def computeDifference(self, fieldA, fieldB, roi, differenceVolume):
referenceVolume = self.createVectorVolumeFromRoi(
roi, self.ReferenceVolumeSpacingMm)
referenceVolume.SetName('ReferenceVolume')
slicer.mrmlScene.AddNode(referenceVolume)
resampledFieldA = self.resampleVolume(fieldA, referenceVolume)
resampledFieldB = self.resampleVolume(fieldB, referenceVolume)
subtractor = vtk.vtkImageMathematics()
subtractor.SetOperationToSubtract()
subtractor.SetInput1Data(resampledFieldA.GetImageData())
subtractor.SetInput2Data(resampledFieldB.GetImageData())
differenceVolume.SetImageDataConnection(subtractor.GetOutputPort())
ijkToRasMatrix = vtk.vtkMatrix4x4()
referenceVolume.GetIJKToRASMatrix(ijkToRasMatrix)
differenceVolume.SetIJKToRASMatrix(ijkToRasMatrix)
differenceVolumeDisplayNode = slicer.vtkMRMLVectorVolumeDisplayNode()
slicer.mrmlScene.AddNode(differenceVolumeDisplayNode)
differenceVolumeDisplayNode.SetAndObserveColorNodeID(
"vtkMRMLColorTableNodeRainbow")
differenceVolume.SetAndObserveNthDisplayNodeID(
0, differenceVolumeDisplayNode.GetID())
slicer.mrmlScene.RemoveNode(resampledFieldA)
slicer.mrmlScene.RemoveNode(resampledFieldB)
slicer.mrmlScene.RemoveNode(referenceVolume)
def run(self, referenceVolumeNode, secondaryVolumeNode):
referenceImageData = referenceVolumeNode.GetImageData()
secondaryImageData = secondaryVolumeNode.GetImageData()
# Apply image convolution to input imagedata
imageMath = vtk.vtkImageMathematics()
imageMath.SetInput1(referenceImageData)
imageMath.SetInput2(secondaryImageData)
imageMath.SetOperationToSubtract()
imageMath.Update()
imageAccumulate = vtk.vtkImageAccumulate()
imageAccumulate.SetInput(referenceImageData)
imageAccumulate.IgnoreZeroOn()
imageAccumulate.Update()
referenceVolumeVoxelCount = imageAccumulate.GetVoxelCount()
# Update the volume with convolutionl operation result
imageAccumulate2 = vtk.vtkImageAccumulate()
imageAccumulate2.SetInput(imageMath.GetOutput())
imageAccumulate2.IgnoreZeroOn()
imageAccumulate2.Update()
differenceVolumeVoxelCount = imageAccumulate2.GetVoxelCount()
self._volumeSimilarity = (
referenceVolumeVoxelCount -
differenceVolumeVoxelCount) / referenceVolumeVoxelCount
def onHelloWorldButtonClicked(self):
print "Hello World !"
#frame volume sera el scalar volume de referencia#
self.__mvNode = self.mvSelector.currentNode()
#NODO REFERENCIA
frameVolume = slicer.vtkMRMLScalarVolumeNode()
frameVolume.SetScene(slicer.mrmlScene)
slicer.mrmlScene.AddNode(frameVolume)
nComponents = self.__mvNode.GetNumberOfFrames()
f=int(self.__veInitial.value)
frameId = min(f,nComponents-1)
ras2ijk = vtk.vtkMatrix4x4()
ijk2ras = vtk.vtkMatrix4x4()
self.__mvNode.GetRASToIJKMatrix(ras2ijk)
self.__mvNode.GetIJKToRASMatrix(ijk2ras)
frameImage = frameVolume.GetImageData()
if frameImage == None:
frameVolume.SetRASToIJKMatrix(ras2ijk)
frameVolume.SetIJKToRASMatrix(ijk2ras)
mvImage = self.__mvNode.GetImageData()
for i in range(nComponents-1):
extract = vtk.vtkImageExtractComponents()
extract.SetInput(mvImage)
extract.SetComponents(i)
extract.Update()
if i == 0:
frameVolume.SetAndObserveImageData(extract.GetOutput())
elif i < frameId+1 :
s=vtk.vtkImageMathematics()
s.SetOperationToAdd()
s.SetInput1(frameVolume.GetImageData())
s.SetInput2(extract.GetOutput())
s.Update()
frameVolume.SetAndObserveImageData(s.GetOutput())
frameName = 'Holaaa'
frameVolume.SetName(frameName)
selectionNode = slicer.app.applicationLogic().GetSelectionNode()
selectionNode.SetReferenceActiveVolumeID(frameVolume.GetID())
slicer.app.applicationLogic().PropagateVolumeSelection(0)
def onHelloWorldButtonClicked(self):
print "Hello World !"
#frame volume sera el scalar volume de referencia#
self.__mvNode = self.mvSelector.currentNode()
#NODO REFERENCIA
frameVolume = slicer.vtkMRMLScalarVolumeNode()
frameVolume.SetScene(slicer.mrmlScene)
slicer.mrmlScene.AddNode(frameVolume)
nComponents = self.__mvNode.GetNumberOfFrames()
f = int(self.__veInitial.value)
frameId = min(f, nComponents - 1)
ras2ijk = vtk.vtkMatrix4x4()
ijk2ras = vtk.vtkMatrix4x4()
self.__mvNode.GetRASToIJKMatrix(ras2ijk)
self.__mvNode.GetIJKToRASMatrix(ijk2ras)
frameImage = frameVolume.GetImageData()
if frameImage == None:
frameVolume.SetRASToIJKMatrix(ras2ijk)
frameVolume.SetIJKToRASMatrix(ijk2ras)
mvImage = self.__mvNode.GetImageData()
for i in range(nComponents - 1):
extract = vtk.vtkImageExtractComponents()
extract.SetInput(mvImage)
extract.SetComponents(i)
extract.Update()
if i == 0:
frameVolume.SetAndObserveImageData(extract.GetOutput())
elif i < frameId + 1:
s = vtk.vtkImageMathematics()
s.SetOperationToAdd()
s.SetInput1(frameVolume.GetImageData())
s.SetInput2(extract.GetOutput())
s.Update()
frameVolume.SetAndObserveImageData(s.GetOutput())
frameName = 'Holaaa'
frameVolume.SetName(frameName)
selectionNode = slicer.app.applicationLogic().GetSelectionNode()
selectionNode.SetReferenceActiveVolumeID(frameVolume.GetID())
slicer.app.applicationLogic().PropagateVolumeSelection(0)
def run(self,inputVolume1,inputVolume2,outputVolume,mathOperationType):
"""
Run the actual algorithm
"""
math = vtk.vtkImageMathematics()
math.SetInput1(inputVolume1.GetImageData())
math.SetInput2(inputVolume2.GetImageData())
if mathOperationType == "Add":
math.SetOperationToAdd()
elif mathOperationType == "Subtract":
math.SetOperationToSubtract()
else:
pass
math.Update()
outputVolume.CopyOrientation(input1VolumeNode)
outputVolume.SetAndObserveImageData(math.GetOutput())
return True
def getSNR(self):
qu=QCLib.QCUtil()
imfirst=self.first.GetImageData()
imsecond=self.second.GetImageData()
if imfirst.GetScalarTypeMin()>=0: #unsigned
imfirst.SetScalarType(imfirst.GetScalarType()-1)
if imsecond.GetScalarTypeMin()>=0: #unsigned
imsecond.SetScalarType(imsecond.GetScalarType()-1)
stat=qu.getROIstats(self.first,self.label)
statfirst=stat.values()[0]
mathv=vtk.vtkImageMathematics()
mathv.SetInput1Data(imfirst)
mathv.SetInput2Data(imsecond)
mathv.SetOperationToSubtract()
mathv.Update()
imsub=mathv.GetOutput()
if imsub.GetScalarTypeMin()>=0: #unsigned
imsub.SetScalarType(imsub.GetScalarType()-1)
