FroggieSurface
Repository source: FroggieSurface
Description¶
Construct surfaces from a segmented frog dataset. Up to fifteen different surfaces may be extracted. The example, FroggieView is similar to this example and uses sliders to control the opacities of the tissues.
By default the frog is oriented so that we look down on the dorsal (posterior) surface and the superior surface faces the top of the screen. The frog is rendered with the skin being translucent so that you can see the internal organs.
In the lower left of the image there is a prop assembly with labelled XYZ axes and a cube labelled with anatomical orientations:
- Sagittal plane
- L - left
- R - right
- Coronal plane
- A - anterior
- P - posterior
- Transverse plane
- S - superior
- I - inferior
This prop assembly can be moved and resized.
Individual tissues can be specified by using the "-t" option e.g. "-t skin skeleton".
We use vtkFlyingEdges3D to take the 3D structured point set and generate the iso-surfaces. However, if desired, you can specify vtkMarchingCubes instead, use the option "-m".
The parameters used to generate the example image are loaded from a JSON file containing the data needed to access and generate the actors for each tissue along with other supplementary data such as the data file names. This means that the user need only load this one file in order to generate the data for rendering. This file is called:
<DATA>/Frog_mhd.json
Where <DATA> is the path to vtk-examples/src/Testing/Data.
For information about the parameters in the JSON file, please see Frog_mhd_format.
The code uses a general way of specifying transformations that can permute image and other geometric data in order to maintain proper orientation regardless of the acquisition order. See the class SliceOrder.
The dataset was prepared at the Lawrence Berkeley National Laboratories and is included with their permission. The data was acquired by physically slicing the frog and photographing the slices. The original segmented data is in the form of tissue masks with one file per tissue. There are 136 slices per tissue and 15 different tissues. Each slice is 470 by 500 pixels.
To accommodate the volume readers in VTK, the mask files were processed and combined into one vtkMetaImageReader file, called frogtissue.mhd. Integer numbers 1-15 are used to represent the 15 tissues. A similar process was done for the frog skin with the result being stored in a file called frog.mhd.
Further information:
Info
Mutually exclusive options "-a, -b, -c, -d" are provided to let you generate approximations to the following figures: Figure 12-9a, Figure 12-9b, Figure 12-9c, and Figure 12-9d in Chapter 12 of the VTK Textbook.
Other languages
See (Cxx), (PythonicAPI)
Question
If you have a question about this example, please use the VTK Discourse Forum
Code¶
FroggieSurface.py
#!/usr/bin/env python3
import copy
import json
from pathlib import Path
# noinspection PyUnresolvedReferences
import vtkmodules.vtkInteractionStyle
# noinspection PyUnresolvedReferences
import vtkmodules.vtkRenderingOpenGL2
from vtkmodules.vtkCommonColor import vtkNamedColors
from vtkmodules.vtkCommonCore import vtkLookupTable
from vtkmodules.vtkCommonMath import vtkMatrix4x4
from vtkmodules.vtkCommonTransforms import vtkTransform
from vtkmodules.vtkFiltersCore import (
vtkDecimatePro,
vtkFlyingEdges3D,
vtkMarchingCubes,
vtkPolyDataNormals,
vtkStripper,
vtkWindowedSincPolyDataFilter
)
from vtkmodules.vtkFiltersGeneral import vtkTransformPolyDataFilter
from vtkmodules.vtkIOImage import vtkMetaImageReader
from vtkmodules.vtkImagingCore import (
vtkImageShrink3D,
vtkImageThreshold
)
from vtkmodules.vtkImagingGeneral import vtkImageGaussianSmooth
from vtkmodules.vtkImagingMorphological import vtkImageIslandRemoval2D
from vtkmodules.vtkInteractionStyle import vtkInteractorStyleTrackballCamera
from vtkmodules.vtkInteractionWidgets import (
vtkCameraOrientationWidget,
vtkOrientationMarkerWidget
)
from vtkmodules.vtkRenderingAnnotation import (
vtkAnnotatedCubeActor,
vtkAxesActor
)
from vtkmodules.vtkRenderingCore import (
vtkActor,
vtkPolyDataMapper,
vtkPropAssembly,
vtkRenderWindow,
vtkRenderWindowInteractor,
vtkRenderer
)
def get_program_parameters(argv):
import argparse
description = 'Construct surfaces from a segmented frog dataset.'
epilogue = '''
Up to fifteen different surfaces may be extracted.
