def test_streamtube_and_line_actors():
scene = window.Scene()
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)
scene.add(c)
c = actor.line(lines, colors, spline_subdiv=5, linewidth=3)
scene.add(c)
# create streamtubes of the same lines and shift them a bit
c2 = actor.streamtube(lines, colors, linewidth=.1)
c2.SetPosition(2, 0, 0)
scene.add(c2)
arr = window.snapshot(scene)
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)
scene.add(c2)
arr = window.snapshot(scene)
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])
c3 = actor.line(lines, colors, depth_cue=True, fake_tube=True)
VTK_9_PLUS = window.vtk.vtkVersion.GetVTKMajorVersion() >= 9
shader_obj = c3.GetShaderProperty() if VTK_9_PLUS else c3.GetMapper()
mapper_code = shader_obj.GetGeometryShaderCode()
file_code = shaders.load("line.geom")
npt.assert_equal(mapper_code, file_code)
npt.assert_equal(c3.GetProperty().GetRenderLinesAsTubes(), True)
def test_order_transparent():
scene = window.Scene()
lines = [
np.array([[1, 0, 1.], [-1, 0, 1.]]),
np.array([[1, 0, -1.], [-1, 0, -1.]])
]
colors = np.array([[1., 0., 0.], [0., 1., 0.]])
stream_actor = actor.streamtube(lines, colors, linewidth=0.3, opacity=0.5)
scene.add(stream_actor)
scene.reset_camera()
scene.reset_clipping_range()
arr = window.snapshot(scene,
fname='green_front.png',
offscreen=True,
order_transparent=False)
green_no_ot = arr[150, 150, 1]
arr = window.snapshot(scene,
fname='red_front.png',
offscreen=True,
order_transparent=True)
# when order transparency is True green should be weaker
green_ot = arr[150, 150, 1]
npt.assert_equal(green_no_ot > green_ot, True)
def bounding_box(molecule, colors=(1, 1, 1), linewidth=0.3):
"""Create a bounding box for a molecule.
Parameters
----------
molecule : Molecule
The molecule around which the bounding box is to be created.
colors : tuple (3,) or ndarray of shape (3,), optional
Color of the bounding box. Default: (1, 1, 1)
linewidth: float, optional
Thickness of tubes used to compose bounding box. Default: 0.3
Returns
-------
bbox_actor : vtkActor
Actor created to serve as a bounding box for a given molecule.
"""
pts = numpy_to_vtk_points(get_all_atomic_positions(molecule))
min_x, max_x, min_y, max_y, min_z, max_z = pts.GetBounds()
lines = np.array([[[min_x, min_y, min_z], [min_x, min_y, max_z]],
[[min_x, max_y, min_z], [min_x, max_y, max_z]],
[[max_x, min_y, min_z], [max_x, min_y, max_z]],
[[max_x, max_y, min_z], [max_x, max_y, max_z]],
[[min_x, min_y, min_z], [max_x, min_y, min_z]],
[[min_x, max_y, min_z], [max_x, max_y, min_z]],
[[min_x, max_y, max_z], [max_x, max_y, max_z]],
[[min_x, min_y, max_z], [max_x, min_y, max_z]],
[[min_x, min_y, min_z], [min_x, max_y, min_z]],
[[max_x, min_y, min_z], [max_x, max_y, min_z]],
[[min_x, min_y, max_z], [min_x, max_y, max_z]],
[[max_x, min_y, max_z], [max_x, max_y, max_z]]])
return streamtube(lines, colors=colors, linewidth=linewidth)
def test_stereo():
scene = window.Scene()
lines = [np.array([[-1, 0, 0.], [1, 0, 0.]]),
np.array([[-1, 1, 0.], [1, 1, 0.]])]
colors = np.array([[1., 0., 0.], [0., 1., 0.]])
stream_actor = actor.streamtube(lines, colors, linewidth=0.3, opacity=0.5)
scene.add(stream_actor)
# green in front
scene.elevation(90)
scene.camera().OrthogonalizeViewUp()
scene.reset_clipping_range()
scene.reset_camera()
mono = window.snapshot(scene, fname='stereo_off.png', offscreen=True,
size=(300, 300), order_transparent=True,
stereo='off')
with npt.assert_warns(UserWarning):
stereo = window.snapshot(scene, fname='stereo_horizontal.png',
offscreen=True, size=(300, 300),
order_transparent=True, stereo='On')
# mono render should have values in the center
# horizontal split stereo render should be empty in the center
npt.assert_raises(AssertionError, npt.assert_array_equal,
mono[150, 150], [0, 0, 0])
npt.assert_array_equal(stereo[150, 150], [0, 0, 0])
def test_order_transparent():
scene = window.Scene()
lines = [
np.array([[-1, 0, 0.], [1, 0, 0.]]),
np.array([[-1, 1, 0.], [1, 1, 0.]])
