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 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 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_model_reco_bundles(model,
recognized_bundle,
folder_name,
file_bundle_name,
interactive=True):
ren = window.Scene()
ren.SetBackground(1, 1, 1)
ren.add(actor.line(model, colors=(.1, .7, .26))) #green
ren.add(actor.line(recognized_bundle, colors=(.1, .1, 6))) #blue
if interactive:
window.show(ren)
ren.set_camera(ren.camera_info())
window.record(ren,
out_path=pjoin(folder_name, file_bundle_name) + '.png',
size=(600, 600))
def save_views_imgs(lines, size=(500, 500), interactive=False, ext='jpg'):
"""
Function to save view images when the input file does fulfill the
requirements of the validator.
:param lines: Streamlines-like object.
:param size: A 2-tuple, containing (width, height) in pixels.
:param interactive: (Boolean) If True, launches a window. Useful for
developing/debugging options.
:param ext: (String) Extension of the output files.
"""
# Start virtual display
if has_xvfbwrapper:
print('Starting Xvfb')
vdisplay = Xvfb()
vdisplay.start()
# Create streamlines actor
streamlines_actor = actor.line(lines)
# Set renderer window
scene = window.Scene()
# Add streamlines to renderer
scene.add(streamlines_actor)
# Loop through views
for param in _VIEW_PARAMS:
# Set camera
scene.set_camera(position=param['cam_pos'],
focal_point=param['focal_pnt'],
view_up=param['view_up'])
if interactive:
window.show(scene, size=size)
# Save imgs
out_file = os.path.join('secondary', param['view'] + '.' + ext)
print('Saving: {}'.format(out_file))
window.record(scene, out_path=out_file, size=size)
# Stop virtual display
if has_xvfbwrapper:
vdisplay.stop()
def show_both_bundles(bundles, colors=None, show=True, fname=None):
if colors is None:
colors = [window.colors.orange, window.colors.red]
scene = window.Scene()
#scene.SetBackground(1., 1, 1)
# scene.set_camera(position=(-176.42, 118.52, 128.20),
# focal_point=(113.30, 128.31, 76.56),
# view_up=(0.18, 0.00, 0.98))
for (i, bundle) in enumerate(bundles):
color = colors[i]
lines_actor = actor.line(bundle, color, linewidth=0.3)
#lines_actor.RotateX(-90)
#lines_actor.RotateZ(90)
scene.add(lines_actor)
if show:
window.show(scene)
if fname is not None:
sleep(1)
window.record(scene, n_frames=1, out_path=fname, size=(900, 900))
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))
sft_target = load_trk(target_file, "same", bbox_valid_check=False)
target = sft_target.streamlines
target_header = create_tractogram_header(atlas_file,
*sft_atlas.space_attribute)
"""
let's visualize atlas tractogram and target tractogram before registration
"""
interactive = False
ren = window.Renderer()
ren.SetBackground(1, 1, 1)
ren.add(actor.line(atlas, colors=(1, 0, 1)))
ren.add(actor.line(target, colors=(1, 1, 0)))
window.record(ren, out_path='tractograms_initial.png', size=(600, 600))
if interactive:
window.show(ren)
"""
.. figure:: tractograms_initial.png
:align: center
Atlas and target before registration.
"""
"""
We will register target tractogram to model atlas' space using streamlinear
registeration (SLR) [Garyfallidis15]_
"""
moved, transform, qb_centroids1, qb_centroids2 = whole_brain_slr(
scene.add(slice_actor2)
scene.reset_camera()
scene.zoom(1.4)
###############################################################################
# In order to interact with the data you will need to uncomment the line below.
# window.show(scene, size=(600, 600), reset_camera=False)
###############################################################################
# Otherwise, you can save a screenshot using the following command.
window.record(scene,
out_path='slices.png',
size=(600, 600),
reset_camera=False)
