def load(self,loadable):
"""Load the selection as a scalar volume, but rescale the values
"""
scalarVolumePlugin = slicer.modules.dicomPlugins['DICOMScalarVolumePlugin']()
vNode = scalarVolumePlugin.loadFilesWithArchetype(loadable.files, loadable.name)
if vNode:
intercept = float(slicer.dicomDatabase.fileValue(loadable.files[0], self.tags['ScaleIntercept']))
slope = float(slicer.dicomDatabase.fileValue(loadable.files[0], self.tags['ScaleSlope']))
privateIntercept = float(slicer.dicomDatabase.fileValue(loadable.files[0], self.tags['PrivateScaleIntercept']))
privateSlope = float(slicer.dicomDatabase.fileValue(loadable.files[0], self.tags['PrivateScaleSlope']))
print('Slope: '+str(slope)+' private: '+str(privateSlope)+' Intercept: '+str(intercept)+' private: '+str(privateIntercept))
# vtkImageShiftScale first shifts, then scales
# First, revert the scaling applied on ITK-level read
reverseShift = vtk.vtkImageShiftScale()
reverseShift.SetShift(-1.*intercept)
reverseShift.SetScale(1)
reverseShift.SetInput(vNode.GetImageData())
reverseShift.SetOutputScalarTypeToFloat()
reverseScale = vtk.vtkImageShiftScale()
reverseScale.SetShift(0)
reverseScale.SetScale(1./slope)
reverseScale.SetInput(reverseShift.GetOutput())
reverseScale.SetOutputScalarTypeToFloat()
# Second, apply scaling using the private tags information
rescale = vtk.vtkImageShiftScale()
rescale.SetShift(-1.*privateIntercept)
rescale.SetScale(1./privateSlope)
rescale.SetOutputScalarTypeToFloat()
rescale.SetInput(reverseScale.GetOutput())
rescale.Update()
imageData = vtk.vtkImageData()
imageData.DeepCopy(rescale.GetOutput())
# Note: the assumption here is that intercept/slope are identical for all
# slices in the series. According to Tom Chenevert, this is typically the
# case: "The exception is when there are multiple image types in a series,
# such as real, imaginary, magnitude and phase images all stored in the
# series. But this is not common."
vNode.SetAndObserveImageData(imageData)
return vNode
def load(self,loadable):
"""Load the selection as a scalar volume, but rescale the values
"""
scalarVolumePlugin = slicer.modules.dicomPlugins['DICOMScalarVolumePlugin']()
vNode = scalarVolumePlugin.loadFilesWithArchetype(loadable.files, loadable.name)
if vNode:
intercept = float(slicer.dicomDatabase.fileValue(loadable.files[0], self.tags['ScaleIntercept']))
slope = float(slicer.dicomDatabase.fileValue(loadable.files[0], self.tags['ScaleSlope']))
privateIntercept = float(slicer.dicomDatabase.fileValue(loadable.files[0], self.tags['PrivateScaleIntercept']))
privateSlope = float(slicer.dicomDatabase.fileValue(loadable.files[0], self.tags['PrivateScaleSlope']))
print('Slope: '+str(slope)+' private: '+str(privateSlope)+' Intercept: '+str(intercept)+' private: '+str(privateIntercept))
# vtkImageShiftScale first shifts, then scales
# First, revert the scaling applied on ITK-level read
reverseShift = vtk.vtkImageShiftScale()
reverseShift.SetShift(-1.*intercept)
reverseShift.SetScale(1)
reverseShift.SetInputData(vNode.GetImageData())
reverseShift.SetOutputScalarTypeToFloat()
reverseScale = vtk.vtkImageShiftScale()
reverseScale.SetShift(0)
reverseScale.SetScale(1./slope)
reverseScale.SetInputData(reverseShift.GetOutput())
reverseScale.SetOutputScalarTypeToFloat()
# Second, apply scaling using the private tags information
rescale = vtk.vtkImageShiftScale()
rescale.SetShift(-1.*privateIntercept)
rescale.SetScale(1./privateSlope)
rescale.SetOutputScalarTypeToFloat()
rescale.SetInputData(reverseScale.GetOutput())
rescale.Update()
imageData = vtk.vtkImageData()
imageData.DeepCopy(rescale.GetOutput())
