[Insight-users] Problem in 3D segmentation
Rodrigo Trujillo
Rodrigo Trujillo" <rodrigo.trujillo at cenpra.gov.br
Fri, 30 Apr 2004 07:27:06 -0300
Luis,
I made some tests: i printed the output of sigmoid and fastmarching filters
after send them to VTK.
The FastMarching filter modifies EXTENT and SPACING (and others attributes):
Sigmoid
Spacing: (0.32, 0.32, 0.6)
Extent: (0, 255, 0, 255, 2, 27)
FastMarching
Spacing: (1, 1, 1)
Extent: (0, 255, 0, 255, 0, 25)
Why does it happen ?
Is it the cause of problem ?
Rodrigo Trujillo
----- Original Message -----
From: "Rodrigo Trujillo" <rodrigo.trujillo at cenpra.gov.br>
To: "Luis Ibanez" <luis.ibanez at kitware.com>
Cc: "ITK Users" <insight-users at itk.org>
Sent: Friday, April 30, 2004 6:54 AM
Subject: Re: [Insight-users] Problem in 3D segmentation
> Hi Luis,
>
> 1- The size is 256 X 256 pixels.
>
> 2- The error happens in first time.
>
>
> Rodrigo Trujillo
>
>
> ----- Original Message -----
> From: "Luis Ibanez" <luis.ibanez at kitware.com>
> To: "Rodrigo Trujillo" <rodrigo.trujillo at cenpra.gov.br>
> Cc: "ITK Users" <insight-users at itk.org>
> Sent: Wednesday, April 28, 2004 9:25 PM
> Subject: Re: [Insight-users] Problem in 3D segmentation
>
>
> >
> > Hi Rodrigo,
> >
> >
> > Two questions:
> >
> >
> > 1) What is the size (in pixels) of the image that
> > you are passing as input to this ITK pipeline ?
> >
> >
> > 2) Does this error happens the first time you run
> > the pipeline, or does it happens when you have
> > ran it once and then you change the input image
> > for another one ?
> >
> >
> >
> > Please let us know,
> >
> >
> > Thanks
> >
> >
> > Luis
> >
> >
> > ------------------------
> > Rodrigo Trujillo wrote:
> >
> > > Hi,
> > >
> > > I'm testing itkShapeDetectionLevelSetImageFilter in Python. With 2D
> > > images (1 slice) my program
> > > works very well, but when i tried to expand the code for 3D images,
the
> > > following error occurs:
> > >
> > > "
> > > Traceback (most recent call last):
> > > File "C:\Meus
> > > Documentos\Rodrigo\Segmentacao\ShapeDetection_3D_MRI.py", line 84, in
?
> > > shapeD.Update()
> > > File "C:/ITK/Release\itkShapeDetectionLevelSetImageFilter.py", line
> > > 692, in Update
> > > def Update(*args): return
> > >
>
apply(_itkShapeDetectionLevelSetImageFilter.itkShapeDetectionLevelSetImageFi
> lterF3F3_Pointer_Update,args)
> > > RuntimeError:
> > > C:\Compilacao\InsightToolkit-1.6.0\Code\Common\itkDataObject.cxx:376:
> > > Requested region is (at least partially) outside the largest possible
> > > region.
> > > "
> > >
> > > Does somebody know the reason of the error ? And how can i solve ?
> > > My code is attached.
> > >
> > >
> > > Thanks,
> > >
> > > Rodrigo Trujillo
> > >
> > >
> >
> ------------------------------------------------------------------------
> > >
> > > import vtk
> > > import ConnectVTKITK as itk
> > > from vtk.tk.vtkTkRenderWidget import *
> > >
> > > reader = vtk.vtkImageReader2()
> > > reader.SetDataByteOrderToLittleEndian()
> > > reader.SetFilePrefix('C://TEMP//InVesalius//Jair')
> > > reader.SetDataSpacing(0.32,0.32,0.6)
> > > reader.SetDataExtent(0,255,0,255,2,27)
> > > reader.Update()
> > >
> > > imageCast = vtk.vtkImageCast()
> > > imageCast.SetOutputScalarTypeToFloat()
> > > imageCast.SetInput(reader.GetOutput())
> > > imageCast.Update()
> > >
> > > vtkExporter = vtk.vtkImageExport()
> > > vtkExporter.SetInput(imageCast.GetOutput())
> > > itkImporter = itk.itkVTKImageImportF3_New()
> > > itk.ConnectVTKToITKF3(vtkExporter, itkImporter.GetPointer())
> > > itkImporter.Update() # Sem este update, dah pau !!!
> > >
> > > # Passando um filtro de SMOOTHING
> > > filter = itk.itkCurvatureAnisotropicDiffusionImageFilterF3F3_New()
> > > filter.SetInput(itkImporter.GetOutput())
> > >
> > > filter.SetNumberOfIterations(6)
> > > filter.SetTimeStep(0.0625)
> > > filter.SetConductanceParameter(3.0)
> > > filter.Update()
> > >
> > > # Criando o gradiente das imagem
> > > gradiente =
> itk.itkGradientMagnitudeRecursiveGaussianImageFilterF3F3_New()
> > > gradiente.SetInput(filter.GetOutput())
> > > gradiente.SetSigma(0.7)
> > > gradiente.Update()
> > >
> > > # Passando sigmoid. Cria a funcao SPEED
> > > sigmoid = itk.itkSigmoidImageFilterF3F3_New()
> > > sigmoid.SetInput(gradiente.GetOutput())
> > > sigmoid.SetOutputMinimum(0)
> > > sigmoid.SetOutputMaximum(4095)
> > > sigmoid.SetAlpha(-1.0) # Deve ser negativo para inverter as cores
> > > sigmoid.SetBeta(14.0)
> > > sigmoid.Update()
> > >
> > > # Pipeline do FastMarching
> > > fastMarching = itk.itkFastMarchingImageFilterF3F3_New()
> > >
> > > sementes = itk.itkNodeContainerF3_New() # Guardara as sementes
> (LevelSetNodes !!)