stat=qu.getROIstatsIM(imsub,self.label.GetImageData())
statsub=stat.values()[0]
len=statfirst.__len__()
SNRvalues={}
for n in range(len):
stat={}
statfirstn=statfirst.values()[n]
statsubn=statsub.values()[n]
stat['count']=statfirstn['count']
stat['mean']=statfirstn['mean']
stat['sd']=statfirstn['sd']
stat['N']=statsubn['sd']
SNRvalues[statfirst.keys()[n]]=stat
return SNRvalues
def computeDifference(self, fieldA, fieldB, roi, differenceVolume):
referenceVolume = self.createVectorVolumeFromRoi(roi, self.ReferenceVolumeSpacingMm)
referenceVolume.SetName('ReferenceVolume')
slicer.mrmlScene.AddNode( referenceVolume )
resampledFieldA = self.resampleVolume(fieldA, referenceVolume)
resampledFieldB = self.resampleVolume(fieldB, referenceVolume)
subtractor = vtk.vtkImageMathematics()
subtractor.SetOperationToSubtract()
subtractor.SetInput1Data(resampledFieldA.GetImageData())
subtractor.SetInput2Data(resampledFieldB.GetImageData())
differenceVolume.SetImageDataConnection(subtractor.GetOutputPort())
ijkToRasMatrix = vtk.vtkMatrix4x4()
referenceVolume.GetIJKToRASMatrix(ijkToRasMatrix)
differenceVolume.SetIJKToRASMatrix(ijkToRasMatrix)
differenceVolumeDisplayNode = slicer.vtkMRMLVectorVolumeDisplayNode()
slicer.mrmlScene.AddNode( differenceVolumeDisplayNode )
differenceVolumeDisplayNode.SetAndObserveColorNodeID("vtkMRMLColorTableNodeRainbow");
differenceVolume.SetAndObserveNthDisplayNodeID(0, differenceVolumeDisplayNode.GetID());
slicer.mrmlScene.RemoveNode( resampledFieldA )
slicer.mrmlScene.RemoveNode( resampledFieldB )
slicer.mrmlScene.RemoveNode( referenceVolume )
def loadPetSeries(self, loadable):
"""Use the conversion factor to load the volume into Slicer"""
conversionFactor = loadable.slope
# Create volume node
imageNode = self.scalarVolumePlugin.loadFilesWithArchetype(loadable.files, loadable.name)
if imageNode:
# apply the conversion factor
multiplier = vtk.vtkImageMathematics()
multiplier.SetOperationToMultiplyByK()
multiplier.SetConstantK(float(conversionFactor))
if vtk.VTK_MAJOR_VERSION <= 5:
multiplier.SetInput1(imageNode.GetImageData())
else:
multiplier.SetInput1Data(imageNode.GetImageData())
multiplier.Update()
imageNode.GetImageData().DeepCopy(multiplier.GetOutput())
# create list of DICOM instance UIDs corresponding to the loaded files
instanceUIDs = ""
for dicomFile in loadable.files:
uid = slicer.dicomDatabase.fileValue(dicomFile,self.tags['sopInstanceUID'])
if uid == "":
uid = "Unknown"
instanceUIDs += uid + " "
instanceUIDs = instanceUIDs[:-1] # strip last space
# get the instance UID for the RWVM object
derivedItemUID = ""
try:
derivedItemUID = slicer.dicomDatabase.fileValue(loadable.rwvFile,self.tags['sopInstanceUID'])
except AttributeError:
# no derived items
pass
# Set Attributes
imageNode.SetAttribute('DICOM.MeasurementUnitsCodeMeaning',loadable.unitName)
imageNode.SetAttribute('DICOM.MeasurementUnitsCodeValue',loadable.units)
# Keep references to the PET instances, as these may be needed to
# establish correspondence between slice annotations and acutal slices,
# but also keep the RWVM instance UID ... it's confusing, but not sure
# if there is a better way in Slicer for now
imageNode.SetAttribute("DICOM.instanceUIDs", instanceUIDs)
imageNode.SetAttribute("DICOM.RWV.instanceUID", derivedItemUID)
# automatically select the volume to display
volumeLogic = slicer.modules.volumes.logic()
appLogic = slicer.app.applicationLogic()
selNode = appLogic.GetSelectionNode()
selNode.SetReferenceActiveVolumeID(imageNode.GetID())
appLogic.PropagateVolumeSelection()
# Change display
displayNode = imageNode.GetVolumeDisplayNode()
displayNode.SetInterpolate(0)
if loadable.referencedModality == 'PT':
radiopharmaceuticalCode = ''
try:
radiopharmaceuticalCode = loadable.RadiopharmaceuticalCodeValue
imageNode.SetAttribute('DICOM.RadiopharmaceuticalCodeValue',radiopharmaceuticalCode)
print('Found Radiopharmaceutical Code ' + radiopharmaceuticalCode)
except AttributeError:
imageNode.SetAttribute('DICOM.RadiopharmaceuticalCodeValue','unknown')
# use radionuclide info instead
radionuclideCode = ''
try:
radionuclideCode = loadable.RadionuclideCodeValue
imageNode.SetAttribute('DICOM.RadionuclideCodeValue',radionuclideCode)
print('Found Radionuclide Code ' + radionuclideCode)
except AttributeError:
imageNode.SetAttribute('DICOM.RadionuclideCodeValue','unknown')
if radiopharmaceuticalCode == 'C-B1031': # FDG
displayNode.AutoWindowLevelOff()
displayNode.SetWindowLevel(6,3)
displayNode.SetAndObserveColorNodeID('vtkMRMLColorTableNodeInvertedGrey')
elif radiopharmaceuticalCode == 'C-B1036': # FLT
displayNode.AutoWindowLevelOff()
displayNode.SetWindowLevel(4,2)
displayNode.SetAndObserveColorNodeID('vtkMRMLColorTableNodeInvertedGrey')
else: # Default W/L if no info about radiopharmaceutical can be found, often FDG
displayNode.AutoWindowLevelOff()
displayNode.SetWindowLevel(6,3)
displayNode.SetAndObserveColorNodeID('vtkMRMLColorTableNodeInvertedGrey')
else:
displayNode.SetAutoWindowLevel(1)
# Change name
name = (loadable.name).replace(' ','_')
imageNode.SetName(name)
# create Subject Hierarchy nodes for the loaded series
self.addSeriesInSubjectHierarchy(loadable,imageNode)
return imageNode
def load(self,loadable):
"""Use the conversion factor to load the volume into Slicer"""
conversionFactor = loadable.slope
# Create volume node
imageNode = self.scalarVolumePlugin.loadFilesWithArchetype(loadable.files, loadable.name)
if imageNode:
# apply the conversion factor
multiplier = vtk.vtkImageMathematics()
multiplier.SetOperationToMultiplyByK()
multiplier.SetConstantK(float(conversionFactor))
multiplier.SetInput1Data(imageNode.GetImageData())
multiplier.Update()
imageNode.GetImageData().DeepCopy(multiplier.GetOutput())
# create Subject Hierarchy nodes for the loaded series
self.addSeriesInSubjectHierarchy(loadable,imageNode)
# create list of DICOM instance UIDs corresponding to the loaded files
instanceUIDs = ""
for dicomFile in loadable.files:
uid = slicer.dicomDatabase.fileValue(dicomFile,self.tags['sopInstanceUID'])
if uid == "":
uid = "Unknown"
instanceUIDs += uid + " "
