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| = FreeSurfer Python Development = | = THIS PAGE HAS BEEN MOVED TO SHAREPOINT! = Please refer to this site/make edits here for the most updated information: https://partnershealthcare.sharepoint.com/sites/LCN/SitePages/Additional-Martinos-Center-Resources.aspx#freesurfer-and-lcn-python-development -------------------------- |
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| To ensure consistency and universal access to python libraries, a custom python (anaconda) distribution for internal freesurfer developers is installed at `/space/freesurfer/python/linux`. This way, as a lab, we can have complete control over the tools available to us. 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.'' | <<BR>> <<BR>> <<BR>> = 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`: |
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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 first 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. '''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. |
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| 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: | The freesurfer python library source, which contains general utilities and various submodules like `gems` and `samseg`, is developed in the repository under `repo/python/freesurfer`. In order to utilize this library for your own local development, you must point your `PYTHONPATH` at it: |
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| export PYTHONPATH=/path/to/freesurfer-repository/python:$PYTHONPATH | export PYTHONPATH=/path/to/your/freesurfer-repository/python:$PYTHONPATH |
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| 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: | This allows you to import your working version of the freesurfer library in any script or python interpreter. Alternatively, there is a nightly build of the freesurfer module, enabling import of the package without cloning or installing the full freesurfer repository. To access this, add the following to your `PYTHONPATH`. Currently, we build for python `3.5-3.8`. |
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| import freesurfer as fs 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 |
export PYTHONPATH=/autofs/cluster/freesurfer/python/fsmodule:$PYTHONPATH |
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= FsPython = |
THIS PAGE HAS BEEN MOVED TO SHAREPOINT!
Please refer to this site/make edits here for the most updated information: https://partnershealthcare.sharepoint.com/sites/LCN/SitePages/Additional-Martinos-Center-Resources.aspx#freesurfer-and-lcn-python-development
FreeSurfer and LCN Python Development
To facilitate straightforward and reproducible python development in the lab, a local conda distribution for internal developers is installed at /autofs/cluster/freesurfer/python/linux. To use this version, make sure all calls to python or python3 point to this install by adding the following to your PATH:
export PATH=/autofs/cluster/freesurfer/python/linux/bin:$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.
Developing and Using the FreeSurfer Python Library
The freesurfer python library source, which contains general utilities and various submodules like gems and samseg, is developed in the repository under repo/python/freesurfer. In order to utilize this library for your own local development, you must point your PYTHONPATH at it:
export PYTHONPATH=/path/to/your/freesurfer-repository/python:$PYTHONPATH
This allows you to import your working version of the freesurfer library in any script or python interpreter. Alternatively, there is a nightly build of the freesurfer module, enabling import of the package without cloning or installing the full freesurfer repository. To access this, add the following to your PYTHONPATH. Currently, we build for python 3.5-3.8.
export PYTHONPATH=/autofs/cluster/freesurfer/python/fsmodule:$PYTHONPATH