3ad8", + "command": "python3.7 /home/pi/PlanktonScope/script/main.py", + "addpay": false, + "append": "", + "useSpawn": "false", + "timer": "", + "oldrc": false, + "name": "", + "x": 910, + "y": 140, "wires": [ [ - "76a6e6bb.a08b98" + "87558394.4e589", + "a11158b1.b7649" + ], + [ + "87558394.4e589", + "a11158b1.b7649" + ], + [ + "87558394.4e589", + "a11158b1.b7649" ] ] }, { - "id": "f25890f5.f2549", - "type": "file", - "z": "259c8713.b50e28", + "id": "62b9a3b1.74dbc4", + "type": "exec", + "z": "e8320d42.9a3ad8", + "command": "ps -ax | grep \"python3.7 /home/pi/PlanktonScope/script/main.py\"| head -1 | awk -F \" \" '{print$1}' ", + "addpay": false, + "append": "", + "useSpawn": "false", + "timer": "", + "oldrc": false, "name": "", - "filename": "/home/pi/PlanktonScope/config.txt", - "appendNewline": true, + "x": 610, + "y": 200, + "wires": [ + [ + "66fb9ed2.8ecd3" + ], + [], + [] + ] + }, + { + "id": "66fb9ed2.8ecd3", + "type": "exec", + "z": "e8320d42.9a3ad8", + "command": "kill", + "addpay": true, + "append": "", + "useSpawn": "false", + "timer": "", + "oldrc": false, + "name": "", + "x": 1050, + "y": 200, + "wires": [ + [ + "87558394.4e589", + "a11158b1.b7649" + ], + [ + "87558394.4e589", + "a11158b1.b7649" + ], + [ + "87558394.4e589", + "a11158b1.b7649" + ] + ] + }, + { + "id": "5df162d7.08eb34", + "type": "ui_button", + "z": "e8320d42.9a3ad8", + "name": "", + "group": "9c86b3b7.54841", + "order": 9, + "width": 12, + "height": 1, + "passthru": false, + "label": "Kill MQTT", + "tooltip": "", + "color": "", + "bgcolor": "", + "icon": "", + "payload": "", + "payloadType": "str", + "topic": "", + "x": 80, + "y": 200, + "wires": [ + [ + "62b9a3b1.74dbc4" + ] + ] + }, + { + "id": "d16389e5.3bc67", + "type": "ui_button", + "z": "e8320d42.9a3ad8", + "name": "", + "group": "9c86b3b7.54841", + "order": 10, + "width": 12, + "height": 1, + "passthru": false, + "label": "Restart MQTT", + "tooltip": "", + "color": "", + "bgcolor": "", + "icon": "", + "payload": "", + "payloadType": "str", + "topic": "", + "x": 100, + "y": 140, + "wires": [ + [ + "a7301ba5.d56d48" + ] + ] + }, + { + "id": "87558394.4e589", + "type": "ui_toast", + "z": "e8320d42.9a3ad8", + "position": "top right", + "displayTime": "3", + "highlight": "", + "sendall": true, + "outputs": 0, + "ok": "OK", + "cancel": "", + "raw": false, + "topic": "", + "name": "", + "x": 1260, + "y": 140, + "wires": [] + }, + { + "id": "500abffa.c7a788", + "type": "file", + "z": "e8320d42.9a3ad8", + "name": "", + "filename": "/home/pi/PlanktonScope/script/main.py", + "appendNewline": false, "createDir": true, "overwriteFile": "true", "encoding": "none", - "x": 1520, + "x": 530, "y": 100, - "wires": [ - [] - ] - }, - { - "id": "f5c1aa13.3cfbf8", - "type": "function", - "z": "bdd6e33e.5db3b8", - "name": "set optical config", - "func": "global.set(msg.topic,msg.payload);\nvar acq_fnumber_objective = String(global.get(msg.topic));\n\nswitch(acq_fnumber_objective) {\n case \"25\":\n global.set(\"magnification\",0.6);\n global.set(\"process_pixel\",1.86);\n global.set(\"sug_min\",60);\n global.set(\"sug_max\",670);\n global.set(\"sug_flowrate\",3);\n break;\n case \"16\":\n global.set(\"magnification\",0.94);\n global.set(\"process_pixel\",1.19);\n global.set(\"sug_min\",40);\n global.set(\"sug_max\",430);\n global.set(\"sug_flowrate\",2.4);\n break;\n case \"12\":\n global.set(\"magnification\",1.20);\n global.set(\"process_pixel\",0.94);\n global.set(\"sug_min\",30);\n global.set(\"sug_max\",340);\n global.set(\"sug_flowrate\",1.25);\n break;\n case \"8\":\n global.set(\"magnification\",1.78);\n global.set(\"process_pixel\",0.63);\n global.set(\"sug_min\",20);\n global.set(\"sug_max\",230);\n global.set(\"sug_flowrate\",0.42);\n break;\n case \"6\":\n global.set(\"magnification\",2.36);\n global.set(\"process_pixel\",0.48);\n global.set(\"sug_min\",15);\n global.set(\"sug_max\",170);\n global.set(\"sug_flowrate\",0.32);\n break;\n}\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 750, - "y": 360, - "wires": [ - [] - ] - }, - { - "id": "eb9181d8.25e01", - "type": "ui_dropdown", - "z": "bdd6e33e.5db3b8", - "name": "acq_fnumber_objective", - "label": "M12 Lens*", - "tooltip": "", - "place": "Select option", - "group": "52159161.72187", - "order": 3, - "width": 0, - "height": 0, - "passthru": true, - "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", - "x": 526, - "y": 360, "wires": [ [ - "f5c1aa13.3cfbf8" + "a7301ba5.d56d48" ] ] }, { - "id": "5aba848a.7a861c", - "type": "ui_numeric", - "z": "bdd6e33e.5db3b8", - "name": "acq_minimum_mesh", - "label": "Min fraction size (μm)", - "tooltip": "", - "group": "52159161.72187", - "order": 8, - "width": 0, - "height": 0, - "wrap": false, - "passthru": true, - "topic": "acq_minimum_mesh", - "format": "{{value}}", - "min": 0, - "max": "300", - "step": "10", - "x": 536, - "y": 160, + "id": "985c65de.0801b", + "type": "template", + "z": "e8320d42.9a3ad8", + "name": "main.py", + "field": "payload", + "fieldType": "msg", + "format": "python", + "syntax": "plain", + "template": "################################################################################\n#Actuator Libraries\n################################################################################\n\n#Library for exchaning messages with Node-RED\nimport paho.mqtt.client as mqtt\n\n#Library to control the PiCamera\nfrom picamera import PiCamera\n\n#Libraries to control the steppers for focusing and pumping\nfrom adafruit_motor import stepper\nfrom adafruit_motorkit import MotorKit\n\n#Library to send command over I2C for the light module on the fan\nimport smbus\n\n################################################################################\n#Practical Libraries\n################################################################################\n\n#Library to get date and time for folder name and filename\nfrom datetime import datetime, timedelta\n\n#Library to be able to sleep for a duration\nfrom time import sleep\n\n#Libraries manipulate json format, execute bash commands\nimport json, shutil, os, subprocess\n\n################################################################################\n#Morphocut Libraries\n################################################################################\n\nfrom skimage.util import img_as_ubyte\nfrom morphocut import Call\nfrom morphocut.contrib.ecotaxa import EcotaxaWriter\nfrom morphocut.contrib.zooprocess import CalculateZooProcessFeatures\nfrom morphocut.core import Pipeline\nfrom morphocut.file import Find\nfrom morphocut.image import (ExtractROI,\n FindRegions,\n ImageReader,\n ImageWriter,\n RescaleIntensity,\n RGB2Gray\n)\nfrom morphocut.stat import RunningMedian\nfrom morphocut.str import Format\nfrom morphocut.stream import TQDM, Enumerate, FilterVariables\n\n################################################################################\n#Other image processing Libraries\n################################################################################\n\nfrom skimage.feature import canny\nfrom skimage.color import rgb2gray, label2rgb\nfrom skimage.morphology import disk\nfrom skimage.morphology import erosion, dilation, closing\nfrom skimage.measure import label, regionprops\nimport cv2\n\n################################################################################\n#Streaming PiCamera over server\n################################################################################\nimport io\nimport picamera\nimport logging\nimport socketserver\nfrom threading import Condition\nfrom http import server\nimport threading\n\n################################################################################\n#Creation of the webpage containing the PiCamera Streaming\n################################################################################\n\nPAGE=\"\"\"\\\n\n\nPlanktonScope v2 | PiCamera Streaming\n\n\n\n\n\n\"\"\"\n\n################################################################################\n#Classes for the PiCamera Streaming\n################################################################################\n\nclass StreamingOutput(object):\n def __init__(self):\n self.frame = None\n self.buffer = io.BytesIO()\n self.condition = Condition()\n\n def write(self, buf):\n if buf.startswith(b'\\xff\\xd8'):\n # New frame, copy the existing buffer's content and notify all\n # clients it's available\n self.buffer.truncate()\n with self.condition:\n self.frame = self.buffer.getvalue()\n self.condition.notify_all()\n self.buffer.seek(0)\n return self.buffer.write(buf)\n\nclass StreamingHandler(server.BaseHTTPRequestHandler):\n def do_GET(self):\n if self.path == '/':\n self.send_response(301)\n self.send_header('Location', '/index.html')\n self.end_headers()\n elif self.path == '/index.html':\n content = PAGE.encode('utf-8')\n self.send_response(200)\n self.send_header('Content-Type', 'text/html')\n self.send_header('Content-Length', len(content))\n self.end_headers()\n self.wfile.write(content)\n elif self.path == '/stream.mjpg':\n self.send_response(200)\n self.send_header('Age', 0)\n self.send_header('Cache-Control', 'no-cache, private')\n self.send_header('Pragma', 'no-cache')\n self.send_header('Content-Type', 'multipart/x-mixed-replace; boundary=FRAME')\n self.end_headers()\n try:\n while True:\n with output.condition:\n output.condition.wait()\n frame = output.frame\n self.wfile.write(b'--FRAME\\r\\n')\n self.send_header('Content-Type', 'image/jpeg')\n self.send_header('Content-Length', len(frame))\n self.end_headers()\n self.wfile.write(frame)\n self.wfile.write(b'\\r\\n')\n except Exception as e:\n logging.warning(\n 'Removed streaming client %s: %s',\n self.client_address, str(e))\n else:\n self.send_error(404)\n self.end_headers()\n\nclass StreamingServer(socketserver.ThreadingMixIn, server.HTTPServer):\n allow_reuse_address = True\n daemon_threads = True\n\n################################################################################\n#MQTT core functions\n################################################################################\n\n#Run this function in order to connect to the client (Node-RED)\ndef on_connect(client, userdata, flags, rc):\n #Print when connected\n print(\"Connected! - \" + str(rc))\n #When connected, run subscribe()\n client.subscribe(\"actuator/#\")\n #Turn green the light module\n rgb(0,255,0)\n\n#Run this function in order to subscribe to all the topics begining by actuator\ndef on_subscribe(client, obj, mid, granted_qos):\n #Print when subscribed\n print(\"Subscribed! - \"+str(mid)+\" \"+str(granted_qos))\n\n#Run this command when Node-RED is sending a message on the subscribed topic\ndef on_message(client, userdata, msg):\n #Print the topic and the message\n print(msg.topic+\" \"+str(msg.qos)+\" \"+str(msg.payload))\n #Update the global variables command, args and counter\n global command\n global args\n global counter\n #Parse the topic to find the command. ex : actuator/pump -> pump\n command=msg.topic.split(\"/\")[1]\n #Decode the message to find the arguments\n args=str(msg.payload.decode())\n #Reset the counter to 0\n counter=0\n\n################################################################################\n#LEDs Actuation\n################################################################################\ndef rgb(R,G,B):\n #Update LED n1\n bus.write_byte_data(0x0d, 0x00, 0)\n bus.write_byte_data(0x0d, 0x01, R)\n bus.write_byte_data(0x0d, 0x02, G)\n bus.write_byte_data(0x0d, 0x03, B)\n\n #Update LED n2\n bus.write_byte_data(0x0d, 0x00, 1)\n bus.write_byte_data(0x0d, 0x01, R)\n bus.write_byte_data(0x0d, 0x02, G)\n bus.write_byte_data(0x0d, 0x03, B)\n\n #Update LED n3\n bus.write_byte_data(0x0d, 0x00, 2)\n bus.write_byte_data(0x0d, 0x01, R)\n bus.write_byte_data(0x0d, 0x02, G)\n bus.write_byte_data(0x0d, 0x03, B)\n\n #Update the I2C Bus in order to really update the LEDs new values\n cmd=\"i2cdetect -y 1\"\n subprocess.Popen(cmd.split(),stdout=subprocess.PIPE)\n\n################################################################################\n#Init function - executed only once\n################################################################################\n\n#define the bus used to actuate the light module on the fan\nbus = smbus.SMBus(1)\n\n#define the names for the 2 exsting steppers\nkit = MotorKit()\npump_stepper = kit.stepper1\nfocus_stepper = kit.stepper2\n#Make sure the steppers are release and do not use any power\npump_stepper.release()\nfocus_stepper.release()\n\n#Precise the settings of the PiCamera\ncamera = PiCamera()\ncamera.resolution = (3280, 2464)\ncamera.iso = 60\ncamera.shutter_speed = 500\ncamera.exposure_mode = 'fixedfps'\n\n#Declare the global variables command, args and counter\ncommand = ''\nargs = ''\ncounter=''\n\n#MQTT Client functions definition\nclient = mqtt.Client()\nclient.connect(\"192.168.4.1\",1883,60)\nclient.on_connect = on_connect\nclient.on_subscribe = on_subscribe\nclient.on_message = on_message\nclient.loop_start()\n\n################################################################################\n#Definition of the few important metadata\n################################################################################\n\nlocal_metadata = {\n \"process_datetime\": datetime.now(),\n \"acq_camera_resolution\" : camera.resolution,\n \"acq_camera_iso\" : camera.iso,\n \"acq_camera_shutter_speed\" : camera.shutter_speed\n}\n\n#Read the content of config.json containing the metadata defined on Node-RED\nconfig_json = open('/home/pi/PlanktonScope/config.json','r')\nnode_red_metadata = json.loads(config_json.read())\n\n#Concat the local metadata and the metadata from Node-RED\nglobal_metadata = {**local_metadata, **node_red_metadata}\n\n#Define the name of the .zip file that will contain the images and the .tsv table for EcoTaxa\narchive_fn = os.path.join(\"/home/pi/PlanktonScope/\",\"export\", \"ecotaxa_export.zip\")\n\n################################################################################\n#MorphoCut Script\n################################################################################\n\n#Define processing pipeline\nwith Pipeline() as p:\n\n #Recursively find .jpg files in import_path.\n #Sort to get consective frames.\n abs_path = Find(\"/home/pi/PlanktonScope/tmp\", [\".jpg\"], sort=True, verbose=True)\n\n #Extract name from abs_path\n name = Call(lambda p: os.path.splitext(os.path.basename(p))[0], abs_path)\n\n #Set the LEDs as Green\n Call(rgb, 0,255,0)\n\n #Read image\n img = ImageReader(abs_path)\n\n #Show progress bar for frames\n TQDM(Format(\"Frame {name}\", name=name))\n\n #Apply running median to approximate the background image\n flat_field = RunningMedian(img, 5)\n\n #Correct image\n img = img / flat_field\n\n #Rescale intensities and convert to uint8 to speed up calculations\n img = RescaleIntensity(img, in_range=(0, 1.1), dtype=\"uint8\")\n\n #Filter variable to reduce memory load\n FilterVariables(name,img)\n\n #Save cleaned images\n #frame_fn = Format(os.path.join(\"/home/pi/PlanktonScope/tmp\",\"CLEAN\", \"{name}.jpg\"), name=name)\n #ImageWriter(frame_fn, img)\n\n #Convert image to uint8 gray\n img_gray = RGB2Gray(img)\n\n #?\n img_gray = Call(img_as_ubyte, img_gray)\n\n #Canny edge detection using OpenCV\n img_canny = Call(cv2.Canny, img_gray, 50,100)\n\n #Dilate using OpenCV\n kernel = Call(cv2.getStructuringElement, cv2.MORPH_ELLIPSE, (15, 15))\n img_dilate = Call(cv2.dilate, img_canny, kernel, iterations=2)\n\n #Close using OpenCV\n kernel = Call(cv2.getStructuringElement, cv2.MORPH_ELLIPSE, (5, 5))\n img_close = Call(cv2.morphologyEx, img_dilate, cv2.MORPH_CLOSE, kernel, iterations=1)\n\n #Erode using OpenCV\n kernel = Call(cv2.getStructuringElement, cv2.MORPH_ELLIPSE, (15, 15))\n mask = Call(cv2.erode, img_close, kernel, iterations=2)\n\n #Find objects\n regionprops = FindRegions(\n mask, img_gray, min_area=1000, padding=10, warn_empty=name\n )\n\n #Set the LEDs as Purple\n Call(rgb, 255,0,255)\n\n # For an object, extract a vignette/ROI from the image\n roi_orig = ExtractROI(img, regionprops, bg_color=255)\n\n # Generate an object identifier\n i = Enumerate()\n\n #Call(print,i)\n\n #Define the ID of each object\n object_id = Format(\"{name}_{i:d}\", name=name, i=i)\n\n #Call(print,object_id)\n\n #Define the name of each object\n object_fn = Format(os.path.join(\"/home/pi/PlanktonScope/\",\"OBJECTS\", \"{name}.jpg\"), name=object_id)\n\n #Save the image of the object with its name\n ImageWriter(object_fn, roi_orig)\n\n #Calculate features. The calculated features are added to the global_metadata.\n #Returns a Variable representing a dict for every object in the stream.\n meta = CalculateZooProcessFeatures(\n regionprops, prefix=\"object_\", meta=global_metadata\n )\n\n #Get all the metadata\n json_meta = Call(json.dumps,meta, sort_keys=True, default=str)\n\n #Publish the json containing all the metadata to via MQTT to Node-RED\n Call(client.publish, \"receiver/segmentation/metric\", json_meta)\n\n #Add object_id to the metadata dictionary\n meta[\"object_id\"] = object_id\n\n #Generate object filenames\n orig_fn = Format(\"{object_id}.jpg\", object_id=object_id)\n\n #Write objects to an EcoTaxa archive:\n #roi image in original color, roi image in grayscale, metadata associated with each object\n EcotaxaWriter(archive_fn, (orig_fn, roi_orig), meta)\n\n #Progress bar for objects\n TQDM(Format(\"Object {object_id}\", object_id=object_id))\n\n #Publish the object_id to via MQTT to Node-RED\n Call(client.publish, \"receiver/segmentation/object_id\", object_id)\n\n #Set the LEDs as Green\n Call(rgb, 0,255,0)\n\n################################################################################\n#While loop for capting commands from Node-RED\n################################################################################\n\noutput = StreamingOutput()\naddress = ('192.168.4.1', 8000)\nserver = StreamingServer(address, StreamingHandler)\nthreading.Thread(target=server.serve_forever).start()\ncamera.start_recording(output, format='mjpeg', resize=(640, 480))\n\nwhile True:\n\n ############################################################################\n #Pump Event\n ############################################################################\n\n #If the command is \"pump\"\n if (command==\"pump\"):\n\n #Set the LEDs as Blue\n rgb(0,0,255)\n\n #Get direction from the different received arguments\n direction=args.split(\" \")[0]\n\n #Get delay (in between steps) from the different received arguments\n delay=float(args.split(\" \")[1])\n\n #Get number of steps from the different received arguments\n nb_step=int(args.split(\" \")[2])\n\n #Print status\n print(\"The pump has been started.\")\n\n #Publish the status \"Start\" to via MQTT to Node-RED\n client.publish(\"receiver/pump\", \"Start\");\n\n ########################################################################\n while True:\n\n #Depending on direction, select the right direction for the pump\n if direction == \"BACKWARD\":\n direction=stepper.BACKWARD\n\n if direction == \"FORWARD\":\n direction=stepper.FORWARD\n\n #Actuate the pump for one step in the right direction\n pump_stepper.onestep(direction=direction, style=stepper.DOUBLE)\n\n #Increment the counter\n counter+=1\n\n #Wait during the delay to pump at the right flowrate\n sleep(delay)\n\n ####################################################################\n #If counter reach the number of step, break\n if counter>nb_step:\n\n #Release the pump stepper to stop power draw\n pump_stepper.release()\n\n #Print status\n print(\"The pumping is done.\")\n\n #Change the command to not re-enter in this while loop\n command=\"wait\"\n\n #Publish the status \"Done\" to via MQTT to Node-RED\n client.publish(\"receiver/pump\", \"Done\");\n\n #Set the LEDs as Green\n rgb(0,255,0)\n\n #Reset the counter to 0\n counter=0\n\n break\n\n ####################################################################\n #If a new received command isn't \"pump\", break this while loop\n if command!=\"pump\":\n\n #Release the pump stepper to stop power draw\n pump_stepper.release()\n\n #Print status\n print(\"The pump has been interrompted.\")\n\n #Publish the status \"Interrompted\" to via MQTT to Node-RED\n client.publish(\"receiver/pump\", \"Interrompted\");\n\n #Set the LEDs as Green\n rgb(0,255,0)\n\n #Reset the counter to 0\n counter=0\n\n break\n\n ############################################################################\n #Focus Event\n ############################################################################\n\n #If the command is \"focus\"\n elif (command==\"focus\"):\n\n #Set the LEDs as Yellow\n rgb(255,255,0)\n\n #Get direction from the different received arguments\n direction=args.split(\" \")[0]\n\n #Get number of steps from the different received arguments\n nb_step=int(args.split(\" \")[1])\n\n #Print status\n print(\"The focus has been started.