instanceUIDs = instanceUIDs[:-1] # strip last space
# get the instance UID for the RWVM object
derivedItemUID = ""
try:
derivedItemUID = slicer.dicomDatabase.fileValue(loadable.derivedItems[0],self.tags['sopInstanceUID'])
except AttributeError:
# no derived items
pass
# Set Attributes
patientName = self.__getSeriesInformation(loadable.files, self.tags['patientName'])
patientBirthDate = self.__getSeriesInformation(loadable.files, self.tags['patientBirthDate'])
patientSex = self.__getSeriesInformation(loadable.files, self.tags['patientSex'])
patientHeight = self.__getSeriesInformation(loadable.files, self.tags['patientHeight'])
patientWeight = self.__getSeriesInformation(loadable.files, self.tags['patientWeight'])
imageNode.SetAttribute('DICOM.PatientID', loadable.patientID)
imageNode.SetAttribute('DICOM.PatientName', patientName)
imageNode.SetAttribute('DICOM.PatientBirthDate', patientBirthDate)
imageNode.SetAttribute('DICOM.PatientSex', patientSex)
imageNode.SetAttribute('DICOM.PatientHeight', patientHeight)
imageNode.SetAttribute('DICOM.PatientWeight', patientWeight)
imageNode.SetAttribute('DICOM.StudyDate', loadable.studyDate)
imageNode.SetAttribute('DICOM.MeasurementUnitsCodeMeaning',loadable.unitName)
imageNode.SetAttribute('DICOM.MeasurementUnitsCodeValue',loadable.units)
imageNode.SetAttribute("DICOM.instanceUIDs", instanceUIDs)
imageNode.SetAttribute("DICOM.RealWorldValueMappingUID", derivedItemUID)
# automatically select the volume to display
volumeLogic = slicer.modules.volumes.logic()
appLogic = slicer.app.applicationLogic()
selNode = appLogic.GetSelectionNode()
selNode.SetReferenceActiveVolumeID(imageNode.GetID())
appLogic.PropagateVolumeSelection()
# Change display
displayNode = imageNode.GetVolumeDisplayNode()
displayNode.SetInterpolate(0)
# Change name
name = (loadable.name).replace(' ','_')
imageNode.SetName(name)
return imageNode
def test_ResectionVolume1(self):
""" Ideally you should have several levels of tests. At the lowest level
tests sould exercise the functionality of the logic with different inputs
(both valid and invalid). At higher levels your tests should emulate the
way the user would interact with your code and confirm that it still works
the way you intended.
One of the most important features of the tests is that it should alert other
developers when their changes will have an impact on the behavior of your
module. For example, if a developer removes a feature that you depend on,
your test should break so they know that the feature is needed.
"""
self.delayDisplay("Starting the test")
#
# first, get some data
#
resectionVolumeWidget = slicer.modules.ResectionVolumeWidget
# Confirm that generate surface checkbox will not stay checked
resectionVolumeWidget.generateSurface.setChecked(True)
self.assertTrue(resectionVolumeWidget.generateSurface.isChecked() == False)
# Data is in local directory currently for initial development
slicer.util.loadMarkupsFiducialList("C:\SlicerTestData\ResectionVolumePoints.fcsv")
slicer.util.loadModel("C:\SlicerTestData\ResectionVolumeModel.vtk")
slicer.util.loadLabelVolume("C:\SlicerTestData\ResectionVolumeTestLabel.nrrd")
slicer.util.loadLabelVolume("C:\SlicerTestData\RecoloredResectionVolumeTestLabel.nrrd")
# Set fiducial points node
fiducialNode = slicer.util.getNode("ResectionVolumePoints")
resectionVolumeWidget.fiducialSelector.setCurrentNode(fiducialNode)
# Confirm that generate surface checkbox will not stay checked
resectionVolumeWidget.generateSurface.setChecked(True)
self.assertTrue(resectionVolumeWidget.generateSurface.isChecked() == False)
# Set model node
testModelNode = slicer.mrmlScene.CreateNodeByClass("vtkMRMLModelNode")
testModelNode.SetName("ResectionVolumeModelTest")
slicer.mrmlScene.AddNode(testModelNode)
resectionVolumeWidget.modelSelector.setCurrentNode(testModelNode)
# Check the generate surface box
resectionVolumeWidget.generateSurface.setChecked(True)
# Confirm that generate surface checkbox stays checked
self.assertTrue(resectionVolumeWidget.generateSurface.isChecked())
# Compare newly generated model with loaded model by determining if
# the maximum distance between the 2 sets of polydata is less than
# a desired value
loadedModelNode = slicer.util.getNode("ResectionVolumeModel")
distanceFilter = vtk.vtkDistancePolyDataFilter()
distanceFilter.SetInputData(0, testModelNode.GetPolyData())
distanceFilter.SetInputData(1, loadedModelNode.GetPolyData())
distanceFilter.Update()
distancePolyData = distanceFilter.GetOutput()
distanceRange = distancePolyData.GetScalarRange()
maxDistance = max(abs(distanceRange[0]),abs(distanceRange[1]))
self.assertTrue(maxDistance < 0.0001) # What value for cutoff
# Recolor the test label
labelNode = slicer.util.getNode("ResectionVolumeTestLabel")
loadedLabelNode = slicer.util.getNode("RecoloredResectionVolumeTestLabel")
resectionVolumeWidget.labelSelector.setCurrentNode(labelNode)
resectionVolumeWidget.initialLabelValueSelector.setValue(1)
resectionVolumeWidget.outputLabelValueSelector.setValue(2)
resectionVolumeWidget.onRecolorLabelMap()
# Compare the recolored test label with the loaded recolored test label
# by subtracting the 2 images (which should be the same) and then finding
# the min/max values, (which should be 0)
imageMath = vtk.vtkImageMathematics()
imageMath.SetOperationToSubtract()
imageMath.SetInput1Data(labelNode.GetImageData())
imageMath.SetInput2Data(loadedLabelNode.GetImageData())
imageMath.Update()
imageStatistics = vtk.vtkImageHistogramStatistics()
imageStatistics.SetInputData(imageMath.GetOutput())
minimumValue = imageStatistics.GetMinimum()
maximumValue = imageStatistics.GetMaximum()
self.assertTrue(minimumValue == maximumValue == 0)
self.delayDisplay('Test passed!')
def test_ResectionVolume1(self):
""" Ideally you should have several levels of tests. At the lowest level
tests sould exercise the functionality of the logic with different inputs
(both valid and invalid). At higher levels your tests should emulate the
way the user would interact with your code and confirm that it still works
the way you intended.
