def getMIP(imageData, color):
"""
A function that will take a volume and do a simple
maximum intensity projection that will be converted to a
wxBitmap
"""
maxval = imageData.GetScalarRange()[1]
imageData.SetUpdateExtent(imageData.GetWholeExtent())
if maxval > 255:
shiftscale = vtk.vtkImageShiftScale()
shiftscale.SetInputConnection(imageData.GetProducerPort())
shiftscale.SetScale(255.0 / maxval)
shiftscale.SetOutputScalarTypeToUnsignedChar()
imageData = shiftscale.GetOutput()
mip = vtkbxd.vtkImageSimpleMIP()
mip.SetInputConnection(imageData.GetProducerPort())
if color == None:
output = optimize.execute_limited(mip)
return output
if mip.GetOutput().GetNumberOfScalarComponents() == 1:
ctf = getColorTransferFunction(color)
maptocolor = vtk.vtkImageMapToColors()
maptocolor.SetInputConnection(mip.GetOutputPort())
maptocolor.SetLookupTable(ctf)
maptocolor.SetOutputFormatToRGB()
imagedata = optimize.execute_limited(maptocolor)
else:
imagedata = output = optimize.execute_limited(mip)
return imagedata
def getMIP(imageData, color):
"""
A function that will take a volume and do a simple
maximum intensity projection that will be converted to a
wxBitmap
"""
maxval = imageData.GetScalarRange()[1]
imageData.SetUpdateExtent(imageData.GetWholeExtent())
if maxval > 255:
shiftscale = vtk.vtkImageShiftScale()
shiftscale.SetInputConnection(imageData.GetProducerPort())
shiftscale.SetScale(255.0 / maxval)
shiftscale.SetOutputScalarTypeToUnsignedChar()
imageData = shiftscale.GetOutput()
mip = vtkbxd.vtkImageSimpleMIP()
mip.SetInputConnection(imageData.GetProducerPort())
if color == None:
output = optimize.execute_limited(mip)
return output
if mip.GetOutput().GetNumberOfScalarComponents() == 1:
ctf = getColorTransferFunction(color)
maptocolor = vtk.vtkImageMapToColors()
maptocolor.SetInputConnection(mip.GetOutputPort())
maptocolor.SetLookupTable(ctf)
maptocolor.SetOutputFormatToRGB()
imagedata = optimize.execute_limited(maptocolor)
else:
imagedata = output = optimize.execute_limited(mip)
return imagedata
def testMIP(self):
reader = vtkbxd.vtkLIFReader()
reader.SetFileName(os.path.join(DATA_PATH, "512x_128y_10z_22t_2ch.lif"))
reader.OpenFile()
reader.Update()
data = reader.GetOutput()
mip = vtkbxd.vtkImageSimpleMIP()
mip.SetInput(data)
pngwriter = vtk.vtkPNGWriter()
pngwriter.SetInput(mip.GetOutput())
mip.Update()
pngwriter.SetFileName("lif.png")
pngwriter.Write()
def testMIP(self):
reader = vtkbxd.vtkLIFReader()
reader.SetFileName(os.path.join(DATA_PATH,
"512x_128y_10z_22t_2ch.lif"))
reader.OpenFile()
reader.Update()
data = reader.GetOutput()
mip = vtkbxd.vtkImageSimpleMIP()
mip.SetInput(data)
pngwriter = vtk.vtkPNGWriter()
pngwriter.SetInput(mip.GetOutput())
mip.Update()
pngwriter.SetFileName("lif.png")
pngwriter.Write()
def processOutputData(self, data):
"""
Process the data before it's send to the preview
"""
data.UpdateInformation()
if self.mode == 0: # MIP mode
if not self.mip:
self.mip = vtkbxd.vtkImageSimpleMIP()
else:
self.mip.RemoveAllInputs()
self.mip.SetInput(data)
data = self.mip.GetOutput()
else: # AIP mode
scalarType = data.GetScalarType()
imgType = "IUC"
if scalarType == 5:
imgType = "IUS"
elif scalarType == 9:
imgType = "IUL"
elif scalarType == 10:
imgType = "IF"
self.convVTKtoITK = eval("itk.VTKImageToImageFilter.%s3.New()" %
imgType)