> > > node = itk.itkLevelSetNodeF3() # Pega a semente e
> transforma num LevelSetNode
> > >
> > > idx = itk.itkIndex3() # Selecionando uma semente
> > > idx.SetElement(0,130)
> > > idx.SetElement(1,114)
> > > idx.SetElement(2,20)
> > >
> > > #node.SetValue(0.0)
> > > node.SetValue(-5.0)
> > > node.SetIndex(idx)
> > >
> > > sementes.Initialize() # Inicializa as sementes
> > > sementes.InsertElement(0,node)
> > >
> > > fastMarching.SetTrialPoints(sementes.GetPointer())
> > > fastMarching.SetOutputSize(
> gradiente.GetOutput().GetBufferedRegion().GetSize())
> > > fastMarching.SetSpeedConstant( 1.0 )
> > > fastMarching.SetStoppingValue(5.0)
> > > fastMarching.Update()
> > >
> > >
> > > # Implementacao do SHAPE
> > >
> > > shapeD = itk.itkShapeDetectionLevelSetImageFilterF3F3_New()
> > >
> > > shapeD.SetInput( fastMarching.GetOutput() )
> > > shapeD.SetFeatureImage( sigmoid.GetOutput() )
> > >
> > > shapeD.SetPropagationScaling( 10.0 )
> > > shapeD.SetCurvatureScaling( 5.0 )
> > >
> > > shapeD.SetMaximumRMSError( 0.02 )
> > > shapeD.SetNumberOfIterations( 400 )
> > > shapeD.Update()
> > >
> > > # Threshold binario na imagem do Shape
> > > bt = itk.itkBinaryThresholdImageFilterF3US3_New() # Retorna UShort
> > > bt.SetInput(shapeD.GetOutput())
> > > bt.SetLowerThreshold(0)
> > > bt.SetUpperThreshold(204)
> > > bt.SetOutsideValue(0)
> > > bt.SetInsideValue(2000)
> > > bt.Update()
> > >
> > > itkExporter = itk.itkVTKImageExportUS3_New()
> > > itkExporter.SetInput(bt.GetOutput())
> > > vtkImporter = vtk.vtkImageImport()
> > > itk.ConnectITKUS3ToVTK(itkExporter.GetPointer(), vtkImporter)
> > > vtkImporter.Update()
> > >
> > >
> > > # Visualizacao
> > >
> > > # Definindo a opacidade: Funcao de transferencia de opacidade
> > >
> > > tfun = vtk.vtkPiecewiseFunction()
> > > tfun.AddPoint(0.0, 0)
> > > tfun.AddPoint(1.0, 0)
> > > #tfun.AddPoint(199.0, 0)
> > > #tfun.AddPoint(200.0, 0.5)
> > > tfun.AddPoint(2.0, 1.0)
> > > tfun.AddPoint(4095.0, 1.0)
> > >
> > > # Definindo a funcao de transferencia de cores
> > >
> > > ctfun = vtk.vtkColorTransferFunction()
> > > ctfun.AddRGBPoint(0.0, 1.0, 0.1, 0.1)
> > > ctfun.AddRGBPoint(4095.0, 1.0, 1.0, 1.0)
> > >
> > >
> > > # Criando o volume
> > > compositeFunction = vtk.vtkVolumeRayCastCompositeFunction()
> > >
> > > volumeMapper = vtk.vtkVolumeRayCastMapper()
> > > volumeMapper.SetInput(vtkImporter.GetOutput())
> > > volumeMapper.SetVolumeRayCastFunction(compositeFunction)
> > >
> > > volumeProperty = vtk.vtkVolumeProperty()
> > > volumeProperty.SetColor(ctfun)
> > > volumeProperty.SetScalarOpacity(tfun)
> > > volumeProperty.SetInterpolationTypeToLinear()
> > > volumeProperty.ShadeOn()
> > >
> > > Ator = vtk.vtkVolume()
> > > Ator.SetMapper(volumeMapper)
> > > Ator.SetProperty(volumeProperty)
> > >
> > > ren = vtk.vtkRenderer()
> > > ren.AddVolume(Ator)
> > >
> > > # Criando a grade em volta do volume
> > > out = vtk.vtkOutlineFilter()
> > > out.SetInput(vtkImporter.GetOutput())
> > >
> > > isoMapper2 = vtk.vtkOpenGLPolyDataMapper()
> > > isoMapper2.SetInput(out.GetOutput())
> > > isoMapper2.ScalarVisibilityOff()
> > >
> > > isoActor2 = vtk.vtkOpenGLActor()
> > > isoActor2.SetMapper(isoMapper2)
> > >
> > > ren.AddActor(isoActor2)
> > >
> > > janela = Tkinter.Tk()
> > >
> > > imageframe = Frame(janela)
> > > imageframe.pack(side=LEFT,fill = BOTH)
> > >
> > > pane = vtkTkRenderWidget(imageframe,width = 512, height = 512)
> > > pane.GetRenderWindow().AddRenderer(ren)
> > > pane.pack()
> > >
> > > janela.mainloop()
> >
> >
> >
> >
>
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