Note:
If you want to use brainbin (the brain with no gaussian smoothing),
instead of brain, then request it with -t brainbin
'''
parser = argparse.ArgumentParser(description=description, epilog=epilogue,
formatter_class=argparse.RawDescriptionHelpFormatter)
group = parser.add_mutually_exclusive_group()
group.add_argument('-a', action='store_const', dest='view', const='a',
help='The view corresponds to Fig 12-9a in the VTK Textbook')
group.add_argument('-b', action='store_const', dest='view', const='b',
help='The view corresponds to Fig 12-9b in the VTK Textbook')
group.add_argument('-c', action='store_const', dest='view', const='c',
help='The view corresponds to Fig 12-9c in the VTK Textbook')
group.add_argument('-d', action='store_const', dest='view', const='d',
help='The view corresponds to Fig 12-9d in the VTK Textbook')
group.add_argument('-l', action='store_const', dest='view', const='l',
help='The view corresponds to looking down on the anterior surface')
group.add_argument('-p', action='store_const', dest='view', const='p',
help='The view corresponds to looking down on the posterior surface (the default)')
parser.set_defaults(type=None)
parser.add_argument('file_name', help='The path to the JSON file e.g. Frog_mhd.json.')
parser.add_argument('-t', nargs='+', dest='tissues', action='append', help='Select one or more tissues.')
parser.add_argument('-m', action='store_false', dest='flying_edges',
help='Use flying edges by default, marching cubes if set.')
# -o: obliterate a synonym for decimation.
parser.add_argument('-o', action='store_true', dest='decimation', help='Decimate if set.')
args = parser.parse_args()
return args.file_name, args.view, args.tissues, args.flying_edges, args.decimation
def main(fn, select_figure, chosen_tissues, flying_edges, decimate):
if not select_figure:
select_figure = 'p'
fn_path = Path(fn)
if not fn_path.suffix:
fn_path = fn_path.with_suffix(".json")
if not fn_path.is_file():
print('Unable to find: ', fn_path)
parsed_ok, parameters = parse_json(fn_path)
if not parsed_ok:
print('Unable to parse the JSON file.')
return
tissues = list()
indices = dict()
for n in parameters['names']:
if n != 'brainbin':
tissues.append(n)
indices[n] = parameters[n]['tissue']
color_lut = create_tissue_lut(indices, parameters['colors'])
if select_figure:
if select_figure == 'b':
# No skin.
tissues = parameters['fig12-9b']
if select_figure in ['c', 'd']:
# No skin, blood and skeleton.
tissues = parameters['fig12-9cd']
if chosen_tissues:
chosen_tissues = [x.lower() for x in chosen_tissues[0]]
res = list()
has_brainbin = False
if 'brainbin' in chosen_tissues:
print('Using brainbin instead of brain.')
res.append('brainbin')
indices.pop('brain', None)
indices['brainbin'] = 2
parameters['colors'].pop('brain', None)
parameters['colors']['brainbin'] = 'beige'
has_brainbin = True
for ct in chosen_tissues:
if has_brainbin and ct in ['brain', 'brainbin']:
continue
if ct in tissues:
res.append(ct)
else:
print(f'Tissue: {ct} is not available.')
print(f'Available tissues are: {", ".join(tissues)} and brainbin')
return
if len(res) == 1 and 'skin' in res:
parameters['skin']['opacity'] = 1.0
tissues = res
colors = vtkNamedColors()
colors.SetColor("ParaViewBkg", [82, 87, 110, 255])
# Setup render window, renderer, and interactor.
ren = vtkRenderer()
ren_win = vtkRenderWindow()
ren_win.AddRenderer(ren)
iren = vtkRenderWindowInteractor()
iren.SetRenderWindow(ren_win)
style = vtkInteractorStyleTrackballCamera()
iren.SetInteractorStyle(style)
color_size = len(max(parameters['colors'].values(), key=len))
name_size = len(max(parameters['names'], key=len))
int_size = 2
line = '-' * (7 + name_size + color_size)
res = [line,
f'{"Tissue":<{name_size}s}{" Label "}{"Color"}',
line]
so = SliceOrder()
for name in tissues:
actor = create_tissue_actor(name, parameters[name], parameters['mhd_files'], flying_edges, decimate,
color_lut, so)
ren.AddActor(actor)
res.append(f'{name:<{name_size}s} {indices[name]:{int_size + 3}d} {parameters["colors"][name]:<{color_size}s}')
res.append(line)
print('\n'.join(res))
ren_win.SetSize(1024, 1024)
ren_win.SetWindowName('FroggieSurface')
ren.SetBackground(colors.GetColor3d('ParaViewBkg'))
