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Add option -E #11

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Add option -E #11

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2450b44
add option -E
Vinalti Dec 19, 2023
a667396
Hotfix / fix README
Vinalti Dec 19, 2023
ea3b544
backup boot_config when copying
Vinalti Dec 19, 2023
c2b6d72
Update README
Vinalti Dec 19, 2023
1a913c0
Update README.md
Vinalti Dec 19, 2023
b8136cb
hotfix requirements.txt
Vinalti Dec 19, 2023
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145 changes: 86 additions & 59 deletions README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -8,77 +8,85 @@ running or service interaction.

# Installation
## Raspberry Pi Configuration
The Raspberry Pi configuration is not covered by this installer as it depends
on the operating system you have installed. Nevertheless here are some
recommendations for the configuration.
Part of the Raspberry Pi configuration is covered by this installer when using
the `-E` or `-A` options.

### Raspi-Config
The following settings should be manually set using `raspi-config`:
Nevertheless, the Camera can be manually activated using `raspi-config`:
- `3 Interface Options` > `1 Camera` > `Yes`

If you have a recent system, you must activate legacy-camera support via:
`3 Interface Options` > `I1 Legacy Camera` > `Enable`
On older system the options are sightly different:
`3 Interface Options` > `1 Camera` > `Yes`
That will automatically add the following lines at the end of `/boot/config.txt`
```toml
[all]
start_x=1
gpu_mem=128
```

### Config File
The following settings should be set in the config file `/boot/config.txt`:
You can also manually edit the same config file to allow LEDs to work correctly:
```conf
dtparam=audio=off
```

- `dtparam=audio=off` (**Required** for LED operations, use `raspi-config nonint set_config_var dtparam=audio off /boot/config.txt`)
- `[all]`
- `start_x=1` (Required for camera, use `raspi-config nonint do_camera 0`)
- `gpu_mem=128`
### Not covered
Network or user configuration is not covered by the installer as it depends on
your setup. During our tests the default user was used, and the connection to
the network was established via cable.

#### Allow software to run as normal user
While this is theoritically feasable, this procedure **has not been tested** and
is therefore not recommended.
To allow the software to run as normal user the following change would be required:
- Connect LED to D10 instead of D18 GPIO PIN
- Change file `open_micro_view.Microscope_light.py`, constant `LED_PIN` to `board.D10`
- Change following configuration in `/boot/config.txt`:
- `dtparam=spi=on`
- `enable_uart=1`
- In file `src/open_micro_view/microscope_light.py`, change constant `LED_PIN`
to `board.D10`

- In `/boot/config.txt` verify/change or add the config:
```conf
dtparam=spi=on
enable_uart=1
```


> **Note**
> Running the process as a normal user may provoke permission errors while
> saving, reading or copying pictures. Temperature may also not be available.
> saving, reading or copying pictures. The setup of directory permissions are
> not detailled here.

## Installation of OpenMicroView
Installation script is located in `install/` directory.
You can launch it with `sudo OpenMicroView/install/install.sh`
Installation script is located in the `install/` directory.

### One-liner installation
You can execute this command, it will do the same as below steps 1, 2, 3 and 4 in a single line.
```
git clone https://github.com/SpaceBiologyGroup/OpenMicroView --depth 1 && sudo OpenMicroView/install/install.sh -A
You can execute this command, it will do the same as below steps 1, 2, 3, 4 and
5 in a single line.
```sh
git clone ssh://[email protected]/SpaceBiologyGroup/OpenMicroView --depth 1 && sudo OpenMicroView/install/install.sh -A
```
Once done, if no error happened you can reboot the Raspberry Pi with
`sudo reboot`.

If you prefer to control every steps, you can do it step by step as shown below.

### 1. Download the project

```sh
git clone ssh://[email protected]/SpaceBiologyGroup/OpenMicroView
git clone ssh://[email protected]/SpaceBiologyGroup/OpenMicroView --depth 1
```

### 2. Install Dependencies
To install dependencies, run the following command as root:
```sh
OpenMicroView/install/install.sh -D
sudo OpenMicroView/install/install.sh -D
```

### 3. Installing as Service (optional)
To install OpenMicroView as a service, run the following command as root:
### 3. Installing as Service
```sh
OpenMicroView/install/install.sh -S
sudo OpenMicroView/install/install.sh -S
```
The software will be copied in `/opt/OpenMicroView/` and a service file
will be created in systemd directory.
will be created in the systemd directory.

### 4. Check your raspberry pi configuration
The install script allows you to check for classical configuration errors,
To do so you can just run the following command as root:
```sh
OpenMicroView/install/install.sh -C
sudo OpenMicroView/install/install.sh -C
```

If every check succeed, the output should look like that:
Expand All @@ -94,19 +102,27 @@ If every check succeed, the output should look like that:
[ OK ] /etc/systemd/system/OpenMicroView.service: XAUTHORITY path seems correct
[INFO] Reboot may be required if you edited the configuration.
```
### 5. Automatically Fix
If required you can try to automatically fix the `/boot/config.txt` file with:
```sh
sudo OpenMicroView/install/install.sh -E
```
then, run step `4.` Once again to check the final config.

### 6. Reboot
Reboot the system (`sudo reboot`). Then, OpenMicroView UI should show up at start.

### Note
You can see full usage of the installation tool using:
```sh
install/install.sh -h
```
or you can execute `-DSC` or `-A` to install dependencies, service, and
to check for configuration errors.

# Starting the interface
## Service
If you installed OpenMicroView as a Service, you can use the following commands
to start/stop/restart or view the status of OpenMicroView:
If you installed OpenMicroView as a Service, you can restart the system
or use the following commands to start/stop/restart or view the status
of OpenMicroView:
```sh
service OpenMicroView start
service OpenMicroView stop
Expand All @@ -120,8 +136,7 @@ systemctl disable OpenMicroView.service
```
In order to view the logs from the service:
```sh
journalctl -u OpenMicroView
# add `-f` to follow logs in real time
journalctl -u OpenMicroView -f
```

## Standalone
Expand All @@ -141,28 +156,40 @@ sudo python3 ./start.py

# Debugging
- `Authentication error`:
- Make sure you are login as root or you prepended `sudo` (e.g. `sudo service OpenMicroView start`)
- Make sure you are logged in as root or you prepended `sudo`
- The software doesn't start at all
- Look at the logs with `journalctl -u OpenMicroView -f`
- Verify 'camera' or 'Legacy Camera' is activated (`sudo raspi-config`
-> `3 Interface` > `1 (Legacy) Camera`)
- If started using the service verify the following
- open `/etc/systemd/system/OpenMicroView.service`
- Check `Environment="DISPLAY=<value>"`: `<value>` is equal to the
output of `echo $DISPLAY` when executed directly on the targeted
screen, not from SSH session (`:0`, `:0.0`, ...).
- Check `Environment="XAUTHORITY=/home/<user>/.Xauthority"`: `<user>`
is you're normal user. You can execute `ls -1 /home/` to find the
correct user. Choose default user if several exists.
- if you make any changes, save, close and reload systemctl with
`systemctl daemon-reload`
- restart service with `service OpenMicroView stop`
- Look at the logs with `journalctl -u OpenMicroView -f`
- Verify 'camera' or 'Legacy Camera' is activated (`sudo raspi-config`
-> `3 Interface` > `1 (Legacy) Camera`)
- If started using the service verify the following
- open `/etc/systemd/system/OpenMicroView.service`
- Check `Environment="DISPLAY=<value>"`: `<value>` is equal to the
output of `echo $DISPLAY` when executed directly on the targeted
screen, not from SSH session (`:0`, `:0.0`, ...).
- Check `Environment="XAUTHORITY=/home/<user>/.Xauthority"`: `<user>`
is you're normal user. You can execute `ls -1 /home/` to find the
correct user. Choose default user if several exists.
- if you make any changes, save, close and reload systemctl with
`systemctl daemon-reload`
- restart service with `service OpenMicroView stop`
- Run `OpenMicroView/install/install.sh -C` to check the configuration
- If error are found, run `OpenMicroView/install/install.sh -E` to fix them.
- If the LED do not switch on correctly:
- Verify `/boot/config.txt` contains `dtparam=audio=off`
- Verify LED is connected on `GPIO D18` connector
- Verify `/boot/config.txt` contains `dtparam=audio=off`
- Verify LED is connected on `GPIO D18` connector
- If the Screen is not calibrated:
- This is likely due to kernel compatibility issue
- Use one of the Compatible OS [listed below](#Versions)
- This is likely due to kernel compatibility issue
- Use one of the Compatible OS [listed below](#operating-system)
- If the screen stays OFF:
- Verify connection of the screen to the raspberry
- Make sure you are using one of the [compatible versions](#operating-system)
- Connect via SSH for debugging
- If the camera is not detected:
- Verify it is activated using `raspi-config`
- Reboot the system
- Make sure you are using one of the [compatible versions](#operating-system)
- Verify current system version with `cat /boot/issue.txt`


# Versions
## Hardware
Expand Down
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