def onApply(self):
# Make sure the user wants to do the operation, even if the segment is not visible
if not self.scriptedEffect.confirmCurrentSegmentVisible():
return
self.scriptedEffect.saveStateForUndo()
# Get modifier labelmap and parameters
modifierLabelmap = self.scriptedEffect.defaultModifierLabelmap()
selectedSegmentLabelmap = self.scriptedEffect.selectedSegmentLabelmap()
# We need to know exactly the value of the segment voxels, apply threshold to make force the selected label value
labelValue = 1
backgroundValue = 0
thresh = vtk.vtkImageThreshold()
thresh.SetInputData(selectedSegmentLabelmap)
thresh.ThresholdByLower(0)
thresh.SetInValue(backgroundValue)
thresh.SetOutValue(labelValue)
thresh.SetOutputScalarType(selectedSegmentLabelmap.GetScalarType())
shellMode = self.scriptedEffect.parameter("ShellMode")
shellThicknessMM = abs(
self.scriptedEffect.doubleParameter("ShellThicknessMm"))
import vtkITK
margin = vtkITK.vtkITKImageMargin()
margin.SetInputConnection(thresh.GetOutputPort())
margin.CalculateMarginInMMOn()
spacing = selectedSegmentLabelmap.GetSpacing()
voxelDiameter = min(selectedSegmentLabelmap.GetSpacing())
if shellMode == MEDIAL_SURFACE:
margin.SetOuterMarginMM(0.5 * shellThicknessMM)
margin.SetInnerMarginMM(-0.5 * shellThicknessMM +
0.5 * voxelDiameter)
elif shellMode == INSIDE_SURFACE:
margin.SetOuterMarginMM(shellThicknessMM + 0.1 * voxelDiameter)
margin.SetInnerMarginMM(
0.0 +
0.1 * voxelDiameter) # Don't include the original border (0.0)
elif shellMode == OUTSIDE_SURFACE:
margin.SetOuterMarginMM(0.0)
margin.SetInnerMarginMM(-shellThicknessMM + voxelDiameter)
modifierLabelmap.DeepCopy(margin.GetOutput())
# This can be a long operation - indicate it to the user
qt.QApplication.setOverrideCursor(qt.Qt.WaitCursor)
margin.Update()
modifierLabelmap.ShallowCopy(margin.GetOutput())
# Apply changes
self.scriptedEffect.modifySelectedSegmentByLabelmap(
modifierLabelmap,
slicer.qSlicerSegmentEditorAbstractEffect.ModificationModeSet)
qt.QApplication.restoreOverrideCursor()
def onApply(self):
# Make sure the user wants to do the operation, even if the segment is not visible
if not self.scriptedEffect.confirmCurrentSegmentVisible():
return
self.scriptedEffect.saveStateForUndo()
# Get modifier labelmap and parameters
modifierLabelmap = self.scriptedEffect.defaultModifierLabelmap()
selectedSegmentLabelmap = self.scriptedEffect.selectedSegmentLabelmap()
marginSizeMM = self.scriptedEffect.doubleParameter("MarginSizeMm")
# We need to know exactly the value of the segment voxels, apply threshold to make force the selected label value
labelValue = 1
backgroundValue = 0
thresh = vtk.vtkImageThreshold()
thresh.SetInputData(selectedSegmentLabelmap)
thresh.ThresholdByLower(0)
thresh.SetInValue(backgroundValue)
thresh.SetOutValue(labelValue)
thresh.SetOutputScalarType(selectedSegmentLabelmap.GetScalarType())
if (marginSizeMM < 0):
# The distance filter used in the margin filter starts at zero at the border voxels,
# so if we need to shrink the margin, it is more accurate to invert the labelmap and
# use positive distance when calculating the margin
thresh.SetInValue(labelValue)
thresh.SetOutValue(backgroundValue)
import vtkITK
margin = vtkITK.vtkITKImageMargin()
margin.SetInputConnection(thresh.GetOutputPort())
margin.CalculateMarginInMMOn()
margin.SetOuterMarginMM(abs(marginSizeMM))
margin.Update()
if marginSizeMM >= 0:
modifierLabelmap.ShallowCopy(margin.GetOutput())
else:
