def __init__(self, module_manager):
# initialise our base class
ModuleBase.__init__(self, module_manager)
# initialise any mixins we might have
NoConfigModuleMixin.__init__(self)
# we'll be playing around with some vtk objects, this could
# be anything
self._thresh = vtk.vtkThresholdPoints()
# this is wacked syntax!
self._thresh.ThresholdByUpper(1)
self._reconstructionFilter = vtk.vtkSurfaceReconstructionFilter()
self._reconstructionFilter.SetInput(self._thresh.GetOutput())
self._mc = vtk.vtkMarchingCubes()
self._mc.SetInput(self._reconstructionFilter.GetOutput())
self._mc.SetValue(0, 0.0)
module_utils.setup_vtk_object_progress(self, self._thresh,
'Extracting points...')
module_utils.setup_vtk_object_progress(self, self._reconstructionFilter,
'Reconstructing...')
module_utils.setup_vtk_object_progress(self, self._mc,
'Extracting surface...')
self._iObj = self._thresh
self._oObj = self._mc
self._viewFrame = self._createViewFrame({'threshold' :
self._thresh,
'reconstructionFilter' :
self._reconstructionFilter,
'marchingCubes' :
self._mc})
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
vtk.vtkThresholdPoints(), 'Processing.',
('vtkDataSet',), ('vtkPolyData',),
replaceDoc=True,
inputFunctions=None, outputFunctions=None)
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(self,
module_manager,
vtk.vtkThresholdPoints(),
'Processing.', ('vtkDataSet', ),
('vtkPolyData', ),
replaceDoc=True,
inputFunctions=None,
outputFunctions=None)
def select(connected):
selector = vtk.vtkThresholdPoints()
selector.SetInput(connected.GetOutput())
print n_regions
for i in range(10,11):#change to n_regions
selector.ThresholdBetween(48,48)
selector.SetInputArrayToProcess(1, 0, 0, vtk.vtkDataObject.FIELD_ASSOCIATION_CELLS, "RegionId" )
selector.Update()
triangles = vtk.vtkTriangleFilter()
triangles.SetInputConnection(selector.GetOutputPort())
[V, A] = getMassProperties(triangles)
print ("The volume is: " + str(V) + "\n")
return selector
def select(connected):
selector = vtk.vtkThresholdPoints()
selector.SetInput(connected.GetOutput())
print n_regions
for i in range(10, 11): #change to n_regions
selector.ThresholdBetween(48, 48)
selector.SetInputArrayToProcess(
1, 0, 0, vtk.vtkDataObject.FIELD_ASSOCIATION_CELLS, "RegionId")
selector.Update()
triangles = vtk.vtkTriangleFilter()
triangles.SetInputConnection(selector.GetOutputPort())
[V, A] = getMassProperties(triangles)
print("The volume is: " + str(V) + "\n")
return selector
TubeMapper = vtk.vtkPolyDataMapper()
TubeMapper.SetInputConnection(Tubes.GetOutputPort())
TubeMapper.ScalarVisibilityOff()
CubeEdges = vtk.vtkActor()
CubeEdges.SetMapper(TubeMapper)
CubeEdges.GetProperty().SetDiffuseColor(GetRGBColor('khaki'))
CubeEdges.GetProperty().SetSpecular(.4)
CubeEdges.GetProperty().SetSpecularPower(10)
# build the vertices of the cube
#
Sphere = vtk.vtkSphereSource()
Sphere.SetRadius(0.04)
Sphere.SetPhiResolution(20)
Sphere.SetThetaResolution(20)
ThresholdIn = vtk.vtkThresholdPoints()
ThresholdIn.SetInputData(grid)
ThresholdIn.ThresholdByUpper(.5)
Vertices = vtk.vtkGlyph3D()
Vertices.SetInputConnection(ThresholdIn.GetOutputPort())
Vertices.SetSourceConnection(Sphere.GetOutputPort())
SphereMapper = vtk.vtkPolyDataMapper()
SphereMapper.SetInputConnection(Vertices.GetOutputPort())
SphereMapper.ScalarVisibilityOff()
CubeVertices = vtk.vtkActor()
CubeVertices.SetMapper(SphereMapper)
CubeVertices.GetProperty().SetDiffuseColor(GetRGBColor('tomato'))
# define the text for the labels
caseLabel = vtk.vtkVectorText()
caseLabel.SetText("Case 1")
def main():
fileName = r"carotid.vtk"
colors = vtk.vtkNamedColors()
ren1 = vtk.vtkRenderer()
renWin = vtk.vtkRenderWindow()
renWin.AddRenderer(ren1)
iren = vtk.vtkRenderWindowInteractor()
iren.SetRenderWindow(renWin)
# Create the pipeline.
reader = vtk.vtkStructuredPointsReader()
reader.SetFileName(fileName)
threshold = vtk.vtkThresholdPoints()
threshold.SetInputConnection(reader.GetOutputPort())
threshold.ThresholdByUpper(200)
mask = vtk.vtkMaskPoints()
mask.SetInputConnection(threshold.GetOutputPort())
mask.SetOnRatio(5)
cone = vtk.vtkConeSource()
cone.SetResolution(11)
cone.SetHeight(1)
cone.SetRadius(0.25)
cones = vtk.vtkGlyph3D()
cones.SetInputConnection(mask.GetOutputPort())
cones.SetSourceConnection(cone.GetOutputPort())
cones.SetScaleFactor(0.4)
cones.SetScaleModeToScaleByVector()
lut = vtk.vtkLookupTable()
lut.SetHueRange(.667, 0.0)
lut.Build()
scalarRange = [0] * 2
cones.Update()
scalarRange[0] = cones.GetOutput().GetPointData().GetScalars().GetRange(
)[0]
scalarRange[1] = cones.GetOutput().GetPointData().GetScalars().GetRange(
)[1]
vectorMapper = vtk.vtkPolyDataMapper()
vectorMapper.SetInputConnection(cones.GetOutputPort())
vectorMapper.SetScalarRange(scalarRange[0], scalarRange[1])
vectorMapper.SetLookupTable(lut)
vectorActor = vtk.vtkActor()
vectorActor.SetMapper(vectorMapper)
# Speed contours.
iso = vtk.vtkContourFilter()
iso.SetInputConnection(reader.GetOutputPort())
iso.SetValue(0, 175)
isoMapper = vtk.vtkPolyDataMapper()
isoMapper.SetInputConnection(iso.GetOutputPort())
isoMapper.ScalarVisibilityOff()
isoActor = vtk.vtkActor()
isoActor.SetMapper(isoMapper)
isoActor.GetProperty().SetRepresentationToWireframe()
isoActor.GetProperty().SetOpacity(0.25)
# Outline
outline = vtk.vtkOutlineFilter()
outline.SetInputConnection(reader.GetOutputPort())
outlineMapper = vtk.vtkPolyDataMapper()
outlineMapper.SetInputConnection(outline.GetOutputPort())
outlineActor = vtk.vtkActor()
outlineActor.SetMapper(outlineMapper)
outlineActor.GetProperty().SetColor(0., 0., 0.)
