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README: remove the repo clone step

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@ -10,596 +10,4 @@ Jump here : http://planktonscope.su.domains/Images_raspberry/Raspbian_Buster_Mor
# 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.
<<<<<<< HEAD
## 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 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/
=======
>>>>>>> 6602696... Update to documentation to use RTD with mkdocs locally