def onApply(self):
# This can be a long operation - indicate it to the user
qt.QApplication.setOverrideCursor(qt.Qt.WaitCursor)
self.scriptedEffect.saveStateForUndo()
# Get parameters
fullyConnected = self.scriptedEffect.integerParameter("FullyConnected")
minimumSize = self.scriptedEffect.integerParameter("MinimumSize")
# Get modifier labelmap
selectedSegmentLabelmap = self.scriptedEffect.selectedSegmentLabelmap()
castIn = vtk.vtkImageCast()
castIn.SetInputData(selectedSegmentLabelmap)
castIn.SetOutputScalarTypeToUnsignedLong()
# Identify the islands in the inverted volume and
# find the pixel that corresponds to the background
islandMath = vtkITK.vtkITKIslandMath()
islandMath.SetInputConnection(castIn.GetOutputPort())
islandMath.SetFullyConnected(fullyConnected)
islandMath.SetMinimumSize(minimumSize)
# Note that island operation happens in unsigned long space
# but the segment editor works in unsigned char
castOut = vtk.vtkImageCast()
castOut.SetInputConnection(islandMath.GetOutputPort())
castOut.SetOutputScalarTypeToUnsignedChar()
castOut.Update()
islandCount = islandMath.GetNumberOfIslands()
islandOrigCount = islandMath.GetOriginalNumberOfIslands()
ignoredIslands = islandOrigCount - islandCount
logging.info("%d islands created (%d ignored)" %
(islandCount, ignoredIslands))
# Create oriented image data from output
import vtkSegmentationCorePython as vtkSegmentationCore
multiLabelImage = vtkSegmentationCore.vtkOrientedImageData()
multiLabelImage.DeepCopy(castOut.GetOutput())
selectedSegmentLabelmapImageToWorldMatrix = vtk.vtkMatrix4x4()
selectedSegmentLabelmap.GetImageToWorldMatrix(
selectedSegmentLabelmapImageToWorldMatrix)
multiLabelImage.SetGeometryFromImageToWorldMatrix(
selectedSegmentLabelmapImageToWorldMatrix)
# Import multi-label labelmap to segmentation
segmentationNode = self.scriptedEffect.parameterSetNode(
).GetSegmentationNode()
selectedSegmentID = self.scriptedEffect.parameterSetNode(
).GetSelectedSegmentID()
selectedSegmentName = segmentationNode.GetSegmentation().GetSegment(
selectedSegmentID).GetName()
slicer.vtkSlicerSegmentationsModuleLogic.ImportLabelmapToSegmentationNode( \
multiLabelImage, segmentationNode, selectedSegmentName )
segmentationNode.GetSegmentation().RemoveSegment(selectedSegmentID)
qt.QApplication.restoreOverrideCursor()
def findLargest2DRegion(segmentationNode):
qrLogic = CustomSegmentEditorLogic
segmentationsLogic = slicer.modules.segmentations.logic()
largestLM = None
largestSize = 0
for segment in qrLogic.getAllSegments(segmentationNode):
imageData = vtkSegmentationCore.vtkOrientedImageData()
segmentID = segmentationNode.GetSegmentation(
).GetSegmentIdBySegment(segment)
segmentationsLogic.GetSegmentBinaryLabelmapRepresentation(
segmentationNode, segmentID, imageData)
extent = imageData.GetExtent()
if extent[1] != -1 and extent[3] != -1 and extent[5] != -1:
tempLabel = slicer.vtkMRMLLabelMapVolumeNode()
tempLabel.SetName(segment.GetName() + "CentroidHelper")
segmentationsLogic.CreateLabelmapVolumeFromOrientedImageData(
imageData, tempLabel)
dims = tempLabel.GetImageData().GetDimensions()
size = dims[0] * dims[1]
if size > largestSize:
largestSize = size
largestLM = tempLabel
return largestLM
def onApply(self):
import vtkSegmentationCorePython as vtkSegmentationCore
# Get modifier labelmap and parameters
operation = self.scriptedEffect.parameter("Operation")
if operation in self.operationsRequireModifierSegment:
# Get modifier segment
segmentationNode = self.scriptedEffect.parameterSetNode().GetSegmentationNode()
segmentation = segmentationNode.GetSegmentation()
modifierSegmentID = self.modifierSegmentID()
if not modifierSegmentID:
logging.error("Operation {0} requires a selected modifier segment".format(operation))
return
modifierSegment = segmentation.GetSegment(modifierSegmentID)
modifierSegmentLabelmap = modifierSegment.GetRepresentation(vtkSegmentationCore.vtkSegmentationConverter.GetSegmentationBinaryLabelmapRepresentationName())
if operation == LOGICAL_COPY:
self.scriptedEffect.modifySelectedSegmentByLabelmap(modifierSegmentLabelmap, slicer.qSlicerSegmentEditorAbstractEffect.ModificationModeSet)
elif operation == LOGICAL_UNION:
self.scriptedEffect.modifySelectedSegmentByLabelmap(modifierSegmentLabelmap, slicer.qSlicerSegmentEditorAbstractEffect.ModificationModeAdd)
elif operation == LOGICAL_SUBTRACT:
self.scriptedEffect.modifySelectedSegmentByLabelmap(modifierSegmentLabelmap, slicer.qSlicerSegmentEditorAbstractEffect.ModificationModeRemove)
elif operation == LOGICAL_INTERSECT:
selectedSegmentLabelmap = self.scriptedEffect.selectedSegmentLabelmap()
intersectionLabelmap = vtkSegmentationCore.vtkOrientedImageData()
vtkSegmentationCore.vtkOrientedImageDataResample.MergeImage(selectedSegmentLabelmap, modifierSegmentLabelmap, intersectionLabelmap, vtkSegmentationCore.vtkOrientedImageDataResample.OPERATION_MINIMUM, selectedSegmentLabelmap.GetExtent())
selectedSegmentLabelmapExtent = selectedSegmentLabelmap.GetExtent()
modifierSegmentLabelmapExtent = modifierSegmentLabelmap.GetExtent()
commonExtent = [max(selectedSegmentLabelmapExtent[0], modifierSegmentLabelmapExtent[0]),
min(selectedSegmentLabelmapExtent[1], modifierSegmentLabelmapExtent[1]),
max(selectedSegmentLabelmapExtent[2], modifierSegmentLabelmapExtent[2]),
min(selectedSegmentLabelmapExtent[3], modifierSegmentLabelmapExtent[3]),
max(selectedSegmentLabelmapExtent[4], modifierSegmentLabelmapExtent[4]),
min(selectedSegmentLabelmapExtent[5], modifierSegmentLabelmapExtent[5])]
self.scriptedEffect.modifySelectedSegmentByLabelmap(intersectionLabelmap, slicer.qSlicerSegmentEditorAbstractEffect.ModificationModeSet, commonExtent)
elif operation == LOGICAL_INVERT:
selectedSegmentLabelmap = self.scriptedEffect.selectedSegmentLabelmap()
inverter = vtk.vtkImageThreshold()
inverter.SetInputData(selectedSegmentLabelmap)
inverter.SetInValue(1)
inverter.SetOutValue(0)
inverter.ReplaceInOn()
inverter.ThresholdByLower(0)
inverter.SetOutputScalarType(vtk.VTK_UNSIGNED_CHAR)
inverter.Update()
selectedSegmentLabelmap.DeepCopy(inverter.GetOutput())
self.scriptedEffect.modifySelectedSegmentByLabelmap(selectedSegmentLabelmap, slicer.qSlicerSegmentEditorAbstractEffect.ModificationModeSet)
elif operation == LOGICAL_CLEAR or operation == LOGICAL_FILL:
selectedSegmentLabelmap = self.scriptedEffect.selectedSegmentLabelmap()
vtkSegmentationCore.vtkOrientedImageDataResample.FillImage(selectedSegmentLabelmap, 1 if operation == LOGICAL_FILL else 0, selectedSegmentLabelmap.GetExtent())
self.scriptedEffect.modifySelectedSegmentByLabelmap(selectedSegmentLabelmap, slicer.qSlicerSegmentEditorAbstractEffect.ModificationModeSet)
else:
logging.error("Uknown operation: {0}".format(operation))
def onApply(self):
# TODO:
# self.logic.undoRedo = self.undoRedo
# Get parameters
fullyConnected = self.scriptedEffect.integerParameter("FullyConnected")
minimumSize = self.scriptedEffect.integerParameter("MinimumSize")
# Get modifier labelmap
selectedSegmentLabelmap = self.scriptedEffect.selectedSegmentLabelmap()
castIn = vtk.vtkImageCast()
castIn.SetInputData(selectedSegmentLabelmap)
castIn.SetOutputScalarTypeToUnsignedLong()
# Identify the islands in the inverted volume and
# find the pixel that corresponds to the background
islandMath = vtkITK.vtkITKIslandMath()
islandMath.SetInputConnection(castIn.GetOutputPort())
islandMath.SetFullyConnected(fullyConnected)
islandMath.SetMinimumSize(minimumSize)
# Note that island operation happens in unsigned long space
# but the segment editor works in unsigned char
castOut = vtk.vtkImageCast()
castOut.SetInputConnection(islandMath.GetOutputPort())
castOut.SetOutputScalarTypeToUnsignedChar()
castOut.Update()
islandCount = islandMath.GetNumberOfIslands()
islandOrigCount = islandMath.GetOriginalNumberOfIslands()
ignoredIslands = islandOrigCount - islandCount
logging.info("%d islands created (%d ignored)" % (islandCount, ignoredIslands))
# Create oriented image data from output
import vtkSegmentationCorePython as vtkSegmentationCore
multiLabelImage = vtkSegmentationCore.vtkOrientedImageData()
multiLabelImage.DeepCopy(castOut.GetOutput())
selectedSegmentLabelmapImageToWorldMatrix = vtk.vtkMatrix4x4()
selectedSegmentLabelmap.GetImageToWorldMatrix(selectedSegmentLabelmapImageToWorldMatrix)
multiLabelImage.SetGeometryFromImageToWorldMatrix(selectedSegmentLabelmapImageToWorldMatrix)
# Import multi-label labelmap to segmentation
segmentationNode = self.scriptedEffect.parameterSetNode().GetSegmentationNode()
selectedSegmentID = self.scriptedEffect.parameterSetNode().GetSelectedSegmentID()
selectedSegmentName = segmentationNode.GetSegmentation().GetSegment(selectedSegmentID).GetName()
slicer.vtkSlicerSegmentationsModuleLogic.ImportLabelmapToSegmentationNode(
multiLabelImage, segmentationNode, selectedSegmentName
)
# Set labelmap visibility to outline for the new segments
displayNode = segmentationNode.GetDisplayNode()
# for index in xrange(1,islandCount+1):
# segmentID = selectedSegmentName + "_" + str(index)
# displayNode.SetSegmentVisibility2DFill(segmentID, False)
# displayNode.SetSegmentVisibility2DOutline(segmentID, True)
displayNode.SetSegmentVisibility(selectedSegmentID, False)
def onApply(self):
#TODO:
#self.logic.undoRedo = self.undoRedo
# Get parameters
fullyConnected = self.scriptedEffect.integerParameter("FullyConnected")
minimumSize = self.scriptedEffect.integerParameter("MinimumSize")
# Get modifier labelmap
selectedSegmentLabelmap = self.scriptedEffect.selectedSegmentLabelmap()
castIn = vtk.vtkImageCast()
castIn.SetInputData(selectedSegmentLabelmap)
castIn.SetOutputScalarTypeToUnsignedLong()
# Identify the islands in the inverted volume and
# find the pixel that corresponds to the background
islandMath = vtkITK.vtkITKIslandMath()
islandMath.SetInputConnection(castIn.GetOutputPort())
islandMath.SetFullyConnected(fullyConnected)
islandMath.SetMinimumSize(minimumSize)
# Note that island operation happens in unsigned long space
# but the segment editor works in unsigned char
castOut = vtk.vtkImageCast()
castOut.SetInputConnection(islandMath.GetOutputPort())
castOut.SetOutputScalarTypeToUnsignedChar()
castOut.Update()
islandCount = islandMath.GetNumberOfIslands()
islandOrigCount = islandMath.GetOriginalNumberOfIslands()
ignoredIslands = islandOrigCount - islandCount
logging.info( "%d islands created (%d ignored)" % (islandCount, ignoredIslands) )
# Create oriented image data from output
import vtkSegmentationCorePython as vtkSegmentationCore
multiLabelImage = vtkSegmentationCore.vtkOrientedImageData()
multiLabelImage.DeepCopy(castOut.GetOutput())
selectedSegmentLabelmapImageToWorldMatrix = vtk.vtkMatrix4x4()
selectedSegmentLabelmap.GetImageToWorldMatrix(selectedSegmentLabelmapImageToWorldMatrix)
multiLabelImage.SetGeometryFromImageToWorldMatrix(selectedSegmentLabelmapImageToWorldMatrix)
# Import multi-label labelmap to segmentation
segmentationNode = self.scriptedEffect.parameterSetNode().GetSegmentationNode()
selectedSegmentID = self.scriptedEffect.parameterSetNode().GetSelectedSegmentID()
selectedSegmentName = segmentationNode.GetSegmentation().GetSegment(selectedSegmentID).GetName()
slicer.vtkSlicerSegmentationsModuleLogic.ImportLabelmapToSegmentationNode( \
multiLabelImage, segmentationNode, selectedSegmentName )
# Set labelmap visibility to outline for the new segments
displayNode = segmentationNode.GetDisplayNode()
#for index in xrange(1,islandCount+1):
# segmentID = selectedSegmentName + "_" + str(index)
# displayNode.SetSegmentVisibility2DFill(segmentID, False)
# displayNode.SetSegmentVisibility2DOutline(segmentID, True)
displayNode.SetSegmentVisibility(selectedSegmentID, False)
def TestSection_2_MergeLabelmapWithDifferentGeometries(self):
# Merge labelmap when segments containing labelmaps with different geometries (both same directions, different directions)
logging.info('Test section 2: Merge labelmap with different geometries')
self.assertIsNotNone(self.sphereSegment)
self.sphereSegment.RemoveRepresentation(self.binaryLabelmapReprName)
self.assertIsNone(self.sphereSegment.GetRepresentation(self.binaryLabelmapReprName))
# Create new segmentation with sphere segment
self.secondSegmentationNode = slicer.vtkMRMLSegmentationNode()
self.secondSegmentationNode.SetName('Second')
self.secondSegmentationNode.GetSegmentation().SetMasterRepresentationName(self.binaryLabelmapReprName)
slicer.mrmlScene.AddNode(self.secondSegmentationNode)
self.secondSegmentationNode.GetSegmentation().AddSegment(self.sphereSegment)
# Check automatically converted labelmap. It is supposed to have the default geometry
# (which is different than the one in the input segmentation)
sphereLabelmap = self.sphereSegment.GetRepresentation(self.binaryLabelmapReprName)
self.assertIsNotNone(sphereLabelmap)
sphereLabelmapSpacing = sphereLabelmap.GetSpacing()
self.assertTrue(sphereLabelmapSpacing[0] == 1.0 and sphereLabelmapSpacing[1] == 1.0 and sphereLabelmapSpacing[2] == 1.0)
# Create binary labelmap in segmentation that will create the merged labelmap from
# different geometries so that labelmap is not removed from sphere segment when adding
self.inputSegmentationNode.GetSegmentation().CreateRepresentation(self.binaryLabelmapReprName)
# Copy segment to input segmentation
self.inputSegmentationNode.GetSegmentation().CopySegmentFromSegmentation(self.secondSegmentationNode.GetSegmentation(), self.sphereSegmentName)
self.assertEqual(self.inputSegmentationNode.GetSegmentation().GetNumberOfSegments(), 3)
# Check merged labelmap
# Reference geometry has the tiny patient spacing, and it is oversampled to have smimilar
# voxel size as the sphere labelmap with the uniform 1mm spacing
mergedLabelmap = vtkSegmentationCore.vtkOrientedImageData()
self.inputSegmentationNode.GenerateMergedLabelmapForAllSegments(mergedLabelmap, 0)
mergedLabelmapSpacing = mergedLabelmap.GetSpacing()
self.assertAlmostEqual(mergedLabelmapSpacing[0], 1.2894736842, 8)
self.assertAlmostEqual(mergedLabelmapSpacing[1], 1.2894736842, 8)
self.assertAlmostEqual(mergedLabelmapSpacing[2], 0.6052631578, 8)
imageStat = vtk.vtkImageAccumulate()
imageStat.SetInputData(mergedLabelmap)
imageStat.SetComponentExtent(0,5,0,0,0,0)
imageStat.SetComponentOrigin(0,0,0)
imageStat.SetComponentSpacing(1,1,1)
imageStat.Update()
self.assertEqual(imageStat.GetVoxelCount(), 54872000)
imageStatResult = imageStat.GetOutput()
for i in range(5):
logging.info("Volume {0}: {1}".format(i, imageStatResult.GetScalarComponentAsDouble(i,0,0,0)))
self.assertEqual(imageStatResult.GetScalarComponentAsDouble(0,0,0,0), 43573723)
self.assertEqual(imageStatResult.GetScalarComponentAsDouble(1,0,0,0), 10601312)
self.assertEqual(imageStatResult.GetScalarComponentAsDouble(2,0,0,0), 251476)
self.assertEqual(imageStatResult.GetScalarComponentAsDouble(3,0,0,0), 445489)
self.assertEqual(imageStatResult.GetScalarComponentAsDouble(4,0,0,0), 0) # Built from color table and color four is removed in previous test section
def onApply(self):
# This can be a long operation - indicate it to the user
qt.QApplication.setOverrideCursor(qt.Qt.WaitCursor)
self.scriptedEffect.saveStateForUndo()
# Get parameters
fullyConnected = self.scriptedEffect.integerParameter("FullyConnected")
minimumSize = self.scriptedEffect.integerParameter("MinimumSize")
# Get modifier labelmap
selectedSegmentLabelmap = self.scriptedEffect.selectedSegmentLabelmap()
castIn = vtk.vtkImageCast()
castIn.SetInputData(selectedSegmentLabelmap)
castIn.SetOutputScalarTypeToUnsignedLong()
# Identify the islands in the inverted volume and
# find the pixel that corresponds to the background
islandMath = vtkITK.vtkITKIslandMath()
islandMath.SetInputConnection(castIn.GetOutputPort())
islandMath.SetFullyConnected(fullyConnected)
islandMath.SetMinimumSize(minimumSize)
# Note that island operation happens in unsigned long space
# but the segment editor works in unsigned char
castOut = vtk.vtkImageCast()
castOut.SetInputConnection(islandMath.GetOutputPort())
castOut.SetOutputScalarTypeToUnsignedChar()
castOut.Update()
islandCount = islandMath.GetNumberOfIslands()
islandOrigCount = islandMath.GetOriginalNumberOfIslands()
ignoredIslands = islandOrigCount - islandCount
logging.info( "%d islands created (%d ignored)" % (islandCount, ignoredIslands) )
# Create oriented image data from output
import vtkSegmentationCorePython as vtkSegmentationCore
multiLabelImage = vtkSegmentationCore.vtkOrientedImageData()
multiLabelImage.DeepCopy(castOut.GetOutput())
selectedSegmentLabelmapImageToWorldMatrix = vtk.vtkMatrix4x4()
selectedSegmentLabelmap.GetImageToWorldMatrix(selectedSegmentLabelmapImageToWorldMatrix)
multiLabelImage.SetGeometryFromImageToWorldMatrix(selectedSegmentLabelmapImageToWorldMatrix)
# Import multi-label labelmap to segmentation
segmentationNode = self.scriptedEffect.parameterSetNode().GetSegmentationNode()
selectedSegmentID = self.scriptedEffect.parameterSetNode().GetSelectedSegmentID()
selectedSegmentName = segmentationNode.GetSegmentation().GetSegment(selectedSegmentID).GetName()
slicer.vtkSlicerSegmentationsModuleLogic.ImportLabelmapToSegmentationNode( \
multiLabelImage, segmentationNode, selectedSegmentName )
segmentationNode.GetSegmentation().RemoveSegment(selectedSegmentID)
qt.QApplication.restoreOverrideCursor()
def TestSection_1_AddRemoveSegment(self):