###############################################################################
# Render slices from FA with your colormap
# ========================================
# It is also possible to set the colormap of your preference. Here we are
# loading an FA image and showing it in a non-standard way using an HSV
# colormap.
fname_fa = os.path.join(os.path.expanduser('~'), '.dipy',
'exp_bundles_and_maps', 'bundles_2_subjects', 'subj_1',
'fa_1x1x1.nii.gz')
img = nib.load(fname_fa)
text += 'Actor ID ' + str(id(picked_info['actor']))
text_block.message = text
showm.render()
###############################################################################
# Bind the callback to the actor
fury_actor.AddObserver('LeftButtonPressEvent', left_click_callback, 1)
###############################################################################
# Make the window appear
showm = window.ShowManager(scene, size=(1024, 768), order_transparent=True)
showm.initialize()
scene.add(panel)
###############################################################################
# Change interactive to True to start interacting with the scene
interactive = False
if interactive:
showm.start()
###############################################################################
# Save the current framebuffer in a PNG file
window.record(showm.scene, size=(1024, 768), out_path="viz_picking.png")
#
# This is the default option when you are using ``line`` or ``streamtube``.
renderer = window.Renderer()
stream_actor = actor.line(bundle_native)
renderer.set_camera(position=(-176.42, 118.52, 128.20),
focal_point=(113.30, 128.31, 76.56),
view_up=(0.18, 0.00, 0.98))
renderer.add(stream_actor)
# Uncomment the line below to show to display the window
# window.show(renderer, size=(600, 600), reset_camera=False)
window.record(renderer, out_path='bundle1.png', size=(600, 600))
###############################################################################
# You may wonder how we knew how to set the camera. This is very easy. You just
# need to run ``window.show`` once see how you want to see the object and then
# close the window and call the ``camera_info`` method which prints the
# position, focal point and view up vectors of the camera.
renderer.camera_info()
###############################################################################
# Show every point with a value from a volume with default colormap
# =================================================================
#
# Here we will need to input the ``fa`` map in ``streamtube`` or ``line``.
# Create a scene to start.
scene = window.Scene()
##############################################################################
# Load an image (png, bmp, jpeg or jpg) using ``io.load_image``. In this
# example, we will use ``read_viz_textures`` to access an image of the
# Earth's surface from the fury Github after using ''fetch_viz_textures()''
# to download the available textures.
fetch_viz_textures()
filename = read_viz_textures("1_earth_8k.jpg")
image = io.load_image(filename)
##############################################################################
# Next, use ``actor.texture_on_sphere`` to add a sphere with the texture from
# your loaded image to the already existing scene.
# To add a texture to your scene as visualized on a plane, use
# ``actor.texture`` instead.
scene.add(actor.texture_on_sphere(image))
##############################################################################
# Lastly, record the scene, or set interactive to True if you would like to
# manipulate your new sphere.
interactive = False
if interactive:
window.show(scene, size=(600, 600), reset_camera=False)
window.record(scene, size=(900, 768), out_path="viz_texture.png")
###############################################################################
# Then we can draw a solid circle, or disk.
disk = ui.Disk2D(outer_radius=50, center=(400, 200), color=(1, 1, 0))
###############################################################################
# Add an inner radius to make a ring.
ring = ui.Disk2D(outer_radius=50, inner_radius=45,
center=(500, 600), color=(0, 1, 1))
###############################################################################
# Now that all the elements have been initialised, we add them to the show
# manager.
current_size = (800, 800)
show_manager = window.ShowManager(size=current_size,
title="FURY Shapes Example")
show_manager.scene.add(rect)
show_manager.scene.add(disk)
show_manager.scene.add(ring)
interactive = False
if interactive:
show_manager.start()
window.record(show_manager.scene, size=current_size, out_path="viz_shapes.png")
p.applyExternalForce(blue_ball, -1,
forceObj=[40000, 0, 0],
posObj=blue_pos,
flags=p.WORLD_FRAME)
apply_force = 0
sync_actor(blue_ball_actor, blue_ball)
sync_actor(red_ball_actor, red_ball)
# Get various collision information using `p.getContactPoints`.
contact = p.getContactPoints(red_ball, blue_ball, -1, -1)
if len(contact) != 0:
tb.message = "Collision!!"
p.stepSimulation()
if cnt == 50:
showm.exit()
showm.add_timer_callback(True, duration, timer_callback)
interactive = False
if interactive:
showm.start()
window.record(scene, size=(900, 700), out_path="viz_ball_collide.png")
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)
showm.scene.azimuth(0.05 * cnt)
sphere_actor.GetProperty().SetOpacity(cnt / 100.)
