def test_ui_line_double_slider_2d(interactive=False):
line_double_slider_2d_test = ui.LineDoubleSlider2D(center=(300, 300),
shape="disk",
outer_radius=15,
min_value=-10,
max_value=10,
initial_values=(-10,
10))
npt.assert_equal(line_double_slider_2d_test.handles[0].size, (30, 30))
npt.assert_equal(line_double_slider_2d_test.left_disk_value, -10)
npt.assert_equal(line_double_slider_2d_test.right_disk_value, 10)
if interactive:
show_manager = window.ShowManager(size=(600, 600),
title="DIPY Line Double Slider")
show_manager.ren.add(line_double_slider_2d_test)
show_manager.start()
line_double_slider_2d_test = ui.LineDoubleSlider2D(center=(300, 300),
shape="square",
handle_side=5,
initial_values=(50, 40))
npt.assert_equal(line_double_slider_2d_test.handles[0].size, (5, 5))
npt.assert_equal(line_double_slider_2d_test._values[0], 39)
npt.assert_equal(line_double_slider_2d_test.right_disk_value, 40)
if interactive:
show_manager = window.ShowManager(size=(600, 600),
title="DIPY Line Double Slider")
show_manager.ren.add(line_double_slider_2d_test)
show_manager.start()
def test_ui_textbox(recording=False):
filename = "test_ui_textbox"
recording_filename = pjoin(DATA_DIR, filename + ".log.gz")
expected_events_counts_filename = pjoin(DATA_DIR, filename + ".pkl")
# TextBox
textbox_test = ui.TextBox2D(height=3, width=10, text="Text")
another_textbox_test = ui.TextBox2D(height=3, width=10, text="Enter Text")
another_textbox_test.set_message("Enter Text")
npt.assert_raises(NotImplementedError, setattr, another_textbox_test,
"center", (10, 100))
# Assign the counter callback to every possible event.
event_counter = EventCounter()
event_counter.monitor(textbox_test)
current_size = (600, 600)
show_manager = window.ShowManager(size=current_size, title="DIPY TextBox")
show_manager.ren.add(textbox_test)
if recording:
show_manager.record_events_to_file(recording_filename)
print(list(event_counter.events_counts.items()))
event_counter.save(expected_events_counts_filename)
else:
show_manager.play_events_from_file(recording_filename)
expected = EventCounter.load(expected_events_counts_filename)
event_counter.check_counts(expected)
def test_text_widget():
interactive = False
renderer = window.Renderer()
axes = actor.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 test_ui_line_slider_2d(recording=False):
filename = "test_ui_line_slider_2d"
recording_filename = pjoin(DATA_DIR, filename + ".log.gz")
expected_events_counts_filename = pjoin(DATA_DIR, filename + ".pkl")
line_slider_2d_test = ui.LineSlider2D(initial_value=-2,
min_value=-5,
max_value=5)
line_slider_2d_test.center = (300, 300)
# Assign the counter callback to every possible event.
event_counter = EventCounter()
event_counter.monitor(line_slider_2d_test)
current_size = (600, 600)
show_manager = window.ShowManager(size=current_size,
title="DIPY Line Slider")
show_manager.ren.add(line_slider_2d_test)
if recording:
show_manager.record_events_to_file(recording_filename)
print(list(event_counter.events_counts.items()))
event_counter.save(expected_events_counts_filename)
else:
show_manager.play_events_from_file(recording_filename)
expected = EventCounter.load(expected_events_counts_filename)
event_counter.check_counts(expected)
def test_rectangle_2d():
window_size = (700, 700)
show_manager = window.ShowManager(size=window_size)
rect = ui.Rectangle2D(size=(100, 50))
rect.set_position((50, 80))
npt.assert_equal(rect.position, (50, 80))
rect.color = (1, 0.5, 0)
npt.assert_equal(rect.color, (1, 0.5, 0))
rect.opacity = 0.5
npt.assert_equal(rect.opacity, 0.5)
# Check the rectangle is drawn at right place.
show_manager.ren.add(rect)
# Uncomment this to start the visualisation
# show_manager.start()
colors = [rect.color]
arr = window.snapshot(show_manager.ren, size=window_size, offscreen=True)
report = window.analyze_snapshot(arr, colors=colors)