# Add/remove segment from segmentation (check display properties, color table, etc.)
logging.info('Test section 1: Add/remove segment')
# Get baseline values
displayNode = self.inputSegmentationNode.GetDisplayNode()
self.assertIsNotNone(displayNode)
# If segments are not found then the returned color is the pre-defined invalid color
bodyColor = displayNode.GetSegmentColor('Body_Contour')
self.assertTrue(int(bodyColor[0]*100) == 33 and int(bodyColor[1]*100) == 66 and bodyColor[2] == 0.0)
tumorColor = displayNode.GetSegmentColor('Tumor_Contour')
self.assertTrue(tumorColor[0] == 1.0 and tumorColor[1] == 0.0 and tumorColor[2] == 0.0)
# Create new segment
sphere = vtk.vtkSphereSource()
sphere.SetCenter(0,50,0)
sphere.SetRadius(50)
sphere.Update()
spherePolyData = vtk.vtkPolyData()
spherePolyData.DeepCopy(sphere.GetOutput())
self.sphereSegment = vtkSegmentationCore.vtkSegment()
self.sphereSegment.SetName(self.sphereSegmentName)
self.sphereSegment.SetDefaultColor(0.0,0.0,1.0)
self.sphereSegment.AddRepresentation(self.closedSurfaceReprName, spherePolyData)
# Add segment to segmentation
self.inputSegmentationNode.GetSegmentation().AddSegment(self.sphereSegment)
self.assertEqual(self.inputSegmentationNode.GetSegmentation().GetNumberOfSegments(), 3)
sphereColor = displayNode.GetSegmentColor(self.sphereSegmentName)
self.assertTrue(sphereColor[0] == 0.0 and sphereColor[1] == 0.0 and sphereColor[2] == 1.0)
# Check merged labelmap
mergedLabelmap = vtkSegmentationCore.vtkOrientedImageData()
self.inputSegmentationNode.GetSegmentation().CreateRepresentation(self.binaryLabelmapReprName)
self.inputSegmentationNode.GenerateMergedLabelmapForAllSegments(mergedLabelmap, 0)
imageStat = vtk.vtkImageAccumulate()
imageStat.SetInputData(mergedLabelmap)
imageStat.SetComponentExtent(0,4,0,0,0,0)
imageStat.SetComponentOrigin(0,0,0)
imageStat.SetComponentSpacing(1,1,1)
imageStat.Update()
self.assertEqual(imageStat.GetVoxelCount(), 1000)
imageStatResult = imageStat.GetOutput()
self.assertEqual(imageStatResult.GetScalarComponentAsDouble(0,0,0,0), 795)
self.assertEqual(imageStatResult.GetScalarComponentAsDouble(1,0,0,0), 194)
self.assertEqual(imageStatResult.GetScalarComponentAsDouble(2,0,0,0), 5)
self.assertEqual(imageStatResult.GetScalarComponentAsDouble(3,0,0,0), 6)
# Remove segment from segmentation
self.inputSegmentationNode.GetSegmentation().RemoveSegment(self.sphereSegmentName)
self.assertEqual(self.inputSegmentationNode.GetSegmentation().GetNumberOfSegments(), 2)
sphereColor = displayNode.GetSegmentColor(self.sphereSegmentName)
self.assertTrue(sphereColor[0] == 0.5 and sphereColor[1] == 0.5 and sphereColor[2] == 0.5)
def jumpToSegmentAndCreateScreenShot(segmentationNode, segment, widgets, center=False, crosshair=False):
imageData = vtkSegmentationCore.vtkOrientedImageData()
segmentID = segmentationNode.GetSegmentation().GetSegmentIdBySegment(segment)
segmentationsLogic = slicer.modules.segmentations.logic()
segmentationsLogic.GetSegmentBinaryLabelmapRepresentation(segmentationNode, segmentID, imageData)
extent = imageData.GetExtent()
if extent[1] != -1 and extent[3] != -1 and extent[5] != -1:
tempLabel = slicer.vtkMRMLLabelMapVolumeNode()
slicer.mrmlScene.AddNode(tempLabel)
tempLabel.SetName(segment.GetName() + "CentroidHelper")
segmentationsLogic.CreateLabelmapVolumeFromOrientedImageData(imageData, tempLabel)
CustomSegmentEditorLogic.applyThreshold(tempLabel, 1)
centroid = ModuleLogicMixin.getCentroidForLabel(tempLabel, 1)
slicer.mrmlScene.RemoveNode(tempLabel)
annotationNodes = []
crosshairButton = None
if crosshair:
crosshairButton = CrosshairButton()
crosshairButton.setSliceIntersectionEnabled(True)
crosshairButton.checked = True
for widget in widgets:
sliceLogic = widget.sliceLogic()
sliceNode = sliceLogic.GetSliceNode()
if not center:
sliceNode.JumpSliceByOffsetting(centroid[0], centroid[1], centroid[2])
else:
markupsLogic = slicer.modules.markups.logic()
markupsLogic.JumpSlicesToLocation(centroid[0], centroid[1], centroid[2], True)
dNodeProperties = ScreenShotHelper.saveSegmentDisplayProperties(segmentationNode, segment)
segmentationNode.GetDisplayNode().SetAllSegmentsVisibility(False)
ScreenShotHelper.setDisplayNodeProperties(segmentationNode, segment,
properties={'fill': True, 'outline': True, 'visible': True})
if crosshairButton:
crosshairButton.crosshairNode.SetCrosshairRAS(centroid)
annotationNode = ScreenShotHelper.takeScreenShot("{}_Screenshot_{}_{}".format(segment.GetName(),
sliceNode.GetName(),
sliceNode.GetOrientation()),
"", widget)
segmentationNode.GetDisplayNode().SetAllSegmentsVisibility(True)
ScreenShotHelper.setDisplayNodeProperties(segmentationNode, segment, dNodeProperties)
annotationNodes.append(annotationNode)
if crosshairButton:
crosshairButton.checked = False
return annotationNodes[0] if len(annotationNodes) == 1 else annotationNodes
def createLabelNodeFromSegment(segmentationNode, segmentID):
labelNode = slicer.vtkMRMLLabelMapVolumeNode()
slicer.mrmlScene.AddNode(labelNode)
segmentationsLogic = slicer.modules.segmentations.logic()
mergedImageData = vtkSegmentationCore.vtkOrientedImageData()
segmentationNode.GenerateMergedLabelmapForAllSegments(mergedImageData, 0, None,
DICOMSegmentationExporter.vtkStringArrayFromList([segmentID]))
if not segmentationsLogic.CreateLabelmapVolumeFromOrientedImageData(mergedImageData, labelNode):
slicer.mrmlScene.RemoveNode(labelNode)
return None
labelNode.SetName("{}_label".format(segmentID))
return labelNode
def onApply(self):
# Apply changes
import vtkSegmentationCorePython as vtkSegmentationCore
segmentationNode = self.scriptedEffect.parameterSetNode().GetSegmentationNode()
if (slicer.app.majorVersion >= 5) or (slicer.app.majorVersion >= 4 and slicer.app.minorVersion >= 11):
modifierLabelmap = vtkSegmentationCore.vtkOrientedImageData()
segmentationNode.GetBinaryLabelmapRepresentation(self.selectedSegmentId, modifierLabelmap)
else:
modifierLabelmap = segmentationNode.GetBinaryLabelmapRepresentation(self.selectedSegmentId)
self.scriptedEffect.modifySelectedSegmentByLabelmap(modifierLabelmap, slicer.qSlicerSegmentEditorAbstractEffect.ModificationModeSet)
self.originalSelectedSegmentLabelmap = None
self.reset()
self.scriptedEffect.selectEffect("")
def updateLabel(self,value):
if not self.fm:
return
self.fm.show(value)
self.fm.Modified()
self.fm.Update()
import vtkSegmentationCorePython as vtkSegmentationCore
newSegmentLabelmap = vtkSegmentationCore.vtkOrientedImageData()
newSegmentLabelmap.ShallowCopy(self.fm.GetOutput())
newSegmentLabelmap.CopyDirections(self.originalSelectedSegmentLabelmap)
segmentationNode = self.scriptedEffect.parameterSetNode().GetSegmentationNode()
slicer.vtkSlicerSegmentationsModuleLogic.SetBinaryLabelmapToSegment(newSegmentLabelmap, segmentationNode, self.selectedSegmentId, slicer.vtkSlicerSegmentationsModuleLogic.MODE_REPLACE, newSegmentLabelmap.GetExtent())
def createLabelNodeFromSegment(segmentationNode, segmentID):
labelNode = slicer.vtkMRMLLabelMapVolumeNode()
slicer.mrmlScene.AddNode(labelNode)
segmentationsLogic = slicer.modules.segmentations.logic()
mergedImageData = vtkSegmentationCore.vtkOrientedImageData()
segmentationNode.GenerateMergedLabelmapForAllSegments(
mergedImageData, 0, None,
DICOMSegmentationExporter.vtkStringArrayFromList([segmentID]))
if not segmentationsLogic.CreateLabelmapVolumeFromOrientedImageData(
mergedImageData, labelNode):
slicer.mrmlScene.RemoveNode(labelNode)
return None
labelNode.SetName("{}_label".format(segmentID))
return labelNode
def getSegmentCentroid(segmentationNode, segment):
imageData = vtkSegmentationCore.vtkOrientedImageData()
segmentID = segmentationNode.GetSegmentation().GetSegmentIdBySegment(segment)
segmentationsLogic = slicer.modules.segmentations.logic()
segmentationsLogic.GetSegmentBinaryLabelmapRepresentation(segmentationNode, segmentID, imageData)
extent = imageData.GetExtent()
if extent[1] != -1 and extent[3] != -1 and extent[5] != -1:
tempLabel = slicer.vtkMRMLLabelMapVolumeNode()
slicer.mrmlScene.AddNode(tempLabel)
tempLabel.SetName(segment.GetName() + "CentroidHelper")
segmentationsLogic.CreateLabelmapVolumeFromOrientedImageData(imageData, tempLabel)
CustomSegmentEditorLogic.applyThreshold(tempLabel, 1)
centroid = ModuleLogicMixin.getCentroidForLabel(tempLabel, 1)
slicer.mrmlScene.RemoveNode(tempLabel)
return centroid
return None
def getSegmentCentroid(segmentationNode, segment):
imageData = vtkSegmentationCore.vtkOrientedImageData()
segmentID = segmentationNode.GetSegmentation().GetSegmentIdBySegment(segment)
segmentationsLogic = slicer.modules.segmentations.logic()
segmentationsLogic.GetSegmentBinaryLabelmapRepresentation(segmentationNode, segmentID, imageData)
extent = imageData.GetExtent()
if extent[1] != -1 and extent[3] != -1 and extent[5] != -1:
tempLabel = slicer.vtkMRMLLabelMapVolumeNode()
slicer.mrmlScene.AddNode(tempLabel)
tempLabel.SetName(segment.GetName() + "CentroidHelper")
segmentationsLogic.CreateLabelmapVolumeFromOrientedImageData(imageData, tempLabel)
CustomSegmentEditorLogic.applyThreshold(tempLabel, 1)
centroid = ModuleLogicMixin.getCentroidForLabel(tempLabel, 1)
slicer.mrmlScene.RemoveNode(tempLabel)
return centroid
return None
def getInvertedBinaryLabelmap(self, modifierLabelmap):
import vtkSegmentationCorePython as vtkSegmentationCore
fillValue = 1
eraseValue = 0
inverter = vtk.vtkImageThreshold()
inverter.SetInputData(modifierLabelmap)
inverter.SetInValue(fillValue)
inverter.SetOutValue(eraseValue)
inverter.ReplaceInOn()
inverter.ThresholdByLower(0)
inverter.SetOutputScalarType(vtk.VTK_UNSIGNED_CHAR)
inverter.Update()
invertedModifierLabelmap = vtkSegmentationCore.vtkOrientedImageData()
invertedModifierLabelmap.ShallowCopy(inverter.GetOutput())
imageToWorldMatrix = vtk.vtkMatrix4x4()
modifierLabelmap.GetImageToWorldMatrix(imageToWorldMatrix)
invertedModifierLabelmap.SetGeometryFromImageToWorldMatrix(imageToWorldMatrix)
return invertedModifierLabelmap
def getInvertedBinaryLabelmap(self, modifierLabelmap):
import vtkSegmentationCorePython as vtkSegmentationCore
fillValue = 1
eraseValue = 0
inverter = vtk.vtkImageThreshold()
inverter.SetInputData(modifierLabelmap)
inverter.SetInValue(fillValue)
inverter.SetOutValue(eraseValue)
inverter.ReplaceInOn()
inverter.ThresholdByLower(0)
inverter.SetOutputScalarType(vtk.VTK_UNSIGNED_CHAR)
inverter.Update()
invertedModifierLabelmap = vtkSegmentationCore.vtkOrientedImageData()
invertedModifierLabelmap.ShallowCopy(inverter.GetOutput())
imageToWorldMatrix = vtk.vtkMatrix4x4()
modifierLabelmap.GetImageToWorldMatrix(imageToWorldMatrix)
invertedModifierLabelmap.SetGeometryFromImageToWorldMatrix(imageToWorldMatrix)
return invertedModifierLabelmap
def clipOrientedImageWithModel(self,
inputOrientedImage,
inputParentTransformNode,
outputOrientedImage,
outputParentTransformNode,
clipOutsideSurface=True,
fillValue=0,
reduceExtent=False):
"""
Fill voxels of the input volume inside/outside the clipping model with the provided fill value
"""
import vtkSegmentationCorePython as vtkSegmentationCore
# Determine the transform between the box and the image IJK coordinate systems
rasToModel = vtk.vtkMatrix4x4()
if self.roiModelNode.GetParentTransformNode() is not None:
self.roiModelNode.GetParentTransformNode(
).GetMatrixTransformFromNode(inputParentTransformNode, rasToModel)
elif inputParentTransformNode is not None:
inputParentTransformNode.GetMatrixTransformToNode(
self.roiModelNode.GetParentTransformNode(), rasToModel)
inputIjkToRas = vtk.vtkMatrix4x4()
inputOrientedImage.GetImageToWorldMatrix(inputIjkToRas)
inputImage = vtk.vtkImageData()
inputImage.ShallowCopy(inputOrientedImage)
inputImage.SetOrigin(0, 0, 0)
inputImage.SetSpacing(1, 1, 1)
clippingPolyData = self.roiModelNode.GetPolyData()
outputIjkToRas = vtk.vtkMatrix4x4()
outputImage = vtkSegmentationCore.vtkOrientedImageData()
self.clipImageWithPolyData(inputImage, outputImage, clippingPolyData,
rasToModel, inputIjkToRas, outputIjkToRas,
clipOutsideSurface, fillValue, reduceExtent)
outputOrientedImage.DeepCopy(outputImage)
outputOrientedImage.SetGeometryFromImageToWorldMatrix(outputIjkToRas)
def findLargest2DRegion(segmentationNode):
qrLogic = CustomSegmentEditorLogic
segmentationsLogic = slicer.modules.segmentations.logic()
largestLM = None
largestSize = 0
for segment in qrLogic.getAllSegments(segmentationNode):
imageData = vtkSegmentationCore.vtkOrientedImageData()
segmentID = segmentationNode.GetSegmentation().GetSegmentIdBySegment(segment)
segmentationsLogic.GetSegmentBinaryLabelmapRepresentation(segmentationNode, segmentID, imageData)
extent = imageData.GetExtent()
if extent[1] != -1 and extent[3] != -1 and extent[5] != -1:
tempLabel = slicer.vtkMRMLLabelMapVolumeNode()
tempLabel.SetName(segment.GetName() + "CentroidHelper")
segmentationsLogic.CreateLabelmapVolumeFromOrientedImageData(imageData, tempLabel)
dims = tempLabel.GetImageData().GetDimensions()
size = dims[0]*dims[1]
if size > largestSize:
largestSize = size
largestLM = tempLabel
return largestLM
def convertSegmentsToSegment(self, probeNode, nodeIds):
thisScene = probeNode.GetScene()
#probeNode.GetSegmentation().CreateRepresentation("Binary labelmap") #added 2/22
#probeNode.GetSegmentation().SetMasterRepresentationName("Binary labelmap") #added 2/22
probeName = "ablation zone"
if len(nodeIds) > 1:
print(
"Found multiple probe nodes, combining them into a single segment!: ",
nodeIds)
probeName = "combined ablation zone"
segmentationNode = slicer.vtkMRMLSegmentationNode()
slicer.mrmlScene.AddNode(segmentationNode)
segmentationNode.CreateDefaultDisplayNodes() # only needed for display
slicer.app.processEvents()
for probeNodeID in nodeIds:
duplicateProbeNode = thisScene.GetNodeByID(probeNodeID)
#duplicateProbeNode.GetSegmentation().SetMasterRepresentationName("Binary labelmap") #ADDED 2/22
segmentType = duplicateProbeNode.GetSegmentation(
).GetMasterRepresentationName()
slicer.app.processEvents()
if (segmentType == "Closed surface"):
mergedImage = vtk.vtkPolyData()
duplicateProbeNode.GetClosedSurfaceRepresentation(
duplicateProbeNode.GetSegmentation().GetNthSegmentID(0),
mergedImage)
newSegmentID = segmentationNode.AddSegmentFromClosedSurfaceRepresentation(
mergedImage, probeNodeID, [0, 1, 0])
newSegment = segmentationNode.GetSegmentation().GetSegment(
newSegmentID)
newSegment.SetName(probeName)
else:
labelmapImage = vtkSegmentationCore.vtkOrientedImageData()
duplicateProbeNode.GetBinaryLabelmapRepresentation(
duplicateProbeNode.GetSegmentation().GetNthSegmentID(0),
labelmapImage)
newSegmentID = segmentationNode.AddSegmentFromBinaryLabelmapRepresentation(
labelmapImage, probeNodeID, [1, 0, 0])
newSegment = segmentationNode.GetSegmentation().GetSegment(
newSegmentID)
newSegment.SetName(probeName)
duplicateProbeNode.GetSegmentation().CreateRepresentation(
"Closed Surface")
#segmentationNode.GetSegmentation().CreateRepresentation("Closed surface")
#segmentationNode.GetSegmentation().SetMasterRepresentationName("Closed surface")
#slicer.mrmlScene.RemoveNode(duplicateProbeNode)
duplicateProbeNode.SetDisplayVisibility(0)
segmentEditorWidget = slicer.qMRMLSegmentEditorWidget()
segmentEditorWidget.setMRMLScene(slicer.mrmlScene)
segmentEditorNode = slicer.mrmlScene.AddNewNodeByClass(
"vtkMRMLSegmentEditorNode")
segmentEditorWidget.setMRMLSegmentEditorNode(segmentEditorNode)
segmentEditorWidget.setSegmentationNode(segmentationNode)
for i in range(
1,
segmentationNode.GetSegmentation().GetNumberOfSegments() +
1): #TWO ADDITIONAL PROBES
segmentEditorWidget.setActiveEffectByName("Logical operators")
effect = segmentEditorWidget.activeEffect()
effect.self().scriptedEffect.setParameter("Operation", "UNION")
effect.self().scriptedEffect.setParameter(
"ModifierSegmentID",
segmentationNode.GetSegmentation().GetNthSegmentID(i))
effect.self().onApply()
#segmentationNode.GetSegmentation().RemoveSegment(segmentationNode.GetSegmentation().GetNthSegmentID(i))
#for i in range(1, segmentationNode.GetSegmentation().GetNumberOfSegments()): #TWO ADDITIONAL PROBES
# segmentationNode.GetSegmentation().RemoveSegment(segmentationNode.GetSegmentation().GetNthSegmentID(i))
segDisplayNode = segmentationNode.GetDisplayNode()
segDisplayNode.SetOpacity(0.3)
segmentationNode.GetSegmentation().CreateRepresentation(
"Closed surface")
segmentationNode.GetSegmentation().SetMasterRepresentationName(
"Closed surface")
segNum = segmentationNode.GetSegmentation().GetNumberOfSegments()
for i in range(0, segNum):
segmentationNode.GetSegmentation().RemoveSegment(
segmentationNode.GetSegmentation().GetNthSegmentID(1))
segmentationNode.SetName("translated probe")
#segmentationNode.GetSegmentation().GetNthSegment(0).SetName(probeName)
return segmentationNode
def preview(self):
# Get master volume image data
import vtkSegmentationCorePython as vtkSegmentationCore
masterImageData = self.scriptedEffect.masterVolumeImageData()
# Get segmentation
segmentationNode = self.scriptedEffect.parameterSetNode().GetSegmentationNode()
previewNode = self.getPreviewNode()
if not previewNode or not self.mergedLabelmapGeometryImage \
or (self.clippedMasterImageDataRequired and not self.clippedMasterImageData):
self.reset()
# Compute merged labelmap extent (effective extent slightly expanded)
self.selectedSegmentIds = vtk.vtkStringArray()
segmentationNode.GetDisplayNode().GetVisibleSegmentIDs(self.selectedSegmentIds)
if self.selectedSegmentIds.GetNumberOfValues() < self.minimumNumberOfSegments:
logging.error("Auto-complete operation skipped: at least {0} visible segments are required".format(self.minimumNumberOfSegments))
return
if not self.mergedLabelmapGeometryImage:
self.mergedLabelmapGeometryImage = vtkSegmentationCore.vtkOrientedImageData()
commonGeometryString = segmentationNode.GetSegmentation().DetermineCommonLabelmapGeometry(
vtkSegmentationCore.vtkSegmentation.EXTENT_UNION_OF_EFFECTIVE_SEGMENTS, self.selectedSegmentIds)
if not commonGeometryString:
logging.info("Auto-complete operation skipped: all visible segments are empty")
return
vtkSegmentationCore.vtkSegmentationConverter.DeserializeImageGeometry(commonGeometryString, self.mergedLabelmapGeometryImage)
masterImageExtent = masterImageData.GetExtent()
labelsEffectiveExtent = self.mergedLabelmapGeometryImage.GetExtent()
margin = [17, 17, 17]
labelsExpandedExtent = [
max(masterImageExtent[0], labelsEffectiveExtent[0]-margin[0]),
min(masterImageExtent[1], labelsEffectiveExtent[1]+margin[0]),
max(masterImageExtent[2], labelsEffectiveExtent[2]-margin[1]),
min(masterImageExtent[3], labelsEffectiveExtent[3]+margin[1]),
max(masterImageExtent[4], labelsEffectiveExtent[4]-margin[2]),
min(masterImageExtent[5], labelsEffectiveExtent[5]+margin[2]) ]
self.mergedLabelmapGeometryImage.SetExtent(labelsExpandedExtent)
previewNode = slicer.mrmlScene.CreateNodeByClass('vtkMRMLSegmentationNode')
previewNode.UnRegister(None)
previewNode = slicer.mrmlScene.AddNode(previewNode)
previewNode.CreateDefaultDisplayNodes()
previewNode.GetDisplayNode().SetVisibility2DOutline(False)
if segmentationNode.GetParentTransformNode():
previewNode.SetAndObserveTransformNodeID(segmentationNode.GetParentTransformNode().GetID())
self.scriptedEffect.parameterSetNode().SetNodeReferenceID(ResultPreviewNodeReferenceRole, previewNode.GetID())
self.scriptedEffect.setCommonParameter("SegmentationResultPreviewOwnerEffect", self.scriptedEffect.name)
self.setPreviewOpacity(0.6)
if self.clippedMasterImageDataRequired:
self.clippedMasterImageData = vtkSegmentationCore.vtkOrientedImageData()
masterImageClipper = vtk.vtkImageConstantPad()
masterImageClipper.SetInputData(masterImageData)
masterImageClipper.SetOutputWholeExtent(self.mergedLabelmapGeometryImage.GetExtent())
masterImageClipper.Update()
self.clippedMasterImageData.ShallowCopy(masterImageClipper.GetOutput())
self.clippedMasterImageData.CopyDirections(self.mergedLabelmapGeometryImage)
previewNode.SetName(segmentationNode.GetName()+" preview")
mergedImage = vtkSegmentationCore.vtkOrientedImageData()
segmentationNode.GenerateMergedLabelmapForAllSegments(mergedImage,
vtkSegmentationCore.vtkSegmentation.EXTENT_UNION_OF_EFFECTIVE_SEGMENTS, self.mergedLabelmapGeometryImage, self.selectedSegmentIds)
outputLabelmap = vtkSegmentationCore.vtkOrientedImageData()
self.computePreviewLabelmap(mergedImage, outputLabelmap)
# Write output segmentation results in segments
for index in xrange(self.selectedSegmentIds.GetNumberOfValues()):
segmentID = self.selectedSegmentIds.GetValue(index)
segment = segmentationNode.GetSegmentation().GetSegment(segmentID)
# Disable save with scene?
# Get only the label of the current segment from the output image
thresh = vtk.vtkImageThreshold()
thresh.ReplaceInOn()
thresh.ReplaceOutOn()
thresh.SetInValue(1)
thresh.SetOutValue(0)
labelValue = index + 1 # n-th segment label value = n + 1 (background label value is 0)
thresh.ThresholdBetween(labelValue, labelValue);
thresh.SetOutputScalarType(vtk.VTK_UNSIGNED_CHAR)
thresh.SetInputData(outputLabelmap)
thresh.Update()
# Write label to segment
newSegmentLabelmap = vtkSegmentationCore.vtkOrientedImageData()
newSegmentLabelmap.ShallowCopy(thresh.GetOutput())
newSegmentLabelmap.CopyDirections(mergedImage)
newSegment = previewNode.GetSegmentation().GetSegment(segmentID)
if not newSegment:
newSegment = vtkSegmentationCore.vtkSegment()
newSegment.SetName(segment.GetName())
color = segmentationNode.GetSegmentation().GetSegment(segmentID).GetColor()
newSegment.SetColor(color)
previewNode.GetSegmentation().AddSegment(newSegment, segmentID)
slicer.vtkSlicerSegmentationsModuleLogic.SetBinaryLabelmapToSegment(newSegmentLabelmap, previewNode, segmentID)
self.updateGUIFromMRML()
def onApply(self):
self.scriptedEffect.saveStateForUndo()
import vtkSegmentationCorePython as vtkSegmentationCore
# Get modifier labelmap and parameters
operation = self.scriptedEffect.parameter("Operation")
bypassMasking = (self.scriptedEffect.integerParameter("BypassMasking")
!= 0)
selectedSegmentID = self.scriptedEffect.parameterSetNode(
).GetSelectedSegmentID()
segmentationNode = self.scriptedEffect.parameterSetNode(
).GetSegmentationNode()
segmentation = segmentationNode.GetSegmentation()
if operation in self.operationsRequireModifierSegment:
# Get modifier segment
modifierSegmentID = self.modifierSegmentID()
if not modifierSegmentID:
logging.error(
"Operation {0} requires a selected modifier segment".
format(operation))
return
modifierSegment = segmentation.GetSegment(modifierSegmentID)
modifierSegmentLabelmap = modifierSegment.GetRepresentation(
vtkSegmentationCore.vtkSegmentationConverter.
