def build_show(self, scene):
show_m = window.ShowManager(scene,
size=(1200, 900),
order_transparent=True,
reset_camera=False)
show_m.initialize()
if self.cluster:
lengths = np.array([self.cla[c]['length'] for c in self.cla])
szs = [self.cla[c]['size'] for c in self.cla]
sizes = np.array(szs)
# global self.panel2, slider_length, slider_size
self.panel2 = ui.Panel2D(size=(300, 200),
position=(850, 320),
color=(1, 1, 1),
opacity=0.1,
align="right")
slider_label_length = build_label(text="Length")
slider_length = ui.LineSlider2D(
min_value=lengths.min(),
max_value=np.percentile(lengths, 98),
initial_value=np.percentile(lengths, 25),
text_template="{value:.0f}",
length=140)
slider_label_size = build_label(text="Size")
slider_size = ui.LineSlider2D(min_value=sizes.min(),
max_value=np.percentile(sizes, 98),
initial_value=np.percentile(
sizes, 50),
text_template="{value:.0f}",
length=140)
# global self.length_min, size_min
self.size_min = sizes.min()
self.length_min = lengths.min()
def hide_clusters_length(slider):
self.length_min = np.round(slider.value)
for k in self.cla:
if (self.cla[k]['length'] < self.length_min
or self.cla[k]['size'] < self.size_min):
self.cla[k]['centroid_actor'].SetVisibility(0)
if k.GetVisibility() == 1:
k.SetVisibility(0)
else:
self.cla[k]['centroid_actor'].SetVisibility(1)
show_m.render()
def hide_clusters_size(slider):
self.size_min = np.round(slider.value)
for k in self.cla:
if (self.cla[k]['length'] < self.length_min
or self.cla[k]['size'] < self.size_min):
self.cla[k]['centroid_actor'].SetVisibility(0)
if k.GetVisibility() == 1:
k.SetVisibility(0)
else:
self.cla[k]['centroid_actor'].SetVisibility(1)
show_m.render()
slider_length.on_change = hide_clusters_length
self.panel2.add_element(slider_label_length, coords=(0.1, 0.333))
self.panel2.add_element(slider_length, coords=(0.4, 0.333))
slider_size.on_change = hide_clusters_size
self.panel2.add_element(slider_label_size, coords=(0.1, 0.6666))
self.panel2.add_element(slider_size, coords=(0.4, 0.6666))
scene.add(self.panel2)
text_block = build_label(HELP_MESSAGE, 16) # ui.TextBlock2D()
text_block.message = HELP_MESSAGE
help_panel = ui.Panel2D(size=(300, 200),
color=(1, 1, 1),
opacity=0.1,
align="left")
help_panel.add_element(text_block, coords=(0.05, 0.1))
scene.add(help_panel)
if len(self.images) > 0:
# !!Only first image loading supported for now')
data, affine = self.images[0]
self.panel = slicer_panel(scene, data, affine, self.world_coords)
else:
data = None
affine = None
self.win_size = scene.GetSize()
def win_callback(obj, event):
if self.win_size != obj.GetSize():
size_old = self.win_size
self.win_size = obj.GetSize()
size_change = [self.win_size[0] - size_old[0], 0]
if data is not None:
self.panel.re_align(size_change)
if self.cluster:
self.panel2.re_align(size_change)
help_panel.re_align(size_change)
show_m.initialize()
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']
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
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)
self.hide_centroids = True
self.select_all = False
def key_press(obj, event):
key = obj.GetKeySym()
if self.cluster:
# hide on/off unselected centroids
if key == 'h' or key == 'H':
if self.hide_centroids:
for ca in self.cea:
if (self.cea[ca]['length'] >= self.length_min
or self.cea[ca]['size'] >= self.size_min):
if self.cea[ca]['selected'] == 0:
ca.VisibilityOff()
else:
for ca in self.cea:
if (self.cea[ca]['length'] >= self.length_min
and self.cea[ca]['size'] >= self.size_min):
if self.cea[ca]['selected'] == 0:
ca.VisibilityOn()
self.hide_centroids = not self.hide_centroids
show_m.render()
# invert selection
if key == 'i' or key == 'I':
for ca in self.cea:
if (self.cea[ca]['length'] >= self.self.length_min
and self.cea[ca]['size'] >= self.size_min):
self.cea[ca]['selected'] = \
not self.cea[ca]['selected']
cas = self.cea[ca]['cluster_actor']
self.cla[cas]['selected'] = \
self.cea[ca]['selected']
show_m.render()
# save current result
if key == 's' or key == 'S':
