def main():
parser = _build_arg_parser()
args = parser.parse_args()
assert_inputs_exist(
parser,
[args.moving_tractogram, args.target_file, args.transformation])
assert_outputs_exist(parser, args, args.out_tractogram)
moving_sft = load_tractogram_with_reference(parser,
args,
args.moving_tractogram,
bbox_check=False)
transfo = np.loadtxt(args.transformation)
if args.inverse:
transfo = np.linalg.inv(transfo)
moved_streamlines = transform_streamlines(moving_sft.streamlines, transfo)
new_sft = StatefulTractogram(
moved_streamlines,
args.target_file,
Space.RASMM,
data_per_point=moving_sft.data_per_point,
data_per_streamline=moving_sft.data_per_streamline)
if args.remove_invalid:
ori_len = len(new_sft)
new_sft.remove_invalid_streamlines()
logging.warning('Removed {} invalid streamlines.'.format(ori_len -
len(new_sft)))
save_tractogram(new_sft, args.out_tractogram)
elif args.keep_invalid:
if not new_sft.is_bbox_in_vox_valid():
logging.warning('Saving tractogram with invalid streamlines.')
save_tractogram(new_sft, args.out_tractogram, bbox_valid_check=False)
else:
save_tractogram(new_sft, args.out_tractogram)
def main():
parser = _build_arg_parser()
args = parser.parse_args()
assert_inputs_exist(parser, [args.moving_tractogram, args.target_file,
args.deformation])
assert_outputs_exist(parser, args, args.out_tractogram)
sft = load_tractogram_with_reference(parser, args, args.moving_tractogram,
bbox_check=False)
deformation = nib.load(args.deformation)
deformation_data = np.squeeze(deformation.get_fdata())
if not is_header_compatible(sft, deformation):
parser.error('Input tractogram/reference do not have the same spatial '
'attribute as the deformation field.')
# Warning: Apply warp in-place
moved_streamlines = warp_streamlines(sft, deformation_data)
new_sft = StatefulTractogram(moved_streamlines, args.target_file,
Space.RASMM,
data_per_point=sft.data_per_point,
data_per_streamline=sft.data_per_streamline)
if args.remove_invalid:
ori_len = len(new_sft)
new_sft.remove_invalid_streamlines()
logging.warning('Removed {} invalid streamlines.'.format(
ori_len - len(new_sft)))
save_tractogram(new_sft, args.out_tractogram)
elif args.keep_invalid:
if not new_sft.is_bbox_in_vox_valid():
logging.warning('Saving tractogram with invalid streamlines.')
save_tractogram(new_sft, args.out_tractogram, bbox_valid_check=False)
else:
save_tractogram(new_sft, args.out_tractogram)
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