GetSegmentationBinaryLabelmapRepresentationName())
if operation == LOGICAL_COPY:
if bypassMasking:
slicer.vtkSlicerSegmentationsModuleLogic.SetBinaryLabelmapToSegment(
modifierSegmentLabelmap, segmentationNode,
selectedSegmentID,
slicer.vtkSlicerSegmentationsModuleLogic.MODE_REPLACE,
modifierSegmentLabelmap.GetExtent())
else:
self.scriptedEffect.modifySelectedSegmentByLabelmap(
modifierSegmentLabelmap, slicer.
qSlicerSegmentEditorAbstractEffect.ModificationModeSet)
elif operation == LOGICAL_UNION:
if bypassMasking:
slicer.vtkSlicerSegmentationsModuleLogic.SetBinaryLabelmapToSegment(
modifierSegmentLabelmap, segmentationNode,
selectedSegmentID, slicer.
vtkSlicerSegmentationsModuleLogic.MODE_MERGE_MAX,
modifierSegmentLabelmap.GetExtent())
else:
self.scriptedEffect.modifySelectedSegmentByLabelmap(
modifierSegmentLabelmap, slicer.
qSlicerSegmentEditorAbstractEffect.ModificationModeAdd)
elif operation == LOGICAL_SUBTRACT:
if bypassMasking:
invertedModifierSegmentLabelmap = self.getInvertedBinaryLabelmap(
modifierSegmentLabelmap)
slicer.vtkSlicerSegmentationsModuleLogic.SetBinaryLabelmapToSegment(
invertedModifierSegmentLabelmap, segmentationNode,
selectedSegmentID, slicer.
vtkSlicerSegmentationsModuleLogic.MODE_MERGE_MIN,
modifierSegmentLabelmap.GetExtent())
else:
self.scriptedEffect.modifySelectedSegmentByLabelmap(
modifierSegmentLabelmap,
slicer.qSlicerSegmentEditorAbstractEffect.
ModificationModeRemove)
elif operation == LOGICAL_INTERSECT:
selectedSegmentLabelmap = self.scriptedEffect.selectedSegmentLabelmap(
)
intersectionLabelmap = vtkSegmentationCore.vtkOrientedImageData(
)
vtkSegmentationCore.vtkOrientedImageDataResample.MergeImage(
selectedSegmentLabelmap, modifierSegmentLabelmap,
intersectionLabelmap, vtkSegmentationCore.
vtkOrientedImageDataResample.OPERATION_MINIMUM,
selectedSegmentLabelmap.GetExtent())
selectedSegmentLabelmapExtent = selectedSegmentLabelmap.GetExtent(
)
modifierSegmentLabelmapExtent = modifierSegmentLabelmap.GetExtent(
)
commonExtent = [
max(selectedSegmentLabelmapExtent[0],
modifierSegmentLabelmapExtent[0]),
min(selectedSegmentLabelmapExtent[1],
modifierSegmentLabelmapExtent[1]),
max(selectedSegmentLabelmapExtent[2],
modifierSegmentLabelmapExtent[2]),
min(selectedSegmentLabelmapExtent[3],
modifierSegmentLabelmapExtent[3]),
max(selectedSegmentLabelmapExtent[4],
modifierSegmentLabelmapExtent[4]),
min(selectedSegmentLabelmapExtent[5],
modifierSegmentLabelmapExtent[5])
]
if bypassMasking:
slicer.vtkSlicerSegmentationsModuleLogic.SetBinaryLabelmapToSegment(
intersectionLabelmap, segmentationNode,
selectedSegmentID,
slicer.vtkSlicerSegmentationsModuleLogic.MODE_REPLACE,
commonExtent)
else:
self.scriptedEffect.modifySelectedSegmentByLabelmap(
intersectionLabelmap, slicer.
qSlicerSegmentEditorAbstractEffect.ModificationModeSet,
commonExtent)
elif operation == LOGICAL_INVERT:
selectedSegmentLabelmap = self.scriptedEffect.selectedSegmentLabelmap(
)
invertedSelectedSegmentLabelmap = self.getInvertedBinaryLabelmap(
selectedSegmentLabelmap)
if bypassMasking:
slicer.vtkSlicerSegmentationsModuleLogic.SetBinaryLabelmapToSegment(
invertedSelectedSegmentLabelmap, segmentationNode,
selectedSegmentID,
slicer.vtkSlicerSegmentationsModuleLogic.MODE_REPLACE)
else:
self.scriptedEffect.modifySelectedSegmentByLabelmap(
invertedSelectedSegmentLabelmap, slicer.
qSlicerSegmentEditorAbstractEffect.ModificationModeSet)
elif operation == LOGICAL_CLEAR or operation == LOGICAL_FILL:
selectedSegmentLabelmap = self.scriptedEffect.selectedSegmentLabelmap(
)
vtkSegmentationCore.vtkOrientedImageDataResample.FillImage(
selectedSegmentLabelmap, 1 if operation == LOGICAL_FILL else 0,
selectedSegmentLabelmap.GetExtent())
if bypassMasking:
slicer.vtkSlicerSegmentationsModuleLogic.SetBinaryLabelmapToSegment(
selectedSegmentLabelmap, segmentationNode,
selectedSegmentID,
slicer.vtkSlicerSegmentationsModuleLogic.MODE_REPLACE)
else:
self.scriptedEffect.modifySelectedSegmentByLabelmap(
selectedSegmentLabelmap, slicer.
qSlicerSegmentEditorAbstractEffect.ModificationModeSet)
else:
logging.error("Unknown operation: {0}".format(operation))
def processInteractionEvents(self, callerInteractor, eventId, viewWidget):
import vtkSegmentationCorePython as vtkSegmentationCore
abortEvent = False
# Only allow in modes where segment selection is needed
if not self.currentOperationRequiresSegmentSelection():
return False
# Only allow for slice views
if viewWidget.className() != "qMRMLSliceWidget":
return abortEvent
if eventId != vtk.vtkCommand.LeftButtonPressEvent:
return abortEvent
abortEvent = True
# 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 abortEvent
self.scriptedEffect.saveStateForUndo()
# This can be a long operation - indicate it to the user
qt.QApplication.setOverrideCursor(qt.Qt.WaitCursor)
operationName = self.scriptedEffect.parameter("Operation")
if operationName == ADD_SELECTED_ISLAND:
inputLabelImage = vtkSegmentationCore.vtkOrientedImageData()
if not segmentationNode.GenerateMergedLabelmapForAllSegments(inputLabelImage,
vtkSegmentationCore.vtkSegmentation.EXTENT_UNION_OF_SEGMENTS_PADDED,
None, visibleSegmentIds):
logging.error('Failed to apply smoothing: cannot get list of visible segments')
qt.QApplication.restoreOverrideCursor()
return abortEvent
else:
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())
thresh.Update()
# Create oriented image data from output
import vtkSegmentationCorePython as vtkSegmentationCore
inputLabelImage = vtkSegmentationCore.vtkOrientedImageData()
inputLabelImage.ShallowCopy(thresh.GetOutput())
selectedSegmentLabelmapImageToWorldMatrix = vtk.vtkMatrix4x4()
selectedSegmentLabelmap.GetImageToWorldMatrix(selectedSegmentLabelmapImageToWorldMatrix)
inputLabelImage.SetImageToWorldMatrix(selectedSegmentLabelmapImageToWorldMatrix)
xy = callerInteractor.GetEventPosition()
ijk = self.xyToIjk(xy, viewWidget, inputLabelImage)
pixelValue = inputLabelImage.GetScalarComponentAsFloat(ijk[0], ijk[1], ijk[2], 0)
try:
floodFillingFilter = vtk.vtkImageThresholdConnectivity()
floodFillingFilter.SetInputData(inputLabelImage)
seedPoints = vtk.vtkPoints()
origin = inputLabelImage.GetOrigin()
spacing = inputLabelImage.GetSpacing()
seedPoints.InsertNextPoint(origin[0]+ijk[0]*spacing[0], origin[1]+ijk[1]*spacing[1], origin[2]+ijk[2]*spacing[2])
floodFillingFilter.SetSeedPoints(seedPoints)
floodFillingFilter.ThresholdBetween(pixelValue, pixelValue)
if operationName == ADD_SELECTED_ISLAND:
floodFillingFilter.SetInValue(1)
floodFillingFilter.SetOutValue(0)
floodFillingFilter.Update()
modifierLabelmap = self.scriptedEffect.defaultModifierLabelmap()
modifierLabelmap.DeepCopy(floodFillingFilter.GetOutput())
self.scriptedEffect.modifySelectedSegmentByLabelmap(modifierLabelmap, slicer.qSlicerSegmentEditorAbstractEffect.ModificationModeAdd)
elif pixelValue != 0: # if clicked on empty part then there is nothing to remove or keep
if operationName == KEEP_SELECTED_ISLAND:
floodFillingFilter.SetInValue(1)
floodFillingFilter.SetOutValue(0)
else: # operationName == REMOVE_SELECTED_ISLAND:
floodFillingFilter.SetInValue(1)
floodFillingFilter.SetOutValue(0)
floodFillingFilter.Update()
modifierLabelmap = self.scriptedEffect.defaultModifierLabelmap()
modifierLabelmap.DeepCopy(floodFillingFilter.GetOutput())
if operationName == KEEP_SELECTED_ISLAND:
self.scriptedEffect.modifySelectedSegmentByLabelmap(modifierLabelmap, slicer.qSlicerSegmentEditorAbstractEffect.ModificationModeSet)
else: # operationName == REMOVE_SELECTED_ISLAND:
self.scriptedEffect.modifySelectedSegmentByLabelmap(modifierLabelmap, slicer.qSlicerSegmentEditorAbstractEffect.ModificationModeRemove)
except IndexError:
logging.error('apply: Failed to threshold master volume!')
finally:
qt.QApplication.restoreOverrideCursor()
return abortEvent
def growCut(self):
# Get master volume image data
import vtkSegmentationCorePython as vtkSegmentationCore
masterImageData = self.scriptedEffect.masterVolumeImageData()
# Get segmentation
segmentationNode = self.scriptedEffect.parameterSetNode().GetSegmentationNode()
# Cast master image if not short
if masterImageData.GetScalarType() != vtk.VTK_SHORT:
imageCast = vtk.vtkImageCast()
imageCast.SetInputData(masterImageData)
imageCast.SetOutputScalarTypeToShort()
imageCast.ClampOverflowOn()
imageCast.Update()
masterImageDataShort = vtkSegmentationCore.vtkOrientedImageData()
masterImageDataShort.DeepCopy(imageCast.GetOutput()) # Copy image data
masterImageDataShort.CopyDirections(masterImageData) # Copy geometry
masterImageData = masterImageDataShort
# Generate merged labelmap as input to GrowCut
mergedImage = vtkSegmentationCore.vtkOrientedImageData()
segmentationNode.GenerateMergedLabelmapForAllSegments(mergedImage, vtkSegmentationCore.vtkSegmentation.EXTENT_UNION_OF_SEGMENTS, masterImageData)
# Make a zero-valued volume for the output
outputLabelmap = vtkSegmentationCore.vtkOrientedImageData()
thresh = vtk.vtkImageThreshold()
thresh.ReplaceInOn()
thresh.ReplaceOutOn()
thresh.SetInValue(0)
thresh.SetOutValue(0)
thresh.SetOutputScalarType( vtk.VTK_SHORT )
thresh.SetInputData( mergedImage )
thresh.SetOutput( outputLabelmap )
thresh.Update()
outputLabelmap.DeepCopy( mergedImage ) #TODO: It was thresholded just above, why deep copy now?
# Perform grow cut
import vtkITK
growCutFilter = vtkITK.vtkITKGrowCutSegmentationImageFilter()
growCutFilter.SetInputData( 0, masterImageData )
growCutFilter.SetInputData( 1, mergedImage )
#TODO: This call sets an empty image for the optional "previous segmentation", and
# is apparently needed for the first segmentation too. Why?
growCutFilter.SetInputConnection( 2, thresh.GetOutputPort() )
#TODO: These are magic numbers inherited from EditorLib/GrowCut.py
objectSize = 5.
contrastNoiseRatio = 0.8
priorStrength = 0.003
segmented = 2
conversion = 1000
spacing = mergedImage.GetSpacing()
voxelVolume = reduce(lambda x,y: x*y, spacing)
voxelAmount = objectSize / voxelVolume
voxelNumber = round(voxelAmount) * conversion
cubeRoot = 1./3.
oSize = int(round(pow(voxelNumber,cubeRoot)))
growCutFilter.SetObjectSize( oSize )
growCutFilter.SetContrastNoiseRatio( contrastNoiseRatio )
growCutFilter.SetPriorSegmentConfidence( priorStrength )
growCutFilter.Update()
outputLabelmap.DeepCopy( growCutFilter.GetOutput() )
# Write output segmentation results in segments
segmentIDs = vtk.vtkStringArray()
segmentationNode.GetSegmentation().GetSegmentIDs(segmentIDs)
for index in xrange(segmentIDs.GetNumberOfValues()):
segmentID = segmentIDs.GetValue(index)
segment = segmentationNode.GetSegmentation().GetSegment(segmentID)
# Get label corresponding to segment in merged labelmap (and so GrowCut output)
colorIndexStr = vtk.mutable("")
tagFound = segment.GetTag(slicer.vtkMRMLSegmentationDisplayNode.GetColorIndexTag(), colorIndexStr);
if not tagFound:
logging.error('Failed to apply GrowCut result on segment ' + segmentID)
continue
colorIndex = int(colorIndexStr.get())
# Get only the label of the current segment from the output image
thresh = vtk.vtkImageThreshold()
thresh.ReplaceInOn()
thresh.ReplaceOutOn()
thresh.SetInValue(1)
thresh.SetOutValue(0)
thresh.ThresholdBetween(colorIndex, colorIndex);
thresh.SetOutputScalarType(vtk.VTK_UNSIGNED_CHAR)
thresh.SetInputData(outputLabelmap)
thresh.Update()
# Write label to segment
newSegmentLabelmap = vtkSegmentationCore.vtkOrientedImageData()
newSegmentLabelmap.ShallowCopy(thresh.GetOutput())
newSegmentLabelmap.CopyDirections(mergedImage)
slicer.vtkSlicerSegmentationsModuleLogic.SetBinaryLabelmapToSegment(newSegmentLabelmap, segmentationNode, segmentID, slicer.vtkSlicerSegmentationsModuleLogic.MODE_REPLACE, newSegmentLabelmap.GetExtent())
def growCut(self):
# Get master volume image data
import vtkSegmentationCorePython as vtkSegmentationCore
masterImageData = self.scriptedEffect.masterVolumeImageData()
# Get segmentation
segmentationNode = self.scriptedEffect.parameterSetNode(
).GetSegmentationNode()
# Cast master image if not short
if masterImageData.GetScalarType() != vtk.VTK_SHORT:
imageCast = vtk.vtkImageCast()
imageCast.SetInputData(masterImageData)
imageCast.SetOutputScalarTypeToShort()
imageCast.ClampOverflowOn()
imageCast.Update()
masterImageDataShort = vtkSegmentationCore.vtkOrientedImageData()
masterImageDataShort.DeepCopy(
imageCast.GetOutput()) # Copy image data
masterImageDataShort.CopyDirections(
masterImageData) # Copy geometry
masterImageData = masterImageDataShort
# Generate merged labelmap as input to GrowCut
mergedImage = vtkSegmentationCore.vtkOrientedImageData()
segmentationNode.GenerateMergedLabelmapForAllSegments(
mergedImage,
vtkSegmentationCore.vtkSegmentation.EXTENT_UNION_OF_SEGMENTS,
masterImageData)
# Make a zero-valued volume for the output
outputLabelmap = vtkSegmentationCore.vtkOrientedImageData()
thresh = vtk.vtkImageThreshold()
thresh.ReplaceInOn()
thresh.ReplaceOutOn()
thresh.SetInValue(0)
thresh.SetOutValue(0)
thresh.SetOutputScalarType(vtk.VTK_SHORT)
thresh.SetInputData(mergedImage)
thresh.SetOutput(outputLabelmap)
thresh.Update()
outputLabelmap.DeepCopy(
mergedImage
) #TODO: It was thresholded just above, why deep copy now?
# Perform grow cut
import vtkITK
growCutFilter = vtkITK.vtkITKGrowCutSegmentationImageFilter()
growCutFilter.SetInputData(0, masterImageData)
growCutFilter.SetInputData(1, mergedImage)
#TODO: This call sets an empty image for the optional "previous segmentation", and
# is apparently needed for the first segmentation too. Why?
growCutFilter.SetInputConnection(2, thresh.GetOutputPort())
#TODO: These are magic numbers inherited from EditorLib/GrowCut.py
objectSize = 5.
contrastNoiseRatio = 0.8
priorStrength = 0.003
segmented = 2
conversion = 1000
spacing = mergedImage.GetSpacing()
voxelVolume = reduce(lambda x, y: x * y, spacing)
voxelAmount = objectSize / voxelVolume
voxelNumber = round(voxelAmount) * conversion
cubeRoot = 1. / 3.
