trf2csv#setup-logfile-extraction

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Ismail ZERGOUG

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May 25, 2020, 3:55:43 PM5/25/20
to PyMedPhys
Hi Simon, I'm trying to get access to "https://gitlab.com/level-0/trf2csv#setup-logfile-extraction" without success. Is there any problem with it?


Best regards

Simon Biggs

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May 25, 2020, 5:27:20 PM5/25/20
to Ismail ZERGOUG, PyMedPhys
Hi Ismail,

Some time ago we actually moved the trf2csv library into PyMedPhys (https://github.com/pymedphys/pymedphys/) away from GitLab. The documentation for converting trf files into csv files via the command line tool can be found at https://docs.pymedphys.com/ref/cli/trf.html

Before being able to use that command line tool you'll need to follow the installation instructions at https://docs.pymedphys.com/howto/get-started.html.

The gist of the docs above are that to install you first need to install Python version 3.7 or higher (making sure to add to path), then in a new terminal/command prompt run:

pip install pymedphys

This will install pymedphys with all the batteries included. If you want to just use pymedphys for trf conversion only, you can have a smaller install by running:

pip install numpy pandas
pip install pymedphys --no-deps

After you have installed pymedphys, open a fresh terminal/command prompt, navigate to a directory where you have some trf files and then run:

pymedphys trf to-csv *.trf

Hopefully this helps,
Cheers,
Simon
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