def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
vtk.vtkImageOpenClose3D(), 'Processing.',
('vtkImageData',), ('vtkImageData',),
replaceDoc=True,
inputFunctions=None, outputFunctions=None)
def openClose3D(image, openValue, closeValue, kernel):
image2 = vtk.vtkImageOpenClose3D()
image2.SetInput(image)
image2.SetOpenValue(openValue)
image2.SetCloseValue(closeValue)
image2.SetKernelSize(kernel[0],kernel[1],kernel[2])
image2.Update()
return image2.GetOutput()
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(self,
module_manager,
vtk.vtkImageOpenClose3D(),
'Processing.', ('vtkImageData', ),
('vtkImageData', ),
replaceDoc=True,
inputFunctions=None,
outputFunctions=None)
def applyOpenClose(self, imgData, oVal, cVal, kernel=[3, 3, 3]):
ocImg = vtk.vtkImageOpenClose3D()
ocImg.SetInputData(imgData.GetOutput())
ocImg.SetOpenValue(oVal)
ocImg.SetCloseValue(cVal)
ocImg.SetKernelSize(kernel[0], kernel[1], kernel[2])
ocImg.Update()
return ocImg
def imageopenclose(image, openvalue, closevalue, kernelsize):
"""Performs opening and closing morphological operations
with a 3D ellipsoidal kernel."""
openClose = vtk.vtkImageOpenClose3D()
openClose.SetInput(image)
openClose.SetOpenValue(openvalue)
openClose.SetCloseValue(closevalue)
openClose.SetKernelSize(kernelsize, kernelsize, kernelsize)
openClose.ReleaseDataFlagOff()
openClose.GetOutput()
openClose.GetCloseValue()
openClose.GetOpenValue()
return openClose.GetOutput()
def OpenCloseImageFilter(self, image, settings):
"""Open or close an image"""
image.SetReleaseDataFlag(1)
_filter = vtk.vtkImageOpenClose3D()
_filter.SetInput(image.GetRealImage())
_filter.AddObserver('ProgressEvent', self.HandleVTKProgressEvent)
_filter.SetProgressText("Opening/Closing...")
_filter.SetKernelSize(settings['KernelSizeX'], settings['KernelSizeY'],
settings['KernelSizeZ'])
_filter.SetOpenValue(settings['OpenValue'])
_filter.SetCloseValue(settings['CloseValue'])
logging.info("Open/close filter applied")
return MVImage.MVImage(_filter.GetOutputPort(), input=image)
def OpenCloseImageFilter(self, image, settings):
"""Open or close an image"""
image.SetReleaseDataFlag(1)
_filter = vtk.vtkImageOpenClose3D()
_filter.SetInput(image.GetRealImage())
_filter.AddObserver('ProgressEvent', self.HandleVTKProgressEvent)
_filter.SetProgressText("Opening/Closing...")
_filter.SetKernelSize(
settings['KernelSizeX'], settings['KernelSizeY'], settings['KernelSizeZ'])
_filter.SetOpenValue(settings['OpenValue'])
_filter.SetCloseValue(settings['CloseValue'])
logging.info("Open/close filter applied")
return MVImage.MVImage(_filter.GetOutputPort(), input=image)
def label_open_close(im, label_id, bg_id, size):
"""
Open or close
Args:
im: vtkImage of the label map
label_id: class id to close
bg_id: class id of background to open
size: number of pixels of the erosion
Return: processed vtk image
"""
filt = vtk.vtkImageOpenClose3D()
filt.SetInputData(im)
filt.SetOpenValue(bg_id)
filt.SetCloseValue(label_id)
filt.SetKernelSize(int(size), int(size), int(size))
filt.Update()
return filt.GetOutput()
def smoothSelectedSegment(self, maskImage=None, maskExtent=None):
try:
# Get modifier labelmap
modifierLabelmap = self.scriptedEffect.defaultModifierLabelmap()
selectedSegmentLabelmap = self.scriptedEffect.selectedSegmentLabelmap(
)
smoothingMethod = self.scriptedEffect.parameter("SmoothingMethod")
if smoothingMethod == GAUSSIAN:
maxValue = 255
radiusFactor = 4.0
standardDeviationMM = self.scriptedEffect.doubleParameter(
"GaussianStandardDeviationMm")
spacing = modifierLabelmap.GetSpacing()
standardDeviationPixel = [1.0, 1.0, 1.0]
radiusPixel = [3, 3, 3]
for idx in range(3):
standardDeviationPixel[
idx] = standardDeviationMM / spacing[idx]
radiusPixel[idx] = int(
