def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
vtk.vtkImageDilateErode3D(), 'Processing.',
('vtkImageData',), ('vtkImageData',),
replaceDoc=True,
inputFunctions=None, outputFunctions=None)
def erode_and_dilate(image_stencil, inval, outval, kernel_size):
erode = vtk.vtkImageDilateErode3D()
if vtk.VTK_MAJOR_VERSION <= 5:
erode.SetInput(image_stencil.GetOutput())
else:
erode.SetInputConnection(image_stencil.GetOutputPort())
erode.SetErodeValue(inval)
erode.SetDilateValue(outval)
erode.SetKernelSize(kernel_size, kernel_size, kernel_size)
erode.ReleaseDataFlagOff()
erode.Update()
dilate = vtk.vtkImageDilateErode3D()
if vtk.VTK_MAJOR_VERSION <= 5:
dilate.SetInput(erode.GetOutput())
else:
dilate.SetInputConnection(erode.GetOutputPort())
dilate.SetDilateValue(inval)
dilate.SetErodeValue(outval)
dilate.SetKernelSize(kernel_size, kernel_size, kernel_size)
dilate.ReleaseDataFlagOff()
dilate.Update()
return dilate
def runMasking(self, ijkPoints, seedLabelmap, outputLabelmap):
kernelSizePixel = self.getKernelSizePixel()
self.floodFillingFilterIsland = vtk.vtkImageThresholdConnectivity()
self.floodFillingFilterIsland.SetInputData(seedLabelmap)
self.floodFillingFilterIsland.SetInValue(BACKGROUND_VALUE)
self.floodFillingFilterIsland.ReplaceInOn()
self.floodFillingFilterIsland.ReplaceOutOff()
self.floodFillingFilterIsland.ThresholdBetween(LABEL_VALUE, LABEL_VALUE)
self.floodFillingFilterIsland.SetSeedPoints(ijkPoints)
self.dilate = vtk.vtkImageDilateErode3D()
self.dilate.SetInputConnection(self.floodFillingFilterIsland.GetOutputPort())
self.dilate.SetDilateValue(LABEL_VALUE)
self.dilate.SetErodeValue(BACKGROUND_VALUE)
self.dilate.SetKernelSize(
2*kernelSizePixel[0]-1,
2*kernelSizePixel[1]-1,
2*kernelSizePixel[2]-1)
self.dilate.Update()
self.imageMask = vtk.vtkImageMask()
self.imageMask.SetInputConnection(self.thresh.GetOutputPort())
self.imageMask.SetMaskedOutputValue(BACKGROUND_VALUE)
self.imageMask.NotMaskOn()
self.imageMask.SetMaskInputData(self.dilate.GetOutput())
self.floodFillingFilter = vtk.vtkImageThresholdConnectivity()
self.floodFillingFilter.SetInputConnection(self.imageMask.GetOutputPort())
self.floodFillingFilter.SetInValue(LABEL_VALUE)
self.floodFillingFilter.SetOutValue(BACKGROUND_VALUE)
self.floodFillingFilter.ThresholdBetween(LABEL_VALUE, LABEL_VALUE)
self.floodFillingFilter.SetSeedPoints(ijkPoints)
self.floodFillingFilter.Update()
outputLabelmap.ShallowCopy(self.floodFillingFilter.GetOutput())
def SeedInitialize(self):
self.PrintLog('Seed initialization.')
queryString = 'Please place seeds'
seeds = self.SeedInput(queryString,0)
self.InitialLevelSets = vtk.vtkImageData()
self.InitialLevelSets.DeepCopy(self.Image)
self.InitialLevelSets.Update()
levelSetsInputScalars = self.InitialLevelSets.GetPointData().GetScalars()
levelSetsInputScalars.FillComponent(0,1.0)
dimensions = self.Image.GetDimensions()
for i in range(seeds.GetNumberOfPoints()):
id = self.Image.FindPoint(seeds.GetPoint(i))
levelSetsInputScalars.SetComponent(id,0,-1.0)
dilateErode = vtk.vtkImageDilateErode3D()
dilateErode.SetInput(self.InitialLevelSets)
dilateErode.SetDilateValue(-1.0)
dilateErode.SetErodeValue(1.0)
dilateErode.SetKernelSize(3,3,3)
dilateErode.Update()
self.InitialLevelSets.DeepCopy(dilateErode.GetOutput())
self.IsoSurfaceValue = 0.0
def SeedInitialize(self):
self.PrintLog('Seed initialization.')
queryString = 'Please place seeds'
seeds = self.SeedInput(queryString,0)
self.InitialLevelSets = vtk.vtkImageData()
self.InitialLevelSets.DeepCopy(self.Image)
self.InitialLevelSets.Update()
levelSetsInputScalars = self.InitialLevelSets.GetPointData().GetScalars()
levelSetsInputScalars.FillComponent(0,1.0)
dimensions = self.Image.GetDimensions()
for i in range(seeds.GetNumberOfPoints()):
id = self.Image.FindPoint(seeds.GetPoint(i))
levelSetsInputScalars.SetComponent(id,0,-1.0)
dilateErode = vtk.vtkImageDilateErode3D()
dilateErode.SetInput(self.InitialLevelSets)
dilateErode.SetDilateValue(-1.0)
dilateErode.SetErodeValue(1.0)
dilateErode.SetKernelSize(3,3,3)
dilateErode.Update()
self.InitialLevelSets.DeepCopy(dilateErode.GetOutput())
self.IsoSurfaceValue = 0.0
def getImageMask(inputVtkImageData):
"""
@type inputVtkImageData: C{vtkImageData}
@param inputVtkImageData: Image data to be normalized
@rtype: C{vtkImageData}
@return: Normalized (0-1) image data
"""
t = vtk.vtkImageThreshold()
#t.ThresholdBetween(1,255)
t.ThresholdByUpper(114)
t.ReplaceInOn()
t.SetReplaceIn(0)
t.ReplaceOutOn()
t.SetReplaceOut(255)
t.SetInput(inputVtkImageData)
norm = vtk.vtkImageNormalize()
norm.SetInput(t.GetOutput())
#norm.SetInput(inputVtkImageData)
norm.Update()
d = vtk.vtkImageDilateErode3D()
d.SetKernelSize(4,4,4)
d.SetDilateValue(1)
d.SetErodeValue(0)
d.SetInput(norm.GetOutput())
return d.GetOutput()
def open_image(image, radius):
openFilter = vtk.vtkImageDilateErode3D()
openFilter.SetDilateValue(255)
openFilter.SetErodeValue(0)
openFilter.SetKernelSize(radius, radius, radius)
openFilter.SetInputData(image)
openFilter.Update()
return openFilter.GetOutput()
def createEyelidSegment(segmentation_node, ref_img_path,
out_segmentation_path):
if segmentation_node is None or not ref_img_path.exists():
print('Could not find: {}'.format(ref_img_path))
return
current_segmentation = segmentation_node.GetSegmentation()
number_of_segments = current_segmentation.GetNumberOfSegments()
if number_of_segments > 2:
# Most probably has an eyelid already, return
return
# Export segment as vtkImageData (via temporary labelmap volume node)
image_node = slicer.util.loadVolume(str(ref_img_path),
{'singleFile': True})
segmentIds = vtk.vtkStringArray()
current_segmentation.GetSegmentIDs(segmentIds)
labelmapVolumeNode = slicer.mrmlScene.AddNewNodeByClass(
'vtkMRMLLabelMapVolumeNode')
slicer.modules.segmentations.logic().ExportSegmentsToLabelmapNode(
segmentation_node, segmentIds, labelmapVolumeNode, image_node,
slicer.vtkSegmentation.EXTENT_REFERENCE_GEOMETRY)
# Manipulate the mask values to add the third label
mask = slicer.util.arrayFromVolume(labelmapVolumeNode)
newmask = mask.copy()
newmask[newmask > 0] = mask.max() + 1
clone = slicer.modules.volumes.logic().CloneVolume(labelmapVolumeNode,
"CloneLabelMap")
slicer.util.updateVolumeFromArray(clone, newmask)
segmentImageData = clone.GetImageData()
kernelSize = [20, 200, 1]
erodeDilate = vtk.vtkImageDilateErode3D()
erodeDilate.SetInputData(segmentImageData)
erodeDilate.SetDilateValue(mask.max() + 1)
erodeDilate.SetErodeValue(0)
erodeDilate.SetKernelSize(*kernelSize)
erodeDilate.Update()
segmentImageData.DeepCopy(erodeDilate.GetOutput())
newmask = slicer.util.arrayFromVolume(clone)
