def bench_length():
repeat = 10
nb_streamlines = DATA['nb_streamlines']
streamlines = DATA["streamlines"] # Streamlines as a list of ndarrays.
print("Timing length() with {0:,} streamlines.".format(nb_streamlines))
python_time = measure("[length_python(s) for s in streamlines]", repeat)
print("Python time: {0:.2}sec".format(python_time))
cython_time = measure("length(streamlines)", repeat)
print("Cython time: {0:.3}sec".format(cython_time))
print("Speed up of {0:.2f}x".format(python_time / cython_time))
# Make sure it produces the same results.
assert_array_equal([length_python(s) for s in DATA["streamlines"]],
length(DATA["streamlines"]))
streamlines = DATA['streamlines_arrseq']
cython_time_arrseq = measure("length(streamlines)", repeat)
print("Cython time (ArrSeq): {0:.3}sec".format(cython_time_arrseq))
print("Speed up of {0:.2f}x".format(python_time / cython_time_arrseq))
# Make sure it produces the same results.
assert_array_equal(length(DATA["streamlines"]),
length(DATA["streamlines_arrseq"]))
def test_length_memory_leaks():
# Test some dtypes
dtypes = [np.float32, np.float64, np.int32, np.int64]
for dtype in dtypes:
rng = np.random.RandomState(1234)
NB_STREAMLINES = 10000
streamlines = [rng.randn(rng.randint(10, 100), 3).astype(dtype)
for _ in range(NB_STREAMLINES)]
list_refcount_before = get_type_refcount()["list"]
lengths = length(streamlines)
list_refcount_after = get_type_refcount()["list"]
# Calling `length` shouldn't increase the refcount of `list`
# since the return value is a numpy array.
assert_equal(list_refcount_after, list_refcount_before)
# Test mixed dtypes
rng = np.random.RandomState(1234)
NB_STREAMLINES = 10000
streamlines = []
for i in range(NB_STREAMLINES):
dtype = dtypes[i % len(dtypes)]
streamlines.append(rng.randn(rng.randint(10, 100), 3).astype(dtype))
list_refcount_before = get_type_refcount()["list"]
lengths = length(streamlines)
list_refcount_after = get_type_refcount()["list"]
# Calling `length` shouldn't increase the refcount of `list`
# since the return value is a numpy array.
assert_equal(list_refcount_after, list_refcount_before)
def test_feature_arclength():
from dipy.tracking.streamline import length
# Test subclassing Feature
class ArcLengthFeature(dipymetric.Feature):
def __init__(self):
super(ArcLengthFeature, self).__init__(is_order_invariant=True)
def infer_shape(self, streamline):
return (1, 1)
def extract(self, streamline):
return length(streamline)[None, None]
for feature in [dipymetric.ArcLengthFeature(), ArcLengthFeature()]:
for s in [s1, s2, s3, s4]:
# Test method infer_shape
assert_equal(feature.infer_shape(s), (1, 1))
# Test method extract
features = feature.extract(s)
assert_equal(features.shape, (1, 1))
assert_array_almost_equal(features, length(s)[None, None])
# This feature type is order invariant
assert_true(feature.is_order_invariant)
for s in [s1, s2, s3, s4]:
features = feature.extract(s)
features_flip = feature.extract(s[::-1])
assert_array_almost_equal(features, features_flip)
def get_endpoints_density_map(streamlines, dimensions, point_to_select=1):
"""
Compute an endpoints density map, supports selecting more than one points
at each end.
Parameters
----------
streamlines: list of ndarray
The list of streamlines to compute endpoints density from.
dimensions: tuple
The shape of the reference volume for the streamlines.
point_to_select: int
Instead of computing the density based on the first and last points,
select more than one at each end. To support compressed streamlines,
a resampling to 0.5mm per segment is performed.
Returns
-------
ndarray: A ndarray where voxel values represent the density of endpoints.
"""
endpoints_map = np.zeros(dimensions)
for streamline in streamlines:
streamline = set_number_of_points(streamline,
int(length(streamline)) * 2)
points_list = list(streamline[0:point_to_select, :].astype(int))
points_list.extend(
streamline[-(point_to_select + 1):-1, :].astype(int))
for xyz in points_list:
x_val = int(np.clip(xyz[0], 0, dimensions[0] - 1))
y_val = int(np.clip(xyz[1], 0, dimensions[1] - 1))
z_val = int(np.clip(xyz[2], 0, dimensions[2] - 1))
endpoints_map[x_val, y_val, z_val] += 1
return endpoints_map
def main():
parser = build_parser()
args = parser.parse_args()
for f in args.datasets:
with Timer("Normalizing step size of dataset '{}'".format(f)):
tractography_data = neurotools.TractographyData.load(f)
t = nib.streamlines.Tractogram(tractography_data.streamlines)
t.apply_affine(
tractography_data.signal.affine) # Bring streamlines to RAS+mm
streamlines = t.streamlines
streamlines._lengths = streamlines._lengths.astype(int)
streamlines._offsets = streamlines._offsets.astype(int)
lengths = length(streamlines)
nb_points = np.ceil(lengths / args.step_size).astype(int)
new_streamlines = (set_number_of_points(s, n)
for s, n in zip(streamlines, nb_points))
t = nib.streamlines.Tractogram(new_streamlines)
t.apply_affine(np.linalg.inv(tractography_data.signal.affine))
t.affine_to_rasmm = np.eye(4)
tractography_data.streamlines = t.streamlines
filename = f[:-4] + "_" + str(args.step_size) + "mm" + f[-4:]
tractography_data.save(filename)
def test_feature_arclength():
from dipy.tracking.streamline import length
# Test subclassing Feature
class ArcLengthFeature(dipymetric.Feature):
def __init__(self):
super(ArcLengthFeature, self).__init__(is_order_invariant=True)
def infer_shape(self, streamline):
return (1, 1)
def extract(self, streamline):
return length(streamline)[None, None]
for feature in [dipymetric.ArcLengthFeature(), ArcLengthFeature()]:
for s in [s1, s2, s3, s4]:
# Test method infer_shape
assert_equal(feature.infer_shape(s), (1, 1))
# Test method extract
features = feature.extract(s)
assert_equal(features.shape, (1, 1))
assert_array_almost_equal(features, length(s)[None, None])
# This feature type is order invariant
assert_true(feature.is_order_invariant)
for s in [s1, s2, s3, s4]:
features = feature.extract(s)
features_flip = feature.extract(s[::-1])
assert_array_almost_equal(features, features_flip)
def test_length(self):
# Test length of only one streamline
length_streamline_cython = dipystreamline.length(self.streamline)
length_streamline_python = length_python(self.streamline)
assert_equal(length_streamline_cython, length_streamline_python)
length_streamline_cython = dipystreamline.length(self.streamline_64bit)
length_streamline_python = length_python(self.streamline_64bit)
assert_equal(length_streamline_cython, length_streamline_python)
# Test computing length of multiple streamlines of different nb_points
length_streamlines_cython = dipystreamline.length(self.streamlines)
for i, s in enumerate(self.streamlines):
length_streamline_python = length_python(s)
assert_array_almost_equal(length_streamlines_cython[i], length_streamline_python)
length_streamlines_cython = dipystreamline.length(self.streamlines_64bit)
for i, s in enumerate(self.streamlines_64bit):
length_streamline_python = length_python(s)
assert_array_almost_equal(length_streamlines_cython[i], length_streamline_python)
# Test streamlines having mixed dtype
streamlines = [self.streamline, self.streamline.astype(np.float64)]
assert_raises(ValueError, dipystreamline.length, streamlines)
# Test streamlines with differente shape
length_streamlines_cython = dipystreamline.length(self.heterogeneous_streamlines)
for i, s in enumerate(self.heterogeneous_streamlines):
length_streamline_python = length_python(s)
assert_array_almost_equal(length_streamlines_cython[i], length_streamline_python)
# Test streamline having integer dtype
length_streamline = dipystreamline.length(self.streamline.astype('int'))
assert_true(length_streamline.dtype == np.float64)
# Test empty list
assert_equal(dipystreamline.length([]), 0.0)
# Test streamline having only one point
assert_equal(dipystreamline.length(np.array([[1, 2, 3]])), 0.0)
# We do not support list of lists, it should be numpy ndarray.
streamline = [[1, 2, 3], [4, 5, 5], [2, 1, 3], [4, 2, 1]]
assert_raises(AttributeError, dipystreamline.length, streamline)
def bench_length():
repeat = 10
nb_streamlines = DATA['nb_streamlines']
msg = "Timing length() with {0:,} streamlines."
