def test_dots(interactive=False):
points = np.array([[0, 0, 0], [0, 1, 0], [1, 0, 0]])
dots_actor = actor.dots(points, color=(0, 255, 0))
scene = window.Scene()
scene.add(dots_actor)
scene.reset_camera()
scene.reset_clipping_range()
if interactive:
window.show(scene, reset_camera=False)
npt.assert_equal(scene.GetActors().GetNumberOfItems(), 1)
extent = scene.GetActors().GetLastActor().GetBounds()
npt.assert_equal(extent, (0.0, 1.0, 0.0, 1.0, 0.0, 0.0))
arr = window.snapshot(scene)
report = window.analyze_snapshot(arr, colors=(0, 255, 0))
npt.assert_equal(report.objects, 3)
# Test one point
points = np.array([0, 0, 0])
dot_actor = actor.dots(points, color=(0, 0, 255))
scene.clear()
scene.add(dot_actor)
scene.reset_camera()
scene.reset_clipping_range()
arr = window.snapshot(scene)
report = window.analyze_snapshot(arr, colors=(0, 0, 255))
npt.assert_equal(report.objects, 1)
def main():
parser = _build_arg_parser()
args = parser.parse_args()
assert_inputs_exist(parser, [args.tractogram])
assert_outputs_exist(parser, args, [], [args.save])
tracts_format = detect_format(args.tractogram)
if tracts_format is not TrkFile:
raise ValueError("Invalid input streamline file format " +
"(must be trk): {0}".format(args.tractogram_filename))
# Load files and data. TRKs can have 'same' as reference
tractogram = load_tractogram(args.tractogram, 'same')
# Streamlines are saved in RASMM but seeds are saved in VOX
# This might produce weird behavior with non-iso
tractogram.to_vox()
streamlines = tractogram.streamlines
if 'seeds' not in tractogram.data_per_streamline:
parser.error('Tractogram does not contain seeds')
seeds = tractogram.data_per_streamline['seeds']
# Make display objects
streamlines_actor = actor.line(streamlines)
points = actor.dots(seeds, color=(1., 1., 1.))
# Add display objects to canvas
s = window.Scene()
s.add(streamlines_actor)
s.add(points)
# Show and record if needed
if args.save is not None:
window.record(s, out_path=args.save, size=(1000, 1000))
window.show(s)
def main():
parser = _build_args_parser()
args = parser.parse_args()
assert_inputs_exist(parser, [args.tractogram])
assert_outputs_exist(parser, args, [], [args.save])
tracts_format = detect_format(args.tractogram)
if tracts_format is not TrkFile:
raise ValueError("Invalid input streamline file format " +
"(must be trk): {0}".format(args.tractogram_filename))
# Load files and data
trk = TrkFile.load(args.tractogram)
tractogram = trk.tractogram
streamlines = tractogram.streamlines
if 'seeds' not in tractogram.data_per_streamline:
parser.error('Tractogram does not contain seeds')
seeds = tractogram.data_per_streamline['seeds']
# Make display objects
streamlines_actor = actor.line(streamlines)
points = actor.dots(seeds, color=(1., 1., 1.))
# Add display objects to canvas
r = window.Renderer()
r.add(streamlines_actor)
r.add(points)
# Show and record if needed
if args.save is not None:
window.record(r, out_path=args.save, size=(1000, 1000))
window.show(r)
def test_selector_manager():
centers, colors, radii = _get_three_cubes()
scene = window.Scene()
cube_actor = actor.cube(centers,
directions=(1, 0, 2),
colors=colors,
scales=radii)
pts = 100 * (np.random.rand(100, 3) - 0.5) + np.array([20, 0, 0.])
pts_actor = actor.dots(pts, dot_size=10)
rgb = 255 * np.ones((400, 400, 3), dtype=np.uint8)
tex_actor = actor.texture(rgb)
scene.add(cube_actor)
scene.add(pts_actor)
scene.add(tex_actor)
showm = window.ShowManager(scene,
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()
selm = pick.SelectionManager(select='faces')
selm.selectable_off([tex_actor])
selm.selectable_on([tex_actor])
selm.selectable_off([tex_actor])
def timer_callback(_obj, _event):
cnt = next(counter)
tb.message = "Let's count up to 15 and exit :" + str(cnt)
if cnt % 10 == 0:
# select large area
info_plus = selm.select((900 // 2, 768 // 2), scene, (30, 30))
for info in info_plus.keys():
if info_plus[info]['actor'] in [cube_actor, pts_actor]:
npt.assert_(True)
else:
npt.assert_(False)
# select single pixel
info_ = selm.pick((900 // 2, 768 // 2), scene)
if info_['actor'] in [cube_actor, pts_actor]:
npt.assert_(True)
else:
npt.assert_(False)
showm.render()
if cnt == 15:
showm.exit()
pass
scene.add(tb)
# Run every 200 milliseconds
showm.add_timer_callback(True, 200, timer_callback)
showm.start()
def get_orbit_actor(orbit_points):
orbit_actor = actor.dots(orbit_points, color=(1, 1, 1),
opacity=1, dot_size=1)
return orbit_actor
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()
