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BF: dipy_horizon now loads .nii.gz and slicer actor apply affine tran… #41

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2 changes: 1 addition & 1 deletion dipy/viz/actor.py
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Original file line number Diff line number Diff line change
Expand Up @@ -157,7 +157,7 @@ def input_connection(self, output):
self.shape = (ex2 + 1, ey2 + 1, ez2 + 1)

def display_extent(self, x1, x2, y1, y2, z1, z2):
self.SetDisplayExtent(x1, x2, y1, y2, z1, z2)
self.SetDisplayExtent(*list(map(int, [x1, x2, y1, y2, z1, z2])))
if vtk.VTK_MAJOR_VERSION > 5:
self.Update()

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36 changes: 15 additions & 21 deletions dipy/workflows/segment.py
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Original file line number Diff line number Diff line change
Expand Up @@ -267,11 +267,11 @@ def recognize_bundles_flow(streamline_files, model_bundle_files,

sf_bundle_file = os.path.join(
out_dir,
base_mb + '_of_' + base_sf + '.trk')
base_mb + '_of_' + base_sf + '.tck')

sf_bundle_file_initial = os.path.join(
out_dir,
base_mb + '_of_' + base_sf + '_initial.trk')
base_mb + '_of_' + base_sf + '_initial.tck')

sf_bundle_labels = os.path.join(
out_dir,
Expand All @@ -281,9 +281,8 @@ def recognize_bundles_flow(streamline_files, model_bundle_files,
# os.makedirs(os.path.dirname(sf_bundle_file))

recognized_tractogram = nib.streamlines.Tractogram(
recognized_bundle)
recognized_trkfile = nib.streamlines.TrkFile(recognized_tractogram)
nib.streamlines.save(recognized_trkfile, sf_bundle_file)
recognized_bundle, affine_to_rasmm=np.eye(4))
nib.streamlines.save(recognized_tractogram, sf_bundle_file)

np.save(sf_bundle_labels, np.array(rb.labels))

Expand All @@ -299,25 +298,23 @@ def recognize_bundles_flow(streamline_files, model_bundle_files,
if debug:
sf_bundle_neighb = os.path.join(
out_dir,
base_mb + '_of_' + base_sf + '_neighb.trk')
base_mb + '_of_' + base_sf + '_neighb.tck')

neighb_tractogram = nib.streamlines.Tractogram(
rb.neighb_streamlines)
neighb_trkfile = nib.streamlines.TrkFile(neighb_tractogram)
nib.streamlines.save(neighb_trkfile, sf_bundle_neighb)
rb.neighb_streamlines, affine_to_rasmm=np.eye(4))
nib.streamlines.save(neighb_tractogram, sf_bundle_neighb)

print('Recognized bundle\'s neighbors saved in \n {} '
.format(sf_bundle_neighb))

if debug:
sf_centroids = os.path.join(
os.path.dirname(sf),
base_sf + '_centroids.trk')
base_sf + '_centroids.tck')

centroid_tractogram = nib.streamlines.Tractogram(
rb.centroids)
centroid_trkfile = nib.streamlines.TrkFile(centroid_tractogram)
nib.streamlines.save(centroid_trkfile, sf_centroids)
rb.centroids, affine_to_rasmm=np.eye(4))
nib.streamlines.save(centroid_tractogram, sf_centroids)

print('Centroids of streamlines saved in \n {} '
.format(sf_centroids))
Expand Down Expand Up @@ -346,15 +343,12 @@ def assign_bundle_labels_flow(streamline_file, labels_files, verbose=True):

labels = np.load(lf)
recognized_bundle = streamlines[labels.tolist()]
recognized_tractogram = nib.streamlines.Tractogram(recognized_bundle)
recognized_trkfile = nib.streamlines.TrkFile(
recognized_tractogram,
header=streamlines_trk.header)
recognized_tractogram = nib.streamlines.Tractogram(recognized_bundle, affine_to_rasmm=np.eye(4))
base = os.path.splitext(os.path.basename(lf))[0].split('_labels')[0]
fname = os.path.join(
os.path.dirname(lf),
base + '_of_' + os.path.basename(streamline_file))
nib.streamlines.save(recognized_trkfile, fname)
nib.streamlines.save(recognized_tractogram, fname)
if verbose:
print('Bundle saved in \n {} '.format(fname))

Expand Down Expand Up @@ -431,9 +425,9 @@ def expand_callback(obj, event):

def button_save_callback(obj, event):
global final_streamlines
ftypes = (("Trackvis file", "*.trk"), ("All Files", "*.*"))
fname = window.save_file_dialog(initial_file='dipy.trk',
default_ext='.trk',
ftypes = (("Trackvis file", "*.tck"), ("All Files", "*.*"))
fname = window.save_file_dialog(initial_file='dipy.tck',
default_ext='.tck',
file_types=ftypes)
if fname != '':
print('Saving new trk file ...')
Expand Down