showm.render()
if cnt == 100:
showm.exit()
scene.add(tb)
# Run every 200 milliseconds
showm.add_timer_callback(True, 200, timer_callback)
showm.start()
window.record(showm.scene, size=(900, 768), out_path="viz_timer.png")
############################################################################
# The below arrow actor is generated by repeating the arrow primitive.
arrow_actor = actor.arrow(centers, dirs, colors=colors, scales=1.5)
############################################################################
# repeating what we did but this time with random centers, directions, and
# colors.
cen2 = np.random.rand(5, 3)
dir2 = np.random.rand(5, 3)
cols2 = np.random.rand(5, 3)
arrow_actor2 = actor.arrow(cen2, dir2, colors=cols2, scales=1.5)
scene = window.Scene()
############################################################################
# Adding our Arrow actors to scene.
scene.add(arrow_actor)
scene.add(arrow_actor2)
interactive = False
if interactive:
window.show(scene, size=(600, 600))
window.record(scene, out_path='viz_arrow.png', size=(600, 600))
colors = np.array([0, 0, 1])
############################################################################
# The below sphere actor is generated by repeating the sphere primitive.
prim_sphere_actor = actor.sphere(centers, colors=colors, radii=5)
############################################################################
# This time, we're using vtkSphereSource to generate the sphere actor
cen2 = np.add(centers, np.array([12, 0, 0]))
cols2 = np.array([1, 0, 0])
vtk_sphere_actor = actor.sphere(cen2, colors=cols2,
radii=5, use_primitive=False)
scene = window.Scene()
############################################################################
# Adding our sphere actors to scene.
scene.add(prim_sphere_actor)
scene.add(vtk_sphere_actor)
interactive = False
if interactive:
window.show(scene, size=(600, 600))
window.record(scene, out_path='viz_sphere.png', size=(600, 600))
# ==================================
#
# Now we create a callback for setting the chosen color.
def change_color(combobox):
label.color = colors[combobox.selected_text]
# `on_change` callback is set to `change_color` method so that
# it's called whenever a different option is selected.
color_combobox.on_change = change_color
###############################################################################
# Show Manager
# ==================================
#
# Now we add label and combobox to the scene.
current_size = (400, 400)
showm = window.ShowManager(size=current_size, title="ComboBox UI Example")
showm.scene.add(label, color_combobox)
# To interact with the UI, set interactive = True
interactive = False
if interactive:
showm.start()
window.record(showm.scene, out_path="combobox_ui.png", size=(400, 400))
orn = p.getQuaternionFromEuler([0, 0, 0])
p.changeConstraint(root_robe_c,
pivot,
jointChildFrameOrientation=orn,
maxForce=500)
# Sync base and chain.
sync_actor(base_actor, rope)
sync_joints(rope_actor, rope)
utils.update_actor(rope_actor)
# Simulate a step.
p.stepSimulation()
# Exit after 2000 steps of simulation.
if cnt == 130:
showm.exit()
# Add the timer callback to showmanager.
# Increasing the duration value will slow down the simulation.
showm.add_timer_callback(True, 1, timer_callback)
interactive = False
# start simulation
if interactive:
showm.start()
window.record(scene, size=(900, 768), out_path="viz_chain.png")
#
# This is the default option when you are using ``line`` or ``streamtube``.
scene = window.Scene()
stream_actor = actor.line(bundle_native)
scene.set_camera(position=(-176.42, 118.52, 128.20),
focal_point=(113.30, 128.31, 76.56),
view_up=(0.18, 0.00, 0.98))
scene.add(stream_actor)
# Uncomment the line below to show to display the window
# window.show(scene, size=(600, 600), reset_camera=False)
window.record(scene, out_path='bundle1.png', size=(600, 600))
###############################################################################
# You may wonder how we knew how to set the camera. This is very easy. You just
# need to run ``window.show`` once see how you want to see the object and then
# close the window and call the ``camera_info`` method which prints the
# position, focal point and view up vectors of the camera.
scene.camera_info()
###############################################################################
# Show every point with a value from a volume with default colormap
# =================================================================
#
# Here we will need to input the ``fa`` map in ``streamtube`` or ``line``.
surface_opacity = 0.5
surface_color = [0, 1, 1]
seedroi_actor = actor.contour_from_roi(seed_mask, affine, surface_color,
surface_opacity)
###############################################################################
# Next, we initialize a ''Scene'' object and add both actors
# to the rendering.
scene = window.Scene()
scene.add(streamlines_actor)
scene.add(seedroi_actor)