# Add the actors to the renderer, set the background and size.
ren1.AddActor(outlineActor)
ren1.AddActor(vectorActor)
ren1.AddActor(isoActor)
ren1.SetBackground(1., 1., 1.)
renWin.SetSize(640, 480)
ren1.ResetCamera()
ren1.ResetCameraClippingRange()
# Render the image.
renWin.Render()
iren.Start()
renderer.SetBackground(0.2, 0.2, 0.2) interactor.Initialize() # Draw Outline outline = vtk.vtkStructuredGridOutlineFilter() outline.SetInputData(b0) outline_mapper = vtk.vtkPolyDataMapper() outline_mapper.SetInputConnection(outline.GetOutputPort()) outline_actor = vtk.vtkActor() outline_actor.SetMapper(outline_mapper) outline_actor.GetProperty().SetColor(1, 1, 1) renderer.AddActor(outline_actor) renderer.ResetCamera() # Threshold points threshold = vtk.vtkThresholdPoints() threshold.SetInputData(b0) threshold.ThresholdByUpper(0.5) # Draw arrows arrow = vtk.vtkArrowSource() glyphs = vtk.vtkGlyph3D() glyphs.SetInputData(b0) glyphs.SetSourceConnection(arrow.GetOutputPort()) glyphs.SetInputConnection(threshold.GetOutputPort()) glyphs.SetVectorModeToUseVector() glyphs.SetScaleModeToScaleByVector() glyphs.SetScaleFactor(0.005) glyphs.SetColorModeToColorByVector()
def __init__(self, parent, data_dir):
super(QGlyphViewer,self).__init__(parent)
# Make tha actual QtWidget a child so that it can be re parented
interactor = QVTKRenderWindowInteractor(self)
self.layout = QtGui.QHBoxLayout()
self.layout.addWidget(interactor)
self.layout.setContentsMargins(0,0,0,0)
self.setLayout(self.layout)
# Read the data
xyx_file = os.path.join(data_dir, "combxyz.bin")
q_file = os.path.join(data_dir, "combq.bin")
pl3d = vtk.vtkMultiBlockPLOT3DReader()
pl3d.SetXYZFileName(xyx_file)
pl3d.SetQFileName(q_file)
pl3d.SetScalarFunctionNumber(100)
pl3d.SetVectorFunctionNumber(202)
pl3d.Update()
blocks = pl3d.GetOutput()
b0 = blocks.GetBlock(0)
# Setup VTK environment
renderer = vtk.vtkRenderer()
render_window = interactor.GetRenderWindow()
render_window.AddRenderer(renderer)
interactor.SetInteractorStyle(vtk.vtkInteractorStyleTrackballCamera())
render_window.SetInteractor(interactor)
renderer.SetBackground(0.2,0.2,0.2)
# Draw Outline
outline = vtk.vtkStructuredGridOutlineFilter()
outline.SetInputData(b0)
outline_mapper = vtk.vtkPolyDataMapper()
outline_mapper.SetInputConnection(outline.GetOutputPort())
outline_actor = vtk.vtkActor()
outline_actor.SetMapper(outline_mapper)
outline_actor.GetProperty().SetColor(1,1,1)
renderer.AddActor(outline_actor)
renderer.ResetCamera()
# Draw Outline
outline = vtk.vtkStructuredGridOutlineFilter()
outline.SetInputData(b0)
outline_mapper = vtk.vtkPolyDataMapper()
outline_mapper.SetInputConnection(outline.GetOutputPort())
outline_actor = vtk.vtkActor()
outline_actor.SetMapper(outline_mapper)
outline_actor.GetProperty().SetColor(1,1,1)
renderer.AddActor(outline_actor)
renderer.ResetCamera()
# Threshold points
threshold = vtk.vtkThresholdPoints()
threshold.SetInputData(b0)
threshold.ThresholdByUpper(0.5)
# Draw arrows
arrow = vtk.vtkArrowSource()
glyphs = vtk.vtkGlyph3D()
glyphs.SetInputData(b0)
glyphs.SetSourceConnection(arrow.GetOutputPort())
glyphs.SetInputConnection(threshold.GetOutputPort())
glyphs.SetVectorModeToUseVector()
glyphs.SetScaleModeToScaleByVector()
glyphs.SetScaleFactor(0.005)
glyphs.SetColorModeToColorByVector()
# Mapper
glyph_mapper = vtk.vtkPolyDataMapper()
glyph_mapper.SetInputConnection(glyphs.GetOutputPort())
glyph_actor = vtk.vtkActor()
glyph_actor.SetMapper(glyph_mapper)
glyph_mapper.UseLookupTableScalarRangeOn()
renderer.AddActor(glyph_actor)
# Set color lookuptable
glyphs.Update()
s0,sf = glyphs.GetOutput().GetScalarRange()
lut = vtk.vtkColorTransferFunction()
lut.AddRGBPoint(s0, 1,0,0)
lut.AddRGBPoint(sf, 0,1,0)
glyph_mapper.SetLookupTable(lut)
self.b0 = b0
self.renderer = renderer
self.interactor = interactor
self.threshold = threshold
def __init__(self, data_dir):
# Read the data
xyx_file = os.path.join(data_dir, "combxyz.bin")
q_file = os.path.join(data_dir, "combq.bin")
pl3d = vtk.vtkMultiBlockPLOT3DReader()
pl3d.SetXYZFileName(xyx_file)
pl3d.SetQFileName(q_file)
pl3d.SetScalarFunctionNumber(100)
pl3d.SetVectorFunctionNumber(202)
pl3d.Update()
blocks = pl3d.GetOutput()
b0 = blocks.GetBlock(0)
# Setup VTK environment
renderer = vtk.vtkRenderer()
render_window = vtk.vtkRenderWindow()
render_window.AddRenderer(renderer)
interactor = vtk.vtkRenderWindowInteractor()
interactor.SetInteractorStyle(vtk.vtkInteractorStyleTrackballCamera())
render_window.SetInteractor(interactor)
renderer.SetBackground(0.2, 0.2, 0.2)
interactor.Initialize()
# Draw Outline
outline = vtk.vtkStructuredGridOutlineFilter()
outline.SetInputData(b0)
outline_mapper = vtk.vtkPolyDataMapper()
outline_mapper.SetInputConnection(outline.GetOutputPort())
outline_actor = vtk.vtkActor()
outline_actor.SetMapper(outline_mapper)
outline_actor.GetProperty().SetColor(1, 1, 1)
renderer.AddActor(outline_actor)
renderer.ResetCamera()
# Draw Outline
outline = vtk.vtkStructuredGridOutlineFilter()
outline.SetInputData(b0)
outline_mapper = vtk.vtkPolyDataMapper()
outline_mapper.SetInputConnection(outline.GetOutputPort())
outline_actor = vtk.vtkActor()
outline_actor.SetMapper(outline_mapper)
outline_actor.GetProperty().SetColor(1, 1, 1)
renderer.AddActor(outline_actor)
renderer.ResetCamera()
# Threshold points
threshold = vtk.vtkThresholdPoints()
threshold.SetInputData(b0)
threshold.ThresholdByUpper(0.5)
# Draw arrows
arrow = vtk.vtkArrowSource()
glyphs = vtk.vtkGlyph3D()
glyphs.SetInputData(b0)
glyphs.SetSourceConnection(arrow.GetOutputPort())
glyphs.SetInputConnection(threshold.GetOutputPort())
glyphs.SetVectorModeToUseVector()
glyphs.SetScaleModeToScaleByVector()
glyphs.SetScaleFactor(0.005)
glyphs.SetColorModeToColorByVector()
# Mapper
glyph_mapper = vtk.vtkPolyDataMapper()
glyph_mapper.SetInputConnection(glyphs.GetOutputPort())
glyph_actor = vtk.vtkActor()
glyph_actor.SetMapper(glyph_mapper)
glyph_mapper.UseLookupTableScalarRangeOn()
renderer.AddActor(glyph_actor)
# Set color lookuptable
glyphs.Update()
s0, sf = glyphs.GetOutput().GetScalarRange()
lut = vtk.vtkColorTransferFunction()
lut.AddRGBPoint(s0, 1, 0, 0)
lut.AddRGBPoint(sf, 0, 1, 0)
glyph_mapper.SetLookupTable(lut)
self.b0 = b0
self.renderer = renderer
self.interactor = interactor
self.threshold = threshold
interactor.Initialize() # Draw Outline outline = vtk.vtkStructuredGridOutlineFilter() outline.SetInputData(b0) outline_mapper = vtk.vtkPolyDataMapper() outline_mapper.SetInputConnection(outline.GetOutputPort()) outline_actor = vtk.vtkActor() outline_actor.SetMapper(outline_mapper) outline_actor.GetProperty().SetColor(1,1,1) renderer.AddActor(outline_actor) renderer.ResetCamera() # Threshold points threshold = vtk.vtkThresholdPoints() threshold.SetInputData(b0) threshold.ThresholdByUpper(0.5) # Draw arrows arrow = vtk.vtkArrowSource() glyphs = vtk.vtkGlyph3D() glyphs.SetInputData(b0) glyphs.SetSourceConnection(arrow.GetOutputPort()) glyphs.SetInputConnection(threshold.GetOutputPort()) glyphs.SetVectorModeToUseVector() glyphs.SetScaleModeToScaleByVector() glyphs.SetScaleFactor(0.005) glyphs.SetColorModeToColorByVector()
points, strength, time_, = ReadPointsCSV.readPoints("events3.csv")
min_strength, max_strength = strength.GetRange()
min_time, max_time = time_.GetRange() # in seconds
# Assign unique names to the scalar arrays
strength.SetName("strength")
time_.SetName("time")
# Create a vtkPolyData object from the earthquake data and specify
# that "strength" should be the active scalar array
points_polydata = vtk.vtkPolyData()
points_polydata.SetPoints(points)
points_polydata.GetPointData().AddArray(strength)
points_polydata.GetPointData().AddArray(time_)
points_polydata.GetPointData().SetActiveScalars("strength")