# Combine both the masks together to add the new labelmap.
newmask[mask > 0] = 0
newmask = newmask + mask
slicer.util.updateVolumeFromArray(clone, newmask)
segmentIds.InsertNextValue('EyeLid')
segmentation_node.GetSegmentation().AddEmptySegment('EyeLid')
slicer.modules.segmentations.logic().ImportLabelmapToSegmentationNode(
clone, segmentation_node, segmentIds)
setSegmentationLabelNames(segmentation_node)
# Save this label to image
slicer.util.saveNode(clone, str(out_segmentation_path))
slicer.mrmlScene.RemoveNode(
labelmapVolumeNode.GetDisplayNode().GetColorNode())
slicer.mrmlScene.RemoveNode(labelmapVolumeNode)
slicer.mrmlScene.RemoveNode(clone.GetDisplayNode().GetColorNode())
slicer.mrmlScene.RemoveNode(clone)
slicer.mrmlScene.RemoveNode(image_node)
def dilateMask(label): imagedata = label.GetImageData() dilateErode = vtk.vtkImageDilateErode3D() dilateErode.SetInputData(imagedata) dilateErode.SetDilateValue(1.0) dilateErode.SetErodeValue(0.0) dilateErode.SetKernelSize(12, 12, 1) dilateErode.Update() label.SetAndObserveImageData(dilateErode.GetOutput())
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(self,
module_manager,
vtk.vtkImageDilateErode3D(),
'Processing.', ('vtkImageData', ),
('vtkImageData', ),
replaceDoc=True,
inputFunctions=None,
outputFunctions=None)
def locate_region_boundary_ids(im, label_id1, label_id2, size=1., bg_id=None):
"""
Locate the boundary coordinates between two regions with different labels
Args:
im: vtkImage of the label map
label_id1: class id of 1st region
label_id2: class id of 2nd region
bg_id: class id of background
Returns
ids: ids of the boundary points
"""
new_Im = vtk.vtkImageData()
new_Im.DeepCopy(im)
if bg_id is not None:
dilateErode = vtk.vtkImageDilateErode3D()
dilateErode.SetInputData(new_Im)
dilateErode.SetDilateValue(label_id1)
dilateErode.SetErodeValue(bg_id)
dilateErode.SetKernelSize(3, 3, 3)
dilateErode.Update()
new_Im = dilateErode.GetOutput()
dilateErode = vtk.vtkImageDilateErode3D()
dilateErode.SetInputData(new_Im)
dilateErode.SetDilateValue(label_id1)
dilateErode.SetErodeValue(label_id2)
#kernel_size = np.rint(size/np.array(im.GetSpacing())).astype(int)
kernel_size = (np.ones(3) * size).astype(int)
dilateErode.SetKernelSize(*kernel_size)
dilateErode.Update()
newIm = dilateErode.GetOutput()
from vtk.util.numpy_support import vtk_to_numpy, numpy_to_vtk
x, y, z = newIm.GetDimensions()
pyIm_new = vtk_to_numpy(newIm.GetPointData().GetScalars()).reshape(
z, y, x).transpose(2, 1, 0)
pyIm = vtk_to_numpy(im.GetPointData().GetScalars()).reshape(z, y,
x).transpose(
2, 1, 0)
ids = np.array(np.where(pyIm_new - pyIm != 0)).transpose()
return ids
def applyDilateErode(self, imgData, dVal, eVal, kernel=[3, 3, 3]):
deImg = vtk.vtkImageDilateErode3D()
deImg.SetInputData(imgData.GetOutput())
deImg.SetDilateValue(dVal)
deImg.SetErodeValue(eVal)
deImg.SetKernelSize(kernel[0], kernel[1], kernel[2])
deImg.Update()
return deImg
def SeedInitialize(self):
self.PrintLog('Seed initialization.')
seedIds = vtk.vtkIdList()
if self.Interactive:
queryString = 'Please place seeds'
seeds = self.SeedInput(queryString, 0)
for i in range(seeds.GetNumberOfPoints()):
seedIds.InsertNextId(self.Image.FindPoint(seeds.GetPoint(i)))
else:
for i in range(len(self.SourcePoints) / 3):
seedIds.InsertNextId(
self.Image.ComputePointId([
self.SourcePoints[3 * i + 0],
self.SourcePoints[3 * i + 1],
self.SourcePoints[3 * i + 2]
]))
for i in range(len(self.TargetPoints) / 3):
seedIds.InsertNextId(
self.Image.ComputePointId([
self.TargetPoints[3 * i + 0],
self.TargetPoints[3 * i + 1],
self.TargetPoints[3 * i + 2]
]))
self.InitialLevelSets = vtk.vtkImageData()
self.InitialLevelSets.DeepCopy(self.Image)
self.InitialLevelSets.Update()
levelSetsInputScalars = self.InitialLevelSets.GetPointData(
).GetScalars()
levelSetsInputScalars.FillComponent(0, 1.0)
dimensions = self.Image.GetDimensions()
for i in range(seedIds.GetNumberOfIds()):
levelSetsInputScalars.SetComponent(seedIds.GetId(i), 0, -1.0)
dilateErode = vtk.vtkImageDilateErode3D()
dilateErode.SetInput(self.InitialLevelSets)
dilateErode.SetDilateValue(-1.0)
dilateErode.SetErodeValue(1.0)
dilateErode.SetKernelSize(3, 3, 3)
dilateErode.Update()
self.InitialLevelSets.DeepCopy(dilateErode.GetOutput())
self.IsoSurfaceValue = 0.0
def dilateMask(label, dilateValue=1.0, erodeValue=0.0, marginSize=5.0):
imagedata = label.GetImageData()
dilateErode = vtk.vtkImageDilateErode3D()
dilateErode.SetInputData(imagedata)
dilateErode.SetDilateValue(dilateValue)
dilateErode.SetErodeValue(erodeValue)
spacing = label.GetSpacing()
kernelSizePixel = [
int(
round((abs(marginSize) / spacing[componentIndex] + 1) / 2) *
2 - 1) for componentIndex in range(3)
]
dilateErode.SetKernelSize(kernelSizePixel[0], kernelSizePixel[1],
kernelSizePixel[2])
dilateErode.Update()
label.SetAndObserveImageData(dilateErode.GetOutput())
def onApply(self):
self.scriptedEffect.saveStateForUndo()
# Get modifier labelmap and parameters
modifierLabelmap = self.scriptedEffect.defaultModifierLabelmap()
selectedSegmentLabelmap = self.scriptedEffect.selectedSegmentLabelmap()
marginSizeMm = self.scriptedEffect.doubleParameter("MarginSizeMm")
kernelSizePixel = self.getKernelSizePixel()
# 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())
erodeDilate = vtk.vtkImageDilateErode3D()
erodeDilate.SetInputConnection(thresh.GetOutputPort())
if marginSizeMm > 0:
# grow
erodeDilate.SetDilateValue(labelValue)
erodeDilate.SetErodeValue(backgroundValue)
else:
# shrink
erodeDilate.SetDilateValue(backgroundValue)
erodeDilate.SetErodeValue(labelValue)
# This can be a long operation - indicate it to the user
qt.QApplication.setOverrideCursor(qt.Qt.WaitCursor)
erodeDilate.SetKernelSize(kernelSizePixel[0], kernelSizePixel[1],
kernelSizePixel[2])
erodeDilate.Update()
modifierLabelmap.DeepCopy(erodeDilate.GetOutput())
# Apply changes
self.scriptedEffect.modifySelectedSegmentByLabelmap(
modifierLabelmap,
slicer.qSlicerSegmentEditorAbstractEffect.ModificationModeSet)
qt.QApplication.restoreOverrideCursor()
def onApply(self):
self.scriptedEffect.saveStateForUndo()
# Get modifier labelmap and parameters
modifierLabelmap = self.scriptedEffect.defaultModifierLabelmap()
selectedSegmentLabelmap = self.scriptedEffect.selectedSegmentLabelmap()
marginSizeMm = self.scriptedEffect.doubleParameter("MarginSizeMm")
kernelSizePixel = self.getKernelSizePixel()
# 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())
erodeDilate = vtk.vtkImageDilateErode3D()
erodeDilate.SetInputConnection(thresh.GetOutputPort())
if marginSizeMm>0:
# grow
erodeDilate.SetDilateValue(labelValue)
erodeDilate.SetErodeValue(backgroundValue)
else:
# shrink
erodeDilate.SetDilateValue(backgroundValue)
erodeDilate.SetErodeValue(labelValue)
# This can be a long operation - indicate it to the user
qt.QApplication.setOverrideCursor(qt.Qt.WaitCursor)
erodeDilate.SetKernelSize(kernelSizePixel[0],kernelSizePixel[1],kernelSizePixel[2])
erodeDilate.Update()
modifierLabelmap.DeepCopy(erodeDilate.GetOutput())
# Apply changes
self.scriptedEffect.modifySelectedSegmentByLabelmap(modifierLabelmap, slicer.qSlicerSegmentEditorAbstractEffect.ModificationModeSet)
qt.QApplication.restoreOverrideCursor()
def ErodeLabelMap(self, LabelMapNode, ErosionKernelSize):
# Initialize new label map node
ErodedLabelMapNode = slicer.vtkMRMLLabelMapVolumeNode()
ErodedLabelMapNode.SetSpacing(LabelMapNode.GetSpacing())
ErodedLabelMapNode.SetOrigin(LabelMapNode.GetOrigin())
# Intialize vtkImageDilateErode3D
Eroder = vtk.vtkImageDilateErode3D()
Eroder.SetErodeValue(1)
Eroder.SetDilateValue(0)
Eroder.SetKernelSize(ErosionKernelSize[0], ErosionKernelSize[1],
ErosionKernelSize[2])
# Erode label map
Eroder.SetInputData(LabelMapNode.GetImageData())
Eroder.Update()
ErodedLabelMapNode.SetAndObserveImageData(Eroder.GetOutput())
return ErodedLabelMapNode
def SeedInitialize(self):
self.PrintLog('Seed initialization.')
seedIds = vtk.vtkIdList()
if self.Interactive:
queryString = 'Please place seeds'
seeds = self.SeedInput(queryString,0)
for i in range(seeds.GetNumberOfPoints()):
seedIds.InsertNextId(self.Image.FindPoint(seeds.GetPoint(i)))
else:
for i in range(len(self.SourcePoints)/3):
seedIds.InsertNextId(self.Image.ComputePointId([self.SourcePoints[3*i+0],self.SourcePoints[3*i+1],self.SourcePoints[3*i+2]]))
for i in range(len(self.TargetPoints)/3):
seedIds.InsertNextId(self.Image.ComputePointId([self.TargetPoints[3*i+0],self.TargetPoints[3*i+1],self.TargetPoints[3*i+2]]))
self.InitialLevelSets = vtk.vtkImageData()
self.InitialLevelSets.DeepCopy(self.Image)
self.InitialLevelSets.Update()
levelSetsInputScalars = self.InitialLevelSets.GetPointData().GetScalars()
levelSetsInputScalars.FillComponent(0,1.0)
dimensions = self.Image.GetDimensions()
for i in range(seedIds.GetNumberOfIds()):
levelSetsInputScalars.SetComponent(seedIds.GetId(i),0,-1.0)
dilateErode = vtk.vtkImageDilateErode3D()
dilateErode.SetInput(self.InitialLevelSets)
dilateErode.SetDilateValue(-1.0)
dilateErode.SetErodeValue(1.0)
dilateErode.SetKernelSize(3,3,3)
dilateErode.Update()
self.InitialLevelSets.DeepCopy(dilateErode.GetOutput())
self.IsoSurfaceValue = 0.0
def label_dilate_erode(im, label_id, bg_id, size):
"""
Dilates a label
Args:
im: vtkImage of the label map
label_id: class id to erode
bg_id: class id of backgroud to dilate
size: num of pixels of the erosion
Returns
newIm: vtkImage with dilated tissue structure
"""
dilateErode = vtk.vtkImageDilateErode3D()
dilateErode.SetInputData(im)
dilateErode.SetDilateValue(label_id)
dilateErode.SetErodeValue(bg_id)
#kernel_size = np.rint(thickness/np.array(im.GetSpacing())).astype(int)
kernel_size = (np.ones(3) * size).astype(int)
dilateErode.SetKernelSize(*kernel_size)
dilateErode.Update()
newIm = dilateErode.GetOutput()
return newIm
def main():
# colors = vtk.vtkNamedColors()
fileName = get_program_parameters()