\")\n\n #Publish the status \"Start\" to via MQTT to Node-RED\n client.publish(\"receiver/focus\", \"Start\");\n\n ########################################################################\n while True:\n\n #Depending on direction, select the right direction for the focus\n if direction == \"FORWARD\":\n direction=stepper.FORWARD\n\n if direction == \"BACKWARD\":\n direction=stepper.BACKWARD\n\n #Actuate the focus for one microstep in the right direction\n focus_stepper.onestep(direction=direction, style=stepper.MICROSTEP)\n\n #Increment the counter\n counter+=1\n\n ####################################################################\n #If counter reach the number of step, break\n if counter>nb_step:\n\n #Release the focus steppers to stop power draw\n focus_stepper.release()\n\n #Print status\n print(\"The focusing is done.\")\n\n #Change the command to not re-enter in this while loop\n command=\"wait\"\n\n #Publish the status \"Done\" to via MQTT to Node-RED\n client.publish(\"receiver/focus\", \"Done\");\n\n #Set the LEDs as Green\n rgb(0,255,0)\n\n #Reset the counter to 0\n counter=0\n\n break\n\n ####################################################################\n #If a new received command isn't \"pump\", break this while loop\n if command!=\"focus\":\n\n #Release the focus steppers to stop power draw\n focus_stepper.release()\n\n #Print status\n print(\"The stage has been interrompted.\")\n\n #Publish the status \"Done\" to via MQTT to Node-RED\n client.publish(\"receiver/focus\", \"Interrompted\");\n\n #Set the LEDs as Green\n rgb(0,255,0)\n\n #Reset the counter to 0\n counter=0\n\n break\n\n ############################################################################\n #Image Event\n ############################################################################\n\n elif (command==\"image\"):\n \n #Publish the status \"Start\" to via MQTT to Node-RED\n client.publish(\"receiver/image\", \"Will do my best dude\");\n\n #Get duration to wait before an image from the different received arguments\n sleep_before=int(args.split(\" \")[0])\n\n #Get number of step in between two images from the different received arguments\n nb_step=int(args.split(\" \")[1])\n\n #Get the number of frames to image from the different received arguments\n nb_frame=int(args.split(\" \")[2])\n\n #Get the segmentation status (true/false) from the different received arguments\n segmentation=str(args.split(\" \")[3])\n\n #Sleep a duration before to start acquisition\n sleep(sleep_before)\n\n #Publish the status \"Start\" to via MQTT to Node-RED\n client.publish(\"receiver/image\", \"Start\");\n\n #Set the LEDs as Blue\n rgb(0,0,255)\n\n #Pump duing a given number of steps (in between each image)\n for i in range(nb_step):\n\n #If the command is still image - pump a defined nb of steps\n if (command==\"image\"):\n\n #Actuate the pump for one step in the FORWARD direction\n pump_stepper.onestep(direction=stepper.FORWARD, style=stepper.DOUBLE)\n\n #The flowrate is fixed for now.\n sleep(0.01)\n\n #If the command isn't image anymore - break\n else:\n\n break\n\n #Set the LEDs as Green\n rgb(0,255,0)\n\n while True:\n\n #Set the LEDs as Cyan\n rgb(0,255,255)\n\n #Increment the counter\n counter+=1\n\n #Get datetime\n datetime_tmp=datetime.now().strftime(\"%H_%M_%S_%f\")\n\n #Print datetime\n print(datetime_tmp)\n\n #Define the filename of the image\n filename = os.path.join(\"/home/pi/PlanktonScope/tmp\",datetime_tmp+\".jpg\")\n\n #Capture an image with the proper filename\n camera.capture(filename)\n\n #Set the LEDs as Green\n rgb(0,255,0)\n\n #Publish the name of the image to via MQTT to Node-RED\n\n client.publish(\"receiver/image\", datetime_tmp+\".jpg has been imaged.\");\n \n #Set the LEDs as Blue\n rgb(0,0,255)\n\n #Pump during a given nb of steps\n for i in range(nb_step):\n\n #Actuate the pump for one step in the FORWARD direction\n pump_stepper.onestep(direction=stepper.FORWARD, style=stepper.DOUBLE)\n\n #The flowrate is fixed for now.\n sleep(0.01)\n\n #Wait a fixed delay which set the framerate as < than 2 imag/sec\n sleep(0.5)\n\n #Set the LEDs as Green\n rgb(0,255,0)\n\n ####################################################################\n #If counter reach the number of frame, break\n if(counter>nb_frame):\n\n #Publish the status \"Completed\" to via MQTT to Node-RED\n client.publish(\"receiver/image\", \"Completed\");\n\n #Release the pump steppers to stop power draw\n pump_stepper.release()\n\n if(segmentation == \"True\"):\n\n #Publish the status \"Start\" to via MQTT to Node-RED\n client.publish(\"receiver/segmentation\", \"Start\");\n\n #Start the MorphoCut Pipeline\n p.run()\n\n #remove directory\n #shutil.rmtree(import_path)\n\n #Publish the status \"Completed\" to via MQTT to Node-RED\n client.publish(\"receiver/segmentation\", \"Completed\");\n\n #Set the LEDs as White\n rgb(255,255,255)\n\n #cmd = os.popen(\"rm -rf /home/pi/PlanktonScope/tmp/*.jpg\")\n\n #Let it happen\n sleep(1)\n\n #Set the LEDs as Green\n rgb(0,255,0)\n\n #End if(segmentation == \"True\"):\n\n #Change the command to not re-enter in this while loop\n command=\"wait\"\n \n #Set the LEDs as Green\n rgb(0,255,255)\n\n #Reset the counter to 0\n counter=0\n\n break\n\n ####################################################################\n #If a new received command isn't \"image\", break this while loop\n if command!=\"image\":\n\n #Release the pump steppers to stop power draw\n pump_stepper.release()\n\n #Print status\n print(\"The imaging has been interrompted.\")\n\n #Publish the status \"Interrompted\" to via MQTT to Node-RED\n client.publish(\"receiver/image\", \"Interrompted\");\n\n #Set the LEDs as Green\n rgb(0,255,0)\n\n #Reset the counter to 0\n counter=0\n\n break\n\n else:\n #Set the LEDs as Black\n rgb(0,0,0)\n #Its just waiting to receive command from Node-RED\n sleep(1)\n #Set the LEDs as White\n rgb(255,255,255)\n #Its just waiting to receive command from Node-RED\n sleep(1)\n", + "output": "str", + "x": 300, + "y": 100, "wires": [ - [] + [ + "500abffa.c7a788" + ] ] }, { - "id": "7cea16e.c42ace8", - "type": "ui_numeric", - "z": "bdd6e33e.5db3b8", - "name": "acq_maximum_mesh", - "label": "Max fraction size (μm)", - "tooltip": "", - "group": "52159161.72187", - "order": 4, - "width": 0, - "height": 0, - "wrap": false, - "passthru": true, - "topic": "acq_maximum_mesh", - "format": "{{value}}", - "min": "200", - "max": "2000", - "step": "100", - "x": 536, + "id": "a11158b1.b7649", + "type": "debug", + "z": "e8320d42.9a3ad8", + "name": "", + "active": true, + "tosidebar": true, + "console": false, + "tostatus": false, + "complete": "true", + "targetType": "full", + "x": 1230, "y": 200, + "wires": [] + }, + { + "id": "cf9e02a2.3feff", + "type": "exec", + "z": "e8320d42.9a3ad8", + "command": "ps -ax | grep \"python3.7 /home/pi/PlanktonScope/script/main.py\"| head -1 | awk -F \" \" '{print$1}' ", + "addpay": false, + "append": "", + "useSpawn": "false", + "timer": "", + "oldrc": false, + "name": "", + "x": 430, + "y": 40, "wires": [ + [ + "945415c5.01217" + ], + [], [] ] }, { - "id": "6ecc9468.0271dc", - "type": "ui_text_input", - "z": "bdd6e33e.5db3b8", - "name": "acq_id", - "label": "Acquisition unique ID*", - "tooltip": "", - "group": "52159161.72187", + "id": "945415c5.01217", + "type": "exec", + "z": "e8320d42.9a3ad8", + "command": "kill", + "addpay": true, + "append": "", + "useSpawn": "false", + "timer": "", + "oldrc": false, + "name": "", + "x": 910, + "y": 40, + "wires": [ + [], + [], + [] + ] + }, + { + "id": "18da28e6.7b000f", + "type": "delay", + "z": "e8320d42.9a3ad8", + "name": "", + "pauseType": "delay", + "timeout": "1", + "timeoutUnits": "seconds", + "rate": "1", + "nbRateUnits": "1", + "rateUnits": "second", + "randomFirst": "1", + "randomLast": "5", + "randomUnits": "seconds", + "drop": false, + "x": 160, + "y": 100, + "wires": [ + [ + "985c65de.0801b" + ] + ] + }, + { + "id": "6384a5e.e34465c", + "type": "subflow", + "name": "Datetime update", + "info": "", + "category": "", + "in": [ + { + "x": 140, + "y": 80, + "wires": [ + { + "id": "42ffcda3.49c30c" + } + ] + } + ], + "out": [], + "env": [], + "color": "#DDAA99", + "icon": "font-awesome/fa-clock-o" + }, + { + "id": "e3824a97.8f2c3", + "type": "exec", + "z": "6384a5e.e34465c", + "command": "sudo date -s", + "addpay": true, + "append": "", + "useSpawn": "false", + "timer": "", + "oldrc": false, + "name": "", + "x": 1010, + "y": 240, + "wires": [ + [], + [], + [] + ] + }, + { + "id": "a5a13db6.4c6958", + "type": "function", + "z": "6384a5e.e34465c", + "name": "", + "func": "d = new Date();\n//get weekday\nvar weekday = new Array(7);\nweekday[0] = \"Sun\";\nweekday[1] = \"Mon\";\nweekday[2] = \"Tue\";\nweekday[3] = \"Wed\";\nweekday[4] = \"Thu\";\nweekday[5] = \"Fri\";\nweekday[6] = \"Sat\";\nvar w = weekday[d.getUTCDay()];\n//get Month\nvar month = new Array(12);\nmonth[0] = \"Jan\";\nmonth[1] = \"Feb\";\nmonth[2] = \"Mar\";\nmonth[3] = \"Apr\";\nmonth[4] = \"May\";\nmonth[5] = \"Jun\";\nmonth[6] = \"Jul\";\nmonth[7] = \"Aug\";\nmonth[8] = \"Sep\";\nmonth[9] = \"Oct\";\nmonth[10] = \"Nov\";\nmonth[11] = \"Dec\";\nvar n = month[d.getUTCMonth()];\n \n//get day\nvar day = d.getUTCDay()\n\n//get Hours\nvar Hours = d.getUTCHours();\n//get Minutes\nvar Minutes = d.getUTCMinutes();\n//get Seconds\nvar Seconds = d.getUTCSeconds();\n//get FullYear\nvar FullYear = d.getUTCFullYear();\n\n//Thu Aug 09 2012 23:34:04 GMT+0200 (GMT+02:00)\n\n//Thu Aug 9 21:31:26 UTC 2012\n\n//msg.payload = \"Thu Aug 9 21:31:26 UTC 2012\"\n\nmsg.payload = '\"'+w+\" \"+n+\" \"+day+\" \"+Hours+\":\"+Minutes+\":\"+Seconds+\" UTC \"+FullYear+'\"';\nreturn msg;", + "outputs": 1, + "noerr": 0, + "x": 490, + "y": 40, + "wires": [ + [ + "bafb69f.a42ea18" + ] + ] + }, + { + "id": "bafb69f.a42ea18", + "type": "ui_template", + "z": "6384a5e.e34465c", + "group": "9c86b3b7.54841", + "name": "", "order": 1, "width": 0, "height": 0, - "passthru": true, - "mode": "number", - "delay": 300, - "topic": "acq_id", - "x": 586, + "format": "
", + "storeOutMessages": true, + "fwdInMessages": true, + "templateScope": "local", + "x": 640, "y": 40, "wires": [ [] ] }, { - "id": "259fd49a.160a3c", - "type": "ui_dropdown", - "z": "bdd6e33e.5db3b8", - "name": "acq_celltype", - "label": "Thickness flowcell*", - "tooltip": "", - "place": "Select option", - "group": "52159161.72187", - "order": 7, - "width": 0, - "height": 0, - "passthru": true, - "options": [ - { - "label": "200 μm µ-Slide I Luer", - "value": 200, - "type": "num" - }, - { - "label": "400 μm µ-Slide I Luer", - "value": 400, - "type": "num" - }, - { - "label": "600 μm µ-Slide I Luer", - "value": 600, - "type": "num" - }, - { - "label": "800 μm µ-Slide I Luer", - "value": 800, - "type": "num" - } - ], - "payload": "", - "topic": "acq_celltype", - "x": 566, - "y": 120, - "wires": [ - [] - ] - }, - { - "id": "66a3425c.79aabc", - "type": "ui_text_input", - "z": "bdd6e33e.5db3b8", - "name": "acq_volume", - "label": "Volume to pass (ml)", - "tooltip": "", - "group": "52159161.72187", - "order": 2, - "width": 0, - "height": 0, - "passthru": true, - "mode": "number", - "delay": 300, - "topic": "acq_volume", - "x": 566, - "y": 240, - "wires": [ - [] - ] - }, - { - "id": "5866c9a4.e1ca88", - "type": "ui_text_input", - "z": "bdd6e33e.5db3b8", - "name": "acq_instrument", - "label": "Acquisition instrument", - "tooltip": "PlanktonScope V2.1", - "group": "52159161.72187", - "order": 6, - "width": 0, - "height": 0, - "passthru": true, - "mode": "text", - "delay": 300, - "topic": "acq_instrument", - "x": 556, - "y": 80, - "wires": [ - [] - ] - }, - { - "id": "76a6e6bb.a08b98", - "type": "json", - "z": "259c8713.b50e28", - "name": "", - "property": "payload", - "action": "str", - "pretty": true, - "x": 1310, - "y": 100, - "wires": [ - [ - "f25890f5.f2549" - ] - ] - }, - { - "id": "594ec843.9d4458", - "type": "file in", - "z": "259c8713.b50e28", - "name": "", - "filename": "/home/pi/PlanktonScope/config.txt", - "format": "utf8", - "chunk": false, - "sendError": false, - "encoding": "none", - "x": 340, - "y": 60, - "wires": [ - [ - "3bc1a977.4e9c76" - ] - ] - }, - { - "id": "d9ca0e54.f8b58", - "type": "inject", - "z": "259c8713.b50e28", - "name": "on_load", - "topic": "", - "payload": "", - "payloadType": "date", - "repeat": "", - "crontab": "", - "once": true, - "onceDelay": 0.1, - "x": 100, - "y": 60, - "wires": [ - [ - "594ec843.9d4458", - "ca38a11d.0ee54", - "807d5cce.2bb1e", - "fda01242.9576a8" - ] - ] - }, - { - "id": "3bc1a977.4e9c76", - "type": "json", - "z": "259c8713.b50e28", - "name": "", - "property": "payload", - "action": "", - "pretty": false, - "x": 550, - "y": 60, - "wires": [ - [ - "7f101b25.0da4a4", - "99b5a67.080f258", - "a71ba4a6.c44c4", - "fe5585e.a1ab078", - "da9f1367.3a17a8", - "d8dbecd.f7b3b9", - "c986ae96.860ec8" - ] - ] - }, - { - "id": "2582798f.eddcc6", - "type": "function", - "z": "173a6e6b.e5ca6a", - "name": "get sample_projet", - "func": "msg.payload = msg.payload.sample_project;\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 250, - "y": 40, - "wires": [ - [ - "a163194f.0b17c8" - ] - ] - }, - { - "id": "1590a418.9166dc", - "type": "function", - "z": "173a6e6b.e5ca6a", - "name": "get sample_ship", - "func": "msg.payload = msg.payload.sample_ship;\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 240, - "y": 120, - "wires": [ - [ - "6d0d6fc7.d30bb" - ] - ] - }, - { - "id": "1d28205b.58a37", - "type": "function", - "z": "173a6e6b.e5ca6a", - "name": "get sample_id", - "func": "msg.payload = msg.payload.sample_id+1;\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 240, - "y": 80, - "wires": [ - [ - "914752eb.af1b" - ] - ] - }, - { - "id": "d96f9fa3.d4cfc", - "type": "function", - "z": "173a6e6b.e5ca6a", - "name": "get sample_operator", - "func": "msg.payload = msg.payload.sample_operator;\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 260, - "y": 160, - "wires": [ - [ - "458408d7.2b3b68" - ] - ] - }, - { - "id": "784e2f78.9b96f", - "type": "function", - "z": "173a6e6b.e5ca6a", - "name": "get sample_sampling_gear", - "func": "msg.payload = msg.payload.sample_sampling_gear;\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 280, - "y": 200, - "wires": [ - [ - "43b12fe4.c5aa3" - ] - ] - }, - { - "id": "47459dcd.81b594", - "type": "function", - "z": "bdd6e33e.5db3b8", - "name": "get acq_id", - "func": "msg.payload = msg.payload.acq_id+1;\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 210, - "y": 40, - "wires": [ - [ - "6ecc9468.0271dc" - ] - ] - }, - { - "id": "eec199a3.a5a768", - "type": "function", - "z": "bdd6e33e.5db3b8", - "name": "get acq_instrument", - "func": "msg.payload = msg.payload.acq_instrument;\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 230, - "y": 80, - "wires": [ - [ - "5866c9a4.e1ca88" - ] - ] - }, - { - "id": "2d278f0a.1a97a", - "type": "function", - "z": "bdd6e33e.5db3b8", - "name": "get acq_celltype", - "func": "msg.payload = msg.payload.acq_celltype;\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 220, - "y": 120, - "wires": [ - [ - "259fd49a.160a3c" - ] - ] - }, - { - "id": "4074b907.e527e8", - "type": "function", - "z": "bdd6e33e.5db3b8", - "name": "get acq_minimum_mesh", - "func": "msg.payload = msg.payload.acq_minimum_mesh;\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 250, - "y": 160, - "wires": [ - [ - "5aba848a.7a861c" - ] - ] - }, - { - "id": "bc37aba3.0d1e78", - "type": "function", - "z": "bdd6e33e.5db3b8", - "name": "get acq_maximum_mesh", - "func": "msg.payload = msg.payload.acq_maximum_mesh;\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 250, - "y": 200, - "wires": [ - [ - "7cea16e.c42ace8" - ] - ] - }, - { - "id": "d973d64a.8801e8", - "type": "function", - "z": "bdd6e33e.5db3b8", - "name": "get acq_volume", - "func": "msg.payload = msg.payload.acq_volume;\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 220, - "y": 240, - "wires": [ - [ - "66a3425c.79aabc" - ] - ] - }, - { - "id": "bc39179c.bb3c08", - "type": "function", - "z": "bdd6e33e.5db3b8", - "name": "get acq_fnumber_objective", - "func": "msg.payload = msg.payload.acq_fnumber_objective;\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 260, - "y": 360, - "wires": [ - [ - "eb9181d8.25e01" - ] - ] - }, - { - "id": "47c7db4d.5eb014", + "id": "81f9cd4c.8540b", "type": "ui_numeric", - "z": "ad5a5663.ce893", - "name": "object_depth_min", - "label": "Minimum depth (m)", + "z": "6384a5e.e34465c", + "name": "tmp_year", + "label": "Year", "tooltip": "", - "group": "cef1e703.bcf3c8", + "group": "9c86b3b7.54841", + "order": 2, + "width": 5, + "height": 1, + "wrap": false, + "passthru": true, + "topic": "tmp_year", + "format": "{{value}}", + "min": "2020", + "max": "2030", + "step": 1, + "x": 640, + "y": 80, + "wires": [ + [ + "8f5a74df.0663f" + ] + ] + }, + { + "id": "274f25fc.9e61ba", + "type": "ui_numeric", + "z": "6384a5e.e34465c", + "name": "tmp_month", + "label": "Month", + "tooltip": "", + "group": "9c86b3b7.54841", "order": 3, - "width": 0, - "height": 0, + "width": 3, + "height": 1, "wrap": false, "passthru": true, - "topic": "object_depth_min", + "topic": "tmp_month", "format": "{{value}}", - "min": "0", - "max": "2000", - "step": "1", - "x": 610, + "min": "1", + "max": "12", + "step": 1, + "x": 650, "y": 120, "wires": [ - [] + [ + "8f5a74df.0663f" + ] ] }, { - "id": "20c46fd4.6b984", + "id": "4ddcb673.905a", "type": "ui_numeric", - "z": "ad5a5663.ce893", - "name": "object_depth_max", - "label": "Maximum depth (m)", + "z": "6384a5e.e34465c", + "name": "tmp_day", + "label": "Day", "tooltip": "", - "group": "cef1e703.bcf3c8", - "order": 2, - "width": 0, - "height": 0, + "group": "9c86b3b7.54841", + "order": 4, + "width": 3, + "height": 1, "wrap": false, "passthru": true, - "topic": "object_depth_max", + "topic": "tmp_day", "format": "{{value}}", - "min": "0", - "max": "2000", - "step": "1", - "x": 610, + "min": "1", + "max": "31", + "step": 1, + "x": 640, "y": 160, "wires": [ - [] + [ + "8f5a74df.0663f" + ] ] }, { - "id": "1a5edafb.a05cf5", + "id": "248eee4c.238282", + "type": "ui_numeric", + "z": "6384a5e.e34465c", + "name": "tmp_hour", + "label": "Hour", + "tooltip": "", + "group": "9c86b3b7.54841", + "order": 5, + "width": 3, + "height": 1, + "wrap": false, + "passthru": true, + "topic": "tmp_hour", + "format": "{{value}}", + "min": "0", + "max": "23", + "step": 1, + "x": 640, + "y": 200, + "wires": [ + [ + "8f5a74df.0663f" + ] + ] + }, + { + "id": "a368c4b7.2dc4b8", + "type": "ui_numeric", + "z": "6384a5e.e34465c", + "name": "tmp_minute", + "label": "Minute", + "tooltip": "", + "group": "9c86b3b7.54841", + "order": 6, + "width": 3, + "height": 1, + "wrap": false, + "passthru": true, + "topic": "tmp_minute", + "format": "{{value}}", + "min": "0", + "max": "59", + "step": 1, + "x": 650, + "y": 240, + "wires": [ + [ + "8f5a74df.0663f" + ] + ] + }, + { + "id": "96cc9953.9496c8", + "type": "ui_numeric", + "z": "6384a5e.e34465c", + "name": "tmp_second", + "label": "Second", + "tooltip": "", + "group": "9c86b3b7.54841", + "order": 7, + "width": 3, + "height": 1, + "wrap": false, + "passthru": true, + "topic": "tmp_second", + "format": "{{value}}", + "min": "0", + "max": "59", + "step": 1, + "x": 650, + "y": 280, + "wires": [ + [ + "8f5a74df.0663f" + ] + ] + }, + { + "id": "d6240495.8429c", + "type": "interval", + "z": "6384a5e.e34465c", + "name": "interval", + "interval": "1", + "onstart": false, + "msg": "ping", + "showstatus": true, + "unit": "seconds", + "statusformat": "YYYY-MM-D HH:mm:ss", + "x": 310, + "y": 40, + "wires": [ + [ + "a5a13db6.4c6958" + ] + ] + }, + { + "id": "e8d38dc0.c7e84", + "type": "ui_button", + "z": "6384a5e.e34465c", + "name": "", + "group": "9c86b3b7.54841", + "order": 8, + "width": 4, + "height": 1, + "passthru": false, + "label": "Update", + "tooltip": "", + "color": "black", + "bgcolor": "white", + "icon": "", + "payload": "", + "payloadType": "str", + "topic": "", + "x": 640, + "y": 320, + "wires": [ + [ + "581f71d3.bde458" + ] + ] + }, + { + "id": "581f71d3.bde458", "type": "function", - "z": "259c8713.b50e28", + "z": "6384a5e.e34465c", + "name": "update datetime", + "func": "var FullYear= global.get(\"year\");\nvar Month= global.get(\"month\");\nvar day= global.get(\"day\");\nvar Hours= global.get(\"hour\");\nvar Minutes= global.get(\"minute\");\nvar Seconds= global.get(\"second\");\n\nmsg.payload = new Date();\n//get Month\nvar month = new Array(12);\nmonth[1] = \"Jan\";\nmonth[2] = \"Feb\";\nmonth[3] = \"Mar\";\nmonth[4] = \"Apr\";\nmonth[5] = \"May\";\nmonth[6] = \"Jun\";\nmonth[7] = \"Jul\";\nmonth[8] = \"Aug\";\nmonth[9] = \"Sep\";\nmonth[10] = \"Oct\";\nmonth[11] = \"Nov\";\nmonth[12] = \"Dec\";\nvar n = month[Month];\n \nmsg.payload = '\"'+day+\" \"+n+\" \"+FullYear+\" \"+Hours+\":\"+Minutes+\":\"+Seconds+'\"';\n\n\nreturn msg;", + "outputs": 1, + "noerr": 0, + "x": 800, + "y": 320, + "wires": [ + [ + "6b023a67.faa104", + "e3824a97.8f2c3" + ] + ] + }, + { + "id": "8f5a74df.0663f", + "type": "function", + "z": "6384a5e.e34465c", "name": "set global", "func": "var value = msg.payload;\nvar key = msg.topic;\n\nglobal.set(key,value);\nreturn msg;", "outputs": 1, "noerr": 0, - "x": 1020, + "x": 840, "y": 60, + "wires": [ + [] + ] + }, + { + "id": "6b023a67.faa104", + "type": "debug", + "z": "6384a5e.e34465c", + "name": "", + "active": true, + "tosidebar": true, + "console": false, + "tostatus": false, + "complete": "false", + "x": 1010, + "y": 300, + "wires": [] + }, + { + "id": "4ab089b9.1098", + "type": "function", + "z": "6384a5e.e34465c", + "name": "", + "func": "d = msg.payload;\n\nvar val = d.getUTCFullYear();\n\nmsg.payload = val;\nreturn msg;", + "outputs": 1, + "noerr": 0, + "x": 490, + "y": 80, "wires": [ [ - "e001a28.555566" + "81f9cd4c.8540b" ] ] }, { - "id": "21f41837.bb6c88", + "id": "42ffcda3.49c30c", "type": "function", - "z": "ad5a5663.ce893", - "name": "get object_depth_min", - "func": "msg.payload = msg.payload.object_depth_min;\nreturn msg;", + "z": "6384a5e.e34465c", + "name": "", + "func": "d = new Date();\nmsg.payload = d\nreturn msg;", "outputs": 1, "noerr": 0, - "x": 304, + "x": 310, + "y": 80, + "wires": [ + [ + "4ab089b9.1098", + "13529b2c.cb9d9d", + "c09bb768.0e7518", + "967b4488.670f08", + "3e3732d.273a04e", + "327729f0.afe466" + ] + ] + }, + { + "id": "13529b2c.cb9d9d", + "type": "function", + "z": "6384a5e.e34465c", + "name": "", + "func": "d = msg.payload;\n\nvar val = d.getUTCMonth();\n\nmsg.payload = val+1;\nreturn msg;", + "outputs": 1, + "noerr": 0, + "x": 490, "y": 120, "wires": [ [ - "47c7db4d.5eb014" + "274f25fc.9e61ba" ] ] }, { - "id": "c2f235f2.eee388", + "id": "c09bb768.0e7518", "type": "function", - "z": "ad5a5663.ce893", - "name": "get object_depth_max", - "func": "msg.payload = msg.payload.object_depth_max;\nreturn msg;", + "z": "6384a5e.e34465c", + "name": "", + "func": "d = msg.payload;\n\nvar val = d.getUTCDay();\n\nmsg.payload = val;\nreturn msg;", "outputs": 1, "noerr": 0, - "x": 304, + "x": 490, "y": 160, "wires": [ [ - "20c46fd4.6b984" + "4ddcb673.905a" ] ] }, { - "id": "23e45d82.a01f82", + "id": "967b4488.670f08", + "type": "function", + "z": "6384a5e.e34465c", + "name": "", + "func": "d = msg.payload;\n\nvar val = d.getUTCHours();\n\nmsg.payload = val;\nreturn msg;", + "outputs": 1, + "noerr": 0, + "x": 490, + "y": 200, + "wires": [ + [ + "248eee4c.238282" + ] + ] + }, + { + "id": "3e3732d.273a04e", + "type": "function", + "z": "6384a5e.e34465c", + "name": "", + "func": "d = msg.payload;\n\nvar val = d.getUTCMinutes();\n\nmsg.payload = val;\nreturn msg;", + "outputs": 1, + "noerr": 0, + "x": 490, + "y": 240, + "wires": [ + [ + "a368c4b7.2dc4b8" + ] + ] + }, + { + "id": "327729f0.afe466", + "type": "function", + "z": "6384a5e.e34465c", + "name": "", + "func": "d = msg.payload;\n\nvar val = d.getUTCSeconds();\n\nmsg.payload = val;\nreturn msg;", + "outputs": 1, + "noerr": 0, + "x": 490, + "y": 280, + "wires": [ + [ + "96cc9953.9496c8" + ] + ] + }, + { + "id": "9c86b3b7.54841", + "type": "ui_group", + "z": "", + "name": "Datetime", + "tab": "2b97fe34.a699fa", + "order": 1, + "disp": true, + "width": "24", + "collapse": false + }, + { + "id": "a156df1e.d37178", + "type": "subflow", + "name": "Acquisition inputs", + "info": "", + "category": "", + "in": [ + { + "x": 40, + "y": 40, + "wires": [ + { + "id": "2dd27be1.476eac" + }, + { + "id": "3883d084.feb708" + }, + { + "id": "4bf1038f.d36f9c" + }, + { + "id": "ae15c276.ec8c68" + } + ] + } + ], + "out": [ + { + "x": 740, + "y": 40, + "wires": [ + { + "id": "b996437b.1a45b8", + "port": 0 + }, + { + "id": "d56a51c1.60023", + "port": 0 + }, + { + "id": "229ade87.b1656a", + "port": 0 + }, + { + "id": "5e093b67.a32f9c", + "port": 0 + } + ] + } + ], + "env": [], + "color": "#A6BBCF", + "icon": "node-red-contrib-camerapi/photo.png" + }, + { + "id": "b996437b.1a45b8", "type": "ui_text_input", - "z": "4475ba6c.45604c", + "z": "a156df1e.d37178", + "name": "custom_nb_step", + "label": "Number of steps in between two images", + "tooltip": "", + "group": "48649115.fcd01", + "order": 2, + "width": 0, + "height": 0, + "passthru": true, + "mode": "number", + "delay": 300, + "topic": "custom_nb_step", + "x": 540, + "y": 80, + "wires": [ + [] + ] + }, + { + "id": "229ade87.b1656a", + "type": "ui_text_input", + "z": "a156df1e.d37178", + "name": "custom_nb_frame", + "label": "Number of images per acquisition", + "tooltip": "", + "group": "48649115.fcd01", + "order": 3, + "width": 0, + "height": 0, + "passthru": true, + "mode": "number", + "delay": 300, + "topic": "custom_nb_frame", + "x": 530, + "y": 120, + "wires": [ + [] + ] + }, + { + "id": "2dd27be1.476eac", + "type": "function", + "z": "a156df1e.d37178", + "name": "get custom_nb_step", + "func": "msg.payload = msg.payload.custom_nb_step;\nreturn msg;", + "outputs": 1, + "noerr": 0, + "x": 220, + "y": 80, + "wires": [ + [ + "b996437b.1a45b8" + ] + ] + }, + { + "id": "4bf1038f.d36f9c", + "type": "function", + "z": "a156df1e.d37178", + "name": "get custom_nb_frame", + "func": "msg.payload = msg.payload.custom_nb_frame;\nreturn msg;", + "outputs": 1, + "noerr": 0, + "x": 220, + "y": 120, + "wires": [ + [ + "229ade87.b1656a" + ] + ] + }, + { + "id": "ae15c276.ec8c68", + "type": "function", + "z": "a156df1e.d37178", + "name": "get custom_segmentation", + "func": "msg.payload = msg.payload.custom_segmentation;\nreturn msg;", + "outputs": 1, + "noerr": 0, + "x": 230, + "y": 160, + "wires": [ + [ + "5e093b67.a32f9c" + ] + ] + }, + { + "id": "3883d084.feb708", + "type": "function", + "z": "a156df1e.d37178", + "name": "get custom_sleep_before", + "func": "msg.payload = msg.payload.custom_sleep_before;\nreturn msg;", + "outputs": 1, + "noerr": 0, + "x": 230, + "y": 40, + "wires": [ + [ + "d56a51c1.60023" + ] + ] + }, + { + "id": "d56a51c1.60023", + "type": "ui_text_input", + "z": "a156df1e.d37178", + "name": "custom_sleep_before", + "label": "Duration before the acquisition (s)", + "tooltip": "", + "group": "48649115.fcd01", + "order": 1, + "width": 0, + "height": 0, + "passthru": true, + "mode": "number", + "delay": 300, + "topic": "custom_sleep_before", + "x": 520, + "y": 40, + "wires": [ + [] + ] + }, + { + "id": "5e093b67.a32f9c", + "type": "ui_switch", + "z": "a156df1e.d37178", + "name": "custom_segmentation", + "label": "Realize the segmentation", + "tooltip": "", + "group": "48649115.fcd01", + "order": 6, + "width": 0, + "height": 0, + "passthru": true, + "decouple": "false", + "topic": "custom_segmentation", + "style": "", + "onvalue": "True", + "onvalueType": "str", + "onicon": "", + "oncolor": "", + "offvalue": "False", + "offvalueType": "str", + "officon": "", + "offcolor": "", + "x": 520, + "y": 160, + "wires": [ + [] + ] + }, + { + "id": "48649115.fcd01", + "type": "ui_group", + "z": "", + "name": "Acquisition inputs", + "tab": "2b97fe34.a699fa", + "order": 9, + "disp": true, + "width": "24", + "collapse": false + }, + { + "id": "99798a85.e62408", + "type": "subflow", + "name": "Process metadata", + "info": "", + "category": "", + "in": [ + { + "x": 40, + "y": 80, + "wires": [ + { + "id": "20414296.54837e" + } + ] + } + ], + "out": [ + { + "x": 700, + "y": 80, + "wires": [ + { + "id": "d5ab9061.b06a9", + "port": 0 + } + ] + } + ], + "env": [], + "color": "#DDAA99" + }, + { + "id": "d5ab9061.b06a9", + "type": "ui_text_input", + "z": "99798a85.e62408", "name": "process_id", "label": "Id of the process", "tooltip": "", - "group": "b1321ea9.cfcf28", + "group": "beeb994e.b67688", "order": 1, "width": 0, "height": 0, @@ -1564,9 +1193,9 @@ ] }, { - "id": "d899c841.e6c178", + "id": "20414296.54837e", "type": "function", - "z": "4475ba6c.45604c", + "z": "99798a85.e62408", "name": "get process_id", "func": "msg.payload = msg.payload.process_id+1;\nreturn msg;", "outputs": 1, @@ -1575,666 +1204,55 @@ "y": 80, "wires": [ [ - "23e45d82.a01f82" + "d5ab9061.b06a9" ] ] }, { - "id": "4fa9647b.8a2ebc", - "type": "gpsd", - "z": "ad5a5663.ce893", - "name": "", - "hostname": "localhost", - "port": "2947", - "tpv": true, - "sky": false, - "info": false, - "device": false, - "gst": false, - "att": false, - "x": 90, - "y": 220, - "wires": [ - [ - "2327c165.8397ae", - "bbb7cb31.15121" - ] - ] - }, - { - "id": "767b43a1.de21dc", - "type": "ui_worldmap", - "z": "ad5a5663.ce893", - "d": true, - "group": "cef1e703.bcf3c8", - "order": 1, - "width": 0, - "height": 0, - "name": "", - "lat": "1.5", - "lon": "1.5", - "zoom": "4", - "layer": "OSM grey", - "cluster": "1", - "maxage": "", - "usermenu": "hide", - "layers": "hide", - "panit": "false", - "panlock": "false", - "zoomlock": "false", - "hiderightclick": "true", - "coords": "deg", - "showgrid": "false", - "path": "/worldmap", - "x": 640, - "y": 200, - "wires": [] - }, - { - "id": "2327c165.8397ae", - "type": "function", - "z": "ad5a5663.ce893", - "name": "get object_lat & object_lon", - "func": "\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 320, - "y": 200, - "wires": [ - [ - "767b43a1.de21dc" - ] - ] - }, - { - "id": "fa47061e.34a218", - "type": "ui_numeric", - "z": "bdd6e33e.5db3b8", - "name": "acq_min_esd", - "label": "Minimum size to segment (μm)", - "tooltip": "", - "group": "52159161.72187", - "order": 9, - "width": 0, - "height": 0, - "wrap": false, - "passthru": true, - "topic": "acq_min_esd", - "format": "{{value}}", - "min": 0, - "max": "300", - "step": "5", - "x": 566, - "y": 280, - "wires": [ - [] - ] - }, - { - "id": "6f36bd6d.154d14", - "type": "ui_numeric", - "z": "bdd6e33e.5db3b8", - "name": "acq_max_esd", - "label": "Maximum size to segment (μm)", - "tooltip": "", - "group": "52159161.72187", - "order": 5, - "width": 0, - "height": 0, - "wrap": false, - "passthru": true, - "topic": "acq_max_esd", - "format": "{{value}}", - "min": "100", - "max": "2000", - "step": "5", - "x": 556, - "y": 320, - "wires": [ - [] - ] - }, - { - "id": "277b6764.edb1f8", - "type": "function", - "z": "bdd6e33e.5db3b8", - "name": "get acq_min_esd", - "func": "msg.payload = msg.payload.acq_min_esd;\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 230, - "y": 280, - "wires": [ - [ - "fa47061e.34a218" - ] - ] - }, - { - "id": "75b10c7c.8433a4", - "type": "function", - "z": "bdd6e33e.5db3b8", - "name": "get acq_max_esd", - "func": "msg.payload = msg.payload.acq_max_esd;\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 230, - "y": 320, - "wires": [ - [ - "6f36bd6d.154d14" - ] - ] - }, - { - "id": "5f4a72d1.9f6adc", - "type": "ui_text_input", - "z": "ae90e3e.7d9fba", - "name": "nb_step", - "label": "Number of step(s)", - "tooltip": "", - "group": "fbd92986.1028c8", - "order": 2, - "width": 8, - "height": 1, - "passthru": true, - "mode": "number", - "delay": 300, - "topic": "nb_step", - "x": 520, - "y": 40, - "wires": [ - [] - ] - }, - { - "id": "81a7627c.bac92", - "type": "function", - "z": "ae90e3e.7d9fba", - "name": "get generic_nb_step", - "func": "msg.payload = msg.payload.generic_nb_step;\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 240, - "y": 40, - "wires": [ - [ - "5f4a72d1.9f6adc" - ] - ] - }, - { - "id": "705dddc5.567bc4", - "type": "ui_button", - "z": "ae90e3e.7d9fba", - "name": "DOWN", - "group": "fbd92986.1028c8", - "order": 3, - "width": 6, - "height": 1, - "passthru": true, - "label": "", - "tooltip": "", - "color": "", - "bgcolor": "", - "icon": "arrow_downward", - "payload": "DOWN", - "payloadType": "str", - "topic": "actuator/focus", - "x": 520, - "y": 120, - "wires": [ - [ - "4f74f017.00a58" - ] - ] - }, - { - "id": "b0aacff7.56651", - "type": "ui_button", - "z": "ae90e3e.7d9fba", - "name": "UP", - "group": "fbd92986.1028c8", - "order": 1, - "width": 6, - "height": 1, - "passthru": false, - "label": "", - "tooltip": "", - "color": "", - "bgcolor": "", - "icon": "arrow_upwards", - "payload": "UP", - "payloadType": "str", - "topic": "actuator/focus", - "x": 530, - "y": 81, - "wires": [ - [ - "4f74f017.00a58" - ] - ] - }, - { - "id": "3e9c4e74.aee022", - "type": "function", - "z": "407d8cdb.3cb7cc", - "name": "pump.js", - "func": "state = global.get(\"state\");\n\nif (state == null){state=\"free\"}\n\nvar manual_volume= global.get(\"manual_volume\");\nvar flowrate= global.get(\"flowrate\");\n\nif (manual_volume === undefined || manual_volume === \"\" || manual_volume === null) {\n msg.topic = \"Missing entry :\"\n msg.payload = \"Volume to pass\";\n \n}else if (flowrate === undefined || flowrate === \"\" || flowrate === null) {\n msg.topic = \"Missing entry :\"\n msg.payload = \"Flowrate\";\n \n}else {\n volume = global.get(\"manual_volume\");\n nb_step=volume*507\n msg.volume = volume;\n flowrate = global.get(\"flowrate\");\n duration=(volume*60)/flowrate\n delay=(duration/nb_step)-0.005\n msg.topic = \"actuator/pump\";\n \n if(msg.payload === \"FORWARD\" & state===\"free\"){\n msg.payload='FORWARD '+delay+' '+nb_step;\n }\n if(msg.payload === \"BACKWARD\" & state===\"free\"){\n msg.payload='BACKWARD '+delay+' '+nb_step;\n }\n}\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 620, - "y": 140, - "wires": [ - [ - "98e2e9e0.fb7418" - ] - ], - "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": "3f0df968.b0d286", - "type": "ui_button", - "z": "407d8cdb.3cb7cc", - "name": "BACKWARD", - "group": "707d9797.c8e798", - "order": 2, - "width": 6, - "height": 1, - "passthru": false, - "label": "", - "tooltip": "", - "color": "", - "bgcolor": "", - "icon": "arrow_back", - "payload": "BACKWARD", - "payloadType": "str", - "topic": "actuator/pump", - "x": 470, - "y": 120, - "wires": [ - [ - "3e9c4e74.aee022" - ] - ] - }, - { - "id": "214fb242.9abb6e", - "type": "ui_button", - "z": "407d8cdb.3cb7cc", - "name": "FORWARD", - "group": "707d9797.c8e798", - "order": 4, - "width": 6, - "height": 1, - "passthru": true, - "label": "", - "tooltip": "", - "color": "", - "bgcolor": "", - "icon": "arrow_forward", - "payload": "FORWARD", - "payloadType": "str", - "topic": "actuator/pump", - "x": 470, - "y": 160, - "wires": [ - [ - "3e9c4e74.aee022" - ] - ] - }, - { - "id": "1d58e86f.a3a9e8", - "type": "rpi-gpio out", - "z": "259c8713.b50e28", - "name": "", - "pin": "40", - "set": "", - "level": "0", - "freq": "", - "out": "out", - "x": 400, - "y": 100, - "wires": [] - }, - { - "id": "3e58f066.366b5", - "type": "ui_template", - "z": "259c8713.b50e28", - "group": "f5194cae.c84688", - "name": "Stream Pi Camera", - "order": 1, + "id": "beeb994e.b67688", + "type": "ui_group", + "z": "", + "name": "Process metadata", + "tab": "2b97fe34.a699fa", + "order": 8, + "disp": true, "width": 24, - "height": 11, - "format": "
", - "storeOutMessages": true, - "fwdInMessages": true, - "templateScope": "local", - "x": 750, - "y": 340, - "wires": [ - [] - ] + "collapse": false }, { - "id": "b7d9455c.026588", - "type": "switch", - "z": "ae90e3e.7d9fba", - "name": "", - "property": "topic", - "propertyType": "msg", - "rules": [ - { - "t": "eq", - "v": "actuator/focus", - "vt": "str" - }, - { - "t": "eq", - "v": "Missing entry :", - "vt": "str" - } - ], - "checkall": "true", - "repair": false, - "outputs": 2, - "x": 810, - "y": 100, - "wires": [ - [ - "fdb3b132.8b341" - ], - [ - "b9d996d6.37c2f8" - ] - ] + "id": "246abd43.838a5a", + "type": "subflow", + "name": "MQTT Receive & Plot", + "info": "", + "category": "", + "in": [], + "out": [], + "env": [], + "color": "#F3B567", + "icon": "node-red/bridge.svg" }, { - "id": "b9d996d6.37c2f8", - "type": "ui_toast", - "z": "ae90e3e.7d9fba", - "position": "dialog", - "displayTime": "3", - "highlight": "", - "sendall": true, - "outputs": 1, - "ok": "OK", - "cancel": "", - "raw": false, - "topic": "", - "name": "", - "x": 970, - "y": 140, - "wires": [ - [] - ] - }, - { - "id": "ca38a11d.0ee54", - "type": "function", - "z": "259c8713.b50e28", - "name": "init LED", - "func": "msg.payload=1;\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 260, - "y": 100, - "wires": [ - [ - "1d58e86f.a3a9e8" - ] - ] - }, - { - "id": "98e2e9e0.fb7418", - "type": "switch", - "z": "407d8cdb.3cb7cc", - "name": "", - "property": "topic", - "propertyType": "msg", - "rules": [ - { - "t": "eq", - "v": "actuator/pump", - "vt": "str" - }, - { - "t": "eq", - "v": "Missing entry :", - "vt": "str" - } - ], - "checkall": "true", - "repair": false, - "outputs": 2, - "x": 770, - "y": 140, - "wires": [ - [ - "61fb057d.3c251c" - ], - [ - "46a536f0.c83138" - ] - ] - }, - { - "id": "46a536f0.c83138", - "type": "ui_toast", - "z": "407d8cdb.3cb7cc", - "position": "dialog", - "displayTime": "3", - "highlight": "", - "sendall": true, - "outputs": 1, - "ok": "OK", - "cancel": "", - "raw": false, - "topic": "", - "name": "", - "x": 930, - "y": 160, - "wires": [ - [] - ] - }, - { - "id": "24ffcf03.2a51b", - "type": "ui_button", - "z": "407d8cdb.3cb7cc", - "name": "stop pump", - "group": "707d9797.c8e798", - "order": 5, - "width": 4, - "height": 1, - "passthru": true, - "label": "STOP PUMP", - "tooltip": "", - "color": "", - "bgcolor": "#AD1625", - "icon": "", - "payload": "off", - "payloadType": "str", - "topic": "actuator/wait", - "x": 470, - "y": 200, - "wires": [ - [ - "e2a7220a.09d43" - ] - ] - }, - { - "id": "4f74f017.00a58", - "type": "function", - "z": "ae90e3e.7d9fba", - "name": "focus.js", - "func": "state = global.get(\"state\");\n\nif (state == null){state=\"free\"}\n\nvar nb_step= global.get(\"nb_step\");\n\nif (nb_step === undefined || nb_step === \"\" || nb_step === null) {\n msg.topic = \"Missing entry :\"\n msg.payload = \"Number of steps\";\n \n}else {\n nb_step= global.get(\"nb_step\");\n if(msg.payload === \"UP\" & state===\"free\"){\n msg.payload=\"FORWARD \"+nb_step;\n }\n if(msg.payload === \"DOWN\" & state===\"free\"){\n msg.payload=\"BACKWARD \"+nb_step;\n }\n}\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 660, - "y": 100, - "wires": [ - [ - "b7d9455c.026588" - ] - ], - "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": "52cc1de5.b78e84", - "type": "ui_button", - "z": "ae90e3e.7d9fba", - "name": "stop focus", - "group": "fbd92986.1028c8", - "order": 4, - "width": 4, - "height": 1, - "passthru": true, - "label": "STOP FOCUS", - "tooltip": "", - "color": "", - "bgcolor": "#AD1625", - "icon": "", - "payload": "off", - "payloadType": "str", - "topic": "actuator/wait", - "x": 510, - "y": 160, - "wires": [ - [ - "e46763fe.7fc83" - ] - ] - }, - { - "id": "39cad6fb.1503ca", - "type": "ui_button", - "z": "35488f4f.00498", - "name": "", - "group": "c6a276ac.3eb74", - "order": 1, - "width": 0, - "height": 0, - "passthru": false, - "label": "Reboot", - "tooltip": "", - "color": "", - "bgcolor": "#AD1625", - "icon": "", - "payload": "off", - "payloadType": "str", - "topic": "reboot", - "x": 220, - "y": 80, - "wires": [ - [ - "95b876d4.07c708" - ] - ] - }, - { - "id": "1f53f29b.feee4d", - "type": "exec", - "z": "35488f4f.00498", - "command": "sudo", - "addpay": true, - "append": "", - "useSpawn": "false", - "timer": "2", - "oldrc": false, - "name": "cmd", - "x": 530, - "y": 80, - "wires": [ - [], - [], - [] - ] - }, - { - "id": "e325458b.95bff8", - "type": "ui_button", - "z": "35488f4f.00498", - "name": "", - "group": "c6a276ac.3eb74", - "order": 2, - "width": 0, - "height": 0, - "passthru": false, - "label": "Shutdown", - "tooltip": "", - "color": "", - "bgcolor": "#AD1625", - "icon": "", - "payload": "off", - "payloadType": "str", - "topic": "shutdown", - "x": 220, - "y": 140, - "wires": [ - [ - "95b876d4.07c708" - ] - ] - }, - { - "id": "95b876d4.07c708", - "type": "python3-function", - "z": "35488f4f.00498", - "name": "action", - "func": "#!