if data.GetNumberOfScalarComponents() > 1:
imageLuminance = vtk.vtkImageLuminance()
imageLuminance.SetInput(data)
data = imageLuminance.GetOutput()
self.convVTKtoITK.SetInput(data)
self.convVTKtoITK.Update()
itkImg = self.convVTKtoITK.GetOutput()
self.pif = eval("itk.MeanProjectionImageFilter.%s3%s2.New()" %
(imgType, imgType))
self.pif.SetInput(itkImg)
output = self.pif.GetOutput()
self.convITKtoVTK = itk.ImageToVTKImageFilter[output].New()
self.convITKtoVTK.SetInput(output)
self.convITKtoVTK.Update()
data = self.convITKtoVTK.GetOutput()
return PreviewFrame.PreviewFrame.processOutputData(self, data)
def processOutputData(self, data):
"""
Process the data before it's send to the preview
"""
data.UpdateInformation()
if self.mode == 0: # MIP mode
if not self.mip:
self.mip = vtkbxd.vtkImageSimpleMIP()
else:
self.mip.RemoveAllInputs()
self.mip.SetInput(data)
data = self.mip.GetOutput()
else: # AIP mode
scalarType = data.GetScalarType()
imgType = "IUC"
if scalarType == 5:
imgType = "IUS"
elif scalarType == 9:
imgType = "IUL"
elif scalarType == 10:
imgType = "IF"
self.convVTKtoITK = eval("itk.VTKImageToImageFilter.%s3.New()"%imgType)
if data.GetNumberOfScalarComponents() > 1:
imageLuminance = vtk.vtkImageLuminance()
imageLuminance.SetInput(data)
data = imageLuminance.GetOutput()
self.convVTKtoITK.SetInput(data)
self.convVTKtoITK.Update()
itkImg = self.convVTKtoITK.GetOutput()
self.pif = eval("itk.MeanProjectionImageFilter.%s3%s2.New()"%(imgType,imgType))
self.pif.SetInput(itkImg)
output = self.pif.GetOutput()
self.convITKtoVTK = itk.ImageToVTKImageFilter[output].New()
self.convITKtoVTK.SetInput(output)
self.convITKtoVTK.Update()
data = self.convITKtoVTK.GetOutput()
return PreviewFrame.PreviewFrame.processOutputData(self, data)
merge = vtkbxd.vtkImageColorMerge()
#merge.SetNumberOfThreads(5)
merge.AddInput(d1)
merge.AddLookupTable(ctf1)
merge.AddIntensityTransferFunction(itf1)
itfmap = vtkbxd.vtkImageMapToIntensities()
itfmap.SetInput(d1)
itfmap.SetIntensityTransferFunction(itf1)
maptocolor = vtk.vtkImageMapToColors()
maptocolor.SetOutputFormatToRGB()
maptocolor.SetInput(itfmap.GetOutput())
maptocolor.SetLookupTable(ctf1)
mip = vtkbxd.vtkImageSimpleMIP()
print "Feeding merge to MIP", elapsed()
mip.SetInput(merge.GetOutput())
#flip =vtk.vtkImageFlip()
#flip.SetFilteredAxis(1)
#flip.SetInput(mip.GetOutput())
writer = vtk.vtkPNGWriter()
writer.SetFileName("ITFmapped.png")
writer.SetInput(mip.GetOutput())
print "Feeding MIP to writer ", elapsed()
writer.Update()
writer.Write()
print "Wrote PNG ", elapsed()
#merge.SetNumberOfThreads(5)
merge.AddInput(d1)
merge.AddLookupTable(ctf1)
merge.AddIntensityTransferFunction(itf1)
itfmap = vtkbxd.vtkImageMapToIntensities()
itfmap.SetInput(d1)
itfmap.SetIntensityTransferFunction(itf1)
maptocolor=vtk.vtkImageMapToColors()
maptocolor.SetOutputFormatToRGB()
maptocolor.SetInput(itfmap.GetOutput())
maptocolor.SetLookupTable(ctf1)
mip=vtkbxd.vtkImageSimpleMIP()
print "Feeding merge to MIP",elapsed()
mip.SetInput(merge.GetOutput())
#flip =vtk.vtkImageFlip()
#flip.SetFilteredAxis(1)
#flip.SetInput(mip.GetOutput())
writer=vtk.vtkPNGWriter()
writer.SetFileName("ITFmapped.png")
writer.SetInput(mip.GetOutput())
print "Feeding MIP to writer ",elapsed()
writer.Update()
writer.Write()
print "Wrote PNG ",elapsed()