def test_MGHImage():
testfile = op.join(datadir, 'example.mgz')
# Load from a file
img = fslmgh.MGHImage(testfile)
nbimg = nib.load(testfile)
v2s = nbimg.header.get_vox2ras_tkr()
w2s = affine.concat(v2s, affine.invert(nbimg.affine))
assert np.all(np.isclose(img[:], np.asanyarray(nbimg.dataobj)))
assert np.all(np.isclose(img.voxToWorldMat, nbimg.affine))
assert np.all(np.isclose(img.voxToSurfMat, v2s))
assert np.all(np.isclose(img.surfToVoxMat, affine.invert(v2s)))
assert np.all(np.isclose(img.worldToSurfMat, w2s))
assert np.all(np.isclose(img.surfToWorldMat, affine.invert(w2s)))
assert img.name == op.basename(testfile)
assert img.dataSource == testfile
assert img.mghImageFile == testfile
# Load from an in-memory nibabel object
img = fslmgh.MGHImage(nbimg)
assert np.all(np.isclose(img[:], np.asanyarray(nbimg.dataobj)))
assert np.all(np.isclose(img.voxToWorldMat, nbimg.affine))
assert img.dataSource is None
assert img.mghImageFile is None
def loadVertexDataFile(infile):
"""Loads the given Freesurfer vertex data, label, or annotation file.
This function return different things depending on what ``infile`` is:
- If ``infile`` is a vertex data file, a ``(nvertices,)`` array is
returned, containing one value for each vertex in the mesh.
- If ``infile`` is a ``mgh``/``mgz`` file, the image data is returned
as-is, with dimensions of length 1 squeezed out (under the assumption
that the image contains scalar vertex data).
- If ``infile`` is a vertex label file, a tuple containing the following
is returned:
- a ``(n,)`` array, containing the indices of all vertices that are
specified in the file.
- a ``(n,)`` array, containing scalar value for each vertex
- If ``infile`` is a vertex annotation file, a tuple containing the
following is returned:
- a ``(n,)`` array containing the indices of all ``n`` vertices that
are specified in the file.
- a ``(l, 5)`` array containing the RGBA colour, and the label value,
for every label that is specified in the file.
- A list of length ``l``, containing the names of every label that is
specified in the file.
"""
if isVertexDataFile(infile):
return nibfs.read_morph_data(infile)
elif isVertexLabelFile(infile):
return nibfs.read_label(infile, read_scalars=True)
elif isVertexAnnotFile(infile):
# nibabel 2.2.1 is broken w.r.t. .annot files.
# raise ValueError('.annot files are not yet supported')
labels, lut, names = nibfs.read_annot(infile, orig_ids=False)
return labels, lut, names
elif isVertexMGHFile(infile):
return fslmgh.MGHImage(infile)[:].squeeze()
else:
raise ValueError('Unrecognised freesurfer '
'file type: {}'.format(infile))
def test_MGHImage_save():
testfile = op.join(datadir, 'example.mgz')
with tempdir.tempdir():
shutil.copy(testfile, 'example.mgz')
testfile = 'example.mgz'
img = fslmgh.MGHImage(testfile)
img.save()
expfile = op.abspath(fslimage.addExt('example', mustExist=False))
assert img.dataSource == op.abspath(expfile)
def test_voxToSurfMat():
testfile = op.join(datadir, 'example.mgz')
img = fslmgh.MGHImage(testfile)
assert np.all(np.isclose(img.voxToSurfMat, fslmgh.voxToSurfMat(img)))