def extract_smooth_mesh(imageVTK,
label_range,
smoothing_iterations=30,
pass_band_param=0.01,
target_reduction=0.95):
'''Extract mesh/contour for labels in imageVTK, smooth and decimate.
Multiple labels can be extracted at once, however touching labels
will share vertices and the label ids are lost during smoothing/decimation.
Processing is slow for small objects in a large volume and should be cropped beforehand.
Args:
imageVTK: vtk image data
label_range: range of labels to extract. A tuple (l,l) will extract
a mesh for a single label id l
smoothing_iterations: number of iterations for vtkWindowedSincPolyDataFilter
pass_band_param: pass band param in range [0.,2.] for vtkWindowedSincPolyDataFilter.
Lower value remove higher frequencies.
target_reduction: target reduction for vtkQuadricDecimation
'''
n_contours = label_range[1] - label_range[0] + 1
# alternative vtkDiscreteMarchingCubes is slower and creates some weird missalignment lines when applied to tight crops
dfe = vtk.vtkDiscreteFlyingEdges3D()
dfe.SetInputData(imageVTK)
dfe.ComputeScalarsOff(
) # numpy image labels --> cells (faces) scalar values
dfe.ComputeNormalsOff()
dfe.ComputeGradientsOff()
dfe.InterpolateAttributesOff()
dfe.GenerateValues(n_contours, label_range[0],
label_range[1]) # numContours, rangeStart, rangeEnd
dfe.Update()
smoother = vtk.vtkWindowedSincPolyDataFilter()
smoother.SetInputConnection(dfe.GetOutputPort())
smoother.SetNumberOfIterations(
smoothing_iterations) #this has little effect on the error!
smoother.BoundarySmoothingOff()
smoother.FeatureEdgeSmoothingOff()
# smoother.SetFeatureAngle(120)
smoother.SetPassBand(
pass_band_param) # from 0 to 2, 2 keeps high frequencies
smoother.NonManifoldSmoothingOn()
smoother.NormalizeCoordinatesOn()
smoother.GenerateErrorScalarsOff()
smoother.GenerateErrorVectorsOff()
smoother.Update()
# vtkQuadricDecimation looks cleaner than vtkDecimatePro (no unexpected sharp edges)
# but drop points scalar value --> can be added back if doing one instance a time
decimate = vtk.vtkQuadricDecimation()
decimate.SetInputConnection(smoother.GetOutputPort())
decimate.SetTargetReduction(target_reduction)
decimate.VolumePreservationOn()
decimate.Update()
return decimate.GetOutput()
def main():
# vtkDiscreteFlyingEdges3D was introduced in VTK >= 8.2
use_flying_edges = vtk_version_ok(8, 2, 0)
n = 20
radius = 8
blob = make_blob(n, radius)
if use_flying_edges:
try:
discrete = vtk.vtkDiscreteFlyingEdges3D()
except AttributeError:
discrete = vtk.vtkDiscreteMarchingCubes()
else:
discrete = vtk.vtkDiscreteMarchingCubes()
discrete.SetInputData(blob)
discrete.GenerateValues(n, 1, n)
lut = make_colors(n)
mapper = vtk.vtkPolyDataMapper()
mapper.SetInputConnection(discrete.GetOutputPort())
mapper.SetLookupTable(lut)
mapper.SetScalarRange(0, lut.GetNumberOfColors())
# Create the RenderWindow, Renderer and both Actors
#
ren = vtk.vtkRenderer()
ren_win = vtk.vtkRenderWindow()
ren_win.AddRenderer(ren)
ren_win.SetWindowName('DiscreteMarchingCubes')
iren = vtk.vtkRenderWindowInteractor()
iren.SetRenderWindow(ren_win)
actor = vtk.vtkActor()
actor.SetMapper(mapper)
ren.AddActor(actor)
colors = vtk.vtkNamedColors()
ren.SetBackground(colors.GetColor3d('Burlywood'))
ren_win.Render()
iren.Start()
thres.Update()
if (i == 0):
blobImage.DeepCopy(thres.GetOutput())
maxValue = vtk.vtkImageMathematics()
maxValue.SetInputData(0, blobImage)
maxValue.SetInputData(1, thres.GetOutput())
maxValue.SetOperationToMax()
maxValue.Modified()
maxValue.Update()
blobImage.DeepCopy(maxValue.GetOutput())
i += 1
discrete = vtk.vtkDiscreteFlyingEdges3D()
discrete.SetInputData(blobImage)
discrete.GenerateValues(n, 1, n)
