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Update the documentation for Read The Docs (#43)

Browse source 
Closes #47 .

* Update to documentation to use RTD with mkdocs locally

Initial setup for Read The Doc using mkdocs to build the documentation.
Most of the doc still needs to be rewritten (Expert Setup is the only
part using MD for now).

* README: remove the repo clone step

* Update to documentation to use RTD with mkdocs locally

Initial setup for Read The Doc using mkdocs to build the documentation.
Most of the doc still needs to be rewritten (Expert Setup is the only
part using MD for now).

* documentation edition guide

* Expert setup changes and main README changes

* software architecture stub

* basic doc structure in place

* mqtt message documentatin

* software architecture

* more images

* First README rewrite

* Add admonition configuration

* Various small updates

* how to get involved

* License! Martyr proposal

* Scripts README

* Assembly guide stub

* mkdocs: add assembly guide

* assembly guide: halfway there

* readme: transition to webp for lighter pictures

* README: add extension to path

* README: add assembly guide link

* assembly: complete guide

* add readthedocs config file

* add docs requirements.txt for pip
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# .readthedocs.yml
# Read the Docs configuration file
# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
# Required
version: 2
# Build documentation with MkDocs
mkdocs:
configuration: mkdocs.yml

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README.md
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# 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.

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# 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)

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# 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. If you have choose the Expert's path, now is a good time to [finish setting up your machine](expert_setup.md).

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# Plankton Net
The simplest device you can use is a plankton net. 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.

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# 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!

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# 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)!

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# 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.

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# 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/

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.. _root:
.. include:: ../README.rst
Table of Contents
=================
.. toctree::
:maxdepth: 1
:numbered:
install
remote_access
license
Indices and tables
==================
* :ref:`genindex`
* :ref:`modindex`
* :ref:`search`

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==========================
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 <https://projects.raspberrypi.org/en/projects/raspberry-pi-getting-started/>`_
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 <https://learn.adafruit.com/circuitpython-on-raspberrypi-linux/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 <https://elinux.org/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 <https://learn.adafruit.com/adafruit-ultimate-gps-hat-for-raspberry-pi/pi-setup>`_
`Use Python Thread with GPS HAT <http://www.danmandle.com/blog/getting-gpsd-to-work-with-python/>`_
::
sudo apt-get install python gpsd gpsd-clients
Install RGB Cooling HAT
=======================
`Installing RGB Cooling HAT <https://www.yahboom.net/study/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 <https://nodered.org/docs/getting-started/raspberrypi>`_
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 <https://raw.githubusercontent.com/tpollina/PlanktonScope/master/scripts/flows_planktonscope.json>`_
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 <https://morphocut.readthedocs.io/en/stable/installation.html>`_
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/

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# 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/).

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license
=======
this is a test

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# 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`

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======================================
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.

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mkdocs==1.1.2

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# 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.

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requiring that modified versions of such material be marked in
reasonable ways as different from the original version; or
d) Limiting the use for publicity purposes of names of licensors or
authors of the material; or
e) Declining to grant rights under trademark law for use of some
trade names, trademarks, or service marks; or
f) Requiring indemnification of licensors and authors of that
material by anyone who conveys the material (or modified versions of
it) with contractual assumptions of liability to the recipient, for
any liability that these contractual assumptions directly impose on
those licensors and authors.
All other non-permissive additional terms are considered "further
restrictions" within the meaning of section 10. If the Program as you
received it, or any part of it, contains a notice stating that it is
governed by this License along with a term that is a further
restriction, you may remove that term. If a license document contains
a further restriction but permits relicensing or conveying under this
License, you may add to a covered work material governed by the terms
of that license document, provided that the further restriction does
not survive such relicensing or conveying.
If you add terms to a covered work in accord with this section, you
must place, in the relevant source files, a statement of the
additional terms that apply to those files, or a notice indicating
where to find the applicable terms.
Additional terms, permissive or non-permissive, may be stated in the
form of a separately written license, or stated as exceptions;
the above requirements apply either way.
8. 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. You are not responsible
for enforcing compliance by third parties with this License.
An "entity transaction" is a transaction transferring control of an
organization, or substantially all assets of one, or subdividing an
organization, or merging organizations. If propagation of a covered
work results from an entity transaction, each party to that
transaction who receives a copy of the work also receives whatever
licenses to the work the party's predecessor in interest had or could
give under the previous paragraph, plus a right to possession of the
Corresponding Source of the work from the predecessor in interest, if
the predecessor has it or can get it with reasonable efforts.
You may not impose any further restrictions on the exercise of the
rights granted or affirmed under this License. For example, you may
not impose a license fee, royalty, or other charge for exercise of
rights granted under this License, and you may not initiate litigation
(including a cross-claim or counterclaim in a lawsuit) alleging that
any patent claim is infringed by making, using, selling, offering for
sale, or importing the Program or any portion of it.
11. Patents.
A "contributor" is a copyright holder who authorizes use under this
License of the Program or a work on which the Program is based. The
work thus licensed is called the contributor's "contributor version".
A contributor's "essential patent claims" are all patent claims
owned or controlled by the contributor, whether already acquired or
hereafter acquired, that would be infringed by some manner, permitted
by this License, of making, using, or selling its contributor version,
but do not include claims that would be infringed only as a
consequence of further modification of the contributor version. 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.
<one line to give the program's name and a brief idea of what it does.>
Copyright (C) <year> <name of author>
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 <https://www.gnu.org/licenses/>.
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:
<program> Copyright (C) <year> <name of author>
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
<https://www.gnu.org/licenses/>.
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
<https://www.gnu.org/licenses/why-not-lgpl.html>.

