def show_bundles(bundles,
colors=None,
show=True,
fname=None,
fa=False,
str_tube=False):
ren = window.Renderer()
ren.SetBackground(1., 1, 1)
if str_tube:
bundle_actor = actor.streamtube(bundles, colors, linewidth=0.5)
ren.add(bundle_actor)
else:
for (i, bundle) in enumerate(bundles):
color = colors[i]
# lines_actor = actor.streamtube(bundle, color, linewidth=0.05
lines_actor = actor.line(bundle, color, linewidth=2.5)
#lines_actor.RotateX(-90)
#lines_actor.RotateZ(90)
ren.add(lines_actor)
if fa:
fa, affine_fa = load_nifti(
'/Users/alex/code/Wenlin/data/wenlin_results/bmfaN54900.nii.gz')
fa_actor = actor.slicer(fa, affine_fa)
ren.add(fa_actor)
if show:
window.show(ren)
if fname is not None:
sleep(1)
window.record(ren, n_frames=1, out_path=fname, size=(900, 900))
def window_show_test(bundles, mask_roi, anat, interactive=True, outpath=None):
"""
:param bundles:
:param mask_roi:
:param anat:
:param interactive:
:param outpath:
:return:
"""
candidate_streamlines_actor = actor.streamtube(
bundles, cmap.line_colors(candidate_sl))
ROI_actor = actor.contour_from_roi(mask_roi,
color=(1., 1., 0.),
opacity=0.5)
ren = window.Renderer()
if anat:
vol_actor = actor.slicer(anat)
vol_actor.display(x=40)
vol_actor2 = vol_actor.copy()
vol_actor2.display(z=35)
# Add display objects to canvas
ren.add(candidate_streamlines_actor)
ren.add(ROI_actor)
ren.add(vol_actor)
ren.add(vol_actor2)
if outpath is not None:
window.record(ren, n_frames=1, out_path=outpath, size=(800, 800))
if interactive:
window.show(ren)
def test_order_transparent():
renderer = window.Renderer()
lines = [
np.array([[-1, 0, 0.], [1, 0, 0.]]),
np.array([[-1, 1, 0.], [1, 1, 0.]])
]
colors = np.array([[1., 0., 0.], [0., .5, 0.]])
stream_actor = actor.streamtube(lines, colors, linewidth=0.3, opacity=0.5)
renderer.add(stream_actor)
renderer.reset_camera()
# green in front
renderer.elevation(90)
renderer.camera().OrthogonalizeViewUp()
renderer.reset_clipping_range()
renderer.reset_camera()
not_xvfb = os.environ.get("TEST_WITH_XVFB", False)
if not_xvfb:
arr = window.snapshot(renderer,
fname='green_front.png',
offscreen=True,
order_transparent=False)
else:
arr = window.snapshot(renderer,
fname='green_front.png',
offscreen=False,
order_transparent=False)
# therefore the green component must have a higher value (in RGB terms)
npt.assert_equal(arr[150, 150][1] > arr[150, 150][0], True)
# red in front
renderer.elevation(-180)
renderer.camera().OrthogonalizeViewUp()
renderer.reset_clipping_range()
if not_xvfb:
arr = window.snapshot(renderer,
fname='red_front.png',
offscreen=True,
order_transparent=True)
else:
arr = window.snapshot(renderer,
fname='red_front.png',
offscreen=False,
order_transparent=True)
# therefore the red component must have a higher value (in RGB terms)
npt.assert_equal(arr[150, 150][0] > arr[150, 150][1], True)
def test_streamtube_and_line_actors():
renderer = window.renderer()
line1 = np.array([[0, 0, 0], [1, 1, 1], [2, 2, 2.]])
line2 = line1 + np.array([0.5, 0., 0.])
lines = [line1, line2]
colors = np.array([[1, 0, 0], [0, 0, 1.]])
c = actor.line(lines, colors, linewidth=3)
window.add(renderer, c)
c = actor.line(lines, colors, spline_subdiv=5, linewidth=3)
window.add(renderer, c)
# create streamtubes of the same lines and shift them a bit
c2 = actor.streamtube(lines, colors, linewidth=.1)
c2.SetPosition(2, 0, 0)
window.add(renderer, c2)
arr = window.snapshot(renderer)
report = window.analyze_snapshot(arr,
colors=[(255, 0, 0), (0, 0, 255)],
find_objects=True)
npt.assert_equal(report.objects, 4)
npt.assert_equal(report.colors_found, [True, True])
# as before with splines
c2 = actor.streamtube(lines, colors, spline_subdiv=5, linewidth=.1)
c2.SetPosition(2, 0, 0)
window.add(renderer, c2)
arr = window.snapshot(renderer)
report = window.analyze_snapshot(arr,
colors=[(255, 0, 0), (0, 0, 255)],
find_objects=True)
npt.assert_equal(report.objects, 4)
npt.assert_equal(report.colors_found, [True, True])
def test_streamtube_and_line_actors():
renderer = window.renderer()
line1 = np.array([[0, 0, 0], [1, 1, 1], [2, 2, 2.]])
line2 = line1 + np.array([0.5, 0., 0.])
lines = [line1, line2]
colors = np.array([[1, 0, 0], [0, 0, 1.]])
c = actor.line(lines, colors, linewidth=3)
window.add(renderer, c)
c = actor.line(lines, colors, spline_subdiv=5, linewidth=3)
window.add(renderer, c)
# create streamtubes of the same lines and shift them a bit
c2 = actor.streamtube(lines, colors, linewidth=.1)
c2.SetPosition(2, 0, 0)
window.add(renderer, c2)
arr = window.snapshot(renderer)
report = window.analyze_snapshot(arr,
colors=[(255, 0, 0), (0, 0, 255)],
find_objects=True)
npt.assert_equal(report.objects, 4)
npt.assert_equal(report.colors_found, [True, True])
# as before with splines
c2 = actor.streamtube(lines, colors, spline_subdiv=5, linewidth=.1)
c2.SetPosition(2, 0, 0)
window.add(renderer, c2)
arr = window.snapshot(renderer)
report = window.analyze_snapshot(arr,
colors=[(255, 0, 0), (0, 0, 255)],
find_objects=True)
npt.assert_equal(report.objects, 4)
npt.assert_equal(report.colors_found, [True, True])
def show_template_bundles(bundles, static, show=True, fname=None):
scene = window.Scene()
template_actor = actor.slicer(static)
scene.add(template_actor)
lines_actor = actor.streamtube(bundles,
window.colors.orange,
linewidth=0.3)
scene.add(lines_actor)
if show:
window.show(scene)
if fname is not None:
window.record(scene, n_frames=1, out_path=fname, size=(900, 900))
def show_both_bundles(bundles, colors=None, show=True, fname=None):
scene = window.Scene()
scene.SetBackground(1., 1, 1)
for (i, bundle) in enumerate(bundles):
color = colors[i]
streamtube_actor = actor.streamtube(bundle, color, linewidth=0.3)
streamtube_actor.RotateX(-90)
streamtube_actor.RotateZ(90)
scene.add(streamtube_actor)
if show:
window.show(scene)
elif fname is not None:
window.record(scene, out_path=fname, size=(900, 900))
def show_fascicles_wholebrain(s_list,
vec_vols,
folder_name,
mask_type,
downsamp=1,
scale=[3, 6],
hue=[0.25, -0.05],
saturation=[0.1, 1.0]):
s_img = folder_name + r'\streamlines' + r'\fascicles_AxCaliber_weighted_3d_' + mask_type + '.png'
#hue = [0.4, 0.7] # blues
#hue = [0.25, -0.05] #Hot
#hue = [0, 1] #All
weighted = True
'''
if weighted:
scale = [0, 3]