mapper = vtk.vtkPolyDataMapper()
mapper.SetInputConnection(discrete.GetOutputPort())
mapper.SetLookupTable(lut)
mapper.SetScalarRange(0, lut.GetNumberOfColors())
actor = vtk.vtkActor()
actor.SetMapper(mapper)
ren1.AddActor(actor)
renWin.Render()
iren.Start()
thres.Update()
if (i == 0):
blobImage.DeepCopy(thres.GetOutput())
maxValue = vtk.vtkImageMathematics()
maxValue.SetInputData(0, blobImage)
maxValue.SetInputData(1, thres.GetOutput())
maxValue.SetOperationToMax()
maxValue.Modified()
maxValue.Update()
blobImage.DeepCopy(maxValue.GetOutput())
i += 1
discrete = vtk.vtkDiscreteFlyingEdges3D()
discrete.SetInputData(blobImage)
discrete.GenerateValues(n, 1, n)
mapper = vtk.vtkPolyDataMapper()
mapper.SetInputConnection(discrete.GetOutputPort())
mapper.SetLookupTable(lut)
mapper.SetScalarRange(0, lut.GetNumberOfColors())
actor = vtk.vtkActor()
actor.SetMapper(mapper)
ren1.AddActor(actor)
renWin.Render()
iren.Start()
def smoothMultipleSegments(self):
import vtkSegmentationCorePython as vtkSegmentationCore
# Generate merged labelmap of all visible segments
segmentationNode = self.scriptedEffect.parameterSetNode(
).GetSegmentationNode()
visibleSegmentIds = vtk.vtkStringArray()
segmentationNode.GetDisplayNode().GetVisibleSegmentIDs(
visibleSegmentIds)
if visibleSegmentIds.GetNumberOfValues() == 0:
logging.info(
"Smoothing operation skipped: there are no visible segments")
return
mergedImage = vtkSegmentationCore.vtkOrientedImageData()
if not segmentationNode.GenerateMergedLabelmapForAllSegments(
mergedImage, vtkSegmentationCore.vtkSegmentation.
EXTENT_UNION_OF_SEGMENTS_PADDED, None, visibleSegmentIds):
logging.error(
'Failed to apply smoothing: cannot get list of visible segments'
)
return
segmentLabelValues = [] # list of [segmentId, labelValue]
for i in range(visibleSegmentIds.GetNumberOfValues()):
segmentId = visibleSegmentIds.GetValue(i)
segmentLabelValues.append([segmentId, i + 1])
# Perform smoothing in voxel space
ici = vtk.vtkImageChangeInformation()
ici.SetInputData(mergedImage)
ici.SetOutputSpacing(1, 1, 1)
ici.SetOutputOrigin(0, 0, 0)
# Convert labelmap to combined polydata
if vtk.VTK_MAJOR_VERSION >= 9:
convertToPolyData = vtk.vtkDiscreteFlyingEdges3D()
convertToPolyData.ComputeGradientsOff()
convertToPolyData.ComputeNormalsOff()
convertToPolyData.ComputeScalarsOff()
else:
convertToPolyData = vtk.vtkDiscreteMarchingCubes()
convertToPolyData.SetInputConnection(ici.GetOutputPort())
convertToPolyData.SetNumberOfContours(len(segmentLabelValues))
contourIndex = 0
for segmentId, labelValue in segmentLabelValues:
convertToPolyData.SetValue(contourIndex, labelValue)
contourIndex += 1
# Low-pass filtering using Taubin's method
smoothingFactor = self.scriptedEffect.doubleParameter(
"JointTaubinSmoothingFactor")
smoothingIterations = 100 # according to VTK documentation 10-20 iterations could be enough but we use a higher value to reduce chance of shrinking
passBand = pow(
10.0, -4.0 * smoothingFactor
) # gives a nice range of 1-0.0001 from a user input of 0-1
smoother = vtk.vtkWindowedSincPolyDataFilter()
smoother.SetInputConnection(convertToPolyData.GetOutputPort())
smoother.SetNumberOfIterations(smoothingIterations)
smoother.BoundarySmoothingOff()
smoother.FeatureEdgeSmoothingOff()
smoother.SetFeatureAngle(90.0)
smoother.SetPassBand(passBand)
smoother.NonManifoldSmoothingOn()
smoother.NormalizeCoordinatesOn()
# Extract a label
threshold = vtk.vtkThreshold()
threshold.SetInputConnection(smoother.GetOutputPort())
# Convert to polydata
geometryFilter = vtk.vtkGeometryFilter()
geometryFilter.SetInputConnection(threshold.GetOutputPort())
# Convert polydata to stencil
polyDataToImageStencil = vtk.vtkPolyDataToImageStencil()