###############################################################################
# If you uncomment the following line, the rendering will pop up in an
# interactive window.
interactive = False
if interactive:
window.show(scene)
scene.zoom(1.5)
scene.reset_clipping_range()
window.record(scene,
out_path='contour_from_roi_tutorial.png',
size=(1200, 900),
reset_camera=False)
size = obj.GetSize()
size_change = [size[0] - size_old[0], 0]
panel.re_align(size_change)
show_m.initialize()
###############################################################################
# Finally, please set the following variable to ``True`` to interact with the
# datasets in 3D.
interactive = False
ren.zoom(1.5)
ren.reset_clipping_range()
if interactive:
show_m.add_window_callback(win_callback)
show_m.render()
show_m.start()
else:
window.record(ren,
out_path='bundles_and_3_slices.png',
size=(1200, 900),
reset_camera=False)
del show_m
[3, 5, 7]], dtype='i8') #good
utils.set_polydata_vertices(my_polydata, my_vertices)
utils.set_polydata_triangles(my_polydata, my_triangles)
file_name = "my_star2D.vtk"
save_polydata(my_polydata, file_name)
print("Surface saved in " + file_name)
star_polydata = load_polydata(file_name)
star_vertices = utils.get_polydata_vertices(star_polydata)
colors = star_vertices * 255
utils.set_polydata_colors(star_polydata, colors)
print("new surface colors")
print(utils.get_polydata_colors(star_polydata))
# get vtkActor
star_actor = utils.get_actor_from_polydata(star_polydata)
star_actor.GetProperty().BackfaceCullingOff()
# Create a scene
scene = window.Scene()
scene.add(star_actor)
scene.set_camera(position=(0, 0, 7), focal_point=(0, 0, 0))
scene.zoom(3)
# display
# window.show(scene, size=(1000, 1000), reset_camera=False) this allows the picture to be moved around
window.record(scene, out_path='star2D.png', size=(600, 600))
flags=p.WORLD_FRAME)
apply_force = False
# Set position and orientation of the ball.
sync_actor(ball_actor, ball)
# Updating the position and orientation of each individual brick.
for idx, brick in enumerate(bricks):
sync_brick(idx, brick)
utils.update_actor(brick_actor)
# Simulate a step.
p.stepSimulation()
# Exit after 2000 steps of simulation.
if cnt == 130:
showm.exit()
# Add the timer callback to showmanager.
# Increasing the duration value will slow down the simulation.
showm.add_timer_callback(True, 1, timer_callback)
interactive = False
# start simulation
if interactive:
showm.start()
window.record(scene, out_path="viz_brick_wall.png", size=(900, 768))
def main():
# reads the tractography data in trk format
# extracts streamlines and the file header. Streamlines should be in the same coordinate system as the FA map (used later).
# input example: '/home/Example_data/tracts.trk'
tractography_file = input(
"Please, specify the file with tracts that you would like to analyse. File should be in the trk format. "
)
streams, hdr = load_trk(tractography_file) # for old DIPY version
# sft = load_trk(tractography_file, tractography_file)
# streams = sft.streamlines
streams_array = np.asarray(streams)
print('imported tractography data:' + tractography_file)
# load T1fs_conform image that operates in the same coordinates as simnibs except for the fact the center of mesh
# is located at the image center
# T1fs_conform image should be generated in advance during the head meshing procedure
# input example: fname_T1='/home/Example_data/T1fs_conform.nii.gz'
fname_T1 = input(
"Please, specify the T1fs_conform image that has been generated during head meshing procedure. "
)
data_T1, affine_T1 = load_nifti(fname_T1)
# load FA image in the same coordinates as tracts
# input example:fname_FA='/home/Example_data/DTI_FA.nii'
fname_FA = input("Please, specify the FA image. ")
data_FA, affine_FA = load_nifti(fname_FA)
print('loaded T1fs_conform.nii and FA images')
# specify the head mesh file that is used later in simnibs to simulate induced electric field
# input example:'/home/Example_data/SUBJECT_MESH.msh'
global mesh_path
mesh_path = input("Please, specify the head mesh file. ")
last_slach = max([i for i, ltr in enumerate(mesh_path) if ltr == '/']) + 1
global subject_name
subject_name = mesh_path[last_slach:-4]
# specify the directory where you would like to save your simulation results
# input example:'/home/Example_data/Output'
global out_dir
out_dir = input(
"Please, specify the directory where you would like to save your simulation results. "
)
out_dir = out_dir + '/simulation_at_pos_'
