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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
extractGiftiSurface
"""
import os.path as op
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.
:arg infile: A GIFTI surface file
"""
import nibabel as nib
surfimg = nib.load(infile)
vertices, indices = extractGiftiSurface(surfimg)
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
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`.
"""
def extractGiftiSurface(surfimg):
"""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