One of the most important features of the tests is that it should alert other
developers when their changes will have an impact on the behavior of your
module. For example, if a developer removes a feature that you depend on,
your test should break so they know that the feature is needed.
"""
self.delayDisplay("Starting the test")
slicer.util.selectModule('ResectionVolume')
resectionVolumeWidget = slicer.modules.ResectionVolumeWidget
# Confirm that generate surface checkbox will not stay checked
resectionVolumeWidget.generateSurface.setChecked(True)
self.assertTrue(
resectionVolumeWidget.generateSurface.isChecked() == False)
# Data is in local directory currently for initial development
dir = os.path.dirname(__file__)
slicer.util.loadMarkupsFiducialList(
dir + "/TestData/ResectionVolumePoints.fcsv")
slicer.util.loadModel(dir + "/TestData/ResectionVolumeModel.vtk")
slicer.util.loadLabelVolume(dir +
"/TestData/ResectionVolumeTestLabel.nrrd")
slicer.util.loadLabelVolume(
dir + "/TestData/RecoloredResectionVolumeTestLabel.nrrd")
# Set fiducial points node
fiducialNode = slicer.util.getNode("ResectionVolumePoints")
resectionVolumeWidget.fiducialSelector.setCurrentNode(fiducialNode)
# Confirm that generate surface checkbox will not stay checked
resectionVolumeWidget.generateSurface.setChecked(True)
self.assertTrue(
resectionVolumeWidget.generateSurface.isChecked() == False)
# Set model node
testModelNode = slicer.mrmlScene.CreateNodeByClass("vtkMRMLModelNode")
testModelNode.SetName("ResectionVolumeModelTest")
slicer.mrmlScene.AddNode(testModelNode)
resectionVolumeWidget.modelSelector.setCurrentNode(testModelNode)
# Check the generate surface box
resectionVolumeWidget.generateSurface.setChecked(True)
# Confirm that generate surface checkbox stays checked
self.assertTrue(resectionVolumeWidget.generateSurface.isChecked())
# Compare newly generated model with loaded model by determining if
# the maximum distance between the 2 sets of polydata is less than
# a desired value
loadedModelNode = slicer.util.getNode("ResectionVolumeModel")
distanceFilter = vtk.vtkDistancePolyDataFilter()
distanceFilter.SetInputData(0, testModelNode.GetPolyData())
distanceFilter.SetInputData(1, loadedModelNode.GetPolyData())
distanceFilter.Update()
distancePolyData = distanceFilter.GetOutput()
distanceRange = distancePolyData.GetScalarRange()
maxDistance = max(abs(distanceRange[0]), abs(distanceRange[1]))
self.assertTrue(maxDistance < 0.0001) # What value for cutoff
self.delayDisplay('Generate Model Test Passed!')
# Recolor the test label
labelNode = slicer.util.getNode("ResectionVolumeTestLabel")
loadedLabelNode = slicer.util.getNode(
"RecoloredResectionVolumeTestLabel")
resectionVolumeWidget.labelSelector.setCurrentNode(labelNode)
resectionVolumeWidget.initialLabelValueSelector.setValue(1)
resectionVolumeWidget.outputLabelValueSelector.setValue(2)
resectionVolumeWidget.onRecolorLabelMap()
# Compare the recolored test label with the loaded recolored test label
# by subtracting the 2 images (which should be the same) and then finding
# the min/max values, (which should be 0)
imageMath = vtk.vtkImageMathematics()
imageMath.SetOperationToSubtract()
imageMath.SetInput1Data(labelNode.GetImageData())
imageMath.SetInput2Data(loadedLabelNode.GetImageData())
imageMath.Update()
imageStatistics = vtk.vtkImageHistogramStatistics()
imageStatistics.SetInputData(imageMath.GetOutput())
minimumValue = imageStatistics.GetMinimum()
maximumValue = imageStatistics.GetMaximum()
self.assertTrue(minimumValue == maximumValue == 0)
self.delayDisplay('Test passed!')
def preview(self,color=None):
if not self.editUtil.getBackgroundImage() or not self.editUtil.getLabelImage():
return
#
# make a lookup table where inside the threshold is opaque and colored
# by the label color, while the background is transparent (black)
# - apply the threshold operation to the currently visible background
# (output of the layer logic's vtkImageReslice instance)
#
if not color:
color = self.getPaintColor
if not self.lut:
self.lut = vtk.vtkLookupTable()
self.lut.SetRampToLinear()
self.lut.SetNumberOfTableValues( 3 )
self.lut.SetTableRange( 0, 2 )
self.lut.SetTableValue( 0, 0, 0, 0, 0 )
r,g,b,a = color
self.lut.SetTableValue( 1, r, g, b, a/3 )
self.lut.SetTableValue( 2, r, g, b, a )
if not self.map:
self.map = vtk.vtkImageMapToRGBA()
self.map.SetOutputFormatToRGBA()
self.map.SetLookupTable( self.lut )
if not self.thresh:
self.thresh = vtk.vtkImageThreshold()
sliceLogic = self.sliceWidget.sliceLogic()
backgroundLogic = sliceLogic.GetBackgroundLayer()
self.thresh.SetInput( backgroundLogic.GetReslice().GetOutput() )
self.thresh.ThresholdBetween( self.min, self.max )
self.thresh.SetInValue( 1 )
self.thresh.SetOutValue( 0 )
self.thresh.SetOutputScalarTypeToUnsignedChar()
if not self.outter_thresh:
self.outter_thresh = vtk.vtkImageThreshold()
sliceLogic = self.sliceWidget.sliceLogic()
backgroundLogic = sliceLogic.GetBackgroundLayer()
self.outter_thresh.SetInput( backgroundLogic.GetReslice().GetOutput() )
self.outter_thresh.ThresholdBetween( self.outer_min, self.outer_max )
self.outter_thresh.SetInValue( 1 )
self.outter_thresh.SetOutValue( 0 )
self.outter_thresh.SetOutputScalarTypeToUnsignedChar()
if not self.add_thresh:
self.add_thresh = vtk.vtkImageMathematics()
self.add_thresh.SetInput1( self.thresh.GetOutput() )
self.add_thresh.SetInput2( self.outter_thresh.GetOutput() )