/usr/bin/python\nimport smbus\nimport time\nbus = smbus.SMBus(1)\ntime.sleep(1)\n#turn off fan RGB\nbus.write_byte_data(0x0d, 0x07, 0x00)\nbus.write_byte_data(0x0d, 0x07, 0x00)\n\nmsg[\"payload\"] = str(msg[\"topic\"])+' now'\nreturn msg", - "outputs": 1, - "x": 390, - "y": 100, - "wires": [ - [ - "d348474b.d756a8", - "1f53f29b.feee4d" - ] - ] - }, - { - "id": "d348474b.d756a8", - "type": "exec", - "z": "35488f4f.00498", - "command": "i2cdetect -y 1", - "addpay": false, - "append": "", - "useSpawn": "false", - "timer": "1", - "oldrc": false, - "name": "i2c update", - "x": 550, - "y": 140, - "wires": [ - [], - [], - [] - ] - }, - { - "id": "cdd1b550.da18e8", + "id": "1aeca49c.10b893", "type": "mqtt in", - "z": "91e5fd54.56f58", + "z": "246abd43.838a5a", "name": "", "topic": "receiver/#", "qos": "0", "datatype": "auto", - "broker": "b77ffa1b.942258", + "broker": "84801dc0.193d88", "x": 80, "y": 40, "wires": [ [ - "6920281d.dc9b48" + "be5de01e.45d56", + "613bee5b.042fe" ] ] }, { - "id": "6920281d.dc9b48", + "id": "be5de01e.45d56", "type": "switch", - "z": "91e5fd54.56f58", + "z": "246abd43.838a5a", "name": "", "property": "topic", "propertyType": "msg", @@ -2267,23 +1285,23 @@ "y": 40, "wires": [ [ - "2f66e917.fee586" + "d39289fb.9f759" ], [ - "363ee47e.ed522c" + "e2ab3af3.e61a8" ], [ - "45a52868.fe37c8" + "e43e94c.c297968" ], [ - "469cc189.903d" + "b06c80f3.f1642" ] ] }, { - "id": "2f66e917.fee586", + "id": "d39289fb.9f759", "type": "switch", - "z": "91e5fd54.56f58", + "z": "246abd43.838a5a", "name": "", "property": "payload", "propertyType": "msg", @@ -2311,20 +1329,20 @@ "y": 40, "wires": [ [ - "5c0d0c35.3bcf14" + "267bd959.17b856" ], [ - "cd01157d.0892d8" + "265e58c6.06de38" ], [ - "68e02bf4.7013e4" + "a433c901.2abd48" ] ] }, { - "id": "5c0d0c35.3bcf14", + "id": "267bd959.17b856", "type": "change", - "z": "91e5fd54.56f58", + "z": "246abd43.838a5a", "name": "The pump has started", "rules": [ { @@ -2343,13 +1361,15 @@ "x": 920, "y": 40, "wires": [ - [] + [ + "3b6b4fd4.8c3368" + ] ] }, { - "id": "cd01157d.0892d8", + "id": "265e58c6.06de38", "type": "change", - "z": "91e5fd54.56f58", + "z": "246abd43.838a5a", "name": "The pump has finished.", "rules": [ { @@ -2368,13 +1388,15 @@ "x": 910, "y": 80, "wires": [ - [] + [ + "3b6b4fd4.8c3368" + ] ] }, { - "id": "68e02bf4.7013e4", + "id": "a433c901.2abd48", "type": "change", - "z": "91e5fd54.56f58", + "z": "246abd43.838a5a", "name": "The pump has been stopped.", "rules": [ { @@ -2393,13 +1415,15 @@ "x": 900, "y": 120, "wires": [ - [] + [ + "3b6b4fd4.8c3368" + ] ] }, { - "id": "363ee47e.ed522c", + "id": "e2ab3af3.e61a8", "type": "switch", - "z": "91e5fd54.56f58", + "z": "246abd43.838a5a", "name": "", "property": "payload", "propertyType": "msg", @@ -2427,20 +1451,20 @@ "y": 200, "wires": [ [ - "c088b72f.326d98" + "bd89c468.5a4f4" ], [ - "36934381.14442c" + "762ab12c.cc7e88" ], [ - "89329cfe.c8f4" + "ecb1efe6.7cb968" ] ] }, { - "id": "c088b72f.326d98", + "id": "bd89c468.5a4f4", "type": "change", - "z": "91e5fd54.56f58", + "z": "246abd43.838a5a", "name": "The focus has started", "rules": [ { @@ -2459,13 +1483,15 @@ "x": 920, "y": 200, "wires": [ - [] + [ + "3b6b4fd4.8c3368" + ] ] }, { - "id": "36934381.14442c", + "id": "762ab12c.cc7e88", "type": "change", - "z": "91e5fd54.56f58", + "z": "246abd43.838a5a", "name": "The focus has finished.", "rules": [ { @@ -2484,13 +1510,15 @@ "x": 910, "y": 240, "wires": [ - [] + [ + "3b6b4fd4.8c3368" + ] ] }, { - "id": "89329cfe.c8f4", + "id": "ecb1efe6.7cb968", "type": "change", - "z": "91e5fd54.56f58", + "z": "246abd43.838a5a", "name": "The focus has been stopped.", "rules": [ { @@ -2509,65 +1537,15 @@ "x": 900, "y": 280, "wires": [ - [] + [ + "3b6b4fd4.8c3368" + ] ] }, { - "id": "fdb3b132.8b341", - "type": "mqtt out", - "z": "ae90e3e.7d9fba", - "name": "", - "topic": "", - "qos": "", - "retain": "", - "broker": "cb2f36fe.1c7038", - "x": 950, - "y": 80, - "wires": [] - }, - { - "id": "e46763fe.7fc83", - "type": "mqtt out", - "z": "ae90e3e.7d9fba", - "name": "", - "topic": "", - "qos": "", - "retain": "", - "broker": "cb2f36fe.1c7038", - "x": 650, - "y": 160, - "wires": [] - }, - { - "id": "61fb057d.3c251c", - "type": "mqtt out", - "z": "407d8cdb.3cb7cc", - "name": "", - "topic": "", - "qos": "", - "retain": "", - "broker": "cb2f36fe.1c7038", - "x": 910, - "y": 120, - "wires": [] - }, - { - "id": "e2a7220a.09d43", - "type": "mqtt out", - "z": "407d8cdb.3cb7cc", - "name": "", - "topic": "", - "qos": "", - "retain": "", - "broker": "cb2f36fe.1c7038", - "x": 610, - "y": 200, - "wires": [] - }, - { - "id": "45a52868.fe37c8", + "id": "e43e94c.c297968", "type": "switch", - "z": "91e5fd54.56f58", + "z": "246abd43.838a5a", "name": "", "property": "payload", "propertyType": "msg", @@ -2600,24 +1578,24 @@ "y": 360, "wires": [ [ - "113c9b93.455814" + "87a2aa4d.3590c8" ], [ - "29a7c6de.6ac2ea" + "da9f9e9b.7c9f5" ], [ - "f1b07b24.b85718" + "1143b916.5047b7" ], [ - "446a811b.25e4b", - "a57fea5b.59eb5" + "fa7f2eaf.0e6f1", + "3b6b4fd4.8c3368" ] ] }, { - "id": "177a91d4.f1016e", + "id": "30c9c4c9.d46e3c", "type": "switch", - "z": "91e5fd54.56f58", + "z": "246abd43.838a5a", "name": "", "property": "payload", "propertyType": "msg", @@ -2640,17 +1618,17 @@ "y": 560, "wires": [ [ - "5d717a25.3437e4" + "23e5c77c.4f63f" ], [ - "7d713b16.235164" + "5491334a.93cbfc" ] ] }, { - "id": "29a7c6de.6ac2ea", + "id": "da9f9e9b.7c9f5", "type": "change", - "z": "91e5fd54.56f58", + "z": "246abd43.838a5a", "name": "The acquisition has finished.", "rules": [ { @@ -2670,14 +1648,14 @@ "y": 400, "wires": [ [ - "a57fea5b.59eb5" + "3b6b4fd4.8c3368" ] ] }, { - "id": "f1b07b24.b85718", + "id": "1143b916.5047b7", "type": "change", - "z": "91e5fd54.56f58", + "z": "246abd43.838a5a", "name": "The acquisition has been stopped.", "rules": [ { @@ -2697,14 +1675,14 @@ "y": 440, "wires": [ [ - "a57fea5b.59eb5" + "3b6b4fd4.8c3368" ] ] }, { - "id": "113c9b93.455814", + "id": "87a2aa4d.3590c8", "type": "change", - "z": "91e5fd54.56f58", + "z": "246abd43.838a5a", "name": "The acquisition has started", "rules": [ { @@ -2724,14 +1702,14 @@ "y": 360, "wires": [ [ - "a57fea5b.59eb5" + "3b6b4fd4.8c3368" ] ] }, { - "id": "446a811b.25e4b", + "id": "fa7f2eaf.0e6f1", "type": "function", - "z": "91e5fd54.56f58", + "z": "246abd43.838a5a", "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;", "outputs": 1, @@ -2740,14 +1718,14 @@ "y": 480, "wires": [ [ - "57014db.1bbe0b4" + "582d7204.ec89fc" ] ] }, { - "id": "803b507f.9e38c", + "id": "498b3d58.58b1a4", "type": "function", - "z": "91e5fd54.56f58", + "z": "246abd43.838a5a", "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;", "outputs": 1, @@ -2756,16 +1734,16 @@ "y": 640, "wires": [ [ - "6ad4ae5e.62f4a" + "67618ae5.b74864" ] ] }, { - "id": "57014db.1bbe0b4", + "id": "582d7204.ec89fc", "type": "ui_chart", - "z": "91e5fd54.56f58", + "z": "246abd43.838a5a", "name": "img_counter", - "group": "8cfadfab.327d7", + "group": "eb610eb9.84fae8", "order": 2, "width": 23, "height": 2, @@ -2803,9 +1781,9 @@ ] }, { - "id": "469cc189.903d", + "id": "b06c80f3.f1642", "type": "switch", - "z": "91e5fd54.56f58", + "z": "246abd43.838a5a", "name": "", "property": "topic", "propertyType": "msg", @@ -2833,20 +1811,20 @@ "y": 560, "wires": [ [ - "177a91d4.f1016e" + "30c9c4c9.d46e3c" ], [ - "803b507f.9e38c" + "498b3d58.58b1a4" ], [ - "73f0f4b.8dd430c" + "33094026.f6e8c" ] ] }, { - "id": "7d713b16.235164", + "id": "5491334a.93cbfc", "type": "change", - "z": "91e5fd54.56f58", + "z": "246abd43.838a5a", "name": "The segmentation has finished.", "rules": [ { @@ -2866,14 +1844,14 @@ "y": 600, "wires": [ [ - "a57fea5b.59eb5" + "3b6b4fd4.8c3368" ] ] }, { - "id": "5d717a25.3437e4", + "id": "23e5c77c.4f63f", "type": "change", - "z": "91e5fd54.56f58", + "z": "246abd43.838a5a", "name": "The segmentation has started", "rules": [ { @@ -2893,16 +1871,16 @@ "y": 560, "wires": [ [ - "a57fea5b.59eb5" + "3b6b4fd4.8c3368" ] ] }, { - "id": "6ad4ae5e.62f4a", + "id": "67618ae5.b74864", "type": "ui_chart", - "z": "91e5fd54.56f58", + "z": "246abd43.838a5a", "name": "obj_counter", - "group": "8cfadfab.327d7", + "group": "eb610eb9.84fae8", "order": 5, "width": 23, "height": 2, @@ -2940,9 +1918,9 @@ ] }, { - "id": "32b535dc.2d85ea", + "id": "3c29eb4.e570414", "type": "function", - "z": "91e5fd54.56f58", + "z": "246abd43.838a5a", "name": "", "func": "msg.payload=msg.payload.object_area\nmsg.topic=\"area\"\n\nreturn msg;", "outputs": 1, @@ -2951,14 +1929,14 @@ "y": 700, "wires": [ [ - "1624f1bf.604bfe" + "84dfe51a.0e9fd" ] ] }, { - "id": "73f0f4b.8dd430c", + "id": "33094026.f6e8c", "type": "json", - "z": "91e5fd54.56f58", + "z": "246abd43.838a5a", "name": "", "property": "payload", "action": "", @@ -2967,14 +1945,14 @@ "y": 700, "wires": [ [ - "32b535dc.2d85ea" + "3c29eb4.e570414" ] ] }, { - "id": "6fc7332f.89431c", + "id": "9b672325.568a18", "type": "exec", - "z": "91e5fd54.56f58", + "z": "246abd43.838a5a", "command": "free -m | grep \"Mem\" | awk -F ' ' '{print $3}'", "addpay": false, "append": "", @@ -2985,16 +1963,16 @@ "y": 780, "wires": [ [ - "42781732.a6ab58" + "76a7ddb6.fbde64" ], [], [] ] }, { - "id": "7cdef10d.cb2f2", + "id": "7c9eaef6.142a4", "type": "inject", - "z": "91e5fd54.56f58", + "z": "246abd43.838a5a", "name": "", "topic": "", "payload": "", @@ -3007,16 +1985,16 @@ "y": 780, "wires": [ [ - "6fc7332f.89431c" + "9b672325.568a18" ] ] }, { - "id": "42781732.a6ab58", + "id": "76a7ddb6.fbde64", "type": "ui_chart", - "z": "91e5fd54.56f58", + "z": "246abd43.838a5a", "name": "", - "group": "8cfadfab.327d7", + "group": "eb610eb9.84fae8", "order": 1, "width": 0, "height": 0, @@ -3026,11 +2004,11 @@ "xformat": "auto", "interpolate": "linear", "nodata": "", - "dot": false, + "dot": true, "ymin": "", "ymax": "", "removeOlder": 1, - "removeOlderPoints": "", + "removeOlderPoints": "200", "removeOlderUnit": "3600", "cutout": 0, "useOneColor": false, @@ -3054,11 +2032,11 @@ ] }, { - "id": "1624f1bf.604bfe", + "id": "84dfe51a.0e9fd", "type": "ui_chart", - "z": "91e5fd54.56f58", + "z": "246abd43.838a5a", "name": "", - "group": "8cfadfab.327d7", + "group": "eb610eb9.84fae8", "order": 8, "width": 0, "height": 0, @@ -3096,496 +2074,9 @@ ] }, { - "id": "7f101b25.0da4a4", - "type": "subflow:173a6e6b.e5ca6a", - "z": "259c8713.b50e28", - "name": "", - "env": [], - "x": 750, - "y": 60, - "wires": [ - [ - "1a5edafb.a05cf5" - ] - ] - }, - { - "id": "d8dbecd.f7b3b9", - "type": "subflow:ae90e3e.7d9fba", - "z": "259c8713.b50e28", - "name": "", - "env": [], - "x": 740, - "y": 260, - "wires": [ - [ - "1a5edafb.a05cf5" - ] - ] - }, - { - "id": "309468bc.ac83f8", - "type": "ui_text_input", - "z": "407d8cdb.3cb7cc", - "name": "manual_volume", - "label": "Volume to pass (ml)", - "tooltip": "", - "group": "707d9797.c8e798", - "order": 3, - "width": 8, - "height": 1, - "passthru": true, - "mode": "number", - "delay": 300, - "topic": "manual_volume", - "x": 460, - "y": 80, - "wires": [ - [] - ] - }, - { - "id": "f859eeef.c59ed", - "type": "function", - "z": "407d8cdb.3cb7cc", - "name": "get generic_manual_volume", - "func": "msg.payload = msg.payload.generic_manual_volume;\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 220, - "y": 80, - "wires": [ - [ - "309468bc.ac83f8" - ] - ] - }, - { - "id": "59b05f7f.9e83f8", - "type": "ui_slider", - "z": "407d8cdb.3cb7cc", - "name": "flowrate", - "label": "Flowrate (ml/min)*", - "tooltip": "", - "group": "707d9797.c8e798", - "order": 1, - "width": 0, - "height": 0, - "passthru": true, - "outs": "end", - "topic": "flowrate", - "min": 0, - "max": "20", - "step": "0.1", - "x": 480, - "y": 40, - "wires": [ - [] - ] - }, - { - "id": "d9a85435.ced5e", - "type": "function", - "z": "407d8cdb.3cb7cc", - "name": "get generic.flowrate", - "func": "msg.payload = msg.payload.generic_flowrate;\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 190, - "y": 40, - "wires": [ - [ - "59b05f7f.9e83f8" - ] - ] - }, - { - "id": "c986ae96.860ec8", - "type": "subflow:407d8cdb.3cb7cc", - "z": "259c8713.b50e28", - "name": "", - "env": [], - "x": 740, - "y": 300, - "wires": [ - [ - "1a5edafb.a05cf5" - ] - ] - }, - { - "id": "99b5a67.080f258", - "type": "subflow:bdd6e33e.5db3b8", - "z": "259c8713.b50e28", - "name": "", - "env": [], - "x": 760, - "y": 100, - "wires": [ - [ - "1a5edafb.a05cf5" - ], - [ - "e001a28.555566" - ] - ] - }, - { - "id": "a71ba4a6.c44c4", - "type": "subflow:ad5a5663.ce893", - "z": "259c8713.b50e28", - "name": "", - "env": [], - "x": 740, - "y": 140, - "wires": [ - [ - "1a5edafb.a05cf5" - ], - [ - "e001a28.555566" - ] - ] - }, - { - "id": "9c301fc6.9a9318", - "type": "subflow:35488f4f.00498", - "z": "259c8713.b50e28", - "name": "System commands", - "env": [], - "x": 750, - "y": 460, - "wires": [] - }, - { - "id": "4d5b9f01.270e88", - "type": "exec", - "z": "344146df.e4d5ba", - "command": "vcgencmd measure_temp | tr -d \"temp=\" | tr -d \"'C\" | tr -d \"\\n\"", - "addpay": false, - "append": "", - "useSpawn": "", - "timer": "", - "name": "RPi Temp.", - "x": 350, - "y": 80, - "wires": [ - [ - "4f3fb60b.912848" - ], - [], - [] - ] - }, - { - "id": "1c4bc7ff.94aa8", - "type": "inject", - "z": "344146df.e4d5ba", - "name": "", - "topic": "", - "payload": "", - "payloadType": "date", - "repeat": "10", - "crontab": "", - "once": false, - "onceDelay": "", - "x": 190, - "y": 80, - "wires": [ - [ - "4d5b9f01.270e88" - ] - ] - }, - { - "id": "4f3fb60b.912848", - "type": "python3-function", - "z": "344146df.e4d5ba", - "name": "fan.py", - "func": "#!/usr/bin/python\nimport smbus\nimport sys\n\ntemp = msg[\"payload\"]\n\ntemp = int(temp.split('.',1)[0])\n\nbus = smbus.SMBus(1)\n\nDEVICE_ADDRESS = 0x0d\n\nif temp < 38:\n bus.write_byte_data(DEVICE_ADDRESS, 0x08, 0x00)\n bus.write_byte_data(DEVICE_ADDRESS, 0x08, 0x00)\nif temp > 42:\n bus.write_byte_data(DEVICE_ADDRESS, 0x08, 0x01)\n bus.write_byte_data(DEVICE_ADDRESS, 0x08, 0x01)", - "outputs": 1, - "x": 530, - "y": 80, - "wires": [ - [] - ] - }, - { - "id": "ee70d541.87713", - "type": "subflow:344146df.e4d5ba", - "z": "259c8713.b50e28", - "name": "", - "env": [], - "x": 300, - "y": 140, - "wires": [] - }, - { - "id": "c14cf94.1413e88", - "type": "ui_text_input", - "z": "b73d5eb8.60ef3", - "name": "duration_flush", - "label": "Duration of the flushing (s)", - "tooltip": "", - "group": "f41d0ecb.8be06", - "order": 2, - "width": 0, - "height": 0, - "passthru": true, - "mode": "number", - "delay": 300, - "topic": "duration_flush", - "x": 520, - "y": 80, - "wires": [ - [] - ] - }, - { - "id": "d7b55d02.e41f1", - "type": "ui_text_input", - "z": "b73d5eb8.60ef3", - "name": "duration_bef_seq", - "label": "Duration before sequence (s)", - "tooltip": "", - "group": "f41d0ecb.8be06", - "order": 4, - "width": 0, - "height": 0, - "passthru": true, - "mode": "number", - "delay": 300, - "topic": "duration_bef_seq", - "x": 510, - "y": 160, - "wires": [ - [] - ] - }, - { - "id": "8729ec5c.cf4ab8", - "type": "ui_text_input", - "z": "b73d5eb8.60ef3", - "name": "nb_img", - "label": "Number of images per acquisition", - "tooltip": "", - "group": "f41d0ecb.8be06", - "order": 3, - "width": 0, - "height": 0, - "passthru": true, - "mode": "number", - "delay": 300, - "topic": "nb_img", - "x": 540, - "y": 120, - "wires": [ - [] - ] - }, - { - "id": "3808d004.94ea28", - "type": "function", - "z": "b73d5eb8.60ef3", - "name": "get duration_flush", - "func": "msg.payload = msg.payload.duration_flush;\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 210, - "y": 80, - "wires": [ - [ - "c14cf94.1413e88" - ] - ] - }, - { - "id": "f7cc1192.5a51e8", - "type": "function", - "z": "b73d5eb8.60ef3", - "name": "get nb_img", - "func": "msg.payload = msg.payload.nb_img;\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 190, - "y": 120, - "wires": [ - [ - "8729ec5c.cf4ab8" - ] - ] - }, - { - "id": "10ce45f6.3036ca", - "type": "function", - "z": "b73d5eb8.60ef3", - "name": "get duration_bef_seq", - "func": "msg.payload = msg.payload.duration_bef_seq;\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 220, - "y": 160, - "wires": [ - [ - "d7b55d02.e41f1" - ] - ] - }, - { - "id": "27bbe0f0.05b2c", - "type": "ui_text_input", - "z": "b73d5eb8.60ef3", - "name": "duration_bef_img", - "label": "Duration before image (s)", - "tooltip": "", - "group": "f41d0ecb.8be06", - "order": 5, - "width": 0, - "height": 0, - "passthru": true, - "mode": "number", - "delay": 300, - "topic": "duration_bef_img", - "x": 510, - "y": 200, - "wires": [ - [] - ] - }, - { - "id": "70dfb6bb.9319", - "type": "function", - "z": "b73d5eb8.60ef3", - "name": "get duration_bef_img", - "func": "msg.payload = msg.payload.duration_bef_img;\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 220, - "y": 200, - "wires": [ - [ - "27bbe0f0.05b2c" - ] - ] - }, - { - "id": "b31fd152.a5489", - "type": "ui_text_input", - "z": "b73d5eb8.60ef3", - "name": "duration_between", - "label": "Duration between acquisition (s)", - "tooltip": "", - "group": "f41d0ecb.8be06", - "order": 6, - "width": 0, - "height": 0, - "passthru": true, - "mode": "number", - "delay": 300, - "topic": "duration_between", - "x": 510, - "y": 240, - "wires": [ - [] - ] - }, - { - "id": "a0b53585.93216", - "type": "function", - "z": "b73d5eb8.60ef3", - "name": "get duration_between", - "func": "msg.payload = msg.payload.duration_between;\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 220, - "y": 240, - "wires": [ - [ - "b31fd152.a5489" - ] - ] - }, - { - "id": "fee8c0fa.108778", - "type": "subflow:91e5fd54.56f58", - "z": "259c8713.b50e28", - "name": "", - "env": [], - "x": 760, - "y": 380, - "wires": [] - }, - { - "id": "fe5585e.a1ab078", - "type": "subflow:4475ba6c.45604c", - "z": "259c8713.b50e28", - "name": "process metadata", - "env": [], - "x": 750, - "y": 180, - "wires": [ - [ - "1a5edafb.a05cf5" - ] - ] - }, - { - "id": "da9f1367.3a17a8", - "type": "subflow:b73d5eb8.60ef3", - "z": "259c8713.b50e28", - "d": true, - "name": "Valve actuation", - "env": [], - "x": 740, - "y": 220, - "wires": [ - [ - "1a5edafb.a05cf5" - ] - ], - "icon": "node-red-dashboard/ui_switch.png" - }, - { - "id": "69799a39.13803c", - "type": "function", - "z": "b73d5eb8.60ef3", - "name": "get duration_bef_cycle", - "func": "msg.payload = msg.payload.duration_bef_cycle;\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 220, - "y": 40, - "wires": [ - [ - "7a0b6294.e887c4" - ] - ] - }, - { - "id": "7a0b6294.e887c4", - "type": "ui_text_input", - "z": "b73d5eb8.60ef3", - "name": "duration_bef_cycle", - "label": "Duration before the cycles (s)", - "tooltip": "", - "group": "f41d0ecb.8be06", - "order": 1, - "width": 0, - "height": 0, - "passthru": true, - "mode": "number", - "delay": 300, - "topic": "duration_bef_cycle", - "x": 510, - "y": 40, - "wires": [ - [] - ] - }, - { - "id": "a57fea5b.59eb5", + "id": "3b6b4fd4.8c3368", "type": "ui_toast", - "z": "91e5fd54.56f58", + "z": "246abd43.838a5a", "position": "top right", "displayTime": "3", "highlight": "", @@ -3601,73 +2092,389 @@ "wires": [] }, { - "id": "f7d3d0c4.0203", - "type": "exec", - "z": "1b486ba8.f8c41c", - "command": "sudo date -s", - "addpay": true, - "append": "", - "useSpawn": "false", - "timer": "", - "oldrc": false, + "id": "613bee5b.042fe", + "type": "debug", + "z": "246abd43.838a5a", "name": "", - "x": 1010, - "y": 240, - "wires": [ - [], - [], - [] - ] + "active": true, + "tosidebar": true, + "console": false, + "tostatus": false, + "complete": "true", + "targetType": "full", + "x": 240, + "y": 140, + "wires": [] }, { - "id": "c5fcaba5.184e88", - "type": "function", - "z": "1b486ba8.f8c41c", + "id": "84801dc0.193d88", + "type": "mqtt-broker", + "z": "", "name": "", - "func": "d = new Date();\n//get weekday\nvar weekday = new Array(7);\nweekday[0] = \"Sun\";\nweekday[1] = \"Mon\";\nweekday[2] = \"Tue\";\nweekday[3] = \"Wed\";\nweekday[4] = \"Thu\";\nweekday[5] = \"Fri\";\nweekday[6] = \"Sat\";\nvar w = weekday[d.getUTCDay()];\n//get Month\nvar month = new Array(12);\nmonth[0] = \"Jan\";\nmonth[1] = \"Feb\";\nmonth[2] = \"Mar\";\nmonth[3] = \"Apr\";\nmonth[4] = \"May\";\nmonth[5] = \"Jun\";\nmonth[6] = \"Jul\";\nmonth[7] = \"Aug\";\nmonth[8] = \"Sep\";\nmonth[9] = \"Oct\";\nmonth[10] = \"Nov\";\nmonth[11] = \"Dec\";\nvar n = month[d.getUTCMonth()];\n \n//get day\nvar day = d.getUTCDay()\n\n//get Hours\nvar Hours = d.getUTCHours();\n//get Minutes\nvar Minutes = d.getUTCMinutes();\n//get Seconds\nvar Seconds = d.getUTCSeconds();\n//get FullYear\nvar FullYear = d.getUTCFullYear();\n\n//Thu Aug 09 2012 23:34:04 GMT+0200 (GMT+02:00)\n\n//Thu Aug 9 21:31:26 UTC 2012\n\n//msg.payload = \"Thu Aug 9 21:31:26 UTC 2012\"\n\nmsg.payload = '\"'+w+\" \"+n+\" \"+day+\" \"+Hours+\":\"+Minutes+\":\"+Seconds+\" UTC \"+FullYear+'\"';\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 490, - "y": 40, + "broker": "127.0.0.1", + "port": "1883", + "clientid": "test", + "usetls": false, + "compatmode": false, + "keepalive": "60", + "cleansession": true, + "birthTopic": "", + "birthQos": "0", + "birthPayload": "", + "closeTopic": "", + "closeQos": "0", + "closePayload": "", + "willTopic": "", + "willQos": "0", + "willPayload": "" + }, + { + "id": "eb610eb9.84fae8", + "type": "ui_group", + "z": "", + "name": "MQTT Plots", + "tab": "2b97fe34.a699fa", + "order": 11, + "disp": true, + "width": "24", + "collapse": false + }, + { + "id": "1273b673.4a35ea", + "type": "subflow", + "name": "System Commands", + "info": "", + "category": "", + "in": [], + "out": [], + "env": [], + "color": "#FFCC66", + "icon": "node-red-dashboard/ui_button.png" + }, + { + "id": "44a78834.e8f8b8", + "type": "ui_button", + "z": "1273b673.4a35ea", + "name": "", + "group": "82b3caaa.0518", + "order": 1, + "width": 0, + "height": 0, + "passthru": false, + "label": "Reboot", + "tooltip": "", + "color": "", + "bgcolor": "#AD1625", + "icon": "", + "payload": "off", + "payloadType": "str", + "topic": "reboot", + "x": 220, + "y": 80, "wires": [ [ - "a1c2a5e3.4aea58" + "aba9aac1.c2d198" ] ] }, { - "id": "807d5cce.2bb1e", - "type": "subflow:1b486ba8.f8c41c", - "z": "259c8713.b50e28", - "name": "", - "env": [], - "x": 280, - "y": 180, - "wires": [] + "id": "a32bfa65.bc6b9", + "type": "exec", + "z": "1273b673.4a35ea", + "command": "sudo", + "addpay": true, + "append": "", + "useSpawn": "false", + "timer": "2", + "oldrc": false, + "name": "cmd", + "x": 530, + "y": 80, + "wires": [ + [], + [], + [] + ] }, { - "id": "a1c2a5e3.4aea58", - "type": "ui_template", - "z": "1b486ba8.f8c41c", - "group": "9214d59d.e7b52", + "id": "825c8791.c0bfb", + "type": "ui_button", + "z": "1273b673.4a35ea", "name": "", - "order": 1, + "group": "82b3caaa.0518", + "order": 2, "width": 0, "height": 0, - "format": "
