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| ## page was renamed from python = FreeSurfer Python Development = |
= FreeSurfer and LCN Python Development = |
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| To ensure consistency and control of python libraries in the lab, a custom python3 (anaconda) distribution for internal freesurfer developers is installed at `/space/freesurfer/python/linux`. To make sure calls to `python` or `python3` point to this version, add the following to your PATH. '''''Note:''' the examples on this page assume you're using bash as your shell.'' | To facilitate straightforward and reproducible python development in the lab, a local conda distribution for internal developers is installed at `/autofs/cluster/freesurfer/python/linux`. To use this version, make sure all calls to `python` or `python3` point to this install by adding the following to your `PATH`: |
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| export PATH=/space/freesurfer/python/linux/bin:$PATH | export PATH=/autofs/cluster/freesurfer/python/linux/bin:$PATH |
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| Keep in mind there's also a `python3` link in `/usr/pubsw/bin`, so it's important that `/space/freesurfer/python/linux/bin` comes before it in your PATH. | Keep in mind there's also a `python3` link in `/usr/pubsw/bin`, so it's important that `/autofs/cluster/freesurfer/python/linux/bin` comes before that in your `PATH`. If you want a python package installed into this distribution, email Andrew. |
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| === Developing and Using the FreeSurfer Python Library === The freesurfer python library, which contains general FS utilities and various submodules like deepsurfer, gems, and samseg, is developed in the repository under `repo/python/freesurfer`. In order to utilize this library during development, you must point your `PYTHONPATH` at it: {{{ export PYTHONPATH=/path/to/your/freesurfer-repository/python:$PYTHONPATH }}} This allows you to import your working version of the freesurfer library in any script or python interpreter. You can test this by calling `python` then running: {{{ import freesurfer as fs status = fs.run('echo hello!') }}} === Tensorflow GPU === By default, the cpu-tensorflow package is installed, but if you're on a machine with cuda installed, you can use the gpu-enabled tensorflow by adding to the following search paths: {{{ export PYTHONPATH=/space/freesurfer/python/linux/tensorflow-gpu:$PYTHONPATH export LD_LIBRARY_PATH=/usr/local/cuda/lib64:$LD_LIBRARY_PATH }}} |
'''NOTE:''' This "lab" conda install is meant for quick access to python utilities. If you're a frequent python developer who uses multiple package versions or environments, please install your own local [[https://docs.conda.io/projects/conda/en/latest/user-guide/install/linux.html|conda distribution]]. It will give you full access and control of the installed packages. |
FreeSurfer and LCN Python Development
To facilitate straightforward and reproducible python development in the lab, a local conda distribution for internal developers is installed at /autofs/cluster/freesurfer/python/linux. To use this version, make sure all calls to python or python3 point to this install by adding the following to your PATH:
export PATH=/autofs/cluster/freesurfer/python/linux/bin:$PATH
Keep in mind there's also a python3 link in /usr/pubsw/bin, so it's important that /autofs/cluster/freesurfer/python/linux/bin comes before that in your PATH. If you want a python package installed into this distribution, email Andrew.
NOTE: This "lab" conda install is meant for quick access to python utilities. If you're a frequent python developer who uses multiple package versions or environments, please install your own local conda distribution. It will give you full access and control of the installed packages.