# Read the image.
readerFactory = vtk.vtkImageReader2Factory()
reader = readerFactory.CreateImageReader2(fileName)
reader.SetFileName(fileName)
reader.Update()
# Dilate
dilate = vtk.vtkImageDilateErode3D()
dilate.SetInputConnection(reader.GetOutputPort())
dilate.SetDilateValue(0)
dilate.SetErodeValue(255)
dilate.SetKernelSize(31, 31, 1)
# Erode
erode = vtk.vtkImageDilateErode3D()
erode.SetInputConnection(reader.GetOutputPort())
erode.SetDilateValue(255)
erode.SetErodeValue(0)
erode.SetKernelSize(31, 31, 1)
# Opening - dilate then erode.
dilate1 = vtk.vtkImageDilateErode3D()
dilate1.SetInputConnection(reader.GetOutputPort())
dilate1.SetDilateValue(0)
dilate1.SetErodeValue(255)
dilate1.SetKernelSize(31, 31, 1)
erode1 = vtk.vtkImageDilateErode3D()
erode1.SetInputConnection(dilate1.GetOutputPort())
erode1.SetDilateValue(255)
erode1.SetErodeValue(0)
erode1.SetKernelSize(31, 31, 1)
# Closing - erode then dilate.
erode2 = vtk.vtkImageDilateErode3D()
erode2.SetInputConnection(reader.GetOutputPort())
erode2.SetDilateValue(255)
erode2.SetErodeValue(0)
erode2.SetKernelSize(31, 31, 1)
dilate2 = vtk.vtkImageDilateErode3D()
dilate2.SetInputConnection(erode2.GetOutputPort())
dilate2.SetDilateValue(0)
dilate2.SetErodeValue(255)
dilate2.SetKernelSize(31, 31, 1)
# Connectivity
con = vtk.vtkImageSeedConnectivity()
con.SetInputConnection(reader.GetOutputPort())
con.AddSeed(300, 200)
con.SetInputConnectValue(0)
con.SetOutputConnectedValue(0)
con.SetOutputUnconnectedValue(255)
# Actors
originalActor = vtk.vtkImageActor()
originalActor.GetMapper().SetInputConnection(reader.GetOutputPort())
originalActor.GetProperty().SetInterpolationTypeToNearest()
connectedActor = vtk.vtkImageActor()
connectedActor.GetMapper().SetInputConnection(con.GetOutputPort())
connectedActor.GetProperty().SetInterpolationTypeToNearest()
erodeActor = vtk.vtkImageActor()
erodeActor.GetMapper().SetInputConnection(erode.GetOutputPort())
erodeActor.GetProperty().SetInterpolationTypeToNearest()
dilateActor = vtk.vtkImageActor()
dilateActor.GetMapper().SetInputConnection(dilate.GetOutputPort())
dilateActor.GetProperty().SetInterpolationTypeToNearest()
openingActor = vtk.vtkImageActor()
openingActor.GetMapper().SetInputConnection(dilate2.GetOutputPort())
openingActor.GetProperty().SetInterpolationTypeToNearest()
closingActor = vtk.vtkImageActor()
closingActor.GetMapper().SetInputConnection(erode1.GetOutputPort())
closingActor.GetProperty().SetInterpolationTypeToNearest()
# Setup renderers
originalRenderer = vtk.vtkRenderer()
originalRenderer.AddActor(originalActor)
connectedRenderer = vtk.vtkRenderer()
connectedRenderer.AddActor(connectedActor)
dilateRenderer = vtk.vtkRenderer()
dilateRenderer.AddActor(dilateActor)
erodeRenderer = vtk.vtkRenderer()
erodeRenderer.AddActor(erodeActor)
closingRenderer = vtk.vtkRenderer()
closingRenderer.AddActor(closingActor)
openingRenderer = vtk.vtkRenderer()
openingRenderer.AddActor(openingActor)
renderers = list()
renderers.append(originalRenderer)
renderers.append(connectedRenderer)
renderers.append(erodeRenderer)
renderers.append(dilateRenderer)
renderers.append(openingRenderer)
renderers.append(closingRenderer)
# Setup viewports for the renderers
rendererSize = 300
xGridDimensions = 2
yGridDimensions = 3
renderWindow = vtk.vtkRenderWindow()
renderWindow.SetSize(rendererSize * xGridDimensions,
rendererSize * yGridDimensions)
for row in range(0, yGridDimensions):
for col in range(xGridDimensions):
index = row * xGridDimensions + col
# (xmin, ymin, xmax, ymax)
viewport = [
float(col) / xGridDimensions,
float(yGridDimensions - (row + 1)) / yGridDimensions,
float(col + 1) / xGridDimensions,
float(yGridDimensions - row) / yGridDimensions
]
renderers[index].SetViewport(viewport)
renderWindow.AddRenderer(renderers[index])
renderWindow.SetWindowName('MorphologyComparison')
renderWindowInteractor = vtk.vtkRenderWindowInteractor()
style = vtk.vtkInteractorStyleImage()
renderWindowInteractor.SetInteractorStyle(style)
renderWindowInteractor.SetRenderWindow(renderWindow)
# The renderers share one camera.
renderWindow.Render()
renderers[0].GetActiveCamera().Dolly(1.5)
renderers[0].ResetCameraClippingRange()
for r in range(1, len(renderers)):
renderers[r].SetActiveCamera(renderers[0].GetActiveCamera())
renderWindowInteractor.Initialize()
renderWindowInteractor.Start()
def onApply(self):
self.scriptedEffect.saveStateForUndo()
# Get modifier labelmap and parameters
modifierLabelmap = self.scriptedEffect.defaultModifierLabelmap()
selectedSegmentLabelmap = self.scriptedEffect.selectedSegmentLabelmap()
shellMode = self.scriptedEffect.parameter("ShellMode")
marginSizeMm = self.scriptedEffect.doubleParameter("MarginSizeMm")
kernelSizePixel = self.getKernelSizePixel()
if shellMode == MEDIAL_SURFACE:
# both erosion and dilation will be applied, so kernel size must be half on each side
kernelSizePixel = [int(kernelSizePixel[0]/2), int(kernelSizePixel[1]/2), int(kernelSizePixel[2]/2)]
# 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()
subtract = vtk.vtkImageMathematics()
subtract.SetOperationToSubtract()
if shellMode == INSIDE_SURFACE or shellMode == MEDIAL_SURFACE:
dilate = vtk.vtkImageDilateErode3D()
dilate.SetInputConnection(thresh.GetOutputPort())
dilate.SetDilateValue(labelValue)
dilate.SetErodeValue(backgroundValue)
dilate.SetKernelSize(kernelSizePixel[0],kernelSizePixel[1],kernelSizePixel[2])
dilate.Update()
subtract.SetInput1Data(dilate.GetOutput())
else:
subtract.SetInput1Data(thresh.GetOutput())
if shellMode == OUTSIDE_SURFACE or shellMode == MEDIAL_SURFACE:
erode = vtk.vtkImageDilateErode3D()
erode.SetInputConnection(thresh.GetOutputPort())
erode.SetDilateValue(backgroundValue)
erode.SetErodeValue(labelValue)
erode.SetKernelSize(kernelSizePixel[0],kernelSizePixel[1],kernelSizePixel[2])
erode.Update()
subtract.SetInput2Data(erode.GetOutput())
else:
subtract.SetInput2Data(thresh.GetOutput())
# This can be a long operation - indicate it to the user
qt.QApplication.setOverrideCursor(qt.Qt.WaitCursor)
subtract.Update()
modifierLabelmap.DeepCopy(subtract.GetOutput())
# Apply changes
self.scriptedEffect.modifySelectedSegmentByLabelmap(modifierLabelmap, slicer.qSlicerSegmentEditorAbstractEffect.ModificationModeSet)
qt.QApplication.restoreOverrideCursor()
def autocontour_buie(img, args):
# these hard-coded constants just make sure that the connectivity filter
# actually works, they don't need to be configuable in my opinion
CONN_SCALAR_RANGE = [1, args.in_value + 1]
CONN_SIZE_RANGE = [0, int(1E10)]
# Step 1 was just loading the AIM
# Step 2: Threshold
s2_threshold = vtk.vtkImageThreshold()
s2_threshold.ThresholdByUpper(args.threshold_1)
s2_threshold.SetInValue(args.in_value)
s2_threshold.SetOutValue(args.out_value)
s2_threshold.SetInputData(img)
# Step 3: Median
s3_median = vtk.vtkImageMedian3D()
s3_median.SetKernelSize(*args.step_3_median_kernel)
s3_median.SetInputConnection(s2_threshold.GetOutputPort())
# Step 4: Dilate
s4_dilate = vtk.vtkImageDilateErode3D()
s4_dilate.SetDilateValue(args.in_value)
s4_dilate.SetErodeValue(args.out_value)
s4_dilate.SetKernelSize(*args.step_4_and_6_dilate_erode_kernel)
s4_dilate.SetInputConnection(s3_median.GetOutputPort())
# Step 5: Connectivity (applied to non-bone)
# first flip 0 <-> 127
s5a_invert = vtk.vtkImageThreshold()
s5a_invert.ThresholdByLower(args.in_value / 2)
s5a_invert.SetInValue(args.in_value)
s5a_invert.SetOutValue(args.out_value)
s5a_invert.SetInputConnection(s4_dilate.GetOutputPort())
# then connectivity
s5b_connectivity = vtk.vtkImageConnectivityFilter()
s5b_connectivity.SetExtractionModeToLargestRegion()
s5b_connectivity.SetScalarRange(*CONN_SCALAR_RANGE)