else:
scale = [0, 6]
vec_vols = np.log(vec_vols)
#vec_vols = vec_vols-np.nanmin(vec_vols)/(np.nanmax(vec_vols)-np.nanmin(vec_vols))
'''
if downsamp != 1:
vec_vols = vec_vols[::downsamp]
s_list = s_list[::downsamp]
lut_cmap = actor.colormap_lookup_table(hue_range=hue,
saturation_range=saturation,
scale_range=scale)
bar = actor.scalar_bar(lut_cmap)
#w_actor = actor.line(s_list, vec_vols, linewidth=1.2, lookup_colormap=lut_cmap)
w_actor = actor.streamtube(s_list,
vec_vols,
linewidth=0.6,
lookup_colormap=lut_cmap)
#w_actor = actor.streamtube(s_list, vec_vols, linewidth=0.3, lookup_colormap=lut_cmap)
#w_actor = actor.line(s_list, linewidth=1.0, lookup_colormap=lut_cmap)
r = window.Renderer()
#r.SetBackground(*window.colors.white)
r.add(w_actor)
r.add(bar)
window.show(r)
r.set_camera(r.camera_info())
window.record(r, out_path=s_img, size=(800, 800))
def show_both_bundles(bundles, colors=None, show=True, fname=None):
ren = window.Renderer()
ren.SetBackground(1., 1, 1)
for (i, bundle) in enumerate(bundles):
color = colors[i]
lines_actor = actor.streamtube(bundle, color, linewidth=0.3)
lines_actor.RotateX(-90)
lines_actor.RotateZ(90)
ren.add(lines_actor)
if show:
window.show(ren)
if fname is not None:
sleep(1)
window.record(ren, n_frames=1, out_path=fname, size=(900, 900))
def show_both_bundles(bundles, colors=None, show=True, fname=None):
ren = window.Renderer()
ren.SetBackground(1., 1, 1)
for (i, bundle) in enumerate(bundles):
color = colors[i]
lines_actor = actor.streamtube(bundle, color, linewidth=0.3)
lines_actor.RotateX(-90)
lines_actor.RotateZ(90)
ren.add(lines_actor)
if show:
window.show(ren)
if fname is not None:
sleep(1)
window.record(ren, n_frames=1, out_path=fname, size=(900, 900))
def viewclusters(clusters,streamlines, outpath=None, interactive=False):
#Linked to viewing clusters. If outpath given, will save info to right location, if interactive, will show window
colormap = actor.create_colormap(np.ravel(clusters.centroids))
colormap_full = np.ones((len(streamlines), 3))
for cluster, color in zip(clusters, colormap):
colormap_full[cluster.indices] = color
scene = window.Scene()
scene.SetBackground(1, 1, 1)
scene.add(actor.streamtube(streamlines, colormap_full))
window.record(scene, out_path=outpath, size=(600, 600))
# Enables/disables interactive visualization
if interactive:
window.show(scene)
def test_order_transparent():
renderer = window.Renderer()
lines = [np.array([[-1, 0, 0.], [1, 0, 0.]]),
np.array([[-1, 1, 0.], [1, 1, 0.]])]
colors = np.array([[1., 0., 0.], [0., .5, 0.]])
stream_actor = actor.streamtube(lines, colors, linewidth=0.3, opacity=0.5)
renderer.add(stream_actor)
renderer.reset_camera()
# green in front
renderer.elevation(90)
renderer.camera().OrthogonalizeViewUp()
renderer.reset_clipping_range()
renderer.reset_camera()
not_xvfb = os.environ.get("TEST_WITH_XVFB", False)
if not_xvfb:
arr = window.snapshot(renderer, fname='green_front.png',
offscreen=True, order_transparent=False)
else:
arr = window.snapshot(renderer, fname='green_front.png',
offscreen=False, order_transparent=False)
# therefore the green component must have a higher value (in RGB terms)
npt.assert_equal(arr[150, 150][1] > arr[150, 150][0], True)
# red in front
renderer.elevation(-180)
renderer.camera().OrthogonalizeViewUp()
renderer.reset_clipping_range()
if not_xvfb:
arr = window.snapshot(renderer, fname='red_front.png',
offscreen=True, order_transparent=True)
else:
arr = window.snapshot(renderer, fname='red_front.png',
offscreen=False, order_transparent=True)
# therefore the red component must have a higher value (in RGB terms)
npt.assert_equal(arr[150, 150][0] > arr[150, 150][1], True)
def show_tracts(hue, saturation, scale, streamlines, mean_vol_per_tract,
folder_name, fig_type):
from dipy.viz import window, actor
lut_cmap = actor.colormap_lookup_table(hue_range=hue,
saturation_range=saturation,
scale_range=scale)
streamlines_actor = actor.streamtube(streamlines,
mean_vol_per_tract,
linewidth=0.5,
lookup_colormap=lut_cmap)
bar = actor.scalar_bar(lut_cmap)
r = window.Scene()
r.add(streamlines_actor)
r.add(bar)
mean_pasi_weighted_img = f'{folder_name}{os.sep}streamlines{os.sep}mean_pasi_weighted{fig_type}.png'
window.show(r)
r.set_camera(r.camera_info())
window.record(r, out_path=mean_pasi_weighted_img, size=(800, 800))
def update(self):
if not self.has_changed:
return # Nothing changed
self.has_changed = False
# Update centroids actor.
# Remove old centroid actors.
self.ren.rm(*self.centroid_actors)
# Create an actor for every centroid.
self.centroid_actors = []
for cluster, color in zip(self.clusters, self.clusters_colors):
centroid_actor = actor.streamtube([cluster.centroid],
colors=color,
linewidth=0.1 +
0.1 * np.log(len(cluster)))
centroid_actor.SetVisibility(self.centroids_visible)
self.ren.add(centroid_actor)
# TODO add a click callback
self.centroid_actors.append(centroid_actor)
def add_actors(ren, bundles):
for name in bundles:
streamlines = None
for filename in files:
if name in os.path.basename(filename):
print("Loading: {}".format(os.path.basename(filename)))
streamlines = nib.streamlines.load(filename).streamlines
break
if streamlines is None:
print("Bundle not found: {}".format(name))
continue
idx = np.arange(len(streamlines))
rng.shuffle(idx)
streamlines = streamlines[idx][:subsample]
color = bundle2color[name]
act = actor.streamtube(
streamlines,
colors=np.asarray(color) / 255.,
opacity=1.,
linewidth=0.3,
)
ren.add(act)
feature = VectorOfEndpointsFeature()
metric = CosineMetric(feature)
qb = QuickBundles(threshold=0.1, metric=metric)
clusters = qb.cluster(streamlines)
# Color each streamline according to the cluster they belong to.
colormap = actor.create_colormap(np.arange(len(clusters)))
colormap_full = np.ones((len(streamlines), 3))
for cluster, color in zip(clusters, colormap):
colormap_full[cluster.indices] = color
# Visualization
scene = window.Scene()
scene.clear()
scene.SetBackground(0, 0, 0)
scene.add(actor.streamtube(streamlines, colormap_full))
window.record(scene, out_path='cosine_metric.png', size=(600, 600))
if interactive:
window.show(scene)
"""
.. figure:: cosine_metric.png
:align: center
Showing the streamlines colored according to their orientation.
