def load_tractogram_with_reference(parser,
args,
filepath,
bbox_check=True,
arg_name=None):
_, ext = os.path.splitext(filepath)
if ext == '.trk':
sft = load_tractogram(filepath, 'same', bbox_valid_check=bbox_check)
elif ext in ['.tck', '.fib', '.vtk', '.dpy']:
if arg_name:
arg_ref = arg_name + '_ref'
if args.__getattribute__(arg_ref):
sft = load_tractogram(filepath,
args.__getattribute__(arg_ref),
bbox_valid_check=bbox_check)
else:
parser.error('--{} is required for this file format '
'{}.'.format(arg_ref, filepath))
elif args.reference is None:
parser.error('--reference is required for this file format '
'{}.'.format(filepath))
else:
sft = load_tractogram(filepath,
args.reference,
bbox_valid_check=bbox_check)
else:
parser.error('{} is an unsupported file format'.format(filepath))
return sft
def read_hcp_atlas_16_bundles():
"""
XXX
"""
bundle_dict = {}
_, folder = fetch_hcp_atlas_16_bundles()
whole_brain = load_tractogram(op.join(folder,
'Atlas_in_MNI_Space_16_bundles',
'whole_brain',
'whole_brain_MNI.trk'),
'same',
bbox_valid_check=False).streamlines
bundle_dict['whole_brain'] = whole_brain
bundle_files = glob(
op.join(folder, "Atlas_in_MNI_Space_16_bundles", "bundles", "*.trk"))
for bundle_file in bundle_files:
bundle = op.splitext(op.split(bundle_file)[-1])[0]
bundle_dict[bundle] = {}
bundle_dict[bundle]['sl'] = load_tractogram(bundle_file,
'same',
bbox_valid_check=False)\
.streamlines
feature = ResampleFeature(nb_points=100)
metric = AveragePointwiseEuclideanMetric(feature)
qb = QuickBundles(np.inf, metric=metric)
cluster = qb.cluster(bundle_dict[bundle]['sl'])
bundle_dict[bundle]['centroid'] = cluster.centroids[0]
# For some reason, this file-name has a 0 in it, instead of an O:
bundle_dict["IFOF_R"] = bundle_dict["IF0F_R"]
del bundle_dict["IF0F_R"]
return bundle_dict
def test_recobundles_flow():
with TemporaryDirectory() as out_dir:
data_path = get_fnames('fornix')
fornix = load_tractogram(data_path, 'same',
bbox_valid_check=False).streamlines
f = Streamlines(fornix)
f1 = f.copy()
f2 = f1[:15].copy()
f2._data += np.array([40, 0, 0])
f.extend(f2)
f2_path = pjoin(out_dir, "f2.trk")
sft = StatefulTractogram(f2, data_path, Space.RASMM)
save_tractogram(sft, f2_path, bbox_valid_check=False)
f1_path = pjoin(out_dir, "f1.trk")
sft = StatefulTractogram(f, data_path, Space.RASMM)
save_tractogram(sft, f1_path, bbox_valid_check=False)
rb_flow = RecoBundlesFlow(force=True)
rb_flow.run(f1_path,
f2_path,
greater_than=0,
clust_thr=10,
model_clust_thr=5.,
reduction_thr=10,
out_dir=out_dir)
labels = rb_flow.last_generated_outputs['out_recognized_labels']
recog_trk = rb_flow.last_generated_outputs['out_recognized_transf']
rec_bundle = load_tractogram(recog_trk, 'same',
bbox_valid_check=False).streamlines
npt.assert_equal(len(rec_bundle) == len(f2), True)
label_flow = LabelsBundlesFlow(force=True)
label_flow.run(f1_path, labels)
recog_bundle = label_flow.last_generated_outputs['out_bundle']
