The following package is for analyzing data collected from Stytra. The Preprocessing script can be used for both freely-swimming and head-fixed fish experiments. The Analysis script is meant for freely-swimming.
Last Updated: 6/12/2024 RR
This repository requires Python 3.12 or higher.
Clone this repository. Then, you'll need to create a virtual environment to be able to run the programs:
cd stytra-analysis
python3 -m venv venv
source venv/bin/activate
pip install -r requirements.txt
You should now have all the dependencies. Anytime you run this software, start by activating the virtual environment by doing this:
cd stytra-analysis
source venv/bin/activate
Before generating analyses, we need to preprocess your raw experimental data:
python preprocess.py <path> --trials <# of repeats per trial>
The --trials parameter is optional. It specifies the number of experiments
per repeats that the analysis should consider aggregations over. If it is not
specified, it will be automatically set to 3. The path to the experiment should be an
absolute path, not a relative path.
If you are on a MacBook, you can just drag and drop the folder into terminal.
To see more information, you can run:
python preprocess.py --help
Now that preprocessing is done, we can run analysis.py to generate plots.
It can be run much like preprocessing:
python analysis.py /path/to/experiment
Running the above command will create all of the plots you need in a folder in
that data directory called plots. It will also generate a latencies.csv file.
Remember, this must be run with the virtual environment enabled. Additionally,
the path to the experiment should be an absolute path, not a relative path.