print(msg.format(nb_streamlines * repeat))
python_time = measure("[length_python(s) for s in streamlines]", repeat)
print("Python time: {0:.2f} sec".format(python_time))
cython_time = measure("length(streamlines)", repeat)
print("Cython time: {0:.3f} sec".format(cython_time))
print("Speed up of {0:.2f}x".format(python_time/cython_time))
# Make sure it produces the same results.
assert_array_almost_equal([length_python(s) for s in DATA["streamlines"]],
length(DATA["streamlines"]))
cython_time_arrseq = measure("length(streamlines)", repeat)
print("Cython time (ArrSeq): {0:.3f} sec".format(cython_time_arrseq))
print("Speed up of {0:.2f}x".format(python_time/cython_time_arrseq))
# Make sure it produces the same results.
assert_array_equal(length(DATA["streamlines"]),
length(DATA["streamlines_arrseq"]))
def test_length_memory_leaks():
# Test some dtypes
dtypes = [np.float32, np.float64, np.int32, np.int64]
for dtype in dtypes:
rng = np.random.RandomState(1234)
NB_STREAMLINES = 10000
streamlines = [
rng.randn(rng.randint(10, 100), 3).astype(dtype)
for _ in range(NB_STREAMLINES)
]
list_refcount_before = get_type_refcount()["list"]
lengths = length(streamlines)
list_refcount_after = get_type_refcount()["list"]
# Calling `length` shouldn't increase the refcount of `list`
# since the return value is a numpy array.
assert_equal(list_refcount_after, list_refcount_before)
# Test mixed dtypes
rng = np.random.RandomState(1234)
NB_STREAMLINES = 10000
streamlines = []
for i in range(NB_STREAMLINES):
dtype = dtypes[i % len(dtypes)]
streamlines.append(rng.randn(rng.randint(10, 100), 3).astype(dtype))
list_refcount_before = get_type_refcount()["list"]
lengths = length(streamlines)
list_refcount_after = get_type_refcount()["list"]
# Calling `length` shouldn't increase the refcount of `list`
# since the return value is a numpy array.
assert_equal(list_refcount_after, list_refcount_before)
def embed_flattened_plus_flipped_plus_length_plus_curvature(streamlines):
lengths = length(streamlines)
# Mean curvature of the streamline (TO BE CHECKED!):
# curvature = np.vstack([np.linalg.norm(np.gradient(s, axis=0), axis=0) for s in streamlines])
curvature = np.array([frenet_serret(s)[3].squeeze() for s in streamlines])
torsion = np.array([frenet_serret(s)[4].squeeze() for s in streamlines])
X = embed_flattened_plus_flipped(streamlines)
X = np.concatenate([
X,
np.concatenate([lengths, lengths])[:, None],
np.vstack([curvature, curvature[::-1]]),
np.vstack([torsion, torsion[::-1]])
],
axis=1)
return X
def get_head_tail_density_maps(streamlines, dimensions, point_to_select=1):
"""
Compute two separate endpoints density maps for the head and tail
Parameters
----------
streamlines: list of ndarray
The list of streamlines to compute endpoints density from.
dimensions: tuple
The shape of the reference volume for the streamlines.
point_to_select: int
Instead of computing the density based on the first and last points,
select more than one at each end. To support compressed streamlines,
a resampling to 0.5mm per segment is performed.
Returns
-------
A tuple containing
ndarray: A ndarray where voxel values represent the density of
head endpoints.
ndarray: A ndarray where voxel values represent the density of
tail endpoints.
"""
endpoints_map_head = np.zeros(dimensions)
endpoints_map_tail = np.zeros(dimensions)
for streamline in streamlines:
nb_point = max(2, int(length(streamline))*2)
streamline = set_number_of_points(streamline,
nb_point)
points_list_head = \
list(streamline[0:point_to_select, :])
points_list_tail = \
list(streamline[-point_to_select:, :])
for xyz in points_list_head:
x_val = np.clip(xyz[0], 0, dimensions[0]-1).astype(int)
y_val = np.clip(xyz[1], 0, dimensions[1]-1).astype(int)
z_val = np.clip(xyz[2], 0, dimensions[2]-1).astype(int)
endpoints_map_head[x_val, y_val, z_val] += 1
for xyz in points_list_tail:
x_val = np.clip(xyz[0], 0, dimensions[0]-1).astype(int)
y_val = np.clip(xyz[1], 0, dimensions[1]-1).astype(int)
z_val = np.clip(xyz[2], 0, dimensions[2]-1).astype(int)
endpoints_map_tail[x_val, y_val, z_val] += 1
return endpoints_map_head, endpoints_map_tail
def computeStats(subjectID,reference,streamlines,classification,outdir):
avg_length = []
avg_curv = []
stream_count = []
mean_x = []
mean_y = []
mean_z = []
num_vox = []
tract_index_labels = np.trim_zeros(np.unique(classification['index'].tolist()))
qb = QuickBundles(np.inf)
for i in tract_index_labels:
indices = [ t for t in range(len(classification['index'].tolist())) if classification['index'].tolist()[int(t)] == i ]
avg_length.append(np.mean(length(streamlines[indices])))
clusters = qb.cluster(streamlines[indices])
avg_curv.append(mean_curvature(clusters.centroids[0]))
orientation = mean_orientation(clusters.centroids[0])
mean_x.append(orientation[0])
mean_y.append(orientation[1])
mean_z.append(orientation[2])
stream_count.append(len(indices))
denmap = density_map(streamlines[indices],reference.affine,reference.shape)
num_vox.append(len(denmap[denmap>0]))
df = pd.DataFrame([],dtype=object)
df['subjectID'] = [ subjectID for f in range(len(classification['names'].tolist())) ]
df['structureID'] = [ f for f in classification['names'].tolist() ]
df['nodeID'] = [ 1 for f in range(len(df['structureID'])) ]
df['streamline_count'] = stream_count
df['average_length'] = avg_length
df['average_curvature'] = avg_curv
df['voxel_count'] = num_vox
df['centroid_x'] = mean_x
df['centroid_y'] = mean_y
df['centroid_z'] = mean_z
df.to_csv('%s/output_FiberStats.csv' %outdir,index=False)
def rois_fiberlen_cellinput(N, cell_streamlines):
# input:
# N: # of ROIs
# cell_streamlines: streamlines connecting ith and jth ROIs
# voxel_size, affine: some parameters to transfore streamlines to voxel
connectcm_len = np.zeros([N, N])
idx = 0
for i in range(1, N):
for j in range(i + 1, N):
tmp_streamlines = cell_streamlines[idx]
idx = idx + 1
tmp_len = 0
for sl in tmp_streamlines:
flen = length(sl)
tmp_len = tmp_len + flen
if (len(tmp_streamlines) > 0):
connectcm_len[i, j] = tmp_len / len(tmp_streamlines)
return connectcm_len
def extract(self, streamline):
""" Extracts features from `streamline`. """
# return np.sum(np.sqrt(np.sum((streamline[1:] - streamline[:-1]) ** 2)))
# or use a Dipy's function that computes the arc length of a streamline.
return length(streamline)
def extract(self, streamline):
""" Extracts features from `streamline`. """
# return np.sum(np.sqrt(np.sum((streamline[1:] - streamline[:-1]) ** 2)))
# or use a Dipy's function that computes the arc length of a streamline.
return length(streamline)
def build_scene(self):
scene = window.Renderer()
for (t, streamlines) in enumerate(self.tractograms):
if self.random_colors:
colors = self.prng.random_sample(3)
else:
colors = None
if self.cluster:
print(' Clustering threshold {} \n'.format(self.cluster_thr))
clusters = qbx_and_merge(streamlines,
[40, 30, 25, 20, self.cluster_thr])
self.tractogram_clusters[t] = clusters
centroids = clusters.centroids
print(' Number of centroids is {}'.format(len(centroids)))
sizes = np.array([len(c) for c in clusters])
linewidths = np.interp(sizes,
[sizes.min(), sizes.max()], [0.1, 2.])
centroid_lengths = np.array([length(c) for c in centroids])
print(' Minimum number of streamlines in cluster {}'.format(
sizes.min()))
print(' Maximum number of streamlines in cluster {}'.format(
sizes.max()))
print(' Construct cluster actors')
for (i, c) in enumerate(centroids):
centroid_actor = actor.streamtube([c],
colors,
linewidth=linewidths[i],
lod=False)
scene.add(centroid_actor)
cluster_actor = actor.line(clusters[i], lod=False)
cluster_actor.GetProperty().SetRenderLinesAsTubes(1)
cluster_actor.GetProperty().SetLineWidth(6)
cluster_actor.GetProperty().SetOpacity(1)
cluster_actor.VisibilityOff()
scene.add(cluster_actor)
# Every centroid actor (cea) is paired to a cluster actor
# (cla).
self.cea[centroid_actor] = {
'cluster_actor': cluster_actor,
'cluster': i,
'tractogram': t,
'size': sizes[i],
'length': centroid_lengths[i],
'selected': 0,
'expanded': 0
}
self.cla[cluster_actor] = {
'centroid_actor': centroid_actor,
'cluster': i,
'tractogram': t,
'size': sizes[i],
'length': centroid_lengths[i],
'selected': 0
}
apply_shader(self, cluster_actor)
apply_shader(self, centroid_actor)
else:
streamline_actor = actor.line(streamlines, colors=colors)
streamline_actor.GetProperty().SetEdgeVisibility(1)
streamline_actor.GetProperty().SetRenderLinesAsTubes(1)
streamline_actor.GetProperty().SetLineWidth(6)
streamline_actor.GetProperty().SetOpacity(1)
scene.add(streamline_actor)
return scene
def main():
parser = buildArgsParser()
args = parser.parse_args()
if not os.path.isfile(args.tracts):
parser.error("Tracts file: {0} does not exist.".format(args.tracts))
if not os.path.isfile(args.aparc):
parser.error("Label file: {0} does not exist.".format(args.aparc))
if not os.path.isfile(args.labels):
parser.error("Requested region file: {0} does not exist.".format(
args.labels))
if not os.path.isfile(args.lut):
parser.error("Freesurfer LUT file: {0} does not exist.".format(
args.lut))
if not os.path.isfile(args.faimage):
parser.error("FA Image file: {0} does not exist.".format(args.faimage))
if not os.path.isfile(args.mdimage):
parser.error("MD Image file: {0} does not exist.".format(args.mdimage))
# Validate that tracts can be processed
if not validate_coordinates(args.aparc, args.tracts, nifti_compliant=True):
parser.error("The tracts file contains points that are invalid.\n" +
"Use the remove_invalid_coordinates.py script to clean.")
