def test_text_widget():
interactive = False
renderer = window.Renderer()
axes = fvtk.axes()
window.add(renderer, axes)
renderer.ResetCamera()
show_manager = window.ShowManager(renderer, size=(900, 900))
if interactive:
show_manager.initialize()
show_manager.render()
fetch_viz_icons()
button_png = read_viz_icons(fname='home3.png')
def button_callback(obj, event):
print('Button Pressed')
button = widget.button(show_manager.iren, show_manager.ren,
button_callback, button_png, (.8, 1.2), (100, 100))
global rulez
rulez = True
def text_callback(obj, event):
global rulez
print('Text selected')
if rulez:
obj.GetTextActor().SetInput("Diffusion Imaging Rulez!!")
rulez = False
else:
obj.GetTextActor().SetInput("Diffusion Imaging in Python")
rulez = True
show_manager.render()
text = widget.text(show_manager.iren,
show_manager.ren,
text_callback,
message="Diffusion Imaging in Python",
left_down_pos=(0., 0.),
right_top_pos=(0.4, 0.05),
opacity=1.,
border=False)
if not interactive:
button.Off()
text.Off()
pass
if interactive:
show_manager.render()
show_manager.start()
arr = window.snapshot(renderer, size=(900, 900))
report = window.analyze_snapshot(arr)
npt.assert_equal(report.objects, 3)
def show_signal(r,S,gradients,offset=np.zeros(3)):
PS = np.dot(np.diag(S),gradients)
#for (i,s) in enumerate(S):
fvtk.add(r,fvtk.point(offset+PS/np.max(PS),fvtk.cyan,point_radius=0.05,theta=8,phi=8))
fvtk.add(r,fvtk.point([offset],fvtk.green,point_radius=0.1,theta=8,phi=8))
fvtk.add(r,fvtk.axes((1,1,1)))
lines = fvtk.line([1.5*np.row_stack((needles3d[0],-needles3d[0])), \
1.5*np.row_stack((needles3d[1],-needles3d[1]))], \
colors=np.row_stack((fvtk.golden,fvtk.aquamarine)),linewidth=10)
fvtk.add(r,lines)
def playing_with_diffusivities_and_simulations():
data,bvals,bvecs=get_data(name='101_32')
#S=data[:,:,42]
#drange=np.linspace(0,40,5)
S1,sticks1=simulations_dipy(bvals,bvecs,d=0.0015,S0=200,angles=[(0,0),(90,0)],fractions=[50,50],snr=None)
S2,sticks2=simulations_dipy(bvals,bvecs,d=0.0015,S0=200,angles=[(0,0),(90,0),(90,90)],fractions=[33,33,33],snr=None)
scale=10**4
ob=-1/bvals[1:]
D1=ob*(np.log(S1[1:])-np.log(S1[0]))*scale
D2=ob*(np.log(S2[1:])-np.log(S2[0]))*scale
Bvecs=np.concatenate([bvecs[1:],-bvecs[1:]])
SS1=np.concatenate([S1[1:],S1[1:]])
SS2=np.concatenate([S2[1:],S2[1:]])
DD1=np.concatenate([D1,D1])
DD2=np.concatenate([D2,D2])
X1=np.dot(np.diag(DD1),Bvecs)
X2=np.dot(np.diag(DD2),Bvecs)
U,s,V=np.linalg.svd(np.dot(X1.T,X2),full_matrices=True)
R=np.dot(U,V.T)
print np.round(R,2)
print np.sum(np.dot(X1,R)-X2,axis=0)
r=fvtk.ren()
fvtk.add(r,fvtk.point(X1,fvtk.red,1,.5,16,16))
fvtk.add(r,fvtk.point(X2,fvtk.green,1,.5,16,16))
fvtk.add(r,fvtk.axes((10,10,10)))
fvtk.show(r)
U1,s1,V1=np.linalg.svd(np.dot(X1.T,X1),full_matrices=True)
U2,s2,V2=np.linalg.svd(np.dot(X2.T,X2),full_matrices=True)
u1=U1[:,2]
u2=U2[:,2]
R2=vec2vecrotmat(u1,u2)
print np.round(R2,2)
print np.rad2deg(np.arccos(np.dot(u1,u2)))
uu1=np.zeros((2,3))
uu1[1]=u1
uu2=np.zeros((2,3))
uu2[1]=u2
kX1=online_kurtosis(X1)
kX2=online_kurtosis(X2)
print 's1',s1
print 's2',s2
print 'kX1',kX1
print 'kX2',kX2
print 'average diffusivity 1',np.mean(np.linalg.norm(X1))
print 'average diffusivity 2',np.mean(np.linalg.norm(X2))
def horizon(tractograms, data, affine, cluster=False, cluster_thr=15.,
random_colors=False,
length_lt=0, length_gt=np.inf, clusters_lt=0, clusters_gt=np.inf):
rng = np.random.RandomState(42)
slicer_opacity = .8
ren = window.Renderer()
global centroid_actors
centroid_actors = []
for streamlines in tractograms:
print(' Number of streamlines loaded {} \n'.format(len(streamlines)))
if not random_colors:
ren.add(actor.line(streamlines, opacity=1., lod_points=10 ** 5))
else:
colors = rng.rand(3)
ren.add(actor.line(streamlines, colors, opacity=1., lod_points=10 ** 5))
class SimpleTrackBallNoBB(window.vtk.vtkInteractorStyleTrackballCamera):
def HighlightProp(self, p):
pass
style = SimpleTrackBallNoBB()
