def contourSequence2Volume(cs, spacing=[1, 1, 1]):
polylines = drt2polylines.contourSequence2PolyLines(cs)
stencil = vtk.vtkPolyDataToImageStencil()
stencil.SetInputData(polylines)
bounds = polylines.GetBounds()
i = 0
bounds2 = []
for x in bounds:
if i & 1:
y = math.ceil(x) + 1
else:
y = math.floor(x) - 1
bounds2.append(y)
i = i + 1
stencil.SetOutputWholeExtent(bounds2[0], bounds2[1], bounds2[2],
bounds2[3], bounds2[4], bounds2[5])
stencil.SetOutputSpacing(spacing[0], spacing[1], spacing[2])
stencil.Update()
sten2img = vtk.vtkImageStencilToImage()
sten2img.SetInputConnection(stencil.GetOutputPort())
sten2img.SetOutsideValue(0)
sten2img.SetInsideValue(255)
sten2img.Update()
vtkimg = sten2img.GetOutput()
return vtkimg
def cutSurfaceWithModel(self, segmentMarkupNode, segmentModel):
import vtkSegmentationCorePython as vtkSegmentationCore
if not segmentMarkupNode:
raise AttributeError("{}: segment markup node not set.".format(
self.__class__.__name__))
if not segmentModel:
raise AttributeError("{}: segment model not set.".format(
self.__class__.__name__))
if segmentMarkupNode and segmentModel.GetPolyData().GetNumberOfPolys(
) > 0:
operationName = self.scriptedEffect.parameter("Operation")
segmentationNode = self.scriptedEffect.parameterSetNode(
).GetSegmentationNode()
if not segmentationNode:
raise AttributeError("{}: Segmentation node not set.".format(
self.__class__.__name__))
modifierLabelmap = self.scriptedEffect.defaultModifierLabelmap()
if not modifierLabelmap:
raise AttributeError(
"{}: ModifierLabelmap not set. This can happen for various reasons:\n"
"No master volume set for segmentation,\n"
"No existing segments for segmentation, or\n"
"No referenceImageGeometry is specified in the segmentation"
.format(self.__class__.__name__))
WorldToModifierLabelmapIjkTransform = vtk.vtkTransform()
WorldToModifierLabelmapIjkTransformer = vtk.vtkTransformPolyDataFilter(
)
WorldToModifierLabelmapIjkTransformer.SetTransform(
WorldToModifierLabelmapIjkTransform)
WorldToModifierLabelmapIjkTransformer.SetInputConnection(
segmentModel.GetPolyDataConnection())
segmentationToSegmentationIjkTransformMatrix = vtk.vtkMatrix4x4()
modifierLabelmap.GetImageToWorldMatrix(
segmentationToSegmentationIjkTransformMatrix)
segmentationToSegmentationIjkTransformMatrix.Invert()
WorldToModifierLabelmapIjkTransform.Concatenate(
segmentationToSegmentationIjkTransformMatrix)
worldToSegmentationTransformMatrix = vtk.vtkMatrix4x4()
slicer.vtkMRMLTransformNode.GetMatrixTransformBetweenNodes(
None, segmentationNode.GetParentTransformNode(),
worldToSegmentationTransformMatrix)
WorldToModifierLabelmapIjkTransform.Concatenate(
worldToSegmentationTransformMatrix)
WorldToModifierLabelmapIjkTransformer.Update()
polyToStencil = vtk.vtkPolyDataToImageStencil()
polyToStencil.SetOutputSpacing(1.0, 1.0, 1.0)
polyToStencil.SetInputConnection(
WorldToModifierLabelmapIjkTransformer.GetOutputPort())
boundsIjk = WorldToModifierLabelmapIjkTransformer.GetOutput(
).GetBounds()
modifierLabelmapExtent = self.scriptedEffect.modifierLabelmap(
).GetExtent()
polyToStencil.SetOutputWholeExtent(modifierLabelmapExtent[0],
modifierLabelmapExtent[1],
modifierLabelmapExtent[2],
modifierLabelmapExtent[3],
int(round(boundsIjk[4])),
int(round(boundsIjk[5])))
polyToStencil.Update()
stencilData = polyToStencil.GetOutput()
stencilExtent = [0, -1, 0, -1, 0, -1]
stencilData.SetExtent(stencilExtent)
stencilToImage = vtk.vtkImageStencilToImage()
stencilToImage.SetInputConnection(polyToStencil.GetOutputPort())
if operationName in ("FILL_INSIDE", "ERASE_INSIDE", "SET"):
stencilToImage.SetInsideValue(1.0)
stencilToImage.SetOutsideValue(0.0)
else:
stencilToImage.SetInsideValue(0.0)
stencilToImage.SetOutsideValue(1.0)
stencilToImage.SetOutputScalarType(
modifierLabelmap.GetScalarType())
stencilPositioner = vtk.vtkImageChangeInformation()
stencilPositioner.SetInputConnection(
stencilToImage.GetOutputPort())
stencilPositioner.SetOutputSpacing(modifierLabelmap.GetSpacing())
stencilPositioner.SetOutputOrigin(modifierLabelmap.GetOrigin())
stencilPositioner.Update()
orientedStencilPositionerOutput = vtkSegmentationCore.vtkOrientedImageData(
)
orientedStencilPositionerOutput.ShallowCopy(
stencilToImage.GetOutput())
imageToWorld = vtk.vtkMatrix4x4()
modifierLabelmap.GetImageToWorldMatrix(imageToWorld)
orientedStencilPositionerOutput.SetImageToWorldMatrix(imageToWorld)
vtkSegmentationCore.vtkOrientedImageDataResample.ModifyImage(
modifierLabelmap, orientedStencilPositionerOutput,
vtkSegmentationCore.vtkOrientedImageDataResample.