rec_bundle_org = load_tractogram(recog_bundle,
'same',
bbox_valid_check=False).streamlines
BMD = BundleMinDistanceMetric()
nb_pts = 20
static = set_number_of_points(f2, nb_pts)
moving = set_number_of_points(rec_bundle_org, nb_pts)
BMD.setup(static, moving)
x0 = np.array([0, 0, 0, 0, 0, 0, 1., 1., 1, 0, 0, 0]) # affine
bmd_value = BMD.distance(x0.tolist())
npt.assert_equal(bmd_value < 1, True)
def to_vox_equivalence():
sft_1 = load_tractogram(filepath_dix['gs.trk'], filepath_dix['gs.nii'],
to_space=Space.RASMM)
sft_2 = load_tractogram(filepath_dix['gs.trk'], filepath_dix['gs.nii'],
to_space=Space.RASMM)
sft_1.to_vox()
sft_2.to_space(Space.VOX)
assert_allclose(sft_1.streamlines.get_data(),
sft_2.streamlines.get_data(), atol=1e-3, rtol=1e-6)
def to_center_equivalence():
sft_1 = load_tractogram(filepath_dix['gs.trk'], filepath_dix['gs.nii'],
to_space=Space.VOX)
sft_2 = load_tractogram(filepath_dix['gs.trk'], filepath_dix['gs.nii'],
to_space=Space.VOX)
sft_1.to_center()
sft_2.to_origin(Origin.NIFTI)
assert_allclose(sft_1.streamlines.get_data(),
sft_2.streamlines.get_data(), atol=1e-3, rtol=1e-6)
def shift_corner_from_voxmm():
sft_1 = load_tractogram(filepath_dix['gs.trk'], filepath_dix['gs.nii'],
to_space=Space.VOX)
sft_1.to_corner()
bbox_1 = sft_1.compute_bounding_box()
sft_2 = load_tractogram(filepath_dix['gs.trk'], filepath_dix['gs.nii'],
to_space=Space.VOXMM)
sft_2.to_corner()
sft_2.to_vox()
bbox_2 = sft_2.compute_bounding_box()
assert_allclose(bbox_1, bbox_2, atol=1e-3, rtol=1e-6)
def dpy_iterative_saving_loading():
sft = load_tractogram(filepath_dix['gs.dpy'], filepath_dix['gs.nii'],
to_space=Space.RASMM)
with InTemporaryDirectory():
save_tractogram(sft, 'gs_iter.dpy')
tmp_points_rasmm = np.loadtxt(filepath_dix['gs_rasmm_space.txt'])
for _ in range(100):
sft_iter = load_tractogram('gs_iter.dpy', filepath_dix['gs.nii'],
to_space=Space.RASMM)
assert_allclose(tmp_points_rasmm,
sft_iter.streamlines.data,
atol=1e-3, rtol=1e-6)
save_tractogram(sft_iter, 'gs_iter.dpy')
def to_corner_equivalence():
sft_1 = load_tractogram(filepath_dix['gs.trk'],
filepath_dix['gs.nii'],
to_space=Space.VOX)
sft_2 = load_tractogram(filepath_dix['gs.trk'],
filepath_dix['gs.nii'],
to_space=Space.VOX)
sft_1.to_corner()
sft_2.to_origin(Origin.TRACKVIS)
assert_allclose(sft_1.streamlines.data,
sft_2.streamlines.data,
atol=1e-3,
rtol=1e-6)
def test_bundle_shape_analysis_flow():
with TemporaryDirectory() as dirpath:
data_path = get_fnames('fornix')
fornix = load_tractogram(data_path, 'same',
bbox_valid_check=False).streamlines
f = Streamlines(fornix)
mb = os.path.join(dirpath, "model_bundles")
sub = os.path.join(dirpath, "subjects")
os.mkdir(mb)
sft = StatefulTractogram(f, data_path, Space.RASMM)
save_tractogram(sft,
os.path.join(mb, "temp.trk"),
bbox_valid_check=False)
os.mkdir(sub)
os.mkdir(os.path.join(sub, "patient"))
os.mkdir(os.path.join(sub, "control"))