self.add_thresh.SetOperationToAdd()
self.map.SetInput( self.add_thresh.GetOutput() )
self.map.Update()
self.cursorMapper.SetInput( self.map.GetOutput() )
self.cursorActor.VisibilityOn()
self.sliceView.scheduleRender()
def run(self, enableScreenshots=0, screenshotScaleFactor=1):
"""
Run the actual algorithm
"""
self.delayDisplay('Running the aglorithm')
self.enableScreenshots = enableScreenshots
self.screenshotScaleFactor = screenshotScaleFactor
# Start in conventional layout
lm = slicer.app.layoutManager()
lm.setLayout(slicer.vtkMRMLLayoutNode.SlicerLayoutConventionalView)
# without this delayed display, when running from the cmd line Slicer starts
# up in a different layout and the seed won't get rendered in the right spot
self.delayDisplay("Conventional view")
# Download MRHead from sample data
import SampleData
sampleDataLogic = SampleData.SampleDataLogic()
print("Getting MR Head Volume")
mrHeadVolume = sampleDataLogic.downloadMRHead()
# Place a fiducial on the red slice
markupsLogic = slicer.modules.markups.logic()
eye = [33.4975, 79.4042, -10.2143]
fidIndex = markupsLogic.AddFiducial(eye[0], eye[1], eye[2])
fidID = markupsLogic.GetActiveListID()
fidNode = slicer.mrmlScene.GetNodeByID(fidID)
self.delayDisplay("Placed a fiducial")
# Pan and zoom
sliceWidget = slicer.app.layoutManager().sliceWidget('Red')
sliceLogic = sliceWidget.sliceLogic()
compositeNode = sliceLogic.GetSliceCompositeNode()
sliceNode = sliceLogic.GetSliceNode()
sliceNode.SetXYZOrigin(-71.7, 129.7, 0.0)
sliceNode.SetFieldOfView(98.3, 130.5, 1.0)
self.delayDisplay("Panned and zoomed")
# Get the seed widget seed location
startingSeedDisplayCoords = [0.0, 0.0, 0.0]
helper = self.getFiducialSliceDisplayableManagerHelper('Red')
if helper != None:
seedWidget = helper.GetWidget(fidNode)
seedRepresentation = seedWidget.GetSeedRepresentation()
handleRep = seedRepresentation.GetHandleRepresentation(fidIndex)
startingSeedDisplayCoords = handleRep.GetDisplayPosition()
print('Starting seed display coords = %d, %d, %d' %
(startingSeedDisplayCoords[0], startingSeedDisplayCoords[1],
startingSeedDisplayCoords[2]))
self.takeScreenshot('FiducialLayoutSwitchBug1914-StartingPosition',
'Fiducial starting position',
slicer.qMRMLScreenShotDialog().Red)
# Switch to red slice only
lm.setLayout(slicer.vtkMRMLLayoutNode.SlicerLayoutOneUpRedSliceView)
self.delayDisplay("Red Slice only")
# Switch to conventional layout
lm.setLayout(slicer.vtkMRMLLayoutNode.SlicerLayoutConventionalView)
self.delayDisplay("Conventional layout")
# Get the current seed widget seed location
endingSeedDisplayCoords = [0.0, 0.0, 0.0]
helper = self.getFiducialSliceDisplayableManagerHelper('Red')
if helper != None:
seedWidget = helper.GetWidget(fidNode)
seedRepresentation = seedWidget.GetSeedRepresentation()
handleRep = seedRepresentation.GetHandleRepresentation(fidIndex)
endingSeedDisplayCoords = handleRep.GetDisplayPosition()
print('Ending seed display coords = %d, %d, %d' %
(endingSeedDisplayCoords[0], endingSeedDisplayCoords[1],
endingSeedDisplayCoords[2]))
self.takeScreenshot('FiducialLayoutSwitchBug1914-EndingPosition',
'Fiducial ending position',
slicer.qMRMLScreenShotDialog().Red)
# Compare to original seed widget location
diff = math.pow(
(startingSeedDisplayCoords[0] - endingSeedDisplayCoords[0]),
2) + math.pow(
(startingSeedDisplayCoords[1] - endingSeedDisplayCoords[1]),
2) + math.pow((startingSeedDisplayCoords[2] -
endingSeedDisplayCoords[2]), 2)
if diff != 0.0:
diff = math.sqrt(diff)
self.delayDisplay(
"Difference between starting and ending seed display coordinates = %g"
% diff)
if diff > 1.0:
# raise Exception("Display coordinate difference is too large!\nExpected < 1.0 but got %g" % (diff))
print(
"Display coordinate difference is too large!\nExpected < 1.0 but got %g"
% (diff))
return False
if enableScreenshots == 1:
# compare the screen snapshots
startView = slicer.mrmlScene.GetFirstNodeByName(
'FiducialLayoutSwitchBug1914-StartingPosition')
startShot = startView.GetScreenShot()
endView = slicer.mrmlScene.GetFirstNodeByName(
'FiducialLayoutSwitchBug1914-EndingPosition')
endShot = endView.GetScreenShot()
imageMath = vtk.vtkImageMathematics()
imageMath.SetOperationToSubtract()
imageMath.SetInput1(startShot)
imageMath.SetInput2(endShot)
imageMath.Update()
shotDiff = imageMath.GetOutput()
# save it as a scene view
annotationLogic = slicer.modules.annotations.logic()
annotationLogic.CreateSnapShot(
"FiducialLayoutSwitchBug1914-Diff",
"Difference between starting and ending fiducial seed positions",
slicer.qMRMLScreenShotDialog().Red, screenshotScaleFactor,
shotDiff)
# calculate the image difference
imageStats = vtk.vtkImageHistogramStatistics()
imageStats.SetInput(shotDiff)
imageStats.GenerateHistogramImageOff()
imageStats.Update()
meanVal = imageStats.GetMean()
self.delayDisplay("Mean of image difference = %g" % meanVal)
if meanVal > 5.0:
# raise Exception("Image difference is too great!\nExpected <= 5.0, but got %g" % (meanVal))
print(
"Image difference is too great!\nExpected <= 5.0, but got %g"
% (meanVal))
return False
self.delayDisplay('Test passed!')
return True
def performInitialization( self, image, lowerThreshold, upperThreshold, sourceSeedIds, targetSeedIds, ignoreSideBranches=0 ):
'''
'''
# import the vmtk libraries
try:
#from libvtkvmtkSegmentationPython import *
import libvtkvmtkSegmentationPython as s
except ImportError:
print "FAILURE: Unable to import the SlicerVmtk libraries!"