s5b_connectivity.SetSizeRange(*CONN_SIZE_RANGE)
s5b_connectivity.SetInputConnection(s5a_invert.GetOutputPort())
# then flip 0 <-> 127 again
s5c_invert = vtk.vtkImageThreshold()
s5c_invert.ThresholdByLower(0.5)
s5c_invert.SetInValue(args.in_value)
s5c_invert.SetOutValue(args.out_value)
s5c_invert.SetInputConnection(s5b_connectivity.GetOutputPort())
# Step 6: Erode
s6_erode = vtk.vtkImageDilateErode3D()
s6_erode.SetDilateValue(args.out_value)
s6_erode.SetErodeValue(args.in_value)
s6_erode.SetKernelSize(*args.step_4_and_6_dilate_erode_kernel)
s6_erode.SetInputConnection(s5c_invert.GetOutputPort())
# Step 7: Threshold
s7_threshold = vtk.vtkImageThreshold()
s7_threshold.ThresholdByLower(args.threshold_2)
s7_threshold.SetInValue(args.in_value)
s7_threshold.SetOutValue(args.out_value)
s7_threshold.SetInputData(img)
# Step 8: Mask
s8a_mask = vtk.vtkImageMask()
s8a_mask.SetInputConnection(0, s7_threshold.GetOutputPort())
s8a_mask.SetInputConnection(1, s6_erode.GetOutputPort())
s8b_invert = vtk.vtkImageThreshold()
s8b_invert.ThresholdByLower(args.in_value / 2)
s8b_invert.SetInValue(args.in_value)
s8b_invert.SetOutValue(args.out_value)
s8b_invert.SetInputConnection(s8a_mask.GetOutputPort())
# Step 9: Dilate
s9_dilate = vtk.vtkImageDilateErode3D()
s9_dilate.SetDilateValue(args.out_value)
s9_dilate.SetErodeValue(args.in_value)
s9_dilate.SetKernelSize(*args.step_9_and_11_dilate_erode_kernel)
s9_dilate.SetInputConnection(s8b_invert.GetOutputPort())
# Step 10: Connectivity
# connectivity
s10a_connectivity = vtk.vtkImageConnectivityFilter()
s10a_connectivity.SetExtractionModeToLargestRegion()
s10a_connectivity.SetScalarRange(*CONN_SCALAR_RANGE)
s10a_connectivity.SetSizeRange(*CONN_SIZE_RANGE)
s10a_connectivity.SetInputConnection(s9_dilate.GetOutputPort())
# then convert to 127 and 0 again
s10b_convert = vtk.vtkImageThreshold()
s10b_convert.ThresholdByLower(0.5)
s10b_convert.SetInValue(args.out_value)
s10b_convert.SetOutValue(args.in_value)
s10b_convert.SetInputConnection(s10a_connectivity.GetOutputPort())
# Step 11: Erode
s11_erode = vtk.vtkImageDilateErode3D()
s11_erode.SetDilateValue(args.in_value)
s11_erode.SetErodeValue(args.out_value)
s11_erode.SetKernelSize(*args.step_9_and_11_dilate_erode_kernel)
s11_erode.SetInputConnection(s10b_convert.GetOutputPort())
# Step 12: Gaussian Smooth
s12_gauss = vtk.vtkImageGaussianSmooth()
s12_gauss.SetStandardDeviation(args.step_12_gaussian_std)
s12_gauss.SetRadiusFactors(*args.step_12_gaussian_kernel)
s12_gauss.SetInputConnection(s11_erode.GetOutputPort())
# Step 13: Threshold
s13_threshold = vtk.vtkImageThreshold()
s13_threshold.ThresholdByLower(S13_THRESH)
s13_threshold.SetInValue(args.out_value)
s13_threshold.SetOutValue(args.in_value)
s13_threshold.SetInputConnection(s12_gauss.GetOutputPort())
# Step 14: Mask
s14_mask = vtk.vtkImageMask()
s14_mask.SetInputConnection(0, s6_erode.GetOutputPort())
s14_mask.SetInputConnection(1, s13_threshold.GetOutputPort())
# Step 15: Invert the Trabecular Mask
s15_invert = vtk.vtkImageThreshold()
s15_invert.ThresholdByLower(args.in_value / 2)
s15_invert.SetInValue(args.in_value)
s15_invert.SetOutValue(args.out_value)
s15_invert.SetInputConnection(s13_threshold.GetOutputPort())
# update the pipeline
s14_mask.Update()
s15_invert.Update()
# get masks
cort_mask = s14_mask.GetOutput()
trab_mask = s15_invert.GetOutput()
return cort_mask, trab_mask
def vortvelvolumei(args):
#inputfile, outputfile, sx, ex, sy, ey, sz, ez, dataset):
p = args[0]
cubenum = args[1]
print("Cube", cubenum)
#Check for additonal parameters
if (p["param1"] != ''):
comptype = p["param1"]
else:
comptype = "q" #Default to q criterion
if (p["param2"] != ''):
thresh = float(p["param2"])
else:
thresh = 783.3 #Default for q threshold on isotropic data
inputfile = p["inputfile"] +str(cubenum) + ".npy"
outputfile = p["outputfile"] + str(cubenum) + ".vti" #always VTK Image Data for this.
sx = p["sx"]
sy = p["sy"]
sz = p["sz"]
ex = p["ex"]
ey = p["ey"]
ez = p["ez"]
print ("Loading file, %s" % inputfile)
#Determine if file is h5 or numpy
rs = timeit.default_timer()
vel = np.load(inputfile)
print ("File Loaded")
re = timeit.default_timer()
#convert numpy array to vtk
cs = timeit.default_timer()
#convert numpy array to vtk
vtkdata = numpy_support.numpy_to_vtk(vel.flat, deep=True, array_type=vtk.VTK_FLOAT)
vtkdata.SetNumberOfComponents(3)
vtkdata.SetName("Velocity")
image = vtk.vtkImageData()
image.GetPointData().SetVectors(vtkdata)
image.SetExtent(sx,ex,sy,ey,sz,ez)
#NOTE: Hardcoding Spacing
image.SetSpacing(.006135923, .006135923, .006135923)
ce = timeit.default_timer()
vs = timeit.default_timer()
print ("Beginning computation: " + comptype)
if (comptype == "v"):
vorticity = vtk.vtkCellDerivatives()
vorticity.SetVectorModeToComputeVorticity()
vorticity.SetTensorModeToPassTensors()
vorticity.SetInputData(image)
vorticity.Update()
elif (comptype == "q"):
vorticity = vtk.vtkGradientFilter()
vorticity.SetInputData(image)
vorticity.SetInputScalars(image.FIELD_ASSOCIATION_POINTS,"Velocity")
vorticity.ComputeQCriterionOn()
vorticity.SetComputeGradient(0)
vorticity.Update()
ve = timeit.default_timer()
print("Initial calculation done")
ms = timeit.default_timer()
if (comptype == "v"):
mag = vtk.vtkImageMagnitude()
cp = vtk.vtkCellDataToPointData()
cp.SetInputData(vorticity.GetOutput())
cp.Update()
image.GetPointData().SetScalars(cp.GetOutput().GetPointData().GetVectors())
mag.SetInputData(image)
mag.Update()
m = mag.GetOutput()
m.GetPointData().RemoveArray("Velocity")
else:
image.GetPointData().SetScalars(vorticity.GetOutput().GetPointData().GetVectors("Q-criterion"))
me = timeit.default_timer()
print("Generating screenshot")
c = vtk.vtkContourFilter()
c.SetValue(0,thresh)
c.SetInputData(image)
c.Update()
contour = c.GetOutput()
mapper = vtk.vtkPolyDataMapper()
mapper.SetInputData(contour)
mapper.ScalarVisibilityOn()
mapper.SetScalarRange(-1,1)
mapper.SetScalarModeToUsePointFieldData()
mapper.ColorByArrayComponent("Velocity", 0)
actor = vtk.vtkActor()
actor.SetMapper(mapper)
ren = vtk.vtkRenderer()
ren.AddActor(actor)
ren.SetBackground(1,1,1)
camera = vtk.vtkCamera()
ren.SetActiveCamera(camera)
ren.ResetCamera()
camera.Zoom(1.5) #This reduces the whitespace around the image
renWin = vtk.vtkRenderWindow()
renWin.SetSize(1024,1024)
renWin.AddRenderer(ren)
renWin.SetOffScreenRendering(1)
windowToImageFilter = vtk.vtkWindowToImageFilter()
windowToImageFilter.SetInput(renWin)
windowToImageFilter.Update()
w = vtk.vtkPNGWriter()
pngfilename = p["outputfile"] + str(cubenum) + ".png"
w.SetFileName(pngfilename)
w.SetInputConnection(windowToImageFilter.GetOutputPort())
w.Write()
#Shift camera angle and take snapshots around the cube.
for aznum in range(4):
camera.Azimuth(90)
windowToImageFilter = vtk.vtkWindowToImageFilter()
windowToImageFilter.SetInput(renWin)
windowToImageFilter.Update()
pngfilename = p["outputfile"] + str(cubenum) + "-r" + str(aznum)+ ".png"
w.SetFileName(pngfilename)
w.SetInputConnection(windowToImageFilter.GetOutputPort())
w.Write()
camera.Elevation(90) #Rotate camera to top
windowToImageFilter = vtk.vtkWindowToImageFilter()
windowToImageFilter.SetInput(renWin)
windowToImageFilter.Update()
pngfilename = p["outputfile"] + str(cubenum) + "-t1.png"
w.SetFileName(pngfilename)
w.SetInputConnection(windowToImageFilter.GetOutputPort())
w.Write()
camera.Elevation(180) #Rotate camera to bottom
windowToImageFilter = vtk.vtkWindowToImageFilter()
windowToImageFilter.SetInput(renWin)
windowToImageFilter.Update()
pngfilename = p["outputfile"] + str(cubenum) + "-b1.png"
w.SetFileName(pngfilename)
w.SetInputConnection(windowToImageFilter.GetOutputPort())
w.Write()
print ("Thresholding.")