]
colors = np.array([[1., 0., 0.], [0., 1., 0.]])
stream_actor = actor.streamtube(lines, colors, linewidth=0.3, opacity=0.5)
scene.add(stream_actor)
scene.reset_camera()
# green in front
scene.elevation(90)
scene.camera().OrthogonalizeViewUp()
scene.reset_clipping_range()
scene.reset_camera()
not_xvfb = os.environ.get("TEST_WITH_XVFB", False)
if not_xvfb:
arr = window.snapshot(scene,
fname='green_front.png',
offscreen=True,
order_transparent=False)
else:
arr = window.snapshot(scene,
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
scene.elevation(-180)
scene.camera().OrthogonalizeViewUp()
scene.reset_clipping_range()
if not_xvfb:
arr = window.snapshot(scene,
fname='red_front.png',
offscreen=True,
order_transparent=True)
else:
arr = window.snapshot(scene,
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_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)
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(final_streamlines, template_path, fname):
import nibabel as nib
from fury import actor, window
renderer = window.Renderer()
template_img_data = nib.load(template_path).get_data().astype('bool')
template_actor = actor.contour_from_roi(template_img_data,
color=(50, 50, 50), opacity=0.05)
renderer.add(template_actor)
lines_actor = actor.streamtube(final_streamlines, window.colors.orange,
linewidth=0.3)
renderer.add(lines_actor)
window.record(renderer, n_frames=1, out_path=fname, size=(900, 900))
return
def show_template_bundles(final_streamlines, template_path, fname):
"""Displayes the template bundles
Parameters
----------
final_streamlines : list
Generated streamlines
template_path : str
Path to reference FA nii.gz file
fname : str
Path of the output file (saved as )
"""
renderer = window.Renderer()
template_img_data = nib.load(template_path).get_data().astype("bool")
template_actor = actor.contour_from_roi(
template_img_data, color=(50, 50, 50), opacity=0.05
)
renderer.add(template_actor)
lines_actor = actor.streamtube(
final_streamlines, window.colors.orange, linewidth=0.3
)
renderer.add(lines_actor)
window.record(renderer, n_frames=1, out_path=fname, size=(900, 900))
##############################################################################
# With box, streamtube and sphere actors, we can create the box, the
# edges of the box and the spheres respectively.
scene = window.Scene()
box_centers = np.array([[0, 0, 0]])
box_directions = np.array([[0, 1, 0]])
box_colors = np.array([[1, 1, 1, 0.2]])
box_actor = actor.box(box_centers,
box_directions,
box_colors,
scales=(box_lx, box_ly, box_lz))
scene.add(box_actor)
lines = box_edges(box_lx, box_ly, box_lz)
line_actor = actor.streamtube(lines, colors=(1, 0.5, 0), linewidth=0.1)
scene.add(line_actor)
sphere_actor = actor.sphere(centers=xyz, colors=colors, radii=radii)
scene.add(sphere_actor)
showm = window.ShowManager(scene,
size=(900, 768),
reset_camera=True,
order_transparent=True)
showm.initialize()
tb = ui.TextBlock2D(bold=True)
scene.zoom(0.8)
scene.azimuth(30)
# use itertools to avoid global variables
def test_frame_rate_and_anti_aliasing():
"""Testing frame rate with/out anti-aliasing"""
length_ = 200
multi_samples = 32
max_peels = 8
st_x = np.arange(length_)
st_y = np.sin(np.arange(length_))
st_z = np.zeros(st_x.shape)
st = np.zeros((length_, 3))
st[:, 0] = st_x
st[:, 1] = st_y
st[:, 2] = st_z
all_st = []
all_st.append(st)
for i in range(1000):
all_st.append(st + i * np.array([0., .5, 0]))
# st_actor = actor.line(all_st, linewidth=1)
# TODO: textblock disappears when lod=True
st_actor = actor.streamtube(all_st, linewidth=0.1, lod=False)
scene = window.Scene()
scene.background((1, 1., 1))
# quick game style antialiasing
scene.fxaa_on()
scene.fxaa_off()
# the good staff is later with multi-sampling
tb = ui.TextBlock2D(font_size=40, color=(1, 0.5, 0))
panel = ui.Panel2D(position=(400, 400), size=(400, 400))
panel.add_element(tb, (0.2, 0.5))
counter = itertools.count()
showm = window.ShowManager(scene,
size=(1980, 1080), reset_camera=False,
order_transparent=True,
multi_samples=multi_samples,
max_peels=max_peels,
occlusion_ratio=0.0)
showm.initialize()
scene.add(panel)
scene.add(st_actor)
scene.reset_camera_tight()
scene.zoom(5)
class FrameRateHolder(object):
fpss = []
frh = FrameRateHolder()
def timer_callback(_obj, _event):
cnt = next(counter)
if cnt % 1 == 0:
fps = np.round(scene.frame_rate, 0)
frh.fpss.append(fps)
msg = "FPS " + str(fps) + ' ' + str(cnt)
tb.message = msg
showm.render()
if cnt > 10:
showm.exit()
# Run every 200 milliseconds
showm.add_timer_callback(True, 200, timer_callback)
showm.start()
arr = window.snapshot(scene, size=(1980, 1080),
offscreen=True,
order_transparent=True,
multi_samples=multi_samples,
max_peels=max_peels,
occlusion_ratio=0.0)