p = os.path.join(sub, "patient", "10001")
os.mkdir(p)
c = os.path.join(sub, "control", "20002")
os.mkdir(c)
for pre in [p, c]:
os.mkdir(os.path.join(pre, "rec_bundles"))
sft = StatefulTractogram(f, data_path, Space.RASMM)
save_tractogram(sft,
os.path.join(pre, "rec_bundles", "temp.trk"),
bbox_valid_check=False)
os.mkdir(os.path.join(pre, "org_bundles"))
sft = StatefulTractogram(f, data_path, Space.RASMM)
save_tractogram(sft,
os.path.join(pre, "org_bundles", "temp.trk"),
bbox_valid_check=False)
os.mkdir(os.path.join(pre, "anatomical_measures"))
fa = np.random.rand(255, 255, 255)
save_nifti(os.path.join(pre, "anatomical_measures", "fa.nii.gz"),
fa,
affine=np.eye(4))
out_dir = os.path.join(dirpath, "output")
os.mkdir(out_dir)
sm_flow = BundleShapeAnalysis()
sm_flow.run(sub, out_dir=out_dir)
assert_true(os.path.exists(os.path.join(out_dir, "temp.npy")))
def test_invalid_streamlines_epsilon():
sft = load_tractogram(filepath_dix['gs.trk'], filepath_dix['gs.nii'])
src_strml_count = len(sft)
epsilon = 1e-6
obtained_idx_to_remove, obtained_idx_to_keep = \
sft.remove_invalid_streamlines(epsilon)
expected_idx_to_keep = list(range(src_strml_count))
assert len(obtained_idx_to_remove) == 0
assert expected_idx_to_keep == obtained_idx_to_keep
assert_(len(sft) == src_strml_count,
msg='A small epsilon should not remove any streamlines')
epsilon = 1.0
obtained_idx_to_remove, obtained_idx_to_keep = \
sft.remove_invalid_streamlines(epsilon)
expected_idx_to_remove = [0, 1, 2, 3, 4, 5, 6, 7]
expected_idx_to_keep = [8, 9, 10, 11, 12]
expected_len_sft = 5
expected_removed_strml_count = src_strml_count - expected_len_sft
assert obtained_idx_to_remove == expected_idx_to_remove
assert obtained_idx_to_keep == expected_idx_to_keep
assert_(
len(sft) == expected_len_sft,
msg='Too big of an epsilon ({} mm) should have removed {} streamlines '
'({} corners)'.format(epsilon, expected_removed_strml_count,
expected_removed_strml_count))
def test_invalid_streamlines():
sft = load_tractogram(filepath_dix['gs.trk'], filepath_dix['gs.nii'])
src_strml_count = len(sft)
obtained_idx_to_remove, obtained_idx_to_keep = \
sft.remove_invalid_streamlines()
expected_idx_to_keep = list(range(src_strml_count))
assert len(obtained_idx_to_remove) == 0
assert expected_idx_to_keep == obtained_idx_to_keep
assert_(
len(sft) == src_strml_count,
msg='An unshifted gold standard should have {} invalid streamlines'.
format(src_strml_count - src_strml_count))
# Change the dimensions so that a few streamlines become invalid
sft.dimensions[2] = 5
obtained_idx_to_remove, obtained_idx_to_keep = \
sft.remove_invalid_streamlines()
expected_idx_to_remove = [1, 3, 5, 7, 8, 9, 10, 11]
expected_idx_to_keep = [0, 2, 4, 6, 12]
expected_len_sft = 5
assert obtained_idx_to_remove == expected_idx_to_remove
assert obtained_idx_to_keep == expected_idx_to_keep
assert_(len(sft) == expected_len_sft,
msg='The shifted gold standard should have {} invalid streamlines'.