# Final view.
camera = ren.GetActiveCamera()
# Superior Anterior Left
labels = 'sal'
if select_figure == 'a':
# Fig 12-9a in the VTK Textbook
camera.SetPosition(742.731237, -441.329635, -877.192015)
camera.SetFocalPoint(247.637687, 120.680880, -253.487473)
camera.SetViewUp(-0.323882, -0.816232, 0.478398)
camera.SetDistance(974.669585)
camera.SetClippingRange(311.646383, 1803.630763)
elif select_figure == 'b':
# Fig 12-9b in the VTK Textbook
camera.SetPosition(717.356065, -429.889054, -845.381584)
camera.SetFocalPoint(243.071719, 100.996487, -247.446340)
camera.SetViewUp(-0.320495, -0.820148, 0.473962)
camera.SetDistance(929.683631)
camera.SetClippingRange(293.464446, 1732.794957)
elif select_figure == 'c':
# Fig 12-9c in the VTK Textbook
camera.SetPosition(447.560023, -136.611491, -454.753689)
camera.SetFocalPoint(253.142277, 91.949451, -238.583973)
camera.SetViewUp(-0.425438, -0.786048, 0.448477)
camera.SetDistance(369.821187)
camera.SetClippingRange(0.829116, 829.115939)
elif select_figure == 'd':
# Fig 12-9d in the VTK Textbook
camera.SetPosition(347.826249, -469.633647, -236.234262)
camera.SetFocalPoint(296.893207, 89.307704, -225.156581)
camera.SetViewUp(-0.687345, -0.076948, 0.722244)
camera.SetDistance(561.366478)
camera.SetClippingRange(347.962064, 839.649856)
elif select_figure == 'l':
# Orient so that we look down on the anterior surface and
# the superior surface faces the top of the screen.
# Left Superior Anterior
labels = 'lsa'
transform = vtkTransform()
transform.SetMatrix(camera.GetModelTransformMatrix())
transform.RotateY(90)
transform.RotateZ(90)
camera.SetModelTransformMatrix(transform.GetMatrix())
ren.ResetCamera()
else:
# The default.
# Orient so that we look down on the posterior surface and
# the superior surface faces the top of the screen.
# Right Superior Posterior
labels = 'rsp'
transform = vtkTransform()
transform.SetMatrix(camera.GetModelTransformMatrix())
transform.RotateY(-90)
transform.RotateZ(90)
camera.SetModelTransformMatrix(transform.GetMatrix())
ren.ResetCamera()
cow = vtkCameraOrientationWidget()
cow.SetParentRenderer(ren)
# Turn off if you do not want it.
cow.On()
cow.EnabledOn()
axes = make_cube_actor(labels, colors)
om = vtkOrientationMarkerWidget()
om.SetOrientationMarker(axes)
# Position upper left in the viewport.
# om.SetViewport(0.0, 0.8, 0.2, 1.0)
# Position lower left in the viewport.
om.SetViewport(0, 0, 0.2, 0.2)
om.SetInteractor(iren)
om.EnabledOn()
om.InteractiveOn()
ren_win.Render()
iren.Start()
def parse_json(fn_path):
"""
Parse the JSON file selecting the components that we want.
We also check that the file paths are valid.
:param fn_path: The path the JSON file.
:return: A dictionary of the parameters that we require.