saving_streamlines = Streamlines()
for bundle in self.cla.keys():
if bundle.GetVisibility():
t = self.cla[bundle]['tractogram']
c = self.cla[bundle]['cluster']
indices = self.tractogram_clusters[t][c]
saving_streamlines.extend(Streamlines(indices))
print('Saving result in tmp.trk')
save_trk('tmp.trk', saving_streamlines, np.eye(4))
if key == 'y' or key == 'Y':
active_streamlines = Streamlines()
for bundle in self.cla.keys():
if bundle.GetVisibility():
t = self.cla[bundle]['tractogram']
c = self.cla[bundle]['cluster']
indices = self.tractogram_clusters[t][c]
active_streamlines.extend(Streamlines(indices))
# self.tractograms = [active_streamlines]
hz2 = horizon([active_streamlines],
self.images,
cluster=True,
cluster_thr=5,
random_colors=self.random_colors,
length_lt=np.inf,
length_gt=0,
clusters_lt=np.inf,
clusters_gt=0,
world_coords=True,
interactive=True)
ren2 = hz2.build_scene()
hz2.build_show(ren2)
if key == 'a' or key == 'A':
if self.select_all is False:
for ca in self.cea:
if (self.cea[ca]['length'] >= self.length_min
and self.cea[ca]['size'] >= self.size_min):
self.cea[ca]['selected'] = 1
cas = self.cea[ca]['cluster_actor']
self.cla[cas]['selected'] = \
self.cea[ca]['selected']
show_m.render()
self.select_all = True
else:
for ca in self.cea:
if (self.cea[ca]['length'] >= self.length_min
and self.cea[ca]['size'] >= self.size_min):
self.cea[ca]['selected'] = 0
cas = self.cea[ca]['cluster_actor']
self.cla[cas]['selected'] = \
self.cea[ca]['selected']
show_m.render()
self.select_all = False
if key == 'e' or key == 'E':
for c in self.cea:
if self.cea[c]['selected']:
if not self.cea[c]['expanded']:
len_ = self.cea[c]['length']
sz_ = self.cea[c]['size']
if (len_ >= self.length_min
and sz_ >= self.size_min):
self.cea[c]['cluster_actor']. \
VisibilityOn()
c.VisibilityOff()
self.cea[c]['expanded'] = 1
show_m.render()
if key == 'r' or key == 'R':
for c in self.cea:
if (self.cea[c]['length'] >= self.length_min
and self.cea[c]['size'] >= self.size_min):
self.cea[c]['cluster_actor'].VisibilityOff()
c.VisibilityOn()
self.cea[c]['expanded'] = 0
show_m.render()
scene.reset_camera()
scene.zoom(1.5)
scene.reset_clipping_range()
if self.interactive:
show_m.add_window_callback(win_callback)
show_m.iren.AddObserver('KeyPressEvent', key_press)
show_m.render()
show_m.start()
else:
window.record(scene,
out_path=self.out_png,
size=(1200, 900),
reset_camera=False)
def build_show(self, scene):
self.show_m = window.ShowManager(scene,
size=(1200, 900),
order_transparent=True,
reset_camera=False)
self.show_m.initialize()
if self.cluster and self.tractograms:
lengths = np.array([self.cla[c]['length'] for c in self.cla])
szs = [self.cla[c]['size'] for c in self.cla]
sizes = np.array(szs)
# global self.panel2, slider_length, slider_size
self.panel2 = ui.Panel2D(size=(400, 400),
position=(850, 520),
color=(1, 1, 1),
opacity=0.1,
align="right")
slider_label_threshold = build_label(text="Threshold")
slider_threshold = ui.LineSlider2D(min_value=5,
max_value=25,
initial_value=15,
text_template="{value:.0f}",
length=140,
shape='square')
_color_slider(slider_threshold)
slider_label_length = build_label(text="Length")
slider_length = ui.LineSlider2D(
min_value=lengths.min(),
max_value=np.percentile(lengths, 98),
initial_value=np.percentile(lengths, 25),
text_template="{value:.0f}",
length=140)
_color_slider(slider_length)
slider_label_size = build_label(text="Size")
slider_size = ui.LineSlider2D(min_value=sizes.min(),
max_value=np.percentile(sizes, 98),
initial_value=np.percentile(
sizes, 50),
text_template="{value:.0f}",
length=140)
_color_slider(slider_size)
# global self.length_min, size_min
self.size_min = sizes.min()
self.length_min = lengths.min()
def change_threshold(istyle, obj, slider):
sv = np.round(slider.value, 0)
self.remove_actors(scene)
self.add_actors(scene, self.tractograms, threshold=sv)
slider_threshold.handle_events(slider_threshold.handle.actor)
slider_threshold.on_left_mouse_button_released = change_threshold
def hide_clusters_length(slider):