.. include:: ../links_names.inc
References
----------
qb = QuickBundles(threshold=25.)
clusters = qb.cluster(s)
print("Nb. clusters:", len(clusters))
print("Cluster sizes:", map(len, clusters))
print("Small clusters:", clusters < 10)
print("Streamlines indices of the first cluster:\n", clusters[0].indices)
print("Centroid of the last cluster:\n", clusters[-1].centroid)
interactive = True
ren = window.Renderer()
'''
ren.SetBackground(1, 1, 1)
ren.add(actor.streamtube(streamlines, window.colors.white))
if interactive:
window.show(ren)
'''
colormap = actor.create_colormap(np.arange(len(clusters)))
window.clear(ren)
ren.SetBackground(1, 1, 1)
ren.add(actor.streamtube(s, window.colors.white, opacity=0.05))
ren.add(
actor.streamtube(
[clusters.centroids[i] for i in np.where(clusters > 9)[0]],
colormap,
linewidth=0.4))
if interactive:
window.show(ren)
[ 66.74534607, 86.00262451, 78.82582092],
[ 64.02451324, 88.43942261, 75.0697403 ]], dtype=float32)
`clusters` has also attributes like `centroids` (cluster representatives), and
methods like `add`, `remove`, and `clear` to modify the clustering result.
Lets first show the initial dataset.
"""
# Enables/disables interactive visualization
interactive = False
ren = window.Renderer()
ren.SetBackground(1, 1, 1)
ren.add(actor.streamtube(streamlines, window.colors.white))
window.record(ren, out_path='fornix_initial.png', size=(600, 600))
if interactive:
window.show(ren)
"""
.. figure:: fornix_initial.png
:align: center
Initial Fornix dataset.
Show the centroids of the fornix after clustering (with random colors):
"""
colormap = actor.create_colormap(np.arange(len(clusters)))
"""
"""
Let's visualize the initial candidate group of streamlines in 3D, relative to
the anatomical structure of this brain:
"""
from dipy.viz import window, actor, colormap as cmap
# Enables/disables interactive visualization
interactive = False
candidate_streamlines_actor = actor.streamtube(candidate_sl,
cmap.line_colors(candidate_sl))
cc_ROI_actor = actor.contour_from_roi(cc_slice, color=(1., 1., 0.),
opacity=0.5)
vol_actor = actor.slicer(t1_data)
vol_actor.display(x=40)
vol_actor2 = vol_actor.copy()
vol_actor2.display(z=35)
# Add display objects to canvas
ren = window.Renderer()
ren.add(candidate_streamlines_actor)
ren.add(cc_ROI_actor)
ren.add(vol_actor)
ren.add(vol_actor2)
[ 66.74534607, 86.00262451, 78.82582092],
[ 64.02451324, 88.43942261, 75.0697403 ]], dtype=float32)
`clusters` has also attributes like `centroids` (cluster representatives), and
methods like `add`, `remove`, and `clear` to modify the clustering result.
Lets first show the initial dataset.
"""
# Enables/disables interactive visualization
interactive = False
scene = window.Scene()
scene.SetBackground(1, 1, 1)
scene.add(actor.streamtube(streamlines, window.colors.white))
window.record(scene, out_path='fornix_initial.png', size=(600, 600))
if interactive:
window.show(scene)
"""
.. figure:: fornix_initial.png
:align: center
Initial Fornix dataset.
Show the centroids of the fornix after clustering (with random colors):
"""
colormap = colormap.create_colormap(np.arange(len(clusters)))
def connective_streamlines_figuremaker(allstreamlines,
ROI_streamlines,
ROI_names,
anat_path,
threshold=10.,
verbose=False):
#streamlines = Streamlines(res['af.left'])
#streamlines.extend(res['cst.right'])
#streamlines.extend(res['cc_1'])
world_coords = True
# Cluster sizes: [64, 191, 47, 1]
# Small clusters: array([False, False, False, True], dtype=bool)
scene = window.Scene()
scene.SetBackground(1, 1, 1)
colors = [
'white', 'cadmium_red_deep', 'misty_rose', 'slate_grey_dark',
'ivory_black', 'chartreuse'
]
colors = [
window.colors.white, window.colors.cadmium_red_deep,
window.colors.misty_rose, window.colors.slate_grey_dark,
window.colors.ivory_black, window.colors.chartreuse
]
i = 0
for ROI in ROI_streamlines:
ROI_streamline = allstreamlines[ROI]
qb = QuickBundles(threshold=threshold)
clusters = qb.cluster(ROI_streamline)
if verbose:
print("Nb. clusters:", len(clusters))
print("Cluster sizes:", map(len, clusters))
print("Small clusters:", clusters < 10)
print("Streamlines indices of the first cluster:\n",
clusters[0].indices)
print("Centroid of the last cluster:\n", clusters[-1].centroid)
#if not world_coords:
# from dipy.tracking.streamline import transform_streamlines
# streamlines = transform_streamlines(ROI_streamline, np.linalg.inv(affine))
scene = window.Scene()
#stream_actor = actor.line(ROI_streamline)
#scene.add(actor.streamtube(ROI_streamline, window.colors.misty_rose))
scene.add(actor.streamtube(ROI_streamline, colors[i]))
#if not world_coords:
# image_actor_z = actor.slicer(data, affine=np.eye(4))
#else:
# image_actor_z = actor.slicer(data, affine)
slicer_opacity = 0.6
i = i + 1
anat_nifti = load_nifti(anat_path)
try:
data = anat_nifti.data
except AttributeError:
data = anat_nifti[0]
try:
affine = anat_nifti.affine
except AttributeError:
affine = anat_nifti[1]
shape = np.shape(data)
image_actor_z = actor.slicer(data[:, :, :, 0], affine)
image_actor_z.opacity(slicer_opacity)
image_actor_x = image_actor_z.copy()
x_midpoint = int(np.round(shape[0] / 2))
image_actor_x.display_extent(x_midpoint, x_midpoint, 0, shape[1] - 1, 0,
shape[2] - 1)
image_actor_y = image_actor_z.copy()
y_midpoint = int(np.round(shape[1] / 2))
image_actor_y.display_extent(0, shape[0] - 1, y_midpoint, y_midpoint, 0,
shape[2] - 1)
scene.add(image_actor_z)
scene.add(image_actor_x)
scene.add(image_actor_y)
global size
size = scene.GetSize()
show_m = window.ShowManager(scene, size=(1200, 900))
show_m.initialize()
interactive = True
interactive = False
if interactive:
show_m.add_window_callback(win_callback)
show_m.render()
show_m.start()
else:
window.record(scene,
out_path='bundles_and_3_slices.png',
size=(1200, 900),
reset_camera=False)
from __future__ import print_function
import numpy as np
from dipy.viz import window, actor, widget
from dipy.data import fetch_viz_icons, read_viz_icons
"""
First, we add a couple of streamtubes to the Renderer
"""
renderer = window.Renderer()
lines = [np.array([[-1, 0, 0.], [1, 0, 0.]]),
np.array([[-1, 1, 0.], [1, 1, 0.]])]
colors = np.array([[1., 0., 0.], [0., .5, 0.]])
stream_actor = actor.streamtube(lines, colors, linewidth=0.3, lod=False)
renderer.add(stream_actor)
"""
The ``ShowManager`` allows to break the visualization process in steps so that
the widgets can be added and updated properly.
"""
show_manager = window.ShowManager(renderer, size=(800, 800),
order_transparent=True)
"""
Next we add the widgets and their callbacks.
"""
qb = QuickBundles(threshold=2., metric=metric)
clusters = qb.cluster(streamlines)
"""
We will now visualize the clustering result.
"""
# Color each streamline according to the cluster they belong to.
colormap = actor.create_colormap(np.ravel(clusters.centroids))
colormap_full = np.ones((len(streamlines), 3))
for cluster, color in zip(clusters, colormap):
colormap_full[cluster.indices] = color
ren = window.Renderer()
ren.SetBackground(1, 1, 1)
ren.add(actor.streamtube(streamlines, colormap_full))
window.record(ren, out_path='fornix_clusters_arclength.png', size=(600, 600))
# Enables/disables interactive visualization
interactive = False
if interactive:
window.show(ren)
"""
.. figure:: fornix_clusters_arclength.png
:align: center
Showing the different clusters obtained by using the arc length.
