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For +the avoidance of doubt, this paragraph does not form part of the public +licenses. + +Creative Commons may be contacted at creativecommons.org. diff --git a/README.md b/README.md index 9020ab0..d5ef8a9 100644 --- a/README.md +++ b/README.md @@ -1,602 +1,36 @@ -# PlanktoScop Main Repository -The PlanktoScop is an open and affordable modular imaging platform for citizen oceanography. +# An open and affordable imaging platform for citizen oceanography -This GitHub is part of a community that you can find on [its website](https://www.planktonscope.org/). +![PlanktoScope Render](docs/readme/planktoscope_cad.webp) -# Fast Setup +![Plankton collage](docs/readme/plankton_collage.webp) -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. +# What is this? +The PlanktoScope is an open-source, affordable imaging platform for citizen oceanography. It's built around a Raspberry Pi, a couple of HATs, some stepper motors and a few centimeters of silicon tubes. Its cost is at about $500 in parts. -## Install and setup Raspbian on your Raspberry Pi +The goal of the PlanktoScope is to allow citizen to engage in scientific programs, either at sea or onshore. You can use the PlanktoScope to image the different species of Plankton living in a body of water. -### 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 +## Get the papers! +The PlanktoScope has been described in a paper available on the [bioRxiv preprint server](https://www.biorxiv.org/content/10.1101/2020.04.23.056978v1). The first results of this program and its outline are also available as a [preprint](https://www.biorxiv.org/content/10.1101/2020.08.31.263442v1). -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. +|[![PlanktoScope Preprint](docs/readme/planktoscope_pub.webp)](https://www.biorxiv.org/content/10.1101/2020.04.23.056978v1)|[![PlanktonPlanet Preprint](docs/readme/planktonplanet_pub.webp)](https://www.biorxiv.org/content/10.1101/2020.08.31.263442v1)| +|--------|--------| -#### Writing an image to the SD card -Download the latest version of [balenaEtcher](https://www.balena.io/etcher/) and install it. +# Key Features +- Image small animals and algae living in water +- Focus stage control +- Pump control +- Automatic image capture +- Automatic segmentation -Connect an SD card reader with the micro SD card inside. +# How do I build one? +You can access the complete documentation on [Read The Docs](https://planktonscope.readthedocs.io/). -Open balenaEtcher and select from your hard drive the image zip file you just downloaded. +# How do I get involved? +There are several ways to join the development effort, share your progress with your build or just ask for help. -Select the SD card you want to write your image to. +We are using slack as a communication platform between interested parties. You can [request to join by filling this form](https://forms.gle/4JnziFjVgjq56aT17). -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 or connect via ssh to the Raspberry, and type in 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 - -### Enable Camera/SSH/I2C in raspi-config - -You can 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! -``` - -Also, to make sure the wiring is good, we are going to use `sudo i2cdetect -y 1` to see if our devices are detected: -``` -pi@planktoscope:~ $ sudo i2cdetect -y 1 - 0 1 2 3 4 5 6 7 8 9 a b c d e f -00: -- -- -- -- -- -- -- -- -- -- 0d -- -- -10: -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -20: -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -30: -- -- -- -- -- -- -- -- -- -- -- -- 3c -- -- -- -40: -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -50: -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -60: 60 -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -70: 70 -- -- -- -- -- -- -- -``` - -The device appearing at addresses 60 and 70 is our motor controller. Address `0d` is the fan controller and `3c` is the oled screen (we'll set up both a bit further down). Your version of the RGB Cooling Hat may not have the screen, it's fine as the screen is not necessary for proper operation of the Planktoscope. - -In case the motor controller does not appear, shutdown your Planktoscope and check the wiring. If your board is using a connector instead of a soldered pin connection (as happens with the Adafruit Bonnet Motor Controller), sometimes the pins on the male side need to be bent a little to make good contact. In any case, do not hesitate to ask for help in Slack. - -### 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 -``` - -Change the autostart setting to No, and then 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 now 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). - -We are going to use gpsd to parse the GPS data. We need to set it up by editing `/etc/default/gpsd`. This file is source just before starting gpsd and allows to configure its working. -```sh -sudo nano /etc/default/gpsd -``` - -Change the `USB_AUTO` line to read `false` -```sh -USBAUTO="false" -``` - -Also change the `DEVICES` line to add the device we are going to use `/dev/serial0`: -```sh -DEVICES="/dev/serial0" -``` - -Finally, we want to add the parameter `-n` to `GPSD_OPTIONS`: -```sh -GPSD_OPTIONS="-n" -``` - -Save your work, and restart gpsd by running the following: -```sh -sudo systemctl restart gpsd.service -``` - -If you wait a bit, you can run `gpsmon` to check that your configuration is correct. You should get an output similar to this: -``` -pi@planktoscope:~ $ gpsmon -/dev/serial0 NMEA0183> -┌──────────────────────────────────────────────────────────────────────────────┐ -│Time: 2020-07-21T11:09:26.000Z Lat: 45 33' 28.08539" Non: 1 03' 44.02019" W│ -└───────────────────────────────── Cooked TPV ─────────────────────────────────┘ -┌──────────────────────────────────────────────────────────────────────────────┐ -│ GPGGA GPGSA GPRMC GPZDA GPGSV │ -└───────────────────────────────── Sentences ──────────────────────────────────┘ -┌──────────────────┐┌────────────────────────────┐┌────────────────────────────┐ -│Ch PRN Az El S/N ││Time: 110926.000 ││Time: 110927.000 │ -│ 0 27 351 78 49 ││Latitude: 4533.4809 N ││Latitude: 4533.4809 │ -│ 1 21 51 69 47 ││Longitude: 00103.7367 W ││Longitude: 00103.7367 │ -│ 2 16 184 61 43 ││Speed: 0.00 ││Altitude: -0.1 │ -│ 3 10 116 51 50 ││Course: 201.75 ││Quality: 2 Sats: 11 │ -│ 4 8 299 47 49 ││Status: A FAA: D ││HDOP: 0.87 │ -│ 5 20 66 42 46 ││MagVar: ││Geoid: 49.3 │ -│ 6 123 138 28 43 │└─────────── RMC ────────────┘└─────────── GGA ────────────┘ -│ 7 26 165 25 30 │┌────────────────────────────┐┌────────────────────────────┐ -│ 8 11 264 23 48 ││Mode: A3 ...s: 27 21 16 10 ││UTC: RMS: │ -│ 9 7 303 15 38 ││DOP: H=0.87 V=1.13 P=1.42 ││MAJ: MIN: │ -│10 18 56 14 44 ││TOFF: 0.530187817 ││ORI: LAT: │ -│11 30 330 5 35 ││PPS: ││LON: ALT: │ -└────── GSV ───────┘└──────── GSA + PPS ─────────┘└─────────── GST ────────────┘ -(42) $GPGSV,4,4,14,15,03,035,36,01,02,238,*72 -(72) $GPRMC,110922.000,A,4533.4809,N,00103.7366,W,0.01,322.19,210720,,,D*7E -(35) $GPZDA,110922.000,21,07,2020,,*5B -(81) $GPGGA,110923.000,4533.4809,N,00103.7367,W,2,11,0.87,-0.1,M,49.3,M,0000,0000*5B -(64) $GPGSA,A,3,16,27,30,10,18,21,20,08,11,07,26,,1.43,0.87,1.13*0B -(72) $GPRMC,110923.000,A,4533.4809,N,00103.7367,W,0.01,188.90,210720,,,D*7D -(35) $GPZDA,110923.000,21,07,2020,,*5A -(81) $GPGGA,110924.000,4533.4809,N,00103.7367,W,2,11,0.87,-0.1,M,49.3,M,0000,0000*5C -(64) $GPGSA,A,3,16,27,30,10,18,21,20,08,11,07,26,,1.43,0.87,1.13*0B -(72) $GPRMC,110924.000,A,4533.4809,N,00103.7367,W,0.01,156.23,210720,,,D*71 -``` - -#### Bonus Configuration: Automatic time update from GPSD - -The Adafruit GPS HAT allows your PlanktoScop to automatically sets its time to the GPS received one. Moreover, since the PPS (Pulse Per Second) output is activated, you can even set your PlanktoScope to act as a stratum 1 timeserver. - -We are first going to make sure that your PlanktoScope receives proper PPS signal. We need to add the following line at the end of `/boot/config.txt`: -``` -sudo nano /boot/config.txt -# Add the following line at the end of the line -dtoverlay=pps-gpio,gpiopin=4 -``` - -We also need to activate the pps module of the kernel, by editing `/etc/modules`: - -``` -sudo nano /etc/modules -# Add the following line at the end of the line -pps-gpio -``` - -Now install `pps-tools` so we can check that this is properly running. -```sh -sudo apt install pps-tools -``` - -Finally, in the `/etc/default/gpsd` file, we need to add our pps device to the line `DEVICES`. Append `/dev/pps0`: -```sh -DEVICES="/dev/serial0 /dev/pps0" -``` - -Reboot your PlanktoScope now and check that the PPS signal is properly parsed by the PlanktoScope. You can do this by running `sudo ppstest /dev/pps0`: -``` -pi@planktoscope:~ $ sudo ppstest /dev/pps0 -trying PPS source "/dev/pps0" -found PPS source "/dev/pps0" -ok, found 1 source(s), now start fetching data... -source 0 - assert 1595329939.946478786, sequence: 4125 - clear 0.000000000, sequence: 0 -source 0 - assert 1595329940.946459463, sequence: 4126 - clear 0.000000000, sequence: 0 -``` - -`gpsmon` should also show a PPS signal in the `GSA + PPS` box. - -We now need to install the software that will act as timeserver, both locally and globally. Its name is Chrony. It's a more modern replacement for `ntp`, using the same underlying protocol. Let's go ahead and install it: -```sh -sudo apt install chrony -``` - -We need to edit the configuration of chrony, to activate both the GPS time synchronization and to allow clients to request time updates directly from our microscope. - -Edit the file `/etc/chrony/chrony.conf` and replace its content with the following: -``` -server 0.pool.ntp.org maxpoll 5 -server 1.pool.ntp.org maxpoll 5 -server 2.pool.ntp.org maxpoll 5 -server 3.pool.ntp.org maxpoll 5 - -driftfile /var/lib/chrony/drift - -allow - -makestep 1 5 - -refclock SHM 2 pps refid NMEA -#refclock PPS /dev/pps0 precision 1e-7 noselect refid GPPS -``` - -Before restarting `chrony`, we need to make sure the timesync service from systemd is deactivated: -```sh -sudo systemctl stop systemd-timesyncd.service -sudo systemctl disable systemd-timesyncd.service -``` - -Final step, let's start `chrony` with its new configuration and restart `gpsd`: -```sh -sudo systemctl restart chrony -sudo systemctl restart gpsd -``` - -To check that everything is working as intended, wait a few minutes, and then type `chronyc sources -v`. This command will show the time sources `chrony` is using, and right at the top there should be our NMEA source. Make sure its line starts with `#*`, which means this source is selected: -``` -pi@planktoscope:~ $ chronyc sources -v -210 Number of sources = 5 - - .-- Source mode '^' = server, '=' = peer, '#' = local clock. - / .- Source state '*' = current synced, '+' = combined , '-' = not combined, -| / '?' = unreachable, 'x' = time may be in error, '~' = time too variable. -|| .