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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.

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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

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GNU GENERAL PUBLIC LICENSE
Version 3, 29 June 2007
Copyright (C) 2007 Free Software Foundation, Inc. <https://fsf.org/>
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. We, the Free Software Foundation, use the
GNU General Public License for most of our software; it applies also to
any other work released this way by its authors. You can apply it to
your programs, too.
When we speak of free software, we are referring to freedom, not
price. Our General Public Licenses are designed to make sure that you
have the freedom to distribute copies of free software (and charge for
them if you wish), that you receive source code or can get it if you
want it, that you can change the software or use pieces of it in new
free programs, and that you know you can do these things.
To protect your rights, we need to prevent others from denying you
these rights or asking you to surrender the rights. Therefore, you have
certain responsibilities if you distribute copies of the software, or if
you modify it: responsibilities to respect the freedom of others.
For example, if you distribute copies of such a program, whether
gratis or for a fee, you must pass on to the recipients the same
freedoms that you received. You must make sure that they, too, receive
or can get the source code. And you must show them these terms so they
know their rights.
Developers that use the GNU GPL protect your rights with two steps:
(1) assert copyright on the software, and (2) offer you this License
giving you legal permission to copy, distribute and/or modify it.
For the developers' and authors' protection, the GPL clearly explains
that there is no warranty for this free software. For both users' and
authors' sake, the GPL requires that modified versions be marked as
changed, so that their problems will not be attributed erroneously to
authors of previous versions.
Some devices are designed to deny users access to install or run
modified versions of the software inside them, although the manufacturer
can do so. This is fundamentally incompatible with the aim of
protecting users' freedom to change the software. The systematic
pattern of such abuse occurs in the area of products for individuals to
use, which is precisely where it is most unacceptable. Therefore, we
have designed this version of the GPL to prohibit the practice for those
products. If such problems arise substantially in other domains, we
stand ready to extend this provision to those domains in future versions
of the GPL, as needed to protect the freedom of users.
Finally, every program is threatened constantly by software patents.
States should not allow patents to restrict development and use of
software on general-purpose computers, but in those that do, we wish to
avoid the special danger that patents applied to a free program could
make it effectively proprietary. To prevent this, the GPL assures that
patents cannot be used to render the program non-free.
The precise terms and conditions for copying, distribution and
modification follow.
TERMS AND CONDITIONS
0. Definitions.
"This License" refers to version 3 of the GNU General Public License.
"Copyright" also means copyright-like laws that apply to other kinds of
works, such as semiconductor masks.
"The Program" refers to any copyrightable work licensed under this
License. Each licensee is addressed as "you". "Licensees" and
"recipients" may be individuals or organizations.
To "modify" a work means to copy from or adapt all or part of the work
in a fashion requiring copyright permission, other than the making of an
exact copy. The resulting work is called a "modified version" of the
earlier work or a work "based on" the earlier work.
A "covered work" means either the unmodified Program or a work based
on the Program.
To "propagate" a work means to do anything with it that, without
permission, would make you directly or secondarily liable for
infringement under applicable copyright law, except executing it on a
computer or modifying a private copy. Propagation includes copying,
distribution (with or without modification), making available to the
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66
scripts/README.md
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@ -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.