self.length_min = np.round(slider.value)
for k in self.cla:
if (self.cla[k]['length'] < self.length_min
or self.cla[k]['size'] < self.size_min):
self.cla[k]['centroid_actor'].SetVisibility(0)
if k.GetVisibility() == 1:
k.SetVisibility(0)
else:
self.cla[k]['centroid_actor'].SetVisibility(1)
self.show_m.render()
def hide_clusters_size(slider):
self.size_min = np.round(slider.value)
for k in self.cla:
if (self.cla[k]['length'] < self.length_min
or self.cla[k]['size'] < self.size_min):
self.cla[k]['centroid_actor'].SetVisibility(0)
if k.GetVisibility() == 1:
k.SetVisibility(0)
else:
self.cla[k]['centroid_actor'].SetVisibility(1)
self.show_m.render()
slider_length.on_change = hide_clusters_length
self.panel2.add_element(slider_label_threshold,
coords=(0.1, 0.133))
self.panel2.add_element(slider_threshold, coords=(0.4, 0.133))
self.panel2.add_element(slider_label_length, coords=(0.1, 0.333))
self.panel2.add_element(slider_length, coords=(0.4, 0.333))
slider_size.on_change = hide_clusters_size
self.panel2.add_element(slider_label_size, coords=(0.1, 0.6666))
self.panel2.add_element(slider_size, coords=(0.4, 0.6666))
scene.add(self.panel2)
text_block = build_label(HELP_MESSAGE, 16)
text_block.message = HELP_MESSAGE
help_panel = ui.Panel2D(size=(300, 200),
color=(1, 1, 1),
opacity=0.1,
align="left")
help_panel.add_element(text_block, coords=(0.05, 0.1))
scene.add(help_panel)
if len(self.images) > 0:
# !!Only first image loading supported for now')
data, affine = self.images[0]
self.vox2ras = affine
if len(self.pams) > 0:
pam = self.pams[0]
else:
pam = None
self.panel = slicer_panel(scene,
self.show_m.iren,
data,
affine,
self.world_coords,
pam=pam)
else:
data = None
affine = None
pam = None
self.win_size = scene.GetSize()
def win_callback(obj, event):
if self.win_size != obj.GetSize():
size_old = self.win_size
self.win_size = obj.GetSize()
size_change = [self.win_size[0] - size_old[0], 0]
if data is not None:
self.panel.re_align(size_change)
if self.cluster:
self.panel2.re_align(size_change)
help_panel.re_align(size_change)
self.show_m.initialize()
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)
self.hide_centroids = True
self.select_all = False
def key_press(obj, event):
key = obj.GetKeySym()
if self.cluster:
# hide on/off unselected centroids
if key == 'h' or key == 'H':
if self.hide_centroids:
for ca in self.cea:
if (self.cea[ca]['length'] >= self.length_min
or self.cea[ca]['size'] >= self.size_min):
if self.cea[ca]['selected'] == 0:
ca.VisibilityOff()
else:
for ca in self.cea:
if (self.cea[ca]['length'] >= self.length_min
and self.cea[ca]['size'] >= self.size_min):
if self.cea[ca]['selected'] == 0:
ca.VisibilityOn()
self.hide_centroids = not self.hide_centroids
self.show_m.render()
# invert selection
if key == 'i' or key == 'I':
for ca in self.cea:
if (self.cea[ca]['length'] >= self.length_min
and self.cea[ca]['size'] >= self.size_min):
self.cea[ca]['selected'] = \
not self.cea[ca]['selected']
cas = self.cea[ca]['cluster_actor']
self.cla[cas]['selected'] = \
self.cea[ca]['selected']
self.show_m.render()
# save current result
if key == 's' or key == 'S':
saving_streamlines = Streamlines()
for bundle in self.cla.keys():
if bundle.GetVisibility():
t = self.cla[bundle]['tractogram']
c = self.cla[bundle]['cluster']
indices = self.tractogram_clusters[t][c]
saving_streamlines.extend(Streamlines(indices))
print('Saving result in tmp.trk')
sft = StatefulTractogram(saving_streamlines, 'same',
Space.RASMM)
save_tractogram(sft, 'tmp.trk', bbox_valid_check=False)
if key == 'y' or key == 'Y':
active_streamlines = Streamlines()
for bundle in self.cla.keys():
if bundle.GetVisibility():
t = self.cla[bundle]['tractogram']
c = self.cla[bundle]['cluster']
indices = self.tractogram_clusters[t][c]
active_streamlines.extend(Streamlines(indices))
# self.tractograms = [active_streamlines]
hz2 = Horizon([active_streamlines],
self.images,
cluster=True,
cluster_thr=5,
random_colors=self.random_colors,
length_lt=np.inf,
length_gt=0,
clusters_lt=np.inf,
clusters_gt=0,