- xxxx [ yyyy ] +/- zzzz -|| Reachability register (octal) -. | xxxx = adjusted offset, -|| Log2(Polling interval) --. | | yyyy = measured offset, -|| \ | | zzzz = estimated error. -|| | | \ -MS Name/IP address Stratum Poll Reach LastRx Last sample -=============================================================================== -#* NMEA 0 4 377 13 -434ns[ -582ns] +/- 444ns -^- mail.raveland.org 3 7 377 215 -18ms[ -18ms] +/- 53ms -^- nio.nucli.net 2 6 377 19 -7340us[-7340us] +/- 63ms -^- ntp4.kashra-server.com 2 8 377 146 -11ms[ -11ms] +/- 50ms -^- pob01.aplu.fr 2 8 377 83 -15ms[ -15ms] +/- 66ms -``` - -The other servers are here just as fallback measures, in case the GPS is not working for an unknown reason. - -This part is now complete! Everytime you start your Planktoscope, it will set its own time after a few minutes (once a GPS signal is acquired). - -The ultimate step will have to be done on the other equipment on the network where you want to use this time source. You will need to add the line `server planktoscope.local` to your ntp configuration file either at `/etc/ntp.conf` or at `/etc/chrony/chrony.conf` and then restart your ntp service. - -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 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). - - - -### 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 -``` -We are also going to activate the Projects feature of Node-Red as this will help us manage and track changes to the flows. Open the file `settings.js` with an editor (for example with `nano settings.js`) so we can change the following lines: -``` -Line 68: uncomment the line (remove the //) that ends with flowFilePretty: true, -Line 296: set enabled to true -``` - -Save you changes. - -The final step before restarting node-red is to link the projects directory from within node-red folder to our main home directory. To do so, just open a terminal and type the following: -```bash -ln -s /home/pi/.node-red/projects/PlanktonScope /home/pi/PlanktonScope -``` - -You can now restart the nodered service: -``` -sudo systemctl restart nodered.service -``` - -#### Import the last GUI - -If you now open the Node-Red GUI in your browser, it will ask you to setup the project, an email and a username (so if you make changes to the flow and want to share them we can know who made them). - -You can now choose to clone an existing repository. Choose a name that makes sense for you, and in the `Git repository URL` field put the main Planktonscope repository: `https://www.github.com/PlanktonPlanet/PlanktonScope.git`. - -The latest flow version will be imported immediately. - - -#### More information -[Installing Node-RED on Raspberry Pi](https://nodered.org/docs/getting-started/raspberrypi) - - -## 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/ +This repository is also a good way to get involved. Please fill in an issue if you witnessed a bug in the software or hardware. If you are able, you can also join the development effort. Look through the [issues opened](https://github.com/PlanktonPlanet/PlanktonScope/labels/good%20first%20issue) and choose one that piques your interest. Let us know you want to work on it in the comments, we may even be able to guide your beginnings around the code. \ No newline at end of file diff --git a/docs/README.md b/docs/README.md new file mode 100644 index 0000000..30aeb58 --- /dev/null +++ b/docs/README.md @@ -0,0 +1,29 @@ +# Welcome to the PlanktoScope build and use documentation + +![PlanktoScope](readme/planktoscope_cad.webp) + +You can find here more information about how to build your own PlanktoScope. + +## Setup + + - [How to setup your PlanktoScope the easy way](easy_install.md) + - [How to setup your PlanktoScope the hard way (also known as the Expert's path)](expert_setup.md) + - [Some information about how to setup a remote access](remote_access.md) + +## Build your machine! + - [Assembly Guide](assembly_guide.md) + +## Usage + - [Information about collection devices](collection_devices.md) + +## Under the hood: + - [Software architecture](software_architecture.md) + - [MQTT Messages](mqtt_messages.md) + - How does the segmentation works (soon) + +## Contribute + - [Find out how to contribute to this documentation and help edit it](edit_this_doc.md) + - [Contribute to the code, here is the getting started](edit_the_code.md) + +## License of our work + - [More information about the licenses that we use](license.md) \ No newline at end of file diff --git a/docs/assembly_guide.md b/docs/assembly_guide.md new file mode 100644 index 0000000..e6e1789 --- /dev/null +++ b/docs/assembly_guide.md @@ -0,0 +1,277 @@ +# Assembly guide of the PlanktoScope +![Complete](assembly_guide/pictures/complete.webp) + +## Step 0: Gather everything you need + +- Laser cut structure +- M12 lenses +- Peristaltic pump and tubing +- Raspberry Pi, motor driver board, GPIO connectors +- Flashed SD card +- Stepper motors +- PiCam and flex cable +- GPIO ribbon connector, headers, HATs, LED +- DC Power terminal +- Magnets +- Super glue +- Standoffs (M2.5), M3 screws and nuts + +Make sure you have your screwdriver kit, soldering iron, and components ready. Also, remember to flash the Planktonscope image disk on the SD card before installing the Raspberry Pi. + +If you are not familiar with any process, such as soldering, tapping, or wiring, try and familiarize yourself with the topics first. + +Soldering deals with high heat and potentially toxic materials, so make sure to use the proper precautions. + +## Step 1: Laser cutting +![Step1](assembly_guide/pictures/step1.webp) + +Laser cut all components using the .ai file ensuring all cuts are complete. The current design should have a 5mm material thickness. Start by placing laser cut base A on a flat workspace. Make sure all holes are complete, and negative space is clear. + +!!! warning + If you are doing the laser cutting yourself, please take the time to check the calibration of the machine and its power output for the material you are using. A tight fit is needed between the different plates to avoid unwanted play between critical parts. + +## Step 2: Standoff installation +![Step2](assembly_guide/pictures/step2.webp) +![Step2 standoff location](assembly_guide/render/Step2.webp) + +Place 8 standoffs (M2.5 6mm) into the designated holes on the laser-cut base A. A pair of pliers make the job more comfortable. Do not overtighten as it is possible to crack the base material. + +![Step3](assembly_guide/pictures/step3.webp) + +## Step 3: Motor HAT preparation +![Step4](assembly_guide/pictures/step4.webp) + +Insert and solder the terminal blocks and headers onto the motor driver PCB. + +![Step5](assembly_guide/pictures/step5.webp) + +Place the motor driver PCB on to the indicated standoffs. + +## Step 4: Magnets setup +![Step6](assembly_guide/pictures/step6.webp) + +Now is a good time to think about how the magnets will function within the microscope. The magnets in the sample stage will need to attract to the magnets on the flow cell holder. The magnets in the objective holder will need to attract the magnets on the mount. Keep this in mind as you are adding your magnets and tapping your respective M12 holders so your orientation will be correct. + +![Step8](assembly_guide/pictures/step8.webp) + +You can now fix your magnets into their appropriate holes on sample stage **B**. +It is recommended to glue the magnets in place. If the magnets are too large to fit in, the holes can be widened with a handheld drill. However, they should be quite snug in place. Before you glue them in place make sure that the polarity is maintained, as they will be impossible to remove after gluing. + +## Step 5: Sample stage assembly +![Step9](assembly_guide/pictures/step9.webp) + +Don’t be alarmed by the color swap, this is the sample stage **B**. You can now fit the pegs on the driver mounts into the corresponding holes on the sample stage. They should be glued in place with superglue or epoxy. You can spin the shaft to align the driver mounts on the 2 steppers if it helps making the process easier. + +![Step10](assembly_guide/pictures/step10.webp) + +You should now have a sample stage and motor assembly that looks like this. + +## Step 6: Lenses tapping and mounting +![Step12](assembly_guide/pictures/step12.webp) + +You now need to tap the holes for the M12 lenses in stage and mount **M** and **D**. It is helpful for alignment to do both the objeDtive and tube lens mount together. It is important to do this as straight as possible. A drop of mineral or olive oil can help the process. Be careful to use a right-hand tap (that goes down when turning clockwise). + +![Step13](assembly_guide/pictures/step13.webp) +![Step14](assembly_guide/pictures/step14.webp) + +![Step6-2](assembly_guide/render/step6-2.webp) + +You can now screw the objective lens (the 25mm one) in part **D**. +![Step14](assembly_guide/pictures/step15.webp) + +## Step 7: Camera preparation +You can now unscrew the lens from the Pi camera, being careful not to disturb the sensor below. +![Image22](assembly_guide/pictures/image22.webp) +![Image30](assembly_guide/pictures/image30.webp) + +## Step 8: Camera mount +![Step17](assembly_guide/pictures/step17.webp) + +You can mount the camera using the appropriate holes on the camera mount **G**. Be careful to avoid getting oil or dust on the sensor. + +## Step 9: LED preparation +![Step18](assembly_guide/pictures/step18.webp) + +The LED can then be wired up and put into its mount **F**. If you wire the LED yourself, remember to give enough length to reach the motor driver on the other end of the microscope. You can also add a bit of glue to fix **F** to the motor mount **E** at this time to make assembly easier, though it is not required. + +## Step 10: Vertical slices assembly +You can now start placing the motor mount/LED assembly- **B**, +![Step5](assembly_guide/render/step5.webp) + +**C**, +![Step6](assembly_guide/render/step6.webp) + +**D**, +![Step7](assembly_guide/render/step7.webp) + +**E**, +![Step8](assembly_guide/render/step8.webp) + +**F**, +![Step8](assembly_guide/render/step9.webp) + +and **G** into the base **A**. + +## Step 11: Pump setup +The pump can then be mounted in place on **H**. Thread the wires through the hole with the pump tubing pointed toward the holes on the mount. +![Step19](assembly_guide/pictures/step19.webp) + +Fix the pump in place. +![Step20](assembly_guide/pictures/step20.webp) + +## Step 12: Pump mounting +You can now mount the pump on base **A**. +![Step15](assembly_guide/render/step15.webp) + +Your setup should look like this. Don't worry about the wiring, we'll have a look at it in the next step! + +![Step21](assembly_guide/pictures/step21.webp) + +## Step 13: Motor HAT wiring +![Step22](assembly_guide/pictures/step22.svg) + +You will now want to wire the steppers and pump to the terminals on the motor driver board. + +If your wires are too short, you can invert the pump and the focus wiring. However, you will have to remember to change the configuration later on. + +!!! tip + Make sure the wires are properly connected by pulling on them a little. They should not come loose. + +## Step 14: Raspberry Pi setup and installation +![Step24](assembly_guide/pictures/step24.webp) + +At this point, you can insert your flashed SD card into your Raspberry Pi. [Consult the guide for flashing your SD card](https://www.planktonscope.org/replicate/prepare-your-pi) before you do this. The heat sink can also be added to the processor. + +!!! note + If you choose the Expert path, you still need to flash your sd card, either with the [lite version](https://downloads.raspberrypi.org/raspios_lite_armhf_latest) of Raspberry OS or with the [desktop version](https://downloads.raspberrypi.org/raspios_armhf_latest). + +![Step16](assembly_guide/render/step16.webp) + +Mount the Raspberry Pi containing the flashed SD card on the standoffs attached to the laser cut base A. + +## Step 15: Standoffs +![Step17](assembly_guide/render/step17.webp) + +Add 8 standoffs (M2.5 15mm) to fix the motor driver board and the Raspberry Pi to the base. + +![Step25](assembly_guide/pictures/step25.webp) + +## Step 16: Camera flex cable +![Step26](assembly_guide/pictures/step26.webp) + +At this point you can use the Pi camera flex cable to connect the camera to the Pi. This is done by gently pulling up the tensioners, inserting the cable in the right orientation, then pushing the tensioners back in place to set the cable. Try not to kink or fold the flex cable too much as it is possible to damage it. + +## Step 17: Power supply wiring +![Step29](assembly_guide/pictures/step29.webp) + +The power wires can be wired into place on the motor