", - "storeOutMessages": true, - "fwdInMessages": true, - "templateScope": "local", - "x": 640, - "y": 40, + "passthru": false, + "label": "Shutdown", + "tooltip": "", + "color": "", + "bgcolor": "#AD1625", + "icon": "", + "payload": "off", + "payloadType": "str", + "topic": "shutdown", + "x": 220, + "y": 140, + "wires": [ + [ + "aba9aac1.c2d198" + ] + ] + }, + { + "id": "aba9aac1.c2d198", + "type": "python3-function", + "z": "1273b673.4a35ea", + "name": "action", + "func": "#!/usr/bin/python\nimport smbus\nimport time\nbus = smbus.SMBus(1)\ntime.sleep(1)\n#turn off fan RGB\nbus.write_byte_data(0x0d, 0x07, 0x00)\nbus.write_byte_data(0x0d, 0x07, 0x00)\n\nmsg[\"payload\"] = str(msg[\"topic\"])+' now'\nreturn msg", + "outputs": 1, + "x": 390, + "y": 100, + "wires": [ + [ + "72b7368a.abad3", + "a32bfa65.bc6b9" + ] + ] + }, + { + "id": "72b7368a.abad3", + "type": "exec", + "z": "1273b673.4a35ea", + "command": "i2cdetect -y 1", + "addpay": false, + "append": "", + "useSpawn": "false", + "timer": "1", + "oldrc": false, + "name": "i2c update", + "x": 550, + "y": 140, + "wires": [ + [], + [], + [] + ] + }, + { + "id": "82b3caaa.0518", + "type": "ui_group", + "z": "", + "name": "Commands", + "tab": "2b97fe34.a699fa", + "order": 12, + "disp": true, + "width": 24, + "collapse": false + }, + { + "id": "506e9090.6e905", + "type": "subflow", + "name": "Object metadata", + "info": "", + "category": "", + "in": [ + { + "x": 40, + "y": 40, + "wires": [ + { + "id": "4ab4976c.eee488" + }, + { + "id": "581c8a23.83fa8c" + }, + { + "id": "52052007.b3d0e" + } + ] + } + ], + "out": [ + { + "x": 1060, + "y": 159, + "wires": [ + { + "id": "26b33a5c.0ef82e", + "port": 0 + }, + { + "id": "9ee0935a.415808", + "port": 0 + } + ] + }, + { + "x": 1060, + "y": 59, + "wires": [ + { + "id": "d3875217.e3b668", + "port": 0 + }, + { + "id": "82fef572.49b5f", + "port": 0 + } + ] + } + ], + "env": [], + "color": "#DDAA99" + }, + { + "id": "26b33a5c.0ef82e", + "type": "ui_numeric", + "z": "506e9090.6e905", + "name": "object_depth_min", + "label": "Minimum depth (m)", + "tooltip": "", + "group": "f377d75b.32d27", + "order": 3, + "width": 0, + "height": 0, + "wrap": false, + "passthru": true, + "topic": "object_depth_min", + "format": "{{value}}", + "min": "0", + "max": "2000", + "step": "1", + "x": 610, + "y": 120, "wires": [ [] ] }, { - "id": "9b1b260f.e4b338", + "id": "9ee0935a.415808", + "type": "ui_numeric", + "z": "506e9090.6e905", + "name": "object_depth_max", + "label": "Maximum depth (m)", + "tooltip": "", + "group": "f377d75b.32d27", + "order": 2, + "width": 0, + "height": 0, + "wrap": false, + "passthru": true, + "topic": "object_depth_max", + "format": "{{value}}", + "min": "0", + "max": "2000", + "step": "1", + "x": 610, + "y": 160, + "wires": [ + [] + ] + }, + { + "id": "4ab4976c.eee488", "type": "function", - "z": "ad5a5663.ce893", + "z": "506e9090.6e905", + "name": "get object_depth_min", + "func": "msg.payload = msg.payload.object_depth_min;\nreturn msg;", + "outputs": 1, + "noerr": 0, + "x": 304, + "y": 120, + "wires": [ + [ + "26b33a5c.0ef82e" + ] + ] + }, + { + "id": "581c8a23.83fa8c", + "type": "function", + "z": "506e9090.6e905", + "name": "get object_depth_max", + "func": "msg.payload = msg.payload.object_depth_max;\nreturn msg;", + "outputs": 1, + "noerr": 0, + "x": 304, + "y": 160, + "wires": [ + [ + "9ee0935a.415808" + ] + ] + }, + { + "id": "472998cd.45f588", + "type": "gpsd", + "z": "506e9090.6e905", + "name": "", + "hostname": "localhost", + "port": "2947", + "tpv": true, + "sky": false, + "info": false, + "device": false, + "gst": false, + "att": false, + "x": 90, + "y": 220, + "wires": [ + [ + "52052007.b3d0e", + "ab40705d.43a5d" + ] + ] + }, + { + "id": "7d5701.1e1981", + "type": "ui_worldmap", + "z": "506e9090.6e905", + "d": true, + "group": "f377d75b.32d27", + "order": 1, + "width": 0, + "height": 0, + "name": "", + "lat": "1.5", + "lon": "1.5", + "zoom": "4", + "layer": "OSM grey", + "cluster": "1", + "maxage": "", + "usermenu": "hide", + "layers": "hide", + "panit": "false", + "panlock": "false", + "zoomlock": "false", + "hiderightclick": "true", + "coords": "deg", + "showgrid": "false", + "path": "/worldmap", + "x": 640, + "y": 200, + "wires": [] + }, + { + "id": "52052007.b3d0e", + "type": "function", + "z": "506e9090.6e905", + "name": "get object_lat & object_lon", + "func": "\nreturn msg;", + "outputs": 1, + "noerr": 0, + "x": 320, + "y": 200, + "wires": [ + [ + "7d5701.1e1981" + ] + ] + }, + { + "id": "d3875217.e3b668", + "type": "function", + "z": "506e9090.6e905", "name": "set object_time", "func": "var time = new Date(msg.payload);\n\nvar hour = time.getUTCHours();\nif (hour<10){hour = \"0\"+hour;}\nvar minute = time.getUTCMinutes();\nif (minute<10){minute = \"0\"+minute;}\n\nvar time_UTC = \"\"+hour+minute;\nglobal.set('object_time',time_UTC);\nreturn msg;", "outputs": 1, @@ -3679,9 +2486,9 @@ ] }, { - "id": "86aa9817.45a2e8", + "id": "82fef572.49b5f", "type": "function", - "z": "ad5a5663.ce893", + "z": "506e9090.6e905", "name": "set object_date", "func": "var date = new Date(msg.payload);\n\nvar year = date.getUTCFullYear();\nvar month = date.getUTCMonth()+1;\nif (month<10){month = \"0\"+month;}\nvar day = date.getUTCDate();\nif (day<10){day = \"0\"+day;}\n\nvar date_UTC = \"\"+year+month+day;\nglobal.set('object_date',date_UTC);\n\nreturn msg;", "outputs": 1, @@ -3693,519 +2500,9 @@ ] }, { - "id": "546376f8.9d25d8", - "type": "ui_numeric", - "z": "1b486ba8.f8c41c", - "name": "year", - "label": "Year", - "tooltip": "", - "group": "9214d59d.e7b52", - "order": 2, - "width": 5, - "height": 1, - "wrap": false, - "passthru": true, - "topic": "year", - "format": "{{value}}", - "min": "2020", - "max": "2030", - "step": 1, - "x": 630, - "y": 80, - "wires": [ - [ - "dc685555.af057" - ] - ] - }, - { - "id": "8a701d46.962ed8", - "type": "ui_numeric", - "z": "1b486ba8.f8c41c", - "name": "month", - "label": "Month", - "tooltip": "", - "group": "9214d59d.e7b52", - "order": 3, - "width": 3, - "height": 1, - "wrap": false, - "passthru": true, - "topic": "month", - "format": "{{value}}", - "min": "1", - "max": "12", - "step": 1, - "x": 630, - "y": 120, - "wires": [ - [ - "dc685555.af057" - ] - ] - }, - { - "id": "3e39bc34.b3042c", - "type": "ui_numeric", - "z": "1b486ba8.f8c41c", - "name": "day", - "label": "Day", - "tooltip": "", - "group": "9214d59d.e7b52", - "order": 4, - "width": 3, - "height": 1, - "wrap": false, - "passthru": true, - "topic": "day", - "format": "{{value}}", - "min": "1", - "max": "31", - "step": 1, - "x": 630, - "y": 160, - "wires": [ - [ - "dc685555.af057" - ] - ] - }, - { - "id": "6edc1533.cd3ab4", - "type": "ui_numeric", - "z": "1b486ba8.f8c41c", - "name": "hour", - "label": "Hour", - "tooltip": "", - "group": "9214d59d.e7b52", - "order": 5, - "width": 3, - "height": 1, - "wrap": false, - "passthru": true, - "topic": "hour", - "format": "{{value}}", - "min": "0", - "max": "23", - "step": 1, - "x": 630, - "y": 200, - "wires": [ - [ - "dc685555.af057" - ] - ] - }, - { - "id": "1ba0f9e6.1be54e", - "type": "ui_numeric", - "z": "1b486ba8.f8c41c", - "name": "minute", - "label": "Minute", - "tooltip": "", - "group": "9214d59d.e7b52", - "order": 6, - "width": 3, - "height": 1, - "wrap": false, - "passthru": true, - "topic": "minute", - "format": "{{value}}", - "min": "0", - "max": "59", - "step": 1, - "x": 630, - "y": 240, - "wires": [ - [ - "dc685555.af057" - ] - ] - }, - { - "id": "fd050fce.2ffe28", - "type": "ui_numeric", - "z": "1b486ba8.f8c41c", - "name": "second", - "label": "Second", - "tooltip": "", - "group": "9214d59d.e7b52", - "order": 7, - "width": 3, - "height": 1, - "wrap": false, - "passthru": true, - "topic": "second", - "format": "{{value}}", - "min": "0", - "max": "59", - "step": 1, - "x": 640, - "y": 280, - "wires": [ - [ - "dc685555.af057" - ] - ] - }, - { - "id": "e1cc68bb.7b045", - "type": "interval", - "z": "1b486ba8.f8c41c", - "name": "interval", - "interval": "1", - "onstart": false, - "msg": "ping", - "showstatus": true, - "unit": "seconds", - "statusformat": "YYYY-MM-D HH:mm:ss", - "x": 310, - "y": 40, - "wires": [ - [ - "c5fcaba5.184e88" - ] - ] - }, - { - "id": "23f1828c.afae3e", - "type": "ui_button", - "z": "1b486ba8.f8c41c", - "name": "", - "group": "9214d59d.e7b52", - "order": 8, - "width": 4, - "height": 1, - "passthru": false, - "label": "Update", - "tooltip": "", - "color": "black", - "bgcolor": "white", - "icon": "", - "payload": "", - "payloadType": "str", - "topic": "", - "x": 640, - "y": 320, - "wires": [ - [ - "cb4c9210.01c958" - ] - ] - }, - { - "id": "cb4c9210.01c958", - "type": "function", - "z": "1b486ba8.f8c41c", - "name": "update datetime", - "func": "var FullYear= global.get(\"year\");\nvar Month= global.get(\"month\");\nvar day= global.get(\"day\");\nvar Hours= global.get(\"hour\");\nvar Minutes= global.get(\"minute\");\nvar Seconds= global.get(\"second\");\n\nmsg.payload = new Date();\n//get Month\nvar month = new Array(12);\nmonth[1] = \"Jan\";\nmonth[2] = \"Feb\";\nmonth[3] = \"Mar\";\nmonth[4] = \"Apr\";\nmonth[5] = \"May\";\nmonth[6] = \"Jun\";\nmonth[7] = \"Jul\";\nmonth[8] = \"Aug\";\nmonth[9] = \"Sep\";\nmonth[10] = \"Oct\";\nmonth[11] = \"Nov\";\nmonth[12] = \"Dec\";\nvar n = month[Month];\n \nmsg.payload = '\"'+day+\" \"+n+\" \"+FullYear+\" \"+Hours+\":\"+Minutes+\":\"+Seconds+'\"';\n\n\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 800, - "y": 320, - "wires": [ - [ - "7c1c8abf.4b984c", - "f7d3d0c4.0203" - ] - ] - }, - { - "id": "dc685555.af057", - "type": "function", - "z": "1b486ba8.f8c41c", - "name": "set global", - "func": "var value = msg.payload;\nvar key = msg.topic;\n\nglobal.set(key,value);\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 840, - "y": 60, - "wires": [ - [] - ] - }, - { - "id": "7c1c8abf.4b984c", + "id": "ab40705d.43a5d", "type": "debug", - "z": "1b486ba8.f8c41c", - "name": "", - "active": true, - "tosidebar": true, - "console": false, - "tostatus": false, - "complete": "false", - "x": 1010, - "y": 300, - "wires": [] - }, - { - "id": "92842b63.e0d7b8", - "type": "function", - "z": "1b486ba8.f8c41c", - "name": "", - "func": "d = msg.payload;\n\nvar val = d.getUTCFullYear();\n\nmsg.payload = val;\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 490, - "y": 80, - "wires": [ - [ - "546376f8.9d25d8" - ] - ] - }, - { - "id": "48033b32.2bca94", - "type": "function", - "z": "1b486ba8.f8c41c", - "name": "", - "func": "d = new Date();\nmsg.payload = d\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 310, - "y": 80, - "wires": [ - [ - "92842b63.e0d7b8", - "94057891.b1a658", - "aab6990b.1cf718", - "42b00a98.b36bb4", - "e2370ad.c8e7ff8", - "9c43dfe1.eb6178" - ] - ] - }, - { - "id": "94057891.b1a658", - "type": "function", - "z": "1b486ba8.f8c41c", - "name": "", - "func": "d = msg.payload;\n\nvar val = d.getUTCMonth();\n\nmsg.payload = val+1;\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 490, - "y": 120, - "wires": [ - [ - "8a701d46.962ed8" - ] - ] - }, - { - "id": "aab6990b.1cf718", - "type": "function", - "z": "1b486ba8.f8c41c", - "name": "", - "func": "d = msg.payload;\n\nvar val = d.getUTCDay();\n\nmsg.payload = val;\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 490, - "y": 160, - "wires": [ - [ - "3e39bc34.b3042c" - ] - ] - }, - { - "id": "42b00a98.b36bb4", - "type": "function", - "z": "1b486ba8.f8c41c", - "name": "", - "func": "d = msg.payload;\n\nvar val = d.getUTCHours();\n\nmsg.payload = val;\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 490, - "y": 200, - "wires": [ - [ - "6edc1533.cd3ab4" - ] - ] - }, - { - "id": "e2370ad.c8e7ff8", - "type": "function", - "z": "1b486ba8.f8c41c", - "name": "", - "func": "d = msg.payload;\n\nvar val = d.getUTCMinutes();\n\nmsg.payload = val;\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 490, - "y": 240, - "wires": [ - [ - "1ba0f9e6.1be54e" - ] - ] - }, - { - "id": "9c43dfe1.eb6178", - "type": "function", - "z": "1b486ba8.f8c41c", - "name": "", - "func": "d = msg.payload;\n\nvar val = d.getUTCSeconds();\n\nmsg.payload = val;\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 490, - "y": 280, - "wires": [ - [ - "fd050fce.2ffe28" - ] - ] - }, - { - "id": "ca843dd8.d1c62", - "type": "exec", - "z": "66c23d37.f72cdc", - "command": "python3.7 /home/pi/PlanktonScope/script/mqtt_pump_focus_image_segment_strem.py", - "addpay": false, - "append": "", - "useSpawn": "false", - "timer": "", - "oldrc": false, - "name": "", - "x": 520, - "y": 100, - "wires": [ - [], - [ - "a49ed5a6.5b73b8" - ], - [] - ] - }, - { - "id": "1af32c3e.856864", - "type": "exec", - "z": "66c23d37.f72cdc", - "command": "ps -ax | grep \"python3.7 /home/pi/PlanktonScope/script/mqtt_pump_focus_image_segment_strem.py\"| head -1 | awk -F \" \" '{print$1}' ", - "addpay": false, - "append": "", - "useSpawn": "false", - "timer": "", - "oldrc": false, - "name": "", - "x": 660, - "y": 160, - "wires": [ - [ - "ddabe48c.369c68" - ], - [], - [] - ] - }, - { - "id": "ddabe48c.369c68", - "type": "exec", - "z": "66c23d37.f72cdc", - "command": "kill", - "addpay": true, - "append": "", - "useSpawn": "false", - "timer": "", - "oldrc": false, - "name": "", - "x": 1210, - "y": 120, - "wires": [ - [ - "6382060e.460ab8" - ], - [ - "6382060e.460ab8" - ], - [ - "6382060e.460ab8" - ] - ] - }, - { - "id": "fcaca139.5ed04", - "type": "ui_button", - "z": "66c23d37.f72cdc", - "name": "", - "group": "9214d59d.e7b52", - "order": 9, - "width": 12, - "height": 1, - "passthru": false, - "label": "Kill MQTT", - "tooltip": "", - "color": "", - "bgcolor": "", - "icon": "", - "payload": "", - "payloadType": "str", - "topic": "", - "x": 80, - "y": 160, - "wires": [ - [ - "1af32c3e.856864" - ] - ] - }, - { - "id": "9d663990.fd2908", - "type": "ui_button", - "z": "66c23d37.f72cdc", - "name": "", - "group": "9214d59d.e7b52", - "order": 10, - "width": 12, - "height": 1, - "passthru": false, - "label": "Restart MQTT", - "tooltip": "", - "color": "", - "bgcolor": "", - "icon": "", - "payload": "", - "payloadType": "str", - "topic": "", - "x": 100, - "y": 100, - "wires": [ - [ - "ca843dd8.d1c62" - ] - ] - }, - { - "id": "a49ed5a6.5b73b8", - "type": "ui_toast", - "z": "66c23d37.f72cdc", - "position": "top right", - "displayTime": "3", - "highlight": "", - "sendall": true, - "outputs": 0, - "ok": "OK", - "cancel": "", - "raw": false, - "topic": "", - "name": "", - "x": 920, - "y": 100, - "wires": [] - }, - { - "id": "fda01242.9576a8", - "type": "subflow:66c23d37.f72cdc", - "z": "259c8713.b50e28", - "name": "", - "env": [], - "x": 270, - "y": 220, - "wires": [] - }, - { - "id": "bbb7cb31.15121", - "type": "debug", - "z": "ad5a5663.ce893", + "z": "506e9090.6e905", "name": "", "active": true, "tosidebar": true, @@ -4218,73 +2515,651 @@ "wires": [] }, { - "id": "6382060e.460ab8", - "type": "debug", - "z": "66c23d37.f72cdc", - "name": "", - "active": true, - "tosidebar": true, - "console": false, - "tostatus": false, - "complete": "false", - "x": 1380, - "y": 120, - "wires": [] + "id": "f377d75b.32d27", + "type": "ui_group", + "z": "", + "name": "Object metadata", + "tab": "2b97fe34.a699fa", + "order": 6, + "disp": true, + "width": "24", + "collapse": false }, { - "id": "b23ae409.085ad8", - "type": "ui_button", - "z": "8d959937.18735", - "name": "", - "group": "d170ac9c.3b4828", - "order": 1, + "id": "97d77aeb.75afd8", + "type": "subflow", + "name": "Acquisition metadata", + "info": "", + "category": "", + "in": [ + { + "x": 50, + "y": 30, + "wires": [ + { + "id": "282cae65.749e9a" + }, + { + "id": "cc899daf.a8d5d8" + }, + { + "id": "9873f1c8.6cb608" + }, + { + "id": "e53df171.eed68" + }, + { + "id": "5f728563.cf6214" + }, + { + "id": "c1a5eaf5.8691c" + }, + { + "id": "86c63d98.eb21" + }, + { + "id": "3707a612.b8619a" + }, + { + "id": "b2d20d5d.fd9e38" + } + ] + } + ], + "out": [ + { + "x": 740, + "y": 40, + "wires": [ + { + "id": "3b267291.1eee26", + "port": 0 + }, + { + "id": "435a2dcf.a1a60c", + "port": 0 + }, + { + "id": "cc6cb58d.b2dbe8", + "port": 0 + }, + { + "id": "8b306bbc.914", + "port": 0 + }, + { + "id": "2a5a2b7a.f218d4", + "port": 0 + }, + { + "id": "28df07d8.d71ba8", + "port": 0 + }, + { + "id": "6cf2c1ac.a0fea8", + "port": 0 + }, + { + "id": "e7c4132f.f4417", + "port": 0 + } + ] + }, + { + "x": 900, + "y": 360, + "wires": [ + { + "id": "1e688c91.1b805b", + "port": 0 + } + ] + } + ], + "env": [], + "color": "#DDAA99" + }, + { + "id": "1e688c91.1b805b", + "type": "function", + "z": "97d77aeb.75afd8", + "name": "set optical config", + "func": "global.set(msg.topic,msg.payload);\nvar acq_fnumber_objective = String(global.get(msg.topic));\n\nswitch(acq_fnumber_objective) {\n case \"25\":\n global.set(\"acq_magnification\",0.6);\n global.set(\"process_pixel\",1.86);\n global.set(\"sug_min\",60);\n global.set(\"sug_max\",670);\n global.set(\"sug_flowrate\",3);\n break;\n case \"16\":\n global.set(\"acq_magnification\",0.94);\n global.set(\"process_pixel\",1.19);\n global.set(\"sug_min\",40);\n global.set(\"sug_max\",430);\n global.set(\"sug_flowrate\",2.4);\n break;\n case \"12\":\n global.set(\"acq_magnification\",1.20);\n global.set(\"process_pixel\",0.94);\n global.set(\"sug_min\",30);\n global.set(\"sug_max\",340);\n global.set(\"sug_flowrate\",1.25);\n break;\n case \"8\":\n global.set(\"acq_magnification\",1.78);\n global.set(\"process_pixel\",0.63);\n global.set(\"sug_min\",20);\n global.set(\"sug_max\",230);\n global.set(\"sug_flowrate\",0.42);\n break;\n case \"6\":\n global.set(\"acq_magnification\",2.36);\n global.set(\"process_pixel\",0.48);\n global.set(\"sug_min\",15);\n global.set(\"sug_max\",170);\n global.set(\"sug_flowrate\",0.32);\n break;\n}\nreturn msg;", + "outputs": 1, + "noerr": 0, + "x": 750, + "y": 360, + "wires": [ + [] + ] + }, + { + "id": "2877f2f.211cc8e", + "type": "ui_dropdown", + "z": "97d77aeb.75afd8", + "name": "acq_fnumber_objective", + "label": "M12 Lens*", + "tooltip": "", + "place": "Select option", + "group": "60b93a5.a032344", + "order": 3, "width": 0, "height": 0, - "passthru": false, - "label": "Start Acquisition", - "tooltip": "", - "color": "", - "bgcolor": "", - "icon": "", + "passthru": true, + "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": "", - "payloadType": "str", - "topic": "actuator/image", - "x": 200, - "y": 100, + "topic": "acq_fnumber_objective", + "x": 526, + "y": 360, "wires": [ [ - "715c6be9.55822c" + "1e688c91.1b805b" ] ] }, { - "id": "715c6be9.55822c", + "id": "8b306bbc.914", + "type": "ui_numeric", + "z": "97d77aeb.75afd8", + "name": "acq_minimum_mesh", + "label": "Min fraction size (μm)", + "tooltip": "", + "group": "60b93a5.a032344", + "order": 8, + "width": 0, + "height": 0, + "wrap": false, + "passthru": true, + "topic": "acq_minimum_mesh", + "format": "{{value}}", + "min": 0, + "max": "300", + "step": "10", + "x": 536, + "y": 160, + "wires": [ + [] + ] + }, + { + "id": "2a5a2b7a.f218d4", + "type": "ui_numeric", + "z": "97d77aeb.75afd8", + "name": "acq_maximum_mesh", + "label": "Max fraction size (μm)", + "tooltip": "", + "group": "60b93a5.a032344", + "order": 4, + "width": 0, + "height": 0, + "wrap": false, + "passthru": true, + "topic": "acq_maximum_mesh", + "format": "{{value}}", + "min": "200", + "max": "2000", + "step": "100", + "x": 536, + "y": 200, + "wires": [ + [] + ] + }, + { + "id": "3b267291.1eee26", + "type": "ui_text_input", + "z": "97d77aeb.75afd8", + "name": "acq_id", + "label": "Acquisition unique ID*", + "tooltip": "", + "group": "60b93a5.a032344", + "order": 1, + "width": 0, + "height": 0, + "passthru": true, + "mode": "number", + "delay": 300, + "topic": "acq_id", + "x": 586, + "y": 40, + "wires": [ + [] + ] + }, + { + "id": "cc6cb58d.b2dbe8", + "type": "ui_dropdown", + "z": "97d77aeb.75afd8", + "name": "acq_celltype", + "label": "Thickness flowcell*", + "tooltip": "", + "place": "Select option", + "group": "60b93a5.a032344", + "order": 7, + "width": 0, + "height": 0, + "passthru": true, + "options": [ + { + "label": "200 μm µ-Slide I Luer", + "value": 200, + "type": "num" + }, + { + "label": "400 μm µ-Slide I Luer", + "value": 400, + "type": "num" + }, + { + "label": "600 μm µ-Slide I Luer", + "value": 600, + "type": "num" + }, + { + "label": "800 μm µ-Slide I Luer", + "value": 800, + "type": "num" + } + ], + "payload": "", + "topic": "acq_celltype", + "x": 566, + "y": 120, + "wires": [ + [] + ] + }, + { + "id": "28df07d8.d71ba8", + "type": "ui_text_input", + "z": "97d77aeb.75afd8", + "name": "acq_volume", + "label": "Volume to pass (ml)", + "tooltip": "", + "group": "60b93a5.a032344", + "order": 2, + "width": 0, + "height": 0, + "passthru": true, + "mode": "number", + "delay": 300, + "topic": "acq_volume", + "x": 566, + "y": 240, + "wires": [ + [] + ] + }, + { + "id": "435a2dcf.a1a60c", + "type": "ui_text_input", + "z": "97d77aeb.75afd8", + "name": "acq_instrument", + "label": "Acquisition instrument", + "tooltip": "PlanktonScope V2.1", + "group": "60b93a5.a032344", + "order": 6, + "width": 0, + "height": 0, + "passthru": true, + "mode": "text", + "delay": 300, + "topic": "acq_instrument", + "x": 556, + "y": 80, + "wires": [ + [] + ] + }, + { + "id": "282cae65.749e9a", "type": "function", - "z": "8d959937.18735", - "name": "image.js", - "func": "state = global.get(\"state\");\nglobal.set('img_counter',0)\nglobal.set('obj_counter',0)\nif (state == null){state=\"free\"}\n\nvar duration_bef_cycle= global.get(\"duration_bef_cycle\");\nvar