[Insight-users] watershed segmentation without RGB?
Laurent Mundeleer
lmundele@ulb.ac.be
Tue May 4 10:06:35 EDT 2004
Hi Luis,
from wich version of itk can I use this filters? Is it ok wich 1.4, or=20
do I need to upgrade?
-------
InsightApplications/Auxiliary/vtk
itkImageToVTKImageFilter.h
itkImageToVTKImageFilter.txx
itkVTKImageToImageFilter.h
itkVTKImageToImageFilter.txx
-------
PS : why the use of extensions .txx instead of .cxx ?
Thanks
Regards,
Laurent
Luis Ibanez wrote:
>
> Hi Laurent,
>
> It is likely that the error you are getting is due to
> the interconnections between the ITK and VTK pipelines
> and not to the use of the Watershed filter itself.
>
> Please do the following:
>
>
> A) Take a look at the python example:
>
> Insight/Examples/Segmentation/
> WatershedSegmentation1.py
>
> This example is taking a graylevel image as input.
> Python code looks pretty much like C++, just replace
> all the "." with "->" and add ";" at the end :-)
>
>
>
> B) Just to double-check
> In your program, replace the Watershed image filter
> with an inocuous filter such as the MedianImageFitler.
> Recompile and rerun your program. If you still get
> the abnormal termination error, at least you rule out
> the Watershed filter as the culprit.
>
>
>
> C) You are now 'manually' connecting ITK and VTK pipelines.
> This is tricky and it is easy to get it wrong.
>
> For your convenience, filters have been made available
> in InsightApplications that will connect the two pipelines
> in a single operation. Please use the filters:
>
> InsightApplications/Auxiliary/vtk
> itkImageToVTKImageFilter.h
> itkImageToVTKImageFilter.txx
> itkVTKImageToImageFilter.h
> itkVTKImageToImageFilter.txx
>
>
> Regards,
>
>
> Luis
>
>
> --------------------------
> Laurent Mundeleer wrote:
>
>> Hi James,
>>
>> I've tried to convert the WatershedSegmentation1.cxx to grayscale=20
>> images, but I still have problems (abnormal termination).
>> Here's my code :
>> --------------------
>> tumorFilterITK.h
>> --------------------
>> #ifndef tumorFilterITK_H
>> #define tumorFilterITK_H
>>
>>
>> #include <itkVTKImageExport.h>
>> #include <itkVTKImageImport.h>
>> #include <vtkImageImport.h>
>> #include <vtkImageExport.h>
>>
>> #include <itkGradientAnisotropicDiffusionImageFilter.h>
>> #include <itkGradientMagnitudeImageFilter.h>
>> #include <itkWatershedImageFilter.h>
>> #include <itkCastImageFilter.h>
>>
>> class tumorFilterITK
>> {
>>
>> public:
>>
>> typedef short pixelType;
>>
>> typedef itk::Image<pixelType, 3> ImageType;
>> typedef itk::Image<unsigned long, 3> ImageTypeOut;
>>
>> typedef itk::VTKImageImport<ImageType> ImageImportType;
>> typedef itk::VTKImageExport<ImageType> ImageExportType;
>>
>> typedef itk::CastImageFilter<ImageTypeOut, ImageType> CastFilterTyp=
e;
>>
>> typedef itk::GradientAnisotropicDiffusionImageFilter<ImageType, =
>> ImageType> DiffusionFilterType;
>> typedef itk::GradientMagnitudeImageFilter<ImageType, ImageType>=20
>> GradientMagnitudeFilterType;
>> typedef itk::WatershedImageFilter<ImageType> WatershedFilterType;
>>
>> tumorFilterITK(vtkImageImport*, vtkImageExport*);
>> void tumorFilterITKExec();
>>
>> private:
>>
>> ImageImportType::Pointer itkImporter;
>> ImageExportType::Pointer itkExporter;
>>
>> CastFilterType::Pointer caster;
>>
>> DiffusionFilterType::Pointer diffusion;
>> GradientMagnitudeFilterType::Pointer gradient;
>> WatershedFilterType::Pointer watershed;
>> };
>>