OPERATION_MAXIMUM)
modMode = slicer.qSlicerSegmentEditorAbstractEffect.ModificationModeAdd
if operationName == "ERASE_INSIDE" or operationName == "ERASE_OUTSIDE":
modMode = slicer.qSlicerSegmentEditorAbstractEffect.ModificationModeRemove
elif operationName == "SET":
modMode = slicer.qSlicerSegmentEditorAbstractEffect.ModificationModeSet
self.scriptedEffect.modifySelectedSegmentByLabelmap(
modifierLabelmap, modMode)
# get fiducial positions as space-separated list
import numpy
n = segmentMarkupNode.GetNumberOfFiducials()
fPos = []
for i in range(n):
coord = [0.0, 0.0, 0.0]
segmentMarkupNode.GetNthFiducialPosition(i, coord)
fPos.extend(coord)
fPosString = ' '.join(map(str, fPos))
segmentID = self.scriptedEffect.parameterSetNode(
).GetSelectedSegmentID()
segment = segmentationNode.GetSegmentation().GetSegment(segmentID)
segment.SetTag("SurfaceCutEffectMarkupPositions", fPosString)
def apply(self, segmentMarkupNode, segmentModel, text, textDepth, mode):
self.updateModel(segmentMarkupNode, segmentModel, text, textDepth)
import vtkSegmentationCore
if not segmentMarkupNode:
raise AttributeError(f"{self.__class__.__name__}: segment markup node not set.")
if not segmentModel:
raise AttributeError(f"{self.__class__.__name__}: segment model not set.")
if segmentMarkupNode and segmentModel.GetPolyData().GetNumberOfCells() > 0:
segmentationNode = self.scriptedEffect.parameterSetNode().GetSegmentationNode()
if not segmentationNode:
raise AttributeError(f"{self.__class__.__name__}: Segmentation node not set.")
modifierLabelmap = self.scriptedEffect.defaultModifierLabelmap()
if not modifierLabelmap:
raise AttributeError("{}: ModifierLabelmap not set. This can happen for various reasons:\n"
"No master volume set for segmentation,\n"
"No existing segments for segmentation, or\n"
"No referenceImageGeometry is specified in the segmentation".format(self.__class__.__name__))
WorldToModifierLabelmapIjkTransform = vtk.vtkTransform()
WorldToModifierLabelmapIjkTransformer = vtk.vtkTransformPolyDataFilter()
WorldToModifierLabelmapIjkTransformer.SetTransform(WorldToModifierLabelmapIjkTransform)
WorldToModifierLabelmapIjkTransformer.SetInputConnection(segmentModel.GetPolyDataConnection())
segmentationToSegmentationIjkTransformMatrix = vtk.vtkMatrix4x4()
modifierLabelmap.GetImageToWorldMatrix(segmentationToSegmentationIjkTransformMatrix)
segmentationToSegmentationIjkTransformMatrix.Invert()
WorldToModifierLabelmapIjkTransform.Concatenate(segmentationToSegmentationIjkTransformMatrix)
worldToSegmentationTransformMatrix = vtk.vtkMatrix4x4()
slicer.vtkMRMLTransformNode.GetMatrixTransformBetweenNodes(None, segmentationNode.GetParentTransformNode(),
worldToSegmentationTransformMatrix)
WorldToModifierLabelmapIjkTransform.Concatenate(worldToSegmentationTransformMatrix)
WorldToModifierLabelmapIjkTransformer.Update()
