[Insight-users] ITK to VTK 3D WatershedImageFilter
Luis Ibanez
luis.ibanez at kitware.com
Wed May 20 22:19:46 EDT 2009
Hi Yusuf,
If you want a volumetric display,
you have two options
A) Use VTK's volume rendering
or
B) First extract surfaces from the watershed image
(one surface per label) and then use surface
rendering with vtkPolyData
Regards,
Luis
--------------------------
Yusuf OEZBEK wrote:
> Hello!
>
> What you have about connection ITK to VTK said, I have made. But the
> result is still a 2D image not 3D. How do I change my code so I get 3D
> image with colors?
>
> My result:
> http://img246.imageshack.us/my.php?image=watershed.jpg
>
> My goal:
> http://www.cs.uni-paderborn.de/fileadmin/Informatik/AG-Domik/bachelor_thesis/bolte/coronary_watershed.jpeg
>
>
> Sorry, I am new with ITK.
>
>
> My codes:
>
>
> typedef unsigned char PixelType;
> const unsigned int Dimension = 3;
>
> typedef itk::OrientedImage< PixelType, Dimension > ImageType;
> typedef itk::ImageSeriesReader< ImageType > ReaderType;
> ReaderType::Pointer reader = ReaderType::New();
>
> typedef itk::GDCMImageIO ImageIOType;
> ImageIOType::Pointer dicomIO = ImageIOType::New();
>
> reader->SetImageIO( dicomIO );
>
> typedef itk::GDCMSeriesFileNames NamesGeneratorType;
> NamesGeneratorType::Pointer nameGenerator = NamesGeneratorType::New();
>
> nameGenerator->SetUseSeriesDetails( true );
> nameGenerator->AddSeriesRestriction("0008|0021" );
>
> nameGenerator->SetDirectory( selectedDirectory);
>
> typedef std::vector< std::string > SeriesIdContainer;
>
> const SeriesIdContainer & seriesUID = nameGenerator->GetSeriesUIDs();
>
> SeriesIdContainer::const_iterator seriesItr = seriesUID.begin();
> SeriesIdContainer::const_iterator seriesEnd = seriesUID.end();
> while( seriesItr != seriesEnd )
> {
> seriesItr++;
> }
>
> std::string seriesIdentifier;
>
> seriesIdentifier = seriesUID.begin()->c_str();
>
> typedef std::vector< std::string > FileNamesContainer;
> FileNamesContainer fileNames;
>
> fileNames = nameGenerator->GetFileNames( seriesIdentifier );
>
> reader->SetFileNames( fileNames );
> reader->Update();
>
>
>
> typedef float InternalPixelType;
> typedef itk::RGBPixel<unsigned char> RGBPixelType;
> typedef itk::Image< RGBPixelType, Dimension > RGBImageType;
> // typedef itk::ImageFileWriter< RGBImageType > WriterType;
> typedef itk::WatershedImageFilter< ImageType > WatershedFilterType;
> // typedef itk::Functor::ScalarToRGBPixelFunctor< unsigned long>
> ColorMapFunctorType;
> typedef WatershedFilterType::OutputImageType LabeledImageType;
> // typedef itk::UnaryFunctorImageFilter<
> LabeledImageType,RGBImageType,ColorMapFunctorType > ColorMapFilterType;
> typedef itk::ImageToVTKImageFilter <LabeledImageType> ConnectorType;
> // typedef itk::GradientMagnitudeImageFilter<ImageType, ImageType>
> GradientMagnitudeFilterType;
>
> // GradientMagnitudeFilterType::Pointer magnitudeFilter =
> GradientMagnitudeFilterType::New();
> // magnitudeFilter->SetInput(reader->GetOutput());
>
> WatershedFilterType::Pointer watershedFilter =
> WatershedFilterType::New();
> watershedFilter->SetInput( reader->GetOutput() );
>
> watershedFilter->SetLevel(this->sliderLevelWatershed->value());
> watershedFilter->SetThreshold(this->sliderLevelWatershed->value());
>
> // ColorMapFilterType::Pointer colorMapFilter = ColorMapFilterType::New();