assert_greater(np.sum(arr), 0)
# TODO: check why in osx we have issues in Azure
if not skip_osx:
assert_greater(np.median(frh.fpss), 0)
frh.fpss = []
counter = itertools.count()
multi_samples = 0
showm = window.ShowManager(scene,
size=(1980, 1080), reset_camera=False,
order_transparent=True,
multi_samples=multi_samples,
max_peels=max_peels,
occlusion_ratio=0.0)
showm.initialize()
showm.add_timer_callback(True, 200, timer_callback)
showm.start()
arr2 = window.snapshot(scene, size=(1980, 1080),
offscreen=True,
order_transparent=True,
multi_samples=multi_samples,
max_peels=max_peels,
occlusion_ratio=0.0)
assert_greater(np.sum(arr2), 0)
if not skip_osx:
assert_greater(np.median(frh.fpss), 0)
def test_bundle_maps():
scene = window.Scene()
bundle = simulated_bundle(no_streamlines=10, waves=False)
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)
scene.add(line)
scene.add(actor.scalar_bar(lut, ' '))
report = window.analyze_scene(scene)
npt.assert_almost_equal(report.actors, 1)
# window.show(scene)
scene.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)
scene.add(line)
# window.show(scene)
report = window.analyze_scene(scene)
npt.assert_equal(report.actors_classnames[0], 'vtkLODActor')
scene.clear()
colors = np.random.rand(nb_points, 3)
# values[:nb_points/2] = 0
line = actor.line(bundle, colors, linewidth=2)
scene.add(line)
# window.show(scene)
report = window.analyze_scene(scene)
npt.assert_equal(report.actors_classnames[0], 'vtkLODActor')
# window.show(scene)
arr = window.snapshot(scene)
report2 = window.analyze_snapshot(arr)
npt.assert_equal(report2.objects, 1)
# try other input options for colors
scene.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)
as model bundles
"""
model_af_l_file, model_cst_l_file = get_two_hcp842_bundles()
sft_af_l = load_trk(model_af_l_file, "same", bbox_valid_check=False)
model_af_l = sft_af_l.streamlines
"""
let's visualize Arcuate Fasiculus Left (AF_L) bundle before assignment maps
"""
interactive = False
scene = window.Scene()
scene.SetBackground(1, 1, 1)
scene.add(actor.streamtube(model_af_l))
scene.set_camera(focal_point=(-18.17281532, -19.55606842, 6.92485857),
position=(-360.11, -340.46, -40.44),
view_up=(-0.03, 0.028, 0.89))
window.record(scene,
out_path='af_l_before_assignment_maps.png',
size=(600, 600))
if interactive:
window.show(scene)
"""
.. figure:: af_l_before_assignment_maps.png
:align: center
AF_L before assignment maps
"""
"""
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)
scene.add(stream_actor9)
if interactive:
window.show(scene, size=(600, 600), reset_camera=False)
window.record(scene, out_path='bundle9.png', size=(600, 600))
###############################################################################
# Render streamlines as tubes
# ============================================================
#
# For yet more realism, we can use ``streamtube``. Note that this actor
# generates much more geometry than ``line``, so it is more computationally
# expensive. For large datasets, it may be better to approximate tubes using
# the methods described above.
scene.clear()
stream_actor10 = actor.streamtube(bundle_native, linewidth=0.5)
scene.add(stream_actor10)
if interactive:
window.show(scene, size=(600, 600), reset_camera=False)
window.record(scene, out_path='bundle10.png', size=(600, 600))
###############################################################################
# In summary, we showed that there are many useful ways for visualizing maps
# on bundles.
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)
report = window.analyze_renderer(renderer)
# import pylab as plt
# plt.imshow(report.labels, origin='lower')
# plt.show()
npt.assert_equal(report.actors, 1)
report = window.analyze_renderer(renderer)
npt.assert_equal(report.actors, 1)
def main():
parser = _build_arg_parser()
args = parser.parse_args()
# The number of labels maps must be equal to the number of bundles
tmp = args.in_bundles + args.in_labels
args.in_labels = args.in_bundles[(len(tmp) // 2):] + args.in_labels
args.in_bundles = args.in_bundles[0:len(tmp) // 2]
assert_inputs_exist(parser, args.in_bundles + args.in_labels)
assert_output_dirs_exist_and_empty(parser,
args, [],
optional=args.save_rendering)
stats = {}
num_digits_labels = 3
scene = window.Scene()
scene.background(tuple(map(int, args.background)))
for i, filename in enumerate(args.in_bundles):
sft = load_tractogram_with_reference(parser, args, filename)
sft.to_vox()
sft.to_corner()
img_labels = nib.load(args.in_labels[i])
# same subject: same header or coregistered subjects: same header
if not is_header_compatible(sft, args.in_bundles[0]) \
or not is_header_compatible(img_labels, args.in_bundles[0]):
parser.error('All headers must be identical.')