polyToStencil = vtk.vtkPolyDataToImageStencil()
polyToStencil.SetOutputSpacing(1.0, 1.0, 1.0)
polyToStencil.SetInputConnection(WorldToModifierLabelmapIjkTransformer.GetOutputPort())
boundsIjk = WorldToModifierLabelmapIjkTransformer.GetOutput().GetBounds()
modifierLabelmapExtent = self.scriptedEffect.modifierLabelmap().GetExtent()
polyToStencil.SetOutputWholeExtent(modifierLabelmapExtent[0], modifierLabelmapExtent[1],
modifierLabelmapExtent[2], modifierLabelmapExtent[3],
int(round(boundsIjk[4])), int(round(boundsIjk[5])))
polyToStencil.Update()
stencilData = polyToStencil.GetOutput()
stencilExtent = [0, -1, 0, -1, 0, -1]
stencilData.SetExtent(stencilExtent)
stencilToImage = vtk.vtkImageStencilToImage()
stencilToImage.SetInputConnection(polyToStencil.GetOutputPort())
stencilToImage.SetInsideValue(1.0)
stencilToImage.SetOutsideValue(0.0)
stencilToImage.SetOutputScalarType(modifierLabelmap.GetScalarType())
stencilPositioner = vtk.vtkImageChangeInformation()
stencilPositioner.SetInputConnection(stencilToImage.GetOutputPort())
stencilPositioner.SetOutputSpacing(modifierLabelmap.GetSpacing())
stencilPositioner.SetOutputOrigin(modifierLabelmap.GetOrigin())
stencilPositioner.Update()
orientedStencilPositionerOutput = vtkSegmentationCore.vtkOrientedImageData()
orientedStencilPositionerOutput.ShallowCopy(stencilToImage.GetOutput())
imageToWorld = vtk.vtkMatrix4x4()
modifierLabelmap.GetImageToWorldMatrix(imageToWorld)
orientedStencilPositionerOutput.SetImageToWorldMatrix(imageToWorld)
vtkSegmentationCore.vtkOrientedImageDataResample.ModifyImage(
modifierLabelmap, orientedStencilPositionerOutput,
vtkSegmentationCore.vtkOrientedImageDataResample.OPERATION_MAXIMUM)
modeName = self.scriptedEffect.parameter("Mode")
if modeName == "EMBOSS":
mode = slicer.qSlicerSegmentEditorAbstractEffect.ModificationModeAdd
elif modeName == "ENGRAVE":
mode = slicer.qSlicerSegmentEditorAbstractEffect.ModificationModeRemove
else:
logging.error("Invalid mode: "+modeName+" (valid modes: EMBOSS, ENGRAVE)")
self.scriptedEffect.modifySelectedSegmentByLabelmap(modifierLabelmap, mode)
# get plane parameters as space-separated string list
planeParameters = []
if segmentMarkupNode.GetIsPlaneValid():
planeParameters.extend(segmentMarkupNode.GetOriginWorld())
xAxis = [1, 0, 0]
yAxis = [0, 1, 0]
zAxis = [0, 0, 1]
segmentMarkupNode.GetAxesWorld(xAxis, yAxis, zAxis)
planeParameters.extend(xAxis)
planeParameters.extend(yAxis)
planeParameters.extend(zAxis)
planeParameters.extend(segmentMarkupNode.GetPlaneBounds())
planeParametersString = ' '.join(map(str, planeParameters))
segmentID = self.scriptedEffect.parameterSetNode().GetSelectedSegmentID()
segment = segmentationNode.GetSegmentation().GetSegment(segmentID)
segment.SetTag("EngraveEffectPlaneParameters", planeParametersString)
def StereologyAnalysis(self):
"""Perform stereology analysis on a sub-region of an image"""
# user have to define an ROI - enforce fore now...
# should allow to use whole image as default
event.notify(ProgressEvent("Stereology...", 0.0))
state = self._app_states[self._current_image_index]
origin = self._Origin
spacing = self._Spacing
# --- generate a mask from stencil ----
self.__stencil_data.Update()
stencil_image = vtk.vtkImageStencilToImage()
stencil_image.SetInput(self.__stencil_data)
stencil_image.SetInsideValue(255)
stencil_image.SetOutsideValue(0)
stencil_image.SetOutputScalarTypeToUnsignedChar()
stencil_image.Update()
# --- image purify -----
event.notify(ProgressEvent("Stereology: Purify...", 0.2))
roi_image_reslice = self.GetROIImage()
# optionally create a purification filter
if state.bEnablePurify:
purify = _MicroView.vtkImagePurify()
purify.SetInputConnection(roi_image_reslice.GetOutputPort())
purify.SetThreshold(self._Threshold)
purify.UpdateInformation()
# --- Create an object to calculate stereology parameters
stereology = _MicroView.vtkImageStereology()
if state.bEnablePurify:
stereology.SetInputConnection(purify.GetOutputPort())
stereology.SetThreshold(1)
else:
stereology.SetInputConnection(roi_image_reslice.GetOutputPort())
stereology.SetThreshold(self._Threshold)
stereology.SetImageMask(stencil_image.GetOutput())
event.notify(ProgressEvent("Stereology...", 0.4))
stereology.Update()
event.notify(ProgressEvent("Stereology...", 0.8))
outfile = StringIO.StringIO()
outfile.write('\n==============\n')
outfile.write('= Stereology\n')
outfile.write('==============\n')
outfile.write(' Total # of points used: {0}\n'.format(
stereology.GetnumVoxels()))
voxel_volume = self._Spacing[0] * self._Spacing[1] * self._Spacing[2]
outfile.write(" Total volume of examined region (mm^3): %10.4f\n" %
(stereology.GetnumVoxels() * voxel_volume, ))
if state.bVerboseOutput:
outfile.write('\n')
outfile.write(
' The total number of voxels occupied by bone: %d\n' %
int(stereology.GetPp() * stereology.GetnumVoxels()))
outfile.write(
' The number of intersections (entering and leaving) for each direction:\n'
)
outfile.write(' %d %d : %d %d : %d %d\n' %
(stereology.GetIntX(), stereology.GetIntXO(),
stereology.GetIntY(), stereology.GetIntYO(),
stereology.GetIntZ(), stereology.GetIntZO()))
outfile.write('\n')
outfile.write(
' The Euler # found using 27 surrounding voxels: {0}\n'.format(
stereology.GetEuler3D()))
outfile.write(
" -Euler # / Volume analyzed (1/mm^3): %0.5f\n" %
(-1.0 * stereology.GetEuler3D() / voxel_volume /
stereology.GetnumVoxels()))
outfile.write('\n')
outfile.write(
' Morphologic variables calculated from total planar intersection counts:\n'
)
outfile.write(
' BV/TV BS/BV Tb.Th Tb.N Tb.Sp\n')
format = '%0.6f %0.6f %0.6f %0.6f %0.6f'
if state.bVerboseOutput:
outfile.write(' (x) ' + format %
(stereology.GetBVTV(), stereology.GetxBSBV(),
stereology.GetxTbTh(), stereology.GetxTbN(),
stereology.GetxTbSp()) + '\n')
outfile.write(' (y) ' + format %
(stereology.GetBVTV(), stereology.GetyBSBV(),
stereology.GetyTbTh(), stereology.GetyTbN(),
stereology.GetyTbSp()) + '\n')
outfile.write(' (z) ' + format %
(stereology.GetBVTV(), stereology.GetzBSBV(),
stereology.GetzTbTh(), stereology.GetzTbN(),
stereology.GetzTbSp()) + '\n')
outfile.write(' (avg) ' + format %
(stereology.GetBVTV(), stereology.GetBSBV(),
stereology.GetTbTh(), stereology.GetTbN(),
stereology.GetTbSp()) + '\n')
outfile.write('\n')
self._ResultsDict['StereologyTotalPoints'] = stereology.GetnumVoxels()
self._ResultsDict['StereologyTotalVolume'] = stereology.GetnumVoxels(
) * voxel_volume
self._ResultsDict['StereologyBoneVoxels'] = int(
stereology.GetPp() * stereology.GetnumVoxels())
self._ResultsDict['StereologyEulerNumber'] = stereology.GetEuler3D()
self._ResultsDict['StereologyEulerVolume'] = -1.0 * \
stereology.GetEuler3D() / voxel_volume / stereology.GetnumVoxels()
self._ResultsDict['StereologyAvgBVTV'] = stereology.GetBVTV()
self._ResultsDict['StereologyAvgBSBV'] = stereology.GetBSBV()
self._ResultsDict['StereologyAvgTbTh'] = stereology.GetTbTh()
self._ResultsDict['StereologyAvgTbN'] = stereology.GetTbN()
self._ResultsDict['StereologyAvgTbSp'] = stereology.GetTbSp()
self._StereologyOutStr = outfile.getvalue()
outfile.close()
event.notify(ProgressEvent("Stereology: Done.", 1.0))
# normal status
return 0