oSize = int(round(pow(voxelNumber, cubeRoot)))
growCutFilter.SetObjectSize(oSize)
growCutFilter.SetContrastNoiseRatio(contrastNoiseRatio)
growCutFilter.SetPriorSegmentConfidence(priorStrength)
growCutFilter.Update()
outputLabelmap.DeepCopy(growCutFilter.GetOutput())
# Write output segmentation results in segments
segmentIDs = vtk.vtkStringArray()
segmentationNode.GetSegmentation().GetSegmentIDs(segmentIDs)
for index in xrange(segmentIDs.GetNumberOfValues()):
segmentID = segmentIDs.GetValue(index)
segment = segmentationNode.GetSegmentation().GetSegment(segmentID)
# Get label corresponding to segment in merged labelmap (and so GrowCut output)
colorIndexStr = vtk.mutable("")
tagFound = segment.GetTag(
slicer.vtkMRMLSegmentationDisplayNode.GetColorIndexTag(),
colorIndexStr)
if not tagFound:
logging.error('Failed to apply GrowCut result on segment ' +
segmentID)
continue
colorIndex = int(colorIndexStr.get())
# Get only the label of the current segment from the output image
thresh = vtk.vtkImageThreshold()
thresh.ReplaceInOn()
thresh.ReplaceOutOn()
thresh.SetInValue(1)
thresh.SetOutValue(0)
thresh.ThresholdBetween(colorIndex, colorIndex)
thresh.SetOutputScalarType(vtk.VTK_UNSIGNED_CHAR)
thresh.SetInputData(outputLabelmap)
thresh.Update()
# Write label to segment
newSegmentLabelmap = vtkSegmentationCore.vtkOrientedImageData()
newSegmentLabelmap.ShallowCopy(thresh.GetOutput())
newSegmentLabelmap.CopyDirections(mergedImage)
slicer.vtkSlicerSegmentationsModuleLogic.SetBinaryLabelmapToSegment(
newSegmentLabelmap, segmentationNode, segmentID,
slicer.vtkSlicerSegmentationsModuleLogic.MODE_REPLACE,
newSegmentLabelmap.GetExtent())
def TestSection_2_qMRMLSegmentationGeometryWidget(self):
logging.info('Test section 2: qMRMLSegmentationGeometryWidget')
import vtkSegmentationCore
binaryLabelmapReprName = vtkSegmentationCore.vtkSegmentationConverter.GetBinaryLabelmapRepresentationName()
closedSurfaceReprName = vtkSegmentationCore.vtkSegmentationConverter.GetClosedSurfaceRepresentationName()
# Use MRHead and Tinypatient for testing
import SampleData
sampleDataLogic = SampleData.SampleDataLogic()
mrVolumeNode = sampleDataLogic.downloadMRHead()
[tinyVolumeNode, tinySegmentationNode] = sampleDataLogic.downloadSample('TinyPatient')
# Convert MRHead to oriented image data
import vtkSlicerSegmentationsModuleLogicPython as vtkSlicerSegmentationsModuleLogic
mrOrientedImageData = vtkSlicerSegmentationsModuleLogic.vtkSlicerSegmentationsModuleLogic.CreateOrientedImageDataFromVolumeNode(mrVolumeNode)
mrOrientedImageData.UnRegister(None)
# Create segmentation node with binary labelmap master and one segment with MRHead geometry
segmentationNode = slicer.vtkMRMLSegmentationNode()
segmentationNode.GetSegmentation().SetMasterRepresentationName(binaryLabelmapReprName)
geometryStr = vtkSegmentationCore.vtkSegmentationConverter.SerializeImageGeometry(mrOrientedImageData)
segmentationNode.GetSegmentation().SetConversionParameter(
vtkSegmentationCore.vtkSegmentationConverter.GetReferenceImageGeometryParameterName(), geometryStr)
slicer.mrmlScene.AddNode(segmentationNode)
threshold = vtk.vtkImageThreshold()
threshold.SetInputData(mrOrientedImageData)
threshold.ThresholdByUpper(16.0)
threshold.SetInValue(1)
threshold.SetOutValue(0)
threshold.SetOutputScalarType(vtk.VTK_UNSIGNED_CHAR)
threshold.Update()
segmentOrientedImageData = vtkSegmentationCore.vtkOrientedImageData()
segmentOrientedImageData.DeepCopy(threshold.GetOutput())
mrImageToWorldMatrix = vtk.vtkMatrix4x4()
mrOrientedImageData.GetImageToWorldMatrix(mrImageToWorldMatrix)
segmentOrientedImageData.SetImageToWorldMatrix(mrImageToWorldMatrix)
segment = vtkSegmentationCore.vtkSegment()
segment.SetName('Brain')
segment.SetColor(0.0,0.0,1.0)
segment.AddRepresentation(binaryLabelmapReprName, segmentOrientedImageData)
segmentationNode.GetSegmentation().AddSegment(segment)
# Create geometry widget
geometryWidget = slicer.qMRMLSegmentationGeometryWidget()
geometryWidget.setSegmentationNode(segmentationNode)
geometryWidget.editEnabled = True
geometryImageData = vtkSegmentationCore.vtkOrientedImageData() # To contain the output later
# Volume source with no transforms
geometryWidget.setSourceNode(tinyVolumeNode)
geometryWidget.geometryImageData(geometryImageData)
self.assertTrue(self.compareOutputGeometry(geometryImageData,
(49,49,23), (248.8439, 248.2890, -123.75),
[[-1.0, 0.0, 0.0], [0.0, -1.0, 0.0], [0.0, 0.0, 1.0]]))
vtkSegmentationCore.vtkOrientedImageDataResample.ResampleOrientedImageToReferenceOrientedImage(
segmentOrientedImageData, geometryImageData, geometryImageData, False, True)
self.assertEqual(self.getForegroundVoxelCount(geometryImageData), 92)
# Transformed volume source
translationTransformMatrix = vtk.vtkMatrix4x4()
translationTransformMatrix.SetElement(0,3,24.5)
translationTransformMatrix.SetElement(1,3,24.5)
translationTransformMatrix.SetElement(2,3,11.5)
translationTransformNode = slicer.vtkMRMLLinearTransformNode()
translationTransformNode.SetName('TestTranslation')
slicer.mrmlScene.AddNode(translationTransformNode)
translationTransformNode.SetMatrixTransformToParent(translationTransformMatrix)
tinyVolumeNode.SetAndObserveTransformNodeID(translationTransformNode.GetID())
geometryWidget.geometryImageData(geometryImageData)
self.assertTrue(self.compareOutputGeometry(geometryImageData,
(49,49,23), (224.3439, 223.7890, -135.25),
[[-1.0, 0.0, 0.0], [0.0, -1.0, 0.0], [0.0, 0.0, 1.0]]))
vtkSegmentationCore.vtkOrientedImageDataResample.ResampleOrientedImageToReferenceOrientedImage(
segmentOrientedImageData, geometryImageData, geometryImageData, False, True)
self.assertEqual(self.getForegroundVoxelCount(geometryImageData), 94)
# Volume source with isotropic spacing
tinyVolumeNode.SetAndObserveTransformNodeID(None)
geometryWidget.setIsotropicSpacing(True)
geometryWidget.geometryImageData(geometryImageData)
self.assertTrue(self.compareOutputGeometry(geometryImageData,
(23,23,23), (248.8439, 248.2890, -123.75),
[[-1.0, 0.0, 0.0], [0.0, -1.0, 0.0], [0.0, 0.0, 1.0]]))
vtkSegmentationCore.vtkOrientedImageDataResample.ResampleOrientedImageToReferenceOrientedImage(
segmentOrientedImageData, geometryImageData, geometryImageData, False, True)
self.assertEqual(self.getForegroundVoxelCount(geometryImageData), 414)
# Volume source with oversampling
geometryWidget.setIsotropicSpacing(False)
geometryWidget.setOversamplingFactor(2.0)
geometryWidget.geometryImageData(geometryImageData)
self.assertTrue(self.compareOutputGeometry(geometryImageData,
(24.5, 24.5, 11.5), (261.0939, 260.5390, -129.5),
[[-1.0, 0.0, 0.0], [0.0, -1.0, 0.0], [0.0, 0.0, 1.0]]))
vtkSegmentationCore.vtkOrientedImageDataResample.ResampleOrientedImageToReferenceOrientedImage(
segmentOrientedImageData, geometryImageData, geometryImageData, False, True)
self.assertEqual(self.getForegroundVoxelCount(geometryImageData), 751)
slicer.util.delayDisplay('Volume source cases - OK')
# Segmentation source with binary labelmap master
geometryWidget.setOversamplingFactor(1.0)
geometryWidget.setSourceNode(tinySegmentationNode)
geometryWidget.geometryImageData(geometryImageData)
self.assertTrue(self.compareOutputGeometry(geometryImageData,
(49,49,23), (248.8439, 248.2890, -123.75),
[[-1.0, 0.0, 0.0], [0.0, -1.0, 0.0], [0.0, 0.0, 1.0]]))
vtkSegmentationCore.vtkOrientedImageDataResample.ResampleOrientedImageToReferenceOrientedImage(
segmentOrientedImageData, geometryImageData, geometryImageData, False, True)
self.assertEqual(self.getForegroundVoxelCount(geometryImageData), 92)
# Segmentation source with closed surface master
tinySegmentationNode.GetSegmentation().SetConversionParameter('Smoothing factor', '0.0')
self.assertTrue(tinySegmentationNode.GetSegmentation().CreateRepresentation(closedSurfaceReprName))
tinySegmentationNode.GetSegmentation().SetMasterRepresentationName(closedSurfaceReprName)
tinySegmentationNode.Modified() # Trigger re-calculation of geometry (only generic Modified event is observed)
geometryWidget.geometryImageData(geometryImageData)
self.assertTrue(self.compareOutputGeometry(geometryImageData,
(1,1,1), (-167.156, -217.711, -135.75),
[[0.0, 0.0, 1.0], [-1.0, 0.0, 0.0], [0.0, -1.0, 0.0]]))
vtkSegmentationCore.vtkOrientedImageDataResample.ResampleOrientedImageToReferenceOrientedImage(
segmentOrientedImageData, geometryImageData, geometryImageData, False, True)
self.assertEqual(self.getForegroundVoxelCount(geometryImageData), 5223846)
slicer.util.delayDisplay('Segmentation source cases - OK')
# Model source with no transform
outputModelHierarchy = slicer.vtkMRMLModelHierarchyNode()
slicer.mrmlScene.AddNode(outputModelHierarchy)
success = vtkSlicerSegmentationsModuleLogic.vtkSlicerSegmentationsModuleLogic.ExportVisibleSegmentsToModelHierarchy(
tinySegmentationNode, outputModelHierarchy )
self.assertTrue(success)
modelNode = slicer.util.getNode('Body_Contour')
geometryWidget.setSourceNode(modelNode)
geometryWidget.geometryImageData(geometryImageData)
self.assertTrue(self.compareOutputGeometry(geometryImageData,
(1,1,1), (-167.156, -217.711, -135.75),
[[0.0, 0.0, 1.0], [-1.0, 0.0, 0.0], [0.0, -1.0, 0.0]]))
vtkSegmentationCore.vtkOrientedImageDataResample.ResampleOrientedImageToReferenceOrientedImage(
segmentOrientedImageData, geometryImageData, geometryImageData, False, True)
self.assertEqual(self.getForegroundVoxelCount(geometryImageData), 5223846)
# Transformed model source
rotationTransform = vtk.vtkTransform()
rotationTransform.RotateX(45)
rotationTransformMatrix = vtk.vtkMatrix4x4()
rotationTransform.GetMatrix(rotationTransformMatrix)
rotationTransformNode = slicer.vtkMRMLLinearTransformNode()
rotationTransformNode.SetName('TestRotation')
slicer.mrmlScene.AddNode(rotationTransformNode)
rotationTransformNode.SetMatrixTransformToParent(rotationTransformMatrix)
modelNode.SetAndObserveTransformNodeID(rotationTransformNode.GetID())
modelNode.Modified()
geometryWidget.geometryImageData(geometryImageData)
self.assertTrue(self.compareOutputGeometry(geometryImageData,
(1,1,1), (-167.156, -58.6623, -249.228),
[[0.0, 0.0, 1.0], [-0.7071, -0.7071, 0.0], [0.7071, -0.7071, 0.0]]))
vtkSegmentationCore.vtkOrientedImageDataResample.ResampleOrientedImageToReferenceOrientedImage(
segmentOrientedImageData, geometryImageData, geometryImageData, False, True)
self.assertEqual(self.getForegroundVoxelCount(geometryImageData), 5221241)
# ROI source
roiNode = slicer.vtkMRMLAnnotationROINode()
roiNode.SetName('SourceROI')
slicer.mrmlScene.AddNode(roiNode)
roiNode.UnRegister(None)
xyz = [0]*3
center = [0]*3
slicer.vtkMRMLSliceLogic.GetVolumeRASBox(tinyVolumeNode, xyz, center)
radius = map(lambda x: x/2.0, xyz)
roiNode.SetXYZ(center)
roiNode.SetRadiusXYZ(radius)
geometryWidget.setSourceNode(roiNode)
geometryWidget.geometryImageData(geometryImageData)
self.assertTrue(self.compareOutputGeometry(geometryImageData,
(1,1,1), (-216.156, -217.711, -135.75),
[[0.0, 0.0, 1.0], [-1.0, 0.0, 0.0], [0.0, -1.0, 0.0]]))
vtkSegmentationCore.vtkOrientedImageDataResample.ResampleOrientedImageToReferenceOrientedImage(
segmentOrientedImageData, geometryImageData, geometryImageData, False, True)
self.assertEqual(self.getForegroundVoxelCount(geometryImageData), 5223846)
slicer.util.delayDisplay('Model and ROI source cases - OK')
slicer.util.delayDisplay('Segmentation geometry widget test passed')
def processInteractionEvents(self, callerInteractor, eventId, viewWidget):
import vtkSegmentationCorePython as vtkSegmentationCore
abortEvent = False
# Only allow in modes where segment selection is needed
if not self.currentOperationRequiresSegmentSelection():
return False
# Only allow for slice views
if viewWidget.className() != "qMRMLSliceWidget":
return abortEvent
if eventId != vtk.vtkCommand.LeftButtonPressEvent:
return abortEvent
abortEvent = True
# 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 abortEvent
self.scriptedEffect.saveStateForUndo()
# This can be a long operation - indicate it to the user
qt.QApplication.setOverrideCursor(qt.Qt.WaitCursor)
operationName = self.scriptedEffect.parameter("Operation")
if operationName == ADD_SELECTED_ISLAND:
inputLabelImage = vtkSegmentationCore.vtkOrientedImageData()
if not segmentationNode.GenerateMergedLabelmapForAllSegments(
inputLabelImage, vtkSegmentationCore.vtkSegmentation.
EXTENT_UNION_OF_SEGMENTS_PADDED, None, visibleSegmentIds):
logging.error(
'Failed to apply smoothing: cannot get list of visible segments'
)
qt.QApplication.restoreOverrideCursor()
return abortEvent
else:
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())
thresh.Update()
# Create oriented image data from output
import vtkSegmentationCorePython as vtkSegmentationCore
inputLabelImage = vtkSegmentationCore.vtkOrientedImageData()
inputLabelImage.ShallowCopy(thresh.GetOutput())
selectedSegmentLabelmapImageToWorldMatrix = vtk.vtkMatrix4x4()
selectedSegmentLabelmap.GetImageToWorldMatrix(
selectedSegmentLabelmapImageToWorldMatrix)
inputLabelImage.SetImageToWorldMatrix(
selectedSegmentLabelmapImageToWorldMatrix)
xy = callerInteractor.GetEventPosition()
ijk = self.xyToIjk(xy, viewWidget, inputLabelImage)
pixelValue = inputLabelImage.GetScalarComponentAsFloat(
ijk[0], ijk[1], ijk[2], 0)
try:
floodFillingFilter = vtk.vtkImageThresholdConnectivity()
floodFillingFilter.SetInputData(inputLabelImage)
seedPoints = vtk.vtkPoints()
origin = inputLabelImage.GetOrigin()
spacing = inputLabelImage.GetSpacing()
seedPoints.InsertNextPoint(origin[0] + ijk[0] * spacing[0],
origin[1] + ijk[1] * spacing[1],
origin[2] + ijk[2] * spacing[2])
floodFillingFilter.SetSeedPoints(seedPoints)
floodFillingFilter.ThresholdBetween(pixelValue, pixelValue)
if operationName == ADD_SELECTED_ISLAND:
floodFillingFilter.SetInValue(1)
floodFillingFilter.SetOutValue(0)
floodFillingFilter.Update()
modifierLabelmap = self.scriptedEffect.defaultModifierLabelmap(
)
modifierLabelmap.DeepCopy(floodFillingFilter.GetOutput())
self.scriptedEffect.modifySelectedSegmentByLabelmap(
modifierLabelmap, slicer.
qSlicerSegmentEditorAbstractEffect.ModificationModeAdd)
elif pixelValue != 0: # if clicked on empty part then there is nothing to remove or keep
if operationName == KEEP_SELECTED_ISLAND:
floodFillingFilter.SetInValue(1)
floodFillingFilter.SetOutValue(0)
else: # operationName == REMOVE_SELECTED_ISLAND:
floodFillingFilter.SetInValue(1)
floodFillingFilter.SetOutValue(0)
floodFillingFilter.Update()
modifierLabelmap = self.scriptedEffect.defaultModifierLabelmap(
)
modifierLabelmap.DeepCopy(floodFillingFilter.GetOutput())
if operationName == KEEP_SELECTED_ISLAND:
self.scriptedEffect.modifySelectedSegmentByLabelmap(
modifierLabelmap, slicer.
qSlicerSegmentEditorAbstractEffect.ModificationModeSet)
else: # operationName == REMOVE_SELECTED_ISLAND:
self.scriptedEffect.modifySelectedSegmentByLabelmap(
modifierLabelmap,
slicer.qSlicerSegmentEditorAbstractEffect.
ModificationModeRemove)
except IndexError:
logging.error('apply: Failed to threshold master volume!')
finally:
qt.QApplication.restoreOverrideCursor()
return abortEvent
def onApply(self):
import vtkSegmentationCorePython as vtkSegmentationCore
# Get modifier labelmap and parameters
operation = self.scriptedEffect.parameter("Operation")
bypassMasking = (self.scriptedEffect.integerParameter("BypassMasking") != 0)
selectedSegmentID = self.scriptedEffect.parameterSetNode().GetSelectedSegmentID()
segmentationNode = self.scriptedEffect.parameterSetNode().GetSegmentationNode()
segmentation = segmentationNode.GetSegmentation()
if operation in self.operationsRequireModifierSegment:
# Get modifier segment
modifierSegmentID = self.modifierSegmentID()
if not modifierSegmentID:
logging.error("Operation {0} requires a selected modifier segment".format(operation))
return
modifierSegment = segmentation.GetSegment(modifierSegmentID)
modifierSegmentLabelmap = modifierSegment.GetRepresentation(vtkSegmentationCore.vtkSegmentationConverter.GetSegmentationBinaryLabelmapRepresentationName())
if operation == LOGICAL_COPY:
if bypassMasking:
slicer.vtkSlicerSegmentationsModuleLogic.SetBinaryLabelmapToSegment(modifierSegmentLabelmap,
segmentationNode, selectedSegmentID, slicer.vtkSlicerSegmentationsModuleLogic.MODE_REPLACE, modifierSegmentLabelmap.GetExtent())
else:
self.scriptedEffect.modifySelectedSegmentByLabelmap(modifierSegmentLabelmap, slicer.qSlicerSegmentEditorAbstractEffect.ModificationModeSet)
elif operation == LOGICAL_UNION:
if bypassMasking:
slicer.vtkSlicerSegmentationsModuleLogic.SetBinaryLabelmapToSegment(modifierSegmentLabelmap,
segmentationNode, selectedSegmentID, slicer.vtkSlicerSegmentationsModuleLogic.MODE_MERGE_MAX, modifierSegmentLabelmap.GetExtent())
else:
self.scriptedEffect.modifySelectedSegmentByLabelmap(modifierSegmentLabelmap, slicer.qSlicerSegmentEditorAbstractEffect.ModificationModeAdd)
elif operation == LOGICAL_SUBTRACT:
if bypassMasking:
invertedModifierSegmentLabelmap = self.getInvertedBinaryLabelmap(modifierSegmentLabelmap)
slicer.vtkSlicerSegmentationsModuleLogic.SetBinaryLabelmapToSegment(invertedModifierSegmentLabelmap, segmentationNode, selectedSegmentID,
slicer.vtkSlicerSegmentationsModuleLogic.MODE_MERGE_MIN, modifierSegmentLabelmap.GetExtent())
else:
self.scriptedEffect.modifySelectedSegmentByLabelmap(modifierSegmentLabelmap, slicer.qSlicerSegmentEditorAbstractEffect.ModificationModeRemove)
elif operation == LOGICAL_INTERSECT:
selectedSegmentLabelmap = self.scriptedEffect.selectedSegmentLabelmap()
intersectionLabelmap = vtkSegmentationCore.vtkOrientedImageData()
vtkSegmentationCore.vtkOrientedImageDataResample.MergeImage(selectedSegmentLabelmap, modifierSegmentLabelmap, intersectionLabelmap, vtkSegmentationCore.vtkOrientedImageDataResample.OPERATION_MINIMUM, selectedSegmentLabelmap.GetExtent())
selectedSegmentLabelmapExtent = selectedSegmentLabelmap.GetExtent()
modifierSegmentLabelmapExtent = modifierSegmentLabelmap.GetExtent()
commonExtent = [max(selectedSegmentLabelmapExtent[0], modifierSegmentLabelmapExtent[0]),
min(selectedSegmentLabelmapExtent[1], modifierSegmentLabelmapExtent[1]),
max(selectedSegmentLabelmapExtent[2], modifierSegmentLabelmapExtent[2]),
min(selectedSegmentLabelmapExtent[3], modifierSegmentLabelmapExtent[3]),
max(selectedSegmentLabelmapExtent[4], modifierSegmentLabelmapExtent[4]),
min(selectedSegmentLabelmapExtent[5], modifierSegmentLabelmapExtent[5])]
if bypassMasking:
slicer.vtkSlicerSegmentationsModuleLogic.SetBinaryLabelmapToSegment(intersectionLabelmap, segmentationNode, selectedSegmentID,
slicer.vtkSlicerSegmentationsModuleLogic.MODE_REPLACE, commonExtent)
else:
self.scriptedEffect.modifySelectedSegmentByLabelmap(intersectionLabelmap, slicer.qSlicerSegmentEditorAbstractEffect.ModificationModeSet, commonExtent)
elif operation == LOGICAL_INVERT:
selectedSegmentLabelmap = self.scriptedEffect.selectedSegmentLabelmap()
invertedSelectedSegmentLabelmap = self.getInvertedBinaryLabelmap(selectedSegmentLabelmap)
if bypassMasking:
slicer.vtkSlicerSegmentationsModuleLogic.SetBinaryLabelmapToSegment(
invertedSelectedSegmentLabelmap, segmentationNode, selectedSegmentID, slicer.vtkSlicerSegmentationsModuleLogic.MODE_REPLACE)
else:
self.scriptedEffect.modifySelectedSegmentByLabelmap(invertedSelectedSegmentLabelmap, slicer.qSlicerSegmentEditorAbstractEffect.ModificationModeSet)
elif operation == LOGICAL_CLEAR or operation == LOGICAL_FILL:
selectedSegmentLabelmap = self.scriptedEffect.selectedSegmentLabelmap()
vtkSegmentationCore.vtkOrientedImageDataResample.FillImage(selectedSegmentLabelmap, 1 if operation == LOGICAL_FILL else 0, selectedSegmentLabelmap.GetExtent())
if bypassMasking:
slicer.vtkSlicerSegmentationsModuleLogic.SetBinaryLabelmapToSegment(
selectedSegmentLabelmap, segmentationNode, selectedSegmentID, slicer.vtkSlicerSegmentationsModuleLogic.MODE_REPLACE)
else:
self.scriptedEffect.modifySelectedSegmentByLabelmap(selectedSegmentLabelmap, slicer.qSlicerSegmentEditorAbstractEffect.ModificationModeSet)
else:
logging.error("Uknown operation: {0}".format(operation))
def addGrayscaleVolumeStatistics(self):
import vtkSegmentationCorePython as vtkSegmentationCore
containsLabelmapRepresentation = self.segmentationNode.GetSegmentation().ContainsRepresentation(
vtkSegmentationCore.vtkSegmentationConverter.GetSegmentationBinaryLabelmapRepresentationName())
if not containsLabelmapRepresentation:
return
if self.grayscaleNode is None or self.grayscaleNode.GetImageData() is None:
return
# Get geometry of grayscale volume node as oriented image data
referenceGeometry_Reference = vtkSegmentationCore.vtkOrientedImageData() # reference geometry in reference node coordinate system
referenceGeometry_Reference.SetExtent(self.grayscaleNode.GetImageData().GetExtent())
ijkToRasMatrix = vtk.vtkMatrix4x4()
self.grayscaleNode.GetIJKToRASMatrix(ijkToRasMatrix)
referenceGeometry_Reference.SetGeometryFromImageToWorldMatrix(ijkToRasMatrix)
# Get transform between grayscale volume and segmentation
segmentationToReferenceGeometryTransform = vtk.vtkGeneralTransform()
slicer.vtkMRMLTransformNode.GetTransformBetweenNodes(self.segmentationNode.GetParentTransformNode(),
self.grayscaleNode.GetParentTransformNode(), segmentationToReferenceGeometryTransform)
cubicMMPerVoxel = reduce(lambda x,y: x*y, referenceGeometry_Reference.GetSpacing())
ccPerCubicMM = 0.001
for segmentID in self.statistics["SegmentIDs"]:
segment = self.segmentationNode.GetSegmentation().GetSegment(segmentID)
segmentLabelmap = segment.GetRepresentation(vtkSegmentationCore.vtkSegmentationConverter.GetSegmentationBinaryLabelmapRepresentationName())
segmentLabelmap_Reference = vtkSegmentationCore.vtkOrientedImageData()
vtkSegmentationCore.vtkOrientedImageDataResample.ResampleOrientedImageToReferenceOrientedImage(
segmentLabelmap, referenceGeometry_Reference, segmentLabelmap_Reference,
False, # nearest neighbor interpolation
False, # no padding
segmentationToReferenceGeometryTransform)
# 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(segmentLabelmap_Reference)
thresh.ThresholdByLower(0)
thresh.SetInValue(backgroundValue)
thresh.SetOutValue(labelValue)
thresh.SetOutputScalarType(vtk.VTK_UNSIGNED_CHAR)
thresh.Update()
# Use binary labelmap as a stencil
stencil = vtk.vtkImageToImageStencil()
stencil.SetInputData(thresh.GetOutput())
stencil.ThresholdByUpper(labelValue)
stencil.Update()
stat = vtk.vtkImageAccumulate()
stat.SetInputData(self.grayscaleNode.GetImageData())
stat.SetStencilData(stencil.GetOutput())
stat.Update()
# Add data to statistics list
self.statistics[segmentID,"GS voxel count"] = stat.GetVoxelCount()
self.statistics[segmentID,"GS volume mm3"] = stat.GetVoxelCount() * cubicMMPerVoxel
self.statistics[segmentID,"GS volume cc"] = stat.GetVoxelCount() * cubicMMPerVoxel * ccPerCubicMM
if stat.GetVoxelCount()>0:
self.statistics[segmentID,"GS min"] = stat.GetMin()[0]
self.statistics[segmentID,"GS max"] = stat.GetMax()[0]
self.statistics[segmentID,"GS mean"] = stat.GetMean()[0]
self.statistics[segmentID,"GS stdev"] = stat.GetStandardDeviation()[0]
def TestSection_1_AddRemoveSegment(self):
# Add/remove segment from segmentation (check display properties, color table, etc.)
logging.info('Test section 1: Add/remove segment')
# Get baseline values
displayNode = self.inputSegmentationNode.GetDisplayNode()
self.assertIsNotNone(displayNode)
# If segments are not found then the returned color is the pre-defined invalid color
bodyColor = self.inputSegmentationNode.GetSegmentation().GetSegment('Body_Contour').GetColor()
logging.info("bodyColor: {0}".format(bodyColor))
self.assertEqual(int(bodyColor[0]*100), 33)
self.assertEqual(int(bodyColor[1]*100), 66)
self.assertEqual(int(bodyColor[2]*100), 0)
tumorColor = self.inputSegmentationNode.GetSegmentation().GetSegment('Tumor_Contour').GetColor()
logging.info("tumorColor: {0}".format(tumorColor))
self.assertEqual(int(tumorColor[0]*100), 100)
self.assertEqual(int(tumorColor[1]*100), 0)
self.assertEqual(int(tumorColor[2]*100), 0)
# Create new segment
sphere = vtk.vtkSphereSource()
sphere.SetCenter(0,50,0)
sphere.SetRadius(50)
sphere.Update()
spherePolyData = vtk.vtkPolyData()
spherePolyData.DeepCopy(sphere.GetOutput())
self.sphereSegment = vtkSegmentationCore.vtkSegment()
self.sphereSegment.SetName(self.sphereSegmentName)
self.sphereSegment.SetColor(0.0,0.0,1.0)
self.sphereSegment.AddRepresentation(self.closedSurfaceReprName, spherePolyData)
# Add segment to segmentation
self.inputSegmentationNode.GetSegmentation().AddSegment(self.sphereSegment)
self.assertEqual(self.inputSegmentationNode.GetSegmentation().GetNumberOfSegments(), 3)
# Check merged labelmap
mergedLabelmap = vtkSegmentationCore.vtkOrientedImageData()
self.inputSegmentationNode.GetSegmentation().CreateRepresentation(self.binaryLabelmapReprName)
self.inputSegmentationNode.GenerateMergedLabelmapForAllSegments(mergedLabelmap, 0)
imageStat = vtk.vtkImageAccumulate()
imageStat.SetInputData(mergedLabelmap)
imageStat.SetComponentExtent(0,4,0,0,0,0)
imageStat.SetComponentOrigin(0,0,0)
imageStat.SetComponentSpacing(1,1,1)
imageStat.Update()
self.assertEqual(imageStat.GetVoxelCount(), 1000)
imageStatResult = imageStat.GetOutput()
for i in range(4):
logging.info("Volume {0}: {1}".format(i, imageStatResult.GetScalarComponentAsDouble(i,0,0,0)))
self.assertEqual(imageStatResult.GetScalarComponentAsDouble(0,0,0,0), 795)
self.assertEqual(imageStatResult.GetScalarComponentAsDouble(1,0,0,0), 194)
self.assertEqual(imageStatResult.GetScalarComponentAsDouble(2,0,0,0), 4)
self.assertEqual(imageStatResult.GetScalarComponentAsDouble(3,0,0,0), 7)
# Check if segment reorder is taken into account in merged labelmap generation
# Change segment order
sphereSegmentId = self.inputSegmentationNode.GetSegmentation().GetSegmentIdBySegment(self.sphereSegment)
self.inputSegmentationNode.GetSegmentation().SetSegmentIndex(sphereSegmentId, 1)
# Re-generate merged labelmap
self.inputSegmentationNode.GenerateMergedLabelmapForAllSegments(mergedLabelmap, 0)
imageStat.SetInputData(mergedLabelmap)
imageStat.Update()
self.assertEqual(imageStat.GetVoxelCount(), 1000)
imageStatResult = imageStat.GetOutput()
for i in range(4):
logging.info("Volume {0}: {1}".format(i, imageStatResult.GetScalarComponentAsDouble(i,0,0,0)))
self.assertEqual(imageStatResult.GetScalarComponentAsDouble(0,0,0,0), 795)
self.assertEqual(imageStatResult.GetScalarComponentAsDouble(1,0,0,0), 194)
self.assertEqual(imageStatResult.GetScalarComponentAsDouble(2,0,0,0), 6)
self.assertEqual(imageStatResult.GetScalarComponentAsDouble(3,0,0,0), 5)
# Remove segment from segmentation
self.inputSegmentationNode.GetSegmentation().RemoveSegment(self.sphereSegmentName)
self.assertEqual(self.inputSegmentationNode.GetSegmentation().GetNumberOfSegments(), 2)
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()