# Load label image
labels_img = nib.load(args.aparc)
full_labels = labels_img.get_data().astype('int')
# Load fibers
tract_format = tc.detect_format(args.tracts)
tract = tract_format(args.tracts, args.aparc)
affine = compute_affine_for_dipy_functions(args.aparc, args.tracts)
#load FA and MD image
fa_img = nib.load(args.faimage)
fa_data = fa_img.get_data()
md_img = nib.load(args.mdimage)
md_data = md_img.get_data()
# ========= processing streamlines =================
fiberlen_range = np.asarray([args.minlen, args.maxlen])
streamlines = [t for t in tract]
print "Subject " + args.sub_id + " has " + str(
len(streamlines)) + " raw streamlines."
f_streamlines = [] #filtered streamlines
lenrecord = []
idx = 0
for sl in streamlines:
# Avoid streamlines having only one point, as they crash the
# Dipy connectivity matrix function.
if sl.shape[0] > 1:
flen = length(sl)
# get fibers having length between 20mm and 200mm
if (flen > fiberlen_range[0]) & (flen < fiberlen_range[1]):
f_streamlines.append(sl)
lenrecord.append(flen)
idx = idx + 1
print "Subject " + args.sub_id + " has " + str(
idx) + " streamlines with lengths between " + str(
args.minlen) + " and " + str(args.maxlen) + "."
# ============= process the parcellation =====================
dilation_para = np.array([args.dilation_dist, args.dilation_windsize])
# Compute the mapping from label name to label id
label_id_mapping = compute_labels_map(args.lut)
# Find which labels were requested by the user.
requested_labels_mapping = compute_requested_labels(
args.labels, label_id_mapping)
# Filter to keep only needed ones
filtered_labels = np.zeros(full_labels.shape, dtype='int')
for label_val in requested_labels_mapping:
if sum(sum(sum(full_labels == label_val))) == 0:
print label_val
print requested_labels_mapping[label_val]
filtered_labels[full_labels == label_val] = label_val
#cortex band dilation
dilated_labels = cortexband_dilation_wm(filtered_labels, full_labels,
dilation_para)
# Reduce the range of labels to avoid a sparse matrix,
# because the ids of labels can range from 0 to the 12000's.
reduced_labels, labels_lut = dpu.reduce_labels(filtered_labels)
reduced_dilated_labels, labels_lut = dpu.reduce_labels(dilated_labels)
# Compute connectivity matrix and extract the fibers
M, grouping = nconnectivity_matrix(f_streamlines,
reduced_dilated_labels,
fiberlen_range,
args.cnpoint,
affine=affine,
symmetric=True,
return_mapping=True,
mapping_as_streamlines=True)
Msize = len(M)
CM_before_outlierremove = M[1:, 1:]
nstream_bf = np.sum(CM_before_outlierremove)
print args.sub_id + ' ' + str(
nstream_bf
) + ' streamlines in the connectivity matrix before outlier removal.'
#===================== process the streamlines =============
print 'Processing streamlines to remove outliers ..............'
outlier_para = 3
average_thrd = 8
M_after_ourlierremove = np.zeros((Msize, Msize))
#downsample streamlines
cell_streamlines = []
cell_id = []
for i in range(1, Msize):
for j in range(i + 1, Msize):
tmp_streamlines = grouping[i, j]
tmp_streamlines = list(tmp_streamlines)
#downsample
tmp_streamlines_downsampled = [
downsample(s, 100) for s in tmp_streamlines
]
#remove outliers, we need to rewrite the QuickBundle method to speed up this process
qb = QuickBundles(threshold=average_thrd)
clusters = qb.cluster(tmp_streamlines_downsampled)
outlier_clusters = clusters < outlier_para #small clusters
nonoutlier_clusters = clusters[np.logical_not(outlier_clusters)]
tmp_nonoutlier_index = []
for tmp_cluster in nonoutlier_clusters:
tmp_nonoutlier_index = tmp_nonoutlier_index + tmp_cluster.indices
clean_streamline_downsampled = [
tmp_streamlines_downsampled[ind]
for ind in tmp_nonoutlier_index
]
cell_streamlines.append(clean_streamline_downsampled)
cell_id.append([i, j])
M_after_ourlierremove[i, j] = len(clean_streamline_downsampled)
CM_after_ourlierremove = M_after_ourlierremove[1:, 1:]
nstream_bf = np.sum(CM_after_ourlierremove)
print args.sub_id + ' ' + str(
nstream_bf
) + ' streamlines in the connectivity matrix after outlier removal.'
#save streamlines and count matrix
cmCountMatrix_fname = args.sub_id + "_" + args.pre + "_cm_count_raw.mat"
cmCountMatrix_processed_fname = args.sub_id + "_" + args.pre + "_cm_count_processed.mat"
cmStreamlineMatrix_fname = args.sub_id + "_" + args.pre + "_cm_streamlines.mat"
reduced_labels_fname = args.sub_id + "_" + args.pre + "_reduced_labels.nii.gz"
dilated_labels_fname = args.sub_id + "_" + args.pre + "_dilated_labels.nii.gz"
RoiInfo_fname = args.sub_id + "_" + args.pre + "_RoiInfo.mat"
# save the raw count matrix
CM = M[1:, 1:]
sio.savemat(cmCountMatrix_fname, {'cm': CM})
sio.savemat(cmCountMatrix_processed_fname, {'cm': CM_after_ourlierremove})
# save the streamline matrix
sio.savemat(cmStreamlineMatrix_fname, {'slines': cell_streamlines})
sio.savemat(RoiInfo_fname, {'ROIinfo': cell_id})
print args.sub_id + 'cell_streamlines.mat, ROIinfo.mat has been saved'
filtered_labels_img = nib.Nifti1Image(filtered_labels,
labels_img.get_affine(),
labels_img.get_header())
nib.save(filtered_labels_img, reduced_labels_fname)
print args.sub_id + 'filtered labels have saved'
dilated_labels_img = nib.Nifti1Image(dilated_labels,
labels_img.get_affine(),
labels_img.get_header())
nib.save(dilated_labels_img, dilated_labels_fname)
print args.sub_id + 'dilated labels have saved'
# ===================== process the streamlines and extract features =============
cm_fa_curve = fa_extraction_use_cellinput(cell_streamlines,
cell_id,
fa_data,
Msize,
affine=affine)
(tmp_cm_fa_mean, tmp_cm_fa_max,
cm_count) = fa_mean_extraction(cm_fa_curve, Msize)
# extract MD values along the streamlines
cm_md_curve = fa_extraction_use_cellinput(cell_streamlines,
cell_id,
md_data,
Msize,
affine=affine)
(tmp_cm_md_mean, tmp_cm_md_max,
testcm) = fa_mean_extraction(cm_md_curve, Msize)
#connected surface area
# extract the connective volume ratio
(tmp_cm_volumn,
tmp_cm_volumn_ratio) = rois_connectedvol_cellinput(reduced_labels,
Msize,
cell_streamlines,
cell_id,
affine=affine)
#fiber length
tmp_connectcm_len = rois_fiberlen_cellinput(Msize, cell_streamlines)
#save cm features
cm_md_mean = tmp_cm_md_mean[1:, 1:]
cm_md_max = tmp_cm_md_max[1:, 1:]
cm_fa_mean = tmp_cm_fa_mean[1:, 1:]
cm_fa_max = tmp_cm_fa_max[1:, 1:]
cm_volumn = tmp_cm_volumn[1:, 1:]
cm_volumn_ratio = tmp_cm_volumn_ratio[1:, 1:]
connectcm_len = tmp_connectcm_len[1:, 1:]
sio.savemat(args.pre + "_cm_processed_mdmean_100.mat",
{'cm_mdmean': cm_md_mean})
sio.savemat(args.pre + "_cm_processed_mdmax_100.mat",
{'cm_mdmax': cm_md_max})
sio.savemat(args.pre + "_cm_processed_famean_100.mat",
{'cm_famean': cm_fa_mean})
sio.savemat(args.pre + "_cm_processed_famax_100.mat",
{'cm_famax': cm_fa_max})
sio.savemat(args.pre + "_cm_processed_volumn_100.mat",
{'cm_volumn': cm_volumn})
sio.savemat(args.pre + "_cm_processed_volumn_ratio_100.mat",
{'cm_volumn_ratio': cm_volumn_ratio})
sio.savemat(args.pre + "_cm_processed_volumn_ratio_100.mat",
{'cm_len': connectcm_len})
# save the diffusion functions matrix
cell_fa = []
for i in range(1, Msize):
for j in range(i + 1, Msize):
tmp_fa = cm_fa_curve[i, j]
tmp_fa = list(tmp_fa)
cell_fa.append(tmp_fa)
sio.savemat(args.pre + "_cm_processed_sfa_100.mat", {'sfa': cell_fa})
print 'cell_fa.mat, fa_roiinfo.mat have been saved'
cell_md = []
for i in range(1, Msize):
for j in range(i + 1, Msize):
tmp_md = cm_md_curve[i, j]
tmp_md = list(tmp_md)
cell_md.append(tmp_md)
sio.savemat(args.pre + "_cm_processed_smd_100.mat", {'smd': cell_md})
def add_cluster_actors(self, scene, tractograms,
threshold, enable_callbacks=True):
""" Add streamline actors to the scene
Parameters
----------
scene : Scene
tractograms : list
list of tractograms
threshold : float
Cluster threshold
enable_callbacks : bool
Enable callbacks for selecting clusters
"""
color_gen = distinguishable_colormap()
for (t, sft) in enumerate(tractograms):
streamlines = sft.streamlines
if self.random_colors:
colors = next(color_gen)
else:
colors = None
if not self.world_coords:
# TODO we need to read the affine of a tractogram
# from a StatefullTractogram
msg = 'Currently native coordinates are not supported'
msg += ' for streamlines'
raise ValueError(msg)
if self.cluster:
print(' Clustering threshold {} \n'.format(threshold))
clusters = qbx_and_merge(streamlines,
[40, 30, 25, 20, threshold])
self.tractogram_clusters[t] = clusters
centroids = clusters.centroids
print(' Number of centroids is {}'.format(len(centroids)))
sizes = np.array([len(c) for c in clusters])
linewidths = np.interp(sizes,
[sizes.min(), sizes.max()], [0.1, 2.])
centroid_lengths = np.array([length(c) for c in centroids])
print(' Minimum number of streamlines in cluster {}'
.format(sizes.min()))
print(' Maximum number of streamlines in cluster {}'
.format(sizes.max()))
print(' Construct cluster actors')
for (i, c) in enumerate(centroids):
centroid_actor = actor.streamtube([c], colors,
linewidth=linewidths[i],
lod=False)
scene.add(centroid_actor)
self.mem.centroid_actors.append(centroid_actor)
cluster_actor = actor.line(clusters[i],
lod=False)
cluster_actor.GetProperty().SetRenderLinesAsTubes(1)
cluster_actor.GetProperty().SetLineWidth(6)
cluster_actor.GetProperty().SetOpacity(1)
cluster_actor.VisibilityOff()
scene.add(cluster_actor)
self.mem.cluster_actors.append(cluster_actor)
# Every centroid actor (cea) is paired to a cluster actor
# (cla).
self.cea[centroid_actor] = {
'cluster_actor': cluster_actor,
'cluster': i, 'tractogram': t,
'size': sizes[i], 'length': centroid_lengths[i],
'selected': 0, 'expanded': 0}
self.cla[cluster_actor] = {
'centroid_actor': centroid_actor,
'cluster': i, 'tractogram': t,
'size': sizes[i], 'length': centroid_lengths[i],
'selected': 0, 'highlighted': 0}
apply_shader(self, cluster_actor)
apply_shader(self, centroid_actor)
else:
streamline_actor = actor.line(streamlines, colors=colors)
streamline_actor.GetProperty().SetEdgeVisibility(1)
streamline_actor.GetProperty().SetRenderLinesAsTubes(1)
streamline_actor.GetProperty().SetLineWidth(6)
streamline_actor.GetProperty().SetOpacity(1)
scene.add(streamline_actor)
self.mem.streamline_actors.append(streamline_actor)
if not enable_callbacks:
return
def left_click_centroid_callback(obj, event):
self.cea[obj]['selected'] = not self.cea[obj]['selected']
self.cla[self.cea[obj]['cluster_actor']]['selected'] = \
self.cea[obj]['selected']
self.show_m.render()
def left_click_cluster_callback(obj, event):
if self.cla[obj]['selected']:
self.cla[obj]['centroid_actor'].VisibilityOn()
ca = self.cla[obj]['centroid_actor']
self.cea[ca]['selected'] = 0
obj.VisibilityOff()
self.cea[ca]['expanded'] = 0
self.show_m.render()
for cl in self.cla:
cl.AddObserver('LeftButtonPressEvent', left_click_cluster_callback,
1.0)
self.cla[cl]['centroid_actor'].AddObserver(
'LeftButtonPressEvent', left_click_centroid_callback, 1.0)
def check_range(streamline, gt, lt):
length_s = length(streamline)
if (length_s > gt) & (length_s < lt):
return True
else:
return False
:align: center
Entire bundle with a specific color.
Show every streamline of a bundle with a different color
========================================================
Let's make a colormap where every streamline of the bundle is colored by its
length.
"""
scene.clear()
from dipy.tracking.streamline import length
lengths = length(bundle_native)
hue = (0.5, 0.5) # blue only
saturation = (0.0, 1.0) # black to white
lut_cmap = actor.colormap_lookup_table(scale_range=(lengths.min(),
lengths.max()),
hue_range=hue,
saturation_range=saturation)
stream_actor5 = actor.line(bundle_native,
lengths,
linewidth=0.1,
lookup_colormap=lut_cmap)
scene.add(stream_actor5)
def extract(self, streamline):
return length(streamline)[None, None]
def embed_flattened_plus_flipped_plus_length(streamlines):
lengths = length(streamlines)
X = embed_flattened_plus_flipped(streamlines)
X = np.concatenate([X, np.concatenate([lengths, lengths])[:, None]],
axis=1)
return X
def main():
parser = _build_args_parser()
args = parser.parse_args()
logging.basicConfig(level=logging.INFO)
# make sure all the given files exist
if not isfile(args.streamlines):
parser.error('The file "{0}" must exist.'.format(args.streamlines))
if not isfile(args.intersections):
parser.error('The file "{0}" must exist.'.format(args.intersections))
# make sure that files are not accidently overwritten
if isfile(args.output):
if args.overwrite:
logging.info('Overwriting "{0}".'.format(args.output))
else:
parser.error('The file "{0}" already exists. Use -f to overwrite it.'.format(args.output))
if not args.output_tracts is None:
if isfile(args.output_tracts):
if args.overwrite:
logging.info('Overwriting "{0}".'.format(args.output_tracts))
else:
parser.error('The file "{0}" already exists. Use -f to overwrite it.'.format(args.output_tracts))
# load the surfaces
logging.info('Loading tractography and intersections.')
# load the intersections file
intersections = np.load(args.intersections, allow_pickle=True)
surf_ids0 = intersections['surf_ids0']
surf_ids1 = intersections['surf_ids1']
tri_ids0 = intersections['tri_ids0']
tri_ids1 = intersections['tri_ids1']
pts0 = intersections['pts0']
pts1 = intersections['pts1']
# load the streamlines
streamlines = load_vtk_streamlines(args.streamlines)
logging.info('Filtering streamlines with angles >= {0} and length outside range {1}-{2}mm.'.format(args.angle, args.min_length, args.max_length))
n = len(tri_ids0)
i = 0
mask = np.zeros(n, np.bool)
# create the mask for filtering
for s in streamlines:
s_filter = (length(s) <= args.max_length) & (length(s) >= args.min_length)
if s_filter:
s_filter = (metrics.winding(s) < args.angle)
mask[i] = s_filter
i = i + 1
# save the filtered tractography if requested
if not args.output_tracts is None:
filtered_tracts = np.array(streamlines)[mask]
save_vtk_streamlines(filtered_tracts, args.output_tracts, binary = True)
remaining = np.sum(mask)
logging.info('Removed {0} streamlines with {1} remaining.'.format(n - remaining, remaining))
# save the results
np.savez_compressed(args.output,
pts0=pts0[mask],
tri_ids0=tri_ids0[mask],
surf_ids0=surf_ids0[mask],
pts1=pts1[mask],
tri_ids1=tri_ids1[mask],
surf_ids1=surf_ids1[mask])
:align: center
**Entire bundle with a specific color**.
Show every streamline of a bundle with a different color
========================================================
Let's make a colormap where every streamline of the bundle is colored by its
length.
"""
renderer.clear()
from dipy.tracking.streamline import length
lengths = length(bundle_native)
hue = [0.5, 0.5] # red only
saturation = [0.0, 1.0] # black to white
lut_cmap = actor.colormap_lookup_table(
scale_range=(lengths.min(), lengths.max()), hue_range=hue, saturation_range=saturation
)
stream_actor5 = actor.line(bundle_native, lengths, linewidth=0.1, lookup_colormap=lut_cmap)
renderer.add(stream_actor5)
bar3 = actor.scalar_bar(lut_cmap)
renderer.add(bar3)
def load_tractography_dataset_from_dwi_and_tractogram(dwi,
tractogram,
volume_manager,
use_sh_coeffs=False,
bvals=None,
bvecs=None,
step_size=None,
mean_centering=True):
# Load signal
signal = nib.load(dwi)
signal.get_data() # Forces loading volume in-memory.
basename = re.sub('(\.gz|\.nii.gz)$', '', dwi)
bvals = basename + '.bvals' if bvals is None else bvals
bvecs = basename + '.bvecs' if bvecs is None else bvecs
gradients = gradient_table(bvals, bvecs)
tracto_data = TractographyData(signal, gradients)
# Load streamlines
tfile = nib.streamlines.load(tractogram)
tractogram = tfile.tractogram
# Resample streamline to have a fixed step size, if needed.
if step_size is not None:
print("Resampling streamlines to have a step size of {}mm".format(
step_size))
streamlines = tractogram.streamlines
streamlines._lengths = streamlines._lengths.astype(int)
streamlines._offsets = streamlines._offsets.astype(int)
lengths = length(streamlines)
nb_points = np.ceil(lengths / step_size).astype(int)
new_streamlines = (set_number_of_points(s, n)
for s, n in zip(streamlines, nb_points))
tractogram = nib.streamlines.Tractogram(new_streamlines,
affine_to_rasmm=np.eye(4))
# Compute matrix that brings streamlines back to diffusion voxel space.
rasmm2vox_affine = np.linalg.inv(signal.affine)
tractogram.apply_affine(rasmm2vox_affine)
# Add streamlines to the TractogramData
tracto_data.add(tractogram.streamlines, "tractogram")
dwi = tracto_data.signal
bvals = tracto_data.gradients.bvals
bvecs = tracto_data.gradients.bvecs
if use_sh_coeffs:
# Use 45 spherical harmonic coefficients to represent the diffusion signal.
volume = neurotools.get_spherical_harmonics_coefficients(
dwi, bvals, bvecs,
mean_centering=mean_centering).astype(np.float32)
else:
# Resample the diffusion signal to have 100 directions.
volume = neurotools.resample_dwi(dwi,
bvals,
bvecs,
mean_centering=mean_centering).astype(
np.float32)
tracto_data.signal.uncache(
) # Free some memory as we don't need the original signal.