#!/usr/bin/env python import vtk from vtk.test import Testing from vtk.util.misc import vtkGetDataRoot VTK_DATA_ROOT = vtkGetDataRoot() # A script to test converting a stencil to a binary image sphere = vtk.vtkSphere() sphere.SetCenter(128, 128, 0) sphere.SetRadius(80) functionToStencil = vtk.vtkImplicitFunctionToImageStencil() functionToStencil.SetInput(sphere) functionToStencil.SetOutputOrigin(0, 0, 0) functionToStencil.SetOutputSpacing(1, 1, 1) functionToStencil.SetOutputWholeExtent(0, 255, 0, 255, 0, 0) stencilToImage = vtk.vtkImageStencilToImage() stencilToImage.SetInputConnection(functionToStencil.GetOutputPort()) stencilToImage.SetOutsideValue(0) stencilToImage.SetInsideValue(255) viewer = vtk.vtkImageViewer() viewer.SetInputConnection(stencilToImage.GetOutputPort()) viewer.SetZSlice(0) viewer.SetColorWindow(255) viewer.SetColorLevel(127.5) viewer.Render() # --- end of script --
def onApply(self):
import vtkSegmentationCorePython as vtkSegmentationCore
# Allow users revert to this state by clicking Undo
self.scriptedEffect.saveStateForUndo()
# This can be a long operation - indicate it to the user
qt.QApplication.setOverrideCursor(qt.Qt.WaitCursor)
if self.segmentMarkupNode and (
self.segmentModel.GetPolyData().GetNumberOfPolys() > 0):
self.observeSegmentation(False)
operationName = self.scriptedEffect.parameter("Operation")
modifierLabelmap = self.scriptedEffect.defaultModifierLabelmap()
segmentationNode = self.scriptedEffect.parameterSetNode(
).GetSegmentationNode()
WorldToModifierLabelmapIjkTransform = vtk.vtkTransform()
WorldToModifierLabelmapIjkTransformer = vtk.vtkTransformPolyDataFilter(
)
WorldToModifierLabelmapIjkTransformer.SetTransform(
WorldToModifierLabelmapIjkTransform)
WorldToModifierLabelmapIjkTransformer.SetInputConnection(
self.segmentModel.GetPolyDataConnection())
segmentationToSegmentationIjkTransformMatrix = vtk.vtkMatrix4x4()
modifierLabelmap.GetImageToWorldMatrix(
segmentationToSegmentationIjkTransformMatrix)
segmentationToSegmentationIjkTransformMatrix.Invert()
WorldToModifierLabelmapIjkTransform.Concatenate(
segmentationToSegmentationIjkTransformMatrix)
worldToSegmentationTransformMatrix = vtk.vtkMatrix4x4()
slicer.vtkMRMLTransformNode.GetMatrixTransformBetweenNodes(
None, segmentationNode.GetParentTransformNode(),
worldToSegmentationTransformMatrix)
WorldToModifierLabelmapIjkTransform.Concatenate(
worldToSegmentationTransformMatrix)
WorldToModifierLabelmapIjkTransformer.Update()
polyToStencil = vtk.vtkPolyDataToImageStencil()
polyToStencil.SetOutputSpacing(1.0, 1.0, 1.0)
polyToStencil.SetInputConnection(
WorldToModifierLabelmapIjkTransformer.GetOutputPort())
boundsIjk = WorldToModifierLabelmapIjkTransformer.GetOutput(
).GetBounds()
modifierLabelmapExtent = self.scriptedEffect.modifierLabelmap(
).GetExtent()
polyToStencil.SetOutputWholeExtent(modifierLabelmapExtent[0],
modifierLabelmapExtent[1],
modifierLabelmapExtent[2],
modifierLabelmapExtent[3],
int(round(boundsIjk[4])),
int(round(boundsIjk[5])))
polyToStencil.Update()
stencilData = polyToStencil.GetOutput()
stencilExtent = [0, -1, 0, -1, 0, -1]
stencilData.SetExtent(stencilExtent)
stencilToImage = vtk.vtkImageStencilToImage()
stencilToImage.SetInputConnection(polyToStencil.GetOutputPort())
if operationName in ("FILL_INSIDE", "ERASE_INSIDE", "SET"):
stencilToImage.SetInsideValue(1.0)
stencilToImage.SetOutsideValue(0.0)
else:
stencilToImage.SetInsideValue(0.0)
stencilToImage.SetOutsideValue(1.0)
stencilToImage.SetOutputScalarType(
modifierLabelmap.GetScalarType())
stencilPositioner = vtk.vtkImageChangeInformation()
stencilPositioner.SetInputConnection(
stencilToImage.GetOutputPort())
stencilPositioner.SetOutputSpacing(modifierLabelmap.GetSpacing())
stencilPositioner.SetOutputOrigin(modifierLabelmap.GetOrigin())
stencilPositioner.Update()
orientedStencilPositionerOuput = vtkSegmentationCore.vtkOrientedImageData(
)
orientedStencilPositionerOuput.ShallowCopy(
stencilToImage.GetOutput())
imageToWorld = vtk.vtkMatrix4x4()
modifierLabelmap.GetImageToWorldMatrix(imageToWorld)
orientedStencilPositionerOuput.SetImageToWorldMatrix(imageToWorld)
vtkSegmentationCore.vtkOrientedImageDataResample.ModifyImage(
modifierLabelmap, orientedStencilPositionerOuput,
vtkSegmentationCore.vtkOrientedImageDataResample.