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
# vtkDiscreteFlyingEdges3D cannot be used here, as in the output of that filter,
# each labeled region is completely disconnected from neighboring regions, and
# for joint smoothing it is essential for the points to move together.
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 jumpToSegmentAndCreateScreenShot(segmentationNode,
segment,
widgets,
center=False,
crosshair=False):
imageData = vtkSegmentationCore.vtkOrientedImageData()
segmentID = segmentationNode.GetSegmentation().GetSegmentIdBySegment(
segment)
segmentationsLogic = slicer.modules.segmentations.logic()
segmentationsLogic.GetSegmentBinaryLabelmapRepresentation(
segmentationNode, segmentID, imageData)
extent = imageData.GetExtent()
if extent[1] != -1 and extent[3] != -1 and extent[5] != -1:
tempLabel = slicer.vtkMRMLLabelMapVolumeNode()
slicer.mrmlScene.AddNode(tempLabel)
tempLabel.SetName(segment.GetName() + "CentroidHelper")
segmentationsLogic.CreateLabelmapVolumeFromOrientedImageData(
imageData, tempLabel)
CustomSegmentEditorLogic.applyThreshold(tempLabel, 1)
centroid = ModuleLogicMixin.getCentroidForLabel(tempLabel, 1)
slicer.mrmlScene.RemoveNode(tempLabel)
annotationNodes = []
crosshairButton = None
if crosshair:
crosshairButton = CrosshairButton()
crosshairButton.setSliceIntersectionEnabled(True)
crosshairButton.checked = True
for widget in widgets:
sliceLogic = widget.sliceLogic()
sliceNode = sliceLogic.GetSliceNode()
if not center:
sliceNode.JumpSliceByOffsetting(centroid[0], centroid[1],
centroid[2])
else:
markupsLogic = slicer.modules.markups.logic()
markupsLogic.JumpSlicesToLocation(centroid[0], centroid[1],
centroid[2], True)
dNodeProperties = ScreenShotHelper.saveSegmentDisplayProperties(
segmentationNode, segment)
segmentationNode.GetDisplayNode().SetAllSegmentsVisibility(
False)
ScreenShotHelper.setDisplayNodeProperties(segmentationNode,
segment,
properties={
'fill': True,
'outline': True,
'visible': True
})
if crosshairButton:
crosshairButton.crosshairNode.SetCrosshairRAS(centroid)
annotationNode = ScreenShotHelper.takeScreenShot(
"{}_Screenshot_{}_{}".format(segment.GetName(),
sliceNode.GetName(),
sliceNode.GetOrientation()),
"", widget)
segmentationNode.GetDisplayNode().SetAllSegmentsVisibility(
True)
ScreenShotHelper.setDisplayNodeProperties(
segmentationNode, segment, dNodeProperties)
annotationNodes.append(annotationNode)
if crosshairButton:
crosshairButton.checked = False
return annotationNodes[0] if len(
annotationNodes) == 1 else annotationNodes
def exportAsDICOMSEG(self, exportablesCollection):
"""Export the given node to a segmentation object and load it in the
DICOM database
This function was copied and modified from the EditUtil.py function of the same name in Slicer.
"""
if hasattr(slicer.modules, 'segmentations'):
exportable = exportablesCollection.GetItemAsObject(0)
subjectHierarchyNode = slicer.mrmlScene.GetNodeByID(
exportable.GetNodeID())
instanceUIDs = subjectHierarchyNode.GetAttribute(
"DICOM.ReferencedInstanceUIDs").split()
if instanceUIDs == "":
raise Exception(
"Editor master node does not have DICOM information")
# get the list of source DICOM files
inputDICOMImageFileNames = ""
for instanceUID in instanceUIDs:
inputDICOMImageFileNames += slicer.dicomDatabase.fileForInstance(
instanceUID) + ","
inputDICOMImageFileNames = inputDICOMImageFileNames[:
-1] # strip last comma
# save the per-structure volumes in the temp directory
inputSegmentationsFileNames = ""
import random # TODO: better way to generate temp file names?
import vtkITK
writer = vtkITK.vtkITKImageWriter()
rasToIJKMatrix = vtk.vtkMatrix4x4()
import vtkSegmentationCore
import vtkSlicerSegmentationsModuleLogic
logic = vtkSlicerSegmentationsModuleLogic.vtkSlicerSegmentationsModuleLogic(
)
segmentationNode = subjectHierarchyNode.GetAssociatedNode()
mergedSegmentationImageData = segmentationNode.GetImageData()
mergedSegmentationLabelmapNode = slicer.vtkMRMLLabelMapVolumeNode()
segmentationNode.GetRASToIJKMatrix(rasToIJKMatrix)
mergedSegmentationLabelmapNode.SetRASToIJKMatrix(rasToIJKMatrix)
mergedSegmentationLabelmapNode.SetAndObserveImageData(
mergedSegmentationImageData)
mergedSegmentationOrientedImageData = logic.CreateOrientedImageDataFromVolumeNode(
mergedSegmentationLabelmapNode)
segmentation = segmentationNode.GetSegmentation()
segmentIDs = vtk.vtkStringArray()
segmentation.GetSegmentIDs(segmentIDs)
segmentationName = segmentationNode.GetName()
for i in range(0, segmentIDs.GetNumberOfValues()):
segmentID = segmentIDs.GetValue(i)
segment = segmentation.GetSegment(segmentID)
segmentName = segment.GetName()
structureName = segmentName[len(segmentationName) + 1:-1 *
len('-label')]
structureFileName = structureName + str(
random.randint(0, vtk.VTK_INT_MAX)) + ".nrrd"
filePath = os.path.join(slicer.app.temporaryPath,
structureFileName)
writer.SetFileName(filePath)
segmentImageData = segment.GetRepresentation(
vtkSegmentationCore.vtkSegmentationConverter.
GetSegmentationBinaryLabelmapRepresentationName())
paddedImageData = vtkSegmentationCore.vtkOrientedImageData()
vtkSegmentationCore.vtkOrientedImageDataResample.PadImageToContainImage(
segmentImageData, mergedSegmentationOrientedImageData,
paddedImageData)
labelmapImageData = slicer.vtkMRMLLabelMapVolumeNode()
logic.CreateLabelmapVolumeFromOrientedImageData(
paddedImageData, labelmapImageData)
writer.SetInputDataObject(labelmapImageData.GetImageData())
labelmapImageData.GetRASToIJKMatrix(rasToIJKMatrix)
writer.SetRasToIJKMatrix(rasToIJKMatrix)
logging.debug("Saving to %s..." % filePath)
writer.Write()
inputSegmentationsFileNames += filePath + ","
inputSegmentationsFileNames = inputSegmentationsFileNames[:
-1] # strip last comma
# save the per-structure volumes label attributes
colorNode = segmentationNode.GetNodeReference('colorNodeID')
terminologyName = colorNode.GetAttribute("TerminologyName")
colorLogic = slicer.modules.colors.logic()
if not terminologyName or not colorLogic:
raise Exception(
"No terminology or color logic - cannot export")
inputLabelAttributesFileNames = ""
for i in range(0, segmentIDs.GetNumberOfValues()):
segmentID = segmentIDs.GetValue(i)
segment = segmentation.GetSegment(segmentID)
segmentName = segment.GetName()
structureName = segmentName[len(segmentationName) + 1:-1 *
len('-label')]
labelIndex = colorNode.GetColorIndexByName(structureName)
rgbColor = [
0,
] * 4
colorNode.GetColor(labelIndex, rgbColor)
rgbColor = map(lambda e: e * 255., rgbColor)
# get the attributes and convert to format CodeValue,CodeMeaning,CodingSchemeDesignator
# or empty strings if not defined
propertyCategoryWithColons = colorLogic.GetSegmentedPropertyCategory(
labelIndex, terminologyName)
if propertyCategoryWithColons == '':
logging.debug(
'ERROR: no segmented property category found for label ',
str(labelIndex))
# Try setting a default as this section is required
propertyCategory = "C94970,NCIt,Reference Region"
else:
propertyCategory = propertyCategoryWithColons.replace(
':', ',')
propertyTypeWithColons = colorLogic.GetSegmentedPropertyType(
labelIndex, terminologyName)
propertyType = propertyTypeWithColons.replace(':', ',')
propertyTypeModifierWithColons = colorLogic.GetSegmentedPropertyTypeModifier(
labelIndex, terminologyName)
propertyTypeModifier = propertyTypeModifierWithColons.replace(
':', ',')
anatomicRegionWithColons = colorLogic.GetAnatomicRegion(
labelIndex, terminologyName)
anatomicRegion = anatomicRegionWithColons.replace(':', ',')
anatomicRegionModifierWithColons = colorLogic.GetAnatomicRegionModifier(
labelIndex, terminologyName)
anatomicRegionModifier = anatomicRegionModifierWithColons.replace(
':', ',')
structureFileName = structureName + str(
random.randint(0, vtk.VTK_INT_MAX)) + ".info"
filePath = os.path.join(slicer.app.temporaryPath,
structureFileName)
# EncodeSEG is expecting a file of format:
# labelNum;SegmentedPropertyCategory:codeValue,codeScheme,codeMeaning;SegmentedPropertyType:v,m,s etc
attributes = "%d" % labelIndex
attributes += ";SegmentedPropertyCategory:" + propertyCategory
if propertyType != "":
attributes += ";SegmentedPropertyType:" + propertyType
if propertyTypeModifier != "":
attributes += ";SegmentedPropertyTypeModifier:" + propertyTypeModifier
if anatomicRegion != "":
attributes += ";AnatomicRegion:" + anatomicRegion
if anatomicRegionModifier != "":
attributes += ";AnatomicRegionModifier:" + anatomicRegionModifier
attributes += ";SegmentAlgorithmType:AUTOMATIC"
attributes += ";SegmentAlgorithmName:SlicerSelfTest"
attributes += ";RecommendedDisplayRGBValue:%g,%g,%g" % tuple(
rgbColor[:-1])
fp = open(filePath, "w")
fp.write(attributes)
fp.close()
logging.debug("filePath: %s", filePath)
logging.debug("attributes: %s", attributes)
inputLabelAttributesFileNames += filePath + ","
inputLabelAttributesFileNames = inputLabelAttributesFileNames[:
-1] # strip last comma'''
try:
user = os.environ['USER']
except KeyError:
user = "******"
segFileName = "editor_export.SEG" + str(
random.randint(0, vtk.VTK_INT_MAX)) + ".dcm"
segFilePath = os.path.join(slicer.app.temporaryPath, segFileName)
# TODO: define a way to set parameters like description
# TODO: determine a good series number automatically by looking in the database
parameters = {
"inputDICOMImageFileNames": inputDICOMImageFileNames,
"inputSegmentationsFileNames": inputSegmentationsFileNames,
"inputLabelAttributesFileNames": inputLabelAttributesFileNames,
"readerId": user,
"sessionId": "1",
"timePointId": "1",
"seriesDescription": "SlicerEditorSEGExport",
"seriesNumber": "100",
"instanceNumber": "1",
"bodyPart": "HEAD",
"algorithmDescriptionFileName": "Editor",
"outputSEGFileName": segFilePath,
"skipEmptySlices": False,
"compress": False,
}
encodeSEG = slicer.modules.encodeseg
cliNode = None
cliNode = slicer.cli.run(encodeSEG,
cliNode,
parameters,
delete_temporary_files=False)
waitCount = 0
while cliNode.IsBusy() and waitCount < 20:
slicer.util.delayDisplay(
"Running SEG Encoding... %d" % waitCount, 1000)
waitCount += 1
if cliNode.GetStatusString() != 'Completed':
raise Exception("encodeSEG CLI did not complete cleanly")
logging.info("Added segmentation to DICOM database (%s)",
segFilePath)
slicer.dicomDatabase.insert(segFilePath)
def processInteractionEvents(self, callerInteractor, eventId, viewWidget):
abortEvent = False
# Only allow for slice views
if viewWidget.className() != "qMRMLSliceWidget":
return abortEvent
if eventId == vtk.vtkCommand.LeftButtonPressEvent:
self.scriptedEffect.saveStateForUndo()
# Get master volume image data
import vtkSegmentationCorePython as vtkSegmentationCore
masterImageData = self.scriptedEffect.masterVolumeImageData()
selectedSegmentLabelmap = self.scriptedEffect.selectedSegmentLabelmap()
# Get modifier labelmap
modifierLabelmap = self.scriptedEffect.defaultModifierLabelmap()
xy = callerInteractor.GetEventPosition()
ijk = self.xyToIjk(xy, viewWidget, masterImageData)
pixelValue = masterImageData.GetScalarComponentAsFloat(ijk[0], ijk[1], ijk[2], 0)
useSegmentationAsStencil = False
try:
# This can be a long operation - indicate it to the user
qt.QApplication.setOverrideCursor(qt.Qt.WaitCursor)
# Perform thresholding
floodFillingFilter = vtk.vtkImageThresholdConnectivity()
floodFillingFilter.SetInputData(masterImageData)
seedPoints = vtk.vtkPoints()
origin = masterImageData.GetOrigin()
spacing = masterImageData.GetSpacing()
seedPoints.InsertNextPoint(origin[0]+ijk[0]*spacing[0], origin[1]+ijk[1]*spacing[1], origin[2]+ijk[2]*spacing[2])
floodFillingFilter.SetSeedPoints(seedPoints)
maskImageData = vtkSegmentationCore.vtkOrientedImageData()
intensityBasedMasking = self.scriptedEffect.parameterSetNode().GetMasterVolumeIntensityMask()
segmentationNode = self.scriptedEffect.parameterSetNode().GetSegmentationNode()
success = segmentationNode.GenerateEditMask(maskImageData,
self.scriptedEffect.parameterSetNode().GetMaskMode(),
masterImageData, # reference geometry
self.scriptedEffect.parameterSetNode().GetSelectedSegmentID(),
self.scriptedEffect.parameterSetNode().GetMaskSegmentID() if self.scriptedEffect.parameterSetNode().GetMaskSegmentID() else "",
masterImageData if intensityBasedMasking else None,
self.scriptedEffect.parameterSetNode().GetMasterVolumeIntensityMaskRange() if intensityBasedMasking else None)
if success:
stencil = vtk.vtkImageToImageStencil()
stencil.SetInputData(maskImageData)
stencil.ThresholdByLower(0)
stencil.Update()
floodFillingFilter.SetStencilData(stencil.GetOutput())
else:
logging.error("Failed to create edit mask")
neighborhoodSizeMm = self.neighborhoodSizeMmSlider.value
floodFillingFilter.SetNeighborhoodRadius(neighborhoodSizeMm,neighborhoodSizeMm,neighborhoodSizeMm)
floodFillingFilter.SetNeighborhoodFraction(0.5)
if useSegmentationAsStencil:
stencilFilter = vtk.vtkImageToImageStencil()
stencilFilter.SetInputData(selectedSegmentLabelmap)
stencilFilter.ThresholdByLower(0)
stencilFilter.Update()
floodFillingFilter.SetStencilData(stencilFilter.GetOutput())
pixelValueTolerance = float(self.intensityToleranceSlider.value)
floodFillingFilter.ThresholdBetween(pixelValue-pixelValueTolerance, pixelValue+pixelValueTolerance)
floodFillingFilter.SetInValue(1)
floodFillingFilter.SetOutValue(0)
floodFillingFilter.Update()
modifierLabelmap.DeepCopy(floodFillingFilter.GetOutput())
except IndexError:
logging.error('apply: Failed to threshold master volume!')
finally:
qt.QApplication.restoreOverrideCursor()
# Apply changes
self.scriptedEffect.modifySelectedSegmentByLabelmap(modifierLabelmap, slicer.qSlicerSegmentEditorAbstractEffect.ModificationModeAdd)
abortEvent = True
return abortEvent
def computeStatistics(self, segmentID):
import vtkSegmentationCorePython as vtkSegmentationCore
requestedKeys = self.getRequestedKeys()
segmentationNode = slicer.mrmlScene.GetNodeByID(self.getParameterNode().GetParameter("Segmentation"))
grayscaleNode = slicer.mrmlScene.GetNodeByID(self.getParameterNode().GetParameter("ScalarVolume"))
if len(requestedKeys)==0:
return {}
containsLabelmapRepresentation = segmentationNode.GetSegmentation().ContainsRepresentation(
vtkSegmentationCore.vtkSegmentationConverter.GetSegmentationBinaryLabelmapRepresentationName())
if not containsLabelmapRepresentation:
return {}
if grayscaleNode is None or grayscaleNode.GetImageData() is None:
return {}
# Get geometry of grayscale volume node as oriented image data
# reference geometry in reference node coordinate system
referenceGeometry_Reference = vtkSegmentationCore.vtkOrientedImageData()
referenceGeometry_Reference.SetExtent(grayscaleNode.GetImageData().GetExtent())
ijkToRasMatrix = vtk.vtkMatrix4x4()
grayscaleNode.GetIJKToRASMatrix(ijkToRasMatrix)
referenceGeometry_Reference.SetGeometryFromImageToWorldMatrix(ijkToRasMatrix)
# Get transform between grayscale volume and segmentation
segmentationToReferenceGeometryTransform = vtk.vtkGeneralTransform()
slicer.vtkMRMLTransformNode.GetTransformBetweenNodes(segmentationNode.GetParentTransformNode(),
grayscaleNode.GetParentTransformNode(), segmentationToReferenceGeometryTransform)
cubicMMPerVoxel = reduce(lambda x,y: x*y, referenceGeometry_Reference.GetSpacing())
ccPerCubicMM = 0.001
segment = segmentationNode.GetSegmentation().GetSegment(segmentID)
segBinaryLabelName = vtkSegmentationCore.vtkSegmentationConverter.GetSegmentationBinaryLabelmapRepresentationName()
segmentLabelmap = segment.GetRepresentation(segBinaryLabelName)
segmentLabelmap_Reference = vtkSegmentationCore.vtkOrientedImageData()
vtkSegmentationCore.vtkOrientedImageDataResample.ResampleOrientedImageToReferenceOrientedImage(
segmentLabelmap, referenceGeometry_Reference, segmentLabelmap_Reference,
False, # nearest neighbor interpolation
False, # no padding
segmentationToReferenceGeometryTransform)
# 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(segmentLabelmap_Reference)
thresh.ThresholdByLower(0)
thresh.SetInValue(backgroundValue)
thresh.SetOutValue(labelValue)
thresh.SetOutputScalarType(vtk.VTK_UNSIGNED_CHAR)
thresh.Update()
# Use binary labelmap as a stencil
stencil = vtk.vtkImageToImageStencil()
stencil.SetInputData(thresh.GetOutput())
stencil.ThresholdByUpper(labelValue)
stencil.Update()
stat = vtk.vtkImageAccumulate()
stat.SetInputData(grayscaleNode.GetImageData())
stat.SetStencilData(stencil.GetOutput())
stat.Update()
# create statistics list
stats = {}
if "voxel_count" in requestedKeys:
stats["voxel_count"] = stat.GetVoxelCount()
if "volume_mm3" in requestedKeys:
stats["volume_mm3"] = stat.GetVoxelCount() * cubicMMPerVoxel
if "volume_cm3" in requestedKeys:
stats["volume_cm3"] = stat.GetVoxelCount() * cubicMMPerVoxel * ccPerCubicMM
if stat.GetVoxelCount()>0:
if "min" in requestedKeys:
stats["min"] = stat.GetMin()[0]
if "max" in requestedKeys:
stats["max"] = stat.GetMax()[0]
if "mean" in requestedKeys:
stats["mean"] = stat.GetMean()[0]
if "stdev" in requestedKeys:
stats["stdev"] = stat.GetStandardDeviation()[0]
return stats
def TestSection_03_qMRMLSegmentationGeometryWidget(self):
logging.info('Test section 2: qMRMLSegmentationGeometryWidget')
import vtkSegmentationCore
binaryLabelmapReprName = vtkSegmentationCore.vtkSegmentationConverter.GetBinaryLabelmapRepresentationName(
)
closedSurfaceReprName = vtkSegmentationCore.vtkSegmentationConverter.GetClosedSurfaceRepresentationName(
)
# Use MRHead and Tinypatient for testing
import SampleData
mrVolumeNode = SampleData.downloadSample("MRHead")
[tinyVolumeNode,
tinySegmentationNode] = SampleData.downloadSamples('TinyPatient')
# Convert MRHead to oriented image data
import vtkSlicerSegmentationsModuleLogicPython as vtkSlicerSegmentationsModuleLogic
mrOrientedImageData = vtkSlicerSegmentationsModuleLogic.vtkSlicerSegmentationsModuleLogic.CreateOrientedImageDataFromVolumeNode(
mrVolumeNode)
mrOrientedImageData.UnRegister(None)
# Create segmentation node with binary labelmap master and one segment with MRHead geometry
segmentationNode = slicer.mrmlScene.AddNewNodeByClass(
'vtkMRMLSegmentationNode')
segmentationNode.GetSegmentation().SetMasterRepresentationName(
binaryLabelmapReprName)
geometryStr = vtkSegmentationCore.vtkSegmentationConverter.SerializeImageGeometry(
mrOrientedImageData)
segmentationNode.GetSegmentation().SetConversionParameter(
vtkSegmentationCore.vtkSegmentationConverter.