# Threshold the earthquake points to extract all points within a
# specified time interval.
#
# If you do not specify which input array to process, i.e., if you
# comment out the SetInputArrayToProcess() call, the thresholding will
# be performed on the active scalar array ("strength", in this case).
threshold_filter = vtk.vtkThresholdPoints()
threshold_filter.SetInput(points_polydata)
threshold_filter.ThresholdBetween(min_time, max_time)
threshold_filter.SetInputArrayToProcess(0, 0, 0, 0, "time")
threshold_filter.Update()
# Connect the output of the threshold filter to a vtkGlyph3D filter
# and proceed with the visualization!
def marching_cubes(mcCases):
color = vtk.vtkNamedColors()
renWin = vtk.vtkRenderWindow()
renWin.SetSize(640, 480)
iren = vtk.vtkRenderWindowInteractor()
iren.SetRenderWindow(renWin)
renderers = list()
gridSize = ((len(mcCases) + 3) // 4) * 4
if len(mcCases) < 4:
gridSize = len(mcCases)
print("gridSize:", gridSize)
for i in range(0, gridSize):
# Create the Renderer
renderer = vtk.vtkRenderer()
renderers.append(renderer)
renWin.AddRenderer(renderer)
for i in range(0, len(mcCases)):
# Define a Single Cube
Scalars = vtk.vtkFloatArray()
Scalars.InsertNextValue(1.0)
Scalars.InsertNextValue(0.0)
Scalars.InsertNextValue(0.0)
Scalars.InsertNextValue(1.0)
Scalars.InsertNextValue(0.0)
Scalars.InsertNextValue(0.0)
Scalars.InsertNextValue(0.0)
Scalars.InsertNextValue(0.0)
Points = vtk.vtkPoints()
Points.InsertNextPoint(0, 0, 0)
Points.InsertNextPoint(1, 0, 0)
Points.InsertNextPoint(1, 1, 0)
Points.InsertNextPoint(0, 1, 0)
Points.InsertNextPoint(0, 0, 1)
Points.InsertNextPoint(1, 0, 1)
Points.InsertNextPoint(1, 1, 1)
Points.InsertNextPoint(0, 1, 1)
Ids = vtk.vtkIdList()
Ids.InsertNextId(0)
Ids.InsertNextId(1)
Ids.InsertNextId(2)
Ids.InsertNextId(3)
Ids.InsertNextId(4)
Ids.InsertNextId(5)
Ids.InsertNextId(6)
Ids.InsertNextId(7)
Grid = vtk.vtkUnstructuredGrid()
Grid.Allocate(10, 10)
Grid.InsertNextCell(12, Ids)
Grid.SetPoints(Points)
Grid.GetPointData().SetScalars(Scalars)
# Find the triangles that lie along the 0.5 contour in this cube.
Marching = vtk.vtkContourFilter()
Marching.SetInputData(Grid)
Marching.SetValue(0, 0.5)
Marching.Update()
# Extract the edges of the triangles just found.
triangleEdges = vtk.vtkExtractEdges()
triangleEdges.SetInputConnection(Marching.GetOutputPort())
# Draw the edges as tubes instead of lines. Also create the associated
# mapper and actor to display the tubes.
triangleEdgeTubes = vtk.vtkTubeFilter()
triangleEdgeTubes.SetInputConnection(triangleEdges.GetOutputPort())
triangleEdgeTubes.SetRadius(.005)
triangleEdgeTubes.SetNumberOfSides(6)
triangleEdgeTubes.UseDefaultNormalOn()
triangleEdgeTubes.SetDefaultNormal(.577, .577, .577)
triangleEdgeMapper = vtk.vtkPolyDataMapper()
triangleEdgeMapper.SetInputConnection(
triangleEdgeTubes.GetOutputPort())
triangleEdgeMapper.ScalarVisibilityOff()
triangleEdgeActor = vtk.vtkActor()
triangleEdgeActor.SetMapper(triangleEdgeMapper)
triangleEdgeActor.GetProperty().SetDiffuseColor(
color.GetColor3d("lamp_black"))
triangleEdgeActor.GetProperty().SetSpecular(.4)
triangleEdgeActor.GetProperty().SetSpecularPower(10)
# Shrink the triangles we found earlier. Create the associated mapper
# and actor. Set the opacity of the shrunken triangles.
aShrinker = vtk.vtkShrinkPolyData()
aShrinker.SetShrinkFactor(1)
aShrinker.SetInputConnection(Marching.GetOutputPort())
aMapper = vtk.vtkPolyDataMapper()
aMapper.ScalarVisibilityOff()
aMapper.SetInputConnection(aShrinker.GetOutputPort())
Triangles = vtk.vtkActor()
Triangles.SetMapper(aMapper)
Triangles.GetProperty().SetDiffuseColor(color.GetColor3d("banana"))
Triangles.GetProperty().SetOpacity(.6)
# Draw a cube the same size and at the same position as the one
# created previously. Extract the edges because we only want to see
# the outline of the cube. Pass the edges through a vtkTubeFilter so
# they are displayed as tubes rather than lines.
CubeModel = vtk.vtkCubeSource()
CubeModel.SetCenter(.5, .5, .5)
Edges = vtk.vtkExtractEdges()
Edges.SetInputConnection(CubeModel.GetOutputPort())
Tubes = vtk.vtkTubeFilter()
Tubes.SetInputConnection(Edges.GetOutputPort())
Tubes.SetRadius(.01)
Tubes.SetNumberOfSides(6)
Tubes.UseDefaultNormalOn()
Tubes.SetDefaultNormal(.577, .577, .577)