subject_id = volume_manager.register(volume)
tracto_data.subject_id = subject_id
return TractographyDataset([tracto_data], "dataset", keep_on_cpu=True)
def check_range(streamline, gt=greater_than, lt=less_than):
if (length(streamline) > gt) & (length(streamline) < lt):
return True
else:
return False
def build_scene(self):
scene = window.Renderer()
for (t, streamlines) in enumerate(self.tractograms):
if self.random_colors:
colors = self.prng.random_sample(3)
else:
colors = None
if self.cluster:
print(' Clustering threshold {} \n'.format(self.cluster_thr))
clusters = qbx_and_merge(streamlines,
[40, 30, 25, 20, self.cluster_thr])
self.tractogram_clusters[t] = clusters
centroids = clusters.centroids
print(' Number of centroids is {}'.format(len(centroids)))
sizes = np.array([len(c) for c in clusters])
linewidths = np.interp(sizes,
[sizes.min(), sizes.max()], [0.1, 2.])
centroid_lengths = np.array([length(c) for c in centroids])
print(' Minimum number of streamlines in cluster {}'
.format(sizes.min()))
print(' Maximum number of streamlines in cluster {}'
.format(sizes.max()))
print(' Construct cluster actors')
for (i, c) in enumerate(centroids):
centroid_actor = actor.streamtube([c], colors,
linewidth=linewidths[i],
lod=False)
scene.add(centroid_actor)
cluster_actor = actor.line(clusters[i],
lod=False)
cluster_actor.GetProperty().SetRenderLinesAsTubes(1)
cluster_actor.GetProperty().SetLineWidth(6)
cluster_actor.GetProperty().SetOpacity(1)
cluster_actor.VisibilityOff()
scene.add(cluster_actor)
# Every centroid actor (cea) is paired to a cluster actor
# (cla).
self.cea[centroid_actor] = {
'cluster_actor': cluster_actor,
'cluster': i, 'tractogram': t,
'size': sizes[i], 'length': centroid_lengths[i],
'selected': 0, 'expanded': 0}
self.cla[cluster_actor] = {
'centroid_actor': centroid_actor,
'cluster': i, 'tractogram': t,
'size': sizes[i], 'length': centroid_lengths[i],
'selected': 0}
apply_shader(self, cluster_actor)
apply_shader(self, centroid_actor)
else:
streamline_actor = actor.line(streamlines, colors=colors)
streamline_actor.GetProperty().SetEdgeVisibility(1)
streamline_actor.GetProperty().SetRenderLinesAsTubes(1)
streamline_actor.GetProperty().SetLineWidth(6)
streamline_actor.GetProperty().SetOpacity(1)
scene.add(streamline_actor)
return scene
def streamline_connectcut_returnfulllength(streamline, streamline_labels,
npoints, fiberlen_range):
""" cut streamline into streamlines that connecting different rois, here we try to return
the full length of the fiber. Note in the function of streamline_connectcut, we only
return the intermedia part of a fiber between two rois. Here we retrun strealimes within
the ROIs.
# input: streamline: one streamline
# streamline_label: the labels along streamline
# npoints: threthhold
"""
unq_label = np.unique(streamline_labels)
Nrois = len(streamline_labels)
num_sl = 0
new_streamlines = []
new_streamlines_startlabel = []
new_streamlines_endlabel = []
# case1: the streamline is in the wm or only connect two rois, we just return this streamline
if (len(unq_label) == 1):
num_sl = num_sl + 1
new_streamlines_startlabel.append(unq_label[0])
new_streamlines_endlabel.append(unq_label[0])
return streamline, num_sl, new_streamlines_startlabel, new_streamlines_endlabel
if (len(unq_label) == 2):
new_streamlines_startlabel.append(streamline_labels[0])
new_streamlines_endlabel.append(streamline_labels[-1])
num_sl = num_sl + 1
return streamline, num_sl, new_streamlines_startlabel, new_streamlines_endlabel
# case2: the streamline connects multiple rois
ct = Counter(streamline_labels)
passed_roi = []
for t in ct:
if ((t != 0) & (ct[t] > npoints)):
passed_roi.append(t)
#cut the streamline into nchoose(len(passed_roi),2) pieces
for i in range(0, len(passed_roi)):
for j in range(i + 1, len(passed_roi)):
roia = passed_roi[i]
roib = passed_roi[j]
#find the part connects roia and roib
label_roia = np.squeeze(
np.asarray(np.where(streamline_labels == roia)))
label_roib = np.squeeze(
np.asarray(np.where(streamline_labels == roib)))
if (label_roia[0] < label_roib[0]): # if roia is in front of roib
startidx = label_roia[1] # start index
endidx = label_roib[-1] #
tmpsl = streamline[startidx:endidx]
if (length(tmpsl) > fiberlen_range[0]
): # for streamlines longer than xx mm, we record it
new_streamlines.append(tmpsl)
new_streamlines_startlabel.append(roia)
new_streamlines_endlabel.append(roib)
num_sl = num_sl + 1
else:
startidx = label_roib[1]
endidx = label_roia[-1] # can be improved here
tmpsl = streamline[startidx:endidx]
if (length(tmpsl) > fiberlen_range[0]
): # for streamlines longer than xx mm, we keep it
new_streamlines.append(tmpsl)
new_streamlines_startlabel.append(roib)
new_streamlines_endlabel.append(roia)
num_sl = num_sl + 1
return new_streamlines, num_sl, new_streamlines_startlabel, new_streamlines_endlabel
def main():
parser = build_argparser()
args = parser.parse_args()
tracto_data = None
if args.signal_source == "raw_signal":
signal = nib.load(args.signal)
signal.get_data() # Forces loading volume in-memory.
basename = re.sub('(\.gz|\.nii.gz)$', '', args.signal)
try:
bvals = basename + '.bvals' if args.bvals is None else args.bvals
bvecs = basename + '.bvecs' if args.bvecs is None else args.bvecs
gradients = gradient_table(bvals, bvecs)
except FileNotFoundError:
try:
bvals = basename + '.bval' if args.bvals is None else args.bvals
bvecs = basename + '.bvec' if args.bvecs is None else args.bvecs
gradients = gradient_table(bvals, bvecs)
except FileNotFoundError as e:
print("Could not find .bvals/.bvecs or .bval/.bvec files...")
raise e
tracto_data = TractographyData(signal, gradients)
elif args.signal_source == "processed_signal":
loaded_tracto_data = TractographyData.load(args.tracto_data)
tracto_data = TractographyData(loaded_tracto_data.signal,
loaded_tracto_data.gradients)
# Compute matrix that brings streamlines back to diffusion voxel space.
rasmm2vox_affine = np.linalg.inv(tracto_data.signal.affine)
# Retrieve data.
with Timer("Retrieving data", newline=args.verbose):
for filename in sorted(args.bundles):
if args.verbose:
print("{}".format(filename))
# Load streamlines
tfile = nib.streamlines.load(filename)
tractogram = tfile.tractogram
original_streamlines = tractogram.streamlines
lengths = length(original_streamlines)
streamlines = [
s for (s, l) in zip(original_streamlines, lengths)
if l >= args.min_length
]
# Make sure file is not empty
if len(streamlines) > 0:
if args.subsample_streamlines:
output_streamlines = subsample_streamlines(
streamlines, args.clustering_threshold,
args.removal_distance)
print("Total difference: {} / {}".format(
len(original_streamlines), len(output_streamlines)))
new_tractogram = nib.streamlines.Tractogram(
output_streamlines,
affine_to_rasmm=tractogram.affine_to_rasmm)
tractogram = new_tractogram
tractogram.apply_affine(rasmm2vox_affine)
# Add streamlines to the TractogramData
bundle_name = os.path.splitext(os.path.basename(filename))[0]
tracto_data.add(tractogram.streamlines, bundle_name)
if args.verbose:
diff = tracto_data.streamlines._data - tracto_data.streamlines._data.astype(
args.dtype)
precision_error = np.sum(np.sqrt(np.sum(diff**2, axis=1)))
avg_precision_error = precision_error / len(
tracto_data.streamlines._data)
print("Precision error: {} (avg. {})".format(precision_error,
avg_precision_error))
# Save streamlines coordinates using either float16 or float32.
tracto_data.streamlines._data = tracto_data.streamlines._data.astype(
args.dtype)
# Save dataset
tracto_data.save(args.out)
def main():
parser = _build_args_parser()
args = parser.parse_args()
logging.basicConfig(level=logging.INFO)
# make sure all the given files exist
if not isfile(args.surfaces):
parser.error('The file "{0}" must exist.'.format(args.surfaces))
if not isfile(args.surface_map):
parser.error('The file "{0}" must exist.'.format(args.surface_map))
if not isfile(args.streamlines):
parser.error('The file "{0}" must exist.'.format(args.streamlines))
# make sure that files are not accidently overwritten
if isfile(args.output):
if args.overwrite:
logging.info('Overwriting "{0}".'.format(args.output))
else:
parser.error(
'The file "{0}" already exists. Use -f to overwrite it.'.
format(args.output))
if isfile(args.out_tracts):
if args.overwrite:
logging.info('Overwriting "{0}".'.format(args.out_tracts))
else:
parser.error(
'The file "{0}" already exists. Use -f to overwrite it.'.