# Note: the assumption here is that intercept/slope are identical for all
# slices in the series. According to Tom Chenevert, this is typically the
# case: "The exception is when there are multiple image types in a series,
# such as real, imaginary, magnitude and phase images all stored in the
# series. But this is not common."
vNode.SetAndObserveImageData(imageData)
return vNode
def run(self,inputVolumeNode,outputVolumeNode,outputScalarType):
"""
Run the actual algorithm
"""
castor = vtk.vtkImageShiftScale()
castor.SetInput(inputVolumeNode.GetImageData())
castor.SetShift(0.0)
castor.SetScale(1.0)
if outputScalarType == "Char":
castor.SetOutputScalarTypeToChar()
elif outputScalarType == "UnsignedChar":
castor.SetOutputScalarTypeToUnsignedChar()
elif outputScalarType == "Short":
castor.SetOutputScalarTypeToShort()
elif outputScalarType == "UnsignedShort":
castor.SetOutputScalarTypeToUnsignedShort()
elif outputScalarType == "Int":
castor.SetOutputScalarTypeToInt()
elif outputScalarType == "UnsignedInt":
castor.SetOutputScalarTypeToUnsignedInt()
elif outputScalarType == "Float":
castor.SetOutputScalarTypeToFloat()
elif outputScalarType == "Double":
castor.SetOutputScalarTypeToDouble()
else:
pass
castor.Update()
outputVolumeNode.CopyOrientation(inputVolumeNode)
outputVolumeNode.SetAndObserveImageData(Castor.GetOutput())
return True
def __init__(self, shaderComputation, textureUnit, volumeNode):
FieldSampler.__init__(self, shaderComputation, textureUnit, volumeNode)
self.shiftScale = vtk.vtkImageShiftScale()
try:
from vtkSlicerShadedActorModuleLogicPython import vtkOpenGLTextureImage
except ImportError:
import vtkAddon
vtkOpenGLTextureImage=vtkAddon.vtkOpenGLTextureImage
self.textureImage=vtkOpenGLTextureImage()
self.textureImage.SetShaderComputation(self.shaderComputation)
self.updateFromMRML()
def __init__(self, shaderComputation, textureUnit, volumeNode):
FieldSampler.__init__(self, shaderComputation, textureUnit, volumeNode)
self.shiftScale = vtk.vtkImageShiftScale()
try:
from vtkSlicerShadedActorModuleLogicPython import vtkOpenGLTextureImage
except ImportError:
import vtkAddon
vtkOpenGLTextureImage = vtkAddon.vtkOpenGLTextureImage
self.textureImage = vtkOpenGLTextureImage()
self.textureImage.SetShaderComputation(self.shaderComputation)
self.updateFromMRML()
def fastMarching(self, percentMax):
self.fm = None
# allocate a new filter each time March is hit
bgImage = self.editUtil.getBackgroundImage()
labelImage = self.editUtil.getLabelImage()
# collect seeds
dim = bgImage.GetWholeExtent()
# initialize the filter
self.fm = slicer.vtkPichonFastMarching()
scalarRange = bgImage.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.SetInput(bgImage)
rescale.SetScale(scaleValue)
rescale.SetShift(shiftValue)
rescale.Update()
bgImage = rescale.GetOutput()
scalarRange = bgImage.GetScalarRange()
depth = scalarRange[1] - scalarRange[0]
print('Input scalar range: ' + str(depth))
self.fm.init(dim[1] + 1, dim[3] + 1, dim[5] + 1, depth, 1, 1, 1)
caster = vtk.vtkImageCast()
caster.SetOutputScalarTypeToShort()
caster.SetInput(bgImage)
caster.Update()
self.fm.SetInput(caster.GetOutput())
# self.fm.SetOutput(labelImage)
npoints = int(
(dim[1] + 1) * (dim[3] + 1) * (dim[5] + 1) * percentMax / 100.)