# Create the mapper and actor to display the cube edges.
TubeMapper = vtk.vtkPolyDataMapper()
TubeMapper.SetInputConnection(Tubes.GetOutputPort())
CubeEdges = vtk.vtkActor()
CubeEdges.SetMapper(TubeMapper)
CubeEdges.GetProperty().SetDiffuseColor(color.GetColor3d("khaki"))
CubeEdges.GetProperty().SetSpecular(.4)
CubeEdges.GetProperty().SetSpecularPower(10)
# Create a sphere to use as a glyph source for vtkGlyph3D.
Sphere = vtk.vtkSphereSource()
Sphere.SetRadius(0.04)
Sphere.SetPhiResolution(20)
Sphere.SetThetaResolution(20)
# Remove the part of the cube with data values below 0.5.
ThresholdIn = vtk.vtkThresholdPoints()
ThresholdIn.SetInputData(Grid)
ThresholdIn.ThresholdByUpper(.5)
# Display spheres at the vertices remaining in the cube data set after
# it was passed through vtkThresholdPoints.
Vertices = vtk.vtkGlyph3D()
Vertices.SetInputConnection(ThresholdIn.GetOutputPort())
Vertices.SetSourceConnection(Sphere.GetOutputPort())
# Create a mapper and actor to display the glyphs.
SphereMapper = vtk.vtkPolyDataMapper()
SphereMapper.SetInputConnection(Vertices.GetOutputPort())
SphereMapper.ScalarVisibilityOff()
CubeVertices = vtk.vtkActor()
CubeVertices.SetMapper(SphereMapper)
CubeVertices.GetProperty().SetDiffuseColor(color.GetColor3d("tomato"))
# Define the text for the label
caseLabel = vtk.vtkVectorText()
caseLabel.SetText("Case 1")
# Set up a transform to move the label to a new position.
aLabelTransform = vtk.vtkTransform()
aLabelTransform.Identity()
aLabelTransform.Translate(-0.2, 0, 1.25)
aLabelTransform.Scale(.05, .05, .05)
# Move the label to a new position.
labelTransform = vtk.vtkTransformPolyDataFilter()
labelTransform.SetTransform(aLabelTransform)
labelTransform.SetInputConnection(caseLabel.GetOutputPort())
# Create a mapper and actor to display the text.
labelMapper = vtk.vtkPolyDataMapper()
labelMapper.SetInputConnection(labelTransform.GetOutputPort())
labelActor = vtk.vtkActor()
labelActor.SetMapper(labelMapper)
# Define the base that the cube sits on. Create its associated mapper
# and actor. Set the position of the actor.
baseModel = vtk.vtkCubeSource()
baseModel.SetXLength(1.5)
baseModel.SetYLength(.01)
baseModel.SetZLength(1.5)
baseMapper = vtk.vtkPolyDataMapper()
baseMapper.SetInputConnection(baseModel.GetOutputPort())
base = vtk.vtkActor()
base.SetMapper(baseMapper)
base.SetPosition(.5, -0.09, .5)
# Set the scalar values for this case of marching cubes.
# A negative case number will generate a complementary case
mcCase = mcCases[i]
if mcCase < 0:
cases[-mcCase](Scalars, caseLabel, 0, 1)
else:
cases[mcCase](Scalars, caseLabel, 1, 0)
# Force the grid to update.
Grid.Modified()
# Add the actors to the renderer
renderers[i].AddActor(triangleEdgeActor)
renderers[i].AddActor(base)
renderers[i].AddActor(labelActor)
renderers[i].AddActor(CubeEdges)
renderers[i].AddActor(CubeVertices)
renderers[i].AddActor(Triangles)
# Set the background color.
renderers[i].SetBackground(color.GetColor3d("slate_grey"))
# Position the camera.
renderers[i].GetActiveCamera().Dolly(1.2)
renderers[i].GetActiveCamera().Azimuth(30)
renderers[i].GetActiveCamera().Elevation(20)
renderers[i].ResetCamera()
renderers[i].ResetCameraClippingRange()
if i > 0:
renderers[i].SetActiveCamera(renderers[0].GetActiveCamera())
# Setup viewports for the renderers
rendererSize = 300
xGridDimensions = 4
if len(mcCases) < 4:
xGridDimensions = len(mcCases)
yGridDimensions = (len(mcCases) - 1) // 4 + 1
print("x, y:", xGridDimensions, ",", yGridDimensions)
renWin.SetSize(rendererSize * xGridDimensions,
rendererSize * yGridDimensions)
for row in range(0, yGridDimensions):
for col in range(0, xGridDimensions):
index = row * xGridDimensions + col
# (xmin, ymin, xmax, ymax)
viewport = [
float(col) / xGridDimensions,
float(yGridDimensions - (row + 1)) / yGridDimensions,
float(col + 1) / xGridDimensions,
float(yGridDimensions - row) / yGridDimensions
]
renderers[index].SetViewport(viewport)
iren.Initialize()
renWin.Render()
iren.Start()
def main():
fileName = r"carotid.vtk"
colors = vtk.vtkNamedColors()
ren1 = vtk.vtkRenderer()
renWin = vtk.vtkRenderWindow()
renWin.AddRenderer(ren1)
iren = vtk.vtkRenderWindowInteractor()
iren.SetRenderWindow(renWin)
# Create the pipeline.
reader = vtk.vtkStructuredPointsReader()
reader.SetFileName(fileName)
psource = vtk.vtkPointSource()
psource.SetNumberOfPoints(25)
psource.SetCenter(133.1, 116.3, 5.0)
psource.SetRadius(2.0)
threshold = vtk.vtkThresholdPoints()
threshold.SetInputConnection(reader.GetOutputPort())
threshold.ThresholdByUpper(275)
streamers = vtk.vtkStreamTracer()
streamers.SetInputConnection(reader.GetOutputPort())
streamers.SetSourceConnection(psource.GetOutputPort())
streamers.SetMaximumPropagation(100.0)
streamers.SetInitialIntegrationStep(0.2)
streamers.SetTerminalSpeed(.01)
streamers.Update()
scalarRange = [0] * 2
scalarRange[0] = streamers.GetOutput().GetPointData().GetScalars(
).GetRange()[0]
scalarRange[1] = streamers.GetOutput().GetPointData().GetScalars(
).GetRange()[1]
tubes = vtk.vtkTubeFilter()
tubes.SetInputConnection(streamers.GetOutputPort())
tubes.SetRadius(0.3)
tubes.SetNumberOfSides(6)
tubes.SetVaryRadius(0)
lut = vtk.vtkLookupTable()
lut.SetHueRange(.667, 0.0)
lut.Build()
streamerMapper = vtk.vtkPolyDataMapper()
streamerMapper.SetInputConnection(tubes.GetOutputPort())
streamerMapper.SetScalarRange(scalarRange[0], scalarRange[1])
streamerMapper.SetLookupTable(lut)
streamerActor = vtk.vtkActor()
streamerActor.SetMapper(streamerMapper)
# Speed contours.
iso = vtk.vtkContourFilter()
iso.SetInputConnection(reader.GetOutputPort())
iso.SetValue(0, 175)
isoMapper = vtk.vtkPolyDataMapper()
isoMapper.SetInputConnection(iso.GetOutputPort())
isoMapper.ScalarVisibilityOff()
isoActor = vtk.vtkActor()
isoActor.SetMapper(isoMapper)
isoActor.GetProperty().SetRepresentationToWireframe()
isoActor.GetProperty().SetOpacity(0.25)
# Outline
outline = vtk.vtkOutlineFilter()
outline.SetInputConnection(reader.GetOutputPort())
outlineMapper = vtk.vtkPolyDataMapper()
outlineMapper.SetInputConnection(outline.GetOutputPort())
outlineActor = vtk.vtkActor()
outlineActor.SetMapper(outlineMapper)
outlineActor.GetProperty().SetColor(0., 0., 0.)