Extending `Metric`
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
polydata_in = load_polydata(fib_file_name)
streamlines_in = get_streamlines(polydata_in)
streamlines = []
for line in streamlines_in:
dist = line[:-1] - line[1:]
line_length = np.sum(np.sqrt(np.sum(np.square(dist), axis=1)))
if line_length > min_length:
streamlines.append(line)
#streamlines_sub = streamlines
streamlines_sub = streamlines[::100]
print len(streamlines_in), len(streamlines_sub)
actor = streamtube(streamlines_sub, linewidth=linewidth, tube_sides=tube_sides, spline_subdiv=spline_subdiv)
renderer = window.Renderer()
renderer.add(actor)
my_window = window.show(renderer)
#objexporter = vtk.vtkOBJExporter()
#objexporter.SetInput(my_window)
#objexporter.SetFileName(save_file)
#objexporter.SetFileName("/home/eti/home_mint/Nic/s100_s100_tube_flow.obj")
#objexporter.Write()
#save_polydata(actor.GetMapper().GetInput(), save_file)
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)
clusters = qb.cluster(streamlines)
# Extract feature of every streamline.
centers = np.asarray(list(map(feature.extract, streamlines)))
# Color each center of mass according to the cluster they belong to.
colormap = colormap.create_colormap(np.arange(len(clusters)))
colormap_full = np.ones((len(streamlines), 3))
for cluster, color in zip(clusters, colormap):
colormap_full[cluster.indices] = color
# Visualization
scene = window.Scene()
scene.clear()
scene.SetBackground(0, 0, 0)
scene.add(actor.streamtube(streamlines, window.colors.white, opacity=0.05))
scene.add(actor.point(centers[:, 0, :], colormap_full, point_radius=0.2))
window.record(scene,
n_frames=1,
out_path='center_of_mass_feature.png',
size=(600, 600))
if interactive:
window.show(scene)
"""
.. figure:: center_of_mass_feature.png
:align: center
Showing the center of mass of each streamline and colored according to
the QuickBundles results.
.. _clustering-examples-MidpointFeature:
clusters = qb.cluster(streamlines)
# Extract feature of every streamline.
centers = np.asarray(list(map(feature.extract, streamlines)))
# Color each center of mass according to the cluster they belong to.
colormap = actor.create_colormap(np.arange(len(clusters)))
colormap_full = np.ones((len(streamlines), 3))
for cluster, color in zip(clusters, colormap):
colormap_full[cluster.indices] = color
# Visualization
ren = window.Renderer()
window.clear(ren)
ren.SetBackground(0, 0, 0)
ren.add(actor.streamtube(streamlines, window.colors.white, opacity=0.05))
ren.add(actor.point(centers[:, 0, :], colormap_full, point_radius=0.2))
window.record(ren, n_frames=1, out_path='center_of_mass_feature.png', size=(600, 600))
if interactive:
window.show(ren)
"""
.. figure:: center_of_mass_feature.png
:align: center
Showing the center of mass of each streamline and colored according to
the QuickBundles results.
.. _clustering-examples-MidpointFeature:
Midpoint Feature
#mean_vol_per_tract.append(np.nanmedian(s))
hue = [0.25, -0.05]
saturation = [0, 1]
scale = [3, 12]
if downsamp != 1:
mean_vol_per_tract = mean_vol_per_tract[::downsamp]
str1 = str1[::downsamp]
mean_pasi_weighted_img = f'{folder_name}{os.sep}streamlines{os.sep}CC_3-12_Exp_DTI_PreReg_1_ds2_tube0p3.png'
lut_cmap = actor.colormap_lookup_table(hue_range=hue,
saturation_range=saturation,
scale_range=scale)
#str2 = transform_streamlines(str1, np.linalg.inv(affine2))
streamlines_actor = actor.streamtube(str1,
mean_vol_per_tract,
linewidth=0.3,
lookup_colormap=lut_cmap)
bar = actor.scalar_bar(lut_cmap)
r = window.Scene()
r.add(streamlines_actor)
r.add(bar)
#r.SetBackground(*window.colors.white)
window.show(r)
r.set_camera(r.camera_info())
window.record(r, out_path=mean_pasi_weighted_img, size=(800, 800))
def viewstreamlines_anat(streamlines_full,
anat_path,
affine,
ratio=1,
threshold=10.,
verbose=False):
scene = window.Scene()
scene.SetBackground(1, 1, 1)
#colors = ['white', 'cadmium_red_deep', 'misty_rose', 'slate_grey_dark', 'ivory_black', 'chartreuse']
colors = [
window.colors.white, window.colors.cadmium_red_deep,
window.colors.misty_rose, window.colors.slate_grey_dark,
window.colors.ivory_black, window.colors.chartreuse
]
streamline_cut = []
i = 0
if ratio != 1:
for streamline in streamlines_full:
if i % ratio == 0:
streamline_cut.append(streamline)
i += 1
else:
streamline_cut = streamlines_full
qb = QuickBundles(threshold=threshold)
clusters = qb.cluster(streamline_cut)
if verbose:
print("Nb. clusters:", len(clusters))
print("Cluster sizes:", map(len, clusters))
print("Small clusters:", clusters < 10)
print("Streamlines indices of the first cluster:\n",
clusters[0].indices)
print("Centroid of the last clustker:\n", clusters[-1].centroid)
j = 0
scene = window.Scene()
scene.add(actor.streamtube(streamline_cut, colors[j]))
slicer_opacity = 0.6
j += 1
if isinstance(anat_path, str) and os.path.exists(anat_path):
anat_nifti = load_nifti(anat_path)
try:
data = anat_nifti.data
except AttributeError:
data = anat_nifti[0]
if affine is None:
try:
affine = anat_nifti.affine
except AttributeError:
affine = anat_nifti[1]
else:
data = anat_path
shape = np.shape(data)
if np.size(shape) == 4:
data = data[:, :, :, 0]
image_actor_z = actor.slicer(data, affine)
image_actor_z.opacity(slicer_opacity)
image_actor_x = image_actor_z.copy()
x_midpoint = int(np.round(shape[0] / 2))
image_actor_x.display_extent(x_midpoint, x_midpoint, 0, shape[1] - 1, 0,
shape[2] - 1)
image_actor_y = image_actor_z.copy()
y_midpoint = int(np.round(shape[1] / 2))
image_actor_y.display_extent(0, shape[0] - 1, y_midpoint, y_midpoint, 0,
shape[2] - 1)
scene.add(image_actor_z)
scene.add(image_actor_x)
scene.add(image_actor_y)
global size
size = scene.GetSize()
show_m = window.ShowManager(scene, size=(1200, 900))
show_m.initialize()
interactive = True
interactive = False
if interactive:
show_m.add_window_callback(win_callback)
show_m.render()
show_m.start()
else:
window.record(scene,
out_path='bundles_and_3_slices.png',
size=(1200, 900),
reset_camera=False)
if num_of_bundles <= 6:
colors = color_list_dis
else:
colors = color_list
fa, affine_fa = load_nifti(
'/Users/alex/code/Wenlin/data/wenlin_results/bmfaN54900.nii.gz')
fa_actor = actor.slicer(fa, affine_fa)
bundle_list_center = [group_clusters.centroids[idx] for idx in top_idx]
bundle_list = [group_clusters.clusters[idx] for idx in top_idx]
ren = window.Renderer()
ren.SetBackground(1., 1, 1)
bundle_actor = actor.streamtube(bundle_list_center, colors, linewidth=0.1)
for (i, bundle) in enumerate(bundle_list):
color = colors[i]
lines_actor = actor.line(bundle, color, opacity=0.9)
ren.add(lines_actor)
ren.add(bundle_actor)
#uncomment this to show fa
#ren.add(fa_actor)
window.show(ren)
# %%
num_of_bundles = 20
top_idx_group1 = sorted(range(len(group1_clusters.clusters_sizes())),
key=lambda i: group1_clusters.clusters_sizes()[i],
def test_button_and_slider_widgets():
interactive = False
renderer = window.Renderer()
# create some minimalistic streamlines
lines = [np.array([[-1, 0, 0.], [1, 0, 0.]]),
np.array([[-1, 1, 0.], [1, 1, 0.]])]