format(args.out_tracts))
# load the surfaces
logging.info('Loading .vtk surfaces and streamlines.')
all_surfaces = load_vtk(args.surfaces)
# load surface map
surface_map = np.load(args.surface_map)
# load mask for intersections
surface_mask = np.load(args.surface_mask)
# find triangles with any vertex within the mask
vertices = ns.vtk_to_numpy(all_surfaces.GetPolys().GetData())
triangles = np.vstack([vertices[1::4], vertices[2::4], vertices[3::4]]).T
surface_mask = surface_mask[triangles]
surface_mask = np.all(surface_mask, axis=1)
surface_map = surface_map[triangles[:, 0]]
# locator for quickly finding intersections
locator = vtk.vtkOBBTree()
locator.SetDataSet(all_surfaces)
locator.BuildLocator()
# load the streamlines
streamlines = load_vtk_streamlines(args.streamlines)
# load label images
label_img = nib.load(args.aparc)
label_data = label_img.get_data().astype('int')
voxel_dim = label_img.get_header()['pixdim'][1:4]
# calculate transform from voxel to mm coordinates
affine = np.array(label_img.affine, dtype=float)
affine = np.linalg.inv(affine)
transform = affine[:3, :3].T
offset = affine[:3, 3] + 0.5
logging.info('Trimming, splitting, and filtering {0} streamlines.'.format(
len(streamlines)))
print(args.rois)
new_streamlines = ROI_Streamlines([], [], [], [], [], [], [])
for i in xrange(len(streamlines)):
# just one segment
# filter as error
if len(streamlines[i]) < 3:
continue
# trim and split cortical intersections
trimmed_streamlines, tri_in, tri_out = trim_cortical_streamline(
streamlines[i], i, locator, surface_mask, surface_map)
# split subcortical intersections
for j in range(len(trimmed_streamlines)):
# resample streamline to allow for fine level
# intersections with subcortical regions
fiber_len = length(trimmed_streamlines[j])
n_points = int(fiber_len / SAMPLE_SIZE)
if n_points < 3:
continue
resampled_streamline = set_number_of_points(
trimmed_streamlines[j], n_points)
# find voxels that the streamline passes through
inds = np.dot(resampled_streamline, transform)
inds = inds + offset
if inds.min().round(decimals=6) < 0:
logging.error(
'Streamline has points that map to negative voxel indices')
ii, jj, kk = inds.astype(int).T
sl_labels = label_data[ii, jj, kk]
# split fibers among intersecting regions and return all intersections
split_streamlines = split_subcortical_streamline(
resampled_streamline, sl_labels, args.rois, tri_in[j],
tri_out[j])
# fill the results arrays
new_streamlines.extend(split_streamlines)
logging.info('Saving {0} final streamlines.'.format(
len(new_streamlines.streamlines)))
# save the results
new_streamlines.save_streamlines(args.out_tracts)
new_streamlines.save_intersections(args.output)
def test_length():
# Test length of only one streamline
length_streamline_cython = length(streamline)
length_streamline_python = length_python(streamline)
assert_almost_equal(length_streamline_cython, length_streamline_python)
length_streamline_cython = length(streamline_64bit)
length_streamline_python = length_python(streamline_64bit)
assert_almost_equal(length_streamline_cython, length_streamline_python)
# Test computing length of multiple streamlines of different nb_points
length_streamlines_cython = length(streamlines)
for i, s in enumerate(streamlines):
length_streamline_python = length_python(s)
assert_array_almost_equal(length_streamlines_cython[i],
length_streamline_python)
length_streamlines_cython = length(streamlines_64bit)
for i, s in enumerate(streamlines_64bit):
length_streamline_python = length_python(s)
assert_array_almost_equal(length_streamlines_cython[i],
length_streamline_python)
# ArraySequence
# Test length of only one streamline
length_streamline_cython = length(streamline_64bit)
length_streamline_arrseq = length(Streamlines([streamline]))
assert_almost_equal(length_streamline_arrseq, length_streamline_cython)
length_streamline_cython = length(streamline_64bit)
length_streamline_arrseq = length(Streamlines([streamline_64bit]))
assert_almost_equal(length_streamline_arrseq, length_streamline_cython)
# Test computing length of multiple streamlines of different nb_points
length_streamlines_cython = length(streamlines)
length_streamlines_arrseq = length(Streamlines(streamlines))
assert_array_almost_equal(length_streamlines_arrseq,
length_streamlines_cython)
length_streamlines_cython = length(streamlines_64bit)
length_streamlines_arrseq = length(Streamlines(streamlines_64bit))
assert_array_almost_equal(length_streamlines_arrseq,
length_streamlines_cython)
# Test on a sliced ArraySequence
length_streamlines_cython = length(streamlines_64bit[::2])
length_streamlines_arrseq = length(Streamlines(streamlines_64bit)[::2])
assert_array_almost_equal(length_streamlines_arrseq,
length_streamlines_cython)
length_streamlines_cython = length(streamlines[::-1])
length_streamlines_arrseq = length(Streamlines(streamlines)[::-1])
assert_array_almost_equal(length_streamlines_arrseq,
length_streamlines_cython)
# Test streamlines having mixed dtype
streamlines_mixed_dtype = [
streamline,
streamline.astype(np.float64),
streamline.astype(np.int32),
streamline.astype(np.int64)
]
lengths_mixed_dtype = [length(s) for s in streamlines_mixed_dtype]
assert_array_equal(length(streamlines_mixed_dtype), lengths_mixed_dtype)
# Test streamlines with different shape
length_streamlines_cython = length(heterogeneous_streamlines)
for i, s in enumerate(heterogeneous_streamlines):
length_streamline_python = length_python(s)
assert_array_almost_equal(length_streamlines_cython[i],
length_streamline_python)
# Test streamline having integer dtype
length_streamline = length(streamline.astype('int'))
assert_equal(length_streamline.dtype, np.float64)
# Test empty list
assert_equal(length([]), 0.0)
# Test streamline having only one point
assert_equal(length(np.array([[1, 2, 3]])), 0.0)
# We do not support list of lists, it should be numpy ndarray.
streamline_unsupported = [[1, 2, 3], [4, 5, 5], [2, 1, 3], [4, 2, 1]]
assert_raises(AttributeError, length, streamline_unsupported)
# Test setting computing length of a numpy with flag WRITABLE=False
streamlines_readonly = []
for s in streamlines:
streamlines_readonly.append(s.copy())
streamlines_readonly[-1].setflags(write=False)
assert_array_almost_equal(length(streamlines_readonly),
[length_python(s) for s in streamlines_readonly])
streamlines_readonly = []
for s in streamlines_64bit:
streamlines_readonly.append(s.copy())
streamlines_readonly[-1].setflags(write=False)
assert_array_almost_equal(length(streamlines_readonly),
[length_python(s) for s in streamlines_readonly])
def check_range(streamline, gt, lt):
length_s = length(streamline)
if (length_s > gt) & (length_s < lt):
return True
else:
return False
def test_length():
# Test length of only one streamline
length_streamline_cython = length(streamline)
length_streamline_python = length_python(streamline)
assert_almost_equal(length_streamline_cython, length_streamline_python)
length_streamline_cython = length(streamline_64bit)
length_streamline_python = length_python(streamline_64bit)
assert_almost_equal(length_streamline_cython, length_streamline_python)
# Test computing length of multiple streamlines of different nb_points
length_streamlines_cython = length(streamlines)
for i, s in enumerate(streamlines):
length_streamline_python = length_python(s)
assert_array_almost_equal(length_streamlines_cython[i],
length_streamline_python)
length_streamlines_cython = length(streamlines_64bit)
for i, s in enumerate(streamlines_64bit):
length_streamline_python = length_python(s)
assert_array_almost_equal(length_streamlines_cython[i],
length_streamline_python)
# ArraySequence
# Test length of only one streamline
length_streamline_cython = length(streamline_64bit)
length_streamline_arrseq = length(Streamlines([streamline]))
assert_almost_equal(length_streamline_arrseq, length_streamline_cython)
length_streamline_cython = length(streamline_64bit)
length_streamline_arrseq = length(Streamlines([streamline_64bit]))
assert_almost_equal(length_streamline_arrseq, length_streamline_cython)
# Test computing length of multiple streamlines of different nb_points
length_streamlines_cython = length(streamlines)
length_streamlines_arrseq = length(Streamlines(streamlines))
assert_array_almost_equal(length_streamlines_arrseq,
length_streamlines_cython)
length_streamlines_cython = length(streamlines_64bit)
length_streamlines_arrseq = length(Streamlines(streamlines_64bit))
assert_array_almost_equal(length_streamlines_arrseq,
length_streamlines_cython)
# Test on a sliced ArraySequence
length_streamlines_cython = length(streamlines_64bit[::2])
length_streamlines_arrseq = length(Streamlines(streamlines_64bit)[::2])
assert_array_almost_equal(length_streamlines_arrseq,
length_streamlines_cython)
length_streamlines_cython = length(streamlines[::-1])
length_streamlines_arrseq = length(Streamlines(streamlines)[::-1])
assert_array_almost_equal(length_streamlines_arrseq,
length_streamlines_cython)
# Test streamlines having mixed dtype
streamlines_mixed_dtype = [streamline,
streamline.astype(np.float64),
streamline.astype(np.int32),
streamline.astype(np.int64)]
lengths_mixed_dtype = [length(s)
for s in streamlines_mixed_dtype]
assert_array_equal(length(streamlines_mixed_dtype),
lengths_mixed_dtype)
# Test streamlines with different shape
length_streamlines_cython = length(
heterogeneous_streamlines)
for i, s in enumerate(heterogeneous_streamlines):
length_streamline_python = length_python(s)
assert_array_almost_equal(length_streamlines_cython[i],
length_streamline_python)
# Test streamline having integer dtype
length_streamline = length(streamline.astype('int'))
assert_true(length_streamline.dtype == np.float64)
# Test empty list
assert_equal(length([]), 0.0)
# Test streamline having only one point
assert_equal(length(np.array([[1, 2, 3]])), 0.0)