standardDeviationPixel[idx] * radiusFactor) + 1
if maskExtent:
clippedSelectedSegmentLabelmap = self.clipImage(
selectedSegmentLabelmap, maskExtent, radiusPixel)
else:
clippedSelectedSegmentLabelmap = selectedSegmentLabelmap
thresh = vtk.vtkImageThreshold()
thresh.SetInputData(clippedSelectedSegmentLabelmap)
thresh.ThresholdByLower(0)
thresh.SetInValue(0)
thresh.SetOutValue(maxValue)
thresh.SetOutputScalarType(vtk.VTK_UNSIGNED_CHAR)
gaussianFilter = vtk.vtkImageGaussianSmooth()
gaussianFilter.SetInputConnection(thresh.GetOutputPort())
gaussianFilter.SetStandardDeviation(*standardDeviationPixel)
gaussianFilter.SetRadiusFactor(radiusFactor)
thresh2 = vtk.vtkImageThreshold()
thresh2.SetInputConnection(gaussianFilter.GetOutputPort())
thresh2.ThresholdByUpper(int(maxValue / 2))
thresh2.SetInValue(1)
thresh2.SetOutValue(0)
thresh2.SetOutputScalarType(
selectedSegmentLabelmap.GetScalarType())
thresh2.Update()
self.modifySelectedSegmentByLabelmap(thresh2.GetOutput(),
selectedSegmentLabelmap,
modifierLabelmap,
maskImage, maskExtent)
else:
# size rounded to nearest odd number. If kernel size is even then image gets shifted.
kernelSizePixel = self.getKernelSizePixel()
if maskExtent:
clippedSelectedSegmentLabelmap = self.clipImage(
selectedSegmentLabelmap, maskExtent, kernelSizePixel)
else:
clippedSelectedSegmentLabelmap = selectedSegmentLabelmap
if smoothingMethod == MEDIAN:
# Median filter does not require a particular label value
smoothingFilter = vtk.vtkImageMedian3D()
smoothingFilter.SetInputData(
clippedSelectedSegmentLabelmap)
else:
# 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(clippedSelectedSegmentLabelmap)
thresh.ThresholdByLower(0)
thresh.SetInValue(backgroundValue)
thresh.SetOutValue(labelValue)
thresh.SetOutputScalarType(
clippedSelectedSegmentLabelmap.GetScalarType())
smoothingFilter = vtk.vtkImageOpenClose3D()
smoothingFilter.SetInputConnection(thresh.GetOutputPort())
if smoothingMethod == MORPHOLOGICAL_OPENING:
smoothingFilter.SetOpenValue(labelValue)
smoothingFilter.SetCloseValue(backgroundValue)
else: # must be smoothingMethod == MORPHOLOGICAL_CLOSING:
smoothingFilter.SetOpenValue(backgroundValue)
smoothingFilter.SetCloseValue(labelValue)
smoothingFilter.SetKernelSize(kernelSizePixel[0],
kernelSizePixel[1],
kernelSizePixel[2])
smoothingFilter.Update()
self.modifySelectedSegmentByLabelmap(
smoothingFilter.GetOutput(), selectedSegmentLabelmap,
modifierLabelmap, maskImage, maskExtent)
except IndexError:
logging.error('apply: Failed to apply smoothing')
def smoothSelectedSegment(self):
try:
# Get master volume image data
import vtkSegmentationCorePython
# Get modifier labelmap
modifierLabelmap = self.scriptedEffect.defaultModifierLabelmap()
selectedSegmentLabelmap = self.scriptedEffect.selectedSegmentLabelmap(
)
smoothingMethod = self.scriptedEffect.parameter("SmoothingMethod")
if smoothingMethod == GAUSSIAN:
maxValue = 255
thresh = vtk.vtkImageThreshold()
thresh.SetInputData(selectedSegmentLabelmap)
thresh.ThresholdByLower(0)
thresh.SetInValue(0)
thresh.SetOutValue(maxValue)
thresh.SetOutputScalarType(vtk.VTK_UNSIGNED_CHAR)
standardDeviationMm = self.scriptedEffect.doubleParameter(
"GaussianStandardDeviationMm")
gaussianFilter = vtk.vtkImageGaussianSmooth()
gaussianFilter.SetInputConnection(thresh.GetOutputPort())
gaussianFilter.SetStandardDeviation(standardDeviationMm)
gaussianFilter.SetRadiusFactor(4)
thresh2 = vtk.vtkImageThreshold()
thresh2.SetInputConnection(gaussianFilter.GetOutputPort())
thresh2.ThresholdByUpper(int(maxValue / 2))
thresh2.SetInValue(1)
thresh2.SetOutValue(0)
thresh2.SetOutputScalarType(
selectedSegmentLabelmap.GetScalarType())
thresh2.Update()
modifierLabelmap.DeepCopy(thresh2.GetOutput())
else:
# size rounded to nearest odd number. If kernel size is even then image gets shifted.
kernelSizePixel = self.getKernelSizePixel()
if smoothingMethod == MEDIAN:
# Median filter does not require a particular label value
smoothingFilter = vtk.vtkImageMedian3D()
smoothingFilter.SetInputData(selectedSegmentLabelmap)
else:
# 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())
smoothingFilter = vtk.vtkImageOpenClose3D()
smoothingFilter.SetInputConnection(thresh.GetOutputPort())
if smoothingMethod == MORPHOLOGICAL_OPENING:
smoothingFilter.SetOpenValue(labelValue)
smoothingFilter.SetCloseValue(backgroundValue)
else: # must be smoothingMethod == MORPHOLOGICAL_CLOSING:
smoothingFilter.SetOpenValue(backgroundValue)
smoothingFilter.SetCloseValue(labelValue)
smoothingFilter.SetKernelSize(kernelSizePixel[0],
kernelSizePixel[1],
kernelSizePixel[2])
smoothingFilter.Update()
modifierLabelmap.DeepCopy(smoothingFilter.GetOutput())
except IndexError:
logging.error('apply: Failed to apply smoothing')
# Apply changes
self.scriptedEffect.modifySelectedSegmentByLabelmap(
modifierLabelmap,
slicer.qSlicerSegmentEditorAbstractEffect.ModificationModeSet)
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
# Tst the OpenClose3D filter.
# Image pipeline
reader = vtk.vtkPNGReader()
reader.SetFileName("" + str(VTK_DATA_ROOT) + "/Data/fullhead15.png")
thresh = vtk.vtkImageThreshold()
thresh.SetInputConnection(reader.GetOutputPort())
thresh.SetOutputScalarTypeToUnsignedChar()
thresh.ThresholdByUpper(2000.0)
thresh.SetInValue(255)
thresh.SetOutValue(0)
thresh.ReleaseDataFlagOff()
my_close = vtk.vtkImageOpenClose3D()
my_close.SetInputConnection(thresh.GetOutputPort())
my_close.SetOpenValue(0)
my_close.SetCloseValue(255)
my_close.SetKernelSize(5, 5, 3)
my_close.ReleaseDataFlagOff()
# for coverage (we could compare results to see if they are correct).
my_close.DebugOn()
my_close.DebugOff()
my_close.GetOutput()
my_close.GetCloseValue()
my_close.GetOpenValue()
#my_close AddObserver ProgressEvent {set pro [my_close GetProgress]; puts "Completed $pro"; flush stdout}
viewer = vtk.vtkImageViewer()
viewer.SetInputConnection(my_close.GetOutputPort())
viewer.SetColorWindow(255)
def smoothSelectedSegment(self):
try:
# Get master volume image data
import vtkSegmentationCorePython
# Get modifier labelmap
modifierLabelmap = self.scriptedEffect.defaultModifierLabelmap()
selectedSegmentLabelmap = self.scriptedEffect.selectedSegmentLabelmap()
smoothingMethod = self.scriptedEffect.parameter("SmoothingMethod")
if smoothingMethod == GAUSSIAN:
maxValue = 255
thresh = vtk.vtkImageThreshold()
thresh.SetInputData(selectedSegmentLabelmap)
thresh.ThresholdByLower(0)
thresh.SetInValue(0)
thresh.SetOutValue(maxValue)
thresh.SetOutputScalarType(vtk.VTK_UNSIGNED_CHAR)
standardDeviationMm = self.scriptedEffect.doubleParameter("GaussianStandardDeviationMm")
gaussianFilter = vtk.vtkImageGaussianSmooth()
gaussianFilter.SetInputConnection(thresh.GetOutputPort())
gaussianFilter.SetStandardDeviation(standardDeviationMm)
gaussianFilter.SetRadiusFactor(4)
thresh2 = vtk.vtkImageThreshold()
thresh2.SetInputConnection(gaussianFilter.GetOutputPort())
thresh2.ThresholdByUpper(int(maxValue / 2))
thresh2.SetInValue(1)
thresh2.SetOutValue(0)
thresh2.SetOutputScalarType(selectedSegmentLabelmap.GetScalarType())
thresh2.Update()
modifierLabelmap.DeepCopy(thresh2.GetOutput())
else:
# size rounded to nearest odd number. If kernel size is even then image gets shifted.
kernelSizePixel = self.getKernelSizePixel()
if smoothingMethod == MEDIAN:
# Median filter does not require a particular label value
smoothingFilter = vtk.vtkImageMedian3D()
smoothingFilter.SetInputData(selectedSegmentLabelmap)
else:
# 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())
smoothingFilter = vtk.vtkImageOpenClose3D()
smoothingFilter.SetInputConnection(thresh.GetOutputPort())
if smoothingMethod == MORPHOLOGICAL_OPENING:
smoothingFilter.SetOpenValue(labelValue)
smoothingFilter.SetCloseValue(backgroundValue)
else: # must be smoothingMethod == MORPHOLOGICAL_CLOSING:
smoothingFilter.SetOpenValue(backgroundValue)
smoothingFilter.SetCloseValue(labelValue)
smoothingFilter.SetKernelSize(kernelSizePixel[0],kernelSizePixel[1],kernelSizePixel[2])
smoothingFilter.Update()
modifierLabelmap.DeepCopy(smoothingFilter.GetOutput())
except IndexError:
logging.error('apply: Failed to apply smoothing')
# Apply changes
self.scriptedEffect.modifySelectedSegmentByLabelmap(modifierLabelmap, slicer.qSlicerSegmentEditorAbstractEffect.ModificationModeSet)
from vtk.test import Testing
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
# Tst the OpenClose3D filter.
# Image pipeline
reader = vtk.vtkPNGReader()
reader.SetFileName("" + str(VTK_DATA_ROOT) + "/Data/fullhead15.png")
thresh = vtk.vtkImageThreshold()
thresh.SetInputConnection(reader.GetOutputPort())
thresh.SetOutputScalarTypeToUnsignedChar()
thresh.ThresholdByUpper(2000.0)
thresh.SetInValue(255)
thresh.SetOutValue(0)
thresh.ReleaseDataFlagOff()
my_close = vtk.vtkImageOpenClose3D()
my_close.SetInputConnection(thresh.GetOutputPort())
my_close.SetOpenValue(0)
my_close.SetCloseValue(255)
my_close.SetKernelSize(5,5,3)
my_close.ReleaseDataFlagOff()
# for coverage (we could compare results to see if they are correct).
my_close.DebugOn()
my_close.DebugOff()
my_close.GetOutput()
my_close.GetCloseValue()
my_close.GetOpenValue()
#my_close AddObserver ProgressEvent {set pro [my_close GetProgress]; puts "Completed $pro"; flush stdout}
viewer = vtk.vtkImageViewer()
viewer.SetInputConnection(my_close.GetOutputPort())
viewer.SetColorWindow(255)
reader.Update()
#check binary
vtk_data = reader.GetOutput().GetPointData().GetScalars()
numpy_data = numpy_support.vtk_to_numpy(vtk_data)
u = np.unique(numpy_data).shape[0]
if u != 2:
print('ERROR: Inputfile is not binary')
sys.exit(2)
del u
del numpy_data
del vtk_data # free memory
#closing filter
print('Apllying closing filter')
close_filter = vtk.vtkImageOpenClose3D()
close_filter.SetInputConnection(reader.GetOutputPort())
close_filter.SetOpenValue(0)
close_filter.SetCloseValue(1)
close_filter.SetKernelSize(3, 3, 3)
close_filter.Update()
del reader # free memory
#convert to float
tofloat = vtk.vtkImageCast()
tofloat.SetInputConnection(close_filter.GetOutputPort())
tofloat.SetOutputScalarTypeToFloat()
tofloat.Update()
del close_filter # free memory
#normalize to 1