GetReferenceImageGeometryParameterName(), geometryStr)
threshold = vtk.vtkImageThreshold()
threshold.SetInputData(mrOrientedImageData)
threshold.ThresholdByUpper(16.0)
threshold.SetInValue(1)
threshold.SetOutValue(0)
threshold.SetOutputScalarType(vtk.VTK_UNSIGNED_CHAR)
threshold.Update()
segmentOrientedImageData = vtkSegmentationCore.vtkOrientedImageData()
segmentOrientedImageData.DeepCopy(threshold.GetOutput())
mrImageToWorldMatrix = vtk.vtkMatrix4x4()
mrOrientedImageData.GetImageToWorldMatrix(mrImageToWorldMatrix)
segmentOrientedImageData.SetImageToWorldMatrix(mrImageToWorldMatrix)
segment = vtkSegmentationCore.vtkSegment()
segment.SetName('Brain')
segment.SetColor(0.0, 0.0, 1.0)
segment.AddRepresentation(binaryLabelmapReprName,
segmentOrientedImageData)
segmentationNode.GetSegmentation().AddSegment(segment)
# Create geometry widget
geometryWidget = slicer.qMRMLSegmentationGeometryWidget()
geometryWidget.setSegmentationNode(segmentationNode)
geometryWidget.editEnabled = True
geometryImageData = vtkSegmentationCore.vtkOrientedImageData(
) # To contain the output later
# Volume source with no transforms
geometryWidget.setSourceNode(tinyVolumeNode)
geometryWidget.geometryImageData(geometryImageData)
self.assertTrue(
self.compareOutputGeometry(
geometryImageData, (49, 49, 23), (248.8439, 248.2890, -123.75),
[[-1.0, 0.0, 0.0], [0.0, -1.0, 0.0], [0.0, 0.0, 1.0]]))
vtkSegmentationCore.vtkOrientedImageDataResample.ResampleOrientedImageToReferenceOrientedImage(
segmentOrientedImageData, geometryImageData, geometryImageData,
False, True)
self.assertEqual(self.getForegroundVoxelCount(geometryImageData), 92)
# Transformed volume source
translationTransformMatrix = vtk.vtkMatrix4x4()
translationTransformMatrix.SetElement(0, 3, 24.5)
translationTransformMatrix.SetElement(1, 3, 24.5)
translationTransformMatrix.SetElement(2, 3, 11.5)
translationTransformNode = slicer.vtkMRMLLinearTransformNode()
translationTransformNode.SetName('TestTranslation')
slicer.mrmlScene.AddNode(translationTransformNode)
translationTransformNode.SetMatrixTransformToParent(
translationTransformMatrix)
tinyVolumeNode.SetAndObserveTransformNodeID(
translationTransformNode.GetID())
geometryWidget.geometryImageData(geometryImageData)
self.assertTrue(
self.compareOutputGeometry(
geometryImageData, (49, 49, 23), (224.3439, 223.7890, -135.25),
[[-1.0, 0.0, 0.0], [0.0, -1.0, 0.0], [0.0, 0.0, 1.0]]))
vtkSegmentationCore.vtkOrientedImageDataResample.ResampleOrientedImageToReferenceOrientedImage(
segmentOrientedImageData, geometryImageData, geometryImageData,
False, True)
self.assertEqual(self.getForegroundVoxelCount(geometryImageData), 94)
# Volume source with isotropic spacing
tinyVolumeNode.SetAndObserveTransformNodeID(None)
geometryWidget.setIsotropicSpacing(True)
geometryWidget.geometryImageData(geometryImageData)
self.assertTrue(
self.compareOutputGeometry(
geometryImageData, (23, 23, 23), (248.8439, 248.2890, -123.75),
[[-1.0, 0.0, 0.0], [0.0, -1.0, 0.0], [0.0, 0.0, 1.0]]))
vtkSegmentationCore.vtkOrientedImageDataResample.ResampleOrientedImageToReferenceOrientedImage(
segmentOrientedImageData, geometryImageData, geometryImageData,
False, True)
self.assertEqual(self.getForegroundVoxelCount(geometryImageData), 414)
# Volume source with oversampling
geometryWidget.setIsotropicSpacing(False)
geometryWidget.setOversamplingFactor(2.0)
geometryWidget.geometryImageData(geometryImageData)
self.assertTrue(
self.compareOutputGeometry(
geometryImageData, (24.5, 24.5, 11.5),
(261.0939, 260.5390, -129.5),
[[-1.0, 0.0, 0.0], [0.0, -1.0, 0.0], [0.0, 0.0, 1.0]]))
vtkSegmentationCore.vtkOrientedImageDataResample.ResampleOrientedImageToReferenceOrientedImage(
segmentOrientedImageData, geometryImageData, geometryImageData,
False, True)
self.assertEqual(self.getForegroundVoxelCount(geometryImageData), 751)
slicer.util.delayDisplay('Volume source cases - OK')
# Segmentation source with binary labelmap master
geometryWidget.setOversamplingFactor(1.0)
geometryWidget.setSourceNode(tinySegmentationNode)
geometryWidget.geometryImageData(geometryImageData)
self.assertTrue(
self.compareOutputGeometry(
geometryImageData, (49, 49, 23), (248.8439, 248.2890, -123.75),
[[-1.0, 0.0, 0.0], [0.0, -1.0, 0.0], [0.0, 0.0, 1.0]]))
vtkSegmentationCore.vtkOrientedImageDataResample.ResampleOrientedImageToReferenceOrientedImage(
segmentOrientedImageData, geometryImageData, geometryImageData,
False, True)
self.assertEqual(self.getForegroundVoxelCount(geometryImageData), 92)
# Segmentation source with closed surface master
tinySegmentationNode.GetSegmentation().SetConversionParameter(
'Smoothing factor', '0.0')
self.assertTrue(
tinySegmentationNode.GetSegmentation().CreateRepresentation(
closedSurfaceReprName))
tinySegmentationNode.GetSegmentation().SetMasterRepresentationName(
closedSurfaceReprName)
tinySegmentationNode.Modified(
) # Trigger re-calculation of geometry (only generic Modified event is observed)
geometryWidget.geometryImageData(geometryImageData)
self.assertTrue(
self.compareOutputGeometry(
geometryImageData, (1, 1, 1), (-167.156, -217.711, -135.75),
[[0.0, 0.0, 1.0], [-1.0, 0.0, 0.0], [0.0, -1.0, 0.0]]))
vtkSegmentationCore.vtkOrientedImageDataResample.ResampleOrientedImageToReferenceOrientedImage(
segmentOrientedImageData, geometryImageData, geometryImageData,
False, True)
self.assertEqual(self.getForegroundVoxelCount(geometryImageData),
5223846)
slicer.util.delayDisplay('Segmentation source cases - OK')
# Model source with no transform
shNode = slicer.vtkMRMLSubjectHierarchyNode.GetSubjectHierarchyNode(
slicer.mrmlScene)
outputFolderId = shNode.CreateFolderItem(shNode.GetSceneItemID(),
'ModelsFolder')
success = vtkSlicerSegmentationsModuleLogic.vtkSlicerSegmentationsModuleLogic.ExportVisibleSegmentsToModels(
tinySegmentationNode, outputFolderId)
self.assertTrue(success)
modelNode = slicer.util.getNode('Body_Contour')
geometryWidget.setSourceNode(modelNode)
geometryWidget.geometryImageData(geometryImageData)
self.assertTrue(
self.compareOutputGeometry(
geometryImageData, (1, 1, 1), (-167.156, -217.711, -135.75),
[[0.0, 0.0, 1.0], [-1.0, 0.0, 0.0], [0.0, -1.0, 0.0]]))
vtkSegmentationCore.vtkOrientedImageDataResample.ResampleOrientedImageToReferenceOrientedImage(
segmentOrientedImageData, geometryImageData, geometryImageData,
False, True)
self.assertEqual(self.getForegroundVoxelCount(geometryImageData),
5223846)
# Transformed model source
rotationTransform = vtk.vtkTransform()
rotationTransform.RotateX(45)
rotationTransformMatrix = vtk.vtkMatrix4x4()
rotationTransform.GetMatrix(rotationTransformMatrix)
rotationTransformNode = slicer.vtkMRMLLinearTransformNode()
rotationTransformNode.SetName('TestRotation')
slicer.mrmlScene.AddNode(rotationTransformNode)
rotationTransformNode.SetMatrixTransformToParent(
rotationTransformMatrix)
modelNode.SetAndObserveTransformNodeID(rotationTransformNode.GetID())
modelNode.Modified()
geometryWidget.geometryImageData(geometryImageData)
self.assertTrue(
self.compareOutputGeometry(
geometryImageData, (1, 1, 1), (-167.156, -58.6623, -249.228),
[[0.0, 0.0, 1.0], [-0.7071, -0.7071, 0.0],
[0.7071, -0.7071, 0.0]]))
vtkSegmentationCore.vtkOrientedImageDataResample.ResampleOrientedImageToReferenceOrientedImage(
segmentOrientedImageData, geometryImageData, geometryImageData,
False, True)
self.assertEqual(self.getForegroundVoxelCount(geometryImageData),
5221241)
# ROI source
roiNode = slicer.vtkMRMLAnnotationROINode()
roiNode.SetName('SourceROI')
slicer.mrmlScene.AddNode(roiNode)
roiNode.UnRegister(None)
xyz = [0] * 3
center = [0] * 3
slicer.vtkMRMLSliceLogic.GetVolumeRASBox(tinyVolumeNode, xyz, center)
radius = [x / 2.0 for x in xyz]
roiNode.SetXYZ(center)
roiNode.SetRadiusXYZ(radius)
geometryWidget.setSourceNode(roiNode)
geometryWidget.geometryImageData(geometryImageData)
self.assertTrue(
self.compareOutputGeometry(
geometryImageData, (1, 1, 1), (-216.156, -217.711, -135.75),
[[0.0, 0.0, 1.0], [-1.0, 0.0, 0.0], [0.0, -1.0, 0.0]]))
vtkSegmentationCore.vtkOrientedImageDataResample.ResampleOrientedImageToReferenceOrientedImage(
segmentOrientedImageData, geometryImageData, geometryImageData,
False, True)
self.assertEqual(self.getForegroundVoxelCount(geometryImageData),
5223846)
slicer.util.delayDisplay('Model and ROI source cases - OK')
slicer.util.delayDisplay('Segmentation geometry widget test passed')
def splitSegments(self, minimumSize = 0, maxNumberOfSegments = 0, split = True):
"""
minimumSize: if 0 then it means that all islands are kept, regardless of size
maxNumberOfSegments: if 0 then it means that all islands are kept, regardless of how many
"""
# This can be a long operation - indicate it to the user
qt.QApplication.setOverrideCursor(qt.Qt.WaitCursor)
self.scriptedEffect.saveStateForUndo()
# Get modifier labelmap
selectedSegmentLabelmap = self.scriptedEffect.selectedSegmentLabelmap()
castIn = vtk.vtkImageCast()
castIn.SetInputData(selectedSegmentLabelmap)
castIn.SetOutputScalarTypeToUnsignedInt()
# Identify the islands in the inverted volume and
# find the pixel that corresponds to the background
islandMath = vtkITK.vtkITKIslandMath()
islandMath.SetInputConnection(castIn.GetOutputPort())
islandMath.SetFullyConnected(False)
islandMath.SetMinimumSize(minimumSize)
islandMath.Update()
# Create a separate image for the first (largest) island
labelValue = 1
backgroundValue = 0
thresh = vtk.vtkImageThreshold()
if split:
thresh.ThresholdBetween(1, 1)
else:
if maxNumberOfSegments != 0:
thresh.ThresholdBetween(1, maxNumberOfSegments)
else:
thresh.ThresholdByUpper(1)
thresh.SetInputData(islandMath.GetOutput())
thresh.SetOutValue(backgroundValue)
thresh.SetInValue(labelValue)
thresh.SetOutputScalarType(selectedSegmentLabelmap.GetScalarType())
thresh.Update()
# Create oriented image data from output
import vtkSegmentationCorePython as vtkSegmentationCore
largestIslandImage = vtkSegmentationCore.vtkOrientedImageData()
largestIslandImage.ShallowCopy(thresh.GetOutput())
selectedSegmentLabelmapImageToWorldMatrix = vtk.vtkMatrix4x4()
selectedSegmentLabelmap.GetImageToWorldMatrix(selectedSegmentLabelmapImageToWorldMatrix)
largestIslandImage.SetImageToWorldMatrix(selectedSegmentLabelmapImageToWorldMatrix)
if split and (maxNumberOfSegments != 1):
thresh2 = vtk.vtkImageThreshold()
# 0 is background, 1 is largest island; we need label 2 and higher
if maxNumberOfSegments != 0:
thresh2.ThresholdBetween(2, maxNumberOfSegments)
else:
thresh2.ThresholdByUpper(2)
thresh2.SetInputData(islandMath.GetOutput())
thresh2.SetOutValue(backgroundValue)
thresh2.ReplaceInOff()
thresh2.Update()
islandCount = islandMath.GetNumberOfIslands()
islandOrigCount = islandMath.GetOriginalNumberOfIslands()
ignoredIslands = islandOrigCount - islandCount
logging.info( "%d islands created (%d ignored)" % (islandCount, ignoredIslands) )
# Create oriented image data from output
import vtkSegmentationCorePython as vtkSegmentationCore
multiLabelImage = vtkSegmentationCore.vtkOrientedImageData()
multiLabelImage.DeepCopy(thresh2.GetOutput())
selectedSegmentLabelmapImageToWorldMatrix = vtk.vtkMatrix4x4()
selectedSegmentLabelmap.GetImageToWorldMatrix(selectedSegmentLabelmapImageToWorldMatrix)
multiLabelImage.SetGeometryFromImageToWorldMatrix(selectedSegmentLabelmapImageToWorldMatrix)
# Import multi-label labelmap to segmentation
segmentationNode = self.scriptedEffect.parameterSetNode().GetSegmentationNode()
selectedSegmentID = self.scriptedEffect.parameterSetNode().GetSelectedSegmentID()
selectedSegmentIndex = segmentationNode.GetSegmentation().GetSegmentIndex(selectedSegmentID)
insertBeforeSegmentID = segmentationNode.GetSegmentation().GetNthSegmentID(selectedSegmentIndex + 1)
selectedSegmentName = segmentationNode.GetSegmentation().GetSegment(selectedSegmentID).GetName()
slicer.vtkSlicerSegmentationsModuleLogic.ImportLabelmapToSegmentationNode( \
multiLabelImage, segmentationNode, selectedSegmentName+" -", insertBeforeSegmentID )
self.scriptedEffect.modifySelectedSegmentByLabelmap(largestIslandImage, slicer.qSlicerSegmentEditorAbstractEffect.ModificationModeSet)
qt.QApplication.restoreOverrideCursor()
def TestSection_1_AddRemoveSegment(self):
# Add/remove segment from segmentation (check display properties, color table, etc.)
logging.info('Test section 1: Add/remove segment')
# Get baseline values
displayNode = self.inputSegmentationNode.GetDisplayNode()
self.assertIsNotNone(displayNode)
# If segments are not found then the returned color is the pre-defined invalid color
bodyColor = self.inputSegmentationNode.GetSegmentation().GetSegment(
'Body_Contour').GetColor()
logging.info("bodyColor: {0}".format(bodyColor))
self.assertEqual(int(bodyColor[0] * 100), 33)
self.assertEqual(int(bodyColor[1] * 100), 66)
self.assertEqual(int(bodyColor[2] * 100), 0)
tumorColor = self.inputSegmentationNode.GetSegmentation().GetSegment(
'Tumor_Contour').GetColor()
logging.info("tumorColor: {0}".format(tumorColor))
self.assertEqual(int(tumorColor[0] * 100), 100)
self.assertEqual(int(tumorColor[1] * 100), 0)
self.assertEqual(int(tumorColor[2] * 100), 0)
# Create new segment
sphere = vtk.vtkSphereSource()
sphere.SetCenter(0, 50, 0)
sphere.SetRadius(50)
sphere.Update()
spherePolyData = vtk.vtkPolyData()
spherePolyData.DeepCopy(sphere.GetOutput())
self.sphereSegment = vtkSegmentationCore.vtkSegment()
self.sphereSegment.SetName(self.sphereSegmentName)
self.sphereSegment.SetColor(0.0, 0.0, 1.0)
self.sphereSegment.AddRepresentation(self.closedSurfaceReprName,
spherePolyData)
# Add segment to segmentation
self.inputSegmentationNode.GetSegmentation().AddSegment(
self.sphereSegment)
self.assertEqual(
self.inputSegmentationNode.GetSegmentation().GetNumberOfSegments(),
3)
# Check merged labelmap
mergedLabelmap = vtkSegmentationCore.vtkOrientedImageData()
self.inputSegmentationNode.GetSegmentation().CreateRepresentation(
self.binaryLabelmapReprName)
self.inputSegmentationNode.GenerateMergedLabelmapForAllSegments(
mergedLabelmap, 0)
imageStat = vtk.vtkImageAccumulate()
imageStat.SetInputData(mergedLabelmap)
imageStat.SetComponentExtent(0, 4, 0, 0, 0, 0)
imageStat.SetComponentOrigin(0, 0, 0)
imageStat.SetComponentSpacing(1, 1, 1)
imageStat.Update()
self.assertEqual(imageStat.GetVoxelCount(), 1000)
imageStatResult = imageStat.GetOutput()
for i in range(4):
logging.info("Volume {0}: {1}".format(
i, imageStatResult.GetScalarComponentAsDouble(i, 0, 0, 0)))
self.assertEqual(
imageStatResult.GetScalarComponentAsDouble(0, 0, 0, 0), 795)
self.assertEqual(
imageStatResult.GetScalarComponentAsDouble(1, 0, 0, 0), 194)
self.assertEqual(
imageStatResult.GetScalarComponentAsDouble(2, 0, 0, 0), 4)
self.assertEqual(
imageStatResult.GetScalarComponentAsDouble(3, 0, 0, 0), 7)
# Check if segment reorder is taken into account in merged labelmap generation
# Change segment order
sphereSegmentId = self.inputSegmentationNode.GetSegmentation(
).GetSegmentIdBySegment(self.sphereSegment)
self.inputSegmentationNode.GetSegmentation().SetSegmentIndex(
sphereSegmentId, 1)
# Re-generate merged labelmap
self.inputSegmentationNode.GenerateMergedLabelmapForAllSegments(
mergedLabelmap, 0)
imageStat.SetInputData(mergedLabelmap)
imageStat.Update()
self.assertEqual(imageStat.GetVoxelCount(), 1000)
imageStatResult = imageStat.GetOutput()
for i in range(4):
logging.info("Volume {0}: {1}".format(
i, imageStatResult.GetScalarComponentAsDouble(i, 0, 0, 0)))
self.assertEqual(
imageStatResult.GetScalarComponentAsDouble(0, 0, 0, 0), 795)
self.assertEqual(
imageStatResult.GetScalarComponentAsDouble(1, 0, 0, 0), 194)
self.assertEqual(
imageStatResult.GetScalarComponentAsDouble(2, 0, 0, 0), 6)
self.assertEqual(
imageStatResult.GetScalarComponentAsDouble(3, 0, 0, 0), 5)
# Remove segment from segmentation
self.inputSegmentationNode.GetSegmentation().RemoveSegment(
self.sphereSegmentName)
self.assertEqual(
self.inputSegmentationNode.GetSegmentation().GetNumberOfSegments(),
2)
def TestSection_2_MergeLabelmapWithDifferentGeometries(self):
# Merge labelmap when segments containing labelmaps with different geometries (both same directions, different directions)
logging.info(
'Test section 2: Merge labelmap with different geometries')
self.assertIsNotNone(self.sphereSegment)
self.sphereSegment.RemoveRepresentation(self.binaryLabelmapReprName)
self.assertIsNone(
self.sphereSegment.GetRepresentation(self.binaryLabelmapReprName))
# Create new segmentation with sphere segment
self.secondSegmentationNode = slicer.vtkMRMLSegmentationNode()
self.secondSegmentationNode.SetName('Second')
self.secondSegmentationNode.GetSegmentation(
).SetMasterRepresentationName(self.binaryLabelmapReprName)
slicer.mrmlScene.AddNode(self.secondSegmentationNode)
self.secondSegmentationNode.GetSegmentation().AddSegment(
self.sphereSegment)
# Check automatically converted labelmap. It is supposed to have the default geometry
# (which is different than the one in the input segmentation)
sphereLabelmap = self.sphereSegment.GetRepresentation(
self.binaryLabelmapReprName)
self.assertIsNotNone(sphereLabelmap)
sphereLabelmapSpacing = sphereLabelmap.GetSpacing()
self.assertTrue(sphereLabelmapSpacing[0] == 1.0
and sphereLabelmapSpacing[1] == 1.0
and sphereLabelmapSpacing[2] == 1.0)
# Create binary labelmap in segmentation that will create the merged labelmap from
# different geometries so that labelmap is not removed from sphere segment when adding
self.inputSegmentationNode.GetSegmentation().CreateRepresentation(
self.binaryLabelmapReprName)
# Copy segment to input segmentation
self.inputSegmentationNode.GetSegmentation(
).CopySegmentFromSegmentation(
self.secondSegmentationNode.GetSegmentation(),
self.sphereSegmentName)
self.assertEqual(
self.inputSegmentationNode.GetSegmentation().GetNumberOfSegments(),
3)
# Check merged labelmap
# Reference geometry has the tiny patient spacing, and it is oversampled to have smimilar
# voxel size as the sphere labelmap with the uniform 1mm spacing
mergedLabelmap = vtkSegmentationCore.vtkOrientedImageData()
self.inputSegmentationNode.GenerateMergedLabelmapForAllSegments(
mergedLabelmap, 0)
mergedLabelmapSpacing = mergedLabelmap.GetSpacing()
self.assertAlmostEqual(mergedLabelmapSpacing[0], 1.2894736842, 8)
self.assertAlmostEqual(mergedLabelmapSpacing[1], 1.2894736842, 8)
self.assertAlmostEqual(mergedLabelmapSpacing[2], 0.6052631578, 8)
imageStat = vtk.vtkImageAccumulate()
imageStat.SetInputData(mergedLabelmap)
imageStat.SetComponentExtent(0, 5, 0, 0, 0, 0)
imageStat.SetComponentOrigin(0, 0, 0)
imageStat.SetComponentSpacing(1, 1, 1)
imageStat.Update()
self.assertEqual(imageStat.GetVoxelCount(), 54872000)
imageStatResult = imageStat.GetOutput()
for i in range(5):
logging.info("Volume {0}: {1}".format(
i, imageStatResult.GetScalarComponentAsDouble(i, 0, 0, 0)))
self.assertEqual(
imageStatResult.GetScalarComponentAsDouble(0, 0, 0, 0), 43573723)
self.assertEqual(
imageStatResult.GetScalarComponentAsDouble(1, 0, 0, 0), 10601312)
self.assertEqual(
imageStatResult.GetScalarComponentAsDouble(2, 0, 0, 0), 251476)
self.assertEqual(
imageStatResult.GetScalarComponentAsDouble(3, 0, 0, 0), 445489)
self.assertEqual(
imageStatResult.GetScalarComponentAsDouble(4, 0, 0, 0), 0
) # Built from color table and color four is removed in previous test section
def addGrayscaleVolumeStatistics(self):
import vtkSegmentationCorePython as vtkSegmentationCore
containsLabelmapRepresentation = self.segmentationNode.GetSegmentation(
).ContainsRepresentation(
vtkSegmentationCore.vtkSegmentationConverter.