# Add the actors to the renderer, set the background and size.
ren1.AddActor(outlineActor)
ren1.AddActor(streamerActor)
ren1.AddActor(isoActor)
ren1.SetBackground(1., 1., 1.)
renWin.SetSize(640, 480)
ren1.ResetCamera()
ren1.ResetCameraClippingRange()
# Render the image.
renWin.Render()
iren.Start()
def main():
fileName = get_program_parameters()
colors = vtk.vtkNamedColors()
ren1 = vtk.vtkRenderer()
renWin = vtk.vtkRenderWindow()
renWin.AddRenderer(ren1)
iren = vtk.vtkRenderWindowInteractor()
iren.SetRenderWindow(renWin)
# Create the pipeline.
#
reader = vtk.vtkStructuredPointsReader()
reader.SetFileName(fileName)
threshold = vtk.vtkThresholdPoints()
threshold.SetInputConnection(reader.GetOutputPort())
threshold.ThresholdByUpper(200)
mask = vtk.vtkMaskPoints()
mask.SetInputConnection(threshold.GetOutputPort())
mask.SetOnRatio(5)
cone = vtk.vtkConeSource()
cone.SetResolution(11)
cone.SetHeight(1)
cone.SetRadius(0.25)
cones = vtk.vtkGlyph3D()
cones.SetInputConnection(mask.GetOutputPort())
cones.SetSourceConnection(cone.GetOutputPort())
cones.SetScaleFactor(0.4)
cones.SetScaleModeToScaleByVector()
lut = vtk.vtkLookupTable()
lut.SetHueRange(.667, 0.0)
lut.Build()
scalarRange = [0] * 2
cones.Update()
scalarRange[0] = cones.GetOutput().GetPointData().GetScalars().GetRange(
)[0]
scalarRange[1] = cones.GetOutput().GetPointData().GetScalars().GetRange(
)[1]
print("range: ", scalarRange[0], ", ", scalarRange[1])
vectorMapper = vtk.vtkPolyDataMapper()
vectorMapper.SetInputConnection(cones.GetOutputPort())
vectorMapper.SetScalarRange(scalarRange[0], scalarRange[1])
vectorMapper.SetLookupTable(lut)
vectorActor = vtk.vtkActor()
vectorActor.SetMapper(vectorMapper)
# Speed contours.
iso = vtk.vtkContourFilter()
iso.SetInputConnection(reader.GetOutputPort())
iso.SetValue(0, 175)
isoMapper = vtk.vtkPolyDataMapper()
isoMapper.SetInputConnection(iso.GetOutputPort())
isoMapper.ScalarVisibilityOff()
isoActor = vtk.vtkActor()
isoActor.SetMapper(isoMapper)
isoActor.GetProperty().SetRepresentationToWireframe()
isoActor.GetProperty().SetOpacity(0.25)
# Outline
outline = vtk.vtkOutlineFilter()
outline.SetInputConnection(reader.GetOutputPort())
outlineMapper = vtk.vtkPolyDataMapper()
outlineMapper.SetInputConnection(outline.GetOutputPort())
outlineActor = vtk.vtkActor()
outlineActor.SetMapper(outlineMapper)
outlineActor.GetProperty().SetColor(colors.GetColor3d("Black"))
# Add the actors to the renderer, set the background and size.
#
ren1.AddActor(outlineActor)
ren1.AddActor(vectorActor)
ren1.AddActor(isoActor)
ren1.SetBackground(colors.GetColor3d("Wheat"))
renWin.SetSize(640, 480)
renWin.SetWindowName('CarotidFlowGlyphs')
cam1 = vtk.vtkCamera()
cam1.SetClippingRange(17.4043, 870.216)
cam1.SetFocalPoint(136.71, 104.025, 23)
cam1.SetPosition(204.747, 258.939, 63.7925)
cam1.SetViewUp(-0.102647, -0.210897, 0.972104)
cam1.Zoom(1.2)
ren1.SetActiveCamera(cam1)
# Render the image.
#
renWin.Render()
iren.Start()
def main():
fileName = get_program_parameters()
colors = vtk.vtkNamedColors()
ren1 = vtk.vtkRenderer()
renWin = vtk.vtkRenderWindow()
renWin.AddRenderer(ren1)
iren = vtk.vtkRenderWindowInteractor()
iren.SetRenderWindow(renWin)
# Create the pipeline.
#
reader = vtk.vtkStructuredPointsReader()
reader.SetFileName(fileName)
psource = vtk.vtkPointSource()
psource.SetNumberOfPoints(25)
psource.SetCenter(133.1, 116.3, 5.0)
psource.SetRadius(2.0)
threshold = vtk.vtkThresholdPoints()
threshold.SetInputConnection(reader.GetOutputPort())
threshold.ThresholdByUpper(275)
streamers = vtk.vtkStreamTracer()
streamers.SetInputConnection(reader.GetOutputPort())
streamers.SetSourceConnection(psource.GetOutputPort())
# streamers.SetMaximumPropagationUnitToTimeUnit()
streamers.SetMaximumPropagation(100.0)
# streamers.SetInitialIntegrationStepUnitToCellLengthUnit()
streamers.SetInitialIntegrationStep(0.2)
streamers.SetTerminalSpeed(.01)
streamers.Update()
scalarRange = [0] * 2
scalarRange[0] = streamers.GetOutput().GetPointData().GetScalars(
).GetRange()[0]
scalarRange[1] = streamers.GetOutput().GetPointData().GetScalars(
).GetRange()[1]
print("range: ", scalarRange[0], ", ", scalarRange[1])
tubes = vtk.vtkTubeFilter()
tubes.SetInputConnection(streamers.GetOutputPort())
tubes.SetRadius(0.3)
tubes.SetNumberOfSides(6)
tubes.SetVaryRadius(0)
lut = vtk.vtkLookupTable()
lut.SetHueRange(.667, 0.0)
lut.Build()
streamerMapper = vtk.vtkPolyDataMapper()
streamerMapper.SetInputConnection(tubes.GetOutputPort())
streamerMapper.SetScalarRange(scalarRange[0], scalarRange[1])
streamerMapper.SetLookupTable(lut)
streamerActor = vtk.vtkActor()
streamerActor.SetMapper(streamerMapper)
# Speed contours.
iso = vtk.vtkContourFilter()
iso.SetInputConnection(reader.GetOutputPort())
iso.SetValue(0, 175)
isoMapper = vtk.vtkPolyDataMapper()
isoMapper.SetInputConnection(iso.GetOutputPort())
isoMapper.ScalarVisibilityOff()
isoActor = vtk.vtkActor()
isoActor.SetMapper(isoMapper)
isoActor.GetProperty().SetRepresentationToWireframe()
isoActor.GetProperty().SetOpacity(0.25)
# Outline
outline = vtk.vtkOutlineFilter()
outline.SetInputConnection(reader.GetOutputPort())
outlineMapper = vtk.vtkPolyDataMapper()
outlineMapper.SetInputConnection(outline.GetOutputPort())
outlineActor = vtk.vtkActor()
outlineActor.SetMapper(outlineMapper)
outlineActor.GetProperty().SetColor(colors.GetColor3d("Black"))