assert report.objects == 1
assert report.colors_found
# Test visibility off.
rect.set_visibility(False)
arr = window.snapshot(show_manager.ren, size=window_size, offscreen=True)
report = window.analyze_snapshot(arr)
assert report.objects == 0
def test_ui_ring_slider_2d(recording=False):
filename = "test_ui_ring_slider_2d"
recording_filename = pjoin(DATA_DIR, filename + ".log.gz")
expected_events_counts_filename = pjoin(DATA_DIR, filename + ".pkl")
ring_slider_2d_test = ui.RingSlider2D()
ring_slider_2d_test.center = (300, 300)
ring_slider_2d_test.value = 90
# Assign the counter callback to every possible event.
event_counter = EventCounter()
event_counter.monitor(ring_slider_2d_test)
current_size = (600, 600)
show_manager = window.ShowManager(size=current_size,
title="DIPY Ring Slider")
show_manager.ren.add(ring_slider_2d_test)
if recording:
# Record the following events
# 1. Left Click on the handle and hold it
# 2. Move to the left the handle and make 1.5 tour
# 3. Release the handle
# 4. Left Click on the handle and hold it
# 5. Move to the right the handle and make 1 tour
# 6. Release the handle
show_manager.record_events_to_file(recording_filename)
print(list(event_counter.events_counts.items()))
event_counter.save(expected_events_counts_filename)
else:
show_manager.play_events_from_file(recording_filename)
expected = EventCounter.load(expected_events_counts_filename)
event_counter.check_counts(expected)
def test_ui_disk_slider_2d(recording=False):
filename = "test_ui_disk_slider_2d"
recording_filename = pjoin(DATA_DIR, filename + ".log.gz")
expected_events_counts_filename = pjoin(DATA_DIR, filename + ".pkl")
disk_slider_2d_test = ui.DiskSlider2D()
disk_slider_2d_test.set_center((300, 300))
disk_slider_2d_test.value = 90
# Assign the counter callback to every possible event.
event_counter = EventCounter()
event_counter.monitor(disk_slider_2d_test)
current_size = (600, 600)
show_manager = window.ShowManager(size=current_size,
title="DIPY Disk Slider")
show_manager.ren.add(disk_slider_2d_test)
if recording:
show_manager.record_events_to_file(recording_filename)
print(list(event_counter.events_counts.items()))
event_counter.save(expected_events_counts_filename)
else:
show_manager.play_events_from_file(recording_filename)
expected = EventCounter.load(expected_events_counts_filename)
event_counter.check_counts(expected)
def test_ui_disk_2d():
window_size = (700, 700)
show_manager = window.ShowManager(size=window_size)
disk = ui.Disk2D(outer_radius=20, inner_radius=5)
disk.position = (50, 80)
npt.assert_equal(disk.position, (50, 80))
disk.color = (1, 0.5, 0)
npt.assert_equal(disk.color, (1, 0.5, 0))
disk.opacity = 0.5
npt.assert_equal(disk.opacity, 0.5)
# Check the rectangle is drawn at right place.
show_manager.ren.add(disk)
# Uncomment this to start the visualisation
# show_manager.start()
colors = [disk.color]
arr = window.snapshot(show_manager.ren, size=window_size, offscreen=True)
report = window.analyze_snapshot(arr, colors=colors)
assert report.objects == 1
assert report.colors_found
# Test visibility off.
disk.set_visibility(False)
arr = window.snapshot(show_manager.ren, size=window_size, offscreen=True)
report = window.analyze_snapshot(arr)
assert report.objects == 0
def test_ui_range_slider(interactive=False):
range_slider_test = ui.RangeSlider(shape="square")
if interactive:
show_manager = window.ShowManager(size=(600, 600),
title="DIPY Line Double Slider")
show_manager.ren.add(range_slider_test)
show_manager.start()
def test_ui_option(interactive=False):
option_test = ui.Option(label="option 1", position=(10, 10))
npt.assert_equal(option_test.checked, False)
if interactive:
showm = window.ShowManager(size=(600, 600))
showm.ren.add(option_test)
showm.start()
def test_timer():
""" Testing add a timer and exit window and app from inside timer.
