[Insight-users] nobody could answer me ? Fw : Please help:problem with wathershed segmentation applied to 3D grayscale Image

[John Dailey]

It's been like 4 hours...

A lot of the people in the western part of the US haven't gotten to
work yet, give them a chance to respond...

I am far from being an expert, but 18 minutes doesn't sound that long
to me for a 3d data set (I don't know how big it is) on unknown
hardware.  Let it run a while longer.

On Fri, Aug 22, 2008 at 8:19 AM, sara meghellati
<sara_meghellati at yahoo.fr> wrote:
> I'm sending again my questions as nobody have answered me.
>
> --- En date de : Ven 22.8.08, sara meghellati <sara_meghellati at yahoo.fr> a
> écrit :
>
> De: sara meghellati <sara_meghellati at yahoo.fr>
> Objet: [Insight-users] Please help:problem with wathershed segmentation
> applied to 3D grayscale Image
> À: "insight itk" <insight-users at itk.org>
> Date: Vendredi 22 Août 2008, 13h48
>
> Dear itk experts,
>
> I'm segmenting a volume (3D grayscale image) using watershed method inspired
> from the WatershedSegmentation1
>
> (2D RGB image as input)example provided within itk.
>
> My code is well working for 2D grayscale images but when I change
>
> the dimension to 3, the code
>  still running as it get stuck in a
>
> loop!! I wait for more than 18min but no results!! Is it normal
>
> that this kind of segmentation takes age to give the result in 3d
>
> image or there is some thing wrong with my code? Please could you help me on
> that? Also, how can I follow the progress of the code?
>
> I pass my code bellow. In this example I used the 3D data provided
>
> in http://public.kitware.com/pub/itk/Data/LiverTumor/.
>
> #include <iostream>
>
> #include "itkImage.h"
>
> #include "itkGradientAnisotropicDiffusionImageFilter.h"
>
> #include "itkGradientMagnitudeImageFilter.h"
>
> #include "itkWatershedImageFilter.h"
>
> #include "itkImageFileReader.h"
>
> #include "itkImageFileWriter.h"
>
> #include "itkVectorCastImageFilter.h"
>
> #include "itkUnaryFunctorImageFilter.h"
>
> #include "itkScalarToRGBPixelFunctor.h"
>
>
>
> #include "itkVTKImageExport.h"
>
> #include "itkVTKImageImport.h"
>
>
>
> #include "vtkImageData.h"
>
> #include "vtkImageImport.h"
>
> #include "vtkImageExport.h"
>
> #include "vtkImageActor.h"
>
> #include "vtkRenderer.h"
>
> #include "vtkRenderWindow.h"
>
> #include "vtkRenderWindowInteractor.h"
>
> #include "vtkInteractorStyleTrackballCamera.h"
>
> #include "vtkImageShiftScale.h"
>
>
>
> // This function will connect the given itk::VTKImageExport filter to the
> given vtkImageImport filter.
>
> template <typename ITK_Exporter, typename VTK_Importer>
>
> void ConnectPipelines(ITK_Exporter exporter, VTK_Importer* importer)
>
> {
>
>
> importer->SetUpdateInformationCallback(exporter->GetUpdateInformationCallback());
>
>
> importer->SetPipelineModifiedCallback(exporter->GetPipelineModifiedCallback());
>
>   importer->SetWholeExtentCallback(exporter->GetWholeExtentCallback());
>
>   importer->SetSpacingCallback(exporter->GetSpacingCallback());
>
>   importer->SetOriginCallback(exporter->GetOriginCallback());
>
>   importer->SetScalarTypeCallback(exporter->GetScalarTypeCallback());
>
>
> importer->SetNumberOfComponentsCallback(exporter->GetNumberOfComponentsCallback());
>
>
> importer->SetPropagateUpdateExtentCallback(exporter->GetPropagateUpdateExtentCallback());
>
>   importer->SetUpdateDataCallback(exporter->GetUpdateDataCallback());
>
>   importer->SetDataExtentCallback(exporter->GetDataExtentCallback());
>
>   importer->SetBufferPointerCallback(exporter->GetBufferPointerCallback());
>
>   importer->SetCallbackUserData(exporter->GetCallbackUserData());
>
> }
>
>
>
> int main( )
>
> {
>
>       typedef itk::Image<float, 3>           ImageType;
>
>       typedef itk::Image<unsigned long, 3>   LabeledImageType;
>
>       typedef itk::Image<float, 3>           ScalarImageType;
>
>       // for visualization purposes
>
>       typedef itk::RGBPixel<unsigned char>   RGBPixelType;
>
>       typedef itk::Image<RGBPixelType, 3>    RGBImageType;
>
>
>
>       typedef itk::ImageFileReader<ImageType> FileReaderType;
>
>       typedef itk::GradientAnisotropicDiffusionImageFilter<ImageType,
> ImageType>  DiffusionFilterType;
>
>       typedef itk::GradientMagnitudeImageFilter<ImageType,ImageType>
> GradientMagnitudeFilterType;
>
>       typedef itk::WatershedImageFilter<ScalarImageType>
> WatershedFilterType;
>
>       typedef itk::ImageFileWriter<RGBImageType> FileWriterType;
>
>
>
>       FileReaderType::Pointer reader = FileReaderType::New
>
>       reader->SetFileName( "c:/images/3DImages/Patient01.mhd"  );
>
>       //reader->SetFileName("c:/Images/BrainProtonDensitySlice.png");
>
>
>
>       DiffusionFilterType::Pointer diffusion = DiffusionFilterType::New();
>
>       diffusion->SetNumberOfIterations( atoi("10") );
>
>       diffusion->SetConductanceParameter( atof("2.0") );
>
>       diffusion->SetTimeStep(0.0625);
>
>
>
>       GradientMagnitudeFilterType::Pointer gradient =
> GradientMagnitudeFilterType::New();
>
>
>
>       WatershedFilterType::Pointer watershed = WatershedFilterType::New();
>
>       watershed->SetLevel( atof("0.15") );
>
>       watershed->SetThreshold( atof("0.001") );
>
>       typedef itk::Functor::ScalarToRGBPixelFunctor<unsigned long>
> ColorMapFunctorType;
>
>       typedef itk::UnaryFunctorImageFilter<LabeledImageType,
> RGBImageType, ColorMapFunctorType> ColorMapFilterType;
>
>       ColorMapFilterType::Pointer colormapper = ColorMapFilterType::New();
>
>
>
>       FileWriterType::Pointer writer = FileWriterType::New();
>
>       writer->SetFileName("c:/Images/WatershedSegImg.mhd");
>
>
>
>       diffusion->SetInput(reader->GetOutput());
>
>       gradient->SetInput(diffusion->GetOutput());
>
>       watershed->SetInput(gradient->GetOutput());
>
>       colormapper->SetInput(watershed->GetOutput());
>
>       writer->SetInput(colormapper->GetOutput());
>
>       writer->Update();
>
>
>
> try
>
>     {
>
>             writer->Update();
>
>     }
>
>   catch (itk::ExceptionObject &e)
>
>     {
>
>             std::cerr << e << std::endl;
>
>     }
>
>
>
>   return 0;
>
>
>
> }
>
> Thanks
>
> Sara
>
> ________________________________
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>
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