polyDataToImageStencil.SetInputConnection(
geometryFilter.GetOutputPort())
polyDataToImageStencil.SetOutputSpacing(1, 1, 1)
polyDataToImageStencil.SetOutputOrigin(0, 0, 0)
polyDataToImageStencil.SetOutputWholeExtent(mergedImage.GetExtent())
# Convert stencil to image
stencil = vtk.vtkImageStencil()
emptyBinaryLabelMap = vtk.vtkImageData()
emptyBinaryLabelMap.SetExtent(mergedImage.GetExtent())
emptyBinaryLabelMap.AllocateScalars(vtk.VTK_UNSIGNED_CHAR, 1)
vtkSegmentationCore.vtkOrientedImageDataResample.FillImage(
emptyBinaryLabelMap, 0)
stencil.SetInputData(emptyBinaryLabelMap)
stencil.SetStencilConnection(polyDataToImageStencil.GetOutputPort())
stencil.ReverseStencilOn()
stencil.SetBackgroundValue(
1
) # General foreground value is 1 (background value because of reverse stencil)
imageToWorldMatrix = vtk.vtkMatrix4x4()
mergedImage.GetImageToWorldMatrix(imageToWorldMatrix)
for segmentId, labelValue in segmentLabelValues:
threshold.ThresholdBetween(labelValue, labelValue)
stencil.Update()
smoothedBinaryLabelMap = vtkSegmentationCore.vtkOrientedImageData()
smoothedBinaryLabelMap.ShallowCopy(stencil.GetOutput())
smoothedBinaryLabelMap.SetImageToWorldMatrix(imageToWorldMatrix)
# Write results to segments directly, bypassing masking
slicer.vtkSlicerSegmentationsModuleLogic.SetBinaryLabelmapToSegment(
smoothedBinaryLabelMap, segmentationNode, segmentId,
slicer.vtkSlicerSegmentationsModuleLogic.MODE_REPLACE,
smoothedBinaryLabelMap.GetExtent())
def main():
# vtkDiscreteFlyingEdges3D was introduced in VTK >= 8.2
use_flying_edges = vtk_version_ok(8, 2, 0)
file_name, start_label, end_label = get_program_parameters()
if start_label > end_label:
end_label, start_label = start_label, end_label
# Create all of the classes we will need
reader = vtk.vtkMetaImageReader()
histogram = vtk.vtkImageAccumulate()
if use_flying_edges:
try:
using_marching_cubes = False
discrete_cubes = vtk.vtkDiscreteFlyingEdges3D()
except AttributeError:
using_marching_cubes = True
discrete_cubes = vtk.vtkDiscreteMarchingCubes()
else:
using_marching_cubes = True
discrete_cubes = vtk.vtkDiscreteMarchingCubes()
smoother = vtk.vtkWindowedSincPolyDataFilter()
selector = vtk.vtkThreshold()
scalars_off = vtk.vtkMaskFields()
geometry = vtk.vtkGeometryFilter()
writer = vtk.vtkXMLPolyDataWriter()
# Define all of the variables
file_prefix = 'Label'
smoothing_iterations = 15
pass_band = 0.001
feature_angle = 120.0
# Generate models from labels
# 1) Read the meta file
# 2) Generate a histogram of the labels
# 3) Generate models from the labeled volume
# 4) Smooth the models
# 5) Output each model into a separate file
reader.SetFileName(file_name)
histogram.SetInputConnection(reader.GetOutputPort())
histogram.SetComponentExtent(0, end_label, 0, 0, 0, 0)
histogram.SetComponentOrigin(0, 0, 0)
histogram.SetComponentSpacing(1, 1, 1)
histogram.Update()
discrete_cubes.SetInputConnection(reader.GetOutputPort())
discrete_cubes.GenerateValues(end_label - start_label + 1, start_label, end_label)
smoother.SetInputConnection(discrete_cubes.GetOutputPort())
smoother.SetNumberOfIterations(smoothing_iterations)
smoother.BoundarySmoothingOff()
smoother.FeatureEdgeSmoothingOff()
smoother.SetFeatureAngle(feature_angle)
smoother.SetPassBand(pass_band)
smoother.NonManifoldSmoothingOn()
smoother.NormalizeCoordinatesOn()
smoother.Update()
selector.SetInputConnection(smoother.GetOutputPort())
if use_flying_edges:
if using_marching_cubes:
selector.SetInputArrayToProcess(0, 0, 0, vtk.vtkDataObject().FIELD_ASSOCIATION_CELLS,
vtk.vtkDataSetAttributes().SCALARS)
else:
selector.SetInputArrayToProcess(0, 0, 0, vtk.vtkDataObject().FIELD_ASSOCIATION_POINTS,