"""
xyzr = np.array([[0, 0, 0, 10], [100, 0, 0, 50], [300, 0, 0, 100]])
xyzr2 = np.array([[0, 200, 0, 30], [100, 200, 0, 50], [300, 200, 0, 100]])
colors = np.array([[1, 0, 0, 0.3], [0, 1, 0, 0.4], [0, 0, 1., 0.45]])
renderer = window.Renderer()
global sphere_actor, tb, cnt
sphere_actor = actor.sphere(centers=xyzr[:, :3], colors=colors[:],
radii=xyzr[:, 3])
sphere = get_sphere('repulsion724')
sphere_actor2 = actor.sphere(centers=xyzr2[:, :3], colors=colors[:],
radii=xyzr2[:, 3], vertices=sphere.vertices,
faces=sphere.faces.astype('i8'))
renderer.add(sphere_actor)
renderer.add(sphere_actor2)
tb = ui.TextBlock2D()
cnt = 0
global showm
showm = window.ShowManager(renderer,
size=(1024, 768), reset_camera=False,
order_transparent=True)
showm.initialize()
def timer_callback(obj, event):
global cnt, sphere_actor, showm, tb
cnt += 1
tb.message = "Let's count to 10 and exit :" + str(cnt)
showm.render()
if cnt > 9:
showm.exit()
renderer.add(tb)
# Run every 200 milliseconds
showm.add_timer_callback(True, 200, timer_callback)
showm.start()
arr = window.snapshot(renderer)
npt.assert_(np.sum(arr) > 0)
def test_ui_file_select_menu_2d(recording=False):
filename = "test_ui_file_select_menu_2d"
recording_filename = pjoin(DATA_DIR, filename + ".log.gz")
expected_events_counts_filename = pjoin(DATA_DIR, filename + ".pkl")
with InTemporaryDirectory() as tmpdir:
for i in range(10):
_ = open("test" + str(i) + ".txt", 'wt').write('some text')
file_select_menu = ui.FileSelectMenu2D(size=(500, 500),
position=(300, 300),
font_size=16,
extensions=["txt"],
directory_path=os.getcwd(),
parent=None)
file_select_menu.set_center((300, 300))
npt.assert_equal(file_select_menu.text_item_list[1].file_name[:4],
"test")
npt.assert_equal(file_select_menu.text_item_list[5].file_name[:4],
"test")
event_counter = EventCounter()
for event in event_counter.events_counts:
file_select_menu.add_callback(file_select_menu.buttons["up"].actor,
event, event_counter.count)
file_select_menu.add_callback(
file_select_menu.buttons["down"].actor, event,
event_counter.count)
file_select_menu.menu.add_callback(
file_select_menu.menu.panel.actor, event, event_counter.count)
for text_ui in file_select_menu.text_item_list:
file_select_menu.add_callback(
text_ui.text_actor.get_actors()[0], event,
event_counter.count)
current_size = (600, 600)
show_manager = window.ShowManager(size=current_size,
title="DIPY File Select Menu")
show_manager.ren.add(file_select_menu)
if recording:
show_manager.record_events_to_file(recording_filename)
print(list(event_counter.events_counts.items()))
event_counter.save(expected_events_counts_filename)
else:
show_manager.play_events_from_file(recording_filename)
expected = EventCounter.load(expected_events_counts_filename)
event_counter.check_counts(expected)
def test_ui_image_container_2d(interactive=False):
fetch_viz_icons()
image_test = ui.ImageContainer2D(img_path=read_viz_icons(
fname='home3.png'))
image_test.center = (300, 300)
npt.assert_equal(image_test.size, (100, 100))
image_test.scale((2, 2))
npt.assert_equal(image_test.size, (200, 200))
current_size = (600, 600)
show_manager = window.ShowManager(size=current_size, title="DIPY Button")
show_manager.ren.add(image_test)
if interactive:
show_manager.start()
def take_snapshot(bundles, interact_with=False):
if interact_with:
showm = window.ShowManager(ren,
size=resolution,
reset_camera=False)
showm.start()
ren.camera_info()
snapshot_fname = "_".join(bundles) + ".png"
print("Saving {}".format(snapshot_fname))
window.snapshot(ren,
fname=snapshot_fname,
size=resolution,
offscreen=True,
order_transparent=False)
return snapshot_fname
def display(self):
ren = window.Renderer()
ren.add(self.volume_image)
ren.add(self.fod)
show_m = window.ShowManager(ren, size=(1200, 900))
show_m.initialize()
interactive = True
ren.zoom(1.5)
ren.reset_clipping_range()
if interactive:
show_m.render()
show_m.start()
path = self.patient_num + ".png"
window.record(ren, out_path=path, size=(1200, 900), reset_camera=False)
