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 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 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
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
self.fm = slicer.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.fm.show(1)
self.fm.Modified()
self.fm.Update()
logging.info('FastMarching march update completed')