world_coords=True,
interactive=True)
ren2 = hz2.build_scene()
hz2.build_show(ren2)
if key == 'a' or key == 'A':
if self.select_all is False:
for ca in self.cea:
if (self.cea[ca]['length'] >= self.length_min
and self.cea[ca]['size'] >= self.size_min):
self.cea[ca]['selected'] = 1
cas = self.cea[ca]['cluster_actor']
self.cla[cas]['selected'] = \
self.cea[ca]['selected']
self.show_m.render()
self.select_all = True
else:
for ca in self.cea:
if (self.cea[ca]['length'] >= self.length_min
and self.cea[ca]['size'] >= self.size_min):
self.cea[ca]['selected'] = 0
cas = self.cea[ca]['cluster_actor']
self.cla[cas]['selected'] = \
self.cea[ca]['selected']
self.show_m.render()
self.select_all = False
if key == 'e' or key == 'E':
for c in self.cea:
if self.cea[c]['selected']:
if not self.cea[c]['expanded']:
len_ = self.cea[c]['length']
sz_ = self.cea[c]['size']
if (len_ >= self.length_min
and sz_ >= self.size_min):
self.cea[c]['cluster_actor']. \
VisibilityOn()
c.VisibilityOff()
self.cea[c]['expanded'] = 1
self.show_m.render()
if key == 'r' or key == 'R':
for c in self.cea:
if (self.cea[c]['length'] >= self.length_min
and self.cea[c]['size'] >= self.size_min):
self.cea[c]['cluster_actor'].VisibilityOff()
c.VisibilityOn()
self.cea[c]['expanded'] = 0
self.show_m.render()
HORIMEM.window_timer_cnt = 0
def timer_callback(obj, event):
HORIMEM.window_timer_cnt += 1
# TODO possibly add automatic rotation option
# cnt = HORIMEM.window_timer_cnt
# show_m.scene.azimuth(0.05 * cnt)
# show_m.render()
scene.reset_camera()
scene.zoom(1.5)
scene.reset_clipping_range()
if self.interactive:
if self.recorded_events is None:
self.show_m.add_window_callback(win_callback)
self.show_m.add_timer_callback(True, 200, timer_callback)
self.show_m.iren.AddObserver('KeyPressEvent', key_press)
self.show_m.render()
self.show_m.start()
else:
self.show_m.add_window_callback(win_callback)
self.show_m.add_timer_callback(True, 200, timer_callback)
self.show_m.iren.AddObserver('KeyPressEvent', key_press)
# set to True if event recording needs updating
recording = False
recording_filename = self.recorded_events
if recording:
self.show_m.record_events_to_file(recording_filename)
else:
self.show_m.play_events_from_file(recording_filename)
else:
window.record(scene,
out_path=self.out_png,
size=(1200, 900),
reset_camera=False)
def build_show(self, scene):
title = 'Horizon ' + horizon_version
self.show_m = window.ShowManager(scene, title=title,
size=(1200, 900),
order_transparent=True,
reset_camera=False)
self.show_m.initialize()
if self.cluster and self.tractograms:
lengths = np.array(
[self.cla[c]['length'] for c in self.cla])
szs = [self.cla[c]['size'] for c in self.cla]
sizes = np.array(szs)
# global self.panel2, slider_length, slider_size
self.panel2 = ui.Panel2D(size=(400, 200),
position=(850, 670),
color=(1, 1, 1),
opacity=0.1,
align="right")
slider_label_threshold = build_label(text="Threshold")
print("Cluster threshold", self.cluster_thr)
slider_threshold = ui.LineSlider2D(
min_value=5,
max_value=25,
initial_value=self.cluster_thr,
text_template="{value:.0f}",
length=140, shape='square')
_color_slider(slider_threshold)
slider_label_length = build_label(text="Length")
slider_length = ui.LineSlider2D(
min_value=lengths.min(),
max_value=np.percentile(lengths, 98),
initial_value=np.percentile(lengths, 25),
text_template="{value:.0f}",
length=140)
_color_slider(slider_length)
slider_label_size = build_label(text="Size")
slider_size = ui.LineSlider2D(
min_value=sizes.min(),
max_value=np.percentile(sizes, 98),
initial_value=np.percentile(sizes, 50),
text_template="{value:.0f}",
length=140)
_color_slider(slider_size)
# global self.length_min, size_min
self.size_min = sizes.min()
self.length_min = lengths.min()
def change_threshold(istyle, obj, slider):
sv = np.round(slider.value, 0)
self.remove_cluster_actors(scene)
self.add_cluster_actors(scene, self.tractograms, threshold=sv)
# TODO need to double check if this section is still needed
lengths = np.array(
[self.cla[c]['length'] for c in self.cla])
