gifti.py 5.76 KB
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#!/usr/bin/env python
#
# gifti.py - GIFTI file support.
#
# Author: Paul McCarthy  <pauldmccarthy@gmail.com>
#         Michiel Cottar <michiel.cottaar@ndcn.ox.ac.uk>
#
"""This class provides classes and functions for working with GIFTI files.

The GIFTI file format specification can be found at
http://www.nitrc.org/projects/gifti/

Support is currently very basic - only the following classes/functions
are available:

  .. autosummary::
     :nosignatures:

     GiftiSurface
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     loadGiftiSurface
     relatedFiles
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"""


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import            glob
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import os.path as op

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import nibabel as nib

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import fsl.utils.path as fslpath
from . import            mesh


class GiftiSurface(mesh.TriangleMesh):
    """Class which represents a GIFTI surface image. This is essentially
    just a 3D model made of triangles.

    In addition to the ``vertices`` and ``indices`` provided by the
    :class:`.TriangleMesh` class (from which the ``GiftiSurface`` class
    derives), a ``GiftiSurface`` instance has the following attributes:

    ============== ====================================================
    ``name``       A name, typically the file name sans-suffix.
    ``dataSource`` Full path to the GIFTI file.
    ``surfImg``    Reference to the loaded ``nibabel.gifti.GiftiImage``
    ============== ====================================================
    """


    def __init__(self, infile):
        """Load the given GIFTI file using ``nibabel``, and extracts surface
        data using the  :func:`extractGiftiSurface` function.

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        :arg infile: A GIFTI surface file (``*.surf.gii``).
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        """

        surfimg           = nib.load(infile)
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        vertices, indices = loadGiftiSurface(surfimg)
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        mesh.TriangleMesh.__init__(self, vertices, indices)

        name   = fslpath.removeExt(op.basename(infile), ALLOWED_EXTENSIONS)
        infile = op.abspath(infile)

        self.name       = name
        self.dataSource = infile
        self.surfImg    = surfimg


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    def loadVertexData(self, dataSource):
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        """Attempts to load data associated with each vertex of this
        ``GiftiSurface`` from the given ``dataSource``.

        Currently, only the first ``DataArray`` contained in the
        file is returned.

         - ``*.func.gii``
         - ``*.shape.gii``
         - ``*.label.gii``
         - ``*.time.gii``
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        """

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        # TODO support 4D 
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        # TODO make this more robust
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        vdata = nib.load(dataSource)
        vdata = vdata.darrays[0].data

        if vdata.size != self.vertices.shape[0]:
            raise ValueError('Incompatible size: {}'.format(dataSource))

        return vdata
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ALLOWED_EXTENSIONS = ['.surf.gii', '.gii']
"""List of file extensions that a file containing Gifti surface data
is expected to have.
"""


EXTENSION_DESCRIPTIONS = ['GIFTI surface file', 'GIFTI surface file']
"""A description for each of the :data:`ALLOWED_EXTENSIONS`.
"""


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def loadGiftiSurface(surfimg):
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    """Extracts surface data from the given ``nibabel.gifti.GiftiImage``.

    The image is expected to contain the following``<DataArray>`` elements:

      - one comprising ``NIFTI_INTENT_POINTSET`` data (the surface vertices)
      - one comprising ``NIFTI_INTENT_TRIANGLE`` data (vertex indices
        defining the triangles).

    A ``ValueError`` will be raised if this is not the case.

    :arg surfimg: A ``GiftiImage`` containing surface data.

    :returns:     A tuple containing these values:

                   - A :math:`N\\times 3` ``numpy`` array containing :math:`N`
                     vertices.
    
                   - A :math:`M\\times 3` ``numpy`` array containing the 
                     vertex indices for :math:`M` triangles.
    """

    from nibabel import gifti

    codes    = gifti.gifti.intent_codes.code
    
    indices  = None
    vertices = None
    
    for darray in surfimg.darrays:
        
        if darray.intent == codes['pointset']:
            
            if vertices is not None:
                raise ValueError('multiple arrays with intent "{}"'.format(
                    darray.intent))
            
            vertices = darray.data
            
        elif darray.intent == codes['triangle']:
            if indices is not None:
                raise ValueError('multiple arrays with intent "{}"'.format(
                    darray.intent))
            
            indices = darray.data
            
    if vertices is None:
        raise ValueError('no array with intent "pointset" found')
    
    if indices is None:
        raise ValueError('no array witbh intent "triangle"found')
    
    return vertices, indices
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def relatedFiles(fname):
    """Given a GIFTI file, returns a list of other GIFTI files in the same
    directory which appear to be related with the given one.  Files which
    share the same prefix are assumed to be related to the given file.

    """

    try:
        # We want to return all files in the same
        # directory which have the following name:

        # 
        # [prefix].*.[type].gii
        #
        #   where
        #     - prefix is the file prefix, and which
        #       may include periods.
        #
        #     - we don't care about the middle
        #
        #     - type is func, shape, label, or time

        # We determine the unique prefix of the
        # given file, and back-up to the most
        # recent period. Then search for other
        # files which have that same (non-unique)
        # prefix.
        prefix = fslpath.uniquePrefix(fname)
        prefix = prefix[:prefix.rfind('.')]

        funcs  = glob.glob('{}*.func.gii' .format(prefix))
        shapes = glob.glob('{}*.shape.gii'.format(prefix))
        labels = glob.glob('{}*.label.gii'.format(prefix))
        times  = glob.glob('{}*.time.gii' .format(prefix))

        return funcs + shapes + labels + times

    except:
        return []