del show_m
def show_results(data,
streamlines,
vol,
affine,
world_coords=True,
opacity=0.6):
from dipy.viz import actor, window, widget
shape = data.shape
if not world_coords:
from dipy.tracking.streamline import transform_streamlines
streamlines = transform_streamlines(streamlines, np.linalg.inv(affine))
ren = window.Renderer()
if streamlines is not None:
stream_actor = actor.line(streamlines)
if not world_coords:
image_actor = actor.slicer(vol, affine=np.eye(4))
else:
image_actor = actor.slicer(vol, affine)
slicer_opacity = opacity #.6
image_actor.opacity(slicer_opacity)
if streamlines is not None:
ren.add(stream_actor)
ren.add(image_actor)
show_m = window.ShowManager(ren, size=(1200, 900))
show_m.initialize()
def change_slice(obj, event):
z = int(np.round(obj.get_value()))
image_actor.display_extent(0, shape[0] - 1, 0, shape[1] - 1, z, z)
slider = widget.slider(show_m.iren,
show_m.ren,
callback=change_slice,
min_value=0,
max_value=shape[2] - 1,
value=shape[2] / 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.))
global size
size = ren.GetSize()
def win_callback(obj, event):
global size
if size != obj.GetSize():
slider.place(ren)
size = obj.GetSize()
show_m.initialize()
show_m.add_window_callback(win_callback)
show_m.render()
show_m.start()
# ren.zoom(1.5)
# ren.reset_clipping_range()
# window.record(ren, out_path='bundles_and_a_slice.png', size=(1200, 900),
# reset_camera=False)
del show_m
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 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)
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)
ren.add(stream_actor)
ren.add(image_actor_z)
ren.add(image_actor_x)
ren.add(image_actor_y)
show_m = window.ShowManager(ren, size=(1200, 900))
# A Sphere widget
sphereWidget = vtk.vtkSphereWidget()
sphereWidget.SetRadius(5)
sphereWidget.SetInteractor(show_m.iren)
sphereWidget.SetRepresentationToSurface()
sphereWidget.On()
# Connect the event to a function
sphereWidget.AddObserver("InteractionEvent", sphereCallback)
show_m.initialize()
# create sliders to move the slices and change their opacity
line_slider_z = ui.LineSlider2D(min_value=0,
max_value=shape[2] - 1,
initial_value=shape[2] / 2,
text_template="{value:.0f}",
def plotAllSubjectLandmarks(subjlist,
fixedLandmarkDict,
curveLandmarkDict,
treatfixedascurve=False,
sphereradius=1,
group=[]):
#show landmarks for all subjects, uses different color for each subject
import vtk
from dipy.viz import window
import numpy as np
def markcurve(x, y, z, landnum, curve, color):
sphere = vtk.vtkSphereSource()
sphere.SetRadius(sphereradius)
res = 20
sphere.SetThetaResolution(res)
sphere.SetPhiResolution(res)
sphere.SetCenter(x, y, z)
mapper = vtk.vtkPolyDataMapper()
mapper.SetInputConnection(sphere.GetOutputPort())
marker = vtk.vtkActor()
marker.SetMapper(mapper)
renderer.AddActor(marker)
marker.GetProperty().SetColor(color)
#add line
if landnum > 0:
lineSource = vtk.vtkLineSource()
lineSource.SetPoint1(curve[landnum - 1])
lineSource.SetPoint2([x, y, z])
mapper = vtk.vtkPolyDataMapper()
mapper.SetInputConnection(lineSource.GetOutputPort())
lineActor = vtk.vtkActor()
lineActor.SetMapper(mapper)
lineActor.GetProperty().SetLineWidth(4)
lineActor.GetProperty().SetColor(color)
renderer.AddActor(lineActor)
show_m.iren.Render()
def markfixed(x, y, z, color):
sphere = vtk.vtkSphereSource()
sphere.SetRadius(sphereradius)
res = 20
sphere.SetThetaResolution(res)
sphere.SetPhiResolution(res)
sphere.SetCenter(x, y, z)
mapper = vtk.vtkPolyDataMapper()
mapper.SetInputConnection(sphere.GetOutputPort())
marker = vtk.vtkActor()
marker.SetMapper(mapper)
renderer.AddActor(marker)
marker.GetProperty().SetColor(color)
show_m.iren.Render()
renderer = window.Renderer()
show_m = window.ShowManager(renderer, size=(800, 800))
colorlist = []
if group:
ngroups = len(np.unique(group))
grpcolors = []
for i in range(ngroups):
grpcolors.append(list(np.random.choice(range(256), size=3) / 256.))
