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 test_recobundles_flow():
with TemporaryDirectory() as out_dir:
data_path = get_fnames('fornix')
streams, hdr = nib.trackvis.read(data_path)
fornix = [s[0] for s in streams]
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")
save_trk(f2_path, f2, affine=np.eye(4))
f1_path = pjoin(out_dir, "f1.trk")
save_trk(f1_path, f, affine=np.eye(4))
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_trk(recog_trk)
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_trk(recog_bundle)
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 evaluate_results(self, model_bundle, pruned_streamlines, slr_select):
""" Compare the similiarity between two given bundles, model bundle,
and extracted bundle.
Parameters
----------
model_bundle : Streamlines
pruned_streamlines : Streamlines
slr_select : tuple
Select the number of streamlines from model to neirborhood of
model to perform the local SLR.
Returns
-------
ba_value : float
bundle adjacency value between model bundle and pruned bundle
bmd_value : float
bundle minimum distance value between model bundle and
pruned bundle
"""
spruned_streamlines = Streamlines(pruned_streamlines)
recog_centroids = self._cluster_model_bundle(
spruned_streamlines,
model_clust_thr=1.25)
mod_centroids = self._cluster_model_bundle(
model_bundle,
model_clust_thr=1.25)
recog_centroids = Streamlines(recog_centroids)
model_centroids = Streamlines(mod_centroids)
ba_value = bundle_adjacency(set_number_of_points(recog_centroids, 20),
set_number_of_points(model_centroids, 20),
threshold=10)
BMD = BundleMinDistanceMetric()
static = select_random_set_of_streamlines(model_bundle,
slr_select[0])
moving = select_random_set_of_streamlines(pruned_streamlines,
slr_select[1])
nb_pts = 20
static = set_number_of_points(static, nb_pts)
moving = set_number_of_points(moving, 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())
return ba_value, bmd_value
def _register_neighb_to_model(self, model_bundle, neighb_streamlines,
metric=None, x0=None, bounds=None,
select_model=400, select_target=600,
method='L-BFGS-B',
nb_pts=20, num_threads=None):
if self.verbose:
print('# Local SLR of neighb_streamlines to model')
t = time()
if metric is None or metric == 'symmetric':
metric = BundleMinDistanceMetric(num_threads=num_threads)
if metric == 'asymmetric':
metric = BundleMinDistanceAsymmetricMetric()
if metric == 'diagonal':
metric = BundleSumDistanceMatrixMetric()
if x0 is None:
x0 = 'similarity'
if bounds is None:
bounds = [(-30, 30), (-30, 30), (-30, 30),
(-45, 45), (-45, 45), (-45, 45), (0.8, 1.2)]
# TODO this can be speeded up by using directly the centroids
static = select_random_set_of_streamlines(model_bundle,
select_model, rng=self.rng)
moving = select_random_set_of_streamlines(neighb_streamlines,
select_target, rng=self.rng)
static = set_number_of_points(static, nb_pts)
moving = set_number_of_points(moving, nb_pts)
slr = StreamlineLinearRegistration(metric=metric, x0=x0,
bounds=bounds,
method=method)
slm = slr.optimize(static, moving)
transf_streamlines = neighb_streamlines.copy()
transf_streamlines._data = apply_affine(
slm.matrix, transf_streamlines._data)
transf_matrix = slm.matrix
slr_bmd = slm.fopt
slr_iterations = slm.iterations
if self.verbose:
print(' Square-root of BMD is %.3f' % (np.sqrt(slr_bmd),))
if slr_iterations is not None:
print(' Number of iterations %d' % (slr_iterations,))
print(' Matrix size {}'.format(slm.matrix.shape))
original = np.get_printoptions()
np.set_printoptions(3, suppress=True)
print(transf_matrix)
print(slm.xopt)
np.set_printoptions(**original)
print(' Duration %0.3f sec. \n' % (time() - t,))
return transf_streamlines, slr_bmd
def evaluate_results(self, model_bundle, pruned_streamlines, slr_select):
""" Comapare the similiarity between two given bundles, model bundle,
and extracted bundle.
Parameters
----------
model_bundle : Streamlines
pruned_streamlines : Streamlines
slr_select : tuple
Select the number of streamlines from model to neirborhood of
model to perform the local SLR.