driver board. + +!!! tip + Make sure the wires are properly connected by pulling on them a little. They should not come loose. + +## Step 18: Prepare the GPS HAT +![Step18-1](assembly_guide/render/step18-1.webp) + +Insert the battery to power the GPS HAT and solder the terminal mounts in place. + +## Step 19: Install the GPS HAT +![Step18](assembly_guide/render/step18.webp) + +Mount the GPS HAT over the motor driver PCB using the standoffs attached to the laser cut base **A**. + +## Step 20: Install the Fan HAT +![Step19](assembly_guide/render/step19.webp) + +Place the cooling fan HAT above the Raspberry Pi by mounting it to the standoffs on base **A**. + +!!! warning + Be careful to slide the camera flat cable in the slot in the HAT above the connector. + +## Step 21: Secure the HATS +![Step20](assembly_guide/render/step20.webp) + +Secure the cooling fan HAT and GPS HAT by tightening the 8 screws to the standoffs on base A + +## Step 22: Install back panel +![Step21](assembly_guide/render/step21.webp) + +Insert the laser cut border **I** into base **A**. + +## Step 23: GPS output connector +![Step22](assembly_guide/render/step22.webp) + +Insert the power and GPS connectors into side plate **J**. + +## Step 24: Install side panel +![Step23](assembly_guide/render/step23.webp) + +Place the side plate **J** into the designated slots on the base. You can connect the GPS cable to its connector on the board. + +!!! warning + The GPS connector is quite fragile, make sure to align it properly before inserting it. + +## Step 25: Install the other side panel +![Step25](assembly_guide/render/step25.webp) + +Mount the side plate **K** on base **A** using the assigned slots. + +## Step 26: Secure the sides together +![Step26](assembly_guide/render/step26.webp) + +Secure the laser cut sides with the screws and nuts. + +## Step 27: Secure the sides to the base plate +![Step27](assembly_guide/render/step27.webp) + +Secure the laser cut sides to the base plate **A** with the screws and nuts. + +!!! warning + To make this easier, you can turn the assembly upside down or on its side. Be careful when doing so as the plates may fall. + +## Step 28: Insert the camera ribbon cable in the camera +![Step28](assembly_guide/pictures/step28.webp) + +You can now connect the camera flex cable into the connector on the camera board. Once again, gently pull up the tensioners, insert the cable in the right orientation, and push the tensioners back in place to set the cable. Try not to kink or fold the flex cable too much as it is possible to damage it. + +## Step 29: Insert the ribbon cable +![Step28](assembly_guide/render/step28.webp) + +Attach the GPIO ribbon to connect the cooling fan HAT to the GPS HAT. + +!!! tip + You can try to route the flat ribbon from the camera under the ribbon cable you are connecting now. + ![Step31](assembly_guide/pictures/step31.webp) + +## Step 30: Fluidic assembly +![Step29](assembly_guide/render/step29.webp) + +Feed in the tubing from syringe 1 to form the fluidic path as shown. + +![Step30](assembly_guide/render/step30.webp) + +Feed in the tubing from syringe 2 to form the fluidic path as shown + +![Step31](assembly_guide/render/step31.webp) + +Feed in a length of tubing as shown through motor mount **H** and illumination mount **FE** + +![Step34](assembly_guide/pictures/step34.webp) + +## Step 31: Close your PlanktoScope + +!!! warning + Take a moment to check your wiring one last time. Also check the routing, make sure the LED wires and the pump stepper wires are in their dedicated channel. + +![Step33](assembly_guide/render/step33.webp) + +Place the top **L** into the slots on the Planktonscope body. Secure it in place with screws and nuts. + +![Step34](assembly_guide/render/step34.webp) + +## Step 32: Enjoy! + +Congratulations on a job well done. You can have some rest, get a tea and some biscuits! + +![Step35](assembly_guide/render/step35.webp) + +You can now plug the machine in and test it. 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It should be made of a fine mesh, down to 20 micron. It can be towed behind a boat at low speed (less than 2 knots) or towed by hand in a river or a lake. + +Plankton nets can be made easily with a good sewind machine and some hardware. \ No newline at end of file diff --git a/docs/easy_install.md b/docs/easy_install.md new file mode 100644 index 0000000..7a49780 --- /dev/null +++ b/docs/easy_install.md @@ -0,0 +1,26 @@ +# PlanktonScope Simple Setup Guide + +## Download the image + +For ease of setup, a preconfigured image is provided. You can download it from [here](http://planktonscope.su.domains/Images_raspberry/Raspbian_Buster_Morphocut_WiFi.img). + +## Writing the 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 previously downloaded img file file you wish to write to the SD card. + +Select the SD card you wish to write your image to. + +Review your selections and click 'Flash!' to begin writing data to the SD card. + +## Inserting the SD card +Once flashing is over, you can unmount the SD card from the computer (usually done by right clicking on the card icon in the taskbar). + +Insert now the card in the Raspberry installed in your PlanktonScope. + +## Start playing! + +Start up your PlanktonScope and connect to its WiFi network. You can now access the webpage at http://planktonscope.local:1880/ui to start using your machine! \ No newline at end of file diff --git a/docs/edit_the_code.md b/docs/edit_the_code.md new file mode 100644 index 0000000..22a1a35 --- /dev/null +++ b/docs/edit_the_code.md @@ -0,0 +1,9 @@ +# How to help development for the PlanktoScope code + +We are using the [Github Flow approach](https://docs.github.com/en/free-pro-team@latest/github/collaborating-with-issues-and-pull-requests) for our development efforts. + +If you want to join us, have a look at the [currently opened issues](https://github.com/PlanktonPlanet/PlanktonScope/issues) and pick one where you feel like you can have an impact. Let us know you want to work it in the comments and get started. + +For working on Node-Red, we recommend to install it directly on your development machine to allow for faster cycles of testing (and ease of use). But feel free to setup a Pi Zero as a portable and compact development environment! (One of us is using one configured as usb gadget to do so!) + +If you don't know how to code, [the documentation could use your help](edit_this_doc)! \ No newline at end of file diff --git a/docs/edit_this_doc.md b/docs/edit_this_doc.md new file mode 100644 index 0000000..9f79221 --- /dev/null +++ b/docs/edit_this_doc.md @@ -0,0 +1,25 @@ +# Edit this documentation! + +This documentation is hosted by [ReadTheDocs.org](https://readthedocs.org/) at https://planktonscope.readthedocs.io/. + +The source files are in the main [github repository](https://www.github.com/PlanktonPlanet/PlanktonScope), in the `docs` folder. + +They are simple [Markdown files](https://www.markdownguide.org/), that you can edit in any text editor of your choice. + +The local development and test is made using [mkdocs](https://www.mkdocs.org/). This allows you to test your documentation changes for styling issues and see what it will look like once rendered. + +If you want to include pictures and diagrams in the documentation, please set the pictures in a dedicated folder to the name of the page you are creating (for example, if your page is named `expert_setup.md`, please put all the related pictures in the `docs/expert_setup/` folder). Each picture should be named with a simple yet descriptive name, using jpg or png format if possible. Try to limit the size of the file by limiting the resolution to what is necessary for the picture to be clear on screen. + +Contributions should be made by creating pull requests on [Github directly](https://github.com/PlanktonPlanet/PlanktonScope/pulls). + + +## Extensions available +In addition to the common markdown syntax, several extensions are activated. If you want more information on any of them, please follow the linked guides. + +- [SmartyPants](https://python-markdown.github.io/extensions/smarty/): Converts ASCII dashes, quotes and ellipses to their HTML entity equivalents. +- [Sane Lists](https://python-markdown.github.io/extensions/sane_lists/): Alters the behavior of the Markdown List syntax to be less surprising. +- [Admonition](https://python-markdown.github.io/extensions/admonition/): Adds rST-style admonitions to Markdown documents. +- [Table of contents](https://python-markdown.github.io/extensions/toc/): Generates a Table of Contents from a Markdown document and adds it into the resulting HTML document. +- [Metadata](https://python-markdown.github.io/extensions/meta_data/): Adds a syntax for defining meta-data about a document. +- [Tables](https://python-markdown.github.io/extensions/tables/): Adds the ability to create tables in Markdown documents. +- [Fenced Code Blocks](https://python-markdown.github.io/extensions/fenced_code_blocks/): Adds a secondary way to define code blocks. diff --git a/docs/expert_setup.md b/docs/expert_setup.md new file mode 100644 index 0000000..82da436 --- /dev/null +++ b/docs/expert_setup.md @@ -0,0 +1,596 @@ +# Expert Setup + +## 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! +``` + +Also, to make sure the wiring is good, we are going to use `sudo i2cdetect -y 1` to see if our devices are detected: +``` +pi@planktoscope:~ $ sudo i2cdetect -y 1 + 0 1 2 3 4 5 6 7 8 9 a b c d e f +00: -- -- -- -- -- -- -- -- -- -- 0d -- -- +10: -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- +20: -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- +30: -- -- -- -- -- -- -- -- -- -- -- -- 3c -- -- -- +40: -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- +50: -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- +60: 60 -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- +70: 70 -- -- -- -- -- -- -- +``` + +The device appearing at addresses 60 and 70 is our motor controller. Address `0d` is the fan controller and `3c` is the oled screen (we'll set up both a bit further down). Your version of the RGB Cooling Hat may not have the screen, it's fine as the screen is not necessary for proper operation of the Planktoscope. + +In case the motor controller does not appear, shutdown your Planktoscope and check the wiring. If your board is using a connector instead of a soldered pin connection (as happens with the Adafruit Bonnet Motor Controller), sometimes the pins on the male side need to be bent a little to make good contact. In any case, do not hesitate to ask for help in Slack. + +### 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 +``` + +Change the autostart setting to No, and then 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 now 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). + +We are going to use gpsd to parse the GPS data. We need to set it up by editing `/etc/default/gpsd`. This file is source just before starting gpsd and allows to configure its working. +```sh +sudo nano /etc/default/gpsd +``` + +Change the `USB_AUTO` line to read `false` +```sh +USBAUTO="false" +``` + +Also change the `DEVICES` line to add the device we are going to use `/dev/serial0`: +```sh +DEVICES="/dev/serial0" +``` + +Finally, we want to add the parameter `-n` to `GPSD_OPTIONS`: +```sh +GPSD_OPTIONS="-n" +``` + +Save your work, and restart gpsd by running the following: +```sh +sudo systemctl restart gpsd.service +``` + +If you wait a bit, you can run `gpsmon` to check that your configuration is correct. You should get an output similar to this: +``` +pi@planktoscope:~ $ gpsmon +/dev/serial0 NMEA0183> +┌──────────────────────────────────────────────────────────────────────────────┐ +│Time: 2020-07-21T11:09:26.000Z Lat: 45 33' 28.08539" Non: 1 03' 44.02019" W│ +└───────────────────────────────── Cooked TPV ─────────────────────────────────┘ +┌──────────────────────────────────────────────────────────────────────────────┐ +│ GPGGA GPGSA GPRMC GPZDA GPGSV │ +└───────────────────────────────── Sentences ──────────────────────────────────┘ +┌──────────────────┐┌────────────────────────────┐┌────────────────────────────┐ +│Ch PRN Az El S/N ││Time: 110926.000 ││Time: 110927.000 │ +│ 0 27 351 78 49 ││Latitude: 4533.4809 N ││Latitude: 4533.4809 │ +│ 1 21 51 69 47 ││Longitude: 00103.7367 W ││Longitude: 00103.7367 │ +│ 2 16 184 61 43 ││Speed: 0.00 ││Altitude: -0.1 │ +│ 3 10 116 51 50 ││Course: 201.75 ││Quality: 2 Sats: 11 │ +│ 4 8 299 47 49 ││Status: A FAA: D ││HDOP: 0.87 │ +│ 5 20 66 42 46 ││MagVar: ││Geoid: 49.3 │ +│ 6 123 138 28 43 │└─────────── RMC ────────────┘└─────────── GGA ────────────┘ +│ 7 26 165 25 30 │┌────────────────────────────┐┌────────────────────────────┐ +│ 8 11 264 23 48 ││Mode: A3 ...s: 27 21 16 10 ││UTC: RMS: │ +│ 9 7 303 15 38 ││DOP: H=0.87 V=1.13 P=1.42 ││MAJ: MIN: │ +│10 18 56 14 44 ││TOFF: 0.530187817 ││ORI: LAT: │ +│11 30 330 5 35 ││PPS: ││LON: ALT: │ +└────── GSV ───────┘└──────── GSA + PPS ─────────┘└─────────── GST ────────────┘ +(42) $GPGSV,4,4,14,15,03,035,36,01,02,238,*72 +(72) $GPRMC,110922.000,A,4533.4809,N,00103.7366,W,0.01,322.19,210720,,,D*7E +(35) $GPZDA,110922.000,21,07,2020,,*5B +(81) $GPGGA,110923.000,4533.4809,N,00103.7367,W,2,11,0.87,-0.1,M,49.3,M,0000,0000*5B +(64) $GPGSA,A,3,16,27,30,10,18,21,20,08,11,07,26,,1.43,0.87,1.13*0B +(72) $GPRMC,110923.000,A,4533.4809,N,00103.7367,W,0.01,188.90,210720,,,D*7D +(35) $GPZDA,110923.000,21,07,2020,,*5A +(81) $GPGGA,110924.000,4533.4809,N,00103.7367,W,2,11,0.87,-0.1,M,49.3,M,0000,0000*5C +(64) $GPGSA,A,3,16,27,30,10,18,21,20,08,11,07,26,,1.43,0.87,1.13*0B +(72) $GPRMC,110924.000,A,4533.4809,N,00103.7367,W,0.01,156.23,210720,,,D*71 +``` + +#### Bonus Configuration: Automatic time update from GPSD + +The Adafruit GPS HAT allows your PlanktoScop to automatically sets its time to the GPS received one. Moreover, since the PPS (Pulse Per Second) output is activated, you can even set your PlanktoScope to act as a stratum 1 timeserver. + +We are first going to make sure that your PlanktoScope receives proper PPS signal. We need to add the following line at the end of `/boot/config.txt`: +``` +sudo nano /boot/config.txt +# Add the following line at the end of the line +dtoverlay=pps-gpio,gpiopin=4 +``` + +We also need to activate the pps module of the kernel, by editing `/etc/modules`: + +``` +sudo nano /etc/modules +# Add the following line at the end of the line +pps-gpio +``` + +Now install `pps-tools` so we can check that this is properly running. +```sh +sudo apt install pps-tools +``` + +Finally, in the `/etc/default/gpsd` file, we need to add our pps device to the line `DEVICES`. Append `/dev/pps0`: +```sh +DEVICES="/dev/serial0 /dev/pps0" +``` + +Reboot your PlanktoScope now and check that the PPS signal is properly parsed by the PlanktoScope. You can do this by running `sudo ppstest /dev/pps0`: +``` +pi@planktoscope:~ $ sudo ppstest /dev/pps0 +trying PPS source "/dev/pps0" +found PPS source "/dev/pps0" +ok, found 1 source(s), now start fetching data... +source 0 - assert 1595329939.946478786, sequence: 4125 - clear 0.000000000, sequence: 0 +source 0 - assert 1595329940.946459463, sequence: 4126 - clear 0.000000000, sequence: 0 +``` + +`gpsmon` should also show a PPS signal in the `GSA + PPS` box. + +We now need to install the software that will act as timeserver, both locally and globally. Its name is Chrony. It's a more modern replacement for `ntp`, using the same underlying protocol. Let's go ahead and install it: +```sh +sudo apt install chrony +``` + +We need to edit the configuration of chrony, to activate both the GPS time synchronization and to allow clients to request time updates directly from our microscope. + +Edit the file `/etc/chrony/chrony.conf` and replace its content with the following: +``` +server 0.pool.ntp.org maxpoll 5 +server 1.pool.ntp.org maxpoll 5 +server 2.pool.ntp.org maxpoll 5 +server 3.pool.ntp.org maxpoll 5 + +driftfile /var/lib/chrony/drift + +allow + +makestep 1 5 + +refclock SHM 2 pps refid NMEA +#refclock PPS /dev/pps0 precision 1e-7 noselect refid GPPS +``` + +Before restarting `chrony`, we need to make sure the timesync service from systemd is deactivated: +```sh +sudo systemctl stop systemd-timesyncd.service +sudo systemctl disable systemd-timesyncd.service +``` + +Final step, let's start `chrony` with its new configuration and restart `gpsd`: +```sh +sudo systemctl restart chrony +sudo systemctl restart gpsd +``` + +To check that everything is working as intended, wait a few minutes, and then type `chronyc sources -v`. This command will show the time sources `chrony` is using, and right at the top there should be our NMEA source. Make sure its line starts with `#*`, which means this source is selected: +``` +pi@planktoscope:~ $ chronyc sources -v +210 Number of sources = 5 + + .-- Source mode '^' = server, '=' = peer, '#' = local clock. + / .- Source state '*' = current synced, '+' = combined , '-' = not combined, +| / '?' = unreachable, 'x' = time may be in error, '~' = time too variable. +|| .- xxxx [ yyyy ] +/- zzzz +|| Reachability register (octal) -. | xxxx = adjusted offset, +|| Log2(Polling interval) --. | | yyyy = measured offset, +|| \ | | zzzz = estimated error. +|| | | \ +MS Name/IP address Stratum Poll Reach LastRx Last sample +=============================================================================== +#* NMEA 0 4 377 13 -434ns[ -582ns] +/- 444ns +^- mail.raveland.org 3 7 377 215 -18ms[ -18ms] +/- 53ms +^- nio.nucli.net 2 6 377 19 -7340us[-7340us] +/- 63ms +^- ntp4.kashra-server.com 2 8 377 146 -11ms[ -11ms] +/- 50ms +^- pob01.aplu.fr 2 8 377 83 -15ms[ -15ms] +/- 66ms +``` + +The other servers are here just as fallback measures, in case the GPS is not working for an unknown reason. + +This part is now complete! Everytime you start your Planktoscope, it will set its own time after a few minutes (once a GPS signal is acquired). + +The ultimate step will have to be done on the other equipment on the network where you want to use this time source. You will need to add the line `server planktoscope.local` to your ntp configuration file either at `/etc/ntp.conf` or at `/etc/chrony/chrony.conf` and then restart your ntp service. + +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 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). + + +### 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 +``` +We are also going to activate the Projects feature of Node-Red as this will help us manage and track changes to the flows. Open the file `settings.js` with an editor (for example with `nano settings.js`) so we can change the following lines: +``` +Line 68: uncomment the line (remove the //) that ends with flowFilePretty: true, +Line 296: set enabled to true +``` + +Save you changes. + +The final step before restarting node-red is to link the projects directory from within node-red folder to our main home directory. To do so, just open a terminal and type the following: +```bash +ln -s /home/pi/.node-red/projects/PlanktonScope /home/pi/PlanktonScope +``` + +You can now restart the nodered service: +``` +sudo systemctl restart nodered.service +``` + +#### Import the last GUI + +If you now open the Node-Red GUI in your browser, it will ask you to setup the project, an email and a username (so if you make changes to the flow and want to share them we can know who made them). + +You can now choose to clone an existing repository. Choose a name that makes sense for you, and in the `Git repository URL` field put the main Planktonscope repository: `https://www.github.com/PlanktonPlanet/PlanktonScope.git`. + +The latest flow version will be imported immediately. + + +#### More information +[Installing Node-RED on Raspberry Pi](https://nodered.org/docs/getting-started/raspberrypi) + + +## 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. + +### Share WiFi via Ethernet + +At this link : https://www.instructables.com/id/Share-WiFi-With-Ethernet-Port-on-a-Raspberry-Pi/ + + + diff --git a/docs/index.rst b/docs/index.rst deleted file mode 100644 index 4870f51..0000000 --- a/docs/index.rst +++ /dev/null @@ -1,24 +0,0 @@ -.. _root: - -.. include:: ../README.rst - - -Table of Contents -================= - -.. toctree:: - :maxdepth: 1 - :numbered: - - install - remote_access - license - - -Indices and tables -================== - -* :ref:`genindex` -* :ref:`modindex` -* :ref:`search` - diff --git a/docs/install.rst b/docs/install.rst deleted file mode 100644 index 5093083..0000000 --- a/docs/install.rst +++ /dev/null @@ -1,235 +0,0 @@ -========================== -PlanktonScope Installation -========================== - -************************************* -Install Raspbian on your Raspberry Pi -************************************* - -Download the image -================== - -Download the .zip file of Raspbian Buster with desktop from the Raspberry Pi website Downloads page. - -Writing an image to the SD card - -Download the latest version of balenaEtcher and install it. - -Connect an SD card reader with the micro SD card inside. - -Open balenaEtcher and select from your hard drive the Raspberry Pi .zip file you wish to write to the SD card. - -Select the SD card you wish 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 `_ - -Plug the SD Card in your Raspberry Pi - -Connect your Pi to a screen, mouse, keyboard and power - -Finish the setup - -Make sure you have access to internet and update/upgrade your fresh raspbian - -Update your Pi first -:: - sudo apt-get update -y - sudo apt-get upgrade -y - -Reboot your Pi safely -:: - sudo reboot now - -*************************** -Raspberry Pi configurations -*************************** - -Enable Camera/SSH/I2C in raspi-config - -Open up the configuration page and select Interfacing Options by typing this command: -:: - sudo raspi-config - -Select **Serial** - -Select **NO** - -Keep the **Serial Port Hardware enabled** - -Reboot your Pi safely -:: - sudo reboot now - - -************************************************** -Install the needed libraries for the PlanktonScope -************************************************** - -Install CircuitPython -===================== -`Installing CircuitPython on Raspberry Pi `_ - -Run the following command to install adafruit_blinka -:: - pip3 install adafruit-blinka - sudo pip3 install adafruit-circuitpython-motorkit - -Install RPi Cam Web Interface -============================= - -`RPi Cam Web Interface `_ - -Clone the code from github and enable and run the install script with the following commands -:: - 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 -Press Enter to start RPi Cam Web Interface now -Found what is the IP of your Raspberry Pi -:: - sudo ip addr show | grep 'inet 1' - -Reach the url on a local browser : http://127.0.0.1/html/ - -Install Ultimate GPS HAT -======================== -`Installing Adafruit GPS HAT `_ - -`Use Python Thread with GPS HAT `_ - -:: - sudo apt-get install python gpsd gpsd-clients - -Install RGB Cooling HAT -======================= -`Installing RGB Cooling HAT `_ -Type these command to install: -:: - git clone https://github.com/WiringPi/WiringPi.git - cd WiringPi - sudo ./build - sudo apt-get install gcc - -Install Node-RED -================== -`Installing Node-RED on Raspberry Pi `_ - -Prerequisites -------------- -Ensure npm is able to build any binary modules it needs to install. -:: - sudo apt-get install build-essential - -Download and installation -------------------------- -To install Node.js, npm and Node-RED onto a Raspberry Pi, run the following command will that download and install them: -:: - bash <(curl -sL https://raw.githubusercontent.com/node-red/linux-installers/master/deb/update-nodejs-and-nodered) - -Due