szs = [self.cla[c]['size'] for c in self.cla]
sizes = np.array(szs)
slider_length.min_value = lengths.min()
slider_length.max_value = lengths.max()
slider_length.value = lengths.min()
slider_length.update()
slider_size.min_value = sizes.min()
slider_size.max_value = sizes.max()
slider_size.value = sizes.min()
slider_size.update()
self.length_min = min(lengths)
self.size_min = min(sizes)
self.show_m.render()
slider_threshold.handle_events(slider_threshold.handle.actor)
slider_threshold.on_left_mouse_button_released = change_threshold
def hide_clusters_length(slider):
self.length_min = np.round(slider.value)
for k in self.cla:
if (self.cla[k]['length'] < self.length_min or
self.cla[k]['size'] < self.size_min):
self.cla[k]['centroid_actor'].SetVisibility(0)
if k.GetVisibility() == 1:
k.SetVisibility(0)
else:
self.cla[k]['centroid_actor'].SetVisibility(1)
self.show_m.render()
def hide_clusters_size(slider):
self.size_min = np.round(slider.value)
for k in self.cla:
if (self.cla[k]['length'] < self.length_min or
self.cla[k]['size'] < self.size_min):
self.cla[k]['centroid_actor'].SetVisibility(0)
if k.GetVisibility() == 1:
k.SetVisibility(0)
else:
self.cla[k]['centroid_actor'].SetVisibility(1)
self.show_m.render()
slider_length.on_change = hide_clusters_length
# Clustering panel
self.panel2.add_element(slider_label_threshold, coords=(0.1, 0.26))
self.panel2.add_element(slider_threshold, coords=(0.4, 0.26))
self.panel2.add_element(slider_label_length, coords=(0.1, 0.52))
self.panel2.add_element(slider_length, coords=(0.4, 0.52))
slider_size.on_change = hide_clusters_size
self.panel2.add_element(slider_label_size, coords=(0.1, 0.78))
self.panel2.add_element(slider_size, coords=(0.4, 0.78))
scene.add(self.panel2)
# Information panel
text_block = build_label(HELP_MESSAGE, 18)
text_block.message = HELP_MESSAGE
self.help_panel = ui.Panel2D(size=(320, 200),
color=(0.8, 0.8, 1),
opacity=0.2,
align="left")
self.help_panel.add_element(text_block, coords=(0.05, 0.1))
scene.add(self.help_panel)
if len(self.images) > 0:
# !!Only first image loading supported for now')
data, affine = self.images[0]
self.vox2ras = affine
if len(self.pams) > 0:
pam = self.pams[0]
else:
pam = None
self.panel = slicer_panel(scene, self.show_m.iren, data, affine,
self.world_coords,
pam=pam, mem=self.mem)
else:
data = None
affine = None
pam = None
self.win_size = scene.GetSize()
def win_callback(obj, event):
if self.win_size != obj.GetSize():
size_old = self.win_size
self.win_size = obj.GetSize()
size_change = [self.win_size[0] - size_old[0], 0]
if data is not None:
self.panel.re_align(size_change)
if self.cluster:
self.panel2.re_align(size_change)
self.help_panel.re_align(size_change)
self.show_m.initialize()
self.hide_centroids = True
self.select_all = False
def hide():
if self.hide_centroids:
for ca in self.cea:
if (self.cea[ca]['length'] >= self.length_min or
self.cea[ca]['size'] >= self.size_min):
if self.cea[ca]['selected'] == 0:
ca.VisibilityOff()
else:
for ca in self.cea:
if (self.cea[ca]['length'] >= self.length_min and
self.cea[ca]['size'] >= self.size_min):
if self.cea[ca]['selected'] == 0:
ca.VisibilityOn()
self.hide_centroids = not self.hide_centroids
self.show_m.render()
def invert():
for ca in self.cea:
if (self.cea[ca]['length'] >= self.length_min and
self.cea[ca]['size'] >= self.size_min):
self.cea[ca]['selected'] = \
not self.cea[ca]['selected']
cas = self.cea[ca]['cluster_actor']
self.cla[cas]['selected'] = \
self.cea[ca]['selected']
self.show_m.render()
def save():
saving_streamlines = Streamlines()
for bundle in self.cla.keys():
if bundle.GetVisibility():
t = self.cla[bundle]['tractogram']
c = self.cla[bundle]['cluster']
indices = self.tractogram_clusters[t][c]
saving_streamlines.extend(Streamlines(indices))
print('Saving result in tmp.trk')
# Using the header of the first of the tractograms
sft_new = StatefulTractogram(saving_streamlines,
self.tractograms[0],
Space.RASMM)
save_tractogram(sft_new, 'tmp.trk', bbox_valid_check=False)
print('Saved!')