duration_flush= global.get(\"duration_flush\");\nvar nb_img= global.get(\"nb_img\");\nvar duration_bef_seq= global.get(\"duration_bef_seq\");\nvar duration_bef_img= global.get(\"duration_bef_img\");\nvar duration_between= global.get(\"duration_between\");\n\nif (duration_bef_cycle === undefined || duration_bef_cycle === \"\" || duration_bef_cycle === null) {\n msg.topic = \"Missing entry :\"\n msg.payload = \"Duration before the cycles\";\n \n}else if (duration_flush === undefined || duration_flush === \"\" || duration_flush === null) {\n msg.topic = \"Missing entry :\"\n msg.payload = \"Duration of the flushing\";\n \n}else if (nb_img === undefined || nb_img === \"\" || nb_img === null) {\n msg.topic = \"Missing entry :\"\n msg.payload = \"Directory to store the images\";\n \n}else if (duration_bef_seq === undefined || duration_bef_seq === \"\" || duration_bef_seq === null) {\n msg.topic = \"Missing entry :\"\n msg.payload = \"Duration before the sequence\";\n \n}else if (duration_bef_img === undefined || duration_bef_img === \"\" || duration_bef_img === null) {\n msg.topic = \"Missing entry :\"\n msg.payload = \"Duration before an image\";\n \n}else if (duration_between === undefined || duration_between === \"\" || duration_between === null) {\n msg.topic = \"Missing entry :\"\n msg.payload = \"Duration between sequence\";\n \n}else {\n nb_img=nb_img-1\n msg.payload=duration_bef_cycle+' '+duration_flush+' '+nb_img+' '+duration_bef_seq+' '+duration_bef_img+' '+duration_between;\n}\nreturn msg;", + "z": "97d77aeb.75afd8", + "name": "get acq_id", + "func": "msg.payload = msg.payload.acq_id+1;\nreturn msg;", "outputs": 1, "noerr": 0, - "x": 360, - "y": 100, + "x": 210, + "y": 40, "wires": [ [ - "bda62ebe.dd2e4" + "3b267291.1eee26" + ] + ] + }, + { + "id": "cc899daf.a8d5d8", + "type": "function", + "z": "97d77aeb.75afd8", + "name": "get acq_instrument", + "func": "msg.payload = msg.payload.acq_instrument;\nreturn msg;", + "outputs": 1, + "noerr": 0, + "x": 230, + "y": 80, + "wires": [ + [ + "435a2dcf.a1a60c" + ] + ] + }, + { + "id": "9873f1c8.6cb608", + "type": "function", + "z": "97d77aeb.75afd8", + "name": "get acq_celltype", + "func": "msg.payload = msg.payload.acq_celltype;\nreturn msg;", + "outputs": 1, + "noerr": 0, + "x": 220, + "y": 120, + "wires": [ + [ + "cc6cb58d.b2dbe8" + ] + ] + }, + { + "id": "e53df171.eed68", + "type": "function", + "z": "97d77aeb.75afd8", + "name": "get acq_minimum_mesh", + "func": "msg.payload = msg.payload.acq_minimum_mesh;\nreturn msg;", + "outputs": 1, + "noerr": 0, + "x": 250, + "y": 160, + "wires": [ + [ + "8b306bbc.914" + ] + ] + }, + { + "id": "5f728563.cf6214", + "type": "function", + "z": "97d77aeb.75afd8", + "name": "get acq_maximum_mesh", + "func": "msg.payload = msg.payload.acq_maximum_mesh;\nreturn msg;", + "outputs": 1, + "noerr": 0, + "x": 250, + "y": 200, + "wires": [ + [ + "2a5a2b7a.f218d4" + ] + ] + }, + { + "id": "c1a5eaf5.8691c", + "type": "function", + "z": "97d77aeb.75afd8", + "name": "get acq_volume", + "func": "msg.payload = msg.payload.acq_volume;\nreturn msg;", + "outputs": 1, + "noerr": 0, + "x": 220, + "y": 240, + "wires": [ + [ + "28df07d8.d71ba8" + ] + ] + }, + { + "id": "b2d20d5d.fd9e38", + "type": "function", + "z": "97d77aeb.75afd8", + "name": "get acq_fnumber_objective", + "func": "msg.payload = msg.payload.acq_fnumber_objective;\nreturn msg;", + "outputs": 1, + "noerr": 0, + "x": 260, + "y": 360, + "wires": [ + [ + "2877f2f.211cc8e" + ] + ] + }, + { + "id": "6cf2c1ac.a0fea8", + "type": "ui_numeric", + "z": "97d77aeb.75afd8", + "name": "acq_min_esd", + "label": "Minimum size to segment (μm)", + "tooltip": "", + "group": "60b93a5.a032344", + "order": 9, + "width": 0, + "height": 0, + "wrap": false, + "passthru": true, + "topic": "acq_min_esd", + "format": "{{value}}", + "min": 0, + "max": "300", + "step": "5", + "x": 566, + "y": 280, + "wires": [ + [] + ] + }, + { + "id": "e7c4132f.f4417", + "type": "ui_numeric", + "z": "97d77aeb.75afd8", + "name": "acq_max_esd", + "label": "Maximum size to segment (μm)", + "tooltip": "", + "group": "60b93a5.a032344", + "order": 5, + "width": 0, + "height": 0, + "wrap": false, + "passthru": true, + "topic": "acq_max_esd", + "format": "{{value}}", + "min": "100", + "max": "2000", + "step": "5", + "x": 556, + "y": 320, + "wires": [ + [] + ] + }, + { + "id": "86c63d98.eb21", + "type": "function", + "z": "97d77aeb.75afd8", + "name": "get acq_min_esd", + "func": "msg.payload = msg.payload.acq_min_esd;\nreturn msg;", + "outputs": 1, + "noerr": 0, + "x": 230, + "y": 280, + "wires": [ + [ + "6cf2c1ac.a0fea8" + ] + ] + }, + { + "id": "3707a612.b8619a", + "type": "function", + "z": "97d77aeb.75afd8", + "name": "get acq_max_esd", + "func": "msg.payload = msg.payload.acq_max_esd;\nreturn msg;", + "outputs": 1, + "noerr": 0, + "x": 230, + "y": 320, + "wires": [ + [ + "e7c4132f.f4417" + ] + ] + }, + { + "id": "60b93a5.a032344", + "type": "ui_group", + "z": "", + "name": "Acquisition metadata", + "tab": "2b97fe34.a699fa", + "order": 7, + "disp": true, + "width": "24", + "collapse": false + }, + { + "id": "9a45991b.365bc8", + "type": "subflow", + "name": "Pump actuation", + "info": "", + "category": "", + "in": [ + { + "x": 40, + "y": 40, + "wires": [ + { + "id": "eb7c01ae.d00358" + }, + { + "id": "642ae1f3.cf7d28" + } + ] + } + ], + "out": [ + { + "x": 700, + "y": 40, + "wires": [ + { + "id": "4485759b.52ee74", + "port": 0 + }, + { + "id": "3283f063.31c548", + "port": 0 + } + ] + } + ], + "env": [], + "color": "#A6BBCF", + "icon": "font-awesome/fa-recycle" + }, + { + "id": "6246d9ef.156bd", + "type": "function", + "z": "9a45991b.365bc8", + "name": "pump.js", + "func": "state = global.get(\"state\");\n\nif (state == null){state=\"free\"}\n\nvar manual_volume= global.get(\"pump_manual_volume\");\nvar flowrate= global.get(\"pump_flowrate\");\n\nif (manual_volume === undefined || manual_volume === \"\" || manual_volume === null) {\n msg.topic = \"Missing entry :\"\n msg.payload = \"Volume to pass\";\n \n}else if (flowrate === undefined || flowrate === \"\" || flowrate === null) {\n msg.topic = \"Missing entry :\"\n msg.payload = \"Flowrate\";\n \n}else {\n volume = global.get(\"pump_manual_volume\");\n nb_step=volume*507\n msg.volume = volume;\n flowrate = global.get(\"pump_flowrate\");\n duration=(volume*60)/flowrate\n delay=(duration/nb_step)-0.005\n msg.topic = \"actuator/pump\";\n \n if(msg.payload === \"FORWARD\" & state===\"free\"){\n msg.payload='FORWARD '+delay+' '+nb_step;\n }\n if(msg.payload === \"BACKWARD\" & state===\"free\"){\n msg.payload='BACKWARD '+delay+' '+nb_step;\n }\n}\nreturn msg;", + "outputs": 1, + "noerr": 0, + "x": 640, + "y": 140, + "wires": [ + [ + "53bef09a.8102e" ] ], "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": "bda62ebe.dd2e4", + "id": "2374d55d.a3e3a2", + "type": "ui_button", + "z": "9a45991b.365bc8", + "name": "BACKWARD", + "group": "4153382f.45437", + "order": 2, + "width": 6, + "height": 1, + "passthru": false, + "label": "", + "tooltip": "", + "color": "", + "bgcolor": "", + "icon": "arrow_back", + "payload": "BACKWARD", + "payloadType": "str", + "topic": "actuator/pump", + "x": 470, + "y": 120, + "wires": [ + [ + "6246d9ef.156bd" + ] + ] + }, + { + "id": "c8aa9753.f51c08", + "type": "ui_button", + "z": "9a45991b.365bc8", + "name": "FORWARD", + "group": "4153382f.45437", + "order": 4, + "width": 6, + "height": 1, + "passthru": true, + "label": "", + "tooltip": "", + "color": "", + "bgcolor": "", + "icon": "arrow_forward", + "payload": "FORWARD", + "payloadType": "str", + "topic": "actuator/pump", + "x": 470, + "y": 160, + "wires": [ + [ + "6246d9ef.156bd" + ] + ] + }, + { + "id": "53bef09a.8102e", "type": "switch", - "z": "8d959937.18735", + "z": "9a45991b.365bc8", "name": "", "property": "topic", "propertyType": "msg", "rules": [ { "t": "eq", - "v": "actuator/image", + "v": "actuator/pump", "vt": "str" }, { @@ -4296,21 +3171,21 @@ "checkall": "true", "repair": false, "outputs": 2, - "x": 510, - "y": 100, + "x": 770, + "y": 140, "wires": [ [ - "366697a.e8f6068" + "4d3bf3c2.6a380c" ], [ - "e2049db5.46682" + "d943e58a.e85fc" ] ] }, { - "id": "e2049db5.46682", + "id": "d943e58a.e85fc", "type": "ui_toast", - "z": "8d959937.18735", + "z": "9a45991b.365bc8", "position": "dialog", "displayTime": "3", "highlight": "", @@ -4321,36 +3196,23 @@ "raw": false, "topic": "", "name": "", - "x": 690, - "y": 120, + "x": 930, + "y": 160, "wires": [ [] ] }, { - "id": "366697a.e8f6068", - "type": "mqtt out", - "z": "8d959937.18735", - "name": "", - "topic": "", - "qos": "", - "retain": "", - "broker": "cb2f36fe.1c7038", - "x": 670, - "y": 80, - "wires": [] - }, - { - "id": "3a85a060.ad2aa", + "id": "eaa22490.6843d", "type": "ui_button", - "z": "8d959937.18735", - "name": "Stop Acquisition", - "group": "d170ac9c.3b4828", - "order": 2, - "width": 0, - "height": 0, + "z": "9a45991b.365bc8", + "name": "stop pump", + "group": "4153382f.45437", + "order": 5, + "width": 4, + "height": 1, "passthru": true, - "label": "STOP ACQUISITION", + "label": "STOP PUMP", "tooltip": "", "color": "", "bgcolor": "#AD1625", @@ -4358,79 +3220,1077 @@ "payload": "off", "payloadType": "str", "topic": "actuator/wait", - "x": 200, - "y": 140, + "x": 470, + "y": 200, "wires": [ [ - "f59d51da.c3b078" + "9e71b7a5.28dff8" ] ] }, { - "id": "f59d51da.c3b078", + "id": "4d3bf3c2.6a380c", "type": "mqtt out", - "z": "8d959937.18735", + "z": "9a45991b.365bc8", "name": "", "topic": "", "qos": "", "retain": "", - "broker": "cb2f36fe.1c7038", - "x": 350, - "y": 140, + "broker": "e8ab36cc.74d77", + "x": 910, + "y": 120, "wires": [] }, { - "id": "8ade1ac1.5c3408", - "type": "ui_switch", - "z": "8d959937.18735", - "name": "Segmentation", - "label": "Segmentation", + "id": "9e71b7a5.28dff8", + "type": "mqtt out", + "z": "9a45991b.365bc8", + "name": "", + "topic": "", + "qos": "", + "retain": "", + "broker": "e8ab36cc.74d77", + "x": 610, + "y": 200, + "wires": [] + }, + { + "id": "3283f063.31c548", + "type": "ui_text_input", + "z": "9a45991b.365bc8", + "name": "pump_manual_volume", + "label": "Volume to pass (ml)", "tooltip": "", - "group": "d170ac9c.3b4828", + "group": "4153382f.45437", + "order": 3, + "width": 8, + "height": 1, + "passthru": true, + "mode": "number", + "delay": 300, + "topic": "pump_manual_volume", + "x": 480, + "y": 80, + "wires": [ + [] + ] + }, + { + "id": "642ae1f3.cf7d28", + "type": "function", + "z": "9a45991b.365bc8", + "name": "get pump_manual_volume", + "func": "msg.payload = msg.payload.pump_manual_volume;\nreturn msg;", + "outputs": 1, + "noerr": 0, + "x": 220, + "y": 80, + "wires": [ + [ + "3283f063.31c548" + ] + ] + }, + { + "id": "4485759b.52ee74", + "type": "ui_slider", + "z": "9a45991b.365bc8", + "name": "pump_flowrate", + "label": "Flowrate (ml/min)*", + "tooltip": "", + "group": "4153382f.45437", + "order": 1, + "width": 0, + "height": 0, + "passthru": true, + "outs": "end", + "topic": "pump_flowrate", + "min": 0, + "max": "20", + "step": "0.1", + "x": 500, + "y": 40, + "wires": [ + [] + ] + }, + { + "id": "eb7c01ae.d00358", + "type": "function", + "z": "9a45991b.365bc8", + "name": "get pump_flowrate", + "func": "msg.payload = msg.payload.pump_flowrate;\nreturn msg;", + "outputs": 1, + "noerr": 0, + "x": 190, + "y": 40, + "wires": [ + [ + "4485759b.52ee74" + ] + ] + }, + { + "id": "4153382f.45437", + "type": "ui_group", + "z": "", + "name": "Pump actuation", + "tab": "2b97fe34.a699fa", + "order": 5, + "disp": true, + "width": "24", + "collapse": false + }, + { + "id": "ac806d39.1682a8", + "type": "subflow", + "name": "Focus actuation", + "info": "", + "category": "", + "in": [ + { + "x": 40, + "y": 40, + "wires": [ + { + "id": "c631467a.569ba" + } + ] + } + ], + "out": [ + { + "x": 800, + "y": 200, + "wires": [ + { + "id": "97bf666e.4d3ad", + "port": 0 + } + ] + } + ], + "env": [], + "color": "#A6BBCF", + "icon": "node-red/sort.svg" + }, + { + "id": "97bf666e.4d3ad", + "type": "ui_text_input", + "z": "ac806d39.1682a8", + "name": "focus_nb_step", + "label": "Number of step(s)", + "tooltip": "", + "group": "69433259.f306fc", + "order": 2, + "width": 8, + "height": 1, + "passthru": true, + "mode": "number", + "delay": 300, + "topic": "focus_nb_step", + "x": 540, + "y": 40, + "wires": [ + [] + ] + }, + { + "id": "c631467a.569ba", + "type": "function", + "z": "ac806d39.1682a8", + "name": "get focus_nb_step", + "func": "msg.payload = msg.payload.focus_nb_step;\nreturn msg;", + "outputs": 1, + "noerr": 0, + "x": 230, + "y": 40, + "wires": [ + [ + "97bf666e.4d3ad" + ] + ] + }, + { + "id": "8346f4af.5c0978", + "type": "ui_button", + "z": "ac806d39.1682a8", + "name": "DOWN", + "group": "69433259.f306fc", + "order": 3, + "width": 6, + "height": 1, + "passthru": true, + "label": "", + "tooltip": "", + "color": "", + "bgcolor": "", + "icon": "arrow_downward", + "payload": "DOWN", + "payloadType": "str", + "topic": "actuator/focus", + "x": 520, + "y": 120, + "wires": [ + [ + "350c388d.12cd28" + ] + ] + }, + { + "id": "7ee30e1c.691bd", + "type": "ui_button", + "z": "ac806d39.1682a8", + "name": "UP", + "group": "69433259.f306fc", + "order": 1, + "width": 6, + "height": 1, + "passthru": false, + "label": "", + "tooltip": "", + "color": "", + "bgcolor": "", + "icon": "arrow_upwards", + "payload": "UP", + "payloadType": "str", + "topic": "actuator/focus", + "x": 530, + "y": 81, + "wires": [ + [ + "350c388d.12cd28" + ] + ] + }, + { + "id": "a2f04fac.5a338", + "type": "switch", + "z": "ac806d39.1682a8", + "name": "", + "property": "topic", + "propertyType": "msg", + "rules": [ + { + "t": "eq", + "v": "actuator/focus", + "vt": "str" + }, + { + "t": "eq", + "v": "Missing entry :", + "vt": "str" + } + ], + "checkall": "true", + "repair": false, + "outputs": 2, + "x": 810, + "y": 100, + "wires": [ + [ + "9fd904e.d1cbcf8" + ], + [ + "ccd4fa1e.152" + ] + ] + }, + { + "id": "ccd4fa1e.152", + "type": "ui_toast", + "z": "ac806d39.1682a8", + "position": "dialog", + "displayTime": "3", + "highlight": "", + "sendall": true, + "outputs": 1, + "ok": "OK", + "cancel": "", + "raw": false, + "topic": "", + "name": "", + "x": 970, + "y": 140, + "wires": [ + [] + ] + }, + { + "id": "350c388d.12cd28", + "type": "function", + "z": "ac806d39.1682a8", + "name": "focus.js", + "func": "state = global.get(\"state\");\n\nif (state == null){state=\"free\"}\n\nvar nb_step= global.get(\"focus_nb_step\");\n\nif (nb_step === undefined || nb_step === \"\" || nb_step === null) {\n msg.topic = \"Missing entry :\"\n msg.payload = \"Number of steps\";\n \n}else {\n nb_step= global.get(\"focus_nb_step\");\n if(msg.payload === \"UP\" & state===\"free\"){\n msg.payload=\"FORWARD \"+nb_step;\n }\n if(msg.payload === \"DOWN\" & state===\"free\"){\n msg.payload=\"BACKWARD \"+nb_step;\n }\n}\nreturn msg;", + "outputs": 1, + "noerr": 0, + "x": 660, + "y": 100, + "wires": [ + [ + "a2f04fac.5a338" + ] + ], + "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": "da904b2b.4a1d68", + "type": "ui_button", + "z": "ac806d39.1682a8", + "name": "stop focus", + "group": "69433259.f306fc", + "order": 4, + "width": 4, + "height": 1, + "passthru": true, + "label": "STOP FOCUS", + "tooltip": "", + "color": "", + "bgcolor": "#AD1625", + "icon": "", + "payload": "off", + "payloadType": "str", + "topic": "actuator/wait", + "x": 510, + "y": 160, + "wires": [ + [ + "8bb9c09d.bc8178" + ] + ] + }, + { + "id": "9fd904e.d1cbcf8", + "type": "mqtt out", + "z": "ac806d39.1682a8", + "name": "", + "topic": "", + "qos": "", + "retain": "", + "broker": "e8ab36cc.74d77", + "x": 950, + "y": 80, + "wires": [] + }, + { + "id": "8bb9c09d.bc8178", + "type": "mqtt out", + "z": "ac806d39.1682a8", + "name": "", + "topic": "", + "qos": "", + "retain": "", + "broker": "e8ab36cc.74d77", + "x": 650, + "y": 160, + "wires": [] + }, + { + "id": "69433259.f306fc", + "type": "ui_group", + "z": "", + "name": "Focus actuation", + "tab": "2b97fe34.a699fa", + "order": 4, + "disp": true, + "width": "24", + "collapse": false + }, + { + "id": "e8ab36cc.74d77", + "type": "mqtt-broker", + "z": "", + "name": "", + "broker": "0.0.0.0", + "port": "1883", + "clientid": "Client_node", + "usetls": false, + "compatmode": false, + "keepalive": "60", + "cleansession": true, + "birthTopic": "", + "birthQos": "0", + "birthPayload": "", + "closeTopic": "", + "closeQos": "0", + "closePayload": "", + "willTopic": "", + "willQos": "0", + "willPayload": "" + }, + { + "id": "5c6dd7ee.546fa8", + "type": "subflow", + "name": "Sample metadata", + "info": "", + "category": "", + "in": [ + { + "x": 40, + "y": 40, + "wires": [ + { + "id": "730e3aa0.75f6dc" + }, + { + "id": "b49441ee.07b358" + }, + { + "id": "77454044.f47e88" + }, + { + "id": "203e3416.6c480c" + }, + { + "id": "3555467a.6ba1ea" + } + ] + } + ], + "out": [ + { + "x": 840, + "y": 40, + "wires": [ + { + "id": "419967b7.b9b5f", + "port": 0 + }, + { + "id": "9b3f7b46.107718", + "port": 0 + }, + { + "id": "6f24740b.fbae5c", + "port": 0 + }, + { + "id": "bf7a47c8.a960b8", + "port": 0 + }, + { + "id": "327afe96.262122", + "port": 0 + } + ] + } + ], + "env": [], + "color": "#DDAA99" + }, + { + "id": "6f24740b.fbae5c", + "type": "ui_text_input", + "z": "5c6dd7ee.546fa8", + "name": "sample_ship", + "label": "Name of the ship", + "tooltip": "", + "group": "417f91c9.193ab", + "order": 2, + "width": 0, + "height": 0, + "passthru": true, + "mode": "text", + "delay": 300, + "topic": "sample_ship", + "x": 590, + "y": 120, + "wires": [ + [] + ] + }, + { + "id": "327afe96.262122", + "type": "ui_dropdown", + "z": "5c6dd7ee.546fa8", + "name": "sample_sampling_gear", + "label": "Sampling gear", + "tooltip": "", + "place": "Select", + "group": "417f91c9.193ab", + "order": 4, + "width": 0, + "height": 0, + "passthru": true, + "options": [ + { + "label": "Plankton net", + "value": "net", + "type": "str" + }, + { + "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" + }, + { + "label": "Flask", + "value": "flask", + "type": "str" + } + ], + "payload": "", + "topic": "sample_sampling_gear", + "x": 550, + "y": 200, + "wires": [ + [] + ] + }, + { + "id": "bf7a47c8.a960b8", + "type": "ui_text_input", + "z": "5c6dd7ee.546fa8", + "name": "sample_operator", + "label": "Name of the operator", + "tooltip": "", + "group": "417f91c9.193ab", "order": 3, "width": 0, "height": 0, - "passthru": false, - "decouple": "false", - "topic": "actuator/segmentation_state", - "style": "", - "onvalue": "true", - "onvalueType": "str", - "onicon": "", - "oncolor": "", - "offvalue": "false", - "offvalueType": "str", - "officon": "", - "offcolor": "", - "x": 200, - "y": 180, + "passthru": true, + "mode": "text", + "delay": 300, + "topic": "sample_operator", + "x": 570, + "y": 160, + "wires": [ + [] + ] + }, + { + "id": "419967b7.b9b5f", + "type": "ui_text_input", + "z": "5c6dd7ee.546fa8", + "name": "sample_project", + "label": "Name of the project*", + "tooltip": "", + "group": "417f91c9.193ab", + "order": 1, + "width": 0, + "height": 0, + "passthru": true, + "mode": "text", + "delay": 300, + "topic": "sample_project", + "x": 580, + "y": 40, + "wires": [ + [] + ] + }, + { + "id": "9b3f7b46.107718", + "type": "ui_text_input", + "z": "5c6dd7ee.546fa8", + "name": "sample_id", + "label": "ID of the station*", + "tooltip": "", + "group": "417f91c9.193ab", + "order": 5, + "width": 0, + "height": 0, + "passthru": true, + "mode": "number", + "delay": 300, + "topic": "sample_id", + "x": 590, + "y": 80, + "wires": [ + [] + ] + }, + { + "id": "730e3aa0.75f6dc", + "type": "function", + "z": "5c6dd7ee.546fa8", + "name": "get sample_projet", + "func": "msg.payload = msg.payload.sample_project;\nreturn msg;", + "outputs": 1, + "noerr": 0, + "x": 250, + "y": 40, "wires": [ [ - "7751b219.9a3e1c" + "419967b7.b9b5f" ] ] }, { - "id": "7751b219.9a3e1c", - "type": "mqtt out", - "z": "8d959937.18735", + "id": "77454044.f47e88", + "type": "function", + "z": "5c6dd7ee.546fa8", + "name": "get sample_ship", + "func": "msg.payload = msg.payload.sample_ship;\nreturn msg;", + "outputs": 1, + "noerr": 0, + "x": 240, + "y": 120, + "wires": [ + [ + "6f24740b.fbae5c" + ] + ] + }, + { + "id": "b49441ee.07b358", + "type": "function", + "z": "5c6dd7ee.546fa8", + "name": "get sample_id", + "func": "msg.payload = msg.payload.sample_id+1;\nreturn msg;", + "outputs": 1, + "noerr": 0, + "x": 240, + "y": 80, + "wires": [ + [ + "9b3f7b46.107718" + ] + ] + }, + { + "id": "203e3416.6c480c", + "type": "function", + "z": "5c6dd7ee.546fa8", + "name": "get sample_operator", + "func": "msg.payload = msg.payload.sample_operator;\nreturn msg;", + "outputs": 1, + "noerr": 0, + "x": 260, + "y": 160, + "wires": [ + [ + "bf7a47c8.a960b8" + ] + ] + }, + { + "id": "3555467a.6ba1ea", + "type": "function", + "z": "5c6dd7ee.546fa8", + "name": "get sample_sampling_gear", + "func": "msg.payload = msg.payload.sample_sampling_gear;\nreturn msg;", + "outputs": 1, + "noerr": 0, + "x": 280, + "y": 200, + "wires": [ + [ + "327afe96.262122" + ] + ] + }, + { + "id": "417f91c9.193ab", + "type": "ui_group", + "z": "", + "name": "Sample metadata", + "tab": "2b97fe34.a699fa", + "order": 