# Add the actors to the renderer, set the background and size.
#
ren1.AddActor(outlineActor)
ren1.AddActor(streamerActor)
ren1.AddActor(isoActor)
ren1.SetBackground(colors.GetColor3d("Wheat"))
renWin.SetSize(640, 480)
cam1 = vtk.vtkCamera()
cam1.SetClippingRange(17.4043, 870.216)
cam1.SetFocalPoint(136.71, 104.025, 23)
cam1.SetPosition(204.747, 258.939, 63.7925)
cam1.SetViewUp(-0.102647, -0.210897, 0.972104)
cam1.Zoom(1.6)
ren1.SetActiveCamera(cam1)
# Render the image.
#
renWin.Render()
iren.Start()
def opyfFindBlobs3D(scalars,
th1,
th2=None,
R=1.,
minArea=None,
CenterType='barycenter'):
if th2 is None:
th2 = np.max(scalars)
[h, w, p] = scalars.shape
scalars = scalars.T.copy()
scalars = scalars.ravel()
# (scalars>=th1)*(scalars<=th2)
# indth=np.where((scalars>=th1)*(scalars<=th2))
# Points XYZ
x, y, z = np.mgrid[0:h, 0:w, 0:p]
pts = np.empty(z.shape + (3, ), dtype=float)
pts[..., 0] = x
pts[..., 1] = y
pts[..., 2] = z
pts = pts.transpose(2, 1, 0, 3).copy()
pts.shape = pts.size / 3, 3
# VTK
points = vtk.vtkPoints()
points.SetDataTypeToDouble()
for [x, y, z] in pts:
points.InsertNextPoint(x, y, z)
Scalarsvtk = vtk.vtkFloatArray()
for s in scalars:
Scalarsvtk.InsertNextValue(s)
Ids = vtk.vtkIdList()
polydata = vtk.vtkPolyData()
# polydata=vtk.vtkUnstructuredGrid()
polydata.SetPoints(points)
polydata.GetPointData().SetScalars(Scalarsvtk)
ThresholdIn = vtk.vtkThresholdPoints()
ThresholdIn.SetInputData(polydata)
# ThresholdIn.ThresholdByLower(230.)
ThresholdIn.ThresholdBetween(th1, th2)
ThresholdIn.Update()
PointsThresh = ThresholdIn.GetOutput().GetPoints()
staticLocator = vtk.vtkStaticPointLocator()
staticLocator.SetDataSet(ThresholdIn.GetOutput())
staticLocator.SetNumberOfPointsPerBucket(5)
staticLocator.AutomaticOn()
staticLocator.BuildLocator()
S = ThresholdIn.GetOutput().GetPointData().GetArray(0)
nppointsArr = vtk_to_numpy(S)
idspointsThresh = np.arange(0, PointsThresh.GetNumberOfPoints())
entitiy = 0
i = idspointsThresh[0]
idsStored = np.array([])
ids1 = [0]
C = 1
blob3D = []
indstore = 0
while len(idspointsThresh) > 0:
C = 1
while C == 1:
ids2 = []
l = len(idsStored)
for i in ids1:
PointswhithinRadius = vtk.vtkIdList()
staticLocator.FindPointsWithinRadius(R,
PointsThresh.GetPoint(i),
PointswhithinRadius)
for j in range(PointswhithinRadius.GetNumberOfIds()):
tempid = PointswhithinRadius.GetId(j)
if len(np.where(idsStored == tempid)[0]) == 0:
idsStored = np.append(idsStored, np.int(tempid))
ids2.append(tempid)
indDel = np.where(idspointsThresh == tempid)
idspointsThresh = np.delete(idspointsThresh, indDel, 0)
if len(idsStored) == l:
C = 0
blob3D.append(idsStored[indstore:].astype(int))
indstore = len(idsStored)
entitiy += 1
if len(idspointsThresh) > 0:
ids1 = [idspointsThresh[0]]
else:
ids1 = ids2
C = np.zeros((len(blob3D), 3))
AreaBlob = []
X = vtk_to_numpy(PointsThresh.GetData())
blob3Dout = []
for i in range(len(blob3D)):
ind = blob3D[i]
Xblob = X[ind]
blob3Dout.append(Xblob)
pxInts = nppointsArr[ind]
if CenterType == 'barycenter':
C[i, :] = np.sum(Xblob * np.array([pxInts, pxInts, pxInts]).T,
axis=0) / (np.sum(pxInts))
elif CenterType == 'geometric':
C[i, :] = np.sum(Xblob, axis=0) / (np.float(len(pxInts)))
AreaBlob.append(len(Xblob))
AreaBlob = np.array(AreaBlob)
blob3Dout = np.array(blob3Dout)
if minArea is not None:
C = C[np.where(AreaBlob > minArea)]
blob3Dout = blob3Dout[np.where(AreaBlob > minArea)]
AreaBlob = AreaBlob[np.where(AreaBlob > minArea)]
return blob3Dout, C, AreaBlob
def plot(self, struct):
# creates self. data1, legend, filename, fieldname, dim, has_field, tracker, revision
if not self.call_config(struct):
return
# creates self.src
if not self.call_src():
return
# wireframe
# test proba
#self.ref0 = vtk.vtkThreshold() # necesario en selrF_
#self.ref0.SetInputConnection(self.src.GetOutputPort())
#self.ref0.ThresholdByLower(0.999) # valor inclusive
self.wireM = vtk.vtkDataSetMapper()
# test proba
#self.wireM.SetInputConnection(self.ref0.GetOutputPort())
self.wireM.SetInputConnection(self.src.GetOutputPort())
self.wireM.ScalarVisibilityOff()
self.wireA = vtk.vtkActor()
self.wireA.SetMapper(self.wireM)
self.wireA.GetProperty().SetRepresentationToWireframe()
self.wireA.GetProperty().SetColor(Plot.mesh3_color)
self.wireA.SetVisibility(0)
self.add_outline_2(self.src)
if self.has_field:
# reference labels
if self.data1.get('fielddomain') == 'point':
self.refsT = vtk.vtkThresholdPoints()
self.refsT.SetInputConnection(self.src.GetOutputPort())
self.refsT.ThresholdByUpper(1.0 - epsilon)
else:
self.refsT = vtk.vtkThreshold() # necesario en selrF_
self.refsT.SetInputConnection(self.src.GetOutputPort())
self.refsT.ThresholdByUpper(1.0 - epsilon)
# self.refsT.SetInputArrayToProcess(1, 0, 0, 0, self.fieldname)
# self.refsT.SetAttributeModeToUseCellData()
if self.data1.get('fielddomain') == 'point':
label_con = self.refsT.GetOutputPort()
else:
self.ccrF = vtk.vtkCellCenters()
self.ccrF.SetInputConnection(self.refsT.GetOutputPort())
label_con = self.ccrF.GetOutputPort()
self.lrM = vtk.vtkLabeledDataMapper()
self.lrM.SetInputConnection(label_con)
self.lrM.SetLabelModeToLabelScalars()
self.lrM.GetLabelTextProperty().SetColor(Plot.label_color)
self.lrA = vtk.vtkActor2D()
self.lrA.SetMapper(self.lrM)
self.lrA.SetVisibility(0)
# CELL POINT FIELD VERTEX EDGE
if self.data1.get('fielddomain') == 'point':
ftype = 1 # vtkSelection::POINT