data_labels = img_labels.get_fdata()
bundle_name, _ = os.path.splitext(os.path.basename(filename))
unique_labels = np.unique(data_labels)[1:].astype(int)
# Empty bundle should at least return a json
if not len(sft):
tmp_dict = {}
for label in unique_labels:
tmp_dict['{}'.format(label).zfill(num_digits_labels)] \
= {'mean': 0.0, 'std': 0.0}
stats[bundle_name] = {'diameter': tmp_dict}
continue
counter = 0
labels_dict = {label: ([], []) for label in unique_labels}
pts_labels = map_coordinates(data_labels,
sft.streamlines._data.T - 0.5,
order=0)
# For each label, all positions and directions are needed to get
# a tube estimation per label.
for streamline in sft.streamlines:
direction = np.gradient(streamline, axis=0).tolist()
curr_labels = pts_labels[counter:counter +
len(streamline)].tolist()
for i, label in enumerate(curr_labels):
if label > 0:
labels_dict[label][0].append(streamline[i])
labels_dict[label][1].append(direction[i])
counter += len(streamline)
centroid = np.zeros((len(unique_labels), 3))
radius = np.zeros((len(unique_labels), 1))
error = np.zeros((len(unique_labels), 1))
for key in unique_labels:
key = int(key)
c, d, e = fit_circle_in_space(labels_dict[key][0],
labels_dict[key][1],
args.fitting_func)
centroid[key - 1], radius[key - 1], error[key - 1] = c, d, e
# Spatial smoothing to avoid degenerate estimation
centroid_smooth = gaussian_filter(centroid,
sigma=[1, 0],
mode='nearest')
centroid_smooth[::len(centroid) - 1] = centroid[::len(centroid) - 1]
radius = gaussian_filter(radius, sigma=1, mode='nearest')
error = gaussian_filter(error, sigma=1, mode='nearest')
tmp_dict = {}
for label in unique_labels:
tmp_dict['{}'.format(label).zfill(num_digits_labels)] \
= {'mean': float(radius[label-1])*2,
'std': float(error[label-1])}
stats[bundle_name] = {'diameter': tmp_dict}
if args.show_rendering or args.save_rendering:
tube_actor = create_tube_with_radii(
centroid_smooth,
radius,
error,
wireframe=args.wireframe,
error_coloring=args.error_coloring)
scene.add(tube_actor)
cmap = plt.get_cmap('jet')
coloring = cmap(pts_labels / np.max(pts_labels))[:, 0:3]
streamlines_actor = actor.streamtube(sft.streamlines,
linewidth=args.width,
opacity=args.opacity,
colors=coloring)
scene.add(streamlines_actor)
slice_actor = actor.slicer(data_labels, np.eye(4))
slice_actor.opacity(0.0)
scene.add(slice_actor)
# If there's actually streamlines to display
if args.show_rendering:
showm = window.ShowManager(scene, reset_camera=True)
showm.initialize()
showm.start()
elif args.save_rendering:
scene.reset_camera()
snapshot(scene,
os.path.join(args.save_rendering, 'superior.png'),
size=(1920, 1080),
offscreen=True)
scene.pitch(180)
scene.reset_camera()
snapshot(scene,
os.path.join(args.save_rendering, 'inferior.png'),
size=(1920, 1080),
offscreen=True)
scene.pitch(90)
scene.set_camera(view_up=(0, 0, 1))
scene.reset_camera()
snapshot(scene,
os.path.join(args.save_rendering, 'posterior.png'),
size=(1920, 1080),
offscreen=True)
scene.pitch(180)
scene.set_camera(view_up=(0, 0, 1))
scene.reset_camera()
snapshot(scene,
os.path.join(args.save_rendering, 'anterior.png'),
size=(1920, 1080),
offscreen=True)
scene.yaw(90)
scene.reset_camera()
snapshot(scene,
os.path.join(args.save_rendering, 'right.png'),
size=(1920, 1080),
offscreen=True)
scene.yaw(180)
scene.reset_camera()
snapshot(scene,
os.path.join(args.save_rendering, 'left.png'),
size=(1920, 1080),
offscreen=True)
print(json.dumps(stats, indent=args.indent, sort_keys=args.sort_keys))
def screenshot_tracking(tracking, t1, directory="."):
"""
Compute 3 view screenshot with streamlines on T1.
Parameters
----------
tracking : string
tractogram filename.
t1 : string
t1 filename.
directory : string
Directory to save the mosaic.