to the limited memory of the Raspberry Pi, you will need to start Node-RED with an additional argument to tell the underlying Node.js process to free up unused memory sooner than it would otherwise. -:: - node-red-pi --max-old-space-size=256 - -Autostart on boot ------------------ -Run Node-RED when the Pi is turned on, or re-booted, enable the service to autostart by running the command: -:: - sudo systemctl enable nodered.service - -Check the installation ----------------------- -Make sure NodeRed is correctly installed by reaching the following page from the broswer of your pi : -:: - http://localhost:1880. - -Install few nodes ------------------ -These nodes will be used in Node-RED: -:: - cd .node-red/ - npm install node-red-dashboard - npm install node-red-contrib-python3-function - npm install node-red-contrib-camerapi - npm install node-red-contrib-gpsd - npm install node-red-contrib-web-worldmap - -Import the last GUI -------------------- - -Import the `lastest version of the GUI `_ - -Install Mosquitto MQTT -====================== - -In order to send and receive from Node-RED: -:: - sudo apt-get install mosquitto mosquitto-clients - - -Install mqtt-paho -================= - -In order to send and receive from python: -:: - pip3 install paho-mqtt - -Install OpenCV -================= - -Use the quick version without virtual env -https://www.pyimagesearch.com/2019/09/16/install-opencv-4-on-raspberry-pi-4-and-raspbian-buster/ - - -Install MorphoCut -================= - -`Installing MorphoCut `_ - -MorphoCut is packaged on PyPI and can be installed with pip: -:: - sudo apt-get install python3-scipy - pip3 install -U git+https://github.com/morphocut/morphocut.git@pyrocystis - -Finishing the install -===================== - -Make sure to update your Pi -:: - sudo apt-get update -y - sudo apt-get full-upgrade -y - -Reboot your Pi safely -:: - sudo reboot now - - -******************* -Usefull later maybe -******************* - -Download the GitHub repo -======================== -At this link : https://github.com/tpollina/PlanktonScope/archive/master.zip -Unzip to a specific location: -:: - unzip /home/pi/Downloads/PlanktonScope-master.zip -d /home/pi/ - mv /home/pi/PlanktonScope-master /home/pi/PlanktonScope - -Update node-RED interface -========================= -To update the interface, you can just download the lastest .json file: -:: - wget -P $HOME/.node-red https://raw.githubusercontent.com/tpollina/PlanktonScope/master/scripts/flows_planktonscope.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/docs/license.md b/docs/license.md new file mode 100644 index 0000000..3d6c9d0 --- /dev/null +++ b/docs/license.md @@ -0,0 +1,12 @@ +# Our work is fully open source + +That's the headline, yes. + +## Hardware files +We released our hardware files (everything in the `hardware` directory) under a [CERN OHL-S license](https://ohwr.org/cern_ohl_s_v2.txt). + +## Software source +Our source code (everything in the directories `flows` and `scripts`) is released under a [GPL-3.0 license](https://www.gnu.org/licenses/gpl-3.0.en.html). + +## Everything else (documentation, pictures, etc...) +Everything else is released under a [Creative Commons CC-BY-SA license](https://creativecommons.org/licenses/by-sa/4.0/). \ No newline at end of file diff --git a/docs/license.rst b/docs/license.rst deleted file mode 100644 index a300841..0000000 --- a/docs/license.rst +++ /dev/null @@ -1,3 +0,0 @@ -license -======= -this is a test diff --git a/docs/mqtt_messages.md b/docs/mqtt_messages.md new file mode 100644 index 0000000..edde1d0 --- /dev/null +++ b/docs/mqtt_messages.md @@ -0,0 +1,175 @@ +# Details about used MQTT messages + +## Topic lists +- [`actuator`](#actuator) + - [`actuator/pump`](#actuatorpump) + - [`actuator/focus`](#actuatorfocus) +- [`imager/image`](#imagerimage) +- [`segmenter/segment`](#segmentersegment) +- [`status`](#status) + - [`status/pump`](#statuspump) + - [`status/focus`](#statusfocus) + - [`status/imager`](#statusimager) + - [`status/segmenter`](#statussegmenter) + - [`status/segmenter/name`](#statussegmentername) + - [`status/segmenter/object_id`](#statussegmenterobject_id) + - [`status/segmenter/metric`](#statussegmentermetric) + + + +## Topic details +### `actuator` +#### `actuator/pump` +Control the movement of the pump. The message is a JSON object: +```json +{ + "action": "move", + "direction": "FORWARD", + "volume": 10, + "flowrate": 1 +} +``` +This messages make the pump move 10mL forward at 1mL/min. + +Another supported message is: +```json +{ + "action": "stop" +} +``` + +- Receive only + +#### `actuator/focus` +Control of the focus stage. The message is a JSON object, speed is optional: +```json +{ + "action": "move", + "direction": "UP", + "distance": 0.26, + "speed": 1 +} +``` + +This message makes the stage move up by 10mm. + +Another supported message is: +```json +{ + "action": "stop" +} +``` + +- Receive only + + +### `imager/image` +This topic controls the camera and capture. The message allowed is a JSON message: +```json +{ + "action": "image", + "sleep": 5, + "volume": 1, + "nb_frame": 200 +} +``` + +Sleep in seconds and volume in mL. + +This topic can also receive a config update message: +```json +{ + "action": "config", + "config": {...} +} +``` + +A camera settings message can also be received here. The fields `iso` and `shutter_speed` are optionals: +```json +{ + "action": "settings", + "iso": 100, + "shutter_speed": 40 +} +``` + +- Receive only + +### `segmenter/segment` +This topic controls the segmentation process. The message is a JSON object: +```json +{ + "action": "segment" +} +``` + +`action` can also be `stop`. + +- Receive only + +### `status` +This high-level topic is used to send information to the Node-Red process. There is no publication or receive at this level. + +#### `status/pump` +State of the pump. It's a JSON object with: +```json +{ + "status": "Started", + "duration": 25 +} +``` + +Duration is a best guess estimate. It should not be used to control the other events. If you want to wait for a movement to finish, the best thing to do is to wait for the message `Done`. + +Status can be `Started`, `Ready`, `Done`, `Interrupted`, `Error`, `Dead`. + +- Publish only + +#### `status/focus` +State of the focus stage. It's a JSON object with: +```json +{ + "status": "Started", + "duration": 25 +} +``` + +Duration is a best guess estimate. It should not be used to control the other events. If you want to wait for a movement to finish, the best thing to do is to wait for the message `Done`. + +Status is one of `Started`, `Ready`, `Done`, `Interrupted`, `Error`, `Dead`. + +- Publish only + +#### `status/imager` +State of the imager. It's a JSON object with: +```json +{ + "status": "Started", + "time_left": 25 +} +``` + +Status is one of `Started`, `Ready`, `Completed` or `12_11_15_0.1.jpg has been imaged`. + +- Publish only + +#### `status/segmenter` +Status of the segmentation. It's a JSON object with: +```json +{ + "status": "Started", +} +``` + +`status` is one of `Started`, `Done`, `Interrupted`, `Busy`, `Ready` or `Dead`. + +- Publish only + +#### `status/segmenter/object_id` +```json +{ + "object_id": "13449" +} +``` + +#### `status/segmenter/metric` \ No newline at end of file diff --git a/docs/readme/copepod.webp b/docs/readme/copepod.webp new file mode 100644 index 0000000..b142b55 Binary files /dev/null and b/docs/readme/copepod.webp differ diff --git a/docs/readme/plankton_collage.webp b/docs/readme/plankton_collage.webp new file mode 100644 index 0000000..80ab8ae Binary files /dev/null and b/docs/readme/plankton_collage.webp differ diff --git a/docs/readme/planktonplanet_pub.webp b/docs/readme/planktonplanet_pub.webp new file mode 100644 index 0000000..7d17152 Binary files /dev/null and b/docs/readme/planktonplanet_pub.webp differ diff --git a/docs/readme/planktoscope_cad.webp b/docs/readme/planktoscope_cad.webp new file mode 100644 index 0000000..3c94b11 Binary files /dev/null and b/docs/readme/planktoscope_cad.webp differ diff --git a/docs/readme/planktoscope_pub.webp b/docs/readme/planktoscope_pub.webp new file mode 100644 index 0000000..77d124f Binary files /dev/null and b/docs/readme/planktoscope_pub.webp differ diff --git a/docs/remote_access.rst b/docs/remote_access.md similarity index 79% rename from docs/remote_access.rst rename to docs/remote_access.md index bc44baa..4708c31 100644 --- a/docs/remote_access.rst +++ b/docs/remote_access.md @@ -1,93 +1,92 @@ -====================================== -Remote access via a standalone network -====================================== +# Remote access via a standalone network -Setting up a Raspberry Pi as an access point in a standalone network (NAT) -========================================================================== +## Setting up a Raspberry Pi as an access point in a standalone network (NAT) -This tutorial is adapted from an official Raspberry Pi tutorial that you can find `here`_. - -.. _here: https://www.raspberrypi.org/documentation/configuration/wireless/access-point.md#internet-sharing +This tutorial is adapted from an official Raspberry Pi tutorial that you can find [here](https://www.raspberrypi.org/documentation/configuration/wireless/access-point.md#internet-sharing). In order to work as an access point, the Raspberry Pi will need to have access point software installed, along with DHCP server software to provide connecting devices with a network address. To create an access point, we'll need DNSMasq and HostAPD. Install all the required software in one go with this command:: - +``` sudo apt install dnsmasq hostapd - -Since the configuration files are not ready yet, turn the new software off as follows:: +``` +Since the configuration files are not ready yet, turn the new software off as follows:: +``` sudo systemctl stop dnsmasq sudo systemctl stop hostapd +``` -Configuring a static IP -======================= +### Configuring a static IP We are configuring a standalone network to act as a server, so the Raspberry Pi needs to have a static IP address assigned to the wireless port. This documentation assumes that we are using the standard 192.168.x.x IP addresses for our wireless network, so we will assign the server the IP address 192.168.4.1. It is also assumed that the wireless device being used is wlan0. To configure the static IP address, edit the dhcpcd configuration file with:: - +``` sudo touch /etc/dhcpcd.conf chmod 777 /etc/dhcpcd.conf +``` Send the desired IP address to the end of the previous generated .conf:: - +``` echo "interface wlan0" >> /etc/dhcpcd.conf echo " static ip_address=192.168.4.1/24" >> /etc/dhcpcd.conf echo " nohook wpa_supplicant" >> /etc/dhcpcd.conf - +``` + Now restart the dhcpcd daemon and set up the new wlan0 configuration:: - +``` sudo service dhcpcd restart +``` -Configuring the DHCP server (dnsmasq) -===================================== +### Configuring the DHCP server (dnsmasq) The DHCP service is provided by dnsmasq. By default, the configuration file contains a lot of information that is not needed, and it is easier to start from scratch. Rename this configuration file, and edit a new one:: - +``` sudo mv /etc/dnsmasq.conf /etc/dnsmasq.conf.orig sudo touch /etc/dnsmasq.conf sudo chmod 777 /etc/dnsmasq.conf +``` Type or copy the following information into the dnsmasq configuration file and save it:: - +``` sudo echo "interface=wlan0" >> /etc/dnsmasq.conf sudo echo " dhcp-range=192.168.4.2,192.168.4.20,255.255.255.0,24h" >> /etc/dnsmasq.conf - +``` + So for wlan0, we are going to provide IP addresses between 192.168.4.2 and 192.168.4.20, with a lease time of 24 hours. If you are providing DHCP services for other network devices (e.g. eth0), you could add more sections with the appropriate interface header, with the range of addresses