[Insight-users] Problem in 3D segmentation
Luis Ibanez
luis.ibanez@kitware.com
Mon May 10 02:44:21 EDT 2004
Hi Rodrigo,
Instead of changing the extent in this way, you
should probably use the RegionOfInterestImageFilter.
http://www.itk.org/Insight/Doxygen/html/classitk_1_1RegionOfInterestImageFilter.html
Regards,
Luis
-----------------------
Rodrigo Trujillo wrote:
> Hi Luis,
>
> First, thanks for help...
>
> Sorry, i didn´t write, but in my tests i was
> feeding to pipeline 20 slices at least.
> So, i think this is not the problem. :-)
>
>
> The problem is not in SPACING, but in EXTENT (i think).
> When i read 3D image and set extent as: SetDataExtent(0,255,0,255, 0 ,
> 25 )
> my pipeline runs very well. But, when i set:
> SetDataExtent(0,255,0,255, 5 , 25 ) , the FastMarching
> modifies to: (0,255,0,255, 0 , 20 ) and then a error occurs
> in ShapeDetection (it receives 2 different EXTENTS).
>
>
> I don´t know if this is a bug, and if it was fixed in CVS, because
> i had problems in the compilation (but, this is another subject).
>
>
> Rodrigo Trujillo
>
>
>
> ----- Original Message -----
> From: "Luis Ibanez" <luis.ibanez@kitware.com>
> To: "Rodrigo Trujillo" <rodrigo.trujillo@cenpra.gov.br>
> Cc: "ITK Users" <insight-users@itk.org>
> Sent: Friday, April 30, 2004 5:45 PM
> Subject: Re: [Insight-users] Problem in 3D segmentation
>
>
>
>>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@kitware.com>
>>>To: "Rodrigo Trujillo" <rodrigo.trujillo@cenpra.gov.br>
>>>Cc: "ITK Users" <insight-users@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@itk.org
>>>http://www.itk.org/mailman/listinfo/insight-users
>>>
>>
>>
>>
>>
>
>
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