colors = np.array([[1., 0., 0.], [0.3, 0.7, 0.]])
stream_actor = actor.streamtube(lines, colors)
renderer.add(stream_actor)
# the show manager allows to break the rendering process
# in steps so that the widgets can be added properly
show_manager = window.ShowManager(renderer, size=(800, 800))
if interactive:
show_manager.initialize()
show_manager.render()
def button_callback(obj, event):
print('Camera pressed')
def button_plus_callback(obj, event):
print('+ pressed')
def button_minus_callback(obj, event):
print('- pressed')
fetch_viz_icons()
button_png = read_viz_icons(fname='camera.png')
button = widget.button(show_manager.iren,
show_manager.ren,
button_callback,
button_png, (.98, 1.), (80, 50))
button_png_plus = read_viz_icons(fname='plus.png')
button_plus = widget.button(show_manager.iren,
show_manager.ren,
button_plus_callback,
button_png_plus, (.98, .9), (120, 50))
button_png_minus = read_viz_icons(fname='minus.png')
button_minus = widget.button(show_manager.iren,
show_manager.ren,
button_minus_callback,
button_png_minus, (.98, .9), (50, 50))
def print_status(obj, event):
rep = obj.GetRepresentation()
stream_actor.SetPosition((rep.GetValue(), 0, 0))
slider = widget.slider(show_manager.iren, show_manager.ren,
callback=print_status,
min_value=-1,
max_value=1,
value=0.,
label="X",
right_normalized_pos=(.98, 0.6),
size=(120, 0), label_format="%0.2lf")
# This callback is used to update the buttons/sliders' position
# so they can stay on the right side of the window when the window
# is being resized.
global size
size = renderer.GetSize()
def win_callback(obj, event):
global size
if size != obj.GetSize():
button.place(renderer)
button_plus.place(renderer)
button_minus.place(renderer)
slider.place(renderer)
size = obj.GetSize()
if interactive:
# show_manager.add_window_callback(win_callback)
# you can also register any callback in a vtk way like this
# show_manager.window.AddObserver(vtk.vtkCommand.ModifiedEvent,
# win_callback)
show_manager.render()
show_manager.start()
if not interactive:
button.Off()
slider.Off()
# Uncomment below to test the slider and button with analyze
# button.place(renderer)
# slider.place(renderer)
arr = window.snapshot(renderer, size=(800, 800))
report = window.analyze_snapshot(arr)
npt.assert_equal(report.objects, 2)
# imshow(report.labels, origin='lower')
report = window.analyze_renderer(renderer)
npt.assert_equal(report.actors, 1)
"""
ren = window.Renderer()
"""
Every streamline will be coloured according to its orientation
"""
from dipy.viz.colormap import line_colors
"""
`actor.line` creates a streamline actor for streamline visualization
and `ren.add` adds this actor to the scene
"""
ren.add(actor.streamtube(tensor_streamlines, line_colors(tensor_streamlines)))
print('Saving illustration as tensor_tracks.png')
ren.SetBackground(1, 1, 1)
window.record(ren, out_path='tensor_tracks.png', size=(600, 600))
# Enables/disables interactive visualization
interactive = False
if interactive:
window.show(ren)
"""
.. figure:: tensor_tracks.png
:align: center
Deterministic streamlines with EuDX on a Tensor Field.
"""
"""
Let's visualize the initial candidate group of streamlines in 3D, relative to
the anatomical structure of this brain:
"""
# Enables/disables interactive visualization
interactive = False
candidate_streamlines_actor = actor.streamtube(candidate_sl,
cmap.line_colors(candidate_sl))
cc_ROI_actor = actor.contour_from_roi(cc_slice, color=(1., 1., 0.),
opacity=0.5)
vol_actor = actor.slicer(t1_data)
vol_actor.display(x=40)
vol_actor2 = vol_actor.copy()
vol_actor2.display(z=35)
# Add display objects to canvas
ren = window.Renderer()
ren.add(candidate_streamlines_actor)
ren.add(cc_ROI_actor)
ren.add(vol_actor)
ren.add(vol_actor2)
bundle_downsampled2 = [approx_polygon_track(s, 0.25) for s in bundle] n_pts_ds2 = [len(streamline) for streamline in bundle_downsampled2] """ Both, ``downsample`` and ``approx_polygon_track`` can be thought as methods for lossy compression of streamlines. """ from dipy.viz import window, actor # Enables/disables interactive visualization interactive = False ren = window.Renderer() ren.SetBackground(*window.colors.white) bundle_actor = actor.streamtube(bundle, window.colors.red, linewidth=0.3) ren.add(bundle_actor) bundle_actor2 = actor.streamtube(bundle_downsampled, window.colors.red, linewidth=0.3) bundle_actor2.SetPosition(0, 40, 0) bundle_actor3 = actor.streamtube(bundle_downsampled2, window.colors.red, linewidth=0.3) bundle_actor3.SetPosition(0, 80, 0) ren.add(bundle_actor2) ren.add(bundle_actor3) ren.set_camera(position=(0, 0, 0), focal_point=(30, 0, 0)) window.record(out_path='simulated_cosine_bundle.png', size=(900, 900)) if interactive:
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 test_custom_interactor_style_events(recording=False):
print("Using VTK {}".format(vtk.vtkVersion.GetVTKVersion()))
filename = "test_custom_interactor_style_events.log.gz"
recording_filename = pjoin(DATA_DIR, filename)
renderer = window.Renderer()
# the show manager allows to break the rendering process
# in steps so that the widgets can be added properly
interactor_style = interactor.CustomInteractorStyle()
show_manager = window.ShowManager(renderer, size=(800, 800), reset_camera=False, interactor_style=interactor_style)
# Create a cursor, a circle that will follow the mouse.
polygon_source = vtk.vtkRegularPolygonSource()
polygon_source.GeneratePolygonOff() # Only the outline of the circle.
polygon_source.SetNumberOfSides(50)
polygon_source.SetRadius(10)
polygon_source.SetRadius
polygon_source.SetCenter(0, 0, 0)
mapper = vtk.vtkPolyDataMapper2D()
vtk_utils.set_input(mapper, polygon_source.GetOutputPort())
cursor = vtk.vtkActor2D()
cursor.SetMapper(mapper)
cursor.GetProperty().SetColor(1, 0.5, 0)
renderer.add(cursor)
def follow_mouse(iren, obj):
obj.SetPosition(*iren.event.position)
iren.force_render()
interactor_style.add_active_prop(cursor)
interactor_style.add_callback(cursor, "MouseMoveEvent", follow_mouse)
# create some minimalistic streamlines
lines = [np.array([[-1, 0, 0.0], [1, 0, 0.0]]), np.array([[-1, 1, 0.0], [1, 1, 0.0]])]
colors = np.array([[1.0, 0.0, 0.0], [0.3, 0.7, 0.0]])
tube1 = actor.streamtube([lines[0]], colors[0])
tube2 = actor.streamtube([lines[1]], colors[1])
renderer.add(tube1)
renderer.add(tube2)
# Define some counter callback.
states = defaultdict(lambda: 0)
def counter(iren, obj):
states[iren.event.name] += 1
# Assign the counter callback to every possible event.
for event in [
"CharEvent",
"MouseMoveEvent",
"KeyPressEvent",
"KeyReleaseEvent",
"LeftButtonPressEvent",
"LeftButtonReleaseEvent",
"RightButtonPressEvent",
"RightButtonReleaseEvent",
"MiddleButtonPressEvent",
"MiddleButtonReleaseEvent",
]:
interactor_style.add_callback(tube1, event, counter)
# Add callback to scale up/down tube1.
def scale_up_obj(iren, obj):
counter(iren, obj)
scale = np.asarray(obj.GetScale()) + 0.1
obj.SetScale(*scale)
iren.force_render()
iren.event.abort() # Stop propagating the event.