# We do not support list of lists, it should be numpy ndarray.
streamline_unsupported = [[1, 2, 3], [4, 5, 5], [2, 1, 3], [4, 2, 1]]
assert_raises(AttributeError, length,
streamline_unsupported)
# Test setting computing length of a numpy with flag WRITABLE=False
streamlines_readonly = []
for s in streamlines:
streamlines_readonly.append(s.copy())
streamlines_readonly[-1].setflags(write=False)
assert_array_almost_equal(length(streamlines_readonly),
[length_python(s) for s in streamlines_readonly])
streamlines_readonly = []
for s in streamlines_64bit:
streamlines_readonly.append(s.copy())
streamlines_readonly[-1].setflags(write=False)
assert_array_almost_equal(length(streamlines_readonly),
[length_python(s) for s in streamlines_readonly])
def main():
parser = buildArgsParser()
args = parser.parse_args()
if not os.path.isfile(args.tracts):
parser.error("Tracts file: {0} does not exist.".format(args.tracts))
if not os.path.isfile(args.org_aparc):
parser.error("Original label file: {0} does not exist.".format(
args.org_aparc))
if not os.path.isfile(args.dilated_aparc):
parser.error("Dilated label file: {0} does not exist.".format(
args.dilated_aparc))
if not os.path.isfile(args.subcortical_labels):
parser.error("Requested region file: {0} does not exist.".format(
args.subcortical_labels))
if not os.path.isfile(args.lut):
parser.error("Freesurfer LUT file: {0} does not exist.".format(
args.lut))
if not os.path.isfile(args.faimage):
parser.error("FA Image file: {0} does not exist.".format(args.faimage))
if not os.path.isfile(args.mdimage):
parser.error("MD Image file: {0} does not exist.".format(args.mdimage))
# Validate that tracts can be processed
if not validate_coordinates(
args.org_aparc, args.tracts, nifti_compliant=True):
parser.error("The tracts file contains points that are invalid.\n" +
"Use the remove_invalid_coordinates.py script to clean.")
# Load label images
org_labels_img = nib.load(args.org_aparc)
org_labels_data = org_labels_img.get_data().astype('int')
dilated_labels_img = nib.load(args.dilated_aparc)
dilated_labels_data = dilated_labels_img.get_data().astype('int')
# Load fibers
tract_format = tc.detect_format(args.tracts)
tract = tract_format(args.tracts, args.org_aparc)
affine = compute_affine_for_dipy_functions(args.org_aparc, args.tracts)
#load FA and MD image
fa_img = nib.load(args.faimage)
fa_data = fa_img.get_data()
md_img = nib.load(args.mdimage)
md_data = md_img.get_data()
# ========= processing streamlines =================
fiberlen_range = np.asarray([args.minlen, args.maxlen])
streamlines = [t for t in tract]
print "Subjeect " + args.sub_id + " has " + str(
len(streamlines)) + " streamlines."
f_streamlines = [] #filtered streamlines
lenrecord = []
idx = 0
for sl in streamlines:
# Avoid streamlines having only one point, as they crash the
# Dipy connectivity matrix function.
if sl.shape[0] > 1:
flen = length(sl)
# get fibers having length between 20mm and 200mm
if (flen > fiberlen_range[0]) & (flen < fiberlen_range[1]):
f_streamlines.append(sl)
lenrecord.append(flen)
idx = idx + 1
print "Subject " + args.sub_id + " has " + str(
idx - 1) + " streamlines after filtering."
# ============= process the parcellation =====================
# Compute the mapping from label name to label id
label_id_mapping = compute_labels_map(args.lut)
# Find which labels were requested by the user.
requested_labels_mapping = compute_requested_labels(
args.subcortical_labels, label_id_mapping)
# Increase aparc_filtered_labels with subcortical regions
# 17 LH_Hippocampus
# 53 RH_Hippocampus
# 11 LH_Caudate
# 50 RH_Caudate
# 12 LH_Putamen
# 51 RH_Putamen
# 13 LH_Pallidum
# 52 RH_Pallidum
# 18 LH_Amygdala
# 54 RH_Amygdala
# 26 LH_Accumbens
# 58 RH_Accumbens
# 10 LH_Thalamus-Proper
# 49 RH_Thalamus-Proper
# 4 LH_Lateral-Ventricle
# 43 RH_Lateral-Ventricle
# 8 LH_Cerebellum-Cortex
# 47 RH_Cerebellum-Cortex
#
# 16 _Brain-Stem (# 7,8 LH_Cerebellum) (# 41 RH_Cerebellum)
sub_cortical_labels = [
17, 53, 11, 50, 12, 51, 13, 52, 18, 54, 26, 58, 10, 49, 4, 43, 8, 47
] # 16
Brain_Stem_cerebellum = [16] #1
aparc_filtered_labels = dilated_labels_data
for label_val in requested_labels_mapping:
if sum(sum(sum(org_labels_data == label_val))) == 0:
print label_val
print requested_labels_mapping[label_val]
aparc_filtered_labels[org_labels_data == label_val] = label_val
for brain_stem_id in Brain_Stem_cerebellum:
if sum(sum(sum(org_labels_data == brain_stem_id))) == 0:
print 'no labels of '
print brain_stem_id
aparc_filtered_labels[
org_labels_data ==
brain_stem_id] = 99 # let the brain stem's label be 30
# Reduce the range of labels to avoid a sparse matrix,
# because the ids of labels can range from 0 to the 12000's.
reduced_dilated_labels, labels_lut = dpu.reduce_labels(
aparc_filtered_labels)
#dilated_labels_fname = args.sub_id + "_" + args.pre + "_dilated_allbrain_labels.nii.gz"
#dilated_labels_img = nib.Nifti1Image(aparc_filtered_labels, org_labels_img.get_affine(),org_labels_img.get_header())
#nib.save(dilated_labels_img,dilated_labels_fname)
#print args.sub_id + 'dilated labels have saved'
#pdb.set_trace()
# Compute connectivity matrix and extract the fibers
M, grouping = nconnectivity_matrix(f_streamlines,
reduced_dilated_labels,
fiberlen_range,
args.cnpoint,
affine=affine,
symmetric=True,
return_mapping=True,
mapping_as_streamlines=True,
keepfiberinroi=True)
Msize = len(M)
CM_before_outlierremove = M[1:, 1:]
nstream_bf = np.sum(CM_before_outlierremove)
print args.sub_id + ' ' + str(
nstream_bf
) + ' streamlines in the connectivity matrix before outlier removal.'
# ===================== process the streamlines =============
print 'Processing streamlines to remove outliers ..............'
outlier_para = 3
average_thrd = 8
M_after_ourlierremove = np.zeros((Msize, Msize))
# downsample streamlines
cell_streamlines = []
cell_id = []
for i in range(1, Msize):
for j in range(i + 1, Msize):
tmp_streamlines = grouping[i, j]
tmp_streamlines = list(tmp_streamlines)
# downsample
tmp_streamlines_downsampled = [
downsample(s, 100) for s in tmp_streamlines
]
# remove outliers, we need to rewrite the QuickBundle method to speed up this process
qb = QuickBundles(threshold=average_thrd)
clusters = qb.cluster(tmp_streamlines_downsampled)
outlier_clusters = clusters < outlier_para # small clusters
nonoutlier_clusters = clusters[np.logical_not(outlier_clusters)]
tmp_nonoutlier_index = []
for tmp_cluster in nonoutlier_clusters:
tmp_nonoutlier_index = tmp_nonoutlier_index + tmp_cluster.indices
clean_streamline_downsampled = [
tmp_streamlines_downsampled[ind]
for ind in tmp_nonoutlier_index
]
cell_streamlines.append(clean_streamline_downsampled)
cell_id.append([i, j])
M_after_ourlierremove[i, j] = len(clean_streamline_downsampled)
CM_after_ourlierremove = M_after_ourlierremove[1:, 1:]
nstream_bf = np.sum(CM_after_ourlierremove)
print args.sub_id + ' ' + str(
nstream_bf
) + ' streamlines in the connectivity matrix after outlier removal.'