ts = timeit.default_timer()
t = vtk.vtkImageThreshold() #Dense represenation (0's included, structured grid)
#t = vtk.vtkThreshold() #sparse representation
if (comptype == "q"):
t.SetInputData(image)
t.ThresholdByUpper(thresh) #.25*67.17^2 = 1127
#t.SetInputArrayToProcess(0,0,0, vorticity.GetOutput().FIELD_ASSOCIATION_POINTS, "Q-criterion")
print("q criterion")
else:
t.SetInputData(m)
t.SetInputArrayToProcess(0,0,0, mag.GetOutput().FIELD_ASSOCIATION_POINTS, "Magnitude")
t.ThresholdByUpper(thresh) #44.79)
#Set values in range to 1 and values out of range to 0
t.SetInValue(1)
t.SetOutValue(0)
#t.ReplaceInOn()
#t.ReplaceOutOn()
print("Update thresh")
t.Update()
#wt = vtk.vtkXMLImageDataWriter()
#wt.SetInputData(t.GetOutput())
#wt.SetFileName("thresh.vti")
#wt.Write()
d = vtk.vtkImageDilateErode3D()
d.SetInputData(t.GetOutput())
d.SetKernelSize(4,4,4)
d.SetDilateValue(1)
d.SetErodeValue(0)
print ("Update dilate")
d.Update()
iis = vtk.vtkImageToImageStencil()
iis.SetInputData(d.GetOutput())
iis.ThresholdByUpper(1)
stencil = vtk.vtkImageStencil()
stencil.SetInputConnection(2, iis.GetOutputPort())
stencil.SetBackgroundValue(0)
#image.GetPointData().RemoveArray("Vorticity")
#Set scalars to velocity so it can be cut by the stencil
image.GetPointData().SetScalars(image.GetPointData().GetVectors())
#if (comptype == "q"): #Use this to get just q-criterion data instead of velocity data. Do we need both?
# image.GetPointData().SetScalars(vorticity.GetOutput().GetPointData().GetScalars("Q-criterion"))
stencil.SetInputData(image)
print ("Update stencil")
stencil.Update()
te = timeit.default_timer()
print("Setting up write")
ws = timeit.default_timer()
#Make velocity a vector again
velarray = stencil.GetOutput().GetPointData().GetScalars()
image.GetPointData().RemoveArray("Velocity")
image.GetPointData().SetVectors(velarray)
w = vtk.vtkXMLImageDataWriter()
w.SetCompressorTypeToZLib()
#w.SetCompressorTypeToNone() Need to figure out why this fails.
w.SetEncodeAppendedData(0) #turn of base 64 encoding for fast write
w.SetFileName(outputfile)
w.SetInputData(image)
if (0):
w.SetCompressorTypeToZfp()
w.GetCompressor().SetNx(ex-sx+1)
w.GetCompressor().SetNy(ey-sy+1)
w.GetCompressor().SetNz(ez-sz+1)
w.GetCompressor().SetTolerance(1e-2)
w.GetCompressor().SetNumComponents(3)
#result = w.Write()
result = 1 #don't write for benchmarking
we = timeit.default_timer()
print("Results:")
print("Read time: %s" % str(re-rs))
print ("Convert to vtk: %s" % str(ce-cs))
if (comptype == "q"):
print ("Q Computation: %s" % str(ve-vs))
print ("Q Magnitude: %s" % str(me-ms))
else:
print ("Vorticity Computation: %s" % str(ve-vs))
print ("Vorticity Magnitude: %s" % str(me-ms))
print ("Threshold: %s" % str(te-ts))
print ("Write %s" % str(we-ws))
print ("Total time: %s" % str(we-rs))
if (result):
p["message"] = "Success"
p["computetime"] = str(we-rs)
return p #return the packet
t.SetInputArrayToProcess(0, 0, 0,
mag.GetOutput().FIELD_ASSOCIATION_POINTS, "Magnitude")
#t.ThresholdByUpper(44.79)
t.ThresholdByUpper(22.39)
#t.ThresholdByUpper(67.17)
#Set values in range to 1 and values out of range to 0
#t.SetInValue(1)
t.SetOutValue(0)
#t.ReplaceInOn()
t.ReplaceOutOn()
t.Update()
rt = t.GetOutput()
d = vtk.vtkImageDilateErode3D()
d.SetInputData(t.GetOutput())
d.SetKernelSize(3, 3, 3)
d.SetDilateValue(1)
d.SetErodeValue(0)
d.Update()
iis = vtk.vtkImageToImageStencil()
iis.SetInputData(d.GetOutput())
iis.ThresholdByUpper(1)
stencil = vtk.vtkImageStencil()
stencil.SetInputConnection(2, iis.GetOutputPort())
image.GetPointData().RemoveArray("Vorticity")
image.GetPointData().SetScalars(image.GetPointData().GetVectors())
stencil.SetInputData(image)
stencil.Update()
def getthresh(args):
inputfile = args[0]
outputfile = args[1]
sx = args[2]
ex = args[3]
sy = args[4]
ey = args[5]
sz = args[6]
ez = args[7]
dataset = args[8]
comptype = args[9]
print("Loading file, %s" % inputfile)
#Determine if file is h5 or numpy
if (inputfile.split(".")[1] == "npy"):
rs = timeit.default_timer()
vel = np.load(inputfile)
re = timeit.default_timer()
else:
#read in file
rs = timeit.default_timer()
data_file = h5py.File(inputfile, 'r')
vel = np.array(data_file[dataset])
data_file.close()
re = timeit.default_timer()
cs = timeit.default_timer()
#convert numpy array to vtk
vtkdata = numpy_support.numpy_to_vtk(vel.flat,
deep=True,
array_type=vtk.VTK_FLOAT)
vtkdata.SetNumberOfComponents(3)
vtkdata.SetName("Velocity")
image = vtk.vtkImageData()
image.GetPointData().SetVectors(vtkdata)
image.SetExtent(sx, ex, sy, ey, sz, ez)
#NOTE: Hardcoding Spacing
image.SetSpacing(.006135923, .006135923, .006135923)
print("Doing computation")
ce = timeit.default_timer()
vs = timeit.default_timer()
if (comptype == "v"):
vorticity = vtk.vtkCellDerivatives()
vorticity.SetVectorModeToComputeVorticity()
vorticity.SetTensorModeToPassTensors()
vorticity.SetInputData(image)
vorticity.Update()
elif (comptype == "q"):
vorticity = vtk.vtkGradientFilter()
vorticity.SetInputData(image)
vorticity.SetInputScalars(image.FIELD_ASSOCIATION_POINTS, "Velocity")
vorticity.ComputeQCriterionOn()
vorticity.SetComputeGradient(0)
vorticity.Update()
ve = timeit.default_timer()
#Generate contour for comparison
c = vtk.vtkContourFilter()
c.SetValue(0, 1128)
if (comptype == "q"):
image.GetPointData().SetScalars(
vorticity.GetOutput().GetPointData().GetVectors("Q-criterion"))
else:
image.GetPointData().SetScalars(
vorticity.GetOutput().GetPointData().GetVectors())
c.SetInputData(image)
c.Update()
w = vtk.vtkXMLPolyDataWriter()
w.SetEncodeAppendedData(0) #turn of base 64 encoding for fast write
w.SetFileName("contour.vtp")
w.SetInputData(c.GetOutput())
ws = timeit.default_timer()
w.Write()
ms = timeit.default_timer()
if (comptype == "v"):
mag = vtk.vtkImageMagnitude()
cp = vtk.vtkCellDataToPointData()
cp.SetInputData(vorticity.GetOutput())
cp.Update()
image.GetPointData().SetScalars(
cp.GetOutput().GetPointData().GetVectors())
mag.SetInputData(image)
mag.Update()
m = mag.GetOutput()
m.GetPointData().RemoveArray("Velocity")
else:
image.GetPointData().SetScalars(
vorticity.GetOutput().GetPointData().GetVectors("Q-criterion"))
me = timeit.default_timer()
print("Thresholding.")
ts = timeit.default_timer()
t = vtk.vtkImageThreshold()
#t = vtk.vtkThreshold() #sparse representation
if (comptype == "q"):
t.SetInputData(image)
t.ThresholdByUpper(783.3) #.25*67.17^2 = 1127
#t.SetInputArrayToProcess(0,0,0, vorticity.GetOutput().FIELD_ASSOCIATION_POINTS, "Q-criterion")
print("q criterion")
else:
t.SetInputData(m)
t.SetInputArrayToProcess(0, 0, 0,
mag.GetOutput().FIELD_ASSOCIATION_POINTS,
"Magnitude")
t.ThresholdByUpper(44.79) #44.79)
#Set values in range to 1 and values out of range to 0
t.SetInValue(1)
t.SetOutValue(0)
#t.ReplaceInOn()
#t.ReplaceOutOn()
print("Update thresh")
t.Update()
#wt = vtk.vtkXMLImageDataWriter()
#wt.SetInputData(t.GetOutput())
#wt.SetFileName("thresh.vti")
#wt.Write()
d = vtk.vtkImageDilateErode3D()
d.SetInputData(t.GetOutput())
d.SetKernelSize(3, 3, 3)
d.SetDilateValue(1)
d.SetErodeValue(0)
print("Update dilate")
d.Update()
iis = vtk.vtkImageToImageStencil()
iis.SetInputData(d.GetOutput())
iis.ThresholdByUpper(1)
stencil = vtk.vtkImageStencil()
stencil.SetInputConnection(2, iis.GetOutputPort())
stencil.SetBackgroundValue(0)
#image.GetPointData().RemoveArray("Vorticity")
#Set scalars to velocity so it can be cut by the stencil
image.GetPointData().SetScalars(image.GetPointData().GetVectors())
#if (comptype == "q"): #Use this to get just q-criterion data instead of velocity data. Do we need both?
