Metadata-Version: 2.1
Name: fslpy
Version: 3.0.1
Summary: FSL Python library
Home-page: https://git.fmrib.ox.ac.uk/fsl/fslpy
Author: Paul McCarthy
Author-email: pauldmccarthy@gmail.com
License: Apache License Version 2.0
Description: fslpy
        =====
        
        .. image:: https://img.shields.io/pypi/v/fslpy.svg
           :target: https://pypi.python.org/pypi/fslpy/
        
        .. image:: https://anaconda.org/conda-forge/fslpy/badges/version.svg
           :target: https://anaconda.org/conda-forge/fslpy
        
        .. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.1470750.svg
           :target: https://doi.org/10.5281/zenodo.1470750
        
        .. image:: https://git.fmrib.ox.ac.uk/fsl/fslpy/badges/master/coverage.svg
           :target: https://git.fmrib.ox.ac.uk/fsl/fslpy/commits/master/
        
        
        The ``fslpy`` project is a `FSL <http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/>`_
        programming library written in Python. It is used by `FSLeyes
        <https://git.fmrib.ox.ac.uk/fsl/fsleyes/fsleyes/>`_.
        
        
        ``fslpy`` is tested against Python versions 3.5, 3.6 and 3.7.
        
        
        Installation
        ------------
        
        
        Install ``fslpy`` and its core dependencies via pip::
        
            pip install fslpy
        
        
        ``fslpy`` is also available on `conda-forge <https://conda-forge.org/>`_::
        
            conda install -c conda-forge fslpy
        
        
        Dependencies
        ------------
        
        
        All of the core dependencies of ``fslpy`` are listed in the
        `requirements.txt <requirements.txt>`_ file.
        
        Some extra dependencies are listed in
        `requirements-extra.txt <requirements-extra.txt>`_
        which provide addditional functionality:
        
        - ``wxPython``: The `fsl.utils.idle <fsl/utils/idle.py>`_ module has
          functionality  to schedule functions on the ``wx`` idle loop.
        
        - ``indexed_gzip``: The `fsl.data.image.Image <fsl/data/image.py>`_ class
          can use ``indexed_gzip`` to keep large compressed images on disk instead
          of decompressing and loading them into memory..
        
        - ``trimesh``/``rtree``: The `fsl.data.mesh.TriangleMesh <fsl/data/mesh.py>`_
          class has some methods which use ``trimesh`` to perform geometric queries
          on the mesh.
        
        - ``Pillow``: The `fsl.data.bitmap.Bitmap <fsl/data/bitmap.py>`_ class uses
          ``Pillow`` to load image files.
        
        
        If you are using Linux, you need to install wxPython first, as binaries are
        not available on PyPI. Install wxPython like so, changing the URL for your
        specific platform::
        
            pip install -f https://extras.wxpython.org/wxPython4/extras/linux/gtk2/ubuntu-16.04/ wxpython
        
        
        Once wxPython has been installed, you can type the following to install the
        rest of the extra dependencies::
        
            pip install fslpy[extras]
        
        
        Dependencies for testing and documentation are listed in the
        `requirements-dev.txt <requirements-dev.txt>`_ file.
        
        
        Non-Python dependencies
        ^^^^^^^^^^^^^^^^^^^^^^^
        
        
        The `fsl.data.dicom <fsl/data/dicom.py>`_ module requires the presence of
        Chris Rorden's `dcm2niix <https://github.com/rordenlab/dcm2niix>`_ program.
        
        
        The ``rtree`` library assumes that ``libspatialindex`` is installed on
        your system.
        
        
        The `fsl.transform.x5 <fsl/transform/x5.py>`_ module uses `h5py
        <https://www.h5py.org/>`_, which requires ``libhdf5``.
        
        
        Documentation
        -------------
        
        ``fslpy`` is documented using `sphinx <http://http://sphinx-doc.org/>`_. You
        can build the API documentation by running::
        
            pip install -r requirements-dev.txt
            python setup.py doc
        
        The HTML documentation will be generated and saved in the ``doc/html/``
        directory.
        
        
        Tests
        -----
        
        Run the test suite via::
        
            pip install -r requirements-dev.txt
            python setup.py test
        
        A test report will be generated at ``report.html``, and a code coverage report
        will be generated in ``htmlcov/``.
        
        
        Contributing
        ------------
        
        
        If you are interested in contributing to ``fslpy``, check out the
        `contributing guide <doc/contributing.rst>`_.
        
        
        Credits
        -------
        
        
        The `fsl.data.dicom <fsl/data/dicom.py>`_ module is little more than a thin
        wrapper around Chris Rorden's `dcm2niix
        <https://github.com/rordenlab/dcm2niix>`_ program.
        
        
        The `example.mgz <tests/testdata/example.mgz>`_ file, used for testing,
        originates from the ``nibabel`` test data set.
        
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Developers
Classifier: License :: OSI Approved :: Apache Software License
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Topic :: Software Development :: Libraries :: Python Modules
Description-Content-Type: text/x-rst
Provides-Extra: extras