def scale_down_obj(iren, obj):
counter(iren, obj)
scale = np.array(obj.GetScale()) - 0.1
obj.SetScale(*scale)
iren.force_render()
iren.event.abort() # Stop propagating the event.
interactor_style.add_callback(tube2, "MouseWheelForwardEvent", scale_up_obj)
interactor_style.add_callback(tube2, "MouseWheelBackwardEvent", scale_down_obj)
# Add callback to hide/show tube1.
def toggle_visibility(iren, obj):
key = iren.event.key
if key.lower() == "v":
obj.SetVisibility(not obj.GetVisibility())
iren.force_render()
interactor_style.add_active_prop(tube1)
interactor_style.add_active_prop(tube2)
interactor_style.remove_active_prop(tube2)
interactor_style.add_callback(tube1, "CharEvent", toggle_visibility)
if recording:
show_manager.record_events_to_file(recording_filename)
print(list(states.items()))
else:
show_manager.play_events_from_file(recording_filename)
msg = "Wrong count for '{}'."
expected = [
("CharEvent", 6),
("KeyPressEvent", 6),
("KeyReleaseEvent", 6),
("MouseMoveEvent", 1652),
("LeftButtonPressEvent", 1),
("RightButtonPressEvent", 1),
("MiddleButtonPressEvent", 2),
("LeftButtonReleaseEvent", 1),
("MouseWheelForwardEvent", 3),
("MouseWheelBackwardEvent", 1),
("MiddleButtonReleaseEvent", 2),
("RightButtonReleaseEvent", 1),
]
# Useful loop for debugging.
for event, count in expected:
if states[event] != count:
print("{}: {} vs. {} (expected)".format(event, states[event], count))
for event, count in expected:
npt.assert_equal(states[event], count, err_msg=msg.format(event))
def test_custom_interactor_style_events(recording=False):
print("Using VTK {}".format(vtk.vtkVersion.GetVTKVersion()))
filename = "test_custom_interactor_style_events.log.gz"
recording_filename = pjoin(DATA_DIR, filename)
renderer = window.Renderer()
# the show manager allows to break the rendering process
# in steps so that the widgets can be added properly
interactor_style = interactor.CustomInteractorStyle()
show_manager = window.ShowManager(renderer,
size=(800, 800),
reset_camera=False,
interactor_style=interactor_style)
# Create a cursor, a circle that will follow the mouse.
polygon_source = vtk.vtkRegularPolygonSource()
polygon_source.GeneratePolygonOff() # Only the outline of the circle.
polygon_source.SetNumberOfSides(50)
polygon_source.SetRadius(10)
# polygon_source.SetRadius
polygon_source.SetCenter(0, 0, 0)
mapper = vtk.vtkPolyDataMapper2D()
vtk_utils.set_input(mapper, polygon_source.GetOutputPort())
cursor = vtk.vtkActor2D()
cursor.SetMapper(mapper)
cursor.GetProperty().SetColor(1, 0.5, 0)
renderer.add(cursor)
def follow_mouse(iren, obj):
obj.SetPosition(*iren.event.position)
iren.force_render()
interactor_style.add_active_prop(cursor)
interactor_style.add_callback(cursor, "MouseMoveEvent", follow_mouse)
# create some minimalistic streamlines
lines = [
np.array([[-1, 0, 0.], [1, 0, 0.]]),
np.array([[-1, 1, 0.], [1, 1, 0.]])
]
colors = np.array([[1., 0., 0.], [0.3, 0.7, 0.]])
tube1 = actor.streamtube([lines[0]], colors[0])
tube2 = actor.streamtube([lines[1]], colors[1])
renderer.add(tube1)
renderer.add(tube2)
# Define some counter callback.
states = defaultdict(lambda: 0)
def counter(iren, obj):
states[iren.event.name] += 1
# Assign the counter callback to every possible event.
for event in [
"CharEvent", "MouseMoveEvent", "KeyPressEvent", "KeyReleaseEvent",
"LeftButtonPressEvent", "LeftButtonReleaseEvent",
"RightButtonPressEvent", "RightButtonReleaseEvent",
"MiddleButtonPressEvent", "MiddleButtonReleaseEvent"
]:
interactor_style.add_callback(tube1, event, counter)
# Add callback to scale up/down tube1.
def scale_up_obj(iren, obj):
counter(iren, obj)
scale = np.asarray(obj.GetScale()) + 0.1
obj.SetScale(*scale)
iren.force_render()
iren.event.abort() # Stop propagating the event.
def scale_down_obj(iren, obj):
counter(iren, obj)
scale = np.array(obj.GetScale()) - 0.1
obj.SetScale(*scale)
iren.force_render()
iren.event.abort() # Stop propagating the event.
interactor_style.add_callback(tube2, "MouseWheelForwardEvent",
scale_up_obj)
interactor_style.add_callback(tube2, "MouseWheelBackwardEvent",
scale_down_obj)
# Add callback to hide/show tube1.
def toggle_visibility(iren, obj):
key = iren.event.key
if key.lower() == "v":
obj.SetVisibility(not obj.GetVisibility())
iren.force_render()
interactor_style.add_active_prop(tube1)
interactor_style.add_active_prop(tube2)
interactor_style.remove_active_prop(tube2)
interactor_style.add_callback(tube1, "CharEvent", toggle_visibility)
if recording:
show_manager.record_events_to_file(recording_filename)
print(list(states.items()))
else:
show_manager.play_events_from_file(recording_filename)
msg = ("Wrong count for '{}'.")
expected = [('CharEvent', 6), ('KeyPressEvent', 6),
('KeyReleaseEvent', 6), ('MouseMoveEvent', 1652),
('LeftButtonPressEvent', 1), ('RightButtonPressEvent', 1),
('MiddleButtonPressEvent', 2),
('LeftButtonReleaseEvent', 1),
('MouseWheelForwardEvent', 3),
('MouseWheelBackwardEvent', 1),
('MiddleButtonReleaseEvent', 2),
('RightButtonReleaseEvent', 1)]
# Useful loop for debugging.
for event, count in expected:
if states[event] != count:
print("{}: {} vs. {} (expected)".format(
event, states[event], count))
for event, count in expected:
npt.assert_equal(states[event], count, err_msg=msg.format(event))
def test_bundle_maps():
renderer = window.renderer()
bundle = fornix_streamlines()
bundle, shift = center_streamlines(bundle)
mat = np.array([[1, 0, 0, 100],
[0, 1, 0, 100],
[0, 0, 1, 100],
[0, 0, 0, 1.]])