GetSegmentationBinaryLabelmapRepresentationName())
if not containsLabelmapRepresentation:
return
if self.grayscaleNode is None or self.grayscaleNode.GetImageData(
) is None:
return
# Get geometry of grayscale volume node as oriented image data
referenceGeometry_Reference = vtkSegmentationCore.vtkOrientedImageData(
) # reference geometry in reference node coordinate system
referenceGeometry_Reference.SetExtent(
self.grayscaleNode.GetImageData().GetExtent())
ijkToRasMatrix = vtk.vtkMatrix4x4()
self.grayscaleNode.GetIJKToRASMatrix(ijkToRasMatrix)
referenceGeometry_Reference.SetGeometryFromImageToWorldMatrix(
ijkToRasMatrix)
# Get transform between grayscale volume and segmentation
segmentationToReferenceGeometryTransform = vtk.vtkGeneralTransform()
slicer.vtkMRMLTransformNode.GetTransformBetweenNodes(
self.segmentationNode.GetParentTransformNode(),
self.grayscaleNode.GetParentTransformNode(),
segmentationToReferenceGeometryTransform)
cubicMMPerVoxel = reduce(lambda x, y: x * y,
referenceGeometry_Reference.GetSpacing())
ccPerCubicMM = 0.001
for segmentID in self.statistics["SegmentIDs"]:
segment = self.segmentationNode.GetSegmentation().GetSegment(
segmentID)
segmentLabelmap = segment.GetRepresentation(
vtkSegmentationCore.vtkSegmentationConverter.
GetSegmentationBinaryLabelmapRepresentationName())
segmentLabelmap_Reference = vtkSegmentationCore.vtkOrientedImageData(
)
vtkSegmentationCore.vtkOrientedImageDataResample.ResampleOrientedImageToReferenceOrientedImage(
segmentLabelmap,
referenceGeometry_Reference,
segmentLabelmap_Reference,
False, # nearest neighbor interpolation
False, # no padding
segmentationToReferenceGeometryTransform)
# 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(segmentLabelmap_Reference)
thresh.ThresholdByLower(0)
thresh.SetInValue(backgroundValue)
thresh.SetOutValue(labelValue)
thresh.SetOutputScalarType(vtk.VTK_UNSIGNED_CHAR)
thresh.Update()
# Use binary labelmap as a stencil
stencil = vtk.vtkImageToImageStencil()
stencil.SetInputData(thresh.GetOutput())
stencil.ThresholdByUpper(labelValue)
stencil.Update()
stat = vtk.vtkImageAccumulate()
stat.SetInputData(self.grayscaleNode.GetImageData())
stat.SetStencilData(stencil.GetOutput())
stat.Update()
# Add data to statistics list
self.statistics[segmentID, "GS voxel count"] = stat.GetVoxelCount()
self.statistics[
segmentID,
"GS volume mm3"] = stat.GetVoxelCount() * cubicMMPerVoxel
self.statistics[segmentID, "GS volume cc"] = stat.GetVoxelCount(
) * cubicMMPerVoxel * ccPerCubicMM
if stat.GetVoxelCount() > 0:
self.statistics[segmentID, "GS min"] = stat.GetMin()[0]
self.statistics[segmentID, "GS max"] = stat.GetMax()[0]
self.statistics[segmentID, "GS mean"] = stat.GetMean()[0]
self.statistics[segmentID,
"GS stdev"] = stat.GetStandardDeviation()[0]
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 getStencilForVolume(self, segmentationNode, segmentID, grayscaleNode):
import vtkSegmentationCorePython as vtkSegmentationCore
containsLabelmapRepresentation = segmentationNode.GetSegmentation(
).ContainsRepresentation(
vtkSegmentationCore.vtkSegmentationConverter.
GetSegmentationBinaryLabelmapRepresentationName())
if not containsLabelmapRepresentation:
return None
if (not grayscaleNode or not grayscaleNode.GetImageData()
or not grayscaleNode.GetImageData().GetPointData() or
not grayscaleNode.GetImageData().GetPointData().GetScalars()):
# Input grayscale node does not contain valid image data
return None
# Get geometry of grayscale volume node as oriented image data
# reference geometry in reference node coordinate system
referenceGeometry_Reference = vtkSegmentationCore.vtkOrientedImageData(
)
referenceGeometry_Reference.SetExtent(
grayscaleNode.GetImageData().GetExtent())
ijkToRasMatrix = vtk.vtkMatrix4x4()
grayscaleNode.GetIJKToRASMatrix(ijkToRasMatrix)
referenceGeometry_Reference.SetGeometryFromImageToWorldMatrix(
ijkToRasMatrix)
# Get transform between grayscale volume and segmentation
segmentationToReferenceGeometryTransform = vtk.vtkGeneralTransform()
slicer.vtkMRMLTransformNode.GetTransformBetweenNodes(
segmentationNode.GetParentTransformNode(),
grayscaleNode.GetParentTransformNode(),
segmentationToReferenceGeometryTransform)
segmentLabelmap = vtkSegmentationCore.vtkOrientedImageData()
segmentationNode.GetBinaryLabelmapRepresentation(
segmentID, segmentLabelmap)
if (not segmentLabelmap or not segmentLabelmap.GetPointData()
or not segmentLabelmap.GetPointData().GetScalars()):
# No input label data
return None
segmentLabelmap_Reference = vtkSegmentationCore.vtkOrientedImageData()
vtkSegmentationCore.vtkOrientedImageDataResample.ResampleOrientedImageToReferenceOrientedImage(
segmentLabelmap,
referenceGeometry_Reference,
segmentLabelmap_Reference,
False, # nearest neighbor interpolation
False, # no padding
segmentationToReferenceGeometryTransform)
# 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(segmentLabelmap_Reference)
thresh.ThresholdByLower(0)
thresh.SetInValue(backgroundValue)
thresh.SetOutValue(labelValue)
thresh.SetOutputScalarType(vtk.VTK_UNSIGNED_CHAR)
thresh.Update()
# Use binary labelmap as a stencil
stencil = vtk.vtkImageToImageStencil()
stencil.SetInputData(thresh.GetOutput())
stencil.ThresholdByUpper(labelValue)
stencil.Update()
return stencil
def TestSection_2_qMRMLSegmentationGeometryWidget(self):
logging.info('Test section 2: qMRMLSegmentationGeometryWidget')
import vtkSegmentationCore
binaryLabelmapReprName = vtkSegmentationCore.vtkSegmentationConverter.GetBinaryLabelmapRepresentationName()
closedSurfaceReprName = vtkSegmentationCore.vtkSegmentationConverter.GetClosedSurfaceRepresentationName()
# Use MRHead and Tinypatient for testing
import SampleData
sampleDataLogic = SampleData.SampleDataLogic()
mrVolumeNode = sampleDataLogic.downloadMRHead()
[tinyVolumeNode, tinySegmentationNode] = sampleDataLogic.downloadSample('TinyPatient')
# Convert MRHead to oriented image data
import vtkSlicerSegmentationsModuleLogicPython as vtkSlicerSegmentationsModuleLogic
mrOrientedImageData = vtkSlicerSegmentationsModuleLogic.vtkSlicerSegmentationsModuleLogic.CreateOrientedImageDataFromVolumeNode(mrVolumeNode)
mrOrientedImageData.UnRegister(None)
# Create segmentation node with binary labelmap master and one segment with MRHead geometry
segmentationNode = slicer.vtkMRMLSegmentationNode()
segmentationNode.GetSegmentation().SetMasterRepresentationName(binaryLabelmapReprName)
geometryStr = vtkSegmentationCore.vtkSegmentationConverter.SerializeImageGeometry(mrOrientedImageData)
segmentationNode.GetSegmentation().SetConversionParameter(
vtkSegmentationCore.vtkSegmentationConverter.GetReferenceImageGeometryParameterName(), geometryStr)
slicer.mrmlScene.AddNode(segmentationNode)
threshold = vtk.vtkImageThreshold()
threshold.SetInputData(mrOrientedImageData)
threshold.ThresholdByUpper(16.0)
threshold.SetInValue(1)
threshold.SetOutValue(0)
threshold.SetOutputScalarType(vtk.VTK_UNSIGNED_CHAR)
threshold.Update()
segmentOrientedImageData = vtkSegmentationCore.vtkOrientedImageData()
segmentOrientedImageData.DeepCopy(threshold.GetOutput())
mrImageToWorldMatrix = vtk.vtkMatrix4x4()
mrOrientedImageData.GetImageToWorldMatrix(mrImageToWorldMatrix)
segmentOrientedImageData.SetImageToWorldMatrix(mrImageToWorldMatrix)
segment = vtkSegmentationCore.vtkSegment()
segment.SetName('Brain')
segment.SetColor(0.0,0.0,1.0)
segment.AddRepresentation(binaryLabelmapReprName, segmentOrientedImageData)
segmentationNode.GetSegmentation().AddSegment(segment)
# Create geometry widget
geometryWidget = slicer.qMRMLSegmentationGeometryWidget()
geometryWidget.setSegmentationNode(segmentationNode)
geometryWidget.editEnabled = True
geometryImageData = vtkSegmentationCore.vtkOrientedImageData() # To contain the output later
# Volume source with no transforms
geometryWidget.setSourceNode(tinyVolumeNode)
geometryWidget.geometryImageData(geometryImageData)
self.assertTrue(self.compareOutputGeometry(geometryImageData,
(49,49,23), (248.8439, 248.2890, -123.75),
[[0.0, 0.0, 1.0], [0.0, 0.0, 1.0], [0.0, 0.0, 1.0]]))
slicer.util.delayDisplay('Volume source with no transforms - OK')
# Transformed volume source
translationTransformMatrix = vtk.vtkMatrix4x4()
translationTransformMatrix.SetElement(0,3,24.5)
translationTransformMatrix.SetElement(1,3,24.5)
translationTransformMatrix.SetElement(2,3,11.5)
translationTransformNode = slicer.vtkMRMLLinearTransformNode()
translationTransformNode.SetName('TestTranslation')
slicer.mrmlScene.AddNode(translationTransformNode)
translationTransformNode.SetMatrixTransformToParent(translationTransformMatrix)
tinyVolumeNode.SetAndObserveTransformNodeID(translationTransformNode.GetID())
geometryWidget.geometryImageData(geometryImageData)
self.assertTrue(self.compareOutputGeometry(geometryImageData,
(49,49,23), (224.3439, 223.7890, -135.25),
[[0.0, 0.0, 1.0], [0.0, 0.0, 1.0], [0.0, 0.0, 1.0]]))
slicer.util.delayDisplay('Transformed volume source - OK')
# Volume source with isotropic spacing
tinyVolumeNode.SetAndObserveTransformNodeID(None)
geometryWidget.setIsotropicSpacing(True)
geometryWidget.geometryImageData(geometryImageData)
self.assertTrue(self.compareOutputGeometry(geometryImageData,
(23,23,23), (248.8439, 248.2890, -123.75),
[[0.0, 0.0, 1.0], [0.0, 0.0, 1.0], [0.0, 0.0, 1.0]]))
slicer.util.delayDisplay('Volume source with isotropic spacing - OK')
# Volume source with oversampling
geometryWidget.setIsotropicSpacing(False)
geometryWidget.setOversamplingFactor(2.0)
geometryWidget.geometryImageData(geometryImageData)
self.assertTrue(self.compareOutputGeometry(geometryImageData,
(24.5, 24.5, 11.5), (261.0939, 260.5390, -129.5),
[[0.0, 0.0, 1.0], [0.0, 0.0, 1.0], [0.0, 0.0, 1.0]]))
slicer.util.delayDisplay('Volume source with oversampling - OK')
# Segmentation source with binary labelmap master
geometryWidget.setOversamplingFactor(1.0)
geometryWidget.setSourceNode(tinySegmentationNode)
geometryWidget.geometryImageData(geometryImageData)
self.assertTrue(self.compareOutputGeometry(geometryImageData,
(49,49,23), (248.8439, 248.2890, -123.75),
[[0.0, 0.0, 1.0], [0.0, 0.0, 1.0], [0.0, 0.0, 1.0]]))
slicer.util.delayDisplay('Segmentation source with binary labelmap master - OK')
# Segmentation source with closed surface master
tinySegmentationNode.GetSegmentation().SetConversionParameter('Smoothing factor', '0.0')
self.assertTrue(tinySegmentationNode.GetSegmentation().CreateRepresentation(closedSurfaceReprName))
tinySegmentationNode.GetSegmentation().SetMasterRepresentationName(closedSurfaceReprName)
tinySegmentationNode.Modified() # Trigger re-calculation of geometry (only generic Modified event is observed)
geometryWidget.geometryImageData(geometryImageData)
# Manually resample and check if the output is non-empty
# Note: This is done for all poly data based geometry calculations below
#TODO: Come up with proper geometry baselines for these too
vtkSegmentationCore.vtkOrientedImageDataResample.ResampleOrientedImageToReferenceOrientedImage(
segmentOrientedImageData, geometryImageData, geometryImageData, False, True)
self.assertTrue(self.imageDataContainsData(geometryImageData))
slicer.util.delayDisplay('Segmentation source with closed surface master - OK')
# Model source with no transform
outputModelHierarchy = slicer.vtkMRMLModelHierarchyNode()
slicer.mrmlScene.AddNode(outputModelHierarchy)
success = vtkSlicerSegmentationsModuleLogic.vtkSlicerSegmentationsModuleLogic.ExportVisibleSegmentsToModelHierarchy(
tinySegmentationNode, outputModelHierarchy )
self.assertTrue(success)
modelNode = slicer.util.getNode('Body_Contour')
geometryWidget.setSourceNode(modelNode)
geometryWidget.geometryImageData(geometryImageData)
vtkSegmentationCore.vtkOrientedImageDataResample.ResampleOrientedImageToReferenceOrientedImage(
segmentOrientedImageData, geometryImageData, geometryImageData, False, True)
self.assertTrue(self.imageDataContainsData(geometryImageData))
slicer.util.delayDisplay('Model source with no transform - OK')
# Transformed model source
rotationTransform = vtk.vtkTransform()
rotationTransform.RotateX(45)
rotationTransformMatrix = vtk.vtkMatrix4x4()
rotationTransform.GetMatrix(rotationTransformMatrix)
rotationTransformNode = slicer.vtkMRMLLinearTransformNode()
rotationTransformNode.SetName('TestRotation')
slicer.mrmlScene.AddNode(rotationTransformNode)
rotationTransformNode.SetMatrixTransformToParent(rotationTransformMatrix)
modelNode.SetAndObserveTransformNodeID(rotationTransformNode.GetID())
modelNode.Modified()
geometryWidget.geometryImageData(geometryImageData)
vtkSegmentationCore.vtkOrientedImageDataResample.ResampleOrientedImageToReferenceOrientedImage(
segmentOrientedImageData, geometryImageData, geometryImageData, False, True)
self.assertTrue(self.imageDataContainsData(geometryImageData))
slicer.util.delayDisplay('Transformed model source - OK')
# ROI source
roiNode = slicer.vtkMRMLAnnotationROINode()
roiNode.SetName('SourceROI')
slicer.mrmlScene.AddNode(roiNode)
roiNode.UnRegister(None)
xyz = [0]*3
center = [0]*3
slicer.vtkMRMLSliceLogic.GetVolumeRASBox(tinyVolumeNode, xyz, center)
radius = map(lambda x: x/2.0, xyz)
roiNode.SetXYZ(center)
roiNode.SetRadiusXYZ(radius)
geometryWidget.setSourceNode(roiNode)
geometryWidget.geometryImageData(geometryImageData)
vtkSegmentationCore.vtkOrientedImageDataResample.ResampleOrientedImageToReferenceOrientedImage(
segmentOrientedImageData, geometryImageData, geometryImageData, False, True)
self.assertTrue(self.imageDataContainsData(geometryImageData))
slicer.util.delayDisplay('ROI source - OK')
slicer.util.delayDisplay('Segmentation geometry widget test passed')
def fastMarching(self, percentMax):
self.fm = None
# Get master volume image data
import vtkSegmentationCorePython as vtkSegmentationCore
masterImageData = self.scriptedEffect.masterVolumeImageData()
# Get segmentation
segmentationNode = self.scriptedEffect.parameterSetNode(
).GetSegmentationNode()
# Cast master image if not short
if masterImageData.GetScalarType() != vtk.VTK_SHORT:
imageCast = vtk.vtkImageCast()
imageCast.SetInputData(masterImageData)
imageCast.SetOutputScalarTypeToShort()
imageCast.ClampOverflowOn()
imageCast.Update()
masterImageDataShort = vtkSegmentationCore.vtkOrientedImageData()
masterImageDataShort.ShallowCopy(
imageCast.GetOutput()) # Copy image data
masterImageDataShort.CopyDirections(
masterImageData) # Copy geometry
masterImageData = masterImageDataShort
if not self.originalSelectedSegmentLabelmap:
segmentationNode = self.scriptedEffect.parameterSetNode(
).GetSegmentationNode()
segmentationNode.GetSegmentation().SeparateSegmentLabelmap(
self.scriptedEffect.parameterSetNode().GetSelectedSegmentID())
selectedSegmentLabelmap = self.scriptedEffect.selectedSegmentLabelmap()
if not self.originalSelectedSegmentLabelmap:
self.originalSelectedSegmentLabelmap = vtkSegmentationCore.vtkOrientedImageData(
)
self.originalSelectedSegmentLabelmap.DeepCopy(
selectedSegmentLabelmap)
self.selectedSegmentId = self.scriptedEffect.parameterSetNode(
).GetSelectedSegmentID()
# 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(vtk.VTK_UNSIGNED_SHORT)
thresh.Update()
labelImage = thresh.GetOutput()
# collect seeds
dim = masterImageData.GetDimensions()
# initialize the filter
import vtkSlicerSegmentEditorFastMarchingModuleLogicPython
self.fm = vtkSlicerSegmentEditorFastMarchingModuleLogicPython.vtkPichonFastMarching(
)
scalarRange = masterImageData.GetScalarRange()
depth = scalarRange[1] - scalarRange[0]
# this is more or less arbitrary; large depth values will bring the
# algorithm to the knees
scaleValue = 0
shiftValue = 0
if depth > 300:
scaleValue = 300. / depth
if scalarRange[0] < 0:
shiftValue = scalarRange[0] * -1
if scaleValue or shiftValue:
rescale = vtk.vtkImageShiftScale()
rescale.SetInputData(masterImageData)
rescale.SetScale(scaleValue)
rescale.SetShift(shiftValue)
rescale.Update()
masterImageData = rescale.GetOutput()
scalarRange = masterImageData.GetScalarRange()
depth = scalarRange[1] - scalarRange[0]
self.fm.init(dim[0], dim[1], dim[2], depth, 1, 1, 1)
caster = vtk.vtkImageCast()
caster.SetOutputScalarTypeToShort()
caster.SetInputData(masterImageData)
self.fm.SetInputConnection(caster.GetOutputPort())
# self.fm.SetOutput(labelImage)
npoints = int(dim[0] * dim[1] * dim[2] * percentMax / 100.)
self.fm.setNPointsEvolution(npoints)
self.fm.setActiveLabel(labelValue)
spacing = self.originalSelectedSegmentLabelmap.GetSpacing()
self.voxelVolume = spacing[0] * spacing[1] * spacing[2]
self.totalNumberOfVoxels = npoints
nSeeds = self.fm.addSeedsFromImage(labelImage)
if nSeeds == 0:
self.totalNumberOfVoxels = 0
return
self.fm.Modified()
self.fm.Update()
# Need to call show() twice for data to be updated.
# There are many other issues with the vtkPichonFastMarching filter
# (expects extents to start at 0, crashes in debug mode, etc).
self.fm.show(1)
self.fm.Modified()
self.fm.Update()
self.updateLabel(self.marcher.value / self.marcher.maximum)
logging.info('FastMarching march update completed')
def splitSegments(self, minimumSize=0, maxNumberOfSegments=0, split=True):
"""
minimumSize: if 0 then it means that all islands are kept, regardless of size
maxNumberOfSegments: if 0 then it means that all islands are kept, regardless of how many
"""
# This can be a long operation - indicate it to the user
qt.QApplication.setOverrideCursor(qt.Qt.WaitCursor)
self.scriptedEffect.saveStateForUndo()
# Get modifier labelmap
selectedSegmentLabelmap = self.scriptedEffect.selectedSegmentLabelmap()
castIn = vtk.vtkImageCast()
castIn.SetInputData(selectedSegmentLabelmap)
castIn.SetOutputScalarTypeToUnsignedInt()
# Identify the islands in the inverted volume and
# find the pixel that corresponds to the background
islandMath = vtkITK.vtkITKIslandMath()
islandMath.SetInputConnection(castIn.GetOutputPort())
islandMath.SetFullyConnected(False)
islandMath.SetMinimumSize(minimumSize)
islandMath.Update()
# Create a separate image for the first (largest) island
labelValue = 1
backgroundValue = 0
thresh = vtk.vtkImageThreshold()
if split:
thresh.ThresholdBetween(1, 1)
else:
if maxNumberOfSegments != 0:
thresh.ThresholdBetween(1, maxNumberOfSegments)
else:
thresh.ThresholdByUpper(1)
thresh.SetInputData(islandMath.GetOutput())
thresh.SetOutValue(backgroundValue)
thresh.SetInValue(labelValue)
thresh.SetOutputScalarType(selectedSegmentLabelmap.GetScalarType())
thresh.Update()
# Create oriented image data from output
import vtkSegmentationCorePython as vtkSegmentationCore
largestIslandImage = vtkSegmentationCore.vtkOrientedImageData()
largestIslandImage.ShallowCopy(thresh.GetOutput())
selectedSegmentLabelmapImageToWorldMatrix = vtk.vtkMatrix4x4()
selectedSegmentLabelmap.GetImageToWorldMatrix(
selectedSegmentLabelmapImageToWorldMatrix)
largestIslandImage.SetImageToWorldMatrix(
selectedSegmentLabelmapImageToWorldMatrix)
if split and (maxNumberOfSegments != 1):
thresh2 = vtk.vtkImageThreshold()
# 0 is background, 1 is largest island; we need label 2 and higher
if maxNumberOfSegments != 0:
thresh2.ThresholdBetween(2, maxNumberOfSegments)
else:
thresh2.ThresholdByUpper(2)
thresh2.SetInputData(islandMath.GetOutput())
thresh2.SetOutValue(backgroundValue)
thresh2.ReplaceInOff()
thresh2.Update()
islandCount = islandMath.GetNumberOfIslands()
islandOrigCount = islandMath.GetOriginalNumberOfIslands()
ignoredIslands = islandOrigCount - islandCount
logging.info("%d islands created (%d ignored)" %
(islandCount, ignoredIslands))
# Create oriented image data from output
import vtkSegmentationCorePython as vtkSegmentationCore
multiLabelImage = vtkSegmentationCore.vtkOrientedImageData()
multiLabelImage.DeepCopy(thresh2.GetOutput())
selectedSegmentLabelmapImageToWorldMatrix = vtk.vtkMatrix4x4()
selectedSegmentLabelmap.GetImageToWorldMatrix(
selectedSegmentLabelmapImageToWorldMatrix)
multiLabelImage.SetGeometryFromImageToWorldMatrix(
selectedSegmentLabelmapImageToWorldMatrix)
# Import multi-label labelmap to segmentation
segmentationNode = self.scriptedEffect.parameterSetNode(
).GetSegmentationNode()
selectedSegmentID = self.scriptedEffect.parameterSetNode(
).GetSelectedSegmentID()
selectedSegmentIndex = segmentationNode.GetSegmentation(
).GetSegmentIndex(selectedSegmentID)
insertBeforeSegmentID = segmentationNode.GetSegmentation(
).GetNthSegmentID(selectedSegmentIndex + 1)
selectedSegmentName = segmentationNode.GetSegmentation(
).GetSegment(selectedSegmentID).GetName()
slicer.vtkSlicerSegmentationsModuleLogic.ImportLabelmapToSegmentationNode( \
multiLabelImage, segmentationNode, selectedSegmentName+" -", insertBeforeSegmentID )
self.scriptedEffect.modifySelectedSegmentByLabelmap(
largestIslandImage,
slicer.qSlicerSegmentEditorAbstractEffect.ModificationModeSet)
qt.QApplication.restoreOverrideCursor()
def onApply(self):
self.scriptedEffect.saveStateForUndo()
import vtkSegmentationCorePython as vtkSegmentationCore
# Get modifier labelmap and parameters
operation = self.scriptedEffect.parameter("Operation")
bypassMasking = (self.scriptedEffect.integerParameter("BypassMasking")
!= 0)
selectedSegmentID = self.scriptedEffect.parameterSetNode(
).GetSelectedSegmentID()
segmentationNode = self.scriptedEffect.parameterSetNode(
).GetSegmentationNode()
segmentation = segmentationNode.GetSegmentation()
if operation in self.operationsRequireModifierSegment:
# Get modifier segment
modifierSegmentID = self.modifierSegmentID()
if not modifierSegmentID:
logging.error(
"Operation {0} requires a selected modifier segment".
format(operation))
return
modifierSegment = segmentation.GetSegment(modifierSegmentID)
modifierSegmentLabelmap = modifierSegment.GetRepresentation(
vtkSegmentationCore.vtkSegmentationConverter.