# Co-registration of T1fs_conform and FA images. Performed in 4 steps.
# Step 1. Calculation of the center of mass transform. Used later as starting transform.
c_of_mass = transform_centers_of_mass(data_T1, affine_T1, data_FA,
affine_FA)
print('calculated c_of_mass transformation')
# Step 2. Calculation of a 3D translation transform. Used in the next step as starting transform.
nbins = 32
sampling_prop = None
metric = MutualInformationMetric(nbins, sampling_prop)
level_iters = [10000, 1000, 100]
sigmas = [3.0, 1.0, 0.0]
factors = [4, 2, 1]
affreg = AffineRegistration(metric=metric,
level_iters=level_iters,
sigmas=sigmas,
factors=factors)
transform = TranslationTransform3D()
params0 = None
starting_affine = c_of_mass.affine
translation = affreg.optimize(data_T1,
data_FA,
transform,
params0,
affine_T1,
affine_FA,
starting_affine=starting_affine)
print('calculated 3D translation transform')
# Step 3. Calculation of a Rigid 3D transform. Used in the next step as starting transform
transform = RigidTransform3D()
params0 = None
starting_affine = translation.affine
rigid = affreg.optimize(data_T1,
data_FA,
transform,
params0,
affine_T1,
affine_FA,
starting_affine=starting_affine)
print('calculated Rigid 3D transform')
# Step 4. Calculation of an affine transform. Used for co-registration of T1 and FA images.
transform = AffineTransform3D()
params0 = None
starting_affine = rigid.affine
affine = affreg.optimize(data_T1,
data_FA,
transform,
params0,
affine_T1,
affine_FA,
starting_affine=starting_affine)
print('calculated Affine 3D transform')
identity = np.eye(4)
inv_affine_FA = np.linalg.inv(affine_FA)
inv_affine_T1 = np.linalg.inv(affine_T1)
inv_affine = np.linalg.inv(affine.affine)
# transforming streamlines to FA space
new_streams_FA = streamline.transform_streamlines(streams, inv_affine_FA)
new_streams_FA_array = np.asarray(new_streams_FA)
T1_to_FA = np.dot(inv_affine_FA, np.dot(affine.affine, affine_T1))
FA_to_T1 = np.linalg.inv(T1_to_FA)
# transforming streamlines from FA to T1 space
new_streams_T1 = streamline.transform_streamlines(new_streams_FA, FA_to_T1)
global new_streams_T1_array
new_streams_T1_array = np.asarray(new_streams_T1)
# calculating amline derivatives along the streamlines to get the local orientation of the streamlines
global streams_array_derivative
streams_array_derivative = copy.deepcopy(new_streams_T1_array)
print('calculating amline derivatives')
for stream in range(len(new_streams_T1_array)):
my_steam = new_streams_T1_array[stream]
for t in range(len(my_steam[:, 0])):
streams_array_derivative[stream][t,
0] = my_deriv(t, my_steam[:, 0])
streams_array_derivative[stream][t,
1] = my_deriv(t, my_steam[:, 1])
streams_array_derivative[stream][t,
2] = my_deriv(t, my_steam[:, 2])
deriv_norm = np.linalg.norm(streams_array_derivative[stream][t, :])
streams_array_derivative[stream][
t, :] = streams_array_derivative[stream][t, :] / deriv_norm
# to create a torus representing a coil in an interactive window
torus = vtk.vtkParametricTorus()
torus.SetRingRadius(5)
torus.SetCrossSectionRadius(2)
torusSource = vtk.vtkParametricFunctionSource()
torusSource.SetParametricFunction(torus)
torusSource.SetScalarModeToPhase()
torusMapper = vtk.vtkPolyDataMapper()
torusMapper.SetInputConnection(torusSource.GetOutputPort())
torusMapper.SetScalarRange(0, 360)
torusActor = vtk.vtkActor()
torusActor.SetMapper(torusMapper)
torus_pos_x = 100
torus_pos_y = 129
torus_pos_z = 211
torusActor.SetPosition(torus_pos_x, torus_pos_y, torus_pos_z)
list_streams_T1 = list(new_streams_T1)
# adding one fictive bundle of length 1 with coordinates [0,0,0] to avoid some bugs with actor.line during visualization
list_streams_T1.append(np.array([0, 0, 0]))
global bundle_native
bundle_native = list_streams_T1
# generating a list of colors to visualize later the stimualtion effects
effect_max = 0.100
effect_min = -0.100
global colors
colors = [
np.random.rand(*current_streamline.shape)
for current_streamline in bundle_native
]
for my_streamline in range(len(bundle_native) - 1):
my_stream = copy.deepcopy(bundle_native[my_streamline])
for point in range(len(my_stream)):
colors[my_streamline][point] = vtkplotter.colors.colorMap(
(effect_min + effect_max) / 2,
name='jet',
vmin=effect_min,
vmax=effect_max)
colors[my_streamline + 1] = vtkplotter.colors.colorMap(effect_min,
name='jet',
vmin=effect_min,
vmax=effect_max)
# Vizualization of fibers over T1
# i_coord = 0
# j_coord = 0
# k_coord = 0
# global number_of_stimulations
number_of_stimulations = 0
actor_line_list = []
scene = window.Scene()
scene.clear()
scene.background((0.5, 0.5, 0.5))
world_coords = False
shape = data_T1.shape
lut = actor.colormap_lookup_table(scale_range=(effect_min, effect_max),
hue_range=(0.4, 1.),
saturation_range=(1, 1.))