bundle = transform_streamlines(bundle, mat)
# metric = np.random.rand(*(200, 200, 200))
metric = 100 * np.ones((200, 200, 200))
# add lower values
metric[100, :, :] = 100 * 0.5
# create a nice orange-red colormap
lut = actor.colormap_lookup_table(scale_range=(0., 100.),
hue_range=(0., 0.1),
saturation_range=(1, 1),
value_range=(1., 1))
line = actor.line(bundle, metric, linewidth=0.1, lookup_colormap=lut)
window.add(renderer, line)
window.add(renderer, actor.scalar_bar(lut, ' '))
report = window.analyze_renderer(renderer)
npt.assert_almost_equal(report.actors, 1)
# window.show(renderer)
renderer.clear()
nb_points = np.sum([len(b) for b in bundle])
values = 100 * np.random.rand(nb_points)
# values[:nb_points/2] = 0
line = actor.streamtube(bundle, values, linewidth=0.1, lookup_colormap=lut)
renderer.add(line)
# window.show(renderer)
report = window.analyze_renderer(renderer)
npt.assert_equal(report.actors_classnames[0], 'vtkLODActor')
renderer.clear()
colors = np.random.rand(nb_points, 3)
# values[:nb_points/2] = 0
line = actor.line(bundle, colors, linewidth=2)
renderer.add(line)
# window.show(renderer)
report = window.analyze_renderer(renderer)
npt.assert_equal(report.actors_classnames[0], 'vtkLODActor')
# window.show(renderer)
arr = window.snapshot(renderer)
report2 = window.analyze_snapshot(arr)
npt.assert_equal(report2.objects, 1)
# try other input options for colors
renderer.clear()
actor.line(bundle, (1., 0.5, 0))
actor.line(bundle, np.arange(len(bundle)))
actor.line(bundle)
colors = [np.random.rand(*b.shape) for b in bundle]
actor.line(bundle, colors=colors)
def test_button_and_slider_widgets():
recording = False
filename = "test_button_and_slider_widgets.log.gz"
recording_filename = pjoin(DATA_DIR, filename)
renderer = window.Renderer()
# create some minimalistic streamlines
lines = [np.array([[-1, 0, 0.], [1, 0, 0.]]),
np.array([[-1, 1, 0.], [1, 1, 0.]])]
colors = np.array([[1., 0., 0.], [0.3, 0.7, 0.]])
stream_actor = actor.streamtube(lines, colors)
states = {'camera_button_count': 0,
'plus_button_count': 0,
'minus_button_count': 0,
'slider_moved_count': 0,
}
renderer.add(stream_actor)
# the show manager allows to break the rendering process
# in steps so that the widgets can be added properly
show_manager = window.ShowManager(renderer, size=(800, 800))
if recording:
show_manager.initialize()
show_manager.render()
def button_callback(obj, event):
print('Camera pressed')
states['camera_button_count'] += 1
def button_plus_callback(obj, event):
print('+ pressed')
states['plus_button_count'] += 1
def button_minus_callback(obj, event):
print('- pressed')
states['minus_button_count'] += 1
fetch_viz_icons()
button_png = read_viz_icons(fname='camera.png')
button = widget.button(show_manager.iren,
show_manager.ren,
button_callback,
button_png, (.98, 1.), (80, 50))
button_png_plus = read_viz_icons(fname='plus.png')
button_plus = widget.button(show_manager.iren,
show_manager.ren,
button_plus_callback,
button_png_plus, (.98, .9), (120, 50))
button_png_minus = read_viz_icons(fname='minus.png')
button_minus = widget.button(show_manager.iren,
show_manager.ren,
button_minus_callback,
button_png_minus, (.98, .9), (50, 50))
def print_status(obj, event):
rep = obj.GetRepresentation()
stream_actor.SetPosition((rep.GetValue(), 0, 0))
states['slider_moved_count'] += 1
slider = widget.slider(show_manager.iren, show_manager.ren,
callback=print_status,
min_value=-1,
max_value=1,
value=0.,
label="X",
right_normalized_pos=(.98, 0.6),
size=(120, 0), label_format="%0.2lf")
# This callback is used to update the buttons/sliders' position
# so they can stay on the right side of the window when the window
# is being resized.
global size
size = renderer.GetSize()
if recording:
show_manager.record_events_to_file(recording_filename)
print(states)
else:
show_manager.play_events_from_file(recording_filename)
npt.assert_equal(states["camera_button_count"], 7)
npt.assert_equal(states["plus_button_count"], 3)
npt.assert_equal(states["minus_button_count"], 4)
npt.assert_equal(states["slider_moved_count"], 116)
if not recording:
button.Off()
slider.Off()
# Uncomment below to test the slider and button with analyze
# button.place(renderer)
# slider.place(renderer)
arr = window.snapshot(renderer, size=(800, 800))
report = window.analyze_snapshot(arr)
# import pylab as plt
# plt.imshow(report.labels, origin='lower')
# plt.show()
npt.assert_equal(report.objects, 4)
report = window.analyze_renderer(renderer)
npt.assert_equal(report.actors, 1)
def test_button_and_slider_widgets():
recording = False
filename = "test_button_and_slider_widgets.log.gz"
recording_filename = pjoin(DATA_DIR, filename)
renderer = window.Renderer()
# create some minimalistic streamlines
lines = [
np.array([[-1, 0, 0.], [1, 0, 0.]]),
np.array([[-1, 1, 0.], [1, 1, 0.]])
]
colors = np.array([[1., 0., 0.], [0.3, 0.7, 0.]])
stream_actor = actor.streamtube(lines, colors)
states = {
'camera_button_count': 0,
'plus_button_count': 0,
'minus_button_count': 0,
'slider_moved_count': 0,
}
renderer.add(stream_actor)
# the show manager allows to break the rendering process
# in steps so that the widgets can be added properly
show_manager = window.ShowManager(renderer, size=(800, 800))
if recording:
show_manager.initialize()
show_manager.render()
def button_callback(obj, event):
print('Camera pressed')
states['camera_button_count'] += 1
def button_plus_callback(obj, event):
print('+ pressed')
states['plus_button_count'] += 1
def button_minus_callback(obj, event):
print('- pressed')
states['minus_button_count'] += 1
fetch_viz_icons()
button_png = read_viz_icons(fname='camera.png')
button = widget.button(show_manager.iren, show_manager.ren,
button_callback, button_png, (.98, 1.), (80, 50))
button_png_plus = read_viz_icons(fname='plus.png')
button_plus = widget.button(show_manager.iren, show_manager.ren,
button_plus_callback, button_png_plus,
(.98, .9), (120, 50))
button_png_minus = read_viz_icons(fname='minus.png')
button_minus = widget.button(show_manager.iren, show_manager.ren,
button_minus_callback, button_png_minus,
(.98, .9), (50, 50))
def print_status(obj, event):
rep = obj.GetRepresentation()
stream_actor.SetPosition((rep.GetValue(), 0, 0))
states['slider_moved_count'] += 1
slider = widget.slider(show_manager.iren,
show_manager.ren,
callback=print_status,
min_value=-1,
max_value=1,
value=0.,
label="X",
right_normalized_pos=(.98, 0.6),
size=(120, 0),
label_format="%0.2lf")
# This callback is used to update the buttons/sliders' position
# so they can stay on the right side of the window when the window
# is being resized.
global size
size = renderer.GetSize()
if recording:
show_manager.record_events_to_file(recording_filename)
print(states)
else:
show_manager.play_events_from_file(recording_filename)
npt.assert_equal(states["camera_button_count"], 7)
npt.assert_equal(states["plus_button_count"], 3)
npt.assert_equal(states["minus_button_count"], 4)
npt.assert_equal(states["slider_moved_count"], 116)
if not recording:
button.Off()
slider.Off()
# Uncomment below to test the slider and button with analyze
# button.place(renderer)
# slider.place(renderer)
arr = window.snapshot(renderer, size=(800, 800))
report = window.analyze_snapshot(arr)
# import pylab as plt
# plt.imshow(report.labels, origin='lower')
# plt.show()
npt.assert_equal(report.objects, 4)
report = window.analyze_renderer(renderer)
npt.assert_equal(report.actors, 1)
bundle_downsampled2 = [approx_polygon_track(s, 0.25) for s in bundle]
n_pts_ds2 = [len(streamline) for streamline in bundle_downsampled2]
"""
Both, ``set_number_of_points`` and ``approx_polygon_track`` can be thought as
methods for lossy compression of streamlines.