vtk.vtkDataSetAttributes().SCALARS)
else:
selector.SetInputArrayToProcess(0, 0, 0, vtk.vtkDataObject().FIELD_ASSOCIATION_CELLS,
vtk.vtkDataSetAttributes().SCALARS)
# Strip the scalars from the output
scalars_off.SetInputConnection(selector.GetOutputPort())
scalars_off.CopyAttributeOff(vtk.vtkMaskFields().POINT_DATA,
vtk.vtkDataSetAttributes().SCALARS)
scalars_off.CopyAttributeOff(vtk.vtkMaskFields().CELL_DATA,
vtk.vtkDataSetAttributes().SCALARS)
geometry.SetInputConnection(scalars_off.GetOutputPort())
writer.SetInputConnection(geometry.GetOutputPort())
for i in range(start_label, end_label + 1):
# see if the label exists, if not skip it
frequency = histogram.GetOutput().GetPointData().GetScalars().GetTuple1(i)
if frequency == 0.0:
continue
# select the cells for a given label
selector.ThresholdBetween(i, i)
# output the polydata
output_fn = '{:s}{:d}.vtp'.format(file_prefix, i)
print('{:s} writing {:s}'.format(os.path.basename(sys.argv[0]), output_fn))
writer.SetFileName(output_fn)
writer.Write()
def main():
# vtkFlyingEdges3D was introduced in VTK >= 8.2
use_flying_edges = vtk_version_ok(8, 2, 0)
colors = vtk.vtkNamedColors()
ifn, index = get_program_parameters()
# Prepare to read the file.
reader_volume = vtk.vtkMetaImageReader()
reader_volume.SetFileName(ifn)
reader_volume.Update()
# Extract the region of interest.
voi = vtk.vtkExtractVOI()
voi.SetInputConnection(reader_volume.GetOutputPort())
voi.SetVOI(0, 517, 0, 228, 0, 392)
voi.SetSampleRate(1, 1, 1)
voi.Update() # Necessary for GetScalarRange().
srange = voi.GetOutput().GetScalarRange() # Needs Update() before!
print('Range', srange)
# Prepare surface generation.
# For label images.
if use_flying_edges:
try:
contour = vtk.vtkDiscreteFlyingEdges3D()
except AttributeError:
contour = vtk.vtkDiscreteMarchingCubes()
else:
contour = vtk.vtkDiscreteMarchingCubes()
contour.SetInputConnection(voi.GetOutputPort())
# contour.ComputeNormalsOn()
print('Doing label', index)
contour.SetValue(0, index)
contour.Update() # Needed for GetNumberOfPolys()!!!
smoother = vtk.vtkWindowedSincPolyDataFilter()
smoother.SetInputConnection(contour.GetOutputPort())
smoother.SetNumberOfIterations(30) # This has little effect on the error!
# smoother.BoundarySmoothingOff()
# smoother.FeatureEdgeSmoothingOff()
# smoother.SetFeatureAngle(120.0)
# smoother.SetPassBand(0.001) # This increases the error a lot!
smoother.NonManifoldSmoothingOn()
smoother.NormalizeCoordinatesOn()
smoother.GenerateErrorScalarsOn()
# smoother.GenerateErrorVectorsOn()
smoother.Update()
smoothed_polys = smoother.GetOutput()
smoother_error = smoothed_polys.GetPointData().GetScalars()
# Find min and max z.
se_range = smoother_error.GetRange()
print('Smoother error range:', se_range)
minz = se_range[0] # min(smoother_error)
maxz = se_range[1] # max(smoother_error)
if maxz > 1:
print('Big smoother error: min/max:', minz, maxz)
# minz = 0.3 # This way colours of different particles are comparable.
# maxz = 1
# minz = 0.3
# maxz = 0.6
minz = 3.25
maxz = 3.85
# Create the color map.
lut = vtk.vtkLookupTable()
lut.SetTableRange(
minz,
maxz) # This does nothing, use mapper.SetScalarRange(minz, maxz).
lut.SetHueRange(2 / 3.0, 1)
# lut.SetSaturationRange(0, 0)
# lut.SetValueRange(1, 0)
# lut.SetNumberOfColors(256) #256 default
lut.Build()
# Calculate cell normals.
triangle_cell_normals = vtk.vtkPolyDataNormals()
triangle_cell_normals.SetInputData(smoothed_polys)
triangle_cell_normals.ComputeCellNormalsOn()
triangle_cell_normals.ComputePointNormalsOff()
triangle_cell_normals.ConsistencyOn()
triangle_cell_normals.AutoOrientNormalsOn()
triangle_cell_normals.Update() # Creates vtkPolyData.
mapper = vtk.vtkPolyDataMapper()
# mapper.SetInput(smoothed_polys) # This has no normals.
mapper.SetInputConnection(
triangle_cell_normals.GetOutputPort()) # this is better for vis;-)
mapper.ScalarVisibilityOn() # Show colour.
mapper.SetScalarRange(minz, maxz)
# mapper.SetScalarModeToUseCellData() # Contains the label eg. 31
mapper.SetScalarModeToUsePointData(
) # The smoother error relates to the verts.
mapper.SetLookupTable(lut)
# Take the isosurface data and create geometry.
actor = vtk.vtkLODActor()
actor.SetNumberOfCloudPoints(100000)
actor.SetMapper(mapper)
# Create the renderer.
ren = vtk.vtkRenderer()
ren.SetBackground(colors.GetColor3d('DimGray'))
ren.AddActor(actor)
# Create a window for the renderer of size 600X600
ren_win = vtk.vtkRenderWindow()
ren_win.AddRenderer(ren)
ren_win.SetSize(600, 600)
# Set a user interface interactor for the render window.
iren = vtk.vtkRenderWindowInteractor()
iren.SetRenderWindow(ren_win)
# Start the initialization and rendering.
iren.Initialize()
ren.GetActiveCamera().SetPosition(-0.004332, -1.771289, -0.754580)
ren.GetActiveCamera().SetFocalPoint(0.000271, -0.001974, 0.006892)
ren.GetActiveCamera().SetViewUp(0.790211, -0.243999, 0.562166)
ren.ResetCameraClippingRange()
ren_win.Render()
ren_win.SetWindowName('MeshLabelImageColor')
ren_win.Render()
iren.Start()
def main():
# vtkFlyingEdges3D was introduced in VTK >= 8.2
use_flying_edges = vtk_version_ok(8, 2, 0)
file_name = get_program_parameters()
colors = vtk.vtkNamedColors()
# Create the RenderWindow, Renderer and Interactor.
#
ren = vtk.vtkRenderer()
ren_win = vtk.vtkRenderWindow()
ren_win.AddRenderer(ren)
iren = vtk.vtkRenderWindowInteractor()
iren.SetRenderWindow(ren_win)
# Create the pipeline.
#
reader = vtk.vtkMetaImageReader()
reader.SetFileName(file_name)
reader.Update()
locator = vtk.vtkMergePoints()
locator.SetDivisions(64, 64, 92)
locator.SetNumberOfPointsPerBucket(2)
locator.AutomaticOff()
if use_flying_edges:
try:
using_marching_cubes = False
iso = vtk.vtkDiscreteFlyingEdges3D()
except AttributeError:
using_marching_cubes = True
iso = vtk.vtkDiscreteMarchingCubes()
else:
using_marching_cubes = True
iso = vtk.vtkDiscreteMarchingCubes()
iso.SetInputConnection(reader.GetOutputPort())
iso.ComputeGradientsOn()
iso.ComputeScalarsOff()
iso.SetValue(0, 1150)
if using_marching_cubes:
iso.SetLocator(locator)
iso_mapper = vtk.vtkPolyDataMapper()
iso_mapper.SetInputConnection(iso.GetOutputPort())
iso_mapper.ScalarVisibilityOff()
iso_actor = vtk.vtkActor()
iso_actor.SetMapper(iso_mapper)
iso_actor.GetProperty().SetColor(colors.GetColor3d('Ivory'))
outline = vtk.vtkOutlineFilter()
outline.SetInputConnection(reader.GetOutputPort())
outline_mapper = vtk.vtkPolyDataMapper()
outline_mapper.SetInputConnection(outline.GetOutputPort())
outline_actor = vtk.vtkActor()
outline_actor.SetMapper(outline_mapper)
# Add the actors to the renderer, set the background and size.
#
ren.AddActor(outline_actor)
ren.AddActor(iso_actor)
ren.SetBackground(colors.GetColor3d('SlateGray'))
ren.GetActiveCamera().SetFocalPoint(0, 0, 0)
ren.GetActiveCamera().SetPosition(0, -1, 0)
ren.GetActiveCamera().SetViewUp(0, 0, -1)
ren.ResetCamera()
ren.GetActiveCamera().Dolly(1.5)
ren.ResetCameraClippingRange()
ren_win.SetSize(640, 480)
ren_win.SetWindowName('HeadBone')
ren_win.Render()
iren.Start()