# image.GetPointData().SetScalars(vorticity.GetOutput().GetPointData().GetScalars("Q-criterion"))
stencil.SetInputData(image)
print("Update stencil")
stencil.Update()
te = timeit.default_timer()
print("Setting up write")
ws = timeit.default_timer()
#Make velocity a vector again
velarray = stencil.GetOutput().GetPointData().GetScalars()
image.GetPointData().RemoveArray("Velocity")
image.GetPointData().SetVectors(velarray)
w = vtk.vtkXMLImageDataWriter()
w.SetCompressorTypeToZLib()
#w.SetCompressorTypeToNone() Need to figure out why this fails.
w.SetEncodeAppendedData(0) #turn of base 64 encoding for fast write
w.SetFileName(outputfile)
w.SetInputData(image)
if (0):
w.SetCompressorTypeToZfp()
w.GetCompressor().SetNx(ex - sx + 1)
w.GetCompressor().SetNy(ey - sy + 1)
w.GetCompressor().SetNz(ez - sz + 1)
w.GetCompressor().SetTolerance(1e-1)
w.GetCompressor().SetNumComponents(3)
w.Write()
we = timeit.default_timer()
print("Results:")
print("Read time: %s" % str(re - rs))
print("Convert to vtk: %s" % str(ce - cs))
if (comptype == "q"):
print("Q Computation: %s" % str(ve - vs))
print("Q Magnitude: %s" % str(me - ms))
else:
print("Vorticity Computation: %s" % str(ve - vs))
print("Vorticity Magnitude: %s" % str(me - ms))
print("Threshold: %s" % str(te - ts))
print("Write %s" % str(we - ws))
print("Total time: %s" % str(we - rs))
def getthresh(args):
inputfile = args[0]
outputfile = args[1]
sx = args[2]
ex = args[3]
sy = args[4]
ey = args[5]
sz = args[6]
ez = args[7]
dataset = args[8]
comptype = args[9]
print ("Loading file, %s" % inputfile)
#Determine if file is h5 or numpy
if (inputfile.split(".")[1] == "npy"):
rs = timeit.default_timer()
vel = np.load(inputfile)
re = timeit.default_timer()
else:
#read in file
rs = timeit.default_timer()
data_file = h5py.File(inputfile, 'r')
vel = np.array(data_file[dataset])
data_file.close()
re = timeit.default_timer()
cs = timeit.default_timer()
#convert numpy array to vtk
vtkdata = numpy_support.numpy_to_vtk(vel.flat, deep=True, array_type=vtk.VTK_FLOAT)
vtkdata.SetNumberOfComponents(3)
vtkdata.SetName("Velocity")
image = vtk.vtkImageData()
image.GetPointData().SetVectors(vtkdata)
image.SetExtent(sx,ex,sy,ey,sz,ez)
#NOTE: Hardcoding Spacing
image.SetSpacing(.006135923, .006135923, .006135923)
print ("Doing computation")
ce = timeit.default_timer()
vs = timeit.default_timer()
if (comptype == "v"):
vorticity = vtk.vtkCellDerivatives()
vorticity.SetVectorModeToComputeVorticity()
vorticity.SetTensorModeToPassTensors()
vorticity.SetInputData(image)
vorticity.Update()
elif (comptype == "q"):
vorticity = vtk.vtkGradientFilter()
vorticity.SetInputData(image)
vorticity.SetInputScalars(image.FIELD_ASSOCIATION_POINTS,"Velocity")
vorticity.ComputeQCriterionOn()
vorticity.SetComputeGradient(0)
vorticity.Update()
ve = timeit.default_timer()
#Generate contour for comparison
c = vtk.vtkContourFilter()
c.SetValue(0,1128)
if (comptype == "q"):
image.GetPointData().SetScalars(vorticity.GetOutput().GetPointData().GetVectors("Q-criterion"))
else:
image.GetPointData().SetScalars(vorticity.GetOutput().GetPointData().GetVectors())
c.SetInputData(image)
c.Update()
w = vtk.vtkXMLPolyDataWriter()
w.SetEncodeAppendedData(0) #turn of base 64 encoding for fast write
w.SetFileName("contour.vtp")
w.SetInputData(c.GetOutput())
ws = timeit.default_timer()
w.Write()
ms = timeit.default_timer()
if (comptype == "v"):
mag = vtk.vtkImageMagnitude()
cp = vtk.vtkCellDataToPointData()
cp.SetInputData(vorticity.GetOutput())
cp.Update()
image.GetPointData().SetScalars(cp.GetOutput().GetPointData().GetVectors())
mag.SetInputData(image)
mag.Update()
m = mag.GetOutput()
m.GetPointData().RemoveArray("Velocity")
else:
image.GetPointData().SetScalars(vorticity.GetOutput().GetPointData().GetVectors("Q-criterion"))
me = timeit.default_timer()
print ("Thresholding.")
ts = timeit.default_timer()
t = vtk.vtkImageThreshold()
#t = vtk.vtkThreshold() #sparse representation
if (comptype == "q"):
t.SetInputData(image)
t.ThresholdByUpper(783.3) #.25*67.17^2 = 1127
#t.SetInputArrayToProcess(0,0,0, vorticity.GetOutput().FIELD_ASSOCIATION_POINTS, "Q-criterion")
print("q criterion")
else:
t.SetInputData(m)
t.SetInputArrayToProcess(0,0,0, mag.GetOutput().FIELD_ASSOCIATION_POINTS, "Magnitude")
t.ThresholdByUpper(44.79) #44.79)
#Set values in range to 1 and values out of range to 0
t.SetInValue(1)
t.SetOutValue(0)
#t.ReplaceInOn()
#t.ReplaceOutOn()
print("Update thresh")
t.Update()
#wt = vtk.vtkXMLImageDataWriter()
#wt.SetInputData(t.GetOutput())
#wt.SetFileName("thresh.vti")
#wt.Write()
d = vtk.vtkImageDilateErode3D()
d.SetInputData(t.GetOutput())
d.SetKernelSize(3,3,3)
d.SetDilateValue(1)
d.SetErodeValue(0)
print ("Update dilate")
d.Update()
iis = vtk.vtkImageToImageStencil()
iis.SetInputData(d.GetOutput())
iis.ThresholdByUpper(1)
stencil = vtk.vtkImageStencil()
stencil.SetInputConnection(2, iis.GetOutputPort())
stencil.SetBackgroundValue(0)
#image.GetPointData().RemoveArray("Vorticity")
#Set scalars to velocity so it can be cut by the stencil
image.GetPointData().SetScalars(image.GetPointData().GetVectors())
#if (comptype == "q"): #Use this to get just q-criterion data instead of velocity data. Do we need both?
# image.GetPointData().SetScalars(vorticity.GetOutput().GetPointData().GetScalars("Q-criterion"))
stencil.SetInputData(image)
print ("Update stencil")
stencil.Update()
te = timeit.default_timer()
print("Setting up write")
ws = timeit.default_timer()
#Make velocity a vector again
velarray = stencil.GetOutput().GetPointData().GetScalars()
image.GetPointData().RemoveArray("Velocity")
image.GetPointData().SetVectors(velarray)
w = vtk.vtkXMLImageDataWriter()
w.SetCompressorTypeToZLib()
#w.SetCompressorTypeToNone() Need to figure out why this fails.
w.SetEncodeAppendedData(0) #turn of base 64 encoding for fast write
w.SetFileName(outputfile)
w.SetInputData(image)
if (0):
w.SetCompressorTypeToZfp()
w.GetCompressor().SetNx(ex-sx+1)
w.GetCompressor().SetNy(ey-sy+1)
w.GetCompressor().SetNz(ez-sz+1)
w.GetCompressor().SetTolerance(1e-1)
w.GetCompressor().SetNumComponents(3)
w.Write()
we = timeit.default_timer()
print("Results:")
print("Read time: %s" % str(re-rs))
print ("Convert to vtk: %s" % str(ce-cs))
if (comptype == "q"):
print ("Q Computation: %s" % str(ve-vs))
print ("Q Magnitude: %s" % str(me-ms))
else:
print ("Vorticity Computation: %s" % str(ve-vs))
print ("Vorticity Magnitude: %s" % str(me-ms))
print ("Threshold: %s" % str(te-ts))
print ("Write %s" % str(we-ws))
print ("Total time: %s" % str(we-rs))
def vortvelvolume(args):
#inputfile, outputfile, sx, ex, sy, ey, sz, ez, dataset):
p = args[0]
cubenum = args[1]
print("Cube", cubenum)
#Check for additonal parameters
if (p["param1"] != ''):
comptype = p["param1"]
else:
comptype = "q" #Default to q criterion
if (p["param2"] != ''):
thresh = float(p["param2"])
else:
thresh = 783.3 #Default for q threshold on isotropic data
#We use 0 for structured grid (vti) and 1 for unstructured grid (vtu)
if (p["param3"] != ''):
grid = 0
else:
grid = 1
if (p["param4"] != ''):
kernelsize = int(p["param4"])
else:
kernelsize = 3
inputfile = p["inputfile"] +str(cubenum) + ".npy"
outputfile = p["outputfile"] + str(cubenum) + ".vti" #always VTK Image Data for this.
sx = p["sx"]
sy = p["sy"]
sz = p["sz"]
ex = p["ex"]
ey = p["ey"]
ez = p["ez"]
print ("Loading file, %s" % inputfile)
#Determine if file is h5 or numpy
rs = timeit.default_timer()
vel = np.load(inputfile)
re = timeit.default_timer()
#convert numpy array to vtk
cs = timeit.default_timer()
#convert numpy array to vtk
vtkdata = numpy_support.numpy_to_vtk(vel.flat, deep=True, array_type=vtk.VTK_FLOAT)
vtkdata.SetNumberOfComponents(3)
vtkdata.SetName("Velocity")
image = vtk.vtkImageData()
image.GetPointData().SetVectors(vtkdata)
image.SetExtent(sx,ex,sy,ey,sz,ez)
#NOTE: Hardcoding Spacing
image.SetSpacing(.006135923, .006135923, .006135923)
ce = timeit.default_timer()
vs = timeit.default_timer()
if (comptype == "v"):
vorticity = vtk.vtkCellDerivatives()
vorticity.SetVectorModeToComputeVorticity()
vorticity.SetTensorModeToPassTensors()
vorticity.SetInputData(image)
vorticity.Update()
elif (comptype == "q"):
vorticity = vtk.vtkGradientFilter()
vorticity.SetInputData(image)
vorticity.SetInputScalars(image.FIELD_ASSOCIATION_POINTS,"Velocity")
vorticity.ComputeQCriterionOn()
vorticity.SetComputeGradient(0)
vorticity.Update()
ve = timeit.default_timer()
ms = timeit.default_timer()
if (comptype == "v"):
mag = vtk.vtkImageMagnitude()
cp = vtk.vtkCellDataToPointData()
cp.SetInputData(vorticity.GetOutput())
cp.Update()
image.GetPointData().SetScalars(cp.GetOutput().GetPointData().GetVectors())
mag.SetInputData(image)
mag.Update()
m = mag.GetOutput()
m.GetPointData().RemoveArray("Velocity")
else:
image.GetPointData().SetScalars(vorticity.GetOutput().GetPointData().GetVectors("Q-criterion"))
me = timeit.default_timer()
print ("Thresholding.")
