def save_tractogram(sft, filename, bbox_valid_check=True):
""" Save the stateful tractogram in any format (trk, tck, vtk, fib, dpy)
Parameters
----------
sft : StatefulTractogram
The stateful tractogram to save
filename : string
Filename with valid extension
bbox_valid_check : bool
Verification for negative voxel coordinates or values above the
volume dimensions. Default is True, to enforce valid file.
Returns
-------
output : bool
True if the saving operation was successful
"""
_, extension = os.path.splitext(filename)
if extension not in ['.trk', '.tck', '.vtk', '.fib', '.dpy']:
raise TypeError('Output filename is not one of the supported format')
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 use the function ' +
'remove_invalid_streamlines to discard invalid ' +
'streamlines or set bbox_valid_check to False')
old_space = deepcopy(sft.space)
old_shift = deepcopy(sft.shifted_origin)
sft.to_rasmm()
sft.to_center()
timer = time.time()
if extension in ['.trk', '.tck']:
tractogram_type = detect_format(filename)
header = create_tractogram_header(tractogram_type,
*sft.space_attributes)
new_tractogram = Tractogram(sft.streamlines, affine_to_rasmm=np.eye(4))
if extension == '.trk':
new_tractogram.data_per_point = sft.data_per_point
new_tractogram.data_per_streamline = sft.data_per_streamline
fileobj = tractogram_type(new_tractogram, header=header)
nib.streamlines.save(fileobj, filename)
elif extension in ['.vtk', '.fib']:
save_vtk_streamlines(sft.streamlines, filename, binary=True)
elif extension in ['.dpy']:
dpy_obj = Dpy(filename, mode='w')
dpy_obj.write_tracks(sft.streamlines)
dpy_obj.close()
logging.debug('Save %s with %s streamlines in %s seconds', filename,
len(sft), round(time.time() - timer, 3))
if old_space == Space.VOX:
sft.to_vox()
elif old_space == Space.VOXMM:
sft.to_voxmm()
if old_shift:
sft.to_corner()
return True
def save_tractogram(sft, filename, bbox_valid_check=True):
""" Save the stateful tractogram in any format (trk, tck, vtk, fib, dpy)
Parameters
----------
sft : StatefulTractogram
The stateful tractogram to save
filename : string
Filename with valid extension
Returns
-------
output : bool
Did the saving work properly
"""
_, extension = os.path.splitext(filename)
if extension not in ['.trk', '.tck', '.vtk', '.fib', '.dpy']:
TypeError('Output filename is not one of the supported format')
if bbox_valid_check and not sft.is_bbox_in_vox_valid():
raise ValueError('Bounding box is not valid in voxel space, cannot ' +
'save a valid file if some coordinates are invalid')
old_space = deepcopy(sft.space)
old_shift = deepcopy(sft.shifted_origin)
sft.to_rasmm()
sft.to_center()
timer = time.time()
if extension in ['.trk', '.tck']:
tractogram_type = detect_format(filename)
header = create_tractogram_header(tractogram_type,
*sft.space_attribute)
new_tractogram = Tractogram(sft.streamlines,
affine_to_rasmm=np.eye(4))
if extension == '.trk':
new_tractogram.data_per_point = sft.data_per_point
new_tractogram.data_per_streamline = sft.data_per_streamline
fileobj = tractogram_type(new_tractogram, header=header)
nib.streamlines.save(fileobj, filename)
elif extension in ['.vtk', '.fib']:
save_vtk_streamlines(sft.streamlines, filename, binary=True)
elif extension in ['.dpy']:
dpy_obj = Dpy(filename, mode='w')
dpy_obj.write_tracks(sft.streamlines)
dpy_obj.close()
logging.debug('Save %s with %s streamlines in %s seconds',
filename, len(sft), round(time.time() - timer, 3))
if old_space == Space.VOX:
sft.to_vox()
elif old_space == Space.VOXMM:
sft.to_voxmm()
if old_shift:
sft.to_corner()
return True