"""
with open(fn_path) as data_file:
json_data = json.load(data_file)
paths_ok = True
parameters = dict()
# The names of the tissues as a list.
parameters['names'] = list()
for k, v in json_data.items():
if k == 'files':
if 'root' in v:
root = Path(v['root'])
if not root.exists():
print(f'Bad path: {root}')
paths_ok = False
else:
if 'mhd_files' not in v:
print('Expected mhd files.')
paths_ok = False
continue
for kk in v:
if kk == 'mhd_files':
if len(v[kk]) != 2:
print(f'Expected two file names.')
paths_ok = False
# The stem of the file path becomes the key.
path_map = dict()
for p in list(map(lambda pp: root / pp, v[kk])):
path_map[p.stem] = p
if not p.is_file():
paths_ok = False
print(f'Not a file {p}')
if paths_ok:
parameters[kk] = path_map
else:
paths_ok = False
print('Missing the key "root" and/or the key "files" for the files.')
else:
if k in ['tissues', 'figures']:
for kk, vv in v.items():
parameters[kk] = vv
if k == "tissue_parameters":
# Assemble the parameters for each tissue.
# Create the base parameters.
bp = dict()
for kk, vv in v['default'].items():
bp[kk.lower()] = vv
frog = copy.deepcopy(bp)
for kk, vv in v['frog'].items():
frog[kk.lower()] = vv
for kk, vv in v.items():
if kk not in ['default', 'frog', 'parameter types']:
if kk == 'skin':
parameters[kk] = copy.deepcopy(bp)
else:
parameters[kk] = copy.deepcopy(frog)
for kkk, vvv in vv.items():
parameters[kk][kkk.lower()] = vvv
if kkk == 'NAME':
parameters['names'].append(vvv)
return paths_ok, parameters
def create_tissue_actor(name, tissue, files, flying_edges, decimate, lut, so):
"""
Create the actor for a specific tissue.
:param name: The tissue name.
:param tissue: The tissue parameters.
:param files: The path to the tissue files.
:param flying_edges: If true use flying edges.
:param decimate: If true decimate.
:param lut: The color lookup table for the tissues.
:param so: The transforms corresponding to the slice order.
:return: The actor.
"""
pixel_size = tissue['pixel_size']
spacing = tissue['spacing']
start_slice = tissue['start_slice']
data_spacing = [pixel_size, pixel_size, spacing]
columns = tissue['columns']
rows = tissue['rows']
data_origin = [-(columns / 2.0) * pixel_size, -(rows / 2.0) * pixel_size, start_slice * spacing]
voi = [
tissue['start_column'],
tissue['end_column'],
tissue['start_row'],
tissue['end_row'],
tissue['start_slice'],
tissue['end_slice'],
]
# Adjust y bounds for PNM coordinate system.
tmp = voi[2]
voi[2] = rows - voi[3] - 1
voi[3] = rows - tmp - 1
if name == 'skin':
fn = files['frog']
else:
fn = files['frogtissue']
reader = vtkMetaImageReader()
reader.SetFileName(str(fn))
reader.SetDataSpacing(data_spacing)
reader.SetDataOrigin(data_origin)
reader.SetDataExtent(voi)
reader.Update()
last_connection = reader
if not name == 'skin':
if tissue['island_replace'] >= 0:
island_remover = vtkImageIslandRemoval2D()
island_remover.SetAreaThreshold(tissue['island_area'])
island_remover.SetIslandValue(tissue['island_replace'])
island_remover.SetReplaceValue(tissue['tissue'])
island_remover.SetInput(last_connection.GetOutput())
island_remover.Update()
last_connection = island_remover
select_tissue = vtkImageThreshold()
select_tissue.ThresholdBetween(tissue['tissue'], tissue['tissue'])
select_tissue.SetInValue(255)
select_tissue.SetOutValue(0)
select_tissue.SetInputConnection(last_connection.GetOutputPort())
last_connection = select_tissue
sample_rate = [
tissue['sample_rate_column'],
tissue['sample_rate_row'],
tissue['sample_rate_slice'],
]
shrinker = vtkImageShrink3D()
shrinker.SetInputConnection(last_connection.GetOutputPort())
shrinker.SetShrinkFactors(sample_rate)
shrinker.AveragingOn()
last_connection = shrinker
gsd = [
tissue['gaussian_standard_deviation_column'],
tissue['gaussian_standard_deviation_row'],
tissue['gaussian_standard_deviation_slice'],
]
if not all(v == 0 for v in gsd):
grf = [
tissue['gaussian_radius_factor_column'],