Returns
-------
name : string
Path of the mosaic
"""
tractogram = nib.streamlines.load(tracking, True).tractogram
t1 = nib.load(t1)
t1_data = t1.get_data()
slice_name = ['sagittal', 'coronal', 'axial']
img_center = [(int(t1_data.shape[0] / 2) + 5, None, None),
(None, int(t1_data.shape[1] / 2), None),
(None, None, int(t1_data.shape[2] / 2))]
center = [(330, 90, 60), (70, 330, 60), (70, 90, 400)]
viewup = [(0, 0, -1), (0, 0, -1), (0, -1, 0)]
size = (1920, 1080)
image = np.array([])
for i, _axis in enumerate(slice_name):
streamlines = []
it = 0
slice_idx = img_center[i][i]
for streamline in tractogram:
if it > 10000:
break
stream = streamline.streamline
if slice_idx in np.array(stream, dtype=int)[:, i]:
it += 1
idx = np.where(np.array(stream, dtype=int)[:, i] == \
slice_idx)[0][0]
lower = idx - 2
if lower < 0:
lower = 0
upper = idx + 2
if upper > len(stream) - 1:
upper = len(stream) - 1
streamlines.append(stream[lower:upper])
ren = window.Renderer()
streamline_actor = actor.line(streamlines, linewidth=0.2)
ren.add(streamline_actor)
min_val = np.min(t1_data[t1_data > 0])
max_val = np.percentile(t1_data[t1_data > 0], 99)
t1_color = np.float32(t1_data - min_val) \
/ np.float32(max_val - min_val) * 255.0
slice_actor = actor.slicer(t1_color, opacity=0.8, value_range=(0, 255),
interpolation='nearest')
ren.add(slice_actor)
slice_actor.display(img_center[i][0], img_center[i][1],
img_center[i][2])
camera = ren.GetActiveCamera()
camera.SetViewUp(viewup[i])
center_cam = streamline_actor.GetCenter()
camera.SetPosition(center[i])
camera.SetFocalPoint((center_cam))
img2 = renderer_to_arr(ren, size)
if image.size == 0:
image = img2
else:
image = np.hstack((image, img2))
streamlines = []
it = 0
for streamline in tractogram:
if it > 10000:
break
it += 1
streamlines.append(streamline.streamline)
ren = window.Renderer()
streamline_actor = actor.streamtube(streamlines, linewidth=0.2)
ren.add(streamline_actor)
camera = ren.GetActiveCamera()
camera.SetViewUp(0, 0, -1)
center = streamline_actor.GetCenter()
camera.SetPosition(center[0], 350, center[2])
camera.SetFocalPoint(center)
img2 = renderer_to_arr(ren, (3 * 1920, 1920))
image = np.vstack((image, img2))
imgs_comb = Image.fromarray(image)
imgs_comb = imgs_comb.resize((3 * 1920, 1920 + 1080))
image_name = os.path.basename(str(tracking)).split(".")[0]
name = os.path.join(directory, image_name + '.png')
imgs_comb.save(name)
return name
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)
scene = window.Scene()
# 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(scene,
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)
scene.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])
scene.add(tube1)
scene.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_manifest_standard(interactive=False):
scene = window.Scene() # Setup scene
# Setup surface
surface_actor = _generate_surface()
material.manifest_standard(surface_actor, ambient_level=.3,
diffuse_level=.25)
scene.add(surface_actor)
arr = window.snapshot(scene)
report = window.analyze_snapshot(arr)
npt.assert_equal(report.objects, 1)
scene.clear() # Reset scene
# Contour from roi setup
data = np.zeros((50, 50, 50))
data[20:30, 25, 25] = 1.
data[25, 20:30, 25] = 1.
affine = np.eye(4)
surface = actor.contour_from_roi(data, affine, color=np.array([1, 0, 1]))
material.manifest_standard(surface_actor, ambient_level=.3,
diffuse_level=.25)
scene.add(surface)
scene.reset_camera()
scene.reset_clipping_range()
arr = window.snapshot(scene)
report = window.analyze_snapshot(arr)
npt.assert_equal(report.objects, 1)
scene.clear() # Reset scene
# Contour from label setup
data = np.zeros((50, 50, 50))
data[5:15, 1:10, 25] = 1.
data[25:35, 1:10, 25] = 2.
data[40:49, 1:10, 25] = 3.
color = np.array([[255, 0, 0],
[0, 255, 0],
[0, 0, 255]])
surface = actor.contour_from_label(data, color=color)
material.manifest_standard(surface_actor, ambient_level=.3,
diffuse_level=.25)
scene.add(surface)
scene.reset_camera()
scene.reset_clipping_range()
arr = window.snapshot(scene)
report = window.analyze_snapshot(arr)
npt.assert_equal(report.objects, 3)
scene.clear() # Reset scene
# Streamtube setup
data1 = np.array([[0, 0, 0], [1, 1, 1], [2, 2, 2.]])
data2 = data1 + np.array([0.5, 0., 0.])
data = [data1, data2]
colors = np.array([[1, 0, 0], [0, 0, 1.]])