> // colorMapFilter->SetInput( watershedFilter->GetOutput() );
>
> this->displayImage3D->show();
> this->displayImage3D->redraw();
>
> ConnectorType::Pointer connector = ConnectorType::New();
> connector->SetInput(watershedFilter->GetOutput());
>
>
> vtkImageShiftScale *shift = vtkImageShiftScale::New();
> shift->SetInput(connector->GetOutput());
> shift->SetOutputScalarTypeToUnsignedChar();
>
>
> vtkImageActor* actor = vtkImageActor::New();
> actor->SetInput(shift->GetOutput());
>
> camera3D = vtkCamera::New();
> camera3D->SetViewUp(0, 0, -1);
> camera3D->SetPosition(0, 1, 0);
> camera3D->SetFocalPoint(0, 0, 0);
> camera3D->ComputeViewPlaneNormal();
> camera3D->Azimuth(20);
>
> renderer3DWaterShed = vtkRenderer::New();
> renderWindow3DWaterShed = vtkRenderWindow::New();
> renderWindow3DWaterShed->AddRenderer(renderer3DWaterShed);
>
> displayImage3D->SetRenderWindow(renderWindow3DWaterShed);
> // displayImage3D->SetInteractorStyle(mode3DWaterShed);
> displayImage3D->Initialize();
>
> renderer3DWaterShed->AddActor(actor);
> renderer3DWaterShed->SetActiveCamera(camera3D);
> renderer3DWaterShed->ResetCamera();
> camera3D->Dolly(1.3);
> renderer3DWaterShed->ResetCameraClippingRange();
> renderer3DWaterShed->Render();
>
>
>
> ------------------------------------------------------------------------
> *Von:* Luis Ibanez <luis.ibanez at kitware.com>
> *An:* ahmet mehmet <nasil122002 at yahoo.de>
> *CC:* vtk-developers at vtk.org; insight-users at itk.org; vtkusers at vtk.org
> *Gesendet:* Dienstag, den 28. April 2009, 18:53:48 Uhr
> *Betreff:* Re: [Insight-users] ITK to VTK 3D WatershedImageFilter
>
>
>
> You are declaring an ITK+VTK connector of type:
>
> typedef itk::ImageToVTKImageFilter <ImageType> ConnectorType;
>
> where ImageType is given by
>
> typedef unsigned char PixelType;
> const unsigned int Dimension = 3;
> typedef itk::OrientedImage< PixelType, Dimension > ImageType;
>
>
> but you are connecting an image of RGB pixels to it.
> (instead of the image of unsigned char that you promised).
>
>
> What you may want to do is to remove the ITK Coloring filter,
> and to pass the image of labels (the output of the watershed)
> directly to VTK.
>
> Note that then the ITK+VTK connector, should be of type:
>
> itk::ImageToVTKImageFilter < LabeledImageType >
>
>
>
> Regards,
>
>
> Luis
>
>
> ------------------
> ahmet mehmet wrote:
> > Hello!
> > I wanted my 3D watershed segmentation combine with VTK and to show
> it in a VTK window. For the connection between ITK and VTK, I used
> itkImageToVTKImageFilter. But it gives following error.
> > /home/hno4d/Desktop/MIRCIT/MIRCIT.cpp: In member function »virtual
> void MIRCIT::imageDisplayingWatershed()«:
> > /home/hno4d/Desktop/MIRCIT/MIRCIT.cpp:1719: Fehler: keine passende
> Funktion für Aufruf von
> »itk::ImageToVTKImageFilter<itk::OrientedImage<unsigned char, 3u>
> >::SetInput(itk::Image<itk::RGBPixel<unsigned char>, 3u>*)«
> > /home/hno4d/Desktop/MIRCIT/itkImageToVTKImageFilter.txx:79:
> Anmerkung: Kandidaten sind: void
> itk::ImageToVTKImageFilter<TInputImage>::SetInput(const TInputImage*)
> [with TInputImage = itk::OrientedImage<unsigned char, 3u>]
> > make[2]: *** [CMakeFiles/MIRCIT.dir/MIRCIT.o] Fehler 1
> > make[1]: *** [CMakeFiles/MIRCIT.dir/all] Fehler 2
> > make: *** [all] Fehler 2
> >
> > How can I use my code with the following ITK VTK connection?