OPERATION_MAXIMUM)
modMode = slicer.qSlicerSegmentEditorAbstractEffect.ModificationModeAdd
if operationName == "ERASE_INSIDE" or operationName == "ERASE_OUTSIDE":
modMode = slicer.qSlicerSegmentEditorAbstractEffect.ModificationModeRemove
elif operationName == "SET":
modMode = slicer.qSlicerSegmentEditorAbstractEffect.ModificationModeSet
self.scriptedEffect.modifySelectedSegmentByLabelmap(
modifierLabelmap, modMode)
import numpy
n = self.segmentMarkupNode.GetNumberOfFiducials()
# get fiducial positions
fPos = numpy.zeros((n, 3))
for i in xrange(n):
coord = [0.0, 0.0, 0.0]
self.segmentMarkupNode.GetNthFiducialPosition(i, coord)
fPos[i] = coord
segmentID = self.scriptedEffect.parameterSetNode(
).GetSelectedSegmentID()
segment = segmentationNode.GetSegmentation().GetSegment(segmentID)
segment.SetTag("fP", fPos.tostring())
segment.SetTag("fN", n)
self.reset()
self.createNewMarkupNode()
self.fiducialPlacementToggle.setCurrentNode(self.segmentMarkupNode)
self.observeSegmentation(True)
qt.QApplication.restoreOverrideCursor()
#!/usr/bin/env python import vtk from vtk.test import Testing from vtk.util.misc import vtkGetDataRoot VTK_DATA_ROOT = vtkGetDataRoot() # A script to test converting a stencil to a binary image sphere = vtk.vtkSphere() sphere.SetCenter(128,128,0) sphere.SetRadius(80) functionToStencil = vtk.vtkImplicitFunctionToImageStencil() functionToStencil.SetInput(sphere) functionToStencil.SetOutputOrigin(0,0,0) functionToStencil.SetOutputSpacing(1,1,1) functionToStencil.SetOutputWholeExtent(0,255,0,255,0,0) stencilToImage = vtk.vtkImageStencilToImage() stencilToImage.SetInputConnection(functionToStencil.GetOutputPort()) stencilToImage.SetOutsideValue(0) stencilToImage.SetInsideValue(255) viewer = vtk.vtkImageViewer() viewer.SetInputConnection(stencilToImage.GetOutputPort()) viewer.SetZSlice(0) viewer.SetColorWindow(255) viewer.SetColorLevel(127.5) viewer.Render() # --- end of script --
def cutSurfaceWithModel(self, segmentMarkupNode, segmentModel):
import vtkSegmentationCore
if not segmentMarkupNode:
raise AttributeError(
f"{self.__class__.__name__}: segment markup node not set.")
if not segmentModel:
raise AttributeError(
f"{self.__class__.__name__}: segment model not set.")
if segmentMarkupNode and segmentModel.GetPolyData().GetNumberOfCells(
) > 0:
segmentationNode = self.scriptedEffect.parameterSetNode(
).GetSegmentationNode()
if not segmentationNode:
raise AttributeError(
f"{self.__class__.__name__}: Segmentation node not set.")