format(src_strml_count - expected_len_sft))
def test_basic_addition():
sft = load_tractogram(filepath_dix['gs.trk'], filepath_dix['gs.nii'])
sft_first_half = sft[0:7]
sft_last_half = sft[7:13]
concatenate_sft = sft_first_half + sft_last_half
assert_(concatenate_sft == sft, msg='sft were not added correctly')
def io_tractogram(extension):
with InTemporaryDirectory():
fname = 'test.{}'.format(extension)
in_affine = np.eye(4)
in_dimensions = np.array([50, 50, 50])
in_voxel_sizes = np.array([2, 1.5, 1.5])
nii_header = create_nifti_header(in_affine, in_dimensions,
in_voxel_sizes)
sft = StatefulTractogram(streamlines, nii_header, space=Space.RASMM)
save_tractogram(sft, fname, bbox_valid_check=False)
if extension == 'trk':
reference = 'same'
else:
reference = nii_header
sft = load_tractogram(fname, reference, bbox_valid_check=False)
affine, dimensions, voxel_sizes, _ = sft.space_attribute
npt.assert_array_equal(in_affine, affine)
npt.assert_array_equal(in_voxel_sizes, voxel_sizes)
npt.assert_array_equal(in_dimensions, dimensions)
npt.assert_equal(len(sft), len(streamlines))
npt.assert_array_almost_equal(sft.streamlines[1], streamline,
decimal=4)
def test_evaluate_streamline_plausibility(dmri_estimation_data,
tractography_estimation_data):
"""
Test evaluate_streamline_plausibility functionality
"""
import nibabel as nib
from pynets.dmri.utils import evaluate_streamline_plausibility
from dipy.io.stateful_tractogram import Space, Origin
from dipy.io.streamline import load_tractogram
from dipy.io import load_pickle
gtab_file = dmri_estimation_data['gtab_file']
dwi_path = dmri_estimation_data['dwi_file']
mask_file = tractography_estimation_data['mask']
streams = tractography_estimation_data['trk']
gtab = load_pickle(gtab_file)
dwi_img = nib.load(dwi_path)
dwi_data = dwi_img.get_fdata()
mask_img = nib.load(mask_file)
mask_data = mask_img.get_fdata()
tractogram = load_tractogram(
streams,
mask_img,
to_origin=Origin.NIFTI,
to_space=Space.VOXMM,
bbox_valid_check=True,
)
streamlines = tractogram.streamlines
cleaned = evaluate_streamline_plausibility(dwi_data, gtab, mask_data,
streamlines)
assert len(cleaned) > 0
assert len(cleaned) <= len(streamlines)
def convert_trk(tractogram, outtype='tck', output=None, force=False):
''' Convert presumed trk file to either a tck file, or a vtk file
'''
# figure out input type, load file
if nib.streamlines.detect_format(tractogram) is not nib.streamlines.TrkFile:
print("Skipping non TRK file: '{}'".format(tractogram))
return
if output:
output_filename = output
else:
output_filename = tractogram[:-4] + '.{}'.format(outtype)
if os.path.isfile(output_filename) and not force:
print("Skipping existing file: '{}'. Use -f to overwrite.".format(output_filename))
return
print("Converting file: {}\n".format(output_filename))
# load tractogram, set origin to the corner
trk = load_tractogram(tractogram, reference='same')
trk.to_corner() # set origin to the corner
if outtype == 'tck':
save_tractogram(trk, output_filename)
else:
dipy.io.vtk.save_vtk_streamlines(trk, output_filename)
def bounding_bbox_valid(shift):
sft = load_tractogram(filepath_dix['gs.trk'],
filepath_dix['gs.nii'],
shifted_origin=shift,
bbox_valid_check=False)
return sft.is_bbox_in_vox_valid()
def prepare_data_for_actors(bundle_filename, reference_filename,
target_template_filename):
sft = load_tractogram(bundle_filename, reference_filename)
streamlines = sft.streamlines
# Load and prepare the data
reference_img = nib.load(reference_filename)
reference_data = reference_img.get_fdata(dtype=np.float32)
reference_affine = reference_img.affine
if target_template_filename:
target_template_img = nib.load(target_template_filename)
target_template_data = target_template_img.get_fdata(dtype=np.float32)
target_template_affine = target_template_img.affine
# Register the DWI data to the template
logging.debug('Starting registration...')
transformed_reference, transformation = register_image(
target_template_data, target_template_affine, reference_data,
reference_affine)
logging.debug('Transforming streamlines...')