you intend to provide to that interface. -There are many more options for dnsmasq; see the dnsmasq `documentation`_ for more details. - -.. _documentation: http://www.thekelleys.org.uk/dnsmasq/doc.html +There are many more options for dnsmasq; see the dnsmasq [documentation](http://www.thekelleys.org.uk/dnsmasq/doc.html) for more details. Reload dnsmasq to use the updated configuration:: - +``` sudo systemctl reload dnsmasq +``` -Configuring the access point host software (hostapd) -==================================================== +### Configuring the access point host software (hostapd) You need to edit the hostapd configuration file, located at /etc/hostapd/hostapd.conf, to add the various parameters for your wireless network. After initial install, this will be a new/empty file. :: - +``` sudo touch /etc/hostapd/hostapd.conf sudo chmod 777 /etc/hostapd/hostapd.conf - +``` + Add the information below to the configuration file. This configuration assumes we are using channel 7, with a network name of NameOfNetwork, and a password AardvarkBadgerHedgehog. Note that the name and password should not have quotes around them. The passphrase should be between 8 and 64 characters in length. To use the 5 GHz band, you can change the operations mode from hw_mode=g to hw_mode=a. Possible values for hw_mode are: -* a = IEEE 802.11a (5 GHz) -* b = IEEE 802.11b (2.4 GHz) -* g = IEEE 802.11g (2.4 GHz) -* ad = IEEE 802.11ad (60 GHz) (Not available on the Raspberry Pi) +- `a` = IEEE 802.11a (5 GHz) +- `b` = IEEE 802.11b (2.4 GHz) +- `g` = IEEE 802.11g (2.4 GHz) +- `ad` = IEEE 802.11ad (60 GHz) (Not available on the Raspberry Pi) -.. warning:: +!!! warning + Make sure you **define the wished name (ssid)** of the future generated Wifi and its **password (wpa_passphrase)**. - Make sure you **define the wished name (ssid)** of the futur generated Wifi and its **password (wpa_passphrase)**. Set up your hoastapd.conf as follow :: - +``` sudo echo "interface=wlan0" >> /etc/hostapd/hostapd.conf sudo echo "driver=nl80211" >> /etc/hostapd/hostapd.conf sudo echo "ssid=NameOfNetwork" >> /etc/hostapd/hostapd.conf @@ -102,62 +101,67 @@ Set up your hoastapd.conf as follow :: sudo echo "wpa_key_mgmt=WPA-PSK" >> /etc/hostapd/hostapd.conf sudo echo "wpa_pairwise=TKIP" >> /etc/hostapd/hostapd.conf sudo echo "rsn_pairwise=CCMP" >> /etc/hostapd/hostapd.conf +``` -We now need to tell the system where to find this configuration file. :: - +We now need to tell the system where to find this configuration file. +``` sudo chmod 777 /etc/default/hostapd - -Find the line with #DAEMON_CONF, and replace it with this :: - +``` + +Find the line with #DAEMON_CONF, and replace it with this +``` sudo echo 'DAEMON_CONF="/etc/hostapd/hostapd.conf"' >> /etc/default/hostapd +``` -Start it up -=========== - -Now enable and start hostapd :: +### Start it up +Now enable and start hostapd +``` sudo systemctl unmask hostapd sudo systemctl enable hostapd sudo systemctl start hostapd +``` -Do a quick check of their status to ensure they are active and running :: - +Do a quick check of their status to ensure they are active and running +``` sudo systemctl status hostapd sudo systemctl status dnsmasq +``` Add routing and masquerade -========================== - -Edit /etc/sysctl.conf and uncomment a line :: +Edit /etc/sysctl.conf and uncomment a line +``` VAR=$(sudo grep -n -m 1 net.ipv4.ip_forward=1 /etc/sysctl.conf | sudo sed 's/\([0-9]*\).*/\1/') sudo sed -i "${VAR}s/# *//" /etc/sysctl.conf - -Add a masquerade for outbound traffic on eth0 :: +``` +Add a masquerade for outbound traffic on eth0 +``` sudo iptables -t nat -A POSTROUTING -o eth0 -j MASQUERADE +``` -Save the iptables rule :: - +Save the iptables rule +``` sudo sh -c "iptables-save > /etc/iptables.ipv4.nat" - -Edit /etc/rc.local and add this just above "exit 0" to install these rules on boot :: +``` +Edit /etc/rc.local and add this just above "exit 0" to install these rules on boot +``` sudo chmod 777 /etc/rc.local sudo sed -i '/exit 0/d' /etc/rc.local sudo echo "iptables-restore < /etc/iptables.ipv4.nat" >> /etc/rc.local sudo echo "exit 0" >> /etc/rc.local - +``` Reboot and ensure it still functions. Using a wireless device, search for networks. The network SSID you specified in the hostapd configuration should now be present, and it should be accessible with the specified password. -If SSH is enabled on the Raspberry Pi access point, it should be possible to connect to it from another Linux box (or a system with SSH connectivity present) as follows, assuming the pi account is present :: - +If SSH is enabled on the Raspberry Pi access point, it should be possible to connect to it from another Linux box (or a system with SSH connectivity present) as follows, assuming the pi account is present +``` ssh pi@192.168.4.1 -.. note:: - - Most likely your password will be **raspberry** +``` +Most likely your password will be `raspberry`. By this point, the Raspberry Pi is acting as an access point, and other devices can associate with it. Associated devices can access the Raspberry Pi access point via its IP address for operations such as rsync, scp, or ssh. diff --git a/docs/requirements.txt b/docs/requirements.txt new file mode 100644 index 0000000..e2c66c6 --- /dev/null +++ b/docs/requirements.txt @@ -0,0 +1,2 @@ +Markdown==3.2.2 +mkdocs==1.1.2 diff --git a/docs/software_architecture.md b/docs/software_architecture.md new file mode 100644 index 0000000..d5dc017 --- /dev/null +++ b/docs/software_architecture.md @@ -0,0 +1,18 @@ +# Our software architecture + +## Node-Red +Node-Red is our main process. We use the flow to manage our user interface through a dashboard instance. + + +## Python +The python code is separated in four main processes, each with a specific set of responsibilities: + +- The main process controls all the others, starts everything up and cleans up on shutdown +- The stepper process manages the stepper movements. +- The imager process controls the camera and the streaming server via a state machine. +- The segmenter process manages the segmentation and its outputs. + + +Those processes all communicates together using MQTT and json messages. Each message is adressed to one topic. The high level topic controls which process receives the message. The details of each topic is at the end of this commit message. You can learn more about the [MQTT Messages here](mqtt_messages). + +The code is architectured around 6 modules and about 10 classes. I encourage you to have a look at the files, they're pretty straightforward to understand. \ No newline at end of file diff --git a/flows/LICENSE b/flows/LICENSE new file mode 100644 index 0000000..f288702 --- /dev/null +++ b/flows/LICENSE @@ -0,0 +1,674 @@ + GNU GENERAL PUBLIC LICENSE + Version 3, 29 June 2007 + + Copyright (C) 2007 Free Software Foundation, Inc. + Everyone is permitted to copy and distribute verbatim copies + of this license document, but changing it is not allowed. + + Preamble + + The GNU General Public License is a free, copyleft license for +software and other kinds of works. + + The licenses for most software and other practical works are designed +to take away your freedom to share and change the works. By contrast, +the GNU General Public License is intended to guarantee your freedom to +share and change all versions of a program--to make sure it remains free +software for all its users. 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Termination. + + You may not propagate or modify a covered work except as expressly +provided under this License. Any attempt otherwise to propagate or +modify it is void, and will automatically terminate your rights under +this License (including any patent licenses granted under the third +paragraph of section 11). + + However, if you cease all violation of this License, then your +license from a particular copyright holder is reinstated (a) +provisionally, unless and until the copyright holder explicitly and +finally terminates your license, and (b) permanently, if the copyright +holder fails to notify you of the violation by some reasonable means +prior to 60 days after the cessation. + + Moreover, your license from a particular copyright holder is +reinstated permanently if the copyright holder notifies you of the +violation by some reasonable means, this is the first time you have +received notice of violation of this License (for any work) from that +copyright holder, and you cure the violation prior to 30 days after +your receipt of the notice. + + Termination of your rights under this section does not terminate the +licenses of parties who have received copies or rights from you under +this License. If your rights have been terminated and not permanently +reinstated, you do not qualify to receive new licenses for the same +material under section 10. + + 9. Acceptance Not Required for Having Copies. + + You are not required to accept this License in order to receive or +run a copy of the Program. Ancillary propagation of a covered work +occurring solely as a consequence of using peer-to-peer transmission +to receive a copy likewise does not require acceptance. However, +nothing other than this License grants you permission to propagate or +modify any covered work. These actions infringe copyright if you do +not accept this License. Therefore, by modifying or propagating a +covered work, you indicate your acceptance of this License to do so. + + 10. Automatic Licensing of Downstream Recipients. + + Each time you convey a covered work, the recipient automatically +receives a license from the original licensors, to run, modify and +propagate that work, subject to this License. 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For +purposes of this definition, "control" includes the right to grant +patent sublicenses in a manner consistent with the requirements of +this License. + + Each contributor grants you a non-exclusive, worldwide, royalty-free +patent license under the contributor's essential patent claims, to +make, use, sell, offer for sale, import and otherwise run, modify and +propagate the contents of its contributor version. + + In the following three paragraphs, a "patent license" is any express +agreement or commitment, however denominated, not to enforce a patent +(such as an express permission to practice a patent or covenant not to +sue for patent infringement). To "grant" such a patent license to a +party means to make such an agreement or commitment not to enforce a +patent against the party. + + If you convey a covered work, knowingly relying on a patent license, +and the Corresponding Source of the work is not available for anyone +to copy, free of charge and under the terms of this License, through a +publicly available network server or other readily accessible means, +then you must either (1) cause the Corresponding Source to be so +available, or (2) arrange to deprive yourself of the benefit of the +patent license for this particular work, or (3) arrange, in a manner +consistent with the requirements of this License, to extend the patent +license to downstream recipients. "Knowingly relying" means you have +actual knowledge that, but for the patent license, your conveying the +covered work in a country, or your recipient's use of the covered work +in a country, would infringe one or more identifiable patents in that +country that you have reason to believe are valid. + + If, pursuant to or in connection with a single transaction or +arrangement, you convey, or propagate by procuring conveyance of, a +covered work, and grant a patent license to some of the parties +receiving the covered work authorizing them to use, propagate, modify +or convey a specific copy of the covered work, then the patent license +you grant is automatically extended to all recipients of the covered +work and