tissue['gaussian_radius_factor_row'],
tissue['gaussian_radius_factor_slice'],
]
gaussian = vtkImageGaussianSmooth()
gaussian.SetStandardDeviation(*gsd)
gaussian.SetRadiusFactors(*grf)
gaussian.SetInputConnection(shrinker.GetOutputPort())
last_connection = gaussian
iso_value = tissue['value']
if flying_edges:
iso_surface = vtkFlyingEdges3D()
iso_surface.SetInputConnection(last_connection.GetOutputPort())
iso_surface.ComputeScalarsOff()
iso_surface.ComputeGradientsOff()
iso_surface.ComputeNormalsOff()
iso_surface.SetValue(0, iso_value)
iso_surface.Update()
else:
iso_surface = vtkMarchingCubes()
iso_surface.SetInputConnection(last_connection.GetOutputPort())
iso_surface.ComputeScalarsOff()
iso_surface.ComputeGradientsOff()
iso_surface.ComputeNormalsOff()
iso_surface.SetValue(0, iso_value)
iso_surface.Update()
transform = so.get(tissue['slice_order'])
tf = vtkTransformPolyDataFilter()
tf.SetTransform(transform)
tf.SetInputConnection(iso_surface.GetOutputPort())
last_connection = tf
if decimate:
decimator = vtkDecimatePro()
decimator.SetInputConnection(last_connection.GetOutputPort())
decimator.SetFeatureAngle(tissue['decimate_angle'])
decimator.PreserveTopologyOn()
decimator.SetErrorIsAbsolute(1)
decimator.SetAbsoluteError(tissue['decimate_error'])
decimator.SetTargetReduction(tissue['decimate_reduction'])
last_connection = decimator
smooth_iterations = tissue['smooth_iterations']
if smooth_iterations != 0:
smoother = vtkWindowedSincPolyDataFilter()
smoother.SetInputConnection(last_connection.GetOutputPort())
smoother.BoundarySmoothingOff()
smoother.FeatureEdgeSmoothingOff()
smoother.SetFeatureAngle(tissue['smooth_angle'])
smoother.SetPassBand(tissue['smooth_factor'])
smoother.NonManifoldSmoothingOn()
smoother.NormalizeCoordinatesOff()
last_connection = smoother
normals = vtkPolyDataNormals()
normals.SetInputConnection(last_connection.GetOutputPort())
normals.SetFeatureAngle(tissue['feature_angle'])
stripper = vtkStripper()
stripper.SetInputConnection(normals.GetOutputPort())
mapper = vtkPolyDataMapper()
mapper.SetInputConnection(stripper.GetOutputPort())
actor = vtkActor()
actor.SetMapper(mapper)
actor.GetProperty().SetOpacity(tissue['opacity'])
actor.GetProperty().SetDiffuseColor(lut.GetTableValue(tissue['tissue'])[:3])
actor.GetProperty().SetSpecular(0.5)
actor.GetProperty().SetSpecularPower(10)
return actor
class SliceOrder:
"""
These transformations permute image and other geometric data to maintain proper
orientation regardless of the acquisition order. After applying these transforms with
vtkTransformFilter, a view up of 0, -1, 0 will result in the body part
facing the viewer.
NOTE: some transformations have a -1 scale factor for one of the components.
To ensure proper polygon orientation and normal direction, you must
apply the vtkPolyDataNormals filter.
Naming (the nomenclature is medical):
si - superior to inferior (top to bottom)
is - inferior to superior (bottom to top)
ap - anterior to posterior (front to back)
pa - posterior to anterior (back to front)
lr - left to right
rl - right to left
"""
def __init__(self):
self.si_mat = vtkMatrix4x4()
self.si_mat.Zero()
self.si_mat.SetElement(0, 0, 1)
self.si_mat.SetElement(1, 2, 1)
self.si_mat.SetElement(2, 1, -1)
self.si_mat.SetElement(3, 3, 1)
self.is_mat = vtkMatrix4x4()
self.is_mat.Zero()
self.is_mat.SetElement(0, 0, 1)
self.is_mat.SetElement(1, 2, -1)
self.is_mat.SetElement(2, 1, -1)
self.is_mat.SetElement(3, 3, 1)
self.lr_mat = vtkMatrix4x4()
self.lr_mat.Zero()
self.lr_mat.SetElement(0, 2, -1)
self.lr_mat.SetElement(1, 1, -1)
self.lr_mat.SetElement(2, 0, 1)
self.lr_mat.SetElement(3, 3, 1)
self.rl_mat = vtkMatrix4x4()
self.rl_mat.Zero()
self.rl_mat.SetElement(0, 2, 1)
self.rl_mat.SetElement(1, 1, -1)
self.rl_mat.SetElement(2, 0, 1)
self.rl_mat.SetElement(3, 3, 1)
"""
The previous transforms assume radiological views of the slices
(viewed from the feet).
