[Insight-users] Problem in 3D segmentation
Luis Ibanez
luis.ibanez at kitware.com
Fri, 30 Apr 2004 16:45:03 -0400
Hi Rodrigo,
It seems that you are feeding a 3D image
with a single slice into an ITK pipeline
configured for 3D images.
This will not work if you have *any* filter
that requires neighborhood information.
1-slice 3D images are degenerate images and
should be processed in a 2D pipeline.
If you want to run a 3D pipeline with level set
filters, you should provide as input a 3D image
that has at least 5 pixels along every dimension.
Regards,
Luis
-----------------------
Rodrigo Trujillo wrote:
> 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()
>>
>>
>>
>>
>
> _______________________________________________
> Insight-users mailing list
> Insight-users at itk.org
> http://www.itk.org/mailman/listinfo/insight-users
>