# # the lines below is for a non-interactive demonstration run only.
# # they should remain commented unless you set "interactive" to False
# lut, colors = change_TMS_effects(torus_pos_x, torus_pos_y, torus_pos_z)
# bar = actor.scalar_bar(lut)
# bar.SetTitle("TMS effect")
# bar.SetHeight(0.3)
# bar.SetWidth(0.10)
# bar.SetPosition(0.85, 0.3)
# scene.add(bar)
actor_line_list.append(
actor.line(bundle_native,
colors,
linewidth=5,
fake_tube=True,
lookup_colormap=lut))
if not world_coords:
image_actor_z = actor.slicer(data_T1, identity)
else:
image_actor_z = actor.slicer(data_T1, identity)
slicer_opacity = 0.6
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)
"""
Connect the actors with the scene.
"""
scene.add(actor_line_list[0])
scene.add(image_actor_z)
scene.add(image_actor_x)
scene.add(image_actor_y)
show_m = window.ShowManager(scene, size=(1200, 900))
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}",
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)
"""
Сallbacks for the sliders.
"""
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
"""
Сreate text labels to identify the sliders.
"""
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")
"""
Create a ``panel`` to contain the sliders and labels.
"""
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))
scene.add(panel)
"""
Create a ``panel`` to show the value of a picked voxel.
"""
label_position = ui.TextBlock2D(text='Position:')
label_value = ui.TextBlock2D(text='Value:')
result_position = ui.TextBlock2D(text='')
result_value = ui.TextBlock2D(text='')
text2 = ui.TextBlock2D(text='Calculate')
panel_picking = ui.Panel2D(size=(250, 125),
color=(1, 1, 1),
opacity=0.1,
align="left")
panel_picking.center = (200, 120)
panel_picking.add_element(label_position, (0.1, 0.75))
panel_picking.add_element(label_value, (0.1, 0.45))
panel_picking.add_element(result_position, (0.45, 0.75))
panel_picking.add_element(result_value, (0.45, 0.45))
panel_picking.add_element(text2, (0.1, 0.15))
icon_files = []
icon_files.append(('left', read_viz_icons(fname='circle-left.png')))
button_example = ui.Button2D(icon_fnames=icon_files, size=(100, 30))
panel_picking.add_element(button_example, (0.5, 0.1))
def change_text_callback(i_ren, obj, button):
text2.message = str(i_coord) + ' ' + str(j_coord) + ' ' + str(k_coord)
torusActor.SetPosition(i_coord, j_coord, k_coord)
print(i_coord, j_coord, k_coord)
lut, colors = change_TMS_effects(i_coord, j_coord, k_coord)
scene.rm(actor_line_list[0])
actor_line_list.append(
actor.line(bundle_native,
colors,
linewidth=5,
fake_tube=True,
lookup_colormap=lut))
scene.add(actor_line_list[1])
nonlocal number_of_stimulations
global bar
if number_of_stimulations > 0:
scene.rm(bar)
else:
number_of_stimulations = number_of_stimulations + 1
bar = actor.scalar_bar(lut)
bar.SetTitle("TMS effect")
bar.SetHeight(0.3)
bar.SetWidth(0.10) # the width is set first
bar.SetPosition(0.85, 0.3)
scene.add(bar)
actor_line_list.pop(0)
i_ren.force_render()
button_example.on_left_mouse_button_clicked = change_text_callback
scene.add(panel_picking)
scene.add(torusActor)
def left_click_callback(obj, ev):
"""Get the value of the clicked voxel and show it in the panel."""