> > My code:
> >
> > typedef unsigned char PixelType;
> > const unsigned int Dimension = 3;
> >
> > typedef itk::OrientedImage< PixelType, Dimension > ImageType;
> > typedef itk::ImageSeriesReader< ImageType > ReaderType;
> >
> > ReaderType::Pointer reader = ReaderType::New();
> >
> > typedef itk::GDCMImageIO ImageIOType;
> > ImageIOType::Pointer dicomIO = ImageIOType::New();
> >
> > reader->SetImageIO( dicomIO );
> > typedef itk::GDCMSeriesFileNames NamesGeneratorType;
> > NamesGeneratorType::Pointer nameGenerator = NamesGeneratorType::New();
> > nameGenerator->SetUseSeriesDetails( true );
> > nameGenerator->AddSeriesRestriction("0008|0021" );
> > nameGenerator->SetDirectory( selectedDirectory);
> > typedef std::vector< std::string > SeriesIdContainer;
> > const SeriesIdContainer & seriesUID = nameGenerator->GetSeriesUIDs();
> > SeriesIdContainer::const_iterator seriesItr = seriesUID.begin();
> > SeriesIdContainer::const_iterator seriesEnd = seriesUID.end();
> > while( seriesItr != seriesEnd )
> > {
> > seriesItr++;
> > }
> >
> > std::string seriesIdentifier;
> > seriesIdentifier = seriesUID.begin()->c_str();
> >
> > typedef std::vector< std::string > FileNamesContainer;
> > FileNamesContainer fileNames;
> > fileNames = nameGenerator->GetFileNames( seriesIdentifier );
> >
> > reader->SetFileNames( fileNames );
> > reader->Update();
> >
> > typedef float InternalPixelType;
> > typedef itk::RGBPixel<unsigned char> RGBPixelType;
> > typedef itk::Image< RGBPixelType, Dimension > RGBImageType;
> > // typedef itk::ImageFileWriter< RGBImageType > WriterType;
> > typedef itk::WatershedImageFilter< ImageType > WatershedFilterType;
> > typedef itk::Functor::ScalarToRGBPixelFunctor< unsigned long>
> ColorMapFunctorType;
> > typedef WatershedFilterType::OutputImageType LabeledImageType;
> > typedef itk::UnaryFunctorImageFilter<
> LabeledImageType,RGBImageType,ColorMapFunctorType > ColorMapFilterType;
> > typedef itk::ImageToVTKImageFilter <ImageType> ConnectorType;
> > typedef itk::GradientMagnitudeImageFilter<ImageType, ImageType>
> GradientMagnitudeFilterType;
> >
> > GradientMagnitudeFilterType::Pointer magnitudeFilter =
> GradientMagnitudeFilterType::New();
> > magnitudeFilter->SetInput(reader->GetOutput());
> >
> > WatershedFilterType::Pointer watershedFilter =
> WatershedFilterType::New();
> > watershedFilter->SetInput( magnitudeFilter->GetOutput() );
> > watershedFilter->SetThreshold(this->sliderLevelWatershed->value());
> > watershedFilter->SetLevel(this->sliderThresholdWatershed->value());
> >
> > ColorMapFilterType::Pointer colorMapFilter = ColorMapFilterType::New();
> > colorMapFilter->SetInput( watershedFilter->GetOutput() );
> >
> > ConnectorType::Pointer connector = ConnectorType::New();
> > connector->SetInput(colorMapFilter->GetOutput());
> >
> > vtkImageActor* actor = vtkImageActor::New();
> > actor->SetInput(connector->GetOutput());
> >
> > vtkInteractorStyleImage * interactorStyle =
> vtkInteractorStyleImage::New();
> >
> > vtkRenderer* renderer = vtkRenderer::New();
> > vtkRenderWindow* renWin = vtkRenderWindow::New();
> > vtkRenderWindowInteractor* iren = vtkRenderWindowInteractor::New();
> >
> > renWin->SetSize(500, 500);
> > renWin->AddRenderer(renderer);
> > iren->SetRenderWindow(renWin);
> > iren->SetInteractorStyle( interactorStyle );
> > renderer->AddActor(actor);
> >
> > renWin->Render();
> > iren->Start();
> >
> > Thank you!
> >
> >
> >
> > ------------------------------------------------------------------------
> >
> > _____________________________________
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>
>
> ------------------------------------------------------------------------
>
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