2, + "disp": true, + "width": "24", + "collapse": false + }, + { + "id": "2b97fe34.a699fa", + "type": "ui_tab", + "z": "", + "name": "GUI", + "icon": "fa-eyedropper", + "order": 2, + "disabled": false, + "hidden": false + }, + { + "id": "bb8dbe68.7e20a", + "type": "tab", + "label": "Main", + "disabled": false, + "info": "" + }, + { + "id": "20340bb6.5f923c", + "type": "function", + "z": "bb8dbe68.7e20a", + "name": "get global", + "func": "msg.payload={\n \n \"sample_project\":global.get(\"sample_project\"),\n \"sample_id\":global.get(\"sample_id\"),\n \"sample_ship\":global.get(\"sample_ship\"),\n \"sample_operator\":global.get(\"sample_operator\"),\n \"sample_sampling_gear\":global.get(\"sample_sampling_gear\"),\n \n \"acq_id\":global.get(\"acq_id\"),\n \"acq_instrument\":global.get(\"acq_instrument\"),\n //\"acq_instrument_id\":global.get(\"acq_instrument_id\"),\n \"acq_celltype\":global.get(\"acq_celltype\"),\n \"acq_minimum_mesh\":global.get(\"acq_minimum_mesh\"),\n \"acq_maximum_mesh\":global.get(\"acq_maximum_mesh\"),\n \"acq_min_esd\":global.get(\"acq_min_esd\"),\n \"acq_max_esd\":global.get(\"acq_max_esd\"),\n \"acq_volume\":global.get(\"acq_volume\"),\n \"acq_magnification\":global.get(\"magnification\"),\n \"acq_fnumber_objective\":global.get(\"acq_fnumber_objective\"),\n \n \"acq_camera_name\":\"Pi Camera V2.1 - 8MP\",\n \n \"object_date\":global.get(\"object_date\"),\n \"object_time\":global.get(\"object_time\"),\n \"object_lat\":global.get(\"object_lat\"),\n \"object_lon\":global.get(\"object_lon\"),\n \"object_depth_min\":global.get(\"object_depth_min\"),\n \"object_depth_max\":global.get(\"object_depth_max\"),\n \n \"custom_nb_frame\":global.get(\"custom_nb_frame\"),\n \"custom_nb_step\":global.get(\"custom_nb_step\"),\n \"custom_segmentation\":global.get(\"custom_segmentation\"),\n \"custom_sleep_before\":global.get(\"custom_sleep_before\"),\n \"focus_nb_step\":global.get(\"focus_nb_step\"),\n \"pump_flowrate\":global.get(\"pump_flowrate\"),\n \"pump_manual_volume\":global.get(\"pump_manual_volume\"),\n \n \"process_pixel\":global.get(\"process_pixel\"),\n \"process_id\":global.get(\"process_id\")\n \n \n};\nreturn msg;", + "outputs": 1, + "noerr": 0, + "x": 1260, + "y": 160, + "wires": [ + [ + "d69f0eb1.d514d" + ] + ] + }, + { + "id": "aed82ae1.3a7558", + "type": "file", + "z": "bb8dbe68.7e20a", "name": "", + "filename": "/home/pi/PlanktonScope/config.json", + "appendNewline": true, + "createDir": true, + "overwriteFile": "true", + "encoding": "none", + "x": 1640, + "y": 160, + "wires": [ + [] + ] + }, + { + "id": "d69f0eb1.d514d", + "type": "json", + "z": "bb8dbe68.7e20a", + "name": "config.json", + "property": "payload", + "action": "str", + "pretty": true, + "x": 1410, + "y": 160, + "wires": [ + [ + "aed82ae1.3a7558" + ] + ] + }, + { + "id": "b57ab8b0.7bfc4", + "type": "file in", + "z": "bb8dbe68.7e20a", + "name": "", + "filename": "/home/pi/PlanktonScope/config.json", + "format": "utf8", + "chunk": false, + "sendError": false, + "encoding": "none", + "x": 360, + "y": 80, + "wires": [ + [ + "5b6059c3.8d4fa8" + ] + ], + "info": "# PlanktonScope Help\nThis Node will read the content of the file named **config.txt** containing all the input placeholders.\n" + }, + { + "id": "7880a269.4817ac", + "type": "inject", + "z": "bb8dbe68.7e20a", + "name": "on_load", "topic": "", - "qos": "", - "retain": "", - "broker": "cb2f36fe.1c7038", - "x": 350, - "y": 180, + "payload": "", + "payloadType": "date", + "repeat": "", + "crontab": "", + "once": true, + "onceDelay": 0.1, + "x": 120, + "y": 80, + "wires": [ + [ + "b57ab8b0.7bfc4", + "10d8393.60498c7", + "dba45961.85d67", + "8231cfcc.0c5dd8" + ] + ], + "info": "# PlanktonScope Help\nWhen the **Pi** is booting, **Node-RED** will be initiated and this node will be activated once and execute the following nodes." + }, + { + "id": "5b6059c3.8d4fa8", + "type": "json", + "z": "bb8dbe68.7e20a", + "name": "config.json", + "property": "payload", + "action": "", + "pretty": false, + "x": 610, + "y": 80, + "wires": [ + [ + "9b872b59.667ee", + "67bab5e1.2c7dcc", + "8e5a1fb0.dc878", + "bfc59fc4.be21a8", + "80434aac.22226", + "a3453d30.ca9a28", + "e25e094c.60fb1" + ] + ] + }, + { + "id": "1b45a311.c993ed", + "type": "function", + "z": "bb8dbe68.7e20a", + "name": "set global", + "func": "var value = msg.payload;\nvar key = msg.topic;\n\nglobal.set(key,value);\nreturn msg;", + "outputs": 1, + "noerr": 0, + "x": 1080, + "y": 80, + "wires": [ + [ + "20340bb6.5f923c" + ] + ] + }, + { + "id": "1d54c0bf.fbcf07", + "type": "rpi-gpio out", + "z": "bb8dbe68.7e20a", + "name": "", + "pin": "40", + "set": "", + "level": "0", + "freq": "", + "out": "out", + "x": 440, + "y": 120, "wires": [] }, { - "id": "2a677ff0.62e0f", - "type": "subflow:8d959937.18735", - "z": "259c8713.b50e28", + "id": "7da863d0.f7d41c", + "type": "ui_template", + "z": "bb8dbe68.7e20a", + "group": "dc721eb.9ef51e", + "name": "Stream Pi Camera", + "order": 1, + "width": 24, + "height": 11, + "format": "
", + "storeOutMessages": true, + "fwdInMessages": true, + "templateScope": "local", + "x": 830, + "y": 320, + "wires": [ + [] + ] + }, + { + "id": "10d8393.60498c7", + "type": "function", + "z": "bb8dbe68.7e20a", + "name": "init LED", + "func": "msg.payload=1;\nreturn msg;", + "outputs": 1, + "noerr": 0, + "x": 280, + "y": 120, + "wires": [ + [ + "1d54c0bf.fbcf07" + ] + ] + }, + { + "id": "9b872b59.667ee", + "type": "subflow:5c6dd7ee.546fa8", + "z": "bb8dbe68.7e20a", "name": "", "env": [], - "x": 750, - "y": 420, + "x": 830, + "y": 80, + "wires": [ + [ + "1b45a311.c993ed" + ] + ] + }, + { + "id": "a3453d30.ca9a28", + "type": "subflow:ac806d39.1682a8", + "z": "bb8dbe68.7e20a", + "name": "", + "env": [], + "x": 820, + "y": 240, + "wires": [ + [ + "1b45a311.c993ed" + ] + ] + }, + { + "id": "e25e094c.60fb1", + "type": "subflow:9a45991b.365bc8", + "z": "bb8dbe68.7e20a", + "name": "", + "env": [], + "x": 820, + "y": 280, + "wires": [ + [ + "1b45a311.c993ed" + ] + ] + }, + { + "id": "67bab5e1.2c7dcc", + "type": "subflow:97d77aeb.75afd8", + "z": "bb8dbe68.7e20a", + "name": "", + "env": [], + "x": 840, + "y": 120, + "wires": [ + [ + "1b45a311.c993ed" + ], + [ + "20340bb6.5f923c" + ] + ] + }, + { + "id": "8e5a1fb0.dc878", + "type": "subflow:506e9090.6e905", + "z": "bb8dbe68.7e20a", + "name": "", + "env": [], + "x": 820, + "y": 160, + "wires": [ + [ + "1b45a311.c993ed" + ], + [ + "20340bb6.5f923c" + ] + ] + }, + { + "id": "14b78383.7457bc", + "type": "subflow:1273b673.4a35ea", + "z": "bb8dbe68.7e20a", + "name": "System commands", + "env": [], + "x": 830, + "y": 480, "wires": [] + }, + { + "id": "e6403eaf.54f7e", + "type": "subflow:246abd43.838a5a", + "z": "bb8dbe68.7e20a", + "name": "", + "env": [], + "x": 840, + "y": 400, + "wires": [] + }, + { + "id": "bfc59fc4.be21a8", + "type": "subflow:99798a85.e62408", + "z": "bb8dbe68.7e20a", + "name": "process metadata", + "env": [], + "x": 830, + "y": 200, + "wires": [ + [ + "1b45a311.c993ed" + ] + ] + }, + { + "id": "80434aac.22226", + "type": "subflow:a156df1e.d37178", + "z": "bb8dbe68.7e20a", + "name": "Acquisition inputs", + "env": [], + "x": 830, + "y": 360, + "wires": [ + [ + "1b45a311.c993ed" + ] + ], + "icon": "node-red-dashboard/ui_switch.png" + }, + { + "id": "dba45961.85d67", + "type": "subflow:6384a5e.e34465c", + "z": "bb8dbe68.7e20a", + "name": "", + "env": [], + "x": 300, + "y": 200, + "wires": [] + }, + { + "id": "8231cfcc.0c5dd8", + "type": "subflow:e8320d42.9a3ad8", + "z": "bb8dbe68.7e20a", + "name": "", + "env": [], + "x": 290, + "y": 240, + "wires": [] + }, + { + "id": "557afe0d.33d97", + "type": "subflow:97600dff.93378", + "z": "bb8dbe68.7e20a", + "name": "", + "env": [], + "x": 830, + "y": 440, + "wires": [] + }, + { + "id": "af4f780b.068368", + "type": "ui_switch", + "z": "bb8dbe68.7e20a", + "name": "", + "label": "LED", + "tooltip": "", + "group": "9c86b3b7.54841", + "order": 10, + "width": 0, + "height": 0, + "passthru": true, + "decouple": "false", + "topic": "", + "style": "", + "onvalue": "true", + "onvalueType": "bool", + "onicon": "", + "oncolor": "", + "offvalue": "false", + "offvalueType": "bool", + "officon": "", + "offcolor": "", + "x": 270, + "y": 160, + "wires": [ + [ + "1d54c0bf.fbcf07" + ] + ] + }, + { + "id": "dc721eb.9ef51e", + "type": "ui_group", + "z": "", + "name": "Streaming camera", + "tab": "2b97fe34.a699fa", + "order": 3, + "disp": true, + "width": 24, + "collapse": false } ] diff --git a/flows/mqtt_nodered.json b/flows/mqtt_nodered.json deleted file mode 100644 index abeb85e..0000000 --- a/flows/mqtt_nodered.json +++ /dev/null @@ -1 +0,0 @@ -[{"id":"259c8713.b50e28","type":"tab","label":"Main","disabled":false,"info":""},{"id":"6d0d6fc7.d30bb","type":"ui_text_input","z":"259c8713.b50e28","name":"sample_ship","label":"Name of the ship","tooltip":"","group":"3e1ba03d.f01d8","order":3,"width":12,"height":1,"passthru":true,"mode":"text","delay":300,"topic":"sample_ship","x":1370,"y":140,"wires":[["de9708c2.d00068"]]},{"id":"43b12fe4.c5aa3","type":"ui_dropdown","z":"259c8713.b50e28","name":"sample_sampling_gear","label":"Sampling gear","tooltip":"","place":"Select","group":"3e1ba03d.f01d8","order":5,"width":0,"height":0,"passthru":true,"options":[{"label":"Plankton net","value":"net","type":"str"},{"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"}],"payload":"","topic":"sample_sampling_gear","x":1330,"y":220,"wires":[["3c6a723.145778e"]]},{"id":"458408d7.2b3b68","type":"ui_text_input","z":"259c8713.b50e28","name":"sample_operator","label":"Name of the operator","tooltip":"","group":"3e1ba03d.f01d8","order":4,"width":12,"height":1,"passthru":true,"mode":"text","delay":300,"topic":"sample_operator","x":1350,"y":180,"wires":[["a2ae6c99.188f2"]]},{"id":"a163194f.0b17c8","type":"ui_text_input","z":"259c8713.b50e28","name":"sample_project","label":"Name of the project*","tooltip":"","group":"3e1ba03d.f01d8","order":1,"width":12,"height":1,"passthru":true,"mode":"text","delay":300,"topic":"sample_project","x":1360,"y":60,"wires":[["1c2c7439.47115c"]]},{"id":"914752eb.af1b","type":"ui_text_input","z":"259c8713.b50e28","name":"sample_id","label":"ID of the station*","tooltip":"","group":"3e1ba03d.f01d8","order":2,"width":12,"height":1,"passthru":true,"mode":"number","delay":300,"topic":"sample_id","x":1370,"y":100,"wires":[["30648de6.8ebc52"]]},{"id":"8a735175.23927","type":"ui_date_picker","z":"259c8713.b50e28","name":"acq_date","label":"Date :","group":"52159161.72187","order":2,"width":12,"height":1,"passthru":true,"topic":"","x":1380,"y":1141,"wires":[["86aa9817.45a2e8"]]},{"id":"16d7de1c.b0c892","type":"ui_text_input","z":"259c8713.b50e28","name":"acq_time","label":"Time :","tooltip":"","group":"52159161.72187","order":3,"width":12,"height":1,"passthru":true,"mode":"time","delay":300,"topic":"","x":1380,"y":1181,"wires":[["9b1b260f.e4b338"]]},{"id":"9b1b260f.e4b338","type":"function","z":"259c8713.b50e28","name":"set object_time","func":"var time = new Date(msg.payload);\n\nvar hour = time.getUTCHours();\nif (hour<10){hour = \"0\"+hour;}\nvar minute = time.getUTCMinutes();\nif (minute<10){minute = \"0\"+minute;}\n\nvar time_UTC = \"\"+hour+minute+\"00\";\nglobal.set('object_time',time_UTC);\nreturn msg;","outputs":1,"noerr":0,"x":1544,"y":1181,"wires":[["829cc940.327648"]]},{"id":"86aa9817.45a2e8","type":"function","z":"259c8713.b50e28","name":"set object_date","func":"var date = new Date(msg.payload);\n\nvar year = date.getUTCFullYear();\nvar month = date.getUTCMonth()+1;\nif (month<10){month = \"0\"+month;}\nvar day = date.getUTCDate();\nif (day<10){day = \"0\"+day;}\n\nvar date_UTC = \"\"+year+month+day;\nglobal.set('object_date',date_UTC);\n\nreturn msg;","outputs":1,"noerr":0,"x":1544,"y":1141,"wires":[["c93577b9.a1e438"]]},{"id":"e001a28.555566","type":"function","z":"259c8713.b50e28","name":"get global","func":"msg.payload={\n \n \"generic_nb_step\":global.get(\"generic_nb_step\"),\n \"generic_flowrate\":global.get(\"generic_flowrate\"),\n \"generic_manual_volume\":global.get(\"generic_manual_volume\"),\n \"generic_sleep_before\":global.get(\"generic_sleep_before\"),\n \"generic_volume_before\":global.get(\"generic_volume_before\"),\n \"generic_path\":global.get(\"generic_path\"),\n \"generic_nb_frame\":global.get(\"generic_nb_frame\"),\n \"generic_sleep_during\":global.get(\"generic_sleep_during\"),\n \n \"sample_project\":global.get(\"sample_project\"),\n \"sample_id\":global.get(\"sample_id\"),\n \"sample_ship\":global.get(\"sample_ship\"),\n \"sample_operator\":global.get(\"sample_operator\"),\n \"sample_sampling_gear\":global.get(\"sample_sampling_gear\"),\n \n \"acq_id\":global.get(\"acq_id\"),\n \"acq_instrument\":global.get(\"acq_instrument\"),\n //\"acq_instrument_id\":global.get(\"acq_instrument_id\"),\n \"acq_celltype\":global.get(\"acq_celltype\"),\n \"acq_minimum_mesh\":global.get(\"acq_minimum_mesh\"),\n \"acq_maximum_mesh\":global.get(\"acq_maximum_mesh\"),\n \"acq_min_esd\":global.get(\"acq_min_esd\"),\n \"acq_max_esd\":global.get(\"acq_max_esd\"),\n \"acq_volume\":global.get(\"acq_volume\"),\n \"acq_magnification\":global.get(\"magnification\"),\n \"acq_fnumber_objective\":global.get(\"acq_fnumber_objective\"),\n \n \"acq_camera_name\":\"Pi Camera V2.1 - 8MP\",\n \n \"object_date\":global.get(\"object_date\"),\n \"object_time\":global.get(\"object_time\"),\n \"object_lat\":global.get(\"object_lat\"),\n \"object_lon\":global.get(\"object_lon\"),\n \"object_depth_min\":global.get(\"object_depth_min\"),\n \"object_depth_max\":global.get(\"object_depth_max\"),\n \n \"process_pixel\":global.get(\"process_pixel\"),\n \"process_id\":global.get(\"process_id\")\n \n};\nreturn msg;","outputs":1,"noerr":0,"x":1880,"y":60,"wires":[["76a6e6bb.a08b98"]]},{"id":"f25890f5.f2549","type":"file","z":"259c8713.b50e28","name":"","filename":"/home/pi/PlanktonScope/config.txt","appendNewline":true,"createDir":true,"overwriteFile":"true","encoding":"none","x":2233,"y":60,"wires":[[]]},{"id":"f5c1aa13.3cfbf8","type":"function","z":"259c8713.b50e28","name":"set optical config","func":"global.set(msg.topic,msg.payload);\nvar acq_fnumber_objective = String(global.get(msg.topic));\n\nswitch(acq_fnumber_objective) {\n case \"25\":\n global.set(\"magnification\",0.6);\n global.set(\"process_pixel\",1.86);\n global.set(\"sug_min\",60);\n global.set(\"sug_max\",670);\n global.set(\"sug_flowrate\",3);\n break;\n case \"16\":\n global.set(\"magnification\",0.94);\n global.set(\"process_pixel\",1.19);\n global.set(\"sug_min\",40);\n global.set(\"sug_max\",430);\n global.set(\"sug_flowrate\",2.4);\n break;\n case \"12\":\n global.set(\"magnification\",1.20);\n global.set(\"process_pixel\",0.94);\n global.set(\"sug_min\",30);\n global.set(\"sug_max\",340);\n global.set(\"sug_flowrate\",1.25);\n break;\n case \"8\":\n global.set(\"magnification\",1.78);\n global.set(\"process_pixel\",0.63);\n global.set(\"sug_min\",20);\n global.set(\"sug_max\",230);\n global.set(\"sug_flowrate\",0.42);\n break;\n case \"6\":\n global.set(\"magnification\",2.36);\n global.set(\"process_pixel\",0.48);\n global.set(\"sug_min\",15);\n global.set(\"sug_max\",170);\n global.set(\"sug_flowrate\",0.32);\n break;\n}\nreturn msg;","outputs":1,"noerr":0,"x":1550,"y":1041,"wires":[["72e1e23b.a8a67c"]]},{"id":"eb9181d8.25e01","type":"ui_dropdown","z":"259c8713.b50e28","name":"acq_fnumber_objective","label":"M12 Lens*","tooltip":"","place":"Select option","group":"52159161.72187","order":7,"width":12,"height":1,"passthru":true,"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","x":1326,"y":1041,"wires":[["f5c1aa13.3cfbf8"]]},{"id":"5aba848a.7a861c","type":"ui_numeric","z":"259c8713.b50e28","name":"acq_minimum_mesh","label":"Min fraction size (μm)","tooltip":"","group":"52159161.72187","order":8,"width":12,"height":1,"wrap":false,"passthru":true,"topic":"acq_minimum_mesh","format":"{{value}}","min":0,"max":"300","step":"10","x":1336,"y":841,"wires":[["510bd72a.b42ea8"]]},{"id":"7cea16e.c42ace8","type":"ui_numeric","z":"259c8713.b50e28","name":"acq_maximum_mesh","label":"Max fraction size (μm)","tooltip":"","group":"52159161.72187","order":9,"width":12,"height":1,"wrap":false,"passthru":true,"topic":"acq_maximum_mesh","format":"{{value}}","min":"200","max":"2000","step":"100","x":1336,"y":881,"wires":[["a3f18257.8a55e"]]},{"id":"6ecc9468.0271dc","type":"ui_text_input","z":"259c8713.b50e28","name":"acq_id","label":"Acquisition unique ID*","tooltip":"","group":"52159161.72187","order":1,"width":0,"height":0,"passthru":true,"mode":"number","delay":300,"topic":"acq_id","x":1386,"y":721,"wires":[["b26183bf.aa217"]]},{"id":"259fd49a.160a3c","type":"ui_dropdown","z":"259c8713.b50e28","name":"acq_celltype","label":"Thickness flowcell*","tooltip":"","place":"Select option","group":"52159161.72187","order":6,"width":12,"height":1,"passthru":true,"options":[{"label":"200 μm µ-Slide I Luer","value":200,"type":"num"},{"label":"400 μm µ-Slide I Luer","value":400,"type":"num"},{"label":"600 μm µ-Slide I Luer","value":600,"type":"num"},{"label":"800 μm µ-Slide I 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If your acquisition differ for each sample you must have different identifier.\n acq_instrument [t] : name of the instrument (UVP, ZOOSCAN, FLOWCAM, etc.)\n acq_*** [f] or [t] : other fields relative to the acquisition\n","x":800,"y":720,"wires":[]},{"id":"734ba3db.3f82fc","type":"comment","z":"259c8713.b50e28","name":"object","info":"OBJECT: one object to be classified, usually one organism. One object can be represented by several images. In this tsv file, there is one line per image which means the object data gets repeated on several lines.\n\n object_id [t] : unique object name (will be displayed in Ecotaxa object page)\n object_link [f] : URL of an associated website\n object_lat [f] : latitude, decimal degrees\n object_lon [f] : longitude, decimal degrees\n object_date [f] : ISO8601 YYYYMMJJ UTC\n object_time [f] : ISO8601 HHMMSS UTC\n object_depth_min [f] : minimum depth of object, meters\n object_depth_max [f] : maximum depth of object, meters\n\nAnd, for already classified objects\n\n object_annotation_date [t] : ISO8601 YYYYMMJJ UTC\n object_annotation_time [t] : ISO8601 YYYYMMJJ UTC\n object_annotation_category [t] : class of the object with optionnaly its direct parent following separated by left angle bracket without whitespace \"Cnidaria","storeOutMessages":true,"fwdInMessages":true,"templateScope":"local","x":1210,"y":300,"wires":[[]]},{"id":"b7d9455c.026588","type":"switch","z":"259c8713.b50e28","name":"","property":"topic","propertyType":"msg","rules":[{"t":"eq","v":"actuator/focus","vt":"str"},{"t":"eq","v":"Missing entry :","vt":"str"}],"checkall":"true","repair":false,"outputs":2,"x":1670,"y":400,"wires":[["fdb3b132.8b341"],["b9d996d6.37c2f8"]]},{"id":"b9d996d6.37c2f8","type":"ui_toast","z":"259c8713.b50e28","position":"dialog","displayTime":"3","highlight":"","sendall":true,"outputs":1,"ok":"OK","cancel":"","raw":false,"topic":"","name":"","x":1830,"y":420,"wires":[[]]},{"id":"ca38a11d.0ee54","type":"function","z":"259c8713.b50e28","name":"init LED","func":"msg.payload=1;\nreturn msg;","outputs":1,"noerr":0,"x":240,"y":161,"wires":[["1d58e86f.a3a9e8"]]},{"id":"75701b99.c6e974","type":"exec","z":"259c8713.b50e28","command":"vcgencmd measure_temp | tr -d \"temp=\" | tr -d \"'C\" | tr -d 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config.txt","info":"","x":1690,"y":20,"wires":[]},{"id":"72e1e23b.a8a67c","type":"link out","z":"259c8713.b50e28","name":"","links":["7532db82.1dcf04","d473399b.081ae8"],"x":1675,"y":1040,"wires":[]},{"id":"d473399b.081ae8","type":"link in","z":"259c8713.b50e28","name":"","links":["72e1e23b.a8a67c","c93577b9.a1e438","829cc940.327648"],"x":1635,"y":100,"wires":[["e001a28.555566"]]},{"id":"c93577b9.a1e438","type":"link out","z":"259c8713.b50e28","name":"","links":["7532db82.1dcf04","d473399b.081ae8"],"x":1675,"y":1140,"wires":[]},{"id":"829cc940.327648","type":"link out","z":"259c8713.b50e28","name":"","links":["7532db82.1dcf04","d473399b.081ae8"],"x":1675,"y":1180,"wires":[]},{"id":"98e2e9e0.fb7418","type":"switch","z":"259c8713.b50e28","name":"","property":"topic","propertyType":"msg","rules":[{"t":"eq","v":"actuator/pump","vt":"str"},{"t":"eq","v":"Missing entry :","vt":"str"}],"checkall":"true","repair":false,"outputs":2,"x":1670,"y":600,"wires":[["61fb057d.3c251c"],["46a536f0.c83138"]]},{"id":"46a536f0.c83138","type":"ui_toast","z":"259c8713.b50e28","position":"dialog","displayTime":"3","highlight":"","sendall":true,"outputs":1,"ok":"OK","cancel":"","raw":false,"topic":"","name":"","x":1830,"y":620,"wires":[[]]},{"id":"24ffcf03.2a51b","type":"ui_button","z":"259c8713.b50e28","name":"stop pump","group":"707d9797.c8e798","order":5,"width":4,"height":1,"passthru":true,"label":"STOP PUMP","tooltip":"","color":"","bgcolor":"#AD1625","icon":"","payload":"off","payloadType":"str","topic":"actuator/wait","x":1370,"y":660,"wires":[["e2a7220a.09d43"]]},{"id":"7eb16c3b.294e54","type":"comment","z":"259c8713.b50e28","name":"turn ON the LED","info":"","x":260,"y":121,"wires":[]},{"id":"4f74f017.00a58","type":"function","z":"259c8713.b50e28","name":"focus.js","func":"state = global.get(\"state\");\n\nif (state == null){state=\"free\"}\n\nvar nb_step= global.get(\"nb_step\");\n\nif (nb_step === undefined || nb_step === \"\" || nb_step === null) {\n msg.topic = \"Missing entry :\"\n msg.payload = \"Number of steps\";\n \n}else {\n nb_step= global.get(\"nb_step\");\n if(msg.payload === \"UP\" & state===\"free\"){\n msg.payload=\"FORWARD \"+nb_step;\n }\n if(msg.payload === \"DOWN\" & state===\"free\"){\n msg.payload=\"BACKWARD \"+nb_step;\n }\n}\nreturn msg;","outputs":1,"noerr":0,"x":1520,"y":400,"wires":[["b7d9455c.026588"]],"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":"52cc1de5.b78e84","type":"ui_button","z":"259c8713.b50e28","name":"stop focus","group":"fbd92986.1028c8","order":5,"width":4,"height":1,"passthru":true,"label":"STOP FOCUS","tooltip":"","color":"","bgcolor":"#AD1625","icon":"","payload":"off","payloadType":"str","topic":"actuator/wait","x":1370,"y":460,"wires":[["e46763fe.7fc83"]]},{"id":"39cad6fb.1503ca","type":"ui_button","z":"259c8713.b50e28","name":"","group":"c6a276ac.3eb74","order":1,"width":12,"height":1,"passthru":false,"label":"Reboot","tooltip":"","color":"","bgcolor":"#AD1625","icon":"","payload":"off","payloadType":"str","topic":"reboot","x":2620,"y":60,"wires":[["95b876d4.07c708","99d61fbe.b244b"]]},{"id":"1f53f29b.feee4d","type":"exec","z":"259c8713.b50e28","command":"sudo","addpay":true,"append":"","useSpawn":"false","timer":"2","oldrc":false,"name":"cmd","x":2930,"y":60,"wires":[[],[],[]]},{"id":"e325458b.95bff8","type":"ui_button","z":"259c8713.b50e28","name":"","group":"c6a276ac.3eb74","order":2,"width":12,"height":1,"passthru":false,"label":"Shutdown","tooltip":"","color":"","bgcolor":"#AD1625","icon":"","payload":"off","payloadType":"str","topic":"shutdown","x":2620,"y":120,"wires":[["95b876d4.07c708","99d61fbe.b244b"]]},{"id":"95b876d4.07c708","type":"python3-function","z":"259c8713.b50e28","name":"action","func":"#!