>> #endif
>> --------------------------------------------
>> --------------------
>> tumorFilterITK.cpp
>> --------------------
>>
>> #include "tumorFilterITK.h"
>>
>> /// connexion de ITK a VTK
>> template <typename ITK_Exporter, typename VTK_Importer>
>> void ConnectPipelines(ITK_Exporter exporter, VTK_Importer* importer)
>> {
>> =20
>> importer->SetUpdateInformationCallback(exporter->GetUpdateInformationC=
allback());=20
>>
>> =20
>> importer->SetPipelineModifiedCallback(exporter->GetPipelineModifiedCal=
lback());=20
>>
>> importer->SetWholeExtentCallback(exporter->GetWholeExtentCallback());=
>> importer->SetSpacingCallback(exporter->GetSpacingCallback());
>> importer->SetOriginCallback(exporter->GetOriginCallback());
>> importer->SetScalarTypeCallback(exporter->GetScalarTypeCallback());
>> =20
>> importer->SetNumberOfComponentsCallback(exporter->GetNumberOfComponent=
sCallback());=20
>>
>> =20
>> importer->SetPropagateUpdateExtentCallback(exporter->GetPropagateUpdat=
eExtentCallback());=20
>>
>> importer->SetUpdateDataCallback(exporter->GetUpdateDataCallback());
>> importer->SetDataExtentCallback(exporter->GetDataExtentCallback());
>> importer->SetBufferPointerCallback(exporter->GetBufferPointerCallback=
());=20
>>
>> importer->SetCallbackUserData(exporter->GetCallbackUserData());
>> }
>>
>> //-----------------------------------------------------------------
>>
>> /// connexion de VTK a ITK
>> template <typename VTK_Exporter, typename ITK_Importer>
>> void ConnectPipelines(VTK_Exporter* exporter, ITK_Importer importer)
>> {
>> =20
>> importer->SetUpdateInformationCallback(exporter->GetUpdateInformationC=
allback());=20
>>
>> =20
>> importer->SetPipelineModifiedCallback(exporter->GetPipelineModifiedCal=
lback());=20
>>
>> importer->SetWholeExtentCallback(exporter->GetWholeExtentCallback());=
>> importer->SetSpacingCallback(exporter->GetSpacingCallback());
>> importer->SetOriginCallback(exporter->GetOriginCallback());
>> importer->SetScalarTypeCallback(exporter->GetScalarTypeCallback());
>> =20
>> importer->SetNumberOfComponentsCallback(exporter->GetNumberOfComponent=
sCallback());=20
>>
>> =20
>> importer->SetPropagateUpdateExtentCallback(exporter->GetPropagateUpdat=
eExtentCallback());=20
>>
>> importer->SetUpdateDataCallback(exporter->GetUpdateDataCallback());
>> importer->SetDataExtentCallback(exporter->GetDataExtentCallback());
>> importer->SetBufferPointerCallback(exporter->GetBufferPointerCallback=
());=20
>>
>> importer->SetCallbackUserData(exporter->GetCallbackUserData());
>> }
>>
>> //-----------------------------------------------------------------
>>
>> ///contructeur initialisant le pipeline ITK
>> tumorFilterITK::tumorFilterITK(vtkImageImport* vtkImporter,=20
>> vtkImageExport *vtkExporter)
>> { itkImporter =3D ImageImportType::New();
>> itkExporter =3D ImageExportType::New();
>>
>> // itkExporter->SetInput(itkImporter->GetOutput());
>> diffusion =3D DiffusionFilterType::New();
>> gradient =3D GradientMagnitudeFilterType::New();
>> caster =3D CastFilterType::New();
>>
>> watershed =3D WatershedFilterType::New();
>> ConnectPipelines(vtkExporter, itkImporter);
>> ConnectPipelines(itkExporter, vtkImporter); tumorFilterITKExec(=
);
>> }
>>
>> //-----------------------------------------------------------------
>>
>> /// execution du filtre de detection de tumeurs
>> void tumorFilterITK::tumorFilterITKExec()
>> {
>>
>> //inputImage outputImage conductanceