A package to easily open trx.mat files in use at the Decision & Bayesian Computation lab at the Pasteur Institute in Paris
Readme
pytrxmat is a Python package designed to facilitate the access and manipulation of data stored in trx.mat files commonly used in behavior screens. These files contain raw tracking data and postprocessing results for multiple larvae in experimental studies. Installation
pip install pytrxmat
The main component of pytrxmat is the TRX class, which provides a convenient interface to interact with trx.mat files.
from pytrxmat.trx import TRX
# Instantiate the TRX class with the path to your 'trx.mat' file
trx = TRX('path/to/trx.mat')
The TRX class allows you to retrieve various fields from the trx.mat file, including scalar, string, time series, and composite array fields.
# Get a scalar field (e.g., 'numero_larva_num')
scalar_data = trx.get('numero_larva_num')
# Get a time series field (e.g., 'x_tail')
time_series_data = trx.get('x_tail')
# Get a composite array field (e.g., 'duration_large')
composite_array_data = trx.get_composite_array('duration_large')
# Get string fields (e.g., 'neuron' and 'protocol')
string_data = trx.get_string(['neuron', 'protocol'])
The trx.mat file format is a standardized way of storing experimental data in the Decision and Bayesian Computation lab at the Pasteur Institute. The file contains multiple fields, each corresponding to different aspects of the larvae's behavior. The fields include univariate and multivariate time series, classification labels and probabilities, behavior summaries, and metadata such as full paths, IDs, and neuron information.
Contributions to this project are welcome. Feel free to open issues for bug reports or feature requests. If you'd like to contribute code, please submit a pull request.
This project is licensed under the MIT License - see the LICENSE file for details.
FAQs
A package to easily open trx.mat files in use at the Decision & Bayesian Computation lab at the Pasteur Institute in Paris
We found that pytrxmat demonstrated a healthy version release cadence and project activity because the last version was released less than a year ago. It has 1 open source maintainer collaborating on the project.
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