event_pos = show_m.iren.GetEventPosition()
obj.picker.Pick(event_pos[0], event_pos[1], 0, scene)
global i_coord, j_coord, k_coord
i_coord, j_coord, k_coord = obj.picker.GetPointIJK()
print(i_coord, j_coord, k_coord)
result_position.message = '({}, {}, {})'.format(
str(i_coord), str(j_coord), str(k_coord))
result_value.message = '%.8f' % data_T1[i_coord, j_coord, k_coord]
torusActor.SetPosition(i_coord, j_coord, k_coord)
image_actor_z.AddObserver('LeftButtonPressEvent', left_click_callback, 1.0)
global size
size = scene.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()
"""
Set the following variable to ``True`` to interact with the datasets in 3D.
"""
interactive = True
scene.zoom(2.0)
scene.reset_clipping_range()
scene.set_camera(position=(-642.07, 495.40, 148.49),
focal_point=(127.50, 127.50, 127.50),
view_up=(0.02, -0.01, 1.00))
if interactive:
show_m.add_window_callback(win_callback)
show_m.render()
show_m.start()
else:
window.record(scene,
out_path=out_dir + '/bundles_and_effects.png',
size=(1200, 900),
reset_camera=True)
def plot_an_odf_slice(odf_4d, full_sphere, background_data, tile_size,
filename, centroid, axis, camera_distance, subtract_iso,
mask_image):
from fury import actor, window
view_up = [(0., 0., 1.), (0., 0., 1.), (0., -1., 0.)]
# Adjust the centroid so it's only a single slice
slicenum = int(np.round(centroid)[axis])
centroid[axis] = 0
position = centroid.copy()
position[axis] = position[axis] + camera_distance
# Roll if viewing an axial slice
roll = 3 if axis == 2 else 0
position[1] = position[1] - roll
# Ensure the dimensions reflect that there is only one slice
new_shape = list(odf_4d.shape)
new_shape[axis] = 1
image_shape = new_shape[:3]
if axis == 0:
odf_slice = odf_4d[slicenum, :, :, :].reshape(new_shape)
image_slice = background_data[slicenum, :, :].reshape(image_shape)
elif axis == 1:
odf_slice = odf_4d[:, slicenum, :, :].reshape(new_shape)
image_slice = background_data[:, slicenum, :].reshape(image_shape)
elif axis == 2:
odf_slice = odf_4d[:, :, slicenum, :].reshape(new_shape)
image_slice = background_data[:, :, slicenum].reshape(image_shape)
# Tile to get the whole ODF
odf_slice = np.tile(odf_slice, (1, 1, 1, 2))
if subtract_iso:
odf_slice = odf_slice - odf_slice.min(3, keepdims=True)
# Make graphics objects
odf_actor = actor.odf_slicer(odf_slice,
sphere=full_sphere,
colormap=None,
scale=0.6,
mask=image_slice)
image_actor = actor.slicer(image_slice,
opacity=0.6,
interpolation='nearest')
image_size = (tile_size, tile_size)
scene = window.Scene()
scene.add(image_actor)
scene.add(odf_actor)
xfov_min, xfov_max = 0, new_shape[0] - 1
yfov_min, yfov_max = 0, new_shape[1] - 1
zfov_min, zfov_max = 0, new_shape[2] - 1
odf_actor.display_extent(xfov_min, xfov_max, yfov_min, yfov_max, zfov_min,
zfov_max)
image_actor.display_extent(xfov_min, xfov_max, yfov_min, yfov_max,
zfov_min, zfov_max)
scene.set_camera(focal_point=tuple(centroid),
position=tuple(position),
view_up=view_up[axis])
window.record(scene,
out_path=filename,
reset_camera=False,
size=image_size)
scene.clear()
def plot_peak_slice(odf_4d,
sphere,
background_data,
out_file,
axis,
slicenum,
mask_data,
tile_size=1200,
normalize_peaks=True):
from fury import actor, window
view_up = [(0., 0., 1.), (0., 0., 1.), (0., -1., 0.)]