def new_window():
active_streamlines = Streamlines()
for bundle in self.cla.keys():
if bundle.GetVisibility():
t = self.cla[bundle]['tractogram']
c = self.cla[bundle]['cluster']
indices = self.tractogram_clusters[t][c]
active_streamlines.extend(Streamlines(indices))
# Using the header of the first of the tractograms
active_sft = StatefulTractogram(active_streamlines,
self.tractograms[0],
Space.RASMM)
hz2 = Horizon([active_sft],
self.images, cluster=True,
cluster_thr=self.cluster_thr/2.,
random_colors=self.random_colors,
length_lt=np.inf,
length_gt=0, clusters_lt=np.inf,
clusters_gt=0,
world_coords=True,
interactive=True)
ren2 = hz2.build_scene()
hz2.build_show(ren2)
def show_all():
if self.select_all is False:
for ca in self.cea:
if (self.cea[ca]['length'] >= self.length_min and
self.cea[ca]['size'] >= self.size_min):
self.cea[ca]['selected'] = 1
cas = self.cea[ca]['cluster_actor']
self.cla[cas]['selected'] = \
self.cea[ca]['selected']
self.show_m.render()
self.select_all = True
else:
for ca in self.cea:
if (self.cea[ca]['length'] >= self.length_min and
self.cea[ca]['size'] >= self.size_min):
self.cea[ca]['selected'] = 0
cas = self.cea[ca]['cluster_actor']
self.cla[cas]['selected'] = \
self.cea[ca]['selected']
self.show_m.render()
self.select_all = False
def expand():
for c in self.cea:
if self.cea[c]['selected']:
if not self.cea[c]['expanded']:
len_ = self.cea[c]['length']
sz_ = self.cea[c]['size']
if (len_ >= self.length_min and
sz_ >= self.size_min):
self.cea[c]['cluster_actor']. \
VisibilityOn()
c.VisibilityOff()
self.cea[c]['expanded'] = 1
self.show_m.render()
def reset():
for c in self.cea:
if (self.cea[c]['length'] >= self.length_min and
self.cea[c]['size'] >= self.size_min):
self.cea[c]['cluster_actor'].VisibilityOff()
c.VisibilityOn()
self.cea[c]['expanded'] = 0
self.show_m.render()
def key_press(obj, event):
key = obj.GetKeySym()
if self.cluster:
# hide on/off unselected centroids
if key == 'h' or key == 'H':
hide()
# invert selection
if key == 'i' or key == 'I':
invert()
# retract help panel
if key == 'o' or key == 'O':
self.help_panel._set_position((-300, 0))
self.show_m.render()
# save current result
if key == 's' or key == 'S':
save()
if key == 'y' or key == 'Y':
new_window()
if key == 'a' or key == 'A':
show_all()
if key == 'e' or key == 'E':
expand()
if key == 'r' or key == 'R':
reset()
options = [r'un\hide centroids', 'invert selection',
r'un\select all', 'expand clusters',
'collapse clusters', 'save streamlines',
'recluster']
listbox = ui.ListBox2D(values=options, position=(10, 300),
size=(200, 270),
multiselection=False, font_size=18)
def display_element():
action = listbox.selected[0]
if action == r'un\hide centroids':
hide()
if action == 'invert selection':
invert()
if action == r'un\select all':
show_all()
if action == 'expand clusters':
expand()
if action == 'collapse clusters':
reset()
if action == 'save streamlines':
save()
if action == 'recluster':
new_window()
listbox.on_change = display_element
listbox.panel.opacity = 0.2
listbox.set_visibility(0)
self.show_m.scene.add(listbox)
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 right_click_centroid_callback(obj, event):
for lactor in listbox._get_actors():
lactor.SetVisibility(not lactor.GetVisibility())
listbox.scroll_bar.set_visibility(False)
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()
def right_click_cluster_callback(obj, event):
print('Cluster Area Selected')
self.show_m.render()
for cl in self.cla:
cl.AddObserver('LeftButtonPressEvent',
left_click_cluster_callback,
1.0)
cl.AddObserver('RightButtonPressEvent',
right_click_cluster_callback,
1.0)
self.cla[cl]['centroid_actor'].AddObserver(
'LeftButtonPressEvent', left_click_centroid_callback, 1.0)