tubes = actor.streamtube(data, colors, linewidth=.1)
material.manifest_standard(surface_actor, ambient_level=.3,
diffuse_level=.25)
scene.add(tubes)
scene.reset_camera()
scene.reset_clipping_range()
arr = window.snapshot(scene)
report = window.analyze_snapshot(arr)
npt.assert_equal(report.objects, 2)
scene.clear() # Reset scene
# ODF slicer setup
if have_dipy:
from dipy.data import get_sphere
from tempfile import mkstemp
sphere = get_sphere('symmetric362')
shape = (11, 11, 11, sphere.vertices.shape[0])
fid, fname = mkstemp(suffix='_odf_slicer.mmap')
odfs = np.memmap(fname, dtype=np.float64, mode='w+', shape=shape)
odfs[:] = 1
affine = np.eye(4)
mask = np.ones(odfs.shape[:3])
mask[:4, :4, :4] = 0
odfs[..., 0] = 1
odf_actor = actor.odf_slicer(odfs, affine, mask=mask, sphere=sphere,
scale=.25, colormap='blues')
material.manifest_standard(surface_actor, ambient_level=.3,
diffuse_level=.25)
k = 5
I, J, _ = odfs.shape[:3]
odf_actor.display_extent(0, I, 0, J, k, k)
odf_actor.GetProperty().SetOpacity(1.0)
scene.add(odf_actor)
scene.reset_camera()
scene.reset_clipping_range()
arr = window.snapshot(scene)
report = window.analyze_snapshot(arr)
npt.assert_equal(report.objects, 11 * 11)
scene.clear() # Reset scene
# Tensor slicer setup
if have_dipy:
from dipy.data import get_sphere
sphere = get_sphere('symmetric724')
evals = np.array([1.4, .35, .35]) * 10 ** (-3)
evecs = np.eye(3)
mevals = np.zeros((3, 2, 4, 3))
mevecs = np.zeros((3, 2, 4, 3, 3))
mevals[..., :] = evals
mevecs[..., :, :] = evecs
affine = np.eye(4)
scene = window.Scene()
tensor_actor = actor.tensor_slicer(mevals, mevecs, affine=affine,
sphere=sphere, scale=.3)
material.manifest_standard(surface_actor, ambient_level=.3,
diffuse_level=.25)
_, J, K = mevals.shape[:3]
tensor_actor.display_extent(0, 1, 0, J, 0, K)
scene.add(tensor_actor)
scene.reset_camera()
scene.reset_clipping_range()
arr = window.snapshot(scene)
report = window.analyze_snapshot(arr)
npt.assert_equal(report.objects, 4)
scene.clear() # Reset scene
# Point setup
points = np.array([[0, 0, 0], [0, 1, 0], [1, 0, 0]])
colors = np.array([[1, 0, 0], [0, 1, 0], [0, 0, 1]])
opacity = 0.5
points_actor = actor.point(points, colors, opacity=opacity)
material.manifest_standard(surface_actor, ambient_level=.3,
diffuse_level=.25)
scene.add(points_actor)
arr = window.snapshot(scene)
report = window.analyze_snapshot(arr)
npt.assert_equal(report.objects, 3)
scene.clear() # Reset scene
# Sphere setup
xyzr = np.array([[0, 0, 0, 10], [100, 0, 0, 25], [200, 0, 0, 50]])
colors = np.array([[1, 0, 0, 0.3], [0, 1, 0, 0.4], [0, 0, 1., 0.99]])
opacity = 0.5
sphere_actor = actor.sphere(centers=xyzr[:, :3], colors=colors[:],
radii=xyzr[:, 3], opacity=opacity)
material.manifest_standard(surface_actor, ambient_level=.3,
diffuse_level=.25)
scene.add(sphere_actor)
scene.reset_camera()
scene.reset_clipping_range()
arr = window.snapshot(scene)
report = window.analyze_snapshot(arr)
npt.assert_equal(report.objects, 3)
scene.clear() # Reset scene
# Advanced geometry actors setup (Arrow, cone, cylinder)
xyz = np.array([[0, 0, 0], [50, 0, 0], [100, 0, 0]])
dirs = np.array([[0, 1, 0], [1, 0, 0], [0, 0.5, 0.5]])
colors = np.array([[1, 0, 0, 0.3], [0, 1, 0, 0.4], [1, 1, 0, 1]])
heights = np.array([5, 7, 10])
actor_list = [[actor.cone, {'directions': dirs, 'resolution': 8}],
[actor.arrow, {'directions': dirs, 'resolution': 9}],
[actor.cylinder, {'directions': dirs}]]
for act_func, extra_args in actor_list:
aga_actor = act_func(centers=xyz, colors=colors[:], heights=heights,
**extra_args)
material.manifest_standard(surface_actor, ambient_level=.3,
diffuse_level=.25)
scene.add(aga_actor)
scene.reset_camera()
scene.reset_clipping_range()
arr = window.snapshot(scene)
report = window.analyze_snapshot(arr)
npt.assert_equal(report.objects, 3)
scene.clear()
# Basic geometry actors (Box, cube, frustum, octagonalprism, rectangle,
# square)
centers = np.array([[4, 0, 0], [0, 4, 0], [0, 0, 0]])
colors = np.array([[1, 0, 0, 0.4], [0, 1, 0, 0.8], [0, 0, 1, 0.5]])
directions = np.array([[1, 1, 0]])