Other modalities such as physical sectioning may view from the head.
The following transforms modify the original with a 180° rotation about y
"""
self.hf_mat = vtkMatrix4x4()
self.hf_mat.Zero()
self.hf_mat.SetElement(0, 0, -1)
self.hf_mat.SetElement(1, 1, 1)
self.hf_mat.SetElement(2, 2, -1)
self.hf_mat.SetElement(3, 3, 1)
self.transform = dict()
si_trans = vtkTransform()
si_trans.SetMatrix(self.si_mat)
self.transform['si'] = si_trans
is_trans = vtkTransform()
is_trans.SetMatrix(self.is_mat)
self.transform['is'] = is_trans
ap_trans = vtkTransform()
ap_trans.Scale(1, -1, 1)
self.transform['ap'] = ap_trans
pa_trans = vtkTransform()
pa_trans.Scale(1, -1, -1)
self.transform['pa'] = pa_trans
lr_trans = vtkTransform()
lr_trans.SetMatrix(self.lr_mat)
self.transform['lr'] = lr_trans
rl_trans = vtkTransform()
rl_trans.SetMatrix(self.rl_mat)
self.transform['rl'] = rl_trans
hf_trans = vtkTransform()
hf_trans.SetMatrix(self.hf_mat)
self.transform['hf'] = hf_trans
hf_si_trans = vtkTransform()
hf_si_trans.SetMatrix(self.hf_mat)
hf_si_trans.Concatenate(self.si_mat)
self.transform['hfsi'] = hf_si_trans
hf_is_trans = vtkTransform()
hf_is_trans.SetMatrix(self.hf_mat)
hf_is_trans.Concatenate(self.is_mat)
self.transform['hfis'] = hf_is_trans
hf_ap_trans = vtkTransform()
hf_ap_trans.SetMatrix(self.hf_mat)
hf_ap_trans.Scale(1, -1, 1)
self.transform['hfap'] = hf_ap_trans
hf_pa_trans = vtkTransform()
hf_pa_trans.SetMatrix(self.hf_mat)
hf_pa_trans.Scale(1, -1, -1)
self.transform['hfpa'] = hf_pa_trans
hf_lr_trans = vtkTransform()
hf_lr_trans.SetMatrix(self.hf_mat)
hf_lr_trans.Concatenate(self.lr_mat)
self.transform['hflr'] = hf_lr_trans
hf_rl_trans = vtkTransform()
hf_rl_trans.SetMatrix(self.hf_mat)
hf_rl_trans.Concatenate(self.rl_mat)
self.transform['hfrl'] = hf_rl_trans
def print_transform(self, order):
"""
Print the homogenous matrix corresponding to the slice order.
:param order: The slice order.
:return:
"""
print(order)
m = self.transform[order].GetMatrix()
for i in range(0, 4):
row = list()
for j in range(0, 4):
row.append(f'{m.GetElement(i, j):6.2g}')
print(' '.join(row))
def print_all_transforms(self):
"""
Print all the homogenous matrices corresponding to the slice orders.
:return:
"""
for k in self.transform.keys():
self.print_transform(k)
def get(self, order):
"""
Returns the vtkTransform corresponding to the slice order.
:param order: The slice order.
:return: The vtkTransform to use.
"""
if order in self.transform.keys():
return self.transform[order]
else:
s = 'No such transform "{:s}" exists.'.format(order)
raise Exception(s)
def create_tissue_lut(indices, colors):
"""
Create the lookup table for the frog tissues.
Each table value corresponds the color of one of the frog tissues.
:param indices: The tissue name and index.
:param colors: The tissue name and color.
:return: The lookup table.
"""
lut = vtkLookupTable()
lut.SetNumberOfColors(len(colors))
lut.SetTableRange(0, len(colors) - 1)
lut.Build()
nc = vtkNamedColors()
for k in indices.keys():
lut.SetTableValue(indices[k], nc.GetColor4d(colors[k]))
return lut
def make_axes_actor(scale, xyz_labels):
"""
:param scale: Sets the scale and direction of the axes.
:param xyz_labels: Labels for the axes.
:return: The axes actor.