self.cla[cl]['centroid_actor'].AddObserver(
'RightButtonPressEvent', right_click_centroid_callback, 1.0)
self.mem.window_timer_cnt = 0
def timer_callback(obj, event):
self.mem.window_timer_cnt += 1
# TODO possibly add automatic rotation option
# self.show_m.scene.azimuth(0.01 * self.mem.window_timer_cnt)
# self.show_m.render()
scene.reset_camera()
scene.zoom(1.5)
scene.reset_clipping_range()
if self.interactive:
self.show_m.add_window_callback(win_callback)
self.show_m.add_timer_callback(True, 200, timer_callback)
self.show_m.iren.AddObserver('KeyPressEvent', key_press)
if self.return_showm:
return self.show_m
if self.recorded_events is None:
self.show_m.render()
self.show_m.start()
else:
# set to True if event recorded file needs updating
recording = False
recording_filename = self.recorded_events
if recording:
self.show_m.record_events_to_file(recording_filename)
else:
self.show_m.play_events_from_file(recording_filename)
else:
window.record(scene, out_path=self.out_png,
size=(1200, 900),
reset_camera=False)
def build_show(self, scene):
show_m = window.ShowManager(scene, size=(1200, 900),
order_transparent=True,
reset_camera=False)
show_m.initialize()
if self.cluster:
lengths = np.array(
[self.cla[c]['length'] for c in self.cla])
szs = [self.cla[c]['size'] for c in self.cla]
sizes = np.array(szs)
# global self.panel2, slider_length, slider_size
self.panel2 = ui.Panel2D(size=(300, 200),
position=(850, 320),
color=(1, 1, 1),
opacity=0.1,
align="right")
slider_label_length = build_label(text="Length")
slider_length = ui.LineSlider2D(
min_value=lengths.min(),
max_value=np.percentile(lengths, 98),
initial_value=np.percentile(lengths, 25),
text_template="{value:.0f}",
length=140)
slider_label_size = build_label(text="Size")
slider_size = ui.LineSlider2D(
min_value=sizes.min(),
max_value=np.percentile(sizes, 98),
initial_value=np.percentile(sizes, 50),
text_template="{value:.0f}",
length=140)
# global self.length_min, size_min
self.size_min = sizes.min()
self.length_min = lengths.min()
def hide_clusters_length(slider):
self.length_min = np.round(slider.value)
for k in self.cla:
if (self.cla[k]['length'] < self.length_min or
self.cla[k]['size'] < self.size_min):
self.cla[k]['centroid_actor'].SetVisibility(0)
if k.GetVisibility() == 1:
k.SetVisibility(0)
else:
self.cla[k]['centroid_actor'].SetVisibility(1)
show_m.render()
def hide_clusters_size(slider):
self.size_min = np.round(slider.value)
for k in self.cla:
if (self.cla[k]['length'] < self.length_min or
self.cla[k]['size'] < self.size_min):
self.cla[k]['centroid_actor'].SetVisibility(0)
if k.GetVisibility() == 1:
k.SetVisibility(0)
else:
self.cla[k]['centroid_actor'].SetVisibility(1)
show_m.render()
slider_length.on_change = hide_clusters_length
self.panel2.add_element(slider_label_length, coords=(0.1, 0.333))
self.panel2.add_element(slider_length, coords=(0.4, 0.333))
slider_size.on_change = hide_clusters_size
self.panel2.add_element(slider_label_size, coords=(0.1, 0.6666))
self.panel2.add_element(slider_size, coords=(0.4, 0.6666))
scene.add(self.panel2)
text_block = build_label(HELP_MESSAGE, 16) # ui.TextBlock2D()
text_block.message = HELP_MESSAGE
help_panel = ui.Panel2D(size=(300, 200),
color=(1, 1, 1),
opacity=0.1,
align="left")
help_panel.add_element(text_block, coords=(0.05, 0.1))
scene.add(help_panel)
if len(self.images) > 0:
# !!Only first image loading supported for now')
data, affine = self.images[0]
self.panel = slicer_panel(scene, data, affine, self.world_coords)
else:
data = None
affine = None
self.win_size = scene.GetSize()
def win_callback(obj, event):
if self.win_size != obj.GetSize():
size_old = self.win_size
self.win_size = obj.GetSize()
size_change = [self.win_size[0] - size_old[0], 0]