self.fm.setNPointsEvolution(npoints)
print('Setting active label to ' + str(self.editUtil.getLabel()))
self.fm.setActiveLabel(self.editUtil.getLabel())
nSeeds = self.fm.addSeedsFromImage(labelImage)
if nSeeds == 0:
return 0
self.fm.Modified()
self.fm.Update()
# TODO: need to call show() twice for data to be updated
self.fm.show(1)
self.fm.Modified()
self.fm.Update()
self.fm.show(1)
self.fm.Modified()
self.fm.Update()
self.undoRedo.saveState()
self.editUtil.getLabelImage().DeepCopy(self.fm.GetOutput())
self.editUtil.markVolumeNodeAsModified(
self.sliceLogic.GetLabelLayer().GetVolumeNode())
# print('FastMarching output image: '+str(output))
print('FastMarching march update completed')
return npoints
def fastMarching(self,percentMax):
self.fm = None
# allocate a new filter each time March is hit
bgImage = EditUtil.getBackgroundImage()
labelImage = EditUtil.getLabelImage()
# collect seeds
if vtk.VTK_MAJOR_VERSION <= 5:
dim = bgImage.GetWholeExtent()
else:
dim = bgImage.GetDimensions()
print dim
# initialize the filter
self.fm = slicer.vtkPichonFastMarching()
scalarRange = bgImage.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()
if vtk.VTK_MAJOR_VERSION <= 5:
rescale.SetInput(bgImage)
else:
rescale.SetInputData(bgImage)
rescale.SetScale(scaleValue)
rescale.SetShift(shiftValue)
rescale.Update()
bgImage = rescale.GetOutput()
scalarRange = bgImage.GetScalarRange()
depth = scalarRange[1]-scalarRange[0]
print('Input scalar range: '+str(depth))
if vtk.VTK_MAJOR_VERSION <= 5:
self.fm.init(dim[1]+1, dim[3]+1, dim[5]+1, depth, 1, 1, 1)
else:
self.fm.init(dim[0], dim[1], dim[2], depth, 1, 1, 1)
caster = vtk.vtkImageCast()
caster.SetOutputScalarTypeToShort()
if vtk.VTK_MAJOR_VERSION <= 5:
caster.SetInput(bgImage)
caster.Update()
self.fm.SetInput(caster.GetOutput())
else:
caster.SetInputData(bgImage)
self.fm.SetInputConnection(caster.GetOutputPort())
# self.fm.SetOutput(labelImage)
if vtk.VTK_MAJOR_VERSION <= 5:
npoints = int((dim[1]+1)*(dim[3]+1)*(dim[5]+1)*percentMax/100.)
else:
npoints = int(dim[0]*dim[1]*dim[2]*percentMax/100.)
self.fm.setNPointsEvolution(npoints)
print('Setting active label to '+str(EditUtil.getLabel()))
self.fm.setActiveLabel(EditUtil.getLabel())
nSeeds = self.fm.addSeedsFromImage(labelImage)
if nSeeds == 0:
return 0
self.fm.Modified()
self.fm.Update()
# TODO: need to call show() twice for data to be updated
self.fm.show(1)
self.fm.Modified()
self.fm.Update()
self.fm.show(1)
self.fm.Modified()
self.fm.Update()
self.undoRedo.saveState()
EditUtil.getLabelImage().DeepCopy(self.fm.GetOutput())
EditUtil.markVolumeNodeAsModified(self.sliceLogic.GetLabelLayer().GetVolumeNode())
# print('FastMarching output image: '+str(output))
print('FastMarching march update completed')
return npoints
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