# very hackish way
style.SetPickColor(0, 0, 0)
# style.HighlightProp(None)
show_m = window.ShowManager(ren, size=(1200, 900), interactor_style=style)
show_m.initialize()
if data is not None:
#from dipy.core.geometry import rodrigues_axis_rotation
#affine[:3, :3] = np.dot(affine[:3, :3], rodrigues_axis_rotation((0, 0, 1), 45))
image_actor = actor.slicer(data, affine)
image_actor.opacity(slicer_opacity)
image_actor.SetInterpolate(False)
ren.add(image_actor)
ren.add(fvtk.axes((10, 10, 10)))
last_value = [10]
def change_slice(obj, event):
new_value = int(np.round(obj.get_value()))
if new_value == image_actor.shape[1] - 1 or new_value == 0:
new_value = last_value[0] + np.sign(new_value - last_value[0])
image_actor.display(None, new_value, None)
obj.set_value(new_value)
last_value[0] = new_value
slider = widget.slider(show_m.iren, show_m.ren,
callback=change_slice,
min_value=0,
max_value=image_actor.shape[1] - 1,
value=image_actor.shape[1] / 2,
label="Move slice",
right_normalized_pos=(.98, 0.6),
size=(120, 0), label_format="%0.lf",
color=(1., 1., 1.),
selected_color=(0.86, 0.33, 1.))
slider.SetAnimationModeToJump()
global size
size = ren.GetSize()
# ren.background((1, 0.5, 0))
ren.background((0, 0, 0))
global picked_actors
picked_actors = {}
def pick_callback(obj, event):
global centroid_actors
global picked_actors
prop = obj.GetProp3D()
ac = np.array(centroid_actors)
index = np.where(ac == prop)[0]
if len(index) > 0:
try:
bundle = picked_actors[prop]
ren.rm(bundle)
del picked_actors[prop]
except:
bundle = actor.line(clusters[visible_cluster_id[index]],
lod=False)
picked_actors[prop] = bundle
ren.add(bundle)
if prop in picked_actors.values():
ren.rm(prop)
def win_callback(obj, event):
global size
if size != obj.GetSize():
if data is not None:
slider.place(ren)
size = obj.GetSize()
global centroid_visibility
centroid_visibility = True
def key_press(obj, event):
global centroid_visibility
key = obj.GetKeySym()
if key == 'h' or key == 'H':
if cluster:
if centroid_visibility is True:
for ca in centroid_actors:
ca.VisibilityOff()
centroid_visibility = False
else:
for ca in centroid_actors:
ca.VisibilityOn()
centroid_visibility = True
show_m.render()
show_m.initialize()
show_m.iren.AddObserver('KeyPressEvent', key_press)
show_m.add_window_callback(win_callback)
#show_m.add_picker_callback(pick_callback)
show_m.render()
show_m.start()
def test_text_widget():
interactive = False
renderer = window.Renderer()
axes = fvtk.axes()
window.add(renderer, axes)
renderer.ResetCamera()
show_manager = window.ShowManager(renderer, size=(900, 900))
if interactive:
show_manager.initialize()
show_manager.render()
fetch_viz_icons()
button_png = read_viz_icons(fname='home3.png')
def button_callback(obj, event):
print('Button Pressed')
button = widget.button(show_manager.iren,
show_manager.ren,
button_callback,
button_png, (.8, 1.2), (100, 100))
global rulez
rulez = True
def text_callback(obj, event):
global rulez
print('Text selected')
if rulez:
obj.GetTextActor().SetInput("Diffusion Imaging Rulez!!")
rulez = False
else:
obj.GetTextActor().SetInput("Diffusion Imaging in Python")
rulez = True
show_manager.render()
text = widget.text(show_manager.iren,
show_manager.ren,
text_callback,
message="Diffusion Imaging in Python",
left_down_pos=(0., 0.),
right_top_pos=(0.4, 0.05),
opacity=1.,
border=False)
if not interactive:
button.Off()
text.Off()
pass
if interactive:
show_manager.render()
show_manager.start()
arr = window.snapshot(renderer, size=(900, 900))
report = window.analyze_snapshot(arr)
npt.assert_equal(report.objects, 3)
def show_peak_directions(peaks, scale=0.3, x=5, y=None, z=None, show_axes=False):
""" visualize peak directions
Parameters
----------
peaks : ndarray,
(X, Y, Z, 15)
scale : float
voxel scaling (0 =< `scale` =< 1)
x : int,
x slice (0 <= x <= X-1)
y : int,
y slice (0 <= y <= Y-1)
z : int,
z slice (0 <= z <= Z-1)
Notes
-----
If x, y, z are Nones then the full volume is shown.