streamlines = transform_streamlines(streamlines,
np.linalg.inv(transformation),
in_place=True)
new_sft = StatefulTractogram(streamlines, target_template_filename,
Space.RASMM)
return new_sft, transformed_reference
return sft, reference_data
def main():
parser = _build_arg_parser()
args = parser.parse_args()
assert_inputs_exist(parser, [args.tractogram])
assert_outputs_exist(parser, args, [], [args.save])
tracts_format = detect_format(args.tractogram)
if tracts_format is not TrkFile:
raise ValueError("Invalid input streamline file format " +
"(must be trk): {0}".format(args.tractogram_filename))
# Load files and data. TRKs can have 'same' as reference
tractogram = load_tractogram(args.tractogram, 'same')
# Streamlines are saved in RASMM but seeds are saved in VOX
# This might produce weird behavior with non-iso
tractogram.to_vox()
streamlines = tractogram.streamlines
if 'seeds' not in tractogram.data_per_streamline:
parser.error('Tractogram does not contain seeds')
seeds = tractogram.data_per_streamline['seeds']
# Make display objects
streamlines_actor = actor.line(streamlines)
points = actor.dots(seeds, color=(1., 1., 1.))
# Add display objects to canvas
s = window.Scene()
s.add(streamlines_actor)
s.add(points)
# Show and record if needed
if args.save is not None:
window.record(s, out_path=args.save, size=(1000, 1000))
window.show(s)
def bounding_bbox_valid(standard):
sft = load_tractogram(filepath_dix['gs.trk'],
filepath_dix['gs.nii'],
to_origin=standard,
bbox_valid_check=False)
return sft.is_bbox_in_vox_valid()
def test_slr_flow():
with TemporaryDirectory() as out_dir:
data_path = get_fnames('fornix')
fornix = load_tractogram(data_path, 'same',
bbox_valid_check=False).streamlines
f = Streamlines(fornix)
f1 = f.copy()
f1_path = pjoin(out_dir, "f1.trk")
sft = StatefulTractogram(f1, data_path, Space.RASMM)
save_tractogram(sft, f1_path, bbox_valid_check=False)
f2 = f1.copy()
f2._data += np.array([50, 0, 0])
f2_path = pjoin(out_dir, "f2.trk")
sft = StatefulTractogram(f2, data_path, Space.RASMM)
save_tractogram(sft, f2_path, bbox_valid_check=False)
slr_flow = SlrWithQbxFlow(force=True)
slr_flow.run(f1_path, f2_path)
out_path = slr_flow.last_generated_outputs['out_moved']
npt.assert_equal(os.path.isfile(out_path), True)
def test_io_streamline():
with InTemporaryDirectory():
fname = 'test.trk'
affine = np.eye(4)
# Test save
save_tractogram(fname, streamlines, affine,
vox_size=np.array([2, 1.5, 1.5]),
shape=np.array([50, 50, 50]))
tfile = nib.streamlines.load(fname)
npt.assert_array_equal(affine, tfile.affine)
npt.assert_array_equal(np.array([2, 1.5, 1.5]),
tfile.header.get('voxel_sizes'))
npt.assert_array_equal(np.array([50, 50, 50]),
tfile.header.get('dimensions'))
npt.assert_equal(len(tfile.streamlines), len(streamlines))
npt.assert_array_almost_equal(tfile.streamlines[1], streamline,
decimal=4)
# Test basic save
save_tractogram(fname, streamlines, affine)
tfile = nib.streamlines.load(fname)
npt.assert_array_equal(affine, tfile.affine)
npt.assert_equal(len(tfile.streamlines), len(streamlines))
npt.assert_array_almost_equal(tfile.streamlines[1], streamline,
decimal=5)
# Test Load
local_streamlines, hdr = load_tractogram(fname)
npt.assert_equal(len(local_streamlines), len(streamlines))
for arr1, arr2 in zip(local_streamlines, streamlines):
npt.assert_allclose(arr1, arr2)
def main():
args = parse_args()
if os.path.exists(args.output) and not args.force:
raise ValueError("Output already exists! Use --force to overwrite.")
sft = load_tractogram(args.input, args.ref,
to_space=Space.RASMM,
trk_header_check=False,
bbox_valid_check=False)
# There may be invalid streamlines in the input tractogram
sft.remove_invalid_streamlines()