"""
axes = vtkAxesActor()
axes.SetScale(scale)
axes.SetShaftTypeToCylinder()
axes.SetXAxisLabelText(xyz_labels[0])
axes.SetYAxisLabelText(xyz_labels[1])
axes.SetZAxisLabelText(xyz_labels[2])
axes.SetCylinderRadius(0.5 * axes.GetCylinderRadius())
axes.SetConeRadius(1.025 * axes.GetConeRadius())
axes.SetSphereRadius(1.5 * axes.GetSphereRadius())
tprop = axes.GetXAxisCaptionActor2D().GetCaptionTextProperty()
tprop.ItalicOn()
tprop.ShadowOn()
tprop.SetFontFamilyToTimes()
# Use the same text properties on the other two axes.
axes.GetYAxisCaptionActor2D().GetCaptionTextProperty().ShallowCopy(tprop)
axes.GetZAxisCaptionActor2D().GetCaptionTextProperty().ShallowCopy(tprop)
return axes
def make_annotated_cube_actor(cube_labels, colors):
"""
:param cube_labels: The labels for the cube faces.
:param colors: Used to determine the cube color.
:return: The annotated cube actor.
"""
# A cube with labeled faces.
cube = vtkAnnotatedCubeActor()
cube.SetXPlusFaceText(cube_labels[0])
cube.SetXMinusFaceText(cube_labels[1])
cube.SetYPlusFaceText(cube_labels[2])
cube.SetYMinusFaceText(cube_labels[3])
cube.SetZPlusFaceText(cube_labels[4])
cube.SetZMinusFaceText(cube_labels[5])
cube.SetFaceTextScale(0.5)
cube.GetCubeProperty().SetColor(colors.GetColor3d('Gainsboro'))
cube.GetTextEdgesProperty().SetColor(colors.GetColor3d('LightSlateGray'))
# Change the vector text colors.
cube.GetXPlusFaceProperty().SetColor(colors.GetColor3d('Tomato'))
cube.GetXMinusFaceProperty().SetColor(colors.GetColor3d('Tomato'))
cube.GetYPlusFaceProperty().SetColor(colors.GetColor3d('DeepSkyBlue'))
cube.GetYMinusFaceProperty().SetColor(colors.GetColor3d('DeepSkyBlue'))
cube.GetZPlusFaceProperty().SetColor(colors.GetColor3d('SeaGreen'))
cube.GetZMinusFaceProperty().SetColor(colors.GetColor3d('SeaGreen'))
return cube
def make_cube_actor(label_selector, colors):
"""
:param label_selector: The selector used to define labels for the axes and cube.
:param colors: Used to set the colors of the cube faces.
:return: The combined axes and annotated cube prop.
"""
if label_selector == 'sal':
# xyz_labels = ['S', 'A', 'L']
xyz_labels = ['+X', '+Y', '+Z']
cube_labels = ['S', 'I', 'A', 'P', 'L', 'R']
scale = [1.5, 1.5, 1.5]
elif label_selector == 'rsp':
# xyz_labels = ['R', 'S', 'P']
xyz_labels = ['+X', '+Y', '+Z']
cube_labels = ['R', 'L', 'S', 'I', 'P', 'A']
scale = [1.5, 1.5, 1.5]
elif label_selector == 'lsa':
# xyz_labels = ['L', 'S', 'A']
xyz_labels = ['+X', '+Y', '+Z']
cube_labels = ['L', 'R', 'S', 'I', 'A', 'P']
scale = [1.5, 1.5, 1.5]
else:
xyz_labels = ['+X', '+Y', '+Z']
cube_labels = ['+X', '-X', '+Y', '-Y', '+Z', '-Z']
scale = [1.5, 1.5, 1.5]
# We are combining a vtkAxesActor and a vtkAnnotatedCubeActor
# into a vtkPropAssembly
cube = make_annotated_cube_actor(cube_labels, colors)
axes = make_axes_actor(scale, xyz_labels)
# Combine orientation markers into one with an assembly.
assembly = vtkPropAssembly()
assembly.AddPart(axes)
assembly.AddPart(cube)
return assembly
if __name__ == '__main__':
import sys
data_folder, view, selected_tissues, use_flying_edges, use_decimate = get_program_parameters(sys.argv)
main(data_folder, view, selected_tissues, use_flying_edges, use_decimate)