[Insight-users] Problem in 3D segmentation
Rodrigo Trujillo
Rodrigo Trujillo" <rodrigo.trujillo at cenpra.gov.br
Fri, 30 Apr 2004 06:54:22 -0300
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()
>
>
>
>