def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
vtk.vtkImageHybridMedian2D(), 'Processing.',
('vtkImageData',), ('vtkImageData',),
replaceDoc=True,
inputFunctions=None, outputFunctions=None)
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(self,
module_manager,
vtk.vtkImageHybridMedian2D(),
'Processing.', ('vtkImageData', ),
('vtkImageData', ),
replaceDoc=True,
inputFunctions=None,
outputFunctions=None)
def __init__(self):
"""
Initialization
"""
lib.ProcessingFilter.ProcessingFilter.__init__(self)
self.vtkfilter = vtk.vtkImageHybridMedian2D()
self.vtkfilter.AddObserver('ProgressEvent', lib.messenger.send)
lib.messenger.connect(self.vtkfilter, "ProgressEvent", self.updateProgress)
self.eventDesc = "Performing hybrid median filtering"
self.filterDesc = "Computes median value from pixel value, median of corner neighbors and median of face neighbors\nInput: Grayscale image\nOutput: Grayscale image"
def median(self):
"""Median filter that preserves thin lines and corners.
It operates on a 5x5 pixel neighborhood. It computes two values initially:
the median of the + neighbors and the median of the x neighbors.
It then computes the median of these two values plus the center pixel.
This result of this second median is the output pixel value.
"""
medf = vtk.vtkImageHybridMedian2D()
medf.SetInputData(self._data)
medf.Update()
return self._update(medf.GetOutput())
def __init__(self):
"""
Initialization
"""
lib.ProcessingFilter.ProcessingFilter.__init__(self)
self.vtkfilter = vtk.vtkImageHybridMedian2D()
self.vtkfilter.AddObserver('ProgressEvent', lib.messenger.send)
lib.messenger.connect(self.vtkfilter, "ProgressEvent",
self.updateProgress)
self.eventDesc = "Performing hybrid median filtering"
self.filterDesc = "Computes median value from pixel value, median of corner neighbors and median of face neighbors\nInput: Grayscale image\nOutput: Grayscale image"
def main():
# colors = vtk.vtkNamedColors()
fileName = get_program_parameters()
# Read the image.
readerFactory = vtk.vtkImageReader2Factory()
reader = readerFactory.CreateImageReader2(fileName)
reader.SetFileName(fileName)
reader.Update()
scalarRange = [0] * 2
scalarRange[0] = reader.GetOutput().GetPointData().GetScalars().GetRange(
)[0]
scalarRange[1] = reader.GetOutput().GetPointData().GetScalars().GetRange(
)[1]
print("Range:", scalarRange)
middleSlice = (reader.GetOutput().GetExtent()[5] -
reader.GetOutput().GetExtent()[4]) // 2
# Work with double images.
cast = vtk.vtkImageCast()
cast.SetInputConnection(reader.GetOutputPort())
cast.SetOutputScalarTypeToDouble()
cast.Update()
originalData = vtk.vtkImageData()
originalData.DeepCopy(cast.GetOutput())
noisyData = vtk.vtkImageData()
AddShotNoise(originalData, noisyData, 2000.0, 0.1,
reader.GetOutput().GetExtent())
median = vtk.vtkImageMedian3D()
median.SetInputData(noisyData)
median.SetKernelSize(5, 5, 1)
hybridMedian1 = vtk.vtkImageHybridMedian2D()
hybridMedian1.SetInputData(noisyData)
hybridMedian = vtk.vtkImageHybridMedian2D()
hybridMedian.SetInputConnection(hybridMedian1.GetOutputPort())
colorWindow = (scalarRange[1] - scalarRange[0]) * 0.8
colorLevel = colorWindow / 2
originalActor = vtk.vtkImageActor()
originalActor.GetMapper().SetInputData(originalData)
originalActor.GetProperty().SetColorWindow(colorWindow)
originalActor.GetProperty().SetColorLevel(colorLevel)
originalActor.GetProperty().SetInterpolationTypeToNearest()
originalActor.SetDisplayExtent(reader.GetDataExtent()[0],
reader.GetDataExtent()[1],
reader.GetDataExtent()[2],
reader.GetDataExtent()[3], middleSlice,
middleSlice)
noisyActor = vtk.vtkImageActor()
noisyActor.GetMapper().SetInputData(noisyData)
noisyActor.GetProperty().SetColorWindow(colorWindow)
noisyActor.GetProperty().SetColorLevel(colorLevel)
noisyActor.GetProperty().SetInterpolationTypeToNearest()
noisyActor.SetDisplayExtent(originalActor.GetDisplayExtent())
hybridMedianActor = vtk.vtkImageActor()
hybridMedianActor.GetMapper().SetInputConnection(
hybridMedian.GetOutputPort())
hybridMedianActor.GetProperty().SetColorWindow(colorWindow)
hybridMedianActor.GetProperty().SetColorLevel(colorLevel)
hybridMedianActor.GetProperty().SetInterpolationTypeToNearest()
hybridMedianActor.SetDisplayExtent(originalActor.GetDisplayExtent())
medianActor = vtk.vtkImageActor()
medianActor.GetMapper().SetInputConnection(median.GetOutputPort())
medianActor.GetProperty().SetColorWindow(colorWindow)
medianActor.GetProperty().SetColorLevel(colorLevel)
medianActor.GetProperty().SetInterpolationTypeToNearest()
# Setup the renderers.
originalRenderer = vtk.vtkRenderer()
originalRenderer.AddActor(originalActor)
noisyRenderer = vtk.vtkRenderer()
noisyRenderer.AddActor(noisyActor)
hybridRenderer = vtk.vtkRenderer()
hybridRenderer.AddActor(hybridMedianActor)
medianRenderer = vtk.vtkRenderer()
medianRenderer.AddActor(medianActor)
renderers = list()
renderers.append(originalRenderer)
renderers.append(noisyRenderer)
renderers.append(hybridRenderer)
renderers.append(medianRenderer)
# Setup viewports for the renderers.
rendererSize = 400
xGridDimensions = 2
yGridDimensions = 2
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])
renderWindowInteractor = vtk.vtkRenderWindowInteractor()
style = vtk.vtkInteractorStyleImage()
renderWindowInteractor.SetInteractorStyle(style)
renderWindowInteractor.SetRenderWindow(renderWindow)
# The renderers share one camera.
renderWindow.Render()
for r in range(1, len(renderers)):
renderers[r].SetActiveCamera(renderers[0].GetActiveCamera())
renderWindowInteractor.Initialize()
renderWindowInteractor.Start()
shotNoiseThresh2.SetInValue(-shotNoiseAmplitude) shotNoiseThresh2.SetOutValue(0.0) shotNoiseThresh2.Update() shotNoise = vtk.vtkImageMathematics() shotNoise.SetInput1Data(shotNoiseThresh1.GetOutput()) shotNoise.SetInput2Data(shotNoiseThresh2.GetOutput()) shotNoise.SetOperationToAdd() shotNoise.Update() add = vtk.vtkImageMathematics() add.SetInput1Data(shotNoise.GetOutput()) add.SetInput2Data(imageCanvas.GetOutput()) add.SetOperationToAdd() median = vtk.vtkImageMedian3D() median.SetInputConnection(add.GetOutputPort()) median.SetKernelSize(3, 3, 1) hybrid1 = vtk.vtkImageHybridMedian2D() hybrid1.SetInputConnection(add.GetOutputPort()) hybrid2 = vtk.vtkImageHybridMedian2D() hybrid2.SetInputConnection(hybrid1.GetOutputPort()) viewer = vtk.vtkImageViewer() viewer.SetInputConnection(hybrid1.GetOutputPort()) viewer.SetColorWindow(256) viewer.SetColorLevel(127.5) viewer.GetRenderWindow().SetSize(256, 256) viewer.Render()
shotNoiseThresh2.SetInValue(-shotNoiseAmplitude) shotNoiseThresh2.SetOutValue(0.0) shotNoiseThresh2.Update() shotNoise = vtk.vtkImageMathematics() shotNoise.SetInput1Data(shotNoiseThresh1.GetOutput()) shotNoise.SetInput2Data(shotNoiseThresh2.GetOutput()) shotNoise.SetOperationToAdd() shotNoise.Update() add = vtk.vtkImageMathematics() add.SetInput1Data(shotNoise.GetOutput()) add.SetInput2Data(imageCanvas.GetOutput()) add.SetOperationToAdd() median = vtk.vtkImageMedian3D() median.SetInputConnection(add.GetOutputPort()) median.SetKernelSize(3, 3, 1) hybrid1 = vtk.vtkImageHybridMedian2D() hybrid1.SetInputConnection(add.GetOutputPort()) hybrid2 = vtk.vtkImageHybridMedian2D() hybrid2.SetInputConnection(hybrid1.GetOutputPort()) viewer = vtk.vtkImageViewer() viewer.SetInputConnection(hybrid1.GetOutputPort()) viewer.SetColorWindow(256) viewer.SetColorLevel(127.5) viewer.GetRenderWindow().SetSize(256, 256) viewer.Render()
import vtk import itk import time FILE="/media/sda12/Data/selli/selli_coloc1_8-bit.lsm" t=time.time() reader=vtk.vtkLSMReader() reader.SetFileName(FILE) reader.SetUpdateChannel(0) reader.SetUpdateTimePoint(0) medfilter = vtk.vtkImageHybridMedian2D() medfilter.SetInput(reader.GetOutput()) print "Doing median filtering",time.time()-t medfilter.Update() print "done",time.time()-t cast = vtk.vtkImageCast() cast.SetOutputScalarTypeToFloat() cast.SetInput(medfilter.GetOutput()) f3 = itk.Image.F3 vtktoitk=itk.VTKImageToImageFilter[f3].New() vtktoitk.SetInput(cast.GetOutput()) print "Moving data over to ITK side",time.time()-t vtktoitk.Update() print "done.",time.time()-t print "Doing gradient magnitude",time.time()-t gradmag = itk.GradientMagnitudeImageFilter[f3,f3].New() gradmag.SetInput(vtktoitk.GetOutput()) gradmag.Update() print "done",time.time()-t