modifierLabelmap = self.scriptedEffect.defaultModifierLabelmap()
if not modifierLabelmap:
raise AttributeError(
"{}: ModifierLabelmap not set. This can happen for various reasons:\n"
"No master volume set for segmentation,\n"
"No existing segments for segmentation, or\n"
"No referenceImageGeometry is specified in the segmentation"
.format(self.__class__.__name__))
WorldToModifierLabelmapIjkTransform = vtk.vtkTransform()
WorldToModifierLabelmapIjkTransformer = vtk.vtkTransformPolyDataFilter(
)
WorldToModifierLabelmapIjkTransformer.SetTransform(
WorldToModifierLabelmapIjkTransform)
WorldToModifierLabelmapIjkTransformer.SetInputConnection(
segmentModel.GetPolyDataConnection())
segmentationToSegmentationIjkTransformMatrix = vtk.vtkMatrix4x4()
modifierLabelmap.GetImageToWorldMatrix(
segmentationToSegmentationIjkTransformMatrix)
segmentationToSegmentationIjkTransformMatrix.Invert()
WorldToModifierLabelmapIjkTransform.Concatenate(
segmentationToSegmentationIjkTransformMatrix)
worldToSegmentationTransformMatrix = vtk.vtkMatrix4x4()
slicer.vtkMRMLTransformNode.GetMatrixTransformBetweenNodes(
None, segmentationNode.GetParentTransformNode(),
worldToSegmentationTransformMatrix)
WorldToModifierLabelmapIjkTransform.Concatenate(
worldToSegmentationTransformMatrix)
WorldToModifierLabelmapIjkTransformer.Update()
polyToStencil = vtk.vtkPolyDataToImageStencil()
polyToStencil.SetOutputSpacing(1.0, 1.0, 1.0)
polyToStencil.SetInputConnection(
WorldToModifierLabelmapIjkTransformer.GetOutputPort())
boundsIjk = WorldToModifierLabelmapIjkTransformer.GetOutput(
).GetBounds()
modifierLabelmapExtent = self.scriptedEffect.modifierLabelmap(
).GetExtent()
polyToStencil.SetOutputWholeExtent(modifierLabelmapExtent[0],
modifierLabelmapExtent[1],
modifierLabelmapExtent[2],
modifierLabelmapExtent[3],
int(round(boundsIjk[4])),
int(round(boundsIjk[5])))
polyToStencil.Update()
stencilData = polyToStencil.GetOutput()
stencilExtent = [0, -1, 0, -1, 0, -1]
stencilData.SetExtent(stencilExtent)
stencilToImage = vtk.vtkImageStencilToImage()
stencilToImage.SetInputConnection(polyToStencil.GetOutputPort())
stencilToImage.SetInsideValue(1.0)
stencilToImage.SetOutsideValue(0.0)
stencilToImage.SetOutputScalarType(
modifierLabelmap.GetScalarType())
stencilPositioner = vtk.vtkImageChangeInformation()
stencilPositioner.SetInputConnection(
stencilToImage.GetOutputPort())
stencilPositioner.SetOutputSpacing(modifierLabelmap.GetSpacing())
stencilPositioner.SetOutputOrigin(modifierLabelmap.GetOrigin())
stencilPositioner.Update()
orientedStencilPositionerOutput = vtkSegmentationCore.vtkOrientedImageData(
)
orientedStencilPositionerOutput.ShallowCopy(
stencilToImage.GetOutput())
imageToWorld = vtk.vtkMatrix4x4()
modifierLabelmap.GetImageToWorldMatrix(imageToWorld)
orientedStencilPositionerOutput.SetImageToWorldMatrix(imageToWorld)
vtkSegmentationCore.vtkOrientedImageDataResample.ModifyImage(
modifierLabelmap, orientedStencilPositionerOutput,
vtkSegmentationCore.vtkOrientedImageDataResample.
OPERATION_MAXIMUM)
self.scriptedEffect.modifySelectedSegmentByLabelmap(
modifierLabelmap,
slicer.qSlicerSegmentEditorAbstractEffect.ModificationModeSet)
fPosString = self.getPointsAsString(segmentMarkupNode)
segmentID = self.scriptedEffect.parameterSetNode(
).GetSelectedSegmentID()
segment = segmentationNode.GetSegmentation().GetSegment(segmentID)
segment.SetTag("DrawTubeEffectMarkupPositions", fPosString)
def StereologyAnalysis(self):
"""Perform stereology analysis on a sub-region of an image"""
