Contains scripts to use the ExTrack python library.
The scripts provide command line tools to run ExTrack on traced localisation files in CSV format, save the arguments and fitted models, and run predictions on the data using the ExTrack model.
Setup the environment as described on the ExTrack documentation. This recommends
using a conda enviroment to install dependencies (cupy is optional).
conda create -n extrack -c conda-forge python pip numpy lmfit xmltodict matplotlib pandas jupyter # cupy
conda activate extrack
Clone the ExTrack repository and install in the enviroment.
The ExTrack documentation uses the deprecated python setup.py install.
This can be replaced with:
[path/to/ExTrack] $ pip install .
The extrack-scripts in this repository can then be added to the PATH.
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run-extrack.py: runs ExTrack on input CSV files, saves the fitted model, and outputs predicted states and positions
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show-model.py: shows details of fitted models