"""
# if x is None and y is None and z is None:
# raise ValueError('A slice should be provided')
pshape = peaks.shape[:-1]
if x is not None:
x = np.clip(x, 0, pshape[0] - 1)
if y is not None:
y = np.clip(y, 0, pshape[0] - 1)
if z is not None:
z = np.clip(z, 0, pshape[0] - 1)
print x, y, z
peaks = np.asarray(peaks)
if peaks.ndim > 4 or peaks.ndim < 4:
raise ValueError("peaks has wrong shape")
r = fvtk.ren()
for index in ndindex(peaks.shape[:-1]):
peak = peaks[index]
directions = peak.reshape(peak.shape[0] / 3, 3)
pos = np.array(index)
if x is not None:
pos[0] = x
if y is not None:
pos[1] = y
if z is not None:
pos[2] = z
for i in xrange(directions.shape[0]):
if np.linalg.norm(directions[i]) != 0:
if (x, y, z) == (None, None, None):
line_actor = fvtk.line(index +
scale * np.vstack((-directions[i], directions[i])),
np.abs(directions[i] / np.linalg.norm(directions[i])))
fvtk.add(r, line_actor)
if tuple(pos) == index:
line_actor = fvtk.line(pos +
scale * np.vstack((-directions[i], directions[i])),
np.abs(directions[i] / np.linalg.norm(directions[i])))
fvtk.add(r, line_actor)
if show_axes:
fvtk.add(r, fvtk.axes((2, 2, 2)))
fvtk.show(r)
def horizon(tractograms, data, affine):
rng = np.random.RandomState(42)
slicer_opacity = .8
ren = window.Renderer()
global centroid_actors
centroid_actors = []
for streamlines in tractograms:
print(' Number of streamlines loaded {} \n'.format(len(streamlines)))
colors = rng.rand(3)
ren.add(actor.line(streamlines, colors, opacity=1., lod_points=10**5))
class SimpleTrackBallNoBB(window.vtk.vtkInteractorStyleTrackballCamera):
def HighlightProp(self, p):
pass
style = SimpleTrackBallNoBB()
# very hackish way
style.SetPickColor(0, 0, 0)
# style.HighlightProp(None)
show_m = window.ShowManager(ren, size=(1200, 900), interactor_style=style)
show_m.initialize()
if data is not None:
#from dipy.core.geometry import rodrigues_axis_rotation
#affine[:3, :3] = np.dot(affine[:3, :3], rodrigues_axis_rotation((0, 0, 1), 45))
image_actor = actor.slicer(data, affine)
image_actor.opacity(slicer_opacity)
image_actor.SetInterpolate(False)
ren.add(image_actor)
ren.add(fvtk.axes((10, 10, 10)))
last_value = [10]
def change_slice(obj, event):
new_value = int(np.round(obj.get_value()))
if new_value == image_actor.shape[1] - 1 or new_value == 0:
new_value = last_value[0] + np.sign(new_value - last_value[0])
image_actor.display(None, new_value, None)
obj.set_value(new_value)
last_value[0] = new_value
slider = widget.slider(show_m.iren,
show_m.ren,
callback=change_slice,
min_value=0,
max_value=image_actor.shape[1] - 1,
value=image_actor.shape[1] / 2,
label="Move slice",
right_normalized_pos=(.98, 0.6),
size=(120, 0),
label_format="%0.lf",
color=(1., 1., 1.),
selected_color=(0.86, 0.33, 1.))
slider.SetAnimationModeToJump()
global size
size = ren.GetSize()
# ren.background((1, 0.5, 0))
ren.background((0, 0, 0))
global picked_actors
picked_actors = {}
def win_callback(obj, event):
global size
if size != obj.GetSize():
if data is not None:
slider.place(ren)
size = obj.GetSize()
global centroid_visibility
centroid_visibility = True
show_m.initialize()
show_m.add_window_callback(win_callback)
show_m.render()
show_m.start()
print invariant_angles(S) Sinit = S.copy() Rot = rotation_matrix(np.array([0, 1, 0]), 30) S = np.dot(Rot, S.T).T + np.array([1, 0, 0]) print "Dummy translated" print invariant_angles(S) from dipy.viz import fvtk r = fvtk.ren() fvtk.add(r, fvtk.line(Sinit, fvtk.red)) fvtk.add(r, fvtk.line(S, fvtk.green)) fvtk.add(r, fvtk.axes()) fvtk.show(r) # helix theta = 2 * np.pi * np.linspace(0, 2, 100) x = np.cos(theta) y = np.sin(theta) z = theta / (2 * np.pi) Shel = np.vstack((x, y, z)).T from dipy.tracking.metrics import downsample Shel = downsample(Shel, 12) print "Helix standard" print invariant_angles(Shel)