GetSegmentationBinaryLabelmapRepresentationName())
# Get common geometry
commonGeometryString = segmentationNode.GetSegmentation(
).DetermineCommonLabelmapGeometry(
vtkSegmentationCore.vtkSegmentation.EXTENT_UNION_OF_SEGMENTS,
None)
if not commonGeometryString:
logging.info(
"Logical operation skipped: all segments are empty")
return
commonGeometryImage = vtkSegmentationCore.vtkOrientedImageData()
vtkSegmentationCore.vtkSegmentationConverter.DeserializeImageGeometry(
commonGeometryString, commonGeometryImage, False)
# Make sure modifier segment has correct geometry
# (if modifier segment has been just copied over from another segment then its geometry may be different)
if not vtkSegmentationCore.vtkOrientedImageDataResample.DoGeometriesMatch(
commonGeometryImage, modifierSegmentLabelmap):
modifierSegmentLabelmap_CommonGeometry = vtkSegmentationCore.vtkOrientedImageData(
)
vtkSegmentationCore.vtkOrientedImageDataResample.ResampleOrientedImageToReferenceOrientedImage(
modifierSegmentLabelmap,
commonGeometryImage,
modifierSegmentLabelmap_CommonGeometry,
False, # nearest neighbor interpolation,
True # make sure resampled modifier segment is not cropped
)
modifierSegmentLabelmap = modifierSegmentLabelmap_CommonGeometry
if operation == LOGICAL_COPY:
if bypassMasking:
slicer.vtkSlicerSegmentationsModuleLogic.SetBinaryLabelmapToSegment(
modifierSegmentLabelmap, segmentationNode,
selectedSegmentID,
slicer.vtkSlicerSegmentationsModuleLogic.MODE_REPLACE,
modifierSegmentLabelmap.GetExtent())
else:
self.scriptedEffect.modifySelectedSegmentByLabelmap(
modifierSegmentLabelmap, slicer.
qSlicerSegmentEditorAbstractEffect.ModificationModeSet)
elif operation == LOGICAL_UNION:
if bypassMasking:
slicer.vtkSlicerSegmentationsModuleLogic.SetBinaryLabelmapToSegment(
modifierSegmentLabelmap, segmentationNode,
selectedSegmentID, slicer.
vtkSlicerSegmentationsModuleLogic.MODE_MERGE_MAX,
modifierSegmentLabelmap.GetExtent())
else:
self.scriptedEffect.modifySelectedSegmentByLabelmap(
modifierSegmentLabelmap, slicer.
qSlicerSegmentEditorAbstractEffect.ModificationModeAdd)
elif operation == LOGICAL_SUBTRACT:
if bypassMasking:
invertedModifierSegmentLabelmap = self.getInvertedBinaryLabelmap(
modifierSegmentLabelmap)
slicer.vtkSlicerSegmentationsModuleLogic.SetBinaryLabelmapToSegment(
invertedModifierSegmentLabelmap, segmentationNode,
selectedSegmentID, slicer.
vtkSlicerSegmentationsModuleLogic.MODE_MERGE_MIN,
modifierSegmentLabelmap.GetExtent())
else:
self.scriptedEffect.modifySelectedSegmentByLabelmap(
modifierSegmentLabelmap,
slicer.qSlicerSegmentEditorAbstractEffect.
ModificationModeRemove)
elif operation == LOGICAL_INTERSECT:
selectedSegmentLabelmap = self.scriptedEffect.selectedSegmentLabelmap(
)
intersectionLabelmap = vtkSegmentationCore.vtkOrientedImageData(
)
vtkSegmentationCore.vtkOrientedImageDataResample.MergeImage(
selectedSegmentLabelmap, modifierSegmentLabelmap,
intersectionLabelmap, vtkSegmentationCore.
vtkOrientedImageDataResample.OPERATION_MINIMUM,
selectedSegmentLabelmap.GetExtent())
selectedSegmentLabelmapExtent = selectedSegmentLabelmap.GetExtent(
)
modifierSegmentLabelmapExtent = modifierSegmentLabelmap.GetExtent(
)
commonExtent = [
max(selectedSegmentLabelmapExtent[0],
modifierSegmentLabelmapExtent[0]),
min(selectedSegmentLabelmapExtent[1],
modifierSegmentLabelmapExtent[1]),
max(selectedSegmentLabelmapExtent[2],
modifierSegmentLabelmapExtent[2]),
min(selectedSegmentLabelmapExtent[3],
modifierSegmentLabelmapExtent[3]),
max(selectedSegmentLabelmapExtent[4],
modifierSegmentLabelmapExtent[4]),
min(selectedSegmentLabelmapExtent[5],
modifierSegmentLabelmapExtent[5])
]
if bypassMasking:
slicer.vtkSlicerSegmentationsModuleLogic.SetBinaryLabelmapToSegment(
intersectionLabelmap, segmentationNode,
selectedSegmentID,
slicer.vtkSlicerSegmentationsModuleLogic.MODE_REPLACE,
commonExtent)
else:
self.scriptedEffect.modifySelectedSegmentByLabelmap(
intersectionLabelmap, slicer.
qSlicerSegmentEditorAbstractEffect.ModificationModeSet,
commonExtent)
elif operation == LOGICAL_INVERT:
selectedSegmentLabelmap = self.scriptedEffect.selectedSegmentLabelmap(
)
invertedSelectedSegmentLabelmap = self.getInvertedBinaryLabelmap(
selectedSegmentLabelmap)
if bypassMasking:
slicer.vtkSlicerSegmentationsModuleLogic.SetBinaryLabelmapToSegment(
invertedSelectedSegmentLabelmap, segmentationNode,
selectedSegmentID,
slicer.vtkSlicerSegmentationsModuleLogic.MODE_REPLACE)
else:
self.scriptedEffect.modifySelectedSegmentByLabelmap(
invertedSelectedSegmentLabelmap, slicer.
qSlicerSegmentEditorAbstractEffect.ModificationModeSet)
elif operation == LOGICAL_CLEAR or operation == LOGICAL_FILL:
selectedSegmentLabelmap = self.scriptedEffect.selectedSegmentLabelmap(
)
vtkSegmentationCore.vtkOrientedImageDataResample.FillImage(
selectedSegmentLabelmap, 1 if operation == LOGICAL_FILL else 0,
selectedSegmentLabelmap.GetExtent())
if bypassMasking:
slicer.vtkSlicerSegmentationsModuleLogic.SetBinaryLabelmapToSegment(
selectedSegmentLabelmap, segmentationNode,
selectedSegmentID,
slicer.vtkSlicerSegmentationsModuleLogic.MODE_REPLACE)
else:
self.scriptedEffect.modifySelectedSegmentByLabelmap(
selectedSegmentLabelmap, slicer.
qSlicerSegmentEditorAbstractEffect.ModificationModeSet)
else:
logging.error("Unknown operation: {0}".format(operation))
def preview(self):
# Get master volume image data
import vtkSegmentationCorePython as vtkSegmentationCore
masterImageData = self.scriptedEffect.masterVolumeImageData()
# Get segmentation
segmentationNode = self.scriptedEffect.parameterSetNode(
).GetSegmentationNode()
previewNode = self.getPreviewNode()
if not previewNode or not self.mergedLabelmapGeometryImage \
or (self.clippedMasterImageDataRequired and not self.clippedMasterImageData):
self.reset()
# Compute merged labelmap extent (effective extent slightly expanded)
self.selectedSegmentIds = vtk.vtkStringArray()
segmentationNode.GetDisplayNode().GetVisibleSegmentIDs(
self.selectedSegmentIds)
if self.selectedSegmentIds.GetNumberOfValues(
) < self.minimumNumberOfSegments:
logging.error(
"Auto-complete operation skipped: at least {0} visible segments are required"
.format(self.minimumNumberOfSegments))
return
if not self.mergedLabelmapGeometryImage:
self.mergedLabelmapGeometryImage = vtkSegmentationCore.vtkOrientedImageData(
)
commonGeometryString = segmentationNode.GetSegmentation(
).DetermineCommonLabelmapGeometry(
vtkSegmentationCore.vtkSegmentation.
EXTENT_UNION_OF_EFFECTIVE_SEGMENTS, self.selectedSegmentIds)
if not commonGeometryString:
logging.info(
"Auto-complete operation skipped: all visible segments are empty"
)
return
vtkSegmentationCore.vtkSegmentationConverter.DeserializeImageGeometry(
commonGeometryString, self.mergedLabelmapGeometryImage)
masterImageExtent = masterImageData.GetExtent()
labelsEffectiveExtent = self.mergedLabelmapGeometryImage.GetExtent(
)
margin = [17, 17, 17]
labelsExpandedExtent = [
max(masterImageExtent[0],
labelsEffectiveExtent[0] - margin[0]),
min(masterImageExtent[1],
labelsEffectiveExtent[1] + margin[0]),
max(masterImageExtent[2],
labelsEffectiveExtent[2] - margin[1]),
min(masterImageExtent[3],
labelsEffectiveExtent[3] + margin[1]),
max(masterImageExtent[4],
labelsEffectiveExtent[4] - margin[2]),
min(masterImageExtent[5], labelsEffectiveExtent[5] + margin[2])
]
self.mergedLabelmapGeometryImage.SetExtent(labelsExpandedExtent)
previewNode = slicer.mrmlScene.CreateNodeByClass(
'vtkMRMLSegmentationNode')
previewNode.UnRegister(None)
previewNode = slicer.mrmlScene.AddNode(previewNode)
previewNode.CreateDefaultDisplayNodes()
previewNode.GetDisplayNode().SetVisibility2DOutline(False)
if segmentationNode.GetParentTransformNode():
previewNode.SetAndObserveTransformNodeID(
segmentationNode.GetParentTransformNode().GetID())
self.scriptedEffect.parameterSetNode().SetNodeReferenceID(
ResultPreviewNodeReferenceRole, previewNode.GetID())
self.scriptedEffect.setCommonParameter(
"SegmentationResultPreviewOwnerEffect",
self.scriptedEffect.name)
self.setPreviewOpacity(0.6)
if self.clippedMasterImageDataRequired:
self.clippedMasterImageData = vtkSegmentationCore.vtkOrientedImageData(
)
masterImageClipper = vtk.vtkImageConstantPad()
masterImageClipper.SetInputData(masterImageData)
masterImageClipper.SetOutputWholeExtent(
self.mergedLabelmapGeometryImage.GetExtent())
masterImageClipper.Update()
self.clippedMasterImageData.ShallowCopy(
masterImageClipper.GetOutput())
self.clippedMasterImageData.CopyDirections(
self.mergedLabelmapGeometryImage)
previewNode.SetName(segmentationNode.GetName() + " preview")
mergedImage = vtkSegmentationCore.vtkOrientedImageData()
segmentationNode.GenerateMergedLabelmapForAllSegments(
mergedImage, vtkSegmentationCore.vtkSegmentation.
EXTENT_UNION_OF_EFFECTIVE_SEGMENTS,
self.mergedLabelmapGeometryImage, self.selectedSegmentIds)
outputLabelmap = vtkSegmentationCore.vtkOrientedImageData()
self.computePreviewLabelmap(mergedImage, outputLabelmap)
# Write output segmentation results in segments
for index in xrange(self.selectedSegmentIds.GetNumberOfValues()):
segmentID = self.selectedSegmentIds.GetValue(index)
segment = segmentationNode.GetSegmentation().GetSegment(segmentID)
# Disable save with scene?
# Get only the label of the current segment from the output image
thresh = vtk.vtkImageThreshold()
thresh.ReplaceInOn()
thresh.ReplaceOutOn()
thresh.SetInValue(1)
thresh.SetOutValue(0)
labelValue = index + 1 # n-th segment label value = n + 1 (background label value is 0)
thresh.ThresholdBetween(labelValue, labelValue)
thresh.SetOutputScalarType(vtk.VTK_UNSIGNED_CHAR)
thresh.SetInputData(outputLabelmap)
thresh.Update()
# Write label to segment
newSegmentLabelmap = vtkSegmentationCore.vtkOrientedImageData()
newSegmentLabelmap.ShallowCopy(thresh.GetOutput())
newSegmentLabelmap.CopyDirections(mergedImage)
newSegment = previewNode.GetSegmentation().GetSegment(segmentID)
if not newSegment:
newSegment = vtkSegmentationCore.vtkSegment()
newSegment.SetName(segment.GetName())
color = segmentationNode.GetSegmentation().GetSegment(
segmentID).GetColor()
newSegment.SetColor(color)
previewNode.GetSegmentation().AddSegment(newSegment, segmentID)
slicer.vtkSlicerSegmentationsModuleLogic.SetBinaryLabelmapToSegment(
newSegmentLabelmap, previewNode, segmentID)
self.updateGUIFromMRML()
def preview(self):
# Get master volume image data
import vtkSegmentationCorePython as vtkSegmentationCore
masterImageData = self.scriptedEffect.masterVolumeImageData()
# Get segmentation
segmentationNode = self.scriptedEffect.parameterSetNode().GetSegmentationNode()
previewNode = self.getPreviewNode()
if (not previewNode or not self.mergedLabelmapGeometryImage
or (self.clippedMasterImageDataRequired and not self.clippedMasterImageData)):
self.reset()
# Compute merged labelmap extent (effective extent slightly expanded)
self.selectedSegmentIds = vtk.vtkStringArray()
segmentationNode.GetDisplayNode().GetVisibleSegmentIDs(self.selectedSegmentIds)
if self.selectedSegmentIds.GetNumberOfValues() < self.minimumNumberOfSegments:
logging.error("Auto-complete operation skipped: at least {0} visible segments are required".format(self.minimumNumberOfSegments))
return
if not self.mergedLabelmapGeometryImage:
self.mergedLabelmapGeometryImage = vtkSegmentationCore.vtkOrientedImageData()
commonGeometryString = segmentationNode.GetSegmentation().DetermineCommonLabelmapGeometry(
vtkSegmentationCore.vtkSegmentation.EXTENT_UNION_OF_EFFECTIVE_SEGMENTS, self.selectedSegmentIds)
if not commonGeometryString:
logging.info("Auto-complete operation skipped: all visible segments are empty")
return
vtkSegmentationCore.vtkSegmentationConverter.DeserializeImageGeometry(commonGeometryString, self.mergedLabelmapGeometryImage)
masterImageExtent = masterImageData.GetExtent()
labelsEffectiveExtent = self.mergedLabelmapGeometryImage.GetExtent()
# Margin size is relative to combined seed region size, but minimum of 3 voxels
print("self.extentGrowthRatio = {0}".format(self.extentGrowthRatio))
margin = [
int(max(3, self.extentGrowthRatio * (labelsEffectiveExtent[1]-labelsEffectiveExtent[0]))),
int(max(3, self.extentGrowthRatio * (labelsEffectiveExtent[3]-labelsEffectiveExtent[2]))),
int(max(3, self.extentGrowthRatio * (labelsEffectiveExtent[5]-labelsEffectiveExtent[4]))) ]
labelsExpandedExtent = [
max(masterImageExtent[0], labelsEffectiveExtent[0]-margin[0]),
min(masterImageExtent[1], labelsEffectiveExtent[1]+margin[0]),
max(masterImageExtent[2], labelsEffectiveExtent[2]-margin[1]),
min(masterImageExtent[3], labelsEffectiveExtent[3]+margin[1]),
max(masterImageExtent[4], labelsEffectiveExtent[4]-margin[2]),
min(masterImageExtent[5], labelsEffectiveExtent[5]+margin[2]) ]
print("masterImageExtent = "+repr(masterImageExtent))
print("labelsEffectiveExtent = "+repr(labelsEffectiveExtent))
print("labelsExpandedExtent = "+repr(labelsExpandedExtent))
self.mergedLabelmapGeometryImage.SetExtent(labelsExpandedExtent)
# Create and setup preview node
previewNode = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLSegmentationNode")
previewNode.CreateDefaultDisplayNodes()
previewNode.GetDisplayNode().SetVisibility2DOutline(False)
if segmentationNode.GetParentTransformNode():
previewNode.SetAndObserveTransformNodeID(segmentationNode.GetParentTransformNode().GetID())
self.scriptedEffect.parameterSetNode().SetNodeReferenceID(ResultPreviewNodeReferenceRole, previewNode.GetID())
self.scriptedEffect.setCommonParameter("SegmentationResultPreviewOwnerEffect", self.scriptedEffect.name)
self.setPreviewOpacity(0.6)
# Disable smoothing for closed surface generation to make it fast
previewNode.GetSegmentation().SetConversionParameter(
slicer.vtkBinaryLabelmapToClosedSurfaceConversionRule.GetSmoothingFactorParameterName(),
"-0.5");
inputContainsClosedSurfaceRepresentation = segmentationNode.GetSegmentation().ContainsRepresentation(
slicer.vtkSegmentationConverter.GetSegmentationClosedSurfaceRepresentationName())
self.setPreviewShow3D(inputContainsClosedSurfaceRepresentation)
if self.clippedMasterImageDataRequired:
self.clippedMasterImageData = vtkSegmentationCore.vtkOrientedImageData()
masterImageClipper = vtk.vtkImageConstantPad()
masterImageClipper.SetInputData(masterImageData)
masterImageClipper.SetOutputWholeExtent(self.mergedLabelmapGeometryImage.GetExtent())
masterImageClipper.Update()
self.clippedMasterImageData.ShallowCopy(masterImageClipper.GetOutput())
self.clippedMasterImageData.CopyDirections(self.mergedLabelmapGeometryImage)
self.clippedMaskImageData = None
if self.clippedMaskImageDataRequired:
self.clippedMaskImageData = vtkSegmentationCore.vtkOrientedImageData()
intensityBasedMasking = self.scriptedEffect.parameterSetNode().GetMasterVolumeIntensityMask()
success = segmentationNode.GenerateEditMask(self.clippedMaskImageData,
self.scriptedEffect.parameterSetNode().GetMaskMode(),
self.clippedMasterImageData, # reference geometry
"", # edited segment ID
self.scriptedEffect.parameterSetNode().GetMaskSegmentID() if self.scriptedEffect.parameterSetNode().GetMaskSegmentID() else "",
self.clippedMasterImageData if intensityBasedMasking else None,
self.scriptedEffect.parameterSetNode().GetMasterVolumeIntensityMaskRange() if intensityBasedMasking else None)
if not success:
logging.error("Failed to create edit mask")
self.clippedMaskImageData = None
previewNode.SetName(segmentationNode.GetName()+" preview")
mergedImage = vtkSegmentationCore.vtkOrientedImageData()
segmentationNode.GenerateMergedLabelmapForAllSegments(mergedImage,
vtkSegmentationCore.vtkSegmentation.EXTENT_UNION_OF_EFFECTIVE_SEGMENTS, self.mergedLabelmapGeometryImage, self.selectedSegmentIds)
outputLabelmap = vtkSegmentationCore.vtkOrientedImageData()
self.computePreviewLabelmap(mergedImage, outputLabelmap)
# Write output segmentation results in segments
for index in xrange(self.selectedSegmentIds.GetNumberOfValues()):
segmentID = self.selectedSegmentIds.GetValue(index)
segment = segmentationNode.GetSegmentation().GetSegment(segmentID)
# Disable save with scene?
# Get only the label of the current segment from the output image
thresh = vtk.vtkImageThreshold()
thresh.ReplaceInOn()
thresh.ReplaceOutOn()
thresh.SetInValue(1)
thresh.SetOutValue(0)
labelValue = index + 1 # n-th segment label value = n + 1 (background label value is 0)
thresh.ThresholdBetween(labelValue, labelValue);
thresh.SetOutputScalarType(vtk.VTK_UNSIGNED_CHAR)
thresh.SetInputData(outputLabelmap)
thresh.Update()
# Write label to segment
newSegmentLabelmap = vtkSegmentationCore.vtkOrientedImageData()
newSegmentLabelmap.ShallowCopy(thresh.GetOutput())
newSegmentLabelmap.CopyDirections(mergedImage)
newSegment = previewNode.GetSegmentation().GetSegment(segmentID)
if not newSegment:
newSegment = vtkSegmentationCore.vtkSegment()
newSegment.SetName(segment.GetName())
color = segmentationNode.GetSegmentation().GetSegment(segmentID).GetColor()
newSegment.SetColor(color)
previewNode.GetSegmentation().AddSegment(newSegment, segmentID)
slicer.vtkSlicerSegmentationsModuleLogic.SetBinaryLabelmapToSegment(newSegmentLabelmap, previewNode, segmentID)
# Automatically hide result segments that are background (all eight corners are non-zero)
previewNode.GetDisplayNode().SetSegmentVisibility3D(segmentID, not self.isBackgroundLabelmap(newSegmentLabelmap))
self.updateGUIFromMRML()