# user have to define an ROI - enforce fore now...
# should allow to use whole image as default
event.notify(ProgressEvent("Stereology...", 0.0))
state = self._app_states[self._current_image_index]
origin = self._Origin
spacing = self._Spacing
# --- generate a mask from stencil ----
self.__stencil_data.Update()
stencil_image = vtk.vtkImageStencilToImage()
stencil_image.SetInput(self.__stencil_data)
stencil_image.SetInsideValue(255)
stencil_image.SetOutsideValue(0)
stencil_image.SetOutputScalarTypeToUnsignedChar()
stencil_image.Update()
# --- image purify -----
event.notify(ProgressEvent("Stereology: Purify...", 0.2))
roi_image_reslice = self.GetROIImage()
# optionally create a purification filter
if state.bEnablePurify:
purify = _MicroView.vtkImagePurify()
purify.SetInputConnection(roi_image_reslice.GetOutputPort())
purify.SetThreshold(self._Threshold)
purify.UpdateInformation()
# --- Create an object to calculate stereology parameters
stereology = _MicroView.vtkImageStereology()
if state.bEnablePurify:
stereology.SetInputConnection(purify.GetOutputPort())
stereology.SetThreshold(1)
else:
stereology.SetInputConnection(roi_image_reslice.GetOutputPort())
stereology.SetThreshold(self._Threshold)
stereology.SetImageMask(stencil_image.GetOutput())
event.notify(ProgressEvent("Stereology...", 0.4))
stereology.Update()
event.notify(ProgressEvent("Stereology...", 0.8))
outfile = StringIO.StringIO()
outfile.write('\n==============\n')
outfile.write('= Stereology\n')
outfile.write('==============\n')
outfile.write(
' Total # of points used: {0}\n'.format(stereology.GetnumVoxels()))
voxel_volume = self._Spacing[0] * self._Spacing[1] * self._Spacing[2]
outfile.write(" Total volume of examined region (mm^3): %10.4f\n" % (
stereology.GetnumVoxels() * voxel_volume,))
if state.bVerboseOutput:
outfile.write('\n')
outfile.write(' The total number of voxels occupied by bone: %d\n' %
int(stereology.GetPp() * stereology.GetnumVoxels()))
outfile.write(
' The number of intersections (entering and leaving) for each direction:\n')
outfile.write(' %d %d : %d %d : %d %d\n' % (
stereology.GetIntX(),
stereology.GetIntXO(),
stereology.GetIntY(),
stereology.GetIntYO(),
stereology.GetIntZ(),
stereology.GetIntZO()))
outfile.write('\n')
outfile.write(' The Euler # found using 27 surrounding voxels: {0}\n'.format(
stereology.GetEuler3D()))
outfile.write(" -Euler # / Volume analyzed (1/mm^3): %0.5f\n" % (
-1.0 * stereology.GetEuler3D() / voxel_volume / stereology.GetnumVoxels()))
outfile.write('\n')
outfile.write(
' Morphologic variables calculated from total planar intersection counts:\n')
outfile.write(
' BV/TV BS/BV Tb.Th Tb.N Tb.Sp\n')
format = '%0.6f %0.6f %0.6f %0.6f %0.6f'
if state.bVerboseOutput:
outfile.write(' (x) ' + format % (
stereology.GetBVTV(),
stereology.GetxBSBV(),
stereology.GetxTbTh(),
stereology.GetxTbN(),
stereology.GetxTbSp()) + '\n')
outfile.write(' (y) ' + format % (
stereology.GetBVTV(),
stereology.GetyBSBV(),
stereology.GetyTbTh(),
stereology.GetyTbN(),
stereology.GetyTbSp()) + '\n')
outfile.write(' (z) ' + format % (
stereology.GetBVTV(),
stereology.GetzBSBV(),
stereology.GetzTbTh(),
stereology.GetzTbN(),
stereology.GetzTbSp()) + '\n')
outfile.write(' (avg) ' + format % (
stereology.GetBVTV(),
stereology.GetBSBV(),
stereology.GetTbTh(),
stereology.GetTbN(),
stereology.GetTbSp()) + '\n')
outfile.write('\n')
self._ResultsDict['StereologyTotalPoints'] = stereology.GetnumVoxels()
self._ResultsDict[
'StereologyTotalVolume'] = stereology.GetnumVoxels() * voxel_volume
self._ResultsDict['StereologyBoneVoxels'] = int(
stereology.GetPp() * stereology.GetnumVoxels())
self._ResultsDict['StereologyEulerNumber'] = stereology.GetEuler3D()
self._ResultsDict['StereologyEulerVolume'] = -1.0 * \
stereology.GetEuler3D() / voxel_volume / stereology.GetnumVoxels()
self._ResultsDict['StereologyAvgBVTV'] = stereology.GetBVTV()
self._ResultsDict['StereologyAvgBSBV'] = stereology.GetBSBV()
self._ResultsDict['StereologyAvgTbTh'] = stereology.GetTbTh()
self._ResultsDict['StereologyAvgTbN'] = stereology.GetTbN()
self._ResultsDict['StereologyAvgTbSp'] = stereology.GetTbSp()
self._StereologyOutStr = outfile.getvalue()
outfile.close()
event.notify(ProgressEvent("Stereology: Done.", 1.0))
# normal status
return 0