# If we are shrinking then the result needs to be inverted.
thresh = vtk.vtkImageThreshold()
thresh.SetInputData(margin.GetOutput())
thresh.ThresholdByLower(0)
thresh.SetInValue(labelValue)
thresh.SetOutValue(backgroundValue)
thresh.SetOutputScalarType(selectedSegmentLabelmap.GetScalarType())
thresh.Update()
modifierLabelmap.ShallowCopy(thresh.GetOutput())
# Apply changes
self.scriptedEffect.modifySelectedSegmentByLabelmap(
modifierLabelmap,
slicer.qSlicerSegmentEditorAbstractEffect.ModificationModeSet)
qt.QApplication.restoreOverrideCursor()
def processHollowing(self):
# Get modifier labelmap and parameters
modifierLabelmap = self.scriptedEffect.defaultModifierLabelmap()
selectedSegmentLabelmap = self.scriptedEffect.selectedSegmentLabelmap()
# We need to know exactly the value of the segment voxels, apply threshold to make force the selected label value
labelValue = 1
backgroundValue = 0
thresh = vtk.vtkImageThreshold()
thresh.SetInputData(selectedSegmentLabelmap)
thresh.ThresholdByLower(0)
thresh.SetInValue(backgroundValue)
thresh.SetOutValue(labelValue)
thresh.SetOutputScalarType(selectedSegmentLabelmap.GetScalarType())
shellMode = self.scriptedEffect.parameter("ShellMode")
shellThicknessMM = abs(
self.scriptedEffect.doubleParameter("ShellThicknessMm"))
import vtkITK
margin = vtkITK.vtkITKImageMargin()
margin.SetInputConnection(thresh.GetOutputPort())
margin.CalculateMarginInMMOn()
spacing = selectedSegmentLabelmap.GetSpacing()
voxelDiameter = min(selectedSegmentLabelmap.GetSpacing())
if shellMode == MEDIAL_SURFACE:
margin.SetOuterMarginMM(0.5 * shellThicknessMM)
margin.SetInnerMarginMM(-0.5 * shellThicknessMM +
0.5 * voxelDiameter)
elif shellMode == INSIDE_SURFACE:
margin.SetOuterMarginMM(shellThicknessMM + 0.1 * voxelDiameter)
margin.SetInnerMarginMM(
0.0 +
0.1 * voxelDiameter) # Don't include the original border (0.0)
elif shellMode == OUTSIDE_SURFACE:
margin.SetOuterMarginMM(0.0)
margin.SetInnerMarginMM(-shellThicknessMM + voxelDiameter)
modifierLabelmap.DeepCopy(margin.GetOutput())
margin.Update()
modifierLabelmap.ShallowCopy(margin.GetOutput())
# Apply changes
self.scriptedEffect.modifySelectedSegmentByLabelmap(
modifierLabelmap,
slicer.qSlicerSegmentEditorAbstractEffect.ModificationModeSet)
def onApply(self):
# Make sure the user wants to do the operation, even if the segment is not visible
if not self.scriptedEffect.confirmCurrentSegmentVisible():
return
self.scriptedEffect.saveStateForUndo()
# Get modifier labelmap and parameters
modifierLabelmap = self.scriptedEffect.defaultModifierLabelmap()
selectedSegmentLabelmap = self.scriptedEffect.selectedSegmentLabelmap()
# We need to know exactly the value of the segment voxels, apply threshold to make force the selected label value
labelValue = 1
backgroundValue = 0
thresh = vtk.vtkImageThreshold()
thresh.SetInputData(selectedSegmentLabelmap)
thresh.ThresholdByLower(0)
thresh.SetInValue(backgroundValue)
thresh.SetOutValue(labelValue)
thresh.SetOutputScalarType(selectedSegmentLabelmap.GetScalarType())
marginSizeMM = self.scriptedEffect.doubleParameter("MarginSizeMm")
if (marginSizeMM < 0):