scale_list = [1, 2, (1, 1, 1), [3, 2, 1], np.array([1, 2, 3]),
np.array([[1, 2, 3], [1, 3, 2], [3, 1, 2]])]
actor_list = [[actor.box, {}], [actor.cube, {}], [actor.frustum, {}],
[actor.octagonalprism, {}], [actor.rectangle, {}],
[actor.square, {}]]
for act_func, extra_args in actor_list:
for scale in scale_list:
scene = window.Scene()
bga_actor = act_func(centers=centers, directions=directions,
colors=colors, scales=scale, **extra_args)
material.manifest_standard(surface_actor, ambient_level=.3,
diffuse_level=.25)
scene.add(bga_actor)
arr = window.snapshot(scene)
report = window.analyze_snapshot(arr)
msg = 'Failed with {}, scale={}'.format(act_func.__name__, scale)
npt.assert_equal(report.objects, 3, err_msg=msg)
scene.clear()
# Cone setup using vertices
centers = np.array([[0, 0, 0], [20, 0, 0], [40, 0, 0]])
directions = np.array([[0, 1, 0], [1, 0, 0], [0, 0, 1]])
colors = np.array([[1, 0, 0, 0.3], [0, 1, 0, 0.4], [0, 0, 1., 0.99]])
vertices = np.array([[0.0, 0.0, 0.0], [0.0, 10.0, 0.0],
[10.0, 0.0, 0.0], [0.0, 0.0, 10.0]])
faces = np.array([[0, 1, 3], [0, 1, 2]])
cone_actor = actor.cone(centers=centers, directions=directions,
colors=colors[:], vertices=vertices, faces=faces)
material.manifest_standard(surface_actor, ambient_level=.3,
diffuse_level=.25)
scene.add(cone_actor)
scene.reset_camera()
scene.reset_clipping_range()
arr = window.snapshot(scene)
report = window.analyze_snapshot(arr)
npt.assert_equal(report.objects, 3)
scene.clear() # Reset scene
# Superquadric setup
centers = np.array([[8, 0, 0], [0, 8, 0], [0, 0, 0]])
colors = np.array([[1, 0, 0], [0, 1, 0], [0, 0, 1]])
directions = np.random.rand(3, 3)
scales = [1, 2, 3]
roundness = np.array([[1, 1], [1, 2], [2, 1]])
sq_actor = actor.superquadric(centers, roundness=roundness,
directions=directions,
colors=colors.astype(np.uint8),
scales=scales)
material.manifest_standard(surface_actor, ambient_level=.3,
diffuse_level=.25)
scene.add(sq_actor)
scene.reset_camera()
scene.reset_clipping_range()
arr = window.snapshot(scene)
report = window.analyze_snapshot(arr)
ft.assert_greater_equal(report.objects, 3)
scene.clear() # Reset scene
# Label setup
text_actor = actor.label("Hello")
material.manifest_standard(surface_actor, ambient_level=.3,
diffuse_level=.25)
scene.add(text_actor)
scene.reset_camera()
scene.reset_clipping_range()
arr = window.snapshot(scene)
report = window.analyze_snapshot(arr)
npt.assert_equal(report.objects, 5)
scene.clear() # Reset scene
# Texture setup
arr = (255 * np.ones((512, 212, 4))).astype('uint8')
arr[20:40, 20:40, :] = np.array([255, 0, 0, 255], dtype='uint8')
tp2 = actor.texture(arr)
material.manifest_standard(surface_actor, ambient_level=.3,
diffuse_level=.25)
scene.add(tp2)
scene.reset_camera()
scene.reset_clipping_range()
arr = window.snapshot(scene)
report = window.analyze_snapshot(arr)
npt.assert_equal(report.objects, 1)
scene.clear() # Reset scene
# Texture on sphere setup
arr = 255 * np.ones((810, 1620, 3), dtype='uint8')
rows, cols, _ = arr.shape
rs = rows // 2
cs = cols // 2
w = 150 // 2
arr[rs - w: rs + w, cs - 10 * w: cs + 10 * w] = np.array([255, 127, 0])
tsa = actor.texture_on_sphere(arr)
material.manifest_standard(surface_actor, ambient_level=.3,
diffuse_level=.25)
scene.add(tsa)
scene.reset_camera()
scene.reset_clipping_range()
arr = window.snapshot(scene)
report = window.analyze_snapshot(arr)
npt.assert_equal(report.objects, 1)
# NOTE: From this point on, these actors don't have full support for PBR
# interpolation. This is, the test passes but there is no evidence of the
# desired effect.
"""
# Setup slicer
data = (255 * np.random.rand(50, 50, 50))
affine = np.eye(4)
slicer = actor.slicer(data, affine, value_range=[data.min(), data.max()])
slicer.display(None, None, 25)
material.manifest_standard(surface_actor, ambient_level=.3,
diffuse_level=.25)
scene.add(slicer)
"""
"""
# Line setup
data1 = np.array([[0, 0, 0], [1, 1, 1], [2, 2, 2.]])
data2 = data1 + np.array([0.5, 0., 0.])
data = [data1, data2]
colors = np.array([[1, 0, 0], [0, 0, 1.]])