if data is not None:
self.panel.re_align(size_change)
if self.cluster:
self.panel2.re_align(size_change)
help_panel.re_align(size_change)
show_m.initialize()
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']
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
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)
self.hide_centroids = True
self.select_all = False
def key_press(obj, event):
key = obj.GetKeySym()
if self.cluster:
# hide on/off unselected centroids
if key == 'h' or key == 'H':
if self.hide_centroids:
for ca in self.cea:
if (self.cea[ca]['length'] >= self.length_min or
self.cea[ca]['size'] >= self.size_min):
if self.cea[ca]['selected'] == 0:
ca.VisibilityOff()
else:
for ca in self.cea:
if (self.cea[ca]['length'] >= self.length_min and
self.cea[ca]['size'] >= self.size_min):
if self.cea[ca]['selected'] == 0:
ca.VisibilityOn()
self.hide_centroids = not self.hide_centroids
show_m.render()
# invert selection
if key == 'i' or key == 'I':
for ca in self.cea:
if (self.cea[ca]['length'] >= self.self.length_min and
self.cea[ca]['size'] >= self.size_min):
self.cea[ca]['selected'] = \
not self.cea[ca]['selected']
cas = self.cea[ca]['cluster_actor']
self.cla[cas]['selected'] = \
self.cea[ca]['selected']
show_m.render()
# save current result
if key == 's' or key == 'S':
saving_streamlines = Streamlines()
for bundle in self.cla.keys():
if bundle.GetVisibility():
t = self.cla[bundle]['tractogram']
c = self.cla[bundle]['cluster']
indices = self.tractogram_clusters[t][c]
saving_streamlines.extend(Streamlines(indices))
print('Saving result in tmp.trk')
save_trk('tmp.trk', saving_streamlines, np.eye(4))
if key == 'y' or key == 'Y':
active_streamlines = Streamlines()
for bundle in self.cla.keys():
if bundle.GetVisibility():
t = self.cla[bundle]['tractogram']
c = self.cla[bundle]['cluster']
indices = self.tractogram_clusters[t][c]
active_streamlines.extend(Streamlines(indices))
# self.tractograms = [active_streamlines]
hz2 = horizon([active_streamlines],
self.images, cluster=True, cluster_thr=5,
random_colors=self.random_colors,
length_lt=np.inf,
length_gt=0, clusters_lt=np.inf,
clusters_gt=0,
world_coords=True,
interactive=True)
ren2 = hz2.build_scene()
hz2.build_show(ren2)
if key == 'a' or key == 'A':
if self.select_all is False:
for ca in self.cea:
if (self.cea[ca]['length'] >= self.length_min and
self.cea[ca]['size'] >= self.size_min):
self.cea[ca]['selected'] = 1
cas = self.cea[ca]['cluster_actor']
self.cla[cas]['selected'] = \
self.cea[ca]['selected']
show_m.render()
self.select_all = True
else:
for ca in self.cea:
if (self.cea[ca]['length'] >= self.length_min and
self.cea[ca]['size'] >= self.size_min):
self.cea[ca]['selected'] = 0
cas = self.cea[ca]['cluster_actor']
self.cla[cas]['selected'] = \
self.cea[ca]['selected']
show_m.render()
self.select_all = False
if key == 'e' or key == 'E':
for c in self.cea:
if self.cea[c]['selected']:
if not self.cea[c]['expanded']:
len_ = self.cea[c]['length']
sz_ = self.cea[c]['size']
if (len_ >= self.length_min and
sz_ >= self.size_min):
self.cea[c]['cluster_actor']. \
VisibilityOn()
c.VisibilityOff()
self.cea[c]['expanded'] = 1
show_m.render()
if key == 'r' or key == 'R':
for c in self.cea:
if (self.cea[c]['length'] >= self.length_min and
self.cea[c]['size'] >= self.size_min):
self.cea[c]['cluster_actor'].VisibilityOff()
c.VisibilityOn()
self.cea[c]['expanded'] = 0
show_m.render()
scene.reset_camera()
scene.zoom(1.5)
scene.reset_clipping_range()
if self.interactive:
show_m.add_window_callback(win_callback)
show_m.iren.AddObserver('KeyPressEvent', key_press)
show_m.render()
show_m.start()
else:
window.record(scene, out_path=self.out_png,
size=(1200, 900),
reset_camera=False)