works based on it. + + A patent license is "discriminatory" if it does not include within +the scope of its coverage, prohibits the exercise of, or is +conditioned on the non-exercise of one or more of the rights that are +specifically granted under this License. You may not convey a covered +work if you are a party to an arrangement with a third party that is +in the business of distributing software, under which you make payment +to the third party based on the extent of your activity of conveying +the work, and under which the third party grants, to any of the +parties who would receive the covered work from you, a discriminatory +patent license (a) in connection with copies of the covered work +conveyed by you (or copies made from those copies), or (b) primarily +for and in connection with specific products or compilations that +contain the covered work, unless you entered into that arrangement, +or that patent license was granted, prior to 28 March 2007. + + Nothing in this License shall be construed as excluding or limiting +any implied license or other defenses to infringement that may +otherwise be available to you under applicable patent law. + + 12. No Surrender of Others' Freedom. + + If conditions are imposed on you (whether by court order, agreement or +otherwise) that contradict the conditions of this License, they do not +excuse you from the conditions of this License. If you cannot convey a +covered work so as to satisfy simultaneously your obligations under this +License and any other pertinent obligations, then as a consequence you may +not convey it at all. For example, if you agree to terms that obligate you +to collect a royalty for further conveying from those to whom you convey +the Program, the only way you could satisfy both those terms and this +License would be to refrain entirely from conveying the Program. + + 13. Use with the GNU Affero General Public License. + + Notwithstanding any other provision of this License, you have +permission to link or combine any covered work with a work licensed +under version 3 of the GNU Affero General Public License into a single +combined work, and to convey the resulting work. The terms of this +License will continue to apply to the part which is the covered work, +but the special requirements of the GNU Affero General Public License, +section 13, concerning interaction through a network will apply to the +combination as such. + + 14. Revised Versions of this License. + + The Free Software Foundation may publish revised and/or new versions of +the GNU General Public License from time to time. Such new versions will +be similar in spirit to the present version, but may differ in detail to +address new problems or concerns. + + Each version is given a distinguishing version number. If the +Program specifies that a certain numbered version of the GNU General +Public License "or any later version" applies to it, you have the +option of following the terms and conditions either of that numbered +version or of any later version published by the Free Software +Foundation. If the Program does not specify a version number of the +GNU General Public License, you may choose any version ever published +by the Free Software Foundation. + + If the Program specifies that a proxy can decide which future +versions of the GNU General Public License can be used, that proxy's +public statement of acceptance of a version permanently authorizes you +to choose that version for the Program. + + Later license versions may give you additional or different +permissions. However, no additional obligations are imposed on any +author or copyright holder as a result of your choosing to follow a +later version. + + 15. Disclaimer of Warranty. + + THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY +APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT +HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY +OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, +THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR +PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM +IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF +ALL NECESSARY SERVICING, REPAIR OR CORRECTION. + + 16. Limitation of Liability. + + IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING +WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS +THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY +GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE +USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF +DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD +PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS), +EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF +SUCH DAMAGES. + + 17. Interpretation of Sections 15 and 16. + + If the disclaimer of warranty and limitation of liability provided +above cannot be given local legal effect according to their terms, +reviewing courts shall apply local law that most closely approximates +an absolute waiver of all civil liability in connection with the +Program, unless a warranty or assumption of liability accompanies a +copy of the Program in return for a fee. + + END OF TERMS AND CONDITIONS + + How to Apply These Terms to Your New Programs + + If you develop a new program, and you want it to be of the greatest +possible use to the public, the best way to achieve this is to make it +free software which everyone can redistribute and change under these terms. + + To do so, attach the following notices to the program. It is safest +to attach them to the start of each source file to most effectively +state the exclusion of warranty; and each file should have at least +the "copyright" line and a pointer to where the full notice is found. + + + Copyright (C) + + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with this program. If not, see . + +Also add information on how to contact you by electronic and paper mail. + + If the program does terminal interaction, make it output a short +notice like this when it starts in an interactive mode: + + Copyright (C) + This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'. + This is free software, and you are welcome to redistribute it + under certain conditions; type `show c' for details. + +The hypothetical commands `show w' and `show c' should show the appropriate +parts of the General Public License. Of course, your program's commands +might be different; for a GUI interface, you would use an "about box". + + You should also get your employer (if you work as a programmer) or school, +if any, to sign a "copyright disclaimer" for the program, if necessary. +For more information on this, and how to apply and follow the GNU GPL, see +. + + The GNU General Public License does not permit incorporating your program +into proprietary programs. If your program is a subroutine library, you +may consider it more useful to permit linking proprietary applications with +the library. If this is what you want to do, use the GNU Lesser General +Public License instead of this License. But first, please read +. diff --git a/hardware/LICENSE b/hardware/LICENSE new file mode 100644 index 0000000..ba24254 --- /dev/null +++ b/hardware/LICENSE @@ -0,0 +1,290 @@ +CERN Open Hardware Licence Version 2 - Strongly Reciprocal + + +Preamble + +CERN has developed this licence to promote collaboration among +hardware designers and to provide a legal tool which supports the +freedom to use, study, modify, share and distribute hardware designs +and products based on those designs. Version 2 of the CERN Open +Hardware Licence comes in three variants: CERN-OHL-P (permissive); and +two reciprocal licences: CERN-OHL-W (weakly reciprocal) and this +licence, CERN-OHL-S (strongly reciprocal). + +The CERN-OHL-S is copyright CERN 2020. Anyone is welcome to use it, in +unmodified form only. + +Use of this Licence does not imply any endorsement by CERN of any +Licensor or their designs nor does it imply any involvement by CERN in +their development. + + +1 Definitions + + 1.1 'Licence' means this CERN-OHL-S. + + 1.2 'Compatible Licence' means + + a) any earlier version of the CERN Open Hardware licence, or + + b) any version of the CERN-OHL-S, or + + c) any licence which permits You to treat the Source to which + it applies as licensed under CERN-OHL-S provided that on + Conveyance of any such Source, or any associated Product You + treat the Source in question as being licensed under + CERN-OHL-S. + + 1.3 'Source' means information such as design materials or digital + code which can be applied to Make or test a Product or to + prepare a Product for use, Conveyance or sale, regardless of its + medium or how it is expressed. It may include Notices. + + 1.4 'Covered Source' means Source that is explicitly made available + under this Licence. + + 1.5 'Product' means any device, component, work or physical object, + whether in finished or intermediate form, arising from the use, + application or processing of Covered Source. + + 1.6 'Make' means to create or configure something, whether by + manufacture, assembly, compiling, loading or applying Covered + Source or another Product or otherwise. + + 1.7 'Available Component' means any part, sub-assembly, library or + code which: + + a) is licensed to You as Complete Source under a Compatible + Licence; or + + b) is available, at the time a Product or the Source containing + it is first Conveyed, to You and any other prospective + licensees + + i) as a physical part with sufficient rights and + information (including any configuration and + programming files and information about its + characteristics and interfaces) to enable it either to + be Made itself, or to be sourced and used to Make the + Product; or + ii) as part of the normal distribution of a tool used to + design or Make the Product. + + 1.8 'Complete Source' means the set of all Source necessary to Make + a Product, in the preferred form for making modifications, + including necessary installation and interfacing information + both for the Product, and for any included Available Components. + If the format is proprietary, it must also be made available in + a format (if the proprietary tool can create it) which is + viewable with a tool available to potential licensees and + licensed under a licence approved by the Free Software + Foundation or the Open Source Initiative. Complete Source need + not include the Source of any Available Component, provided that + You include in the Complete Source sufficient information to + enable a recipient to Make or source and use the Available + Component to Make the Product. + + 1.9 'Source Location' means a location where a Licensor has placed + Covered Source, and which that Licensor reasonably believes will + remain easily accessible for at least three years for anyone to + obtain a digital copy. + + 1.10 'Notice' means copyright, acknowledgement and trademark notices, + Source Location references, modification notices (subsection + 3.3(b)) and all notices that refer to this Licence and to the + disclaimer of warranties that are included in the Covered + Source. + + 1.11 'Licensee' or 'You' means any person exercising rights under + this Licence. + + 1.12 'Licensor' means a natural or legal person who creates or + modifies Covered Source. A person may be a Licensee and a + Licensor at the same time. + + 1.13 'Convey' means to communicate to the public or distribute. + + +2 Applicability + + 2.1 This Licence governs the use, copying, modification, Conveying + of Covered Source and Products, and the Making of Products. By + exercising any right granted under this Licence, You irrevocably + accept these terms and conditions. + + 2.2 This Licence is granted by the Licensor directly to You, and + shall apply worldwide and without limitation in time. + + 2.3 You shall not attempt to restrict by contract