# The border voxel starts at zero, if we need to account for this single voxel thickness in the margin size.
# Currently this is done by reducing the magnitude of the margin size by 0.9 * the smallest spacing.
voxelDiameter = min(selectedSegmentLabelmap.GetSpacing())
marginSizeMM += 0.9 * voxelDiameter
import vtkITK
margin = vtkITK.vtkITKImageMargin()
margin.SetInputConnection(thresh.GetOutputPort())
margin.CalculateMarginInMMOn()
margin.SetOuterMarginMM(marginSizeMM)
margin.Update()
modifierLabelmap.ShallowCopy(margin.GetOutput())
# Apply changes
self.scriptedEffect.modifySelectedSegmentByLabelmap(
modifierLabelmap,
slicer.qSlicerSegmentEditorAbstractEffect.ModificationModeSet)
qt.QApplication.restoreOverrideCursor()
def _extractCavity(self, shrunkenPd):
spacing = self._inputSpacing / self.remeshOversampling
outsideObjectLabelmap = WrapSolidifyLogic._polydataToLabelmap(
shrunkenPd, spacing) # 0=outside, 1=inside
inputLabelmap = WrapSolidifyLogic._polydataToLabelmap(
self._inputPd, referenceImage=outsideObjectLabelmap)
if self.splitCavities:
# It is less accurate but more robust to dilate labelmap than grow polydata.
# Since accuracy is not important here, we dilate labelmap.
splitCavitiesRadius = self.splitCavitiesDiameter / 2.0
# Dilate
import vtkITK
margin = vtkITK.vtkITKImageMargin()
margin.SetInputData(inputLabelmap)
margin.CalculateMarginInMMOn()
margin.SetOuterMarginMM(splitCavitiesRadius)
margin.Update()
# extendedInputLabelmap: 255 near original inputLabelmap voxels, 0 elsewhere
extendedInputLabelmap = margin.GetOutput()
self._saveIntermediateResult(
"SplitCavitiesGrown",
WrapSolidifyLogic._labelmapToPolydata(extendedInputLabelmap,
255))
else:
extendedInputLabelmap = inputLabelmap
outsideObjectLabelmapInverter = vtk.vtkImageThreshold()
outsideObjectLabelmapInverter.SetInputData(outsideObjectLabelmap)
outsideObjectLabelmapInverter.ThresholdByLower(0)
outsideObjectLabelmapInverter.SetInValue(1) # backgroundValue
outsideObjectLabelmapInverter.SetOutValue(0) # labelValue
outsideObjectLabelmapInverter.SetOutputScalarType(
outsideObjectLabelmap.GetScalarType())
outsideObjectLabelmapInverter.Update()
addImage = vtk.vtkImageMathematics()
addImage.SetInput1Data(outsideObjectLabelmapInverter.GetOutput())
addImage.SetInput2Data(extendedInputLabelmap)
addImage.SetOperationToMax()
addImage.Update()
internalHolesLabelmap = addImage.GetOutput()
# internal holes are 0, elsewhere >=1
self._saveIntermediateResult(
"SplitCavitiesAll",
WrapSolidifyLogic._labelmapToPolydata(internalHolesLabelmap, 0))
# Find largest internal hole
largestHoleExtract = vtk.vtkImageConnectivityFilter()
largestHoleExtract.SetScalarRange(-0.5, 0.5)
largestHoleExtract.SetInputData(internalHolesLabelmap)
largestHoleExtract.SetExtractionModeToLargestRegion()
largestHoleExtract.Update()
largestHolesLabelmap = largestHoleExtract.GetOutput()
# Convert back to polydata
initialRegionPd = vtk.vtkPolyData()
initialRegionPd.DeepCopy(
WrapSolidifyLogic._labelmapToPolydata(largestHolesLabelmap, 0))
self._saveIntermediateResult("SplitCavitiesLargest", initialRegionPd)
if self.splitCavities:
return self._shrinkWrap(initialRegionPd)
else:
return initialRegionPd
def _getInitialRegionPd(self):
"""Get initial shape that will be snapped to closest point of the input segment"""
spacing = self._inputSpacing / self.remeshOversampling
if self.carveHolesInOuterSurface:
# Grow input polydata to close holes between outer surface and internal cavities.
# It is less accurate but more robust to dilate labelmap than grow polydata.
# Since accuracy is not important here, we dilate labelmap.
# Convert to labelmap
carveHolesInOuterSurfaceRadius = self.carveHolesInOuterSurfaceDiameter / 2.0
# add self.carveHolesInOuterSurfaceDiameter extra to bounds to ensure that the grown input still has an margin around
inputLabelmap = WrapSolidifyLogic._polydataToLabelmap(
self._inputPd,
spacing,
extraMarginToBounds=carveHolesInOuterSurfaceRadius)
self._saveIntermediateResult(
"InitialRegionResampled",
WrapSolidifyLogic._labelmapToPolydata(inputLabelmap, 1))
# Dilate
import vtkITK
margin = vtkITK.vtkITKImageMargin()
margin.SetInputData(inputLabelmap)
margin.CalculateMarginInMMOn()
margin.SetOuterMarginMM(carveHolesInOuterSurfaceRadius)
margin.Update()
# extendedInputLabelmap: 255 near original inputLabelmap voxels, 0 elsewhere
extendedInputLabelmap = margin.GetOutput()
self._saveIntermediateResult(
"InitialRegionGrown",
WrapSolidifyLogic._labelmapToPolydata(extendedInputLabelmap,
255))
# Region growing from a corner of the image
seedPoints = vtk.vtkPoints()
seedPoints.InsertNextPoint(
inputLabelmap.GetOrigin()[0] + spacing / 2,
inputLabelmap.GetOrigin()[1] + spacing / 2,
inputLabelmap.GetOrigin()[2] + spacing / 2)
seedScalars = vtk.vtkUnsignedCharArray()
seedScalars.InsertNextValue(
255) # this will be the label value to the grown region
seedData = vtk.vtkPolyData()
seedData.SetPoints(seedPoints)
seedData.GetPointData().SetScalars(seedScalars)
regionGrowing = vtk.vtkImageConnectivityFilter()
regionGrowing.SetSeedData(seedData)
regionGrowing.SetScalarRange(-10, 10)
regionGrowing.SetInputData(extendedInputLabelmap)
regionGrowing.Update()
# outsideObjectImage: 255 outside the object, 0 inside
outsideObjectLabelmap = regionGrowing.GetOutput()
# Cavity extraction and outer surface extraction starts from the same outer surface shrinkwrap
if self.region == REGION_OUTER_SURFACE or self.region == REGION_LARGEST_CAVITY:
if self.carveHolesInOuterSurface:
# Convert back to polydata
initialRegionPd = vtk.vtkPolyData()
initialRegionPd.DeepCopy(
WrapSolidifyLogic._labelmapToPolydata(
outsideObjectLabelmap, 255))
else:
# create sphere that encloses entire segment content
bounds = np.zeros(6)
self._inputPd.GetBounds(bounds)
diameters = np.array([
bounds[1] - bounds[0], bounds[3] - bounds[2],
bounds[5] - bounds[4]
])
maxRadius = max(diameters) / 2.0
sphereSource = vtk.vtkSphereSource()
# to make sure the volume is fully included in the sphere, radius must be sqrt(2) times larger
sphereSource.SetRadius(maxRadius * 1.5)
# Set resolution to be about one magnitude lower than the final resolution
# (by creating an initial surface element for about every 100th final element).
sphereSurfaceArea = 4 * math.pi * maxRadius * maxRadius
voxelSurfaceArea = spacing * spacing
numberOfSurfaceElements = sphereSurfaceArea / voxelSurfaceArea
numberOfIinitialSphereSurfaceElements = numberOfSurfaceElements / 100
sphereResolution = math.sqrt(
numberOfIinitialSphereSurfaceElements)
# Set resolution to minimum 10
sphereResolution = max(int(sphereResolution), 10)
sphereSource.SetPhiResolution(sphereResolution)
sphereSource.SetThetaResolution(sphereResolution)
sphereSource.SetCenter((bounds[0] + bounds[1]) / 2.0,
(bounds[2] + bounds[3]) / 2.0,
(bounds[4] + bounds[5]) / 2.0)
sphereSource.Update()
initialRegionPd = sphereSource.GetOutput()
elif self.region == REGION_SEGMENT:
# create initial region from segment (that will be grown)
if not self.regionSegmentId:
raise ValueError("Region segment is not set")
if self.regionSegmentId == self.segmentId:
raise ValueError(
"Region segment cannot be the same segment as the current segment"
)
initialRegionPd = vtk.vtkPolyData()
self.segmentationNode.GetClosedSurfaceRepresentation(
self.regionSegmentId, initialRegionPd)
if not initialRegionPd or initialRegionPd.GetNumberOfPoints() == 0:
raise ValueError("Region segment is empty")
# initialRegionPd = self._remeshPolydata(initialRegionPd, self._inputSpacing*5.0) # simplify the mesh
else:
raise ValueError("Invalid region: " + self.region)
cleanPolyData = vtk.vtkCleanPolyData()
cleanPolyData.SetInputData(initialRegionPd)
cleanPolyData.Update()
initialRegionPd = cleanPolyData.GetOutput()
self._saveIntermediateResult("InitialRegion", initialRegionPd)
return initialRegionPd