else:
ftype = 0 # vtkSelection::CELL
# selected edges
self.selr = vtk.vtkSelectionSource()
self.selr.SetContentType(7) # vtkSelection::THRESHOLDS
self.selr.SetFieldType(ftype)
if self.data1.get(
'fielddomain'
) == 'point': # necesario para los puntos, sino colapsa
self.selr.SetContainingCells(0)
# unselected edges
self.selr_ = vtk.vtkSelectionSource()
self.selr_.SetContentType(7) # vtkSelection::THRESHOLDS
self.selr_.SetFieldType(ftype)
if self.data1.get(
'fielddomain'
) == 'point': # necesario para los puntos, sino colapsa
self.selr_.SetContainingCells(0)
self.selr_.SetInverse(1)
self.selrF = vtk.vtkExtractSelectedThresholds()
#self.selrF.SetInputConnection(self.src.GetOutputPort()) # por que era asi? # x1sbc
self.selrF.SetInputConnection(self.refsT.GetOutputPort())
self.selrF.SetSelectionConnection(self.selr.GetOutputPort())
self.selrF_ = vtk.vtkExtractSelectedThresholds()
self.selrF_.SetInputConnection(self.refsT.GetOutputPort()) #
self.selrF_.SetSelectionConnection(self.selr_.GetOutputPort())
self.selrM = vtk.vtkDataSetMapper()
self.selrM.SetInputConnection(self.selrF.GetOutputPort())
if not several_colors:
self.selrM.ScalarVisibilityOff()
self.selrM_ = vtk.vtkDataSetMapper()
self.selrM_.SetInputConnection(self.selrF_.GetOutputPort())
self.selrM_.ScalarVisibilityOff()
self.selrM.SetScalarRange(self.change_range(self.src))
self.selrA = vtk.vtkActor()
self.selrA.SetMapper(self.selrM)
if not several_colors:
self.selrA.GetProperty().SetColor(Plot.mesh2_color)
if self.data1.get('fielddomain') == 'point':
self.selrA.GetProperty().SetRepresentationToPoints()
else:
self.selrA.GetProperty().SetRepresentationToSurface()
self.selrA_ = vtk.vtkActor()
self.selrA_.SetMapper(self.selrM_)
if several_colors:
self.selrA_.GetProperty().SetColor(Plot.unselected_color)
else:
self.selrA_.GetProperty().SetColor(Plot.mesh_color)
if self.data1.get('fielddomain') == 'point':
self.selrA_.GetProperty().SetRepresentationToPoints()
else:
self.selrA_.GetProperty().SetRepresentationToWireframe()
if self.data1.get('fielddomain') == 'point':
self.selrA.GetProperty().SetPointSize(3.0)
self.selrA_.GetProperty().SetPointSize(2.0)
# lóxica dudosa: depende do nome do campo
if self.data1.get('fieldname') == 'edge_ref':
self.selrA.GetProperty().SetLineWidth(5.0)
self.selrA_.GetProperty().SetLineWidth(5.0)
self.update_thresholds(struct, True)
# Add the actors to the render
self.rens[0].AddActor(self.selrA_) # unselected
self.rens[0].AddActor(self.selrA) # selected
self.rens[0].AddActor(self.lrA) # labels
self.rens[0].AddActor(self.wireA) # mesh
self.set_iren()
self.iren.AddObserver("LeftButtonPressEvent", self.ButtonEvent)
if self.data1.get('fielddomain') == 'cell':
self.picker = vtk.vtkCellPicker()
else:
self.picker = vtk.vtkPointPicker()
self.picker.AddObserver("EndPickEvent", self.EndPick)
self.iren.SetPicker(self.picker)
self.done = True
def main():
fileNames = [''] * 2
fileNames[0], fileNames[1] = get_program_parameters()
# Generate the other vecAnim file names. There are 8 of them.
tmpFn = fileNames[1][:-5]
for i in range(2, 9):
fileNames.append(tmpFn + str(i) + '.vtk')
colors = vtk.vtkNamedColors()
# Setup the render window, renderer, and interactor.
renderer = vtk.vtkRenderer()
renderWindow = vtk.vtkRenderWindow()
renderWindow.AddRenderer(renderer)
interactor = vtk.vtkRenderWindowInteractor()
interactor.SetRenderWindow(renderWindow)
# Read the data.
#
# Create the pipeline.
#
reader = vtk.vtkStructuredPointsReader()
reader.SetFileName(fileNames[0])
threshold = vtk.vtkThresholdPoints()
threshold.SetInputConnection(reader.GetOutputPort())
threshold.ThresholdByUpper(200)
line = vtk.vtkLineSource()
line.SetResolution(1)
lines = vtk.vtkGlyph3D()
lines.SetInputConnection(threshold.GetOutputPort())
lines.SetSourceConnection(line.GetOutputPort())
lines.SetScaleFactor(0.005)
lines.SetScaleModeToScaleByScalar()
lines.Update()
vectorMapper = vtk.vtkPolyDataMapper()
vectorMapper.SetInputConnection(lines.GetOutputPort())
vectorMapper.SetScalarRange(lines.GetOutput().GetScalarRange())
vectorActor = vtk.vtkActor()
vectorActor.SetMapper(vectorMapper)
vectorActor.GetProperty().SetOpacity(0.99)
vectorActor.GetProperty().SetLineWidth(1.5)
# Outline
outline = vtk.vtkOutlineFilter()
outline.SetInputConnection(reader.GetOutputPort())
outlineMapper = vtk.vtkPolyDataMapper()
outlineMapper.SetInputConnection(outline.GetOutputPort())
outlineActor = vtk.vtkActor()
outlineActor.SetMapper(outlineMapper)
outlineActor.GetProperty().SetColor(colors.GetColor3d('Black'))
# Texture maps.
textureMaps = list()
for i in range(2, len(fileNames)):
tmap = vtk.vtkStructuredPointsReader()
tmap.SetFileName(fileNames[i])
texture = vtk.vtkTexture()
texture.SetInputConnection(tmap.GetOutputPort())
texture.InterpolateOff()
texture.RepeatOff()
textureMaps.append(texture)
vectorActor.SetTexture(textureMaps[0])
# Add the actors to the renderer, set the background and size.
#
renderer.AddActor(vectorActor)
renderer.AddActor(outlineActor)
cam1 = vtk.vtkCamera()
cam1.SetClippingRange(17.4043, 870.216)
cam1.SetFocalPoint(136.71, 104.025, 23)
cam1.SetPosition(204.747, 258.939, 63.7925)
cam1.SetViewUp(-0.102647, -0.210897, 0.972104)
cam1.Zoom(1.2)
renderer.SetActiveCamera(cam1)
renderer.SetBackground(colors.GetColor3d('Wheat'))
renderWindow.SetSize(640, 480)
renderWindow.SetWindowName('AnimateVectors')