#===================== save the data =======================
if (args.saving_indicator == 1): # save the whole brain connectivity
cmCountMatrix_fname = args.sub_id + "_" + args.pre + "_allbrain" + "_cm_count_raw.mat"
cmCountMatrix_processed_fname = args.sub_id + "_" + args.pre + "_allbrain" + "_cm_count_processed.mat"
cmStreamlineMatrix_fname = args.sub_id + "_" + args.pre + "_allbrain" + "_cm_streamlines.mat"
reduced_dilated_labels_fname = args.sub_id + "_" + args.pre + "_allbrain" + "_reduced_dilated_labels.nii.gz"
RoiInfo_fname = args.sub_id + "_" + args.pre + "_allbrain_RoiInfo.mat"
# save the raw count matrix
CM = M[1:, 1:]
sio.savemat(cmCountMatrix_fname, {'cm': CM})
sio.savemat(cmCountMatrix_processed_fname,
{'cm': CM_after_ourlierremove})
# save the streamline matrix
sio.savemat(cmStreamlineMatrix_fname, {'slines': cell_streamlines})
sio.savemat(RoiInfo_fname, {'ROIinfo': cell_id})
print args.sub_id + 'cell_streamlines.mat, ROIinfo.mat has been saved'
filtered_labels_img = nib.Nifti1Image(aparc_filtered_labels,
org_labels_img.get_affine(),
org_labels_img.get_header())
nib.save(filtered_labels_img, reduced_dilated_labels_fname)
print args.sub_id + 'all brain dilated labels have saved'
# ===================== process the streamlines and extract features =============
cm_fa_curve = fa_extraction_use_cellinput(cell_streamlines,
cell_id,
fa_data,
Msize,
affine=affine)
(tmp_cm_fa_mean, tmp_cm_fa_max,
cm_count) = fa_mean_extraction(cm_fa_curve, Msize)
# extract MD values along the streamlines
cm_md_curve = fa_extraction_use_cellinput(cell_streamlines,
cell_id,
md_data,
Msize,
affine=affine)
(tmp_cm_md_mean, tmp_cm_md_max,
testcm) = fa_mean_extraction(cm_md_curve, Msize)
# connected surface area
# extract the connective volume ratio
(tmp_cm_volumn, tmp_cm_volumn_ratio) = rois_connectedvol_cellinput(
reduced_dilated_labels,
Msize,
cell_streamlines,
cell_id,
affine=affine)
# fiber length
tmp_connectcm_len = rois_fiberlen_cellinput(Msize, cell_streamlines)
# save cm features
cm_md_mean = tmp_cm_md_mean[1:, 1:]
cm_md_max = tmp_cm_md_max[1:, 1:]
cm_fa_mean = tmp_cm_fa_mean[1:, 1:]
cm_fa_max = tmp_cm_fa_max[1:, 1:]
cm_volumn = tmp_cm_volumn[1:, 1:]
cm_volumn_ratio = tmp_cm_volumn_ratio[1:, 1:]
connectcm_len = tmp_connectcm_len[1:, 1:]
sio.savemat(args.pre + "_allbrain" + "_cm_processed_mdmean_100.mat",
{'cm_mdmean': cm_md_mean})
sio.savemat(args.pre + "_allbrain" + "_cm_processed_mdmax_100.mat",
{'cm_mdmax': cm_md_max})
sio.savemat(args.pre + "_allbrain" + "_cm_processed_famean_100.mat",
{'cm_famean': cm_fa_mean})
sio.savemat(args.pre + "_allbrain" + "_cm_processed_famax_100.mat",
{'cm_famax': cm_fa_max})
sio.savemat(args.pre + "_allbrain" + "_cm_processed_volumn_100.mat",
{'cm_volumn': cm_volumn})
sio.savemat(
args.pre + "_allbrain" + "_cm_processed_volumn_ratio_100.mat",
{'cm_volumn_ratio': cm_volumn_ratio})
sio.savemat(args.pre + "_allbrain" + "_cm_processed_fiberlen_100.mat",
{'cm_len': connectcm_len})
# save the streamline matrix
cell_fa = []
for i in range(1, Msize):
for j in range(i + 1, Msize):
tmp_fa = cm_fa_curve[i, j]
tmp_fa = list(tmp_fa)
cell_fa.append(tmp_fa)
sio.savemat(args.pre + "_allbrain" + "_cm_processed_sfa_100.mat",
{'sfa': cell_fa})
print args.pre + '_allbrain" + "_cm_processed_sfa_100.mat' + ' has been saved'
cell_md = []
for i in range(1, Msize):
for j in range(i + 1, Msize):
tmp_md = cm_md_curve[i, j]
tmp_md = list(tmp_md)
cell_md.append(tmp_md)
sio.savemat(args.pre + "_allbrain" + "_cm_processed_smd_100.mat",
{'smd': cell_md})
print args.pre + '_allbrain" + "_cm_processed_smd_100.mat' + ' has been saved'
if (
args.saving_indicator == 0
): # save the part of the connection: connection between subcortical region
Nsubcortical_reg = len(sub_cortical_labels) + 1 # should be 19
cmCountMatrix_fname = args.sub_id + "_" + args.pre + "_partbrain_subcort" + "_cm_count_raw.mat"
cmCountMatrix_processed_fname = args.sub_id + "_" + args.pre + "_partbrain_subcort" + "_cm_count_processed.mat"
cmStreamlineMatrix_fname = args.sub_id + "_" + args.pre + "_partbrain_subcort" + "_cm_streamlines.mat"
reduced_dilated_labels_fname = args.sub_id + "_" + args.pre + "_partbrain_subcort" + "_reduced_dilated_labels.nii.gz"
subcortical_RoiInfo_fname = args.sub_id + "_" + args.pre + "_partbrain_subcort_RoiInfo.mat"
# save the raw count matrix
CM = M[1:, 1:]
sio.savemat(cmCountMatrix_fname, {'cm': CM})
sio.savemat(cmCountMatrix_processed_fname,
{'cm': CM_after_ourlierremove})
filtered_labels_img = nib.Nifti1Image(aparc_filtered_labels,
org_labels_img.get_affine(),
org_labels_img.get_header())
nib.save(filtered_labels_img, reduced_dilated_labels_fname)
print args.sub_id + ' all brain dilated labels have saved'
# ===================== process the streamlines and extract features =============
cm_fa_curve = fa_extraction_use_cellinput(cell_streamlines,
cell_id,
fa_data,
Msize,
affine=affine)
(tmp_cm_fa_mean, tmp_cm_fa_max,
cm_count) = fa_mean_extraction(cm_fa_curve, Msize)
# extract MD values along the streamlines
cm_md_curve = fa_extraction_use_cellinput(cell_streamlines,
cell_id,
md_data,
Msize,
affine=affine)
(tmp_cm_md_mean, tmp_cm_md_max,
testcm) = fa_mean_extraction(cm_md_curve, Msize)
# connected surface area
# extract the connective volume ratio
(tmp_cm_volumn, tmp_cm_volumn_ratio) = rois_connectedvol_cellinput(
reduced_dilated_labels,
Msize,
cell_streamlines,
cell_id,
affine=affine)
# fiber length
tmp_connectcm_len = rois_fiberlen_cellinput(Msize, cell_streamlines)
# save cm features
cm_md_mean = tmp_cm_md_mean[1:, 1:]
cm_md_max = tmp_cm_md_max[1:, 1:]
cm_fa_mean = tmp_cm_fa_mean[1:, 1:]
cm_fa_max = tmp_cm_fa_max[1:, 1:]
cm_volumn = tmp_cm_volumn[1:, 1:]
cm_volumn_ratio = tmp_cm_volumn_ratio[1:, 1:]
connectcm_len = tmp_connectcm_len[1:, 1:]
sio.savemat(
args.pre + "_partbrain_subcort" + "_cm_processed_mdmean_100.mat",
{'cm_mdmean': cm_md_mean})
sio.savemat(
args.pre + "_partbrain_subcort" + "_cm_processed_mdmax_100.mat",
{'cm_mdmax': cm_md_max})
sio.savemat(
args.pre + "_partbrain_subcort" + "_cm_processed_famean_100.mat",
{'cm_famean': cm_fa_mean})
sio.savemat(
args.pre + "_partbrain_subcort" + "_cm_processed_famax_100.mat",
{'cm_famax': cm_fa_max})
sio.savemat(
args.pre + "_partbrain_subcort" + "_cm_processed_volumn_100.mat",
{'cm_volumn': cm_volumn})
sio.savemat(
args.pre + "_partbrain_subcort" +
"_cm_processed_volumn_ratio_100.mat",
{'cm_volumn_ratio': cm_volumn_ratio})
sio.savemat(
args.pre + "_partbrain_subcort" + "_cm_processed_fiberlen_100.mat",
{'cm_len': connectcm_len})
# save the streamline matrix
cell_fa = []
cell_id = []
for i in range(1, Nsubcortical_reg):
for j in range(i + 1, Msize):
tmp_fa = cm_fa_curve[i, j]
tmp_fa = list(tmp_fa)
cell_fa.append(tmp_fa)
cell_id.append([i, j])
sio.savemat(
args.pre + "_partbrain_subcort" + "_cm_processed_sfa_100.mat",
{'sfa': cell_fa})
print args.pre + '_partbrain_subcort' + '_cm_processed_sfa_100.mat' + 'has been saved.'
cell_md = []
for i in range(1, Nsubcortical_reg):
for j in range(i + 1, Msize):
tmp_md = cm_md_curve[i, j]
tmp_md = list(tmp_md)
cell_md.append(tmp_md)
sio.savemat(args.pre + "_partbrain" + "_cm_processed_smd_100.mat",
{'smd': cell_md})
print args.pre + '_partbrain' + '_cm_processed_smd_100.mat' + 'has been saved.'
# save the streamline matrix
subcortical_cell_streamlines = []
cell_id = []
idx = 0
for i in range(1, Nsubcortical_reg):
for j in range(i + 1, Msize):
tmp_sls = cell_streamlines[idx]
idx = idx + 1
subcortical_cell_streamlines.append(tmp_sls)
cell_id.append([i, j])
sio.savemat(cmStreamlineMatrix_fname,
{'slines': subcortical_cell_streamlines})
sio.savemat(subcortical_RoiInfo_fname, {'ROIinfo': cell_id})
print cmStreamlineMatrix_fname + ' has been saved'
def check_range(streamline, gt=greater_than, lt=less_than):
if (length(streamline) > gt) & (length(streamline) < lt):
return True
else:
return False
def extract(self, streamline):
return length(streamline)[None, None]
