def test_low_io_vtk():
with InTemporaryDirectory():
fname = 'test.fib'
# Test save
save_vtk_streamlines(streamlines, fname, binary=True)
tracks = load_vtk_streamlines(fname)
npt.assert_equal(len(tracks), len(streamlines))
npt.assert_array_almost_equal(tracks[1], streamline, decimal=4)
def get_tractogram_in_voxel_space(tract_fname,
ref_anat_fname,
tracts_attribs={'orientation': 'unknown'},
origin=Origin.NIFTI):
if tracts_attribs['orientation'] != 'unknown':
to_lps = tracts_attribs['orientation'] == 'LPS'
streamlines = load_vtk_streamlines(tract_fname, to_lps)
sft = StatefulTractogram(streamlines, ref_anat_fname, Space.RASMM)
else:
sft = load_tractogram(tract_fname,
ref_anat_fname,
bbox_valid_check=False,
trk_header_check=False)
sft.to_vox()
sft.to_origin(origin)
return sft
def load_tractogram(filename,
reference,
to_space=Space.RASMM,
shifted_origin=False,
bbox_valid_check=True,
trk_header_check=True):
""" Load the stateful tractogram from any format (trk, tck, vtk, fib, dpy)
Parameters
----------
filename : string
Filename with valid extension
reference : Nifti or Trk filename, Nifti1Image or TrkFile, Nifti1Header or
trk.header (dict), or 'same' if the input is a trk file.
Reference that provides the spatial attribute.
Typically a nifti-related object from the native diffusion used for
streamlines generation
to_space : Enum (dipy.io.stateful_tractogram.Space)
Space to which the streamlines will be transformed after loading.
shifted_origin : bool
Information on the position of the origin,
False is Trackvis standard, default (center of the voxel)
True is NIFTI standard (corner of the voxel)
bbox_valid_check : bool
Verification for negative voxel coordinates or values above the
volume dimensions. Default is True, to enforce valid file.
trk_header_check : bool
Verification that the reference has the same header as the spatial
attributes as the input tractogram when a Trk is loaded
Returns
-------
output : StatefulTractogram
The tractogram to load (must have been saved properly)
"""
_, extension = os.path.splitext(filename)
if extension not in ['.trk', '.tck', '.vtk', '.fib', '.dpy']:
logging.error('Output filename is not one of the supported format')
return False
if to_space not in Space:
logging.error('Space MUST be one of the 3 choices (Enum)')
return False
if reference == 'same':
if extension == '.trk':
reference = filename
else:
logging.error('Reference must be provided, "same" is only ' +
'available for Trk file.')
return False
if trk_header_check and extension == '.trk':
if not is_header_compatible(filename, reference):
logging.error('Trk file header does not match the provided ' +
'reference')
return False
timer = time.time()
data_per_point = None
data_per_streamline = None
if extension in ['.trk', '.tck']:
tractogram_obj = nib.streamlines.load(filename).tractogram
streamlines = tractogram_obj.streamlines
if extension == '.trk':
data_per_point = tractogram_obj.data_per_point
data_per_streamline = tractogram_obj.data_per_streamline
elif extension in ['.vtk', '.fib']:
streamlines = load_vtk_streamlines(filename)
elif extension in ['.dpy']:
dpy_obj = Dpy(filename, mode='r')
streamlines = list(dpy_obj.read_tracks())
dpy_obj.close()
logging.debug('Load %s with %s streamlines in %s seconds', filename,
len(streamlines), round(time.time() - timer, 3))
sft = StatefulTractogram(streamlines,
reference,
Space.RASMM,
shifted_origin=shifted_origin,
data_per_point=data_per_point,
data_per_streamline=data_per_streamline)
if to_space == Space.VOX:
sft.to_vox()
elif to_space == Space.VOXMM:
sft.to_voxmm()
if bbox_valid_check and not sft.is_bbox_in_vox_valid():
raise ValueError('Bounding box is not valid in voxel space, cannot ' +
'load a valid file if some coordinates are invalid.' +
'Please set bbox_valid_check to False and then use' +
'the function remove_invalid_streamlines to discard' +
'invalid streamlines.')
return sft
