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Python interface to libminc

Project description

Pyminc is a python interface to the MINC 2 library, allowing use of numpy arrays to access MINC data, and other such similar goodies, developed by Jason Lerch.


Documentation can be found in the tutorial section of the MINC Wikibooks (Programming with MINC2 in Python):

http://en.wikibooks.org/wiki/MINC/Tutorials


Requirements:

Pyminc is compatible with both Python 2 and Python 3. It requires numpy (the python numerical arrays package) to work; this can be installed automatically from PyPI via setuptools. Also, it needs MINC2 compiled as a shared object and accessible through the standard search paths. For the tests, you also need the minc-tools suite of command-line utilities.

Currently pyminc is geared towards the develop branch of libminc, because that is the version of MINC that is installed through the minc-toolkit (https://github.com/BIC-MNI/minc-toolkit). There are some substantial differences between that branch and the master branch of libminc in terms of the argument types of several functions.


Installing pyminc:

Pyminc is installable from PyPI via setuptools, pip, etc. To install from source:

  1. Untar the tarball if applicable
  2. Run ‘python setup.py install’ with an optional –prefix if you want to install it in a non-default location.
  3. Test the installation. To test the installation of pyminc library, run “python setup.py test”. At your option, also run the pyminc_test2.py script in the scripts folder. This program has 3 arguments: a minc file, a method for smoothing the volume (numpy, blitz or weave) and an output file name.

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