[Insight-users] Problem in 3D segmentation
Luis Ibanez
luis.ibanez at kitware.com
Fri, 30 Apr 2004 16:41:06 -0400
Hi Rodrigo,
The Fastmarching filter sets the spacing of the output
image to the spacing of the input image. When no input
image is provided, then it is up to the user to set the
spacing by calling the method:
SetOutputSpacing();
Note that this has been configured recently in the
CVS version of ITK. If you are using ITK 1.6, the
FastMarching is still forcing the output spacing to
be 1.0 along every dimension.
--
Something that you should try is to call
UpdateLargestPossibleRegion();
instead of the traditional:
Update()
in the last filter of the ITK pipeline.
Regards,
Luis
------------------------
Rodrigo Trujillo wrote:
> 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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>>
>
>
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