for i in range(len(group)):
colorlist.append(grpcolors[list(np.unique(group)).index(group[i])])
else:
for i in range(len(subjlist)):
colorlist.append(list(np.random.choice(range(256), size=3) / 256.))
for subj in range(len(subjlist)):
color = colorlist[subj]
if type(fixedLandmarkDict) is dict:
if treatfixedascurve:
for lnum in range(len(fixedLandmarkDict[subjlist[subj]])):
lm = fixedLandmarkDict[subjlist[subj]][lnum]
markcurve(lm[0], lm[1], lm[2], lnum,
fixedLandmarkDict[subjlist[subj]], color)
else:
for lnum in range(len(fixedLandmarkDict[subjlist[subj]])):
lm = fixedLandmarkDict[subjlist[subj]][lnum]
markfixed(lm[0], lm[1], lm[2], color)
if type(curveLandmarkDict) is dict:
for c in curveLandmarkDict[subjlist[subj]]:
for lnum in range(len(c)):
lm = c[lnum]
markcurve(lm[0], lm[1], lm[2], lnum, c, color)
show_m.initialize()
show_m.render()
show_m.start()
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)
def visualize_volume(volume,
x=None,
y=None,
z=None,
figure=None,
flip_axes=None,
opacity=0.6,
inline=True,
interact=False):
"""
Visualize a volume
Parameters
----------
volume : ndarray or str
3d volume to visualize.
figure : fury Scene object, optional
If provided, the visualization will be added to this Scene. Default:
Initialize a new Scene.
flip_axes : None
This parameter is to conform fury and plotly APIs.
opacity : float, optional
Initial opacity of slices.
Default: 0.6
interact : bool
Whether to provide an interactive VTK window for interaction.
Default: False
inline : bool
Whether to embed the visualization inline in a notebook. Only works
in the notebook context. Default: False.
Returns
-------
Fury Scene object
"""
volume = vut.load_volume(volume)
if figure is None:
figure = window.Scene()
shape = volume.shape
image_actor_z = actor.slicer(volume)
slicer_opacity = opacity
image_actor_z.opacity(slicer_opacity)
image_actor_x = image_actor_z.copy()
if x is None:
x = int(np.round(shape[0] / 2))
image_actor_x.display_extent(x, x, 0, shape[1] - 1, 0, shape[2] - 1)
image_actor_y = image_actor_z.copy()
if y is None:
y = int(np.round(shape[1] / 2))
image_actor_y.display_extent(0, shape[0] - 1, y, y, 0, shape[2] - 1)
figure.add(image_actor_z)
figure.add(image_actor_x)
figure.add(image_actor_y)
show_m = window.ShowManager(figure, size=(1200, 900))
show_m.initialize()
if interact:
line_slider_z = ui.LineSlider2D(min_value=0,
max_value=shape[2] - 1,
initial_value=shape[2] / 2,
text_template="{value:.0f}",
length=140)
line_slider_x = ui.LineSlider2D(min_value=0,
max_value=shape[0] - 1,
initial_value=shape[0] / 2,
text_template="{value:.0f}",
length=140)
line_slider_y = ui.LineSlider2D(min_value=0,
max_value=shape[1] - 1,
initial_value=shape[1] / 2,
text_template="{value:.0f}",
length=140)
opacity_slider = ui.LineSlider2D(min_value=0.0,
max_value=1.0,
initial_value=slicer_opacity,
length=140)
def change_slice_z(slider):
z = int(np.round(slider.value))
image_actor_z.display_extent(0, shape[0] - 1, 0, shape[1] - 1, z,
z)
def change_slice_x(slider):
x = int(np.round(slider.value))
image_actor_x.display_extent(x, x, 0, shape[1] - 1, 0,
shape[2] - 1)
def change_slice_y(slider):
y = int(np.round(slider.value))
image_actor_y.display_extent(0, shape[0] - 1, y, y, 0,
shape[2] - 1)
def change_opacity(slider):
slicer_opacity = slider.value
image_actor_z.opacity(slicer_opacity)
image_actor_x.opacity(slicer_opacity)
image_actor_y.opacity(slicer_opacity)
line_slider_z.on_change = change_slice_z
line_slider_x.on_change = change_slice_x
line_slider_y.on_change = change_slice_y
opacity_slider.on_change = change_opacity
def build_label(text):
label = ui.TextBlock2D()
label.message = text
label.font_size = 18
label.font_family = 'Arial'
label.justification = 'left'
label.bold = False
label.italic = False
label.shadow = False
label.background = (0, 0, 0)
label.color = (1, 1, 1)
return label
line_slider_label_z = build_label(text="Z Slice")
line_slider_label_x = build_label(text="X Slice")
line_slider_label_y = build_label(text="Y Slice")
opacity_slider_label = build_label(text="Opacity")
panel = ui.Panel2D(size=(300, 200),
color=(1, 1, 1),
opacity=0.1,
align="right")
panel.center = (1030, 120)
panel.add_element(line_slider_label_x, (0.1, 0.75))
panel.add_element(line_slider_x, (0.38, 0.75))
panel.add_element(line_slider_label_y, (0.1, 0.55))
panel.add_element(line_slider_y, (0.38, 0.55))
panel.add_element(line_slider_label_z, (0.1, 0.35))
panel.add_element(line_slider_z, (0.38, 0.35))
panel.add_element(opacity_slider_label, (0.1, 0.15))
panel.add_element(opacity_slider, (0.38, 0.15))
show_m.scene.add(panel)
global size
size = figure.GetSize()
def win_callback(obj, event):
global size
if size != obj.GetSize():
size_old = size
size = obj.GetSize()
size_change = [size[0] - size_old[0], 0]
panel.re_align(size_change)
show_m.initialize()
figure.zoom(1.5)
figure.reset_clipping_range()
if interact:
show_m.add_window_callback(win_callback)
show_m.render()
show_m.start()
return _inline_interact(figure, inline, interact)
def test_ui_listbox_2d(recording=False):
filename = "test_ui_listbox_2d"
recording_filename = pjoin(DATA_DIR, filename + ".log.gz")
expected_events_counts_filename = pjoin(DATA_DIR, filename + ".pkl")
# Values that will be displayed by the listbox.
values = list(range(1, 42 + 1))
listbox = ui.ListBox2D(values=values,
size=(500, 500),
multiselection=True,
reverse_scrolling=False)
listbox.center = (300, 300)
# We will collect the sequence of values that have been selected.
selected_values = []
def _on_change():
selected_values.append(list(listbox.selected))
# Set up a callback when selection changes.
listbox.on_change = _on_change
# Assign the counter callback to every possible event.
event_counter = EventCounter()
event_counter.monitor(listbox)
# Create a show manager and record/play events.
show_manager = window.ShowManager(size=(600, 600), title="DIPY ListBox")
show_manager.ren.add(listbox)
if recording:
# Record the following events:
# 1. Click on 1
# 2. Ctrl + click on 2,
# 3. Ctrl + click on 2.
# 4. Click on down arrow (4 times).
# 5. Click on 21.
# 6. Click on up arrow (5 times).
# 7. Click on 1
# 8. Use mouse wheel to scroll down.
# 9. Shift + click on 42.
# 10. Use mouse wheel to scroll back up.
show_manager.record_events_to_file(recording_filename)
print(list(event_counter.events_counts.items()))
event_counter.save(expected_events_counts_filename)
else:
show_manager.play_events_from_file(recording_filename)
expected = EventCounter.load(expected_events_counts_filename)
event_counter.check_counts(expected)
# Check if the right values were selected.
expected = [[1], [1, 2], [1], [21], [1], values]
assert len(selected_values) == len(expected)
assert_arrays_equal(selected_values, expected)
# Test without multiselection enabled.
listbox.multiselection = False
del selected_values[:] # Clear the list.