cast = vtk.vtkImageCast()
cast.SetInput( image )
cast.SetOutputScalarTypeToFloat()
cast.Update()
image = cast.GetOutput()
scalarRange = image.GetScalarRange()
imageDimensions = image.GetDimensions()
maxImageDimensions = max( imageDimensions )
threshold = vtk.vtkImageThreshold()
threshold.SetInput( image )
threshold.ThresholdBetween( lowerThreshold, upperThreshold )
threshold.ReplaceInOff()
threshold.ReplaceOutOn()
threshold.SetOutValue( scalarRange[0] - scalarRange[1] )
threshold.Update()
thresholdedImage = threshold.GetOutput()
scalarRange = thresholdedImage.GetScalarRange()
shiftScale = vtk.vtkImageShiftScale()
shiftScale.SetInput( thresholdedImage )
shiftScale.SetShift( -scalarRange[0] )
shiftScale.SetScale( 1.0 / ( scalarRange[1] - scalarRange[0] ) )
shiftScale.Update()
speedImage = shiftScale.GetOutput()
if ignoreSideBranches:
# ignore sidebranches, use colliding fronts
fastMarching = s.vtkvmtkCollidingFrontsImageFilter()
fastMarching.SetInput( speedImage )
fastMarching.SetSeeds1( sourceSeedIds )
fastMarching.SetSeeds2( targetSeedIds )
fastMarching.ApplyConnectivityOn()
fastMarching.StopOnTargetsOn()
fastMarching.Update()
subtract = vtk.vtkImageMathematics()
subtract.SetInput( fastMarching.GetOutput() )
subtract.SetOperationToAddConstant()
subtract.SetConstantC( -10 * fastMarching.GetNegativeEpsilon() )
subtract.Update()
else:
fastMarching = s.vtkvmtkFastMarchingUpwindGradientImageFilter()
fastMarching.SetInput( speedImage )
fastMarching.SetSeeds( sourceSeedIds )
fastMarching.GenerateGradientImageOn()
fastMarching.SetTargetOffset( 0.0 )
fastMarching.SetTargets( targetSeedIds )
if targetSeedIds.GetNumberOfIds() > 0:
fastMarching.SetTargetReachedModeToOneTarget()
else:
fastMarching.SetTargetReachedModeToNoTargets()
fastMarching.Update()
if targetSeedIds.GetNumberOfIds() > 0:
subtract = vtk.vtkImageMathematics()
subtract.SetInput( fastMarching.GetOutput() )
subtract.SetOperationToAddConstant()
subtract.SetConstantC( -fastMarching.GetTargetValue() )
subtract.Update()
else:
subtract = vtk.vtkImageThreshold()
subtract.SetInput( fastMarching.GetOutput() )
subtract.ThresholdByLower( 2000 ) # TODO find robuste value
subtract.ReplaceInOff()
subtract.ReplaceOutOn()
subtract.SetOutValue( -1 )
subtract.Update()
outImageData = vtk.vtkImageData()
outImageData.DeepCopy( subtract.GetOutput() )
outImageData.Update()
return outImageData
def performInitialization(self,
image,
lowerThreshold,
upperThreshold,
sourceSeedIds,
targetSeedIds,
ignoreSideBranches=0):
'''
'''
# import the vmtk libraries
try:
import vtkvmtkSegmentationPython as vtkvmtkSegmentation
except ImportError:
logging.error("Unable to import the SlicerVmtk libraries")
cast = vtk.vtkImageCast()
cast.SetInputData(image)
cast.SetOutputScalarTypeToFloat()
cast.Update()
image = cast.GetOutput()
scalarRange = image.GetScalarRange()
imageDimensions = image.GetDimensions()
maxImageDimensions = max(imageDimensions)
threshold = vtk.vtkImageThreshold()
threshold.SetInputData(image)
threshold.ThresholdBetween(lowerThreshold, upperThreshold)
threshold.ReplaceInOff()
threshold.ReplaceOutOn()
threshold.SetOutValue(scalarRange[0] - scalarRange[1])
threshold.Update()
thresholdedImage = threshold.GetOutput()
scalarRange = thresholdedImage.GetScalarRange()
shiftScale = vtk.vtkImageShiftScale()
shiftScale.SetInputData(thresholdedImage)
shiftScale.SetShift(-scalarRange[0])
shiftScale.SetScale(1.0 / (scalarRange[1] - scalarRange[0]))
shiftScale.Update()
speedImage = shiftScale.GetOutput()
if ignoreSideBranches:
# ignore sidebranches, use colliding fronts
fastMarching = vtkvmtkSegmentation.vtkvmtkCollidingFrontsImageFilter(
)
fastMarching.SetInputData(speedImage)
fastMarching.SetSeeds1(sourceSeedIds)
fastMarching.SetSeeds2(targetSeedIds)
fastMarching.ApplyConnectivityOn()
fastMarching.StopOnTargetsOn()
fastMarching.Update()
subtract = vtk.vtkImageMathematics()
subtract.SetInputData(fastMarching.GetOutput())
subtract.SetOperationToAddConstant()
subtract.SetConstantC(-10 * fastMarching.GetNegativeEpsilon())
subtract.Update()
else:
fastMarching = vtkvmtkSegmentation.vtkvmtkFastMarchingUpwindGradientImageFilter(
)
fastMarching.SetInputData(speedImage)
fastMarching.SetSeeds(sourceSeedIds)
fastMarching.GenerateGradientImageOn()
fastMarching.SetTargetOffset(0.0)
fastMarching.SetTargets(targetSeedIds)
if targetSeedIds.GetNumberOfIds() > 0:
fastMarching.SetTargetReachedModeToOneTarget()
else:
fastMarching.SetTargetReachedModeToNoTargets()
fastMarching.Update()
if targetSeedIds.GetNumberOfIds() > 0:
subtract = vtk.vtkImageMathematics()
subtract.SetInputData(fastMarching.GetOutput())
subtract.SetOperationToAddConstant()
subtract.SetConstantC(-fastMarching.GetTargetValue())
subtract.Update()
else:
subtract = vtk.vtkImageThreshold()
subtract.SetInputData(fastMarching.GetOutput())
subtract.ThresholdByLower(2000) # TODO find robuste value
subtract.ReplaceInOff()
subtract.ReplaceOutOn()
subtract.SetOutValue(-1)
subtract.Update()
outImageData = vtk.vtkImageData()
outImageData.DeepCopy(subtract.GetOutput())
return outImageData
def loadPetSeries(self, loadable):
"""Use the conversion factor to load the volume into Slicer"""
conversionFactor = loadable.slope
# Create volume node
imageNode = self.scalarVolumePlugin.loadFilesWithArchetype(loadable.files, loadable.name)
if imageNode:
# apply the conversion factor
multiplier = vtk.vtkImageMathematics()
multiplier.SetOperationToMultiplyByK()
multiplier.SetConstantK(float(conversionFactor))
if vtk.VTK_MAJOR_VERSION <= 5:
multiplier.SetInput1(imageNode.GetImageData())
else:
multiplier.SetInput1Data(imageNode.GetImageData())
multiplier.Update()
imageNode.GetImageData().DeepCopy(multiplier.GetOutput())
# create list of DICOM instance UIDs corresponding to the loaded files
instanceUIDs = ""
for dicomFile in loadable.files:
uid = slicer.dicomDatabase.fileValue(dicomFile,self.tags['sopInstanceUID'])
if uid == "":
uid = "Unknown"
instanceUIDs += uid + " "
instanceUIDs = instanceUIDs[:-1] # strip last space
# get the instance UID for the RWVM object
derivedItemUID = ""
try:
derivedItemUID = slicer.dicomDatabase.fileValue(loadable.rwvFile,self.tags['sopInstanceUID'])
except AttributeError:
# no derived items
pass
if loadable.quantity:
imageNode.SetVoxelValueQuantity(loadable.quantity)
if loadable.units:
imageNode.SetVoxelValueUnits(loadable.units)
# Keep references to the PET instances, as these may be needed to
# establish correspondence between slice annotations and acutal slices,
# but also keep the RWVM instance UID ... it's confusing, but not sure
# if there is a better way in Slicer for now
imageNode.SetAttribute("DICOM.instanceUIDs", instanceUIDs)
imageNode.SetAttribute("DICOM.RWV.instanceUID", derivedItemUID)