Returns
-------
ba_value : float
bundle analytics value between model bundle and pruned bundle
bmd_value : float
bundle minimum distance value between model bundle and
pruned bundle
"""
spruned_streamlines = Streamlines(pruned_streamlines)
recog_centroids = self._cluster_model_bundle(
spruned_streamlines,
model_clust_thr=1.25)
mod_centroids = self._cluster_model_bundle(
model_bundle,
model_clust_thr=1.25)
recog_centroids = Streamlines(recog_centroids)
model_centroids = Streamlines(mod_centroids)
ba_value = ba_analysis(recog_centroids, model_centroids, threshold=10)
BMD = BundleMinDistanceMetric()
static = select_random_set_of_streamlines(model_bundle,
slr_select[0])
moving = select_random_set_of_streamlines(pruned_streamlines,
slr_select[1])
nb_pts = 20
static = set_number_of_points(static, nb_pts)
moving = set_number_of_points(moving, 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())
return ba_value, bmd_value
def test_recobundles_flow():
with TemporaryDirectory() as out_dir:
data_path = get_fnames('fornix')
streams, hdr = nib.trackvis.read(data_path)
fornix = [s[0] for s in streams]
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")
save_trk(f2_path, f2, affine=np.eye(4))
f1_path = pjoin(out_dir, "f1.trk")
save_trk(f1_path, f, affine=np.eye(4))
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_trk(recog_trk)
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_trk(recog_bundle)
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 test_min_vs_min_fast_precision():
static = fornix_streamlines()[:20]
moving = fornix_streamlines()[:20]
static = [s.astype('f8') for s in static]
moving = [m.astype('f8') for m in moving]
bmd = BundleMinDistanceMatrixMetric()
bmd.setup(static, moving)
bmdf = BundleMinDistanceMetric()
bmdf.setup(static, moving)
x_test = [0.01, 0, 0, 0, 0, 0]
print(bmd.distance(x_test))
print(bmdf.distance(x_test))
assert_equal(bmd.distance(x_test), bmdf.distance(x_test))
def _affine_slr(sft_bundle, sft_centroid):
x0 = np.zeros((7, ))
bounds_dof = [(-10, 10), (-10, 10), (-10, 10), (-5, 5), (-5, 5), (-5, 5),
(0.95, 1.05)]
metric = BundleMinDistanceMetric(num_threads=1)
slr = StreamlineLinearRegistration(metric=metric,
method="L-BFGS-B",
bounds=bounds_dof,
x0=x0,
num_threads=1)
tmp_bundle = set_number_of_points(sft_bundle.streamlines.copy(), 20)
tmp_centroid = set_number_of_points(sft_centroid.streamlines.copy(), 20)
slm = slr.optimize(tmp_bundle, tmp_centroid)
sft_centroid.streamlines = transform_streamlines(sft_centroid.streamlines,
slm.matrix)
return sft_centroid
def test_min_vs_min_fast_precision():
static = fornix_streamlines()[:20]
moving = fornix_streamlines()[:20]
static = [s.astype('f8') for s in static]
moving = [m.astype('f8') for m in moving]
bmd = BundleMinDistanceMatrixMetric()
bmd.setup(static, moving)
bmdf = BundleMinDistanceMetric()
bmdf.setup(static, moving)
x_test = [0.01, 0, 0, 0, 0, 0]
print(bmd.distance(x_test))
print(bmdf.distance(x_test))
assert_equal(bmd.distance(x_test), bmdf.distance(x_test))
def _register_model_to_neighb(self,
slr_num_thread=1,
select_model=1000,
select_target=1000,
slr_transform_type='scaling'):
"""
Parameters
----------
slr_num_thread : int
Number of threads for SLR.
Should remain 1 for nearly all use-case.
select_model : int
Maximum number of clusters to select from the model.
select_target : int
Maximum number of clusters to select from the neighborhood.
slr_transform_type : str
Define the transformation for the local SLR.
[translation, rigid, similarity, scaling].
Returns
-------
transf_neighbor : list
The neighborhood clusters transformed into model space.
"""
possible_slr_transform_type = {
'translation': 0,
'rigid': 1,
'similarity': 2,
'scaling': 3
}
static = select_random_set_of_streamlines(self.model_centroids,
select_model, self.rng)
moving = select_random_set_of_streamlines(self.neighb_centroids,
select_target, self.rng)
# Tuple 0,1,2 are the min & max bound in x,y,z for translation
# Tuple 3,4,5 are the min & max bound in x,y,z for rotation
# Tuple 6,7,8 are the min & max bound in x,y,z for scaling
# For uniform scaling (similarity), tuple #6 is enough
bounds_dof = [(-20, 20), (-20, 20), (-20, 20), (-10, 10), (-10, 10),
(-10, 10), (0.8, 1.2), (0.8, 1.2), (0.8, 1.2)]
metric = BundleMinDistanceMetric(num_threads=slr_num_thread)
slr_transform_type_id = possible_slr_transform_type[slr_transform_type]
if slr_transform_type_id >= 0:
init_transfo_dof = np.zeros(3)
slr = StreamlineLinearRegistration(metric=metric,
method="Powell",
x0=init_transfo_dof,
bounds=bounds_dof[:3],
num_threads=slr_num_thread)
slm = slr.optimize(static, moving)
if slr_transform_type_id >= 1:
init_transfo_dof = np.zeros(6)
init_transfo_dof[:3] = slm.xopt
slr = StreamlineLinearRegistration(metric=metric,
x0=init_transfo_dof,
bounds=bounds_dof[:6],
num_threads=slr_num_thread)
slm = slr.optimize(static, moving)
if slr_transform_type_id >= 2:
if slr_transform_type_id == 2:
init_transfo_dof = np.zeros(7)
init_transfo_dof[:6] = slm.xopt
init_transfo_dof[6] = 1.
slr = StreamlineLinearRegistration(metric=metric,
x0=init_transfo_dof,
bounds=bounds_dof[:7],
num_threads=slr_num_thread)
slm = slr.optimize(static, moving)
else:
init_transfo_dof = np.zeros(9)
init_transfo_dof[:6] = slm.xopt[:6]
init_transfo_dof[6:] = np.array((slm.xopt[6], ) * 3)
slr = StreamlineLinearRegistration(metric=metric,
x0=init_transfo_dof,
bounds=bounds_dof[:9],
num_threads=slr_num_thread)
slm = slr.optimize(static, moving)
self.model_centroids = transform_streamlines(self.model_centroids,
np.linalg.inv(slm.matrix))