# Make a slice mask to reduce memory
new_shape = list(odf_4d.shape)
new_shape[axis] = 1
image_shape = new_shape[:3]
midpoint = (new_shape[0] / 2., new_shape[1] / 2., new_shape[2] / 2.)
if axis == 0:
odf_slice = odf_4d[slicenum, :, :, :].reshape(new_shape)
image_slice = background_data[slicenum, :, :].reshape(image_shape)
mask_slice = mask_data[slicenum, :, :].reshape(image_shape)
camera_dist = max(midpoint[1], midpoint[2]) * np.pi
elif axis == 1:
odf_slice = odf_4d[:, slicenum, :, :].reshape(new_shape)
image_slice = background_data[:, slicenum, :].reshape(image_shape)
mask_slice = mask_data[:, slicenum, :].reshape(image_shape)
camera_dist = max(midpoint[0], midpoint[2]) * np.pi
elif axis == 2:
odf_slice = odf_4d[:, :, slicenum, :].reshape(new_shape)
image_slice = background_data[:, :, slicenum].reshape(image_shape)
mask_slice = mask_data[:, :, slicenum].reshape(image_shape)
camera_dist = max(midpoint[0], midpoint[1]) * np.pi
position = list(midpoint)
position[axis] += camera_dist
# Find the actual peaks
peak_dirs, peak_values = peaks_from_odfs(odf_slice,
sphere,
relative_peak_threshold=.1,
min_separation_angle=15,
mask=mask_slice,
normalize_peaks=normalize_peaks,
npeaks=3)
if normalize_peaks:
peak_values = peak_values / peak_values.max() * np.pi
peak_actor = actor.peak_slicer(peak_dirs, peak_values, colors=None)
image_actor = actor.slicer(image_slice,
opacity=0.6,
interpolation='nearest')
image_size = (tile_size, tile_size)
scene = window.Scene()
scene.add(image_actor)
scene.add(peak_actor)
xfov_min, xfov_max = 0, new_shape[0] - 1
yfov_min, yfov_max = 0, new_shape[1] - 1
zfov_min, zfov_max = 0, new_shape[2] - 1
peak_actor.display_extent(xfov_min, xfov_max, yfov_min, yfov_max, zfov_min,
zfov_max)
image_actor.display_extent(xfov_min, xfov_max, yfov_min, yfov_max,
zfov_min, zfov_max)
scene.set_camera(focal_point=tuple(midpoint),
position=tuple(position),
view_up=view_up[axis])
window.record(scene,
out_path=out_file,
reset_camera=False,
size=image_size)
scene.clear()
-1,
forceObj=[-500, 0, 0],
posObj=pos,
flags=p.WORLD_FRAME)
apply_force = False
pos = p.getLinkState(rope, p.getNumJoints(rope) - 1)[4]
ball_actor.SetPosition(*pos)
sync_chain(rope_actor, rope)
utils.update_actor(brick_actor)
utils.update_actor(rope_actor)
# Simulate a step.
p.stepSimulation()
if cnt == 130:
showm.exit()
# Add the timer callback to showmanager.
# Increasing the duration value will slow down the simulation.
showm.add_timer_callback(True, 1, timer_callback)
interactive = False
# start simulation
if interactive:
showm.start()
window.record(scene, size=(900, 768), out_path="viz_wrecking_ball.png")
showm.initialize()
counter = itertools.count()
# After some steps we will remove the no_depth_test effect
def timer_callback(obj, event):
cnt = next(counter)
showm.render()
# we will rotate the visualization just to help you to see
# the results of each specifc opengl-state
showm.scene.azimuth(1)
if cnt == 400:
remove_observer_from_actor(actor_no_depth_test, id_observer)
shader_apply_effects(showm.window,
actor_no_depth_test,
effects=window.gl_set_additive_blending)
if cnt == 1000:
showm.exit()
interactive = False
showm.add_timer_callback(interactive, 5, timer_callback)
if interactive:
showm.start()
window.record(scene,
out_path='viz_fine_tuning_gl_context.png',
size=(600, 600))
###############################################################################
# The final step! Visualize the result of our creation! Also, we need to move
# the camera a little bit farther from the network. you can increase the
# parameter max_iteractions of the timer callback to let the animation run for
# more time.
showm = window.ShowManager(scene,
reset_camera=False,
size=(900, 768),
order_transparent=True,
multi_samples=8)
showm.initialize()
scene.set_camera(position=(0, 0, -300))
timer_callback = new_layout_timer(showm,
edges,
vertices_count,
max_iterations=200,
vertex_initial_positions=positions)
# Run every 16 milliseconds
showm.add_timer_callback(True, 16, timer_callback)
showm.start()
window.record(showm.scene,
size=(900, 768),
out_path="viz_animated_networks.png")