# automatically select the volume to display
volumeLogic = slicer.modules.volumes.logic()
appLogic = slicer.app.applicationLogic()
selNode = appLogic.GetSelectionNode()
selNode.SetReferenceActiveVolumeID(imageNode.GetID())
appLogic.PropagateVolumeSelection()
# Change display
displayNode = imageNode.GetVolumeDisplayNode()
displayNode.SetInterpolate(0)
if loadable.referencedModality == 'PT':
radiopharmaceuticalCode = ''
try:
radiopharmaceuticalCode = loadable.RadiopharmaceuticalCodeValue
imageNode.SetAttribute('DICOM.RadiopharmaceuticalCodeValue',radiopharmaceuticalCode)
print('Found Radiopharmaceutical Code ' + radiopharmaceuticalCode)
except AttributeError:
imageNode.SetAttribute('DICOM.RadiopharmaceuticalCodeValue','unknown')
# use radionuclide info instead
radionuclideCode = ''
try:
radionuclideCode = loadable.RadionuclideCodeValue
imageNode.SetAttribute('DICOM.RadionuclideCodeValue',radionuclideCode)
print('Found Radionuclide Code ' + radionuclideCode)
except AttributeError:
imageNode.SetAttribute('DICOM.RadionuclideCodeValue','unknown')
if radiopharmaceuticalCode == 'C-B1031': # FDG
displayNode.AutoWindowLevelOff()
displayNode.SetWindowLevel(6,3)
displayNode.SetAndObserveColorNodeID('vtkMRMLColorTableNodeInvertedGrey')
elif radiopharmaceuticalCode == 'C-B1036': # FLT
displayNode.AutoWindowLevelOff()
displayNode.SetWindowLevel(4,2)
displayNode.SetAndObserveColorNodeID('vtkMRMLColorTableNodeInvertedGrey')
else: # Default W/L if no info about radiopharmaceutical can be found, often FDG
displayNode.AutoWindowLevelOff()
displayNode.SetWindowLevel(6,3)
displayNode.SetAndObserveColorNodeID('vtkMRMLColorTableNodeInvertedGrey')
else:
displayNode.SetAutoWindowLevel(1)
# Change name
name = (loadable.name).replace(' ','_')
imageNode.SetName(name)
# create Subject Hierarchy nodes for the loaded series
self.addSeriesInSubjectHierarchy(loadable,imageNode)
return imageNode
def run(self,enableScreenshots=0,screenshotScaleFactor=1):
"""
Run the actual algorithm
"""
self.delayDisplay('Running the aglorithm')
self.enableScreenshots = enableScreenshots
self.screenshotScaleFactor = screenshotScaleFactor
# Start in conventional layout
lm = slicer.app.layoutManager()
lm.setLayout(slicer.vtkMRMLLayoutNode.SlicerLayoutConventionalView)
# without this delayed display, when running from the cmd line Slicer starts
# up in a different layout and the seed won't get rendered in the right spot
self.delayDisplay("Conventional view")
# Download MRHead from sample data
import SampleData
sampleDataLogic = SampleData.SampleDataLogic()
print("Getting MR Head Volume")
mrHeadVolume = sampleDataLogic.downloadMRHead()
# Place a fiducial on the red slice
markupsLogic = slicer.modules.markups.logic()
eye = [33.4975, 79.4042, -10.2143]
fidIndex = markupsLogic.AddFiducial(eye[0], eye[1], eye[2])
fidID = markupsLogic.GetActiveListID()
fidNode = slicer.mrmlScene.GetNodeByID(fidID)
self.delayDisplay("Placed a fiducial")
# Pan and zoom
sliceWidget = slicer.app.layoutManager().sliceWidget('Red')
sliceLogic = sliceWidget.sliceLogic()
compositeNode = sliceLogic.GetSliceCompositeNode()
sliceNode = sliceLogic.GetSliceNode()
sliceNode.SetXYZOrigin(-71.7, 129.7, 0.0)
sliceNode.SetFieldOfView(98.3, 130.5, 1.0)
self.delayDisplay("Panned and zoomed")
# Get the seed widget seed location
startingSeedDisplayCoords = [0.0, 0.0, 0.0]
helper = self.getFiducialSliceDisplayableManagerHelper('Red')
if helper != None:
seedWidget = helper.GetWidget(fidNode)
seedRepresentation = seedWidget.GetSeedRepresentation()
handleRep = seedRepresentation.GetHandleRepresentation(fidIndex)
startingSeedDisplayCoords = handleRep.GetDisplayPosition()
print('Starting seed display coords = %d, %d, %d' % (startingSeedDisplayCoords[0], startingSeedDisplayCoords[1], startingSeedDisplayCoords[2]))
self.takeScreenshot('FiducialLayoutSwitchBug1914-StartingPosition','Fiducial starting position',slicer.qMRMLScreenShotDialog().Red)
# Switch to red slice only
lm.setLayout(slicer.vtkMRMLLayoutNode.SlicerLayoutOneUpRedSliceView)
self.delayDisplay("Red Slice only")
# Switch to conventional layout
lm.setLayout(slicer.vtkMRMLLayoutNode.SlicerLayoutConventionalView)
self.delayDisplay("Conventional layout")
# Get the current seed widget seed location
endingSeedDisplayCoords = [0.0, 0.0, 0.0]
helper = self.getFiducialSliceDisplayableManagerHelper('Red')
if helper != None:
seedWidget = helper.GetWidget(fidNode)
seedRepresentation = seedWidget.GetSeedRepresentation()
handleRep = seedRepresentation.GetHandleRepresentation(fidIndex)
endingSeedDisplayCoords = handleRep.GetDisplayPosition()
print('Ending seed display coords = %d, %d, %d' % (endingSeedDisplayCoords[0], endingSeedDisplayCoords[1], endingSeedDisplayCoords[2]))
self.takeScreenshot('FiducialLayoutSwitchBug1914-EndingPosition','Fiducial ending position',slicer.qMRMLScreenShotDialog().Red)
# Compare to original seed widget location
diff = math.pow((startingSeedDisplayCoords[0] - endingSeedDisplayCoords[0]),2) + math.pow((startingSeedDisplayCoords[1] - endingSeedDisplayCoords[1]),2) + math.pow((startingSeedDisplayCoords[2] - endingSeedDisplayCoords[2]),2)
if diff != 0.0:
diff = math.sqrt(diff)
self.delayDisplay("Difference between starting and ending seed display coordinates = %g" % diff)
if diff > 1.0:
# raise Exception("Display coordinate difference is too large!\nExpected < 1.0 but got %g" % (diff))
print("Display coordinate difference is too large!\nExpected < 1.0 but got %g" % (diff))
return False
if enableScreenshots == 1:
# compare the screen snapshots
startView = slicer.mrmlScene.GetFirstNodeByName('FiducialLayoutSwitchBug1914-StartingPosition')
startShot = startView.GetScreenShot()
endView = slicer.mrmlScene.GetFirstNodeByName('FiducialLayoutSwitchBug1914-EndingPosition')
endShot = endView.GetScreenShot()
imageMath = vtk.vtkImageMathematics()
imageMath.SetOperationToSubtract()
imageMath.SetInput1(startShot)
imageMath.SetInput2(endShot)
imageMath.Update()
shotDiff = imageMath.GetOutput()
# save it as a scene view
annotationLogic = slicer.modules.annotations.logic()
annotationLogic.CreateSnapShot("FiducialLayoutSwitchBug1914-Diff", "Difference between starting and ending fiducial seed positions",slicer.qMRMLScreenShotDialog().Red, screenshotScaleFactor, shotDiff)
# calculate the image difference
imageStats = vtk.vtkImageHistogramStatistics()
imageStats.SetInput(shotDiff)
imageStats.GenerateHistogramImageOff()
imageStats.Update()
meanVal = imageStats.GetMean()
self.delayDisplay("Mean of image difference = %g" % meanVal)
if meanVal > 5.0:
# raise Exception("Image difference is too great!\nExpected <= 5.0, but got %g" % (meanVal))
print("Image difference is too great!\nExpected <= 5.0, but got %g" % (meanVal))
return False
self.delayDisplay('Test passed!')