show_manager.play_events_from_file(recording_filename)
# Check if the right values were selected.
expected = [[1], [2], [2], [21], [1], [42]]
assert len(selected_values) == len(expected)
assert_arrays_equal(selected_values, expected)
""" Image Container ====== """ img = ui.ImageContainer2D(img_path=read_viz_icons(fname='home3.png')) """ Adding Elements to the ShowManager ================================== Once all elements have been initialised, they have to be added to the show manager in the following manner. """ current_size = (600, 600) show_manager = window.ShowManager(size=current_size, title="DIPY UI Example") show_manager.ren.add(cube_actor_1) show_manager.ren.add(cube_actor_2) show_manager.ren.add(panel) show_manager.ren.add(text) show_manager.ren.add(line_slider) show_manager.ren.add(ring_slider) show_manager.ren.add(listbox) show_manager.ren.add(img) show_manager.ren.reset_camera() show_manager.ren.reset_clipping_range() show_manager.ren.azimuth(30) # Uncomment this to start the visualisation # show_manager.start()
def change_axis_length(i_ren, obj, slider):
# A function to change the semi-major axis length
# using the slider callback
global a, show_manager, sphere_actor
a = slider.value
print(a)
show_manager.ren.rm(sphere_actor)
sphere_actor = vertices_triangles(a, 1., 1.)
show_manager.ren.add(sphere_actor)
show_manager.render()
#Relevant callbacks
line_slider = ui.LineSlider2D(initial_value=1, min_value=0, max_value=1)
line_slider.add_callback(line_slider.slider_disk, "MouseMoveEvent",
change_axis_length)
line_slider.add_callback(line_slider.slider_line, "LeftButtonPressEvent",
change_axis_length)
global show_manager
# renderer and scene
show_manager = window.ShowManager(size=(600, 600), title="Ellipsoid")
show_manager.initialize()
show_manager.ren.add(sphere_actor)
show_manager.ren.add(line_slider)
show_manager.start()
import numpy as np
from dipy.viz import window, actor, ui
import itertools
xyz = 10 * np.random.rand(100, 3)
colors = np.random.rand(100, 4)
radii = np.random.rand(100) + 0.5
renderer = window.Renderer()
sphere_actor = actor.sphere(centers=xyz, colors=colors, radii=radii)
renderer.add(sphere_actor)
showm = window.ShowManager(renderer,
size=(900, 768),
reset_camera=False,
order_transparent=True)
showm.initialize()
tb = ui.TextBlock2D(bold=True)
# use itertools to avoid global variables
counter = itertools.count()
def timer_callback(obj, event):
cnt = next(counter)
tb.message = "Let's count up to 100 and exit :" + str(cnt)
renderer.azimuth(0.05 * cnt)
sphere_actor.GetProperty().SetOpacity(cnt / 100.)
def test_text_block_2d_justification():
window_size = (700, 700)
show_manager = window.ShowManager(size=window_size)
# To help visualize the text positions.
grid_size = (500, 500)
bottom, middle, top = 50, 300, 550
left, center, right = 50, 300, 550
line_color = (1, 0, 0)
grid_top = (center, top), (grid_size[0], 1)
grid_bottom = (center, bottom), (grid_size[0], 1)
grid_left = (left, middle), (1, grid_size[1])
grid_right = (right, middle), (1, grid_size[1])
grid_middle = (center, middle), (grid_size[0], 1)
grid_center = (center, middle), (1, grid_size[1])
grid_specs = [
grid_top, grid_bottom, grid_left, grid_right, grid_middle, grid_center
]
for spec in grid_specs:
line = ui.Rectangle2D(size=spec[1], color=line_color)
line.center = spec[0]
show_manager.ren.add(line)
font_size = 60
bg_color = (1, 1, 1)
texts = []
texts += [
ui.TextBlock2D("HH",
position=(left, top),
font_size=font_size,
color=(1, 0, 0),
bg_color=bg_color,
justification="left",
vertical_justification="top")
]
texts += [
ui.TextBlock2D("HH",
position=(center, top),
font_size=font_size,
color=(0, 1, 0),
bg_color=bg_color,
justification="center",
vertical_justification="top")
]
texts += [
ui.TextBlock2D("HH",
position=(right, top),
font_size=font_size,
color=(0, 0, 1),
bg_color=bg_color,
justification="right",
vertical_justification="top")
]
texts += [
ui.TextBlock2D("HH",
