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| # Portiloop software | |
| This software works with the [Coral implementation](https://github.com/Portiloop/portiloop-hardware) of the `Portiloop` EEG closed-loop stimulation device. | |
| It enables controlling the `Portiloop` from a simple Graphical User Interface (GUI). | |
| ## Quick links | |
| - [Installation on the Portiloop](#installation) | |
| - [GUI usage](#usage) | |
| ## Usage: | |
| The `Portiloop` GUI is a web-based interface running as a `jupyter` server. | |
| - Connect to the `Portiloop` WiFi network. | |
| - Open your favorite web browser | |
| - Enter the following address: `192.168.0.1:9000` | |
| You should now be connected to the `jupyter` server. | |
| _If the jupyter notebook is not yet created:_ | |
| - Hit `New` and select `Python 3`. | |
| This creates a `jupyter` notebook, in which you can simply paste and execute te following: | |
| ```python | |
| from portiloop.capture import Capture | |
| cap = Capture() | |
| ``` | |
| _When the jupyter notebook is created:_ | |
| You can open the notebook and simply execute the cell. | |
| The GUI now looks like this: | |
|  | |
| ### Channels: | |
| The `Channels` pannel enables you to configure each electrode: | |
| - `disabled`: the electrode is not used | |
| - `simple`: the electrode is simply used to measure signal (not recommended) | |
| - `with bias`: the electrode is used to measure signal and to compute a bias ("ground") signal | |
| - `bias out`: the electrode is used to output the bias ("ground") signal | |
| ### General controls: | |
| - `Freq` is the desired sampling rate | |
| - `Time` is the maximum duration of the experiment (you can also stop the experiment manually) | |
| - `Recording` is the name of the `.edf` output file if you wish to record the signal locally | |
| - Tick `Filter` to enable the online filtering pipeline | |
| - Tick `Detect` to enable the online detection pipeline | |
| - Tick `Stimulate` to enable the online stimulation pipeline | |
| - Tick `Record EDF` to record the signal in the file designated in `Recording` | |
| - Tick `Stream LSL` to broadcast the signal on the local network via [LSL](https://labstreaminglayer.readthedocs.io/info/intro.html) | |
| - Tick `Display` to display the signal in the GUI | |
| - `Threshold` enables customizing the optional detection threshold from the GUI (e.g., for classifiers) | |
| - The `Clock` widget lets you select the sampling method: | |
| - `Coral` sets the `ADS1299` sampling rate to twice your target sampling rate, and uses the Coral Real-Time clock to stick to your target sampling rate | |
| - `ADS` sets the `ADS1299` sampling rate to the closest compatible to your target sampling rate and uses the ADS interrupts | |
| ### Custom Filtering | |
| The `Filtering` section lets you customize the filtering pipeline from the GUI. | |
| - The `FIR filter` switch lets you select between the default low-pass FIR filter (used in the Portiloop [paper](https://arxiv.org/abs/2107.13473)), or customize this filter according to your needs (`FIR order` and `FIR cutoff`) | |
| - `Polyak mean`, `Polyak std` and `Epsilon` let you customize the online standardization pipeline, which also acts as a high-pass filter | |
| ### Capture | |
| The `Capture` switch lets you start and stop the experiment at any point in time | |
| _Note: once the experiment is started, all widgets are deactivated until you stop the experiment._ | |
| ## Installation: | |
| Follow these instruction if the software is not readily installed on your `Portiloop` device. | |
| ### Install the library: | |
| _(Requires python 3)_ | |
| #### Install the following libraries from apt to avoid issues: | |
| - `sudo apt install python3-numpy` | |
| - `sudo apt install python3-scipy` | |
| - `sudo apt install python3-pycoral` | |
| - Clone this repository on the `Coral` board | |
| - `cd` to he root of the repository where the `setup.py` file is located | |
| - Execute `pip3 install -e .` | |
| ### Setup the Coral board as a wifi access point | |
| You can find instructions [here](https://www.linux.com/training-tutorials/create-secure-linux-based-wireless-access-point/) to set Linux as a WiFi access point. | |
| ### Setup a jupyter server: | |
| - On your `Portiloop` device, execute `pip3 install notebook` | |
| - Generate a `jupyter` password and copy the result: | |
| ```python | |
| from notebook.auth import passwd | |
| passwd() | |
| ``` | |
| - Execute `jupyter notebook --generate-config` | |
| - `cd` to the `.jupyter` folder and edit `jupyter_notebook_config.py` | |
| - Find the relevant lines, and uncomment them while setting the following values: | |
| - `c.NotebookApp.ip = '*'` | |
| - `c.NotebookApp.open_browser = False` | |
| - `c.NotebookApp.password = u'your_generated_password_here'` | |
| - `c.NotebookApp.port = 9000` | |
| ### Setup a service for your jupyter server to start automatically: | |
| - `cd /etc/systemd/system` | |
| - create an empty file named `notebook.service` and open it. | |
| - paste the following and save: | |
| ```bash | |
| [Unit] | |
| Description=Autostarts jupyter server | |
| [Service] | |
| User=mendel | |
| WorkingDirectory=~ | |
| ExecStart=jupyter notebook | |
| Restart=always | |
| [Install] | |
| WantedBy=multi-user.target | |
| ``` | |
| - Execute `sudo systemctl daemon-reload` | |
| - Execute `sudo systemctl start notebook.service` | |
| - Check that your service is up and running: `sudo systemctl status notebook.service` | |