Commit fe5c855a authored by Paul McCarthy's avatar Paul McCarthy
Browse files

N-d gifti vertex data arrays can be loaded.

parent ed2a830f
Pipeline #273 failed with stage
......@@ -25,9 +25,11 @@ are available:
import glob
import os.path as op
import numpy as np
import nibabel as nib
import fsl.utils.path as fslpath
from . import constants
from . import mesh
......@@ -52,10 +54,12 @@ class GiftiSurface(mesh.TriangleMesh):
data using the :func:`extractGiftiSurface` function.
:arg infile: A GIFTI surface file (``*.surf.gii``).
.. todo:: Allow loading from a ``.topo.gii`` and ``.coord.gii`` file?
surfimg = nib.load(infile)
vertices, indices = loadGiftiSurface(surfimg)
surfimg, vertices, indices = loadGiftiSurface(infile)
mesh.TriangleMesh.__init__(self, vertices, indices)
......@@ -71,27 +75,15 @@ class GiftiSurface(mesh.TriangleMesh):
"""Overrides the :meth:`.TriangleMesh.loadVertexData` method.
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``
``GiftiSurface`` from the given ``dataSource``, which may be
a GIFTI file or a plain text file which contains vertex data.
if dataSource.endswith('.gii'):
# TODO support 4D
# TODO make this more robust
vdata = nib.load(dataSource)
vdata = vdata.darrays[0].data
vdata = loadGiftiVertexData(dataSource)[1]
vdata = None
return mesh.TriangleMesh.loadVertexData(self, dataSource, vdata)
......@@ -106,7 +98,7 @@ EXTENSION_DESCRIPTIONS = ['GIFTI surface file', 'GIFTI surface file']
def loadGiftiSurface(surfimg):
def loadGiftiSurface(filename):
"""Extracts surface data from the given ``nibabel.gifti.GiftiImage``.
The image is expected to contain the following``<DataArray>`` elements:
......@@ -117,10 +109,12 @@ def loadGiftiSurface(surfimg):
A ``ValueError`` will be raised if this is not the case.
:arg surfimg: A ``GiftiImage`` containing surface data.
:arg filename: Name of a GIFTI file containing surface data.
:returns: A tuple containing these values:
- The loaded ``nibabel.gifti.GiftiImage`` instance
- A :math:`N\\times 3` ``numpy`` array containing :math:`N`
......@@ -128,37 +122,84 @@ def loadGiftiSurface(surfimg):
vertex indices for :math:`M` triangles.
from nibabel import gifti
gimg = nib.load(filename)
codes = gifti.gifti.intent_codes.code
pointsetCode = constants.NIFTI_INTENT_POINTSET
triangleCode = constants.NIFTI_INTENT_TRIANGLE
pointsets = [d for d in gimg.darrays if d.intent == pointsetCode]
triangles = [d for d in gimg.darrays if d.intent == triangleCode]
if len(gimg.darrays) != 2:
raise ValueError('GIFTI surface files must contain exactly '
'one pointset array and one triangle array')
indices = None
vertices = None
if len(pointsets) != 1:
raise ValueError('GIFTI surface files must contain '
'exactly one pointset array')
for darray in surfimg.darrays:
if darray.intent == codes['pointset']:
if vertices is not None:
raise ValueError('multiple arrays with intent "{}"'.format(
vertices =
elif darray.intent == codes['triangle']:
if indices is not None:
raise ValueError('multiple arrays with intent "{}"'.format(
indices =
if vertices is None:
raise ValueError('no array with intent "pointset" found')
if len(triangles) != 1:
raise ValueError('GIFTI surface files must contain '
'exactly one triangle array')
vertices = pointsets[0].data
indices = triangles[0].data
return gimg, vertices, indices
def loadGiftiVertexData(filename):
"""Loads vertex data from the given GIFTI file.
It is assumed that the given file does not contain any
which contains either:
- One ``(M, N)`` data array containing ``N`` data points for ``M``
- One or more ``(M, 1)`` data arrays each containing a single data point
for ``M`` vertices, and all with the same intent code
Returns a tuple containing:
if indices is None:
raise ValueError('no array witbh intent "triangle"found')
- The loaded ``nibabel.gifti.GiftiImage`` object
- A ``(M, N)`` numpy array containing ``N`` data points for ``M``
gimg = nib.load(filename)
intents = set([d.intent for d in gimg.darrays])
if len(intents) != 1:
raise ValueError('{} contains multiple (or no) intents'
': {}'.format(filename, intents))
intent = intents.pop()
if intent in (constants.NIFTI_INTENT_POINTSET,
raise ValueError('{} contains surface data'.format(filename))
# Just a single array - return it as-is.
# n.b. Storing (M, N) data in a single
# DataArray goes against the GIFTI spec,
# but hey, it happens.
if len(gimg.darrays) == 1:
return gimg.darrays[0].data
# Otherwise extract and concatenate
# multiple 1-dimensional arrays
vdata = [ for d in gimg.darrays]
if any([len(d.shape) != 1 for d in vdata]):
raise ValueError('{} contains one or more non-vector '
return vertices, indices
return gimg, np.vstack(vdata).T
def relatedFiles(fname):
......@@ -139,6 +139,9 @@ class TriangleMesh(object):
:arg dataSource: Path to the vertex data to load
:arg vertexData: The vertex data itself, if it has already been
:returns: A ``(M, N)``) array, which contains ``N`` data points
for ``M`` vertices.
nvertices = self.vertices.shape[0]
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