ts = timeit.default_timer()
t = vtk.vtkImageThreshold()
#t = vtk.vtkThreshold() #sparse representation
if (comptype == "q"):
t.SetInputData(image)
t.ThresholdByUpper(thresh) #.25*67.17^2 = 1127
#t.SetInputArrayToProcess(0,0,0, vorticity.GetOutput().FIELD_ASSOCIATION_POINTS, "Q-criterion")
print("q criterion")
else:
t.SetInputData(m)
t.SetInputArrayToProcess(0,0,0, mag.GetOutput().FIELD_ASSOCIATION_POINTS, "Magnitude")
t.ThresholdByUpper(thresh) #44.79)
#Set values in range to 1 and values out of range to 0
t.SetInValue(1)
t.SetOutValue(0)
#t.ReplaceInOn()
#t.ReplaceOutOn()
print("Update thresh")
t.Update()
#wt = vtk.vtkXMLImageDataWriter()
#wt.SetInputData(t.GetOutput())
#wt.SetFileName("thresh.vti")
#wt.Write()
d = vtk.vtkImageDilateErode3D()
d.SetInputData(t.GetOutput())
d.SetKernelSize(kernelsize,kernelsize,kernelsize)
d.SetDilateValue(1)
d.SetErodeValue(0)
print ("Update dilate")
d.Update()
iis = vtk.vtkImageToImageStencil()
iis.SetInputData(d.GetOutput())
iis.ThresholdByUpper(1)
stencil = vtk.vtkImageStencil()
stencil.SetInputConnection(2, iis.GetOutputPort())
stencil.SetBackgroundValue(0)
#image.GetPointData().RemoveArray("Vorticity")
#Set scalars to velocity so it can be cut by the stencil
image.GetPointData().SetScalars(image.GetPointData().GetVectors())
#if (comptype == "q"): #Use this to get just q-criterion data instead of velocity data. Do we need both?
# image.GetPointData().SetScalars(vorticity.GetOutput().GetPointData().GetScalars("Q-criterion"))
stencil.SetInputData(image)
print ("Update stencil")
stencil.Update()
te = timeit.default_timer()
print("Setting up write")
ws = timeit.default_timer()
#Make velocity a vector again
velarray = stencil.GetOutput().GetPointData().GetScalars()
image.GetPointData().RemoveArray("Velocity")
image.GetPointData().SetVectors(velarray)
if (grid == 0):
w = vtk.vtkXMLImageDataWriter()
else:
w = vtk.vtkXMLUnstructuredGridWriter()
w.SetCompressorTypeToZLib()
#w.SetCompressorTypeToNone() Need to figure out why this fails.
w.SetEncodeAppendedData(0) #turn of base 64 encoding for fast write
w.SetFileName(outputfile)
w.SetInputData(image)
if (0):
w.SetCompressorTypeToZfp()
w.GetCompressor().SetNx(ex-sx+1)
w.GetCompressor().SetNy(ey-sy+1)
w.GetCompressor().SetNz(ez-sz+1)
w.GetCompressor().SetTolerance(1e-2)
w.GetCompressor().SetNumComponents(3)
result = w.Write()
result = 1 #don't write for benchmarking
we = timeit.default_timer()
print("Results:")
print("Read time: %s" % str(re-rs))
print ("Convert to vtk: %s" % str(ce-cs))
if (comptype == "q"):
print ("Q Computation: %s" % str(ve-vs))
print ("Q Magnitude: %s" % str(me-ms))
else:
print ("Vorticity Computation: %s" % str(ve-vs))
print ("Vorticity Magnitude: %s" % str(me-ms))
print ("Threshold: %s" % str(te-ts))
print ("Write %s" % str(we-ws))
print ("Total time: %s" % str(we-rs))
if (result):
p["message"] = "Success"
p["computetime"] = str(we-rs)
return p #return the packet
def apply(self, ijkPoints):
kernelSizePixel = self.getKernelSizePixel()
if kernelSizePixel[0]<=0 and kernelSizePixel[1]<=0 and kernelSizePixel[2]<=0:
return
qt.QApplication.setOverrideCursor(qt.Qt.WaitCursor)
# Get parameter set node
parameterSetNode = self.scriptedEffect.parameterSetNode()
# Get parameters
minimumThreshold = self.scriptedEffect.doubleParameter("MinimumThreshold")
maximumThreshold = self.scriptedEffect.doubleParameter("MaximumThreshold")
# Get modifier labelmap
modifierLabelmap = self.scriptedEffect.defaultModifierLabelmap()
# Get master volume image data
masterImageData = self.scriptedEffect.masterVolumeImageData()
# Set intensity range
oldMasterVolumeIntensityMask = parameterSetNode.GetMasterVolumeIntensityMask()
parameterSetNode.MasterVolumeIntensityMaskOn()
oldIntensityMaskRange = parameterSetNode.GetMasterVolumeIntensityMaskRange()
intensityRange = [265.00, 1009.00]
if oldMasterVolumeIntensityMask:
intensityRange = [max(oldIntensityMaskRange[0], minimumThreshold), min(oldIntensityMaskRange[1], maximumThreshold)]
parameterSetNode.SetMasterVolumeIntensityMaskRange(intensityRange)
roiNode = lumbarSeed ##self.roiSelector.currentNode()
clippedMasterImageData = masterImageData
if roiNode is not None:
worldToImageMatrix = vtk.vtkMatrix4x4()
masterImageData.GetWorldToImageMatrix(worldToImageMatrix)
bounds = [0,0,0,0,0,0]
roiNode.GetRASBounds(bounds)
corner1RAS = [bounds[0], bounds[2], bounds[4], 1]
corner1IJK = [0, 0, 0, 0]
worldToImageMatrix.MultiplyPoint(corner1RAS, corner1IJK)
corner2RAS = [bounds[1], bounds[3], bounds[5], 1]
corner2IJK = [0, 0, 0, 0]
worldToImageMatrix.MultiplyPoint(corner2RAS, corner2IJK)
extent = [0, -1, 0, -1, 0, -1]
for i in range(3):
lowerPoint = min(corner1IJK[i], corner2IJK[i])
upperPoint = max(corner1IJK[i], corner2IJK[i])
extent[2*i] = int(math.floor(lowerPoint))
extent[2*i+1] = int(math.ceil(upperPoint))
imageToWorldMatrix = vtk.vtkMatrix4x4()
masterImageData.GetImageToWorldMatrix(imageToWorldMatrix)
clippedMasterImageData = slicer.vtkOrientedImageData()
self.padder = vtk.vtkImageConstantPad()
self.padder.SetInputData(masterImageData)
self.padder.SetOutputWholeExtent(extent)
self.padder.Update()
clippedMasterImageData.ShallowCopy(self.padder.GetOutput())
clippedMasterImageData.SetImageToWorldMatrix(imageToWorldMatrix)
# Pipeline
self.thresh = vtk.vtkImageThreshold()
self.thresh.SetInValue(LABEL_VALUE)
self.thresh.SetOutValue(BACKGROUND_VALUE)
self.thresh.SetInputData(clippedMasterImageData)
self.thresh.ThresholdBetween(minimumThreshold, maximumThreshold)
self.thresh.SetOutputScalarTypeToUnsignedChar()
self.thresh.Update()
self.erode = vtk.vtkImageDilateErode3D()
self.erode.SetInputConnection(self.thresh.GetOutputPort())
self.erode.SetDilateValue(BACKGROUND_VALUE)
self.erode.SetErodeValue(LABEL_VALUE)
self.erode.SetKernelSize(
kernelSizePixel[0],
kernelSizePixel[1],
kernelSizePixel[2])
self.erodeCast = vtk.vtkImageCast()
self.erodeCast.SetInputConnection(self.erode.GetOutputPort())
self.erodeCast.SetOutputScalarTypeToUnsignedInt()
self.erodeCast.Update()
# Remove small islands
self.islandMath = vtkITK.vtkITKIslandMath()
self.islandMath.SetInputConnection(self.erodeCast.GetOutputPort())
self.islandMath.SetFullyConnected(False)
self.islandMath.SetMinimumSize(125) # remove regions smaller than 5x5x5 voxels
self.islandThreshold = vtk.vtkImageThreshold()
self.islandThreshold.SetInputConnection(self.islandMath.GetOutputPort())
self.islandThreshold.ThresholdByLower(BACKGROUND_VALUE)
self.islandThreshold.SetInValue(BACKGROUND_VALUE)
self.islandThreshold.SetOutValue(LABEL_VALUE)
self.islandThreshold.SetOutputScalarTypeToUnsignedChar()
self.islandThreshold.Update()