# Work in voxel space, and move streamlines to corner so we can use floor()
# to compare with valid voxel coordinates.
sft.to_vox()
sft.to_corner()
mask = nib.load(args.mask)
valid_voxels = np.where(mask.get_fdata() > 0.5)
valid_streamlines = []
for s in sft.streamlines:
if _is_coords_valid(s[0], valid_voxels):
valid_streamlines.append(s)
elif _is_coords_valid(s[-1], valid_voxels):
valid_streamlines.append(s[::-1])
valid_sft = StatefulTractogram(valid_streamlines, args.ref, space=sft.space, shifted_origin=sft.shifted_origin)
save_tractogram(valid_sft, args.output)
def compute_voxel_measures(args):
bundle_filename, bundle_reference = args[0]
tracking_mask = args[1]
gs_binary_3d = args[2]
bundle_sft = load_tractogram(bundle_filename, bundle_reference)
bundle_sft.to_vox()
bundle_sft.to_corner()
bundle_streamlines = bundle_sft.streamlines
_, bundle_dimensions, _, _ = bundle_sft.space_attributes
if not bundle_streamlines:
logging.info('{} is empty'.format(bundle_filename))
return None
binary_3d = compute_tract_counts_map(bundle_streamlines, bundle_dimensions)
binary_3d[binary_3d > 0] = 1
binary_3d_indices = np.where(binary_3d.flatten() > 0)[0]
gs_binary_3d_indices = np.where(gs_binary_3d.flatten() > 0)[0]
voxels_binary = binary_classification(
binary_3d_indices,
gs_binary_3d_indices,
int(np.prod(tracking_mask.shape)),
mask_count=np.count_nonzero(tracking_mask))
return dict(
zip([
'sensitivity_voxels', 'specificity_voxels', 'precision_voxels',
'accuracy_voxels', 'dice_voxels', 'kappa_voxels', 'youden_voxels'
], voxels_binary))
def test_LSCv2(verbose=False):
xyz1 = np.array([[1, 0, 0], [2, 0, 0], [3, 0, 0]], dtype='float32')
xyz2 = np.array([[1, 0, 0], [1, 2, 0], [1, 3, 0]], dtype='float32')
xyz3 = np.array([[1.1, 0, 0], [1, 2, 0], [1, 3, 0]], dtype='float32')
xyz4 = np.array([[1, 0, 0], [2.1, 0, 0], [3, 0, 0]], dtype='float32')
xyz5 = np.array([[100, 0, 0], [200, 0, 0], [300, 0, 0]], dtype='float32')
xyz6 = np.array([[0, 20, 0], [0, 40, 0], [300, 50, 0]], dtype='float32')
T = [xyz1, xyz2, xyz3, xyz4, xyz5, xyz6]
pf.local_skeleton_clustering(T, 0.2)
pf.local_skeleton_clustering_3pts(T, 0.2)
for i in range(40):
xyz = np.random.rand(3, 3).astype('f4')
T.append(xyz)
from time import time
t1 = time()
C3 = pf.local_skeleton_clustering(T, .5)
t2 = time()
if verbose:
print(t2 - t1)
print(len(C3))
t1 = time()
C4 = pf.local_skeleton_clustering_3pts(T, .5)
t2 = time()
if verbose:
print(t2 - t1)
print(len(C4))
for c in C3:
assert_equal(np.sum(C3[c]['hidden'] - C4[c]['hidden']), 0)
T2 = []
for i in range(10**4):
xyz = np.random.rand(10, 3).astype('f4')
T2.append(xyz)
t1 = time()
C5 = pf.local_skeleton_clustering(T2, .5)
t2 = time()
if verbose:
print(t2 - t1)
print(len(C5))
fname = get_fnames('fornix')
fornix = load_tractogram(fname, 'same', bbox_valid_check=False).streamlines
T3 = set_number_of_points(fornix, 6)
if verbose:
print('lenT3', len(T3))
C = pf.local_skeleton_clustering(T3, 10.)