"""
from dipy.viz import window, actor
# Enables/disables interactive visualization
interactive = False
ren = window.Renderer()
ren.SetBackground(*window.colors.white)
bundle_actor = actor.streamtube(bundle, window.colors.red, linewidth=0.3)
ren.add(bundle_actor)
bundle_actor2 = actor.streamtube(bundle_downsampled,
window.colors.red,
linewidth=0.3)
bundle_actor2.SetPosition(0, 40, 0)
bundle_actor3 = actor.streamtube(bundle_downsampled2,
window.colors.red,
linewidth=0.3)
bundle_actor3.SetPosition(0, 80, 0)
ren.add(bundle_actor2)
ren.add(bundle_actor3)
# Enables/disables interactive visualization
interactive = False
"""
To speed up visualization, we will select a random sub-set of streamlines to
display. This is particularly important, if you track from seeds throughout the
entire white matter, generating many streamlines. In this case, for
demonstration purposes, we subselect 900 streamlines.
"""
from dipy.tracking.streamline import select_random_set_of_streamlines
plot_streamlines = select_random_set_of_streamlines(streamlines, 900)
streamlines_actor = actor.streamtube(
list(move_streamlines(plot_streamlines, inv(t1_aff))),
cmap.line_colors(streamlines), linewidth=0.1)
vol_actor = actor.slicer(t1_data)
vol_actor.display(40, None, None)
vol_actor2 = vol_actor.copy()
vol_actor2.display(None, None, 35)
ren = window.Renderer()
ren.add(streamlines_actor)
ren.add(vol_actor)
ren.add(vol_actor2)
window.record(ren, out_path='sfm_streamlines.png', size=(800, 800))
if interactive:
'''
for line in streamlines:
print(line.shape)
'''
# Do steamline clustering using QuickBundles (QB) using Eular's Method
# dist_thr (distance threshold) which affects number of clusters and their size
# pts (number of points in each streamline) which will be used for downsampling before clustering
# Default values : dist_thr = 4 & pts = 12
qb = QuickBundles(streamlines, dist_thr=20, pts=20)
clusters = qb.clusters()
print('Number of clusters %i' % qb.total_clusters)
print('Cluster size', qb.clusters_sizes())
# Display streamlines
ren = window.Renderer()
ren.add(actor.streamtube(streamlines, window.colors.white))
window.show(ren)
window.record(ren, out_path=filename + '_stream_lines_eu.png', size=(600, 600))
# Display centroids
window.clear(ren)
colormap = actor.create_colormap(np.arange(qb.total_clusters))
ren.add(actor.streamtube(streamlines, window.colors.white, opacity=0.1))
ren.add(actor.streamtube(qb.centroids, colormap, linewidth=0.5))
window.show(ren)
window.record(ren, out_path=filename + '_centroids_eu.png', size=(600, 600))
# Display tracks
window.clear(ren)
colormap_full = np.ones((len(streamlines), 3))
for cluster, color in zip(clusters.items(), colormap):
def test_button_and_slider_widgets():
interactive = False
renderer = window.Renderer()
# create some minimalistic streamlines
lines = [
np.array([[-1, 0, 0.], [1, 0, 0.]]),
np.array([[-1, 1, 0.], [1, 1, 0.]])
]
colors = np.array([[1., 0., 0.], [0.3, 0.7, 0.]])
stream_actor = actor.streamtube(lines, colors)
renderer.add(stream_actor)
# the show manager allows to break the rendering process
# in steps so that the widgets can be added properly
show_manager = window.ShowManager(renderer, size=(800, 800))
if interactive:
show_manager.initialize()
show_manager.render()
def button_callback(obj, event):
print('Camera pressed')
def button_plus_callback(obj, event):
print('+ pressed')
def button_minus_callback(obj, event):
print('- pressed')
fetch_viz_icons()
button_png = read_viz_icons(fname='camera.png')
button = widget.button(show_manager.iren, show_manager.ren,
button_callback, button_png, (.98, 1.), (80, 50))
button_png_plus = read_viz_icons(fname='plus.png')
button_plus = widget.button(show_manager.iren, show_manager.ren,
button_plus_callback, button_png_plus,
(.98, .9), (120, 50))
button_png_minus = read_viz_icons(fname='minus.png')
button_minus = widget.button(show_manager.iren, show_manager.ren,
button_minus_callback, button_png_minus,
(.98, .9), (50, 50))
def print_status(obj, event):
rep = obj.GetRepresentation()
stream_actor.SetPosition((rep.GetValue(), 0, 0))
slider = widget.slider(show_manager.iren,
show_manager.ren,
callback=print_status,
min_value=-1,
max_value=1,
value=0.,
label="X",
right_normalized_pos=(.98, 0.6),
size=(120, 0),
label_format="%0.2lf")
# This callback is used to update the buttons/sliders' position
# so they can stay on the right side of the window when the window
# is being resized.
global size
size = renderer.GetSize()
def win_callback(obj, event):
global size
if size != obj.GetSize():
button.place(renderer)
button_plus.place(renderer)
button_minus.place(renderer)
slider.place(renderer)
size = obj.GetSize()
if interactive:
# show_manager.add_window_callback(win_callback)
# you can also register any callback in a vtk way like this
# show_manager.window.AddObserver(vtk.vtkCommand.ModifiedEvent,
# win_callback)
show_manager.render()
show_manager.start()
if not interactive:
button.Off()
slider.Off()
# Uncomment below to test the slider and button with analyze
# button.place(renderer)
# slider.place(renderer)
arr = window.snapshot(renderer, size=(800, 800))
report = window.analyze_snapshot(arr)
npt.assert_equal(report.objects, 2)
# imshow(report.labels, origin='lower')
report = window.analyze_renderer(renderer)
npt.assert_equal(report.actors, 1)
# Enables/disables interactive visualization
interactive = False
"""
To speed up visualization, we will select a random sub-set of streamlines to
display. This is particularly important, if you track from seeds throughout the
entire white matter, generating many streamlines. In this case, for
demonstration purposes, we subselect 900 streamlines.
"""
from dipy.tracking.streamline import select_random_set_of_streamlines
plot_streamlines = select_random_set_of_streamlines(streamlines, 900)
streamlines_actor = actor.streamtube(
list(move_streamlines(plot_streamlines, inv(t1_aff))),
cmap.line_colors(streamlines), linewidth=0.1)
vol_actor = actor.slicer(t1_data)
vol_actor.display(40, None, None)
vol_actor2 = vol_actor.copy()
vol_actor2.display(None, None, 35)
ren = window.Renderer()
ren.add(streamlines_actor)
ren.add(vol_actor)
ren.add(vol_actor2)
window.record(ren, out_path='sfm_streamlines.png', size=(800, 800))
if interactive:
"""
Create a scene.
"""
ren = window.Renderer()
"""
Every streamline will be coloured according to its orientation
"""
from dipy.viz.colormap import line_colors
"""
`actor.line` creates a streamline actor for streamline visualization
and `ren.add` adds this actor to the scene
"""
ren.add(actor.streamtube(tensor_streamlines, line_colors(tensor_streamlines)))
print('Saving illustration as tensor_tracks.png')
ren.SetBackground(1, 1, 1)
window.record(ren, out_path='tensor_tracks.png', size=(600, 600))
# Enables/disables interactive visualization
interactive = False
if interactive:
window.show(ren)
"""
.. figure:: tensor_tracks.png
:align: center
Deterministic streamlines with EuDX on a Tensor Field.