# Go into a loop.
for j in range(0, 100):
for i in range(0, len(textureMaps)):
vectorActor.SetTexture(textureMaps[i])
renderWindow.Render()
interactor.Start()
def __init__(self, parent, data_dir):
super(QGlyphViewer, self).__init__(parent)
# Make tha actual QtWidget a child so that it can be re parented
interactor = QVTKRenderWindowInteractor(self)
self.layout = QtWidgets.QHBoxLayout()
self.layout.addWidget(interactor)
self.layout.setContentsMargins(0, 0, 0, 0)
self.setLayout(self.layout)
# Read the data
xyx_file = os.path.join(data_dir, "combxyz.bin")
q_file = os.path.join(data_dir, "combq.bin")
pl3d = vtk.vtkMultiBlockPLOT3DReader()
pl3d.SetXYZFileName(xyx_file)
pl3d.SetQFileName(q_file)
pl3d.SetScalarFunctionNumber(100)
pl3d.SetVectorFunctionNumber(202)
pl3d.Update()
blocks = pl3d.GetOutput()
b0 = blocks.GetBlock(0)
# Setup VTK environment
renderer = vtk.vtkRenderer()
render_window = interactor.GetRenderWindow()
render_window.AddRenderer(renderer)
interactor.SetInteractorStyle(vtk.vtkInteractorStyleTrackballCamera())
render_window.SetInteractor(interactor)
renderer.SetBackground(0.2, 0.2, 0.2)
# Draw Outline
outline = vtk.vtkStructuredGridOutlineFilter()
outline.SetInputData(b0)
outline_mapper = vtk.vtkPolyDataMapper()
outline_mapper.SetInputConnection(outline.GetOutputPort())
outline_actor = vtk.vtkActor()
outline_actor.SetMapper(outline_mapper)
outline_actor.GetProperty().SetColor(1, 1, 1)
renderer.AddActor(outline_actor)
renderer.ResetCamera()
# Draw Outline
outline = vtk.vtkStructuredGridOutlineFilter()
outline.SetInputData(b0)
outline_mapper = vtk.vtkPolyDataMapper()
outline_mapper.SetInputConnection(outline.GetOutputPort())
outline_actor = vtk.vtkActor()
outline_actor.SetMapper(outline_mapper)
outline_actor.GetProperty().SetColor(1, 1, 1)
renderer.AddActor(outline_actor)
renderer.ResetCamera()
# Threshold points
threshold = vtk.vtkThresholdPoints()
threshold.SetInputData(b0)
threshold.ThresholdByUpper(0.5)
# Draw arrows
arrow = vtk.vtkArrowSource()
glyphs = vtk.vtkGlyph3D()
glyphs.SetInputData(b0)
glyphs.SetSourceConnection(arrow.GetOutputPort())
glyphs.SetInputConnection(threshold.GetOutputPort())
glyphs.SetVectorModeToUseVector()
glyphs.SetScaleModeToScaleByVector()
glyphs.SetScaleFactor(0.005)
glyphs.SetColorModeToColorByVector()
# Mapper
glyph_mapper = vtk.vtkPolyDataMapper()
glyph_mapper.SetInputConnection(glyphs.GetOutputPort())
glyph_actor = vtk.vtkActor()
glyph_actor.SetMapper(glyph_mapper)
glyph_mapper.UseLookupTableScalarRangeOn()
renderer.AddActor(glyph_actor)
# Set color lookuptable
glyphs.Update()
s0, sf = glyphs.GetOutput().GetScalarRange()
lut = vtk.vtkColorTransferFunction()
lut.AddRGBPoint(s0, 1, 0, 0)
lut.AddRGBPoint(sf, 0, 1, 0)
glyph_mapper.SetLookupTable(lut)
# Register pick listener
self.b0 = b0
self.renderer = renderer
self.interactor = interactor
self.threshold = threshold
self.render_window = render_window
self.picker = vtk.vtkCellPicker()
self.picker.AddObserver("EndPickEvent", self.process_pick)
self.interactor.SetPicker(self.picker)
self.glyphs = glyphs
Tubes.UseDefaultNormalOn()
Tubes.SetDefaultNormal(.577, .577, .577)
TubeMapper = vtk.vtkPolyDataMapper()
TubeMapper.SetInputConnection(Tubes.GetOutputPort())
CubeEdges = vtk.vtkActor()
CubeEdges.SetMapper(TubeMapper)
CubeEdges.GetProperty().SetDiffuseColor(khaki)
CubeEdges.GetProperty().SetSpecular(.4)
CubeEdges.GetProperty().SetSpecularPower(10)
# build the vertices of the cube
#
Sphere = vtk.vtkSphereSource()
Sphere.SetRadius(0.04)
Sphere.SetPhiResolution(20)
Sphere.SetThetaResolution(20)
ThresholdIn = vtk.vtkThresholdPoints()
ThresholdIn.SetInputData(Grid)
ThresholdIn.ThresholdByUpper(.5)
Vertices = vtk.vtkGlyph3D()
Vertices.SetInputConnection(ThresholdIn.GetOutputPort())
Vertices.SetSourceConnection(Sphere.GetOutputPort())
SphereMapper = vtk.vtkPolyDataMapper()
SphereMapper.SetInputConnection(Vertices.GetOutputPort())
SphereMapper.ScalarVisibilityOff()
CubeVertices = vtk.vtkActor()
CubeVertices.SetMapper(SphereMapper)
CubeVertices.GetProperty().SetDiffuseColor(tomato)
CubeVertices.GetProperty().SetDiffuseColor(tomato)
#define the text for the labels
caseLabel = vtk.vtkVectorText()
caseLabel.SetText("Case 2")
def normalizeVessels2(case_dir,
dist_from_bif_inlet=35,
dist_from_bif_outlet=35):
# phases = ["baseline","baseline-post","12months","followup"]
phases = ["baseline"]
centerlines = {}
surfaces = {}
for phase in phases:
if not os.path.exists(os.path.join(case_dir, phase, "centerline.vtp")):
continue
# load the centerline file
reader = vtk.vtkXMLPolyDataReader()
reader.SetFileName(os.path.join(case_dir, phase, "centerline.vtp"))
reader.Update()
centerline = reader.GetOutput()
centerlines.update({phase: centerline})
# load surface files
if not os.path.exists(os.path.join(case_dir, phase, "surface.stl")):
continue
# reader = vtk.vtkGenericDataObjectReader()
reader = vtk.vtkSTLReader()
reader.SetFileName(os.path.join(case_dir, phase, "surface.stl"))
reader.Update()
surface = reader.GetOutput()
surfaces.update({phase: surface})
# get the bifurcation point from baseline data
# split the polydata by centerline id
splitter = vtk.vtkThreshold()
splitter.SetInputData(centerlines["baseline"])
splitter.ThresholdBetween(0, 0)
splitter.SetInputArrayToProcess(0, 0, 0,
vtk.vtkDataObject.FIELD_ASSOCIATION_CELLS,
"GroupIds")
splitter.Update()
mainBranch = splitter.GetOutput()
maxAbsc = 0
maxAbscId = 0
for i in range(mainBranch.GetNumberOfPoints()):
absc = mainBranch.GetPointData().GetArray("Abscissas").GetComponent(
i, 0)
if absc > maxAbsc:
maxAbsc = absc
maxAbscId = i
bifPoint = mainBranch.GetPoint(maxAbscId)
thresholdFilter = vtk.vtkThresholdPoints()
thresholdFilter.SetInputData(centerlines["baseline"])
thresholdFilter.ThresholdBetween(4.4156, 74.4156)
thresholdFilter.SetInputArrayToProcess(
0, 0, 0, vtk.vtkDataObject.FIELD_ASSOCIATION_POINTS, "Abscissas")
thresholdFilter.Update()
vtpWriter = vtk.vtkXMLPolyDataWriter()
vtpWriter.SetFileName(
os.path.join(case_dir, phase, "centerline_clipped.vtp"))
vtpWriter.SetInputData(thresholdFilter.GetOutput())
vtpWriter.Update()