# Points may be outside the region after it is eroded.
# Snap the points to LABEL_VALUE voxels,
snappedIJKPoints = self.snapIJKPointsToLabel(ijkPoints, self.islandThreshold.GetOutput())
if snappedIJKPoints.GetNumberOfPoints() == 0:
qt.QApplication.restoreOverrideCursor()
return
# Convert points to real data coordinates. Required for vtkImageThresholdConnectivity.
seedPoints = vtk.vtkPoints()
origin = masterImageData.GetOrigin()
spacing = masterImageData.GetSpacing()
for i in range(snappedIJKPoints.GetNumberOfPoints()):
ijkPoint = snappedIJKPoints.GetPoint(i)
seedPoints.InsertNextPoint(
origin[0]+ijkPoint[0]*spacing[0],
origin[1]+ijkPoint[1]*spacing[1],
origin[2]+ijkPoint[2]*spacing[2])
segmentationAlgorithm = self.scriptedEffect.parameter(SEGMENTATION_ALGORITHM_PARAMETER_NAME)
if segmentationAlgorithm == SEGMENTATION_ALGORITHM_MASKING:
self.runMasking(seedPoints, self.islandThreshold.GetOutput(), modifierLabelmap)
else:
self.floodFillingFilterIsland = vtk.vtkImageThresholdConnectivity()
self.floodFillingFilterIsland.SetInputConnection(self.islandThreshold.GetOutputPort())
self.floodFillingFilterIsland.SetInValue(SELECTED_ISLAND_VALUE)
self.floodFillingFilterIsland.ReplaceInOn()
self.floodFillingFilterIsland.ReplaceOutOff()
self.floodFillingFilterIsland.ThresholdBetween(265.00, 1009.00)
self.floodFillingFilterIsland.SetSeedPoints(seedPoints)
self.floodFillingFilterIsland.Update()
self.maskCast = vtk.vtkImageCast()
self.maskCast.SetInputData(self.thresh.GetOutput())
self.maskCast.SetOutputScalarTypeToUnsignedChar()
self.maskCast.Update()
self.imageMask = vtk.vtkImageMask()
self.imageMask.SetInputConnection(self.floodFillingFilterIsland.GetOutputPort())
self.imageMask.SetMaskedOutputValue(OUTSIDE_THRESHOLD_VALUE)
self.imageMask.SetMaskInputData(self.maskCast.GetOutput())
self.imageMask.Update()
imageMaskOutput = slicer.vtkOrientedImageData()
imageMaskOutput.ShallowCopy(self.imageMask.GetOutput())
imageMaskOutput.CopyDirections(clippedMasterImageData)
imageToWorldMatrix = vtk.vtkMatrix4x4()
imageMaskOutput.GetImageToWorldMatrix(imageToWorldMatrix)
segmentOutputLabelmap = slicer.vtkOrientedImageData()
if segmentationAlgorithm == SEGMENTATION_ALGORITHM_GROWCUT:
self.runGrowCut(clippedMasterImageData, imageMaskOutput, segmentOutputLabelmap)
elif segmentationAlgorithm == SEGMENTATION_ALGORITHM_WATERSHED:
self.runWatershed(clippedMasterImageData, imageMaskOutput, segmentOutputLabelmap)
else:
logging.error("Unknown segmentation algorithm: \"" + segmentationAlgorithm + "\"")
segmentOutputLabelmap.SetImageToWorldMatrix(imageToWorldMatrix)
self.selectedSegmentThreshold = vtk.vtkImageThreshold()
self.selectedSegmentThreshold.SetInputData(segmentOutputLabelmap)
self.selectedSegmentThreshold.ThresholdBetween(SELECTED_ISLAND_VALUE, SELECTED_ISLAND_VALUE)
self.selectedSegmentThreshold.SetInValue(LABEL_VALUE)
self.selectedSegmentThreshold.SetOutValue(BACKGROUND_VALUE)
self.selectedSegmentThreshold.SetOutputScalarType(modifierLabelmap.GetScalarType())
self.selectedSegmentThreshold.Update()
modifierLabelmap.ShallowCopy(self.selectedSegmentThreshold.GetOutput())
self.scriptedEffect.saveStateForUndo()
self.scriptedEffect.modifySelectedSegmentByLabelmap(modifierLabelmap, slicer.qSlicerSegmentEditorAbstractEffect.ModificationModeAdd)
parameterSetNode.SetMasterVolumeIntensityMask(oldMasterVolumeIntensityMask)
parameterSetNode.SetMasterVolumeIntensityMaskRange(oldIntensityMaskRange)
qt.QApplication.restoreOverrideCursor()
t.SetInputData(mag.GetOutput())
t.SetInputArrayToProcess(0,0,0, mag.GetOutput().FIELD_ASSOCIATION_POINTS, "Magnitude")
#t.ThresholdByUpper(44.79)
t.ThresholdByUpper(22.39)
#t.ThresholdByUpper(67.17)
#Set values in range to 1 and values out of range to 0
#t.SetInValue(1)
t.SetOutValue(0)
#t.ReplaceInOn()
t.ReplaceOutOn()
t.Update()
rt = t.GetOutput()
d = vtk.vtkImageDilateErode3D()
d.SetInputData(t.GetOutput())
d.SetKernelSize(3,3,3)
d.SetDilateValue(1)
d.SetErodeValue(0)
d.Update()
iis = vtk.vtkImageToImageStencil()
iis.SetInputData(d.GetOutput())
iis.ThresholdByUpper(1)
stencil = vtk.vtkImageStencil()
stencil.SetInputConnection(2, iis.GetOutputPort())
image.GetPointData().RemoveArray("Vorticity")
image.GetPointData().SetScalars(image.GetPointData().GetVectors())
stencil.SetInputData(image)
stencil.Update()
def onApply(self):
self.scriptedEffect.saveStateForUndo()
# Get modifier labelmap and parameters
modifierLabelmap = self.scriptedEffect.defaultModifierLabelmap()
selectedSegmentLabelmap = self.scriptedEffect.selectedSegmentLabelmap()
shellMode = self.scriptedEffect.parameter("ShellMode")
marginSizeMm = self.scriptedEffect.doubleParameter("MarginSizeMm")
kernelSizePixel = self.getKernelSizePixel()
if shellMode == MEDIAL_SURFACE:
# both erosion and dilation will be applied, so kernel size must be half on each side
kernelSizePixel = [int(kernelSizePixel[0],2), int(kernelSizePixel[1],2), int(kernelSizePixel[2],2)]
# 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()
subtract = vtk.vtkImageMathematics()
subtract.SetOperationToSubtract()
if shellMode == INSIDE_SURFACE or shellMode == MEDIAL_SURFACE:
dilate = vtk.vtkImageDilateErode3D()
dilate.SetInputConnection(thresh.GetOutputPort())
dilate.SetDilateValue(labelValue)
dilate.SetErodeValue(backgroundValue)
dilate.SetKernelSize(kernelSizePixel[0],kernelSizePixel[1],kernelSizePixel[2])
dilate.Update()
subtract.SetInput1Data(dilate.GetOutput())
else:
subtract.SetInput1Data(thresh.GetOutput())
if shellMode == OUTSIDE_SURFACE or shellMode == MEDIAL_SURFACE:
erode = vtk.vtkImageDilateErode3D()
erode.SetInputConnection(thresh.GetOutputPort())
erode.SetDilateValue(backgroundValue)
erode.SetErodeValue(labelValue)
erode.SetKernelSize(kernelSizePixel[0],kernelSizePixel[1],kernelSizePixel[2])
erode.Update()
subtract.SetInput2Data(erode.GetOutput())
else:
subtract.SetInput2Data(thresh.GetOutput())
# This can be a long operation - indicate it to the user
qt.QApplication.setOverrideCursor(qt.Qt.WaitCursor)
subtract.Update()
modifierLabelmap.DeepCopy(subtract.GetOutput())
# Apply changes
self.scriptedEffect.modifySelectedSegmentByLabelmap(modifierLabelmap, slicer.qSlicerSegmentEditorAbstractEffect.ModificationModeSet)
qt.QApplication.restoreOverrideCursor()
def onApply(self):
self.scriptedEffect.saveStateForUndo()
# Get modifier labelmap and parameters
modifierLabelmap = self.scriptedEffect.defaultModifierLabelmap()
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()
subtract = vtk.vtkImageMathematics()
subtract.SetOperationToSubtract()
kernelSizePixel = self.getKernelSizePixel()
shellMode = self.scriptedEffect.parameter("ShellMode")
if shellMode == MEDIAL_SURFACE:
dilateKernelSizePixel = [int((kernelSizePixel[i]+1.0)/4.0)*2+1 for i in range(3)]
erodeKernelSizePixel = [int((kernelSizePixel[i]-1.0)/4.0)*2+1 for i in range(3)]
elif shellMode == INSIDE_SURFACE:
dilateKernelSizePixel = kernelSizePixel
erodeKernelSizePixel = [1, 1, 1]
elif shellMode == OUTSIDE_SURFACE:
dilateKernelSizePixel = [1, 1, 1]
erodeKernelSizePixel = kernelSizePixel
if dilateKernelSizePixel[0]>1 or dilateKernelSizePixel[1]>1 or dilateKernelSizePixel[2]>1:
dilate = vtk.vtkImageDilateErode3D()
dilate.SetInputConnection(thresh.GetOutputPort())
dilate.SetDilateValue(labelValue)
dilate.SetErodeValue(backgroundValue)
dilate.SetKernelSize(*dilateKernelSizePixel)
dilate.Update()
subtract.SetInput1Data(dilate.GetOutput())
else:
subtract.SetInput1Data(thresh.GetOutput())
if erodeKernelSizePixel[0]>1 or erodeKernelSizePixel[1]>1 or erodeKernelSizePixel[2]>1:
erode = vtk.vtkImageDilateErode3D()
erode.SetInputConnection(thresh.GetOutputPort())
erode.SetDilateValue(backgroundValue)
erode.SetErodeValue(labelValue)
erode.SetKernelSize(*erodeKernelSizePixel)
erode.Update()
subtract.SetInput2Data(erode.GetOutput())
else:
subtract.SetInput2Data(thresh.GetOutput())
# This can be a long operation - indicate it to the user
qt.QApplication.setOverrideCursor(qt.Qt.WaitCursor)
subtract.Update()
modifierLabelmap.DeepCopy(subtract.GetOutput())
# Apply changes
self.scriptedEffect.modifySelectedSegmentByLabelmap(modifierLabelmap, slicer.qSlicerSegmentEditorAbstractEffect.ModificationModeSet)
qt.QApplication.restoreOverrideCursor()