position=(left, middle),
font_size=font_size,
color=(1, 1, 0),
bg_color=bg_color,
justification="left",
vertical_justification="middle")
]
texts += [
ui.TextBlock2D("HH",
position=(center, middle),
font_size=font_size,
color=(0, 1, 1),
bg_color=bg_color,
justification="center",
vertical_justification="middle")
]
texts += [
ui.TextBlock2D("HH",
position=(right, middle),
font_size=font_size,
color=(1, 0, 1),
bg_color=bg_color,
justification="right",
vertical_justification="middle")
]
texts += [
ui.TextBlock2D("HH",
position=(left, bottom),
font_size=font_size,
color=(0.5, 0, 1),
bg_color=bg_color,
justification="left",
vertical_justification="bottom")
]
texts += [
ui.TextBlock2D("HH",
position=(center, bottom),
font_size=font_size,
color=(1, 0.5, 0),
bg_color=bg_color,
justification="center",
vertical_justification="bottom")
]
texts += [
ui.TextBlock2D("HH",
position=(right, bottom),
font_size=font_size,
color=(0, 1, 0.5),
bg_color=bg_color,
justification="right",
vertical_justification="bottom")
]
show_manager.ren.add(*texts)
# Uncomment this to start the visualisation
# show_manager.start()
arr = window.snapshot(show_manager.ren, size=window_size, offscreen=True)
if vtk.vtkVersion.GetVTKVersion() == "6.0.0":
expected = np.load(pjoin(DATA_DIR, "test_ui_text_block.npz"))
npt.assert_array_almost_equal(arr, expected["arr_0"])
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_ui_button_panel(recording=False):
filename = "test_ui_button_panel"
recording_filename = pjoin(DATA_DIR, filename + ".log.gz")
expected_events_counts_filename = pjoin(DATA_DIR, filename + ".pkl")
# Rectangle
rectangle_test = ui.Rectangle2D(size=(10, 10))
another_rectangle_test = ui.Rectangle2D(size=(1, 1))
# Button
fetch_viz_icons()
icon_files = []
icon_files.append(('stop', read_viz_icons(fname='stop2.png')))
icon_files.append(('play', read_viz_icons(fname='play3.png')))
button_test = ui.Button2D(icon_fnames=icon_files)
button_test.center = (20, 20)
def make_invisible(i_ren, obj, button):
# i_ren: CustomInteractorStyle
# obj: vtkActor picked
# button: Button2D
button.set_visibility(False)
i_ren.force_render()
i_ren.event.abort()
def modify_button_callback(i_ren, obj, button):
# i_ren: CustomInteractorStyle
# obj: vtkActor picked
# button: Button2D
button.next_icon()
i_ren.force_render()
button_test.on_right_mouse_button_pressed = make_invisible
button_test.on_left_mouse_button_pressed = modify_button_callback
button_test.scale((2, 2))
button_color = button_test.color
button_test.color = button_color
# TextBlock
text_block_test = ui.TextBlock2D()
text_block_test.message = 'TextBlock'
text_block_test.color = (0, 0, 0)
# Panel
panel = ui.Panel2D(size=(300, 150),
position=(290, 15),
color=(1, 1, 1),
align="right")
panel.add_element(rectangle_test, (290, 135))
panel.add_element(button_test, (0.1, 0.1))
panel.add_element(text_block_test, (0.7, 0.7))
npt.assert_raises(ValueError, panel.add_element, another_rectangle_test,
(10., 0.5))
npt.assert_raises(ValueError, panel.add_element, another_rectangle_test,
(-0.5, 0.5))
# Assign the counter callback to every possible event.
event_counter = EventCounter()
event_counter.monitor(button_test)
event_counter.monitor(panel.background)
current_size = (600, 600)
show_manager = window.ShowManager(size=current_size, title="DIPY Button")
show_manager.ren.add(panel)
if recording:
show_manager.record_events_to_file(recording_filename)
print(list(event_counter.events_counts.items()))
event_counter.save(expected_events_counts_filename)
else:
show_manager.play_events_from_file(recording_filename)
expected = EventCounter.load(expected_events_counts_filename)
event_counter.check_counts(expected)
def test_wrong_interactor_style():
panel = ui.Panel2D(size=(300, 150))
dummy_renderer = window.Renderer()
dummy_show_manager = window.ShowManager(dummy_renderer,
interactor_style='trackball')
npt.assert_raises(TypeError, panel.add_to_renderer, dummy_renderer)