if verbose:
print('lenC', len(C))
"""
def compute_streamlines_measures(args):
bundle_filename, bundle_reference = args[0]
wb_streamlines = args[1]
gs_streamlines_indices = args[2]
if not os.path.isfile(bundle_filename):
logging.info('{} does not exist'.format(bundle_filename))
return None
bundle_sft = load_tractogram(bundle_filename, bundle_reference)
bundle_sft.to_vox()
bundle_sft.to_corner()
bundle_streamlines = bundle_sft.streamlines
_, bundle_dimensions, _, _ = bundle_sft.space_attributes
if not bundle_streamlines:
logging.info('{} is empty'.format(bundle_filename))
return None
_, streamlines_indices = perform_streamlines_operation(
intersection, [wb_streamlines, bundle_streamlines], precision=0)
streamlines_binary = binary_classification(streamlines_indices,
gs_streamlines_indices,
len(wb_streamlines))
return dict(
zip([
'sensitivity_streamlines', 'specificity_streamlines',
'precision_streamlines', 'accuracy_streamlines',
'dice_streamlines', 'kappa_streamlines', 'youden_streamlines'
], streamlines_binary))
def random_streamline_color():
np.random.seed(0)
sft = load_tractogram(filepath_dix['gs.tck'], filepath_dix['gs.nii'])
uniform_colors_x = np.random.randint(0, 255, (13, 1))
uniform_colors_y = np.random.randint(0, 255, (13, 1))
uniform_colors_z = np.random.randint(0, 255, (13, 1))
uniform_colors_x = np.expand_dims(
np.repeat(uniform_colors_x, 8, axis=1), axis=-1)
uniform_colors_y = np.expand_dims(
np.repeat(uniform_colors_y, 8, axis=1), axis=-1)
uniform_colors_z = np.expand_dims(
np.repeat(uniform_colors_z, 8, axis=1), axis=-1)
coloring_dict = {}
coloring_dict['color_x'] = uniform_colors_x
coloring_dict['color_y'] = uniform_colors_y
coloring_dict['color_z'] = uniform_colors_z
try:
sft.data_per_point = coloring_dict
with InTemporaryDirectory():
save_tractogram(sft, 'random_streamlines_color.trk')
return True
except (TypeError, ValueError):
return False
def remove_invalid_streamlines(resize):
sft = load_tractogram(filepath_dix['gs.trk'], filepath_dix['gs.nii'])
if resize:
sft._dimensions[2] = 5
sft.remove_invalid_streamlines()
return len(sft)
def get_streamlines():
from dipy.data import get_fnames
from dipy.io.streamline import load_tractogram
fname = get_fnames('fornix')
fornix = load_tractogram(fname, 'same', bbox_valid_check=False)
return fornix.streamlines
def fib_equal_in_rasmm_space():
if not have_fury:
return
sft = load_tractogram(filepath_dix['gs.fib'], filepath_dix['gs.nii'],
to_space=Space.RASMM)
tmp_points_rasmm = np.loadtxt(filepath_dix['gs_rasmm_space.txt'])
assert_allclose(tmp_points_rasmm,
sft.streamlines.get_data(), atol=1e-3, rtol=1e-6)
def fornix_streamlines(no_pts=12):
fname = get_fnames('fornix')
fornix = load_tractogram(fname, 'same', bbox_valid_check=False).streamlines
fornix_streamlines = Streamlines(fornix)
streamlines = set_number_of_points(fornix_streamlines, no_pts)
return streamlines
def load_bundles(self,
bundle_names,
file_path='./',
file_suffix='.trk',
affine=np.eye(4),
bbox_valid_check=False):
"""
load tractograms from file.
Parameters
----------
bundle_names : list of strings
Names of bundles to load.
file_path : string, optional.
Path to load trk files from.
Default: './'
file_suffix : string, optional.
File name will be the bundle name + file_suffix.
Default: '.trk'
affine : array_like (4, 4), optional.
The mapping from the file's reference to this object's reference.
Default: np.eye(4)
bbox_valid_check : boolean, optional.
Whether to verify that the bounding box is valid in voxel space.
Default: False
"""
for bundle_name in bundle_names:
full_path = os.path.join(file_path, f"{bundle_name}{file_suffix}")
if self.reference == 'same':
sft = load_tractogram(full_path,
self.reference,
bbox_valid_check=bbox_valid_check)
self.reference = sft
self.origin = sft.origin
self.space = sft.space
else:
sft = load_tractogram(full_path,
self.reference,
to_space=self.space,
bbox_valid_check=bbox_valid_check)
sft = self._apply_affine_sft(sft, affine, self.reference,
self.origin)
self.add_bundle(bundle_name, sft)
logging.disable(level=logging.WARNING)
logging.disable(logging.NOTSET)