return True
def GetDistanceMap(self,edgeImg,altedgeImg):
tmpimage=vtk.vtkImageData()
cast=vtk.vtkImageCast()
cast.SetOutputScalarTypeToDouble()
cast.SetInputData(edgeImg)
cast.Update()
#invert edge image edge=0 and background=2x
Math=vtk.vtkImageMathematics()
Math.SetInput1Data(cast.GetOutput())
Math.SetConstantC(0)
Math.SetConstantK(2)
Math.SetOperationToReplaceCByK()
Math.Update()
tmpimage.DeepCopy(Math.GetOutput())
Math.SetInput1Data(tmpimage)
Math.SetConstantC(1)
Math.SetConstantK(0)
Math.Update()
cast.SetInputData(Math.GetOutput())
cast.Update()
tmpimage.DeepCopy(cast.GetOutput())
tmpimage2=vtk.vtkImageData()
#calculate distance map
if self.distalg==0:
dm=slicer.vtkITKSignedDistanceTransform()
# tmpimage.SetSpacing(self.input.GetSpacing())
# dm.SetUseImageSpacing(True)
dm.SetAlgorithmToSignedMaurer()
dm.SetInputData(tmpimage)
dm.Update()
tmpimage2.DeepCopy(dm.GetOutput())
elif self.distalg==1:
dm=slicer.vtkITKSignedDistanceTransform()
dm.SetAlgorithmToApproximateSigned()
dm.SetInputData(tmpimage)
dm.Update()
tmpimage2.DeepCopy(dm.GetOutput())
elif self.distalg==2:
dm=slicer.vtkITKSignedDistanceTransform()
# tmpimage.SetSpacing(self.input.GetSpacing())
# dm.SetUseImageSpacing(True)
dm.SetAlgorithmToSignedDanielsson()
dm.SetObjectValue(2)
dm.SetInputData(tmpimage)
dm.Update()
tmpimage2.DeepCopy(dm.GetOutput())
elif self.distalg==3:
dm=vtk.vtkImageEuclideanDistance()
#tmpimage.SetSpacing(self.input.GetSpacing())
dm.InitializeOn()
#dm.ConsiderAnisotropyOn()
dm.SetInputData(tmpimage)
dm.Update()
Math.SetInputData(dm.GetOutput())
Math.SetOperationToSquareRoot()
Math.Update()
tmpimage2.DeepCopy(Math.GetOutput())
if not altedgeImg:
altedgeImg=tmpimage2
qu=QCLib.QCUtil()
rect=qu.minRectangle(self.ROI)
for i in range(rect['xmin'].__len__()):
if rect['xmin'][i]>=0:
index=i
break
xmin=rect['xmin'][index]
xmax=rect['xmax'][index]
ymin=rect['ymin'][index]
ymax=rect['ymax'][index]
distMap=vtk.vtkImageData()
distMap.DeepCopy(edgeImg)
for x in range(xmin,xmax+1):
for y in range(ymin,ymax+1):
isedge=math.copysign(edgeImg.GetScalarComponentAsDouble(x,y,index,0)-1,1)
if self.distalg!=3:
val=math.copysign((math.fabs(tmpimage2.GetScalarComponentAsDouble(x,y,index,0))+1)*isedge,altedgeImg.GetScalarComponentAsDouble(x,y,index,0))
else:
val=math.copysign((math.fabs(tmpimage2.GetScalarComponentAsDouble(x,y,index,0)))*isedge,altedgeImg.GetScalarComponentAsDouble(x,y,index,0))
distMap.SetScalarComponentFromDouble(x,y,index,0,val)
return distMap
def load(self,loadable):
"""Use the conversion factor to load the volume into Slicer"""
conversionFactor = loadable.slope
# Create volume node
imageNode = self.scalarVolumePlugin.loadFilesWithArchetype(loadable.files, loadable.name)
if imageNode:
# apply the conversion factor
multiplier = vtk.vtkImageMathematics()
multiplier.SetOperationToMultiplyByK()
multiplier.SetConstantK(float(conversionFactor))
if vtk.VTK_MAJOR_VERSION <= 5:
multiplier.SetInput1(imageNode.GetImageData())
else:
multiplier.SetInput1Data(imageNode.GetImageData())
multiplier.Update()
imageNode.GetImageData().DeepCopy(multiplier.GetOutput())
# create list of DICOM instance UIDs corresponding to the loaded files
instanceUIDs = ""
for dicomFile in loadable.files:
uid = slicer.dicomDatabase.fileValue(dicomFile,self.tags['sopInstanceUID'])
if uid == "":
uid = "Unknown"
instanceUIDs += uid + " "
instanceUIDs = instanceUIDs[:-1] # strip last space
# get the instance UID for the RWVM object
derivedItemUID = ""
try:
derivedItemUID = slicer.dicomDatabase.fileValue(loadable.rwvFile,self.tags['sopInstanceUID'])
except AttributeError:
# no derived items
pass
# Set Attributes
imageNode.SetAttribute('DICOM.MeasurementUnitsCodeMeaning',loadable.unitName)
imageNode.SetAttribute('DICOM.MeasurementUnitsCodeValue',loadable.units)
# Keep references to the PET instances, as these may be needed to
# establish correspondence between slice annotations and acutal slices,
# but also keep the RWVM instance UID ... it's confusing, but not sure
# if there is a better way in Slicer for now
imageNode.SetAttribute("DICOM.instanceUIDs", instanceUIDs)
imageNode.SetAttribute("DICOM.RWV.instanceUID", derivedItemUID)
# automatically select the volume to display
volumeLogic = slicer.modules.volumes.logic()
appLogic = slicer.app.applicationLogic()
selNode = appLogic.GetSelectionNode()
selNode.SetReferenceActiveVolumeID(imageNode.GetID())
appLogic.PropagateVolumeSelection()
# Change display
displayNode = imageNode.GetVolumeDisplayNode()
displayNode.SetInterpolate(0)
# Change name
name = (loadable.name).replace(' ','_')
imageNode.SetName(name)
# create Subject Hierarchy nodes for the loaded series
self.addSeriesInSubjectHierarchy(loadable,imageNode)
return imageNode