or otherwise the + rights granted under this Licence to other Licensees. + + 2.4 This Licence is not intended to restrict fair use, fair dealing, + or any other similar right. + + +3 Copying, Modifying and Conveying Covered Source + + 3.1 You may copy and Convey verbatim copies of Covered Source, in + any medium, provided You retain all Notices. + + 3.2 You may modify Covered Source, other than Notices, provided that + You irrevocably undertake to make that modified Covered Source + available from a Source Location should You Convey a Product in + circumstances where the recipient does not otherwise receive a + copy of the modified Covered Source. In each case subsection 3.3 + shall apply. + + You may only delete Notices if they are no longer applicable to + the corresponding Covered Source as modified by You and You may + add additional Notices applicable to Your modifications. + Including Covered Source in a larger work is modifying the + Covered Source, and the larger work becomes modified Covered + Source. + + 3.3 You may Convey modified Covered Source (with the effect that You + shall also become a Licensor) provided that You: + + a) retain Notices as required in subsection 3.2; + + b) add a Notice to the modified Covered Source stating that You + have modified it, with the date and brief description of how + You have modified it; + + c) add a Source Location Notice for the modified Covered Source + if You Convey in circumstances where the recipient does not + otherwise receive a copy of the modified Covered Source; and + + d) license the modified Covered Source under the terms and + conditions of this Licence (or, as set out in subsection + 8.3, a later version, if permitted by the licence of the + original Covered Source). Such modified Covered Source must + be licensed as a whole, but excluding Available Components + contained in it, which remain licensed under their own + applicable licences. + + +4 Making and Conveying Products + +You may Make Products, and/or Convey them, provided that You either +provide each recipient with a copy of the Complete Source or ensure +that each recipient is notified of the Source Location of the Complete +Source. That Complete Source is Covered Source, and You must +accordingly satisfy Your obligations set out in subsection 3.3. If +specified in a Notice, the Product must visibly and securely display +the Source Location on it or its packaging or documentation in the +manner specified in that Notice. + + +5 Research and Development + +You may Convey Covered Source, modified Covered Source or Products to +a legal entity carrying out development, testing or quality assurance +work on Your behalf provided that the work is performed on terms which +prevent the entity from both using the Source or Products for its own +internal purposes and Conveying the Source or Products or any +modifications to them to any person other than You. Any modifications +made by the entity shall be deemed to be made by You pursuant to +subsection 3.2. + + +6 DISCLAIMER AND LIABILITY + + 6.1 DISCLAIMER OF WARRANTY -- The Covered Source and any Products + are provided 'as is' and any express or implied warranties, + including, but not limited to, implied warranties of + merchantability, of satisfactory quality, non-infringement of + third party rights, and fitness for a particular purpose or use + are disclaimed in respect of any Source or Product to the + maximum extent permitted by law. The Licensor makes no + representation that any Source or Product does not or will not + infringe any patent, copyright, trade secret or other + proprietary right. The entire risk as to the use, quality, and + performance of any Source or Product shall be with You and not + the Licensor. This disclaimer of warranty is an essential part + of this Licence and a condition for the grant of any rights + granted under this Licence. + + 6.2 EXCLUSION AND LIMITATION OF LIABILITY -- The Licensor shall, to + the maximum extent permitted by law, have no liability for + direct, indirect, special, incidental, consequential, exemplary, + punitive or other damages of any character including, without + limitation, procurement of substitute goods or services, loss of + use, data or profits, or business interruption, however caused + and on any theory of contract, warranty, tort (including + negligence), product liability or otherwise, arising in any way + in relation to the Covered Source, modified Covered Source + and/or the Making or Conveyance of a Product, even if advised of + the possibility of such damages, and You shall hold the + Licensor(s) free and harmless from any liability, costs, + damages, fees and expenses, including claims by third parties, + in relation to such use. + + +7 Patents + + 7.1 Subject to the terms and conditions of this Licence, each + Licensor hereby grants to You a perpetual, worldwide, + non-exclusive, no-charge, royalty-free, irrevocable (except as + stated in subsections 7.2 and 8.4) patent license to Make, have + Made, use, offer to sell, sell, import, and otherwise transfer + the Covered Source and Products, where such licence applies only + to those patent claims licensable by such Licensor that are + necessarily infringed by exercising rights under the Covered + Source as Conveyed by that Licensor. + + 7.2 If You institute patent litigation against any entity (including + a cross-claim or counterclaim in a lawsuit) alleging that the + Covered Source or a Product constitutes direct or contributory + patent infringement, or You seek any declaration that a patent + licensed to You under this Licence is invalid or unenforceable + then any rights granted to You under this Licence shall + terminate as of the date such process is initiated. + + +8 General + + 8.1 If any provisions of this Licence are or subsequently become + invalid or unenforceable for any reason, the remaining + provisions shall remain effective. + + 8.2 You shall not use any of the name (including acronyms and + abbreviations), image, or logo by which the Licensor or CERN is + known, except where needed to comply with section 3, or where + the use is otherwise allowed by law. Any such permitted use + shall be factual and shall not be made so as to suggest any kind + of endorsement or implication of involvement by the Licensor or + its personnel. + + 8.3 CERN may publish updated versions and variants of this Licence + which it considers to be in the spirit of this version, but may + differ in detail to address new problems or concerns. New + versions will be published with a unique version number and a + variant identifier specifying the variant. If the Licensor has + specified that a given variant applies to the Covered Source + without specifying a version, You may treat that Covered Source + as being released under any version of the CERN-OHL with that + variant. If no variant is specified, the Covered Source shall be + treated as being released under CERN-OHL-S. The Licensor may + also specify that the Covered Source is subject to a specific + version of the CERN-OHL or any later version in which case You + may apply this or any later version of CERN-OHL with the same + variant identifier published by CERN. + + 8.4 This Licence shall terminate with immediate effect if You fail + to comply with any of its terms and conditions. + + 8.5 However, if You cease all breaches of this Licence, then Your + Licence from any Licensor is reinstated unless such Licensor has + terminated this Licence by giving You, while You remain in + breach, a notice specifying the breach and requiring You to cure + it within 30 days, and You have failed to come into compliance + in all material respects by the end of the 30 day period. Should + You repeat the breach after receipt of a cure notice and + subsequent reinstatement, this Licence will terminate + immediately and permanently. Section 6 shall continue to apply + after any termination. + + 8.6 This Licence shall not be enforceable except by a Licensor + acting as such, and third party beneficiary rights are + specifically excluded. + diff --git a/mkdocs.yml b/mkdocs.yml new file mode 100644 index 0000000..b1ab9b9 --- /dev/null +++ b/mkdocs.yml @@ -0,0 +1,27 @@ +site_name: PlanktoScope +nav: + - Setup: + - Basic Install: easy_install.md + - Expert Setup: expert_setup.md + - Remote Access: remote_access.md + - Assembly: + - Assembly guide: assembly_guide.md + - Usage: + - Collection devices: collection_devices.md + - Under the hood: + - Software architecture: software_architecture.md + - MQTT Messages: mqtt_messages.md + - Contribute: + - Edit this documentation: edit_this_doc.md + - Edit the code: edit_the_code.md + - About: + - License: license.md +theme: + name: readthedocs + +markdown_extensions: + - smarty + - sane_lists + - admonition + - toc: + permalink: true diff --git a/scripts/LICENSE b/scripts/LICENSE new file mode 100644 index 0000000..f288702 --- /dev/null +++ b/scripts/LICENSE @@ -0,0 +1,674 @@ + GNU GENERAL PUBLIC LICENSE + Version 3, 29 June 2007 + + Copyright (C) 2007 Free Software Foundation, Inc. + Everyone is permitted to copy and distribute verbatim copies + of this license document, but changing it is not allowed. + + Preamble + + The GNU General Public License is a free, copyleft license for +software and other kinds of works. + + The licenses for most software and other practical works are designed +to take away your freedom to share and change the works. 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But first, please read +. diff --git a/scripts/README.md b/scripts/README.md index 609d679..af46d2a 100644 --- a/scripts/README.md +++ b/scripts/README.md @@ -1,60 +1,14 @@ -_________________ -### Focusing -##### focus.py `nb_step` `orientation` +# Python scripts of the PlanktoScope -- `nb_step` : **integer** (from 1 to 100000) - number of step to perform by the stage (about 31um/step) -- `orientation` : **string** - orientation of the focus either `up` or `down` +This directory contains the various scripts needed for the PlanktoScope to run properly. -Example: +You should start your exploration with the file `main.py` as this is the file started by Node-Red. - python3.7 $HOME/PlanktonScope/scripts/focus.py 650 up +The `planktoscope` directory contains the various modules loaded at runtime: -_________________ -### Pumping -##### pump.py `volume` `flowrate` `action` - -- `volume` : **integer** -- `flowrate` : **float** -- `action` : **string** - -Example: - - python3.7 $HOME/PlanktonScope/scripts/pump.py 1 10 suck - -_________________ -### Image -##### image.py `in_path` `sample_project` `sample_id` `acq_id` `volume` `flowrate` - -- `in_path` : **string** - directory to store acquisitions **the path has to end with /** -- `sample_project` : **string** -- `sample_id` : **string** -- `acq_id` : **string** -- `volume` : **integer** -- `flowrate` : **float** - -Example: - - python3.7 $HOME/PlanktonScope/scripts/image.py $HOME/PlanktonScope/Acquisitions/ tara_pacific station_125 exp_1 24 3.2 - - -_________________ - -### Light -##### light.py `state` - -- `state` : **string** - `on` OR `off` - -Example: - - python3.7 $HOME/PlanktonScope/scripts/light.py on - - -_________________ -### Fan -##### fan.py `state` - -- `state` : **string** - `on` OR `off` - -Example: - - python3.7 $HOME/PlanktonScope/scripts/fan.py on +- `imager_state_machine.py` is the state machine class of the imager process. +- `imager.py` is the process that runs the camera and the streaming server for the liveview. +- `light.py` manages the state of the light messages displayed by the Yahboom HAT. +- `mqtt.py` is the class managing the mqtt dialogue with Mosquitto and Node-Red. +- `segmenter.py` is the process that controls the segmentation. +- `stepper.py` is the process that manages the stepper motors and their movements.