lines = actor.line(data, colors, linewidth=5)
material.manifest_standard(surface_actor, ambient_level=.3,
diffuse_level=.25)
scene.add(lines)
"""
"""
# Scalar bar setup
lut = actor.colormap_lookup_table(
scale_range=(0., 100.), hue_range=(0., 0.1), saturation_range=(1, 1),
value_range=(1., 1))
sb_actor = actor.scalar_bar(lut, ' ')
material.manifest_standard(surface_actor, ambient_level=.3,
diffuse_level=.25)
scene.add(sb_actor)
"""
"""
# Axes setup
axes = actor.axes()
material.manifest_standard(surface_actor, ambient_level=.3,
diffuse_level=.25)
scene.add(axes)
"""
"""
# Peak slicer setup
_peak_dirs = np.array([[1, 0, 0], [0, 1, 0], [0, 0, 1]], dtype='f4')
# peak_dirs.shape = (1, 1, 1) + peak_dirs.shape
peak_dirs = np.zeros((11, 11, 11, 3, 3))
peak_dirs[:, :, :] = _peak_dirs
peak_actor = actor.peak_slicer(peak_dirs)
material.manifest_standard(surface_actor, ambient_level=.3,
diffuse_level=.25)
scene.add(peak_actor)
"""
"""
# Dots setup
points = np.array([[0, 0, 0], [0, 1, 0], [1, 0, 0]])
dots_actor = actor.dots(points, color=(0, 255, 0))
material.manifest_standard(surface_actor, ambient_level=.3,
diffuse_level=.25)
scene.add(dots_actor)
"""
"""
# Text3D setup
msg = 'I \nlove\n FURY'
txt_actor = actor.text_3d(msg)
material.manifest_standard(surface_actor, ambient_level=.3,
diffuse_level=.25)
scene.add(txt_actor)
"""
"""
# Figure setup
arr = (255 * np.ones((512, 212, 4))).astype('uint8')
arr[20:40, 20:40, 3] = 0
tp = actor.figure(arr)
material.manifest_standard(surface_actor, ambient_level=.3,
diffuse_level=.25)
scene.add(tp)
"""
"""
# SDF setup
centers = np.array([[2, 0, 0], [0, 2, 0], [0, 0, 0]]) * 11
colors = np.array([[1, 0, 0], [0, 1, 0], [0, 0, 1]])
directions = np.array([[0, 1, 0], [1, 0, 0], [0, 0, 1]])
scales = [1, 2, 3]
primitive = ['sphere', 'ellipsoid', 'torus']
sdf_actor = actor.sdf(centers, directions=directions, colors=colors,
primitives=primitive, scales=scales)
material.manifest_standard(surface_actor, ambient_level=.3,
diffuse_level=.25)
scene.add(sdf_actor)
"""
# NOTE: For these last set of actors, there is not support for PBR
# interpolation at all.
"""
# Billboard setup
centers = np.array([[0, 0, 0], [5, -5, 5], [-7, 7, -7], [10, 10, 10],
[10.5, 11.5, 11.5], [12, -12, -12], [-17, 17, 17],
[-22, -22, 22]])
colors = np.array([[1, 1, 0], [0, 0, 0], [1, 0, 1], [0, 0, 1], [1, 1, 1],
[1, 0, 0], [0, 1, 0], [0, 1, 1]])
scales = [6, .4, 1.2, 1, .2, .7, 3, 2]
"""
fake_sphere = \
"""
float len = length(point);
float radius = 1.;
if (len > radius)
discard;
vec3 normalizedPoint = normalize(vec3(point.xy, sqrt(1. - len)));
vec3 direction = normalize(vec3(1., 1., 1.));
float df_1 = max(0, dot(direction, normalizedPoint));
float sf_1 = pow(df_1, 24);
fragOutput0 = vec4(max(df_1 * color, sf_1 * vec3(1)), 1);
"""
"""
billboard_actor = actor.billboard(centers, colors=colors, scales=scales,
fs_impl=fake_sphere)
material.manifest_pbr(billboard_actor)
scene.add(billboard_actor)
"""
if interactive:
window.show(scene)
def render(
self,
tractogram: Tractogram = None,
filename: str = None
):
""" Render the streamlines, either directly or through a file
Might render from "outside" the environment, like for comet
Parameters:
-----------
tractogram: Tractogram, optional
Object containing the streamlines and seeds
path: str, optional
If set, save the image at the specified location instead
of displaying directly
"""
from fury import window, actor
# Might be rendering from outside the environment
if tractogram is None:
tractogram = Tractogram(
streamlines=self.streamlines[:, :self.length],
data_per_streamline={
'seeds': self.starting_points
})
# Reshape peaks for displaying
X, Y, Z, M = self.peaks.data.shape
peaks = np.reshape(self.peaks.data, (X, Y, Z, 5, M//5))
# Setup scene and actors
scene = window.Scene()
stream_actor = actor.streamtube(tractogram.streamlines)
peak_actor = actor.peak_slicer(peaks,
np.ones((X, Y, Z, M)),
colors=(0.2, 0.2, 1.),
opacity=0.5)
dot_actor = actor.dots(tractogram.data_per_streamline['seeds'],
color=(1, 1, 1),
opacity=1,
dot_size=2.5)
scene.add(stream_actor)
scene.add(peak_actor)
scene.add(dot_actor)
scene.reset_camera_tight(0.95)
# Save or display scene
if filename is not None:
directory = os.path.dirname(pjoin(self.experiment_path, 'render'))
if not os.path.exists(directory):
os.makedirs(directory)
dest = pjoin(directory, filename)
window.snapshot(
scene,
fname=dest,
offscreen=True,
size=(800, 800))
else:
showm = window.ShowManager(scene, reset_camera=True)
showm.initialize()
showm.start()
