[Insight-users] nobody could answer me ? Fw : Pleasehelp:problem with wathershed segmentation applied to 3Dgrayscale Image
wassim_belhadj at topnet.tn
wassim_belhadj at topnet.tn
Mon Aug 25 03:28:34 EDT 2008
Hi
I tried the code that you have join to Sara but I was one exception:
"list iteraror not dereferencable"
Can we list the parameters to pass as arguments
inputImage Patient01.mhd
outputImage = res.mhd
lowerThreshold =?
outputScaleLevel =?
Thanks in advance
On Fri, 22 Aug 2008 12:59:06 -0400, "Luis Ibanez" <luis.ibanez at kitware.com>
wrote:
> Hi Sara,
>
> Thanks for your detailed question regarding Watersheds.
>
>
> Please take a look at the attached code.
>
> It process the image "Patient01" from
>
> http://public.kitware.com/pub/itk/Data/LiverTumor/.
>
> in a time of
>
> 4 minutes 38 seconds.
>
> This was profiled in an QuadCore Intel Xeon 2.66 Ghz. (with 16Gb RAM).
> (although the process uses only one of the cores)
>
> Note that the process peaks 1Gb of memory allocation when it is running.
>
> Depending on the configuration of your system, it may be that the program
> started swapping memory at some point.
>
> Please give a try at the attached code and let us know what you find.
>
>
> Regards,
>
>
> Luis
>
>
>
-----------------------------------------------------------------------------------------------------------------------------------
> On Fri, Aug 22, 2008 at 11:19 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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>>
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