/usr/bin/python\nimport smbus\nimport time\nbus = smbus.SMBus(1)\ntime.sleep(1)\n#turn off fan RGB\nbus.write_byte_data(0x0d, 0x07, 0x00)\nbus.write_byte_data(0x0d, 0x07, 0x00)\n\nmsg[\"payload\"] = str(msg[\"topic\"])+' now'\nreturn msg","outputs":1,"x":2790,"y":80,"wires":[["d348474b.d756a8","1f53f29b.feee4d"]]},{"id":"d348474b.d756a8","type":"exec","z":"259c8713.b50e28","command":"i2cdetect -y 1","addpay":false,"append":"","useSpawn":"false","timer":"1","oldrc":false,"name":"i2c update","x":2950,"y":120,"wires":[[],[],[]]},{"id":"99d61fbe.b244b","type":"link out","z":"259c8713.b50e28","name":"","links":["3517d063.27073"],"x":2735,"y":20,"wires":[]},{"id":"cdd1b550.da18e8","type":"mqtt in","z":"259c8713.b50e28","name":"","topic":"receiver/#","qos":"0","datatype":"auto","broker":"b77ffa1b.942258","x":720,"y":2000,"wires":[["6920281d.dc9b48"]]},{"id":"6920281d.dc9b48","type":"switch","z":"259c8713.b50e28","name":"","property":"topic","propertyType":"msg","rules":[{"t":"eq","v":"receiver/pump","vt":"str"},{"t":"eq","v":"receiver/focus","vt":"str"},{"t":"eq","v":"receiver/image","vt":"str"},{"t":"cont","v":"receiver/segmentation","vt":"str"}],"checkall":"true","repair":false,"outputs":4,"x":870,"y":2000,"wires":[["2f66e917.fee586"],["363ee47e.ed522c"],["45a52868.fe37c8"],["469cc189.903d"]]},{"id":"2f66e917.fee586","type":"switch","z":"259c8713.b50e28","name":"","property":"payload","propertyType":"msg","rules":[{"t":"eq","v":"Start","vt":"str"},{"t":"eq","v":"Done","vt":"str"},{"t":"eq","v":"Interrompted","vt":"str"}],"checkall":"true","repair":false,"outputs":3,"x":1050,"y":1800,"wires":[["5c0d0c35.3bcf14"],["cd01157d.0892d8"],["68e02bf4.7013e4"]]},{"id":"5c0d0c35.3bcf14","type":"change","z":"259c8713.b50e28","name":"The pump has started","rules":[{"t":"set","p":"payload","pt":"msg","to":"The pump has started","tot":"str"}],"action":"","property":"","from":"","to":"","reg":false,"x":1440,"y":1760,"wires":[[]]},{"id":"cd01157d.0892d8","type":"change","z":"259c8713.b50e28","name":"The pump has finished.","rules":[{"t":"set","p":"payload","pt":"msg","to":"The pump has finished.","tot":"str"}],"action":"","property":"","from":"","to":"","reg":false,"x":1430,"y":1800,"wires":[[]]},{"id":"68e02bf4.7013e4","type":"change","z":"259c8713.b50e28","name":"The pump has been stopped.","rules":[{"t":"set","p":"payload","pt":"msg","to":"The pump has been stopped.","tot":"str"}],"action":"","property":"","from":"","to":"","reg":false,"x":1420,"y":1840,"wires":[[]]},{"id":"363ee47e.ed522c","type":"switch","z":"259c8713.b50e28","name":"","property":"payload","propertyType":"msg","rules":[{"t":"eq","v":"Start","vt":"str"},{"t":"eq","v":"Done","vt":"str"},{"t":"eq","v":"Interrompted","vt":"str"}],"checkall":"true","repair":false,"outputs":3,"x":1050,"y":1920,"wires":[["c088b72f.326d98"],["36934381.14442c"],["89329cfe.c8f4"]]},{"id":"c088b72f.326d98","type":"change","z":"259c8713.b50e28","name":"The focus has started","rules":[{"t":"set","p":"payload","pt":"msg","to":"The focus has started","tot":"str"}],"action":"","property":"","from":"","to":"","reg":false,"x":1440,"y":1880,"wires":[[]]},{"id":"36934381.14442c","type":"change","z":"259c8713.b50e28","name":"The focus has finished.","rules":[{"t":"set","p":"payload","pt":"msg","to":"The focus has 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out","z":"259c8713.b50e28","name":"","topic":"","qos":"","retain":"","broker":"cb2f36fe.1c7038","x":1510,"y":660,"wires":[]},{"id":"577f7f72.6b68b","type":"ui_button","z":"259c8713.b50e28","name":"","group":"8cfadfab.327d7","order":7,"width":19,"height":1,"passthru":false,"label":"Start Acquisition","tooltip":"","color":"","bgcolor":"","icon":"","payload":"","payloadType":"str","topic":"actuator/image","x":1360,"y":1660,"wires":[["5218ba30.bbe844"]]},{"id":"d5111b87.2a64a8","type":"ui_text_input","z":"259c8713.b50e28","name":"generic_sleep_before","label":"Sleep duration before acquisition (s)","tooltip":"","group":"8cfadfab.327d7","order":1,"width":12,"height":1,"passthru":true,"mode":"number","delay":300,"topic":"generic_sleep_before","x":1340,"y":1360,"wires":[["3d141631.d548ba"]]},{"id":"3d141631.d548ba","type":"link out","z":"259c8713.b50e28","name":"","links":["7532db82.1dcf04"],"x":1475,"y":1360,"wires":[]},{"id":"74c89905.79d968","type":"ui_text_input","z":"259c8713.b50e28","name":"generic_sleep_during","label":"Sleep duration between acquisition (s)","tooltip":"","group":"8cfadfab.327d7","order":2,"width":12,"height":1,"passthru":true,"mode":"number","delay":300,"topic":"generic_sleep_during","x":1340,"y":1520,"wires":[["644e95b9.04b7ac"]]},{"id":"644e95b9.04b7ac","type":"link out","z":"259c8713.b50e28","name":"","links":["7532db82.1dcf04"],"x":1475,"y":1520,"wires":[]},{"id":"b50cf2f4.bfb84","type":"link out","z":"259c8713.b50e28","name":"","links":["7532db82.1dcf04"],"x":1475,"y":501,"wires":[]},{"id":"1e75fd6c.234753","type":"ui_slider","z":"259c8713.b50e28","name":"flowrate","label":"Flowrate (ml/min)*","tooltip":"","group":"707d9797.c8e798","order":1,"width":0,"height":0,"passthru":true,"outs":"end","topic":"flowrate","min":0,"max":"20","step":"0.1","x":1380,"y":501,"wires":[["b50cf2f4.bfb84"]]},{"id":"3345fc41.8341b4","type":"function","z":"259c8713.b50e28","name":"get generic.flowrate","func":"msg.payload = msg.payload.generic_flowrate;\nreturn msg;","outputs":1,"noerr":0,"x":1030,"y":501,"wires":[["1e75fd6c.234753"]]},{"id":"32510458.f42f9c","type":"link in","z":"259c8713.b50e28","name":"","links":["b368cae7.dd66b8"],"x":895,"y":501,"wires":[["3345fc41.8341b4"]]},{"id":"3cd0a17b.0cc42e","type":"link out","z":"259c8713.b50e28","name":"","links":["7532db82.1dcf04"],"x":1475,"y":1440,"wires":[]},{"id":"62fea790.2840a8","type":"ui_text_input","z":"259c8713.b50e28","name":"generic_path","label":"DIrectory to store the images","tooltip":"","group":"8cfadfab.327d7","order":3,"width":12,"height":1,"passthru":true,"mode":"text","delay":300,"topic":"generic_path","x":1370,"y":1440,"wires":[["3cd0a17b.0cc42e"]]},{"id":"73e051a8.5875e","type":"ui_text_input","z":"259c8713.b50e28","name":"generic_volume_before","label":"Volume to pass before to begin","tooltip":"","group":"8cfadfab.327d7","order":5,"width":12,"height":1,"passthru":true,"mode":"number","delay":300,"topic":"generic_volume_before","x":1330,"y":1400,"wires":[["5ea01613.8cc9d8"]]},{"id":"5ea01613.8cc9d8","type":"link out","z":"259c8713.b50e28","name":"","links":["7532db82.1dcf04"],"x":1475,"y":1400,"wires":[]},{"id":"26549e4b.5dbf72","type":"ui_text_input","z":"259c8713.b50e28","name":"generic_nb_frame","label":"Number of frame per acquisition","tooltip":"","group":"8cfadfab.327d7","order":4,"width":12,"height":1,"passthru":true,"mode":"number","delay":300,"topic":"generic_nb_frame","x":1350,"y":1480,"wires":[["61382d0b.60c534"]]},{"id":"61382d0b.60c534","type":"link out","z":"259c8713.b50e28","name":"","links":["7532db82.1dcf04"],"x":1475,"y":1480,"wires":[]},{"id":"d5df5489.6523e8","type":"function","z":"259c8713.b50e28","name":"get generic_sleep_before","func":"msg.payload = msg.payload.generic_sleep_before;\nreturn msg;","outputs":1,"noerr":0,"x":1050,"y":1360,"wires":[["d5111b87.2a64a8"]]},{"id":"835c262e.00b468","type":"link in","z":"259c8713.b50e28","name":"","links":["b368cae7.dd66b8"],"x":895,"y":1360,"wires":[["d5df5489.6523e8"]]},{"id":"9b2fe59b.be48c8","type":"function","z":"259c8713.b50e28","name":"get generic_volume_before","func":"msg.payload = msg.payload.generic_volume_before;\nreturn msg;","outputs":1,"noerr":0,"x":1060,"y":1400,"wires":[["73e051a8.5875e"]]},{"id":"a07dad70.7c48","type":"link 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msg.payload.generic_sleep_during;\nreturn msg;","outputs":1,"noerr":0,"x":1050,"y":1520,"wires":[["74c89905.79d968"]]},{"id":"3fa20f41.11e61","type":"link in","z":"259c8713.b50e28","name":"","links":["b368cae7.dd66b8"],"x":895,"y":1520,"wires":[["ce6ded0a.8ee37"]]},{"id":"5218ba30.bbe844","type":"function","z":"259c8713.b50e28","name":"image.js","func":"state = global.get(\"state\");\nglobal.set('img_counter',0)\nglobal.set('obj_counter',0)\nif (state == null){state=\"free\"}\n\nvar generic_sleep_before= global.get(\"generic_sleep_before\");\nvar generic_volume_before= global.get(\"generic_volume_before\");\nvar generic_path= global.get(\"generic_path\");\nvar generic_nb_frame= global.get(\"generic_nb_frame\");\nvar generic_sleep_during= global.get(\"generic_sleep_during\");\n\nif (generic_sleep_before === undefined || generic_sleep_before === \"\" || generic_sleep_before === null) {\n msg.topic = \"Missing entry :\"\n msg.payload = \"Duration before start the acquisition\";\n \n}else 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"order": 1, - "width": 0, - "height": 0, - "passthru": true, - "mode": "text", - "delay": 300, - "topic": "sample_project", - "x": 1160, - "y": 60, - "wires": [ - [ - "e17096e4.74caf8" - ] - ] - }, - { - "id": "75615576.3a38cc", - "type": "ui_text_input", - "z": "103f6179.d5012f", - "name": "sample_id", - "label": "ID of the station*", - "tooltip": "", - "group": "aac2eaf7.0cdab8", - "order": 2, - "width": 0, - "height": 0, - "passthru": true, - "mode": "number", - "delay": 300, - "topic": "sample_id", - "x": 1170, - "y": 140, - "wires": [ - [ - "e17096e4.74caf8" - ] - ] - }, - { - "id": "b77eb8b0.a222a8", - "type": "ui_date_picker", - "z": "103f6179.d5012f", - "name": "acq_date", - "label": "Date :", - "group": "aac2eaf7.0cdab8", - "order": 10, - "width": 0, - "height": 0, - "passthru": true, - "topic": "", - "x": 1176, - "y": 640, - "wires": [ - [ - "4fa687df.1aa1d8" - ] - ] - }, - { - "id": "86d5ed81.6dc99", - "type": "ui_text_input", - "z": "103f6179.d5012f", - "name": "acq_time", - "label": "Time :", - "tooltip": "", - "group": "aac2eaf7.0cdab8", - "order": 11, - "width": 0, - "height": 0, - "passthru": true, - "mode": "time", - "delay": 300, - "topic": "", - "x": 1176, - "y": 680, - "wires": [ - [ - "26461e30.b461b2" - ] - ] - }, - { - "id": "26461e30.b461b2", - "type": "function", - "z": "103f6179.d5012f", - "name": "set time global", - "func": "var time = new Date(msg.payload);\nglobal.set('generic_acq_time',time);\n\nvar hour = time.getUTCHours();\nif (hour<10){hour = \"0\"+hour;}\nvar minute = time.getUTCMinutes();\nif (minute<10){minute = \"0\"+minute;}\n\nvar time_UTC = \"\"+hour+minute+\"00\";\nglobal.set('object_time',time_UTC);\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 1396, - "y": 680, - "wires": [ - [ - "da16d746.4b12e8" - ] - ] - }, - { - "id": "4fa687df.1aa1d8", - "type": "function", - "z": "103f6179.d5012f", - "name": "set date global", - "func": "var date = new Date(msg.payload);\nglobal.set('generic_acq_date',date);\n\nvar year = date.getUTCFullYear();\nvar month = date.getUTCMonth()+1;\nif (month<10){month = \"0\"+month;}\nvar day = date.getUTCDate();\nif (day<10){day = \"0\"+day;}\n\nvar date_UTC = \"\"+year+month+day;\nglobal.set('object_date',date_UTC);\n\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 1396, - "y": 640, - "wires": [ - [ - "da16d746.4b12e8" - ] - ] - }, - { - "id": "da16d746.4b12e8", - "type": "function", - "z": "103f6179.d5012f", - "name": "get global", - "func": "msg.payload={\n generic:{\n \"generic_sample_date\":global.get(\"generic_sample_date\"),\n \"generic_sample_time\":global.get(\"generic_sample_time\"),\n \"generic_acq_date\":global.get(\"generic_acq_date\"),\n \"generic_acq_time\":global.get(\"generic_acq_time\")\n },\n sample:{\n \"sample_id\":global.get(\"sample_id\"),\n \"sample_date\":global.get(\"sample_date\"),\n \"sample_time\":global.get(\"sample_time\"),\n \"sample_operator\":global.get(\"sample_operator\"),\n \"sample_project\":global.get(\"sample_project\"),\n \"sample_sampling_gear\":global.get(\"sample_sampling_gear\")\n },\n acquisition:{\n \"acq_id\":global.get(\"acq_id\"),\n \"acq_celltype\":global.get(\"acq_celltype\"),\n \"acq_fnumber_objective\":global.get(\"acq_fnumber_objective\"),\n \"acq_instrument\":global.get(\"acq_instrument\"),\n \"acq_minimum_mesh\":global.get(\"acq_minimum_mesh\"),\n \"acq_maximum_mesh\":global.get(\"acq_maximum_mesh\"),\n \"acq_volume\":global.get(\"acq_volume\"),\n \"acq_magnification\":global.get(\"magnification\")\n },\n object:{\n \"object_date\":global.get(\"object_date\"),\n \"object_time\":global.get(\"object_time\"),\n \"object_depth_min\":global.get(\"object_depth_min\"),\n \"object_depth_max\":global.get(\"object_depth_max\")\n \n },\n process:{\n //PROCESS\n \"process_pixel\":global.get(\"process_pixel\"),\n \"process_id\":global.get(\"process_id\")\n }\n};\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 1693, - "y": 60, - "wires": [ - [ - "28df8fd6.06fb7" - ] - ] - }, - { - "id": "6dd1657e.c52e4c", - "type": "file", - "z": "103f6179.d5012f", - "name": "", - "filename": "/home/pi/PlanktonScope/log/config.txt", - "appendNewline": true, - "createDir": true, - "overwriteFile": "true", - "encoding": "none", - "x": 2043, - "y": 60, - "wires": [ - [] - ] - }, - { - "id": "3a43748d.52464c", - "type": "function", - "z": "103f6179.d5012f", - "name": "set optical config", - "func": "global.set(msg.topic,msg.payload);\nvar acq_fnumber_objective = String(global.get(msg.topic));\n\nswitch(acq_fnumber_objective) {\n case \"25\":\n global.set(\"magnification\",0.6);\n global.set(\"process_pixel\",1.86);\n global.set(\"sug_min\",60);\n global.set(\"sug_max\",670);\n global.set(\"sug_flowrate\",3);\n break;\n case \"16\":\n global.set(\"magnification\",0.94);\n global.set(\"process_pixel\",1.19);\n global.set(\"sug_min\",40);\n global.set(\"sug_max\",430);\n global.set(\"sug_flowrate\",2.4);\n break;\n case \"12\":\n global.set(\"magnification\",1.20);\n global.set(\"process_pixel\",0.94);\n global.set(\"sug_min\",30);\n global.set(\"sug_max\",340);\n global.set(\"sug_flowrate\",1.25);\n break;\n case \"8\":\n global.set(\"magnification\",1.78);\n global.set(\"process_pixel\",0.63);\n global.set(\"sug_min\",20);\n global.set(\"sug_max\",230);\n global.set(\"sug_flowrate\",0.42);\n break;\n case \"6\":\n global.set(\"magnification\",2.36);\n global.set(\"process_pixel\",0.48);\n global.set(\"sug_min\",15);\n global.set(\"sug_max\",170);\n global.set(\"sug_flowrate\",0.32);\n break;\n}\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 1386, - "y": 720, - "wires": [ - [ - "da16d746.4b12e8" - ] - ] - }, - { - "id": "ff1b2069.b8273", - "type": "ui_dropdown", - "z": "103f6179.d5012f", - "name": "acq_fnumber_objective", - "label": "M12 Lens*", - "tooltip": "", - "place": "Select option", - "group": "aac2eaf7.0cdab8", - "order": 15, - "width": 0, - "height": 0, - "passthru": true, - "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", - "x": 1126, - "y": 720, - "wires": [ - [ - "3a43748d.52464c" - ] - ] - }, - { - "id": "4d38113f.08c6d", - "type": "ui_numeric", - "z": "103f6179.d5012f", - "name": "acq_minimum_mesh", - "label": "Min fraction size (μm)", - "tooltip": "", - "group": "aac2eaf7.0cdab8", - "order": 16, - "width": 0, - "height": 0, - "wrap": false, - "passthru": true, - "topic": "acq_minimum_mesh", - "format": "{{value}}", - "min": 0, - "max": "300", - "step": "10", - "x": 1136, - "y": 520, - "wires": [ - [ - "d911efe0.ea7f1" - ] - ] - }, - { - "id": "220c7464.306a8c", - "type": "ui_numeric", - "z": "103f6179.d5012f", - "name": "acq_maximum_mesh", - "label": "Max fraction size (μm)", - "tooltip": "", - "group": "aac2eaf7.0cdab8", - "order": 17, - "width": 0, - "height": 0, - "wrap": false, - "passthru": true, - "topic": "acq_maximum_mesh", - "format": "{{value}}", - "min": "200", - "max": "2000", - "step": "100", - "x": 1136, - "y": 560, - "wires": [ - [ - "d911efe0.ea7f1" - ] - ] - }, - { - "id": "c3b1ab59.484178", - "type": "ui_text_input", - "z": "103f6179.d5012f", - "name": "acq_id", - "label": "Acquisition unique ID*", - "tooltip": "", - "group": "aac2eaf7.0cdab8", - "order": 9, - "width": 0, - "height": 0, - "passthru": true, - "mode": "number", - "delay": 300, - "topic": "acq_id", - "x": 1186, - "y": 400, - "wires": [ - [ - "d911efe0.ea7f1" - ] - ] - }, - { - "id": "3bb0adb4.de5412", - "type": "ui_dropdown", - "z": "103f6179.d5012f", - "name": "acq_celltype", - "label": "Thickness flowcell*", - "tooltip": "", - "place": "Select option", - "group": "aac2eaf7.0cdab8", - "order": 13, - "width": 0, - "height": 0, - "passthru": true, - "options": [ - { - "label": "200 μm µ-Slide I Luer", - "value": 200, - "type": "num" - }, - { - "label": "400 μm µ-Slide I Luer", - "value": 400, - "type": "num" - }, - { - "label": "600 μm µ-Slide I Luer", - "value": 600, - "type": "num" - }, - { - "label": "800 μm µ-Slide I Luer", - "value": 800, - "type": "num" - } - ], - "payload": "", - "topic": "acq_celltype", - "x": 1166, - "y": 480, - "wires": [ - [ - "d911efe0.ea7f1" - ] - ] - }, - { - "id": "c19a2c73.7512f", - "type": "ui_text_input", - "z": "103f6179.d5012f", - "name": "acq_volume", - "label": "Volume to pass (ml)", - "tooltip": "", - "group": "aac2eaf7.0cdab8", - "order": 14, - "width": 0, - "height": 0, - "passthru": true, - "mode": "number", - "delay": 300, - "topic": "acq_volume", - "x": 1166, - "y": 600, - "wires": [ - [ - "d911efe0.ea7f1" - ] - ] - }, - { - "id": "c9b2c48c.40d068", - "type": "comment", - "z": "103f6179.d5012f", - "name": "sample", - "info": "SAMPLE: a collection event\n\n sample_id [t] : unique identifier\n sample_*** [f] or [t] : other fields relative to the sample\n", - "x": 990, - "y": 20, - "wires": [] - }, - { - "id": "8abc2578.2ebcf8", - "type": "comment", - "z": "103f6179.d5012f", - "name": "acquisition", - "info": "ACQUISITION: metadata relative to the image acquisition\n\n acq_id [t] : unique identifier. If your acquisition differ for each sample you must have different identifier.\n acq_instrument [t] : name of the instrument (UVP, ZOOSCAN, FLOWCAM, etc.)\n acq_*** [f] or [t] : other fields relative to the acquisition\n", - "x": 996, - "y": 360, - "wires": [] - }, - { - "id": "91ab2c80.0f453", - "type": "comment", - "z": "103f6179.d5012f", - "name": "object", - "info": "OBJECT: one object to be classified, usually one organism. One object can be represented by several images. In this tsv file, there is one line per image which means the object data gets repeated on several lines.\n\n object_id [t] : unique object name (will be displayed in Ecotaxa object page)\n object_link [f] : URL of an associated website\n object_lat [f] : latitude, decimal degrees\n object_lon [f] : longitude, decimal degrees\n object_date [f] : ISO8601 YYYYMMJJ UTC\n object_time [f] : ISO8601 HHMMSS UTC\n object_depth_min [f] : minimum depth of object, meters\n object_depth_max [f] : maximum depth of object, meters\n\nAnd, for already classified objects\n\n object_annotation_date [t] : ISO8601 YYYYMMJJ UTC\n object_annotation_time [t] : ISO8601 YYYYMMJJ UTC\n object_annotation_category [t] : class of the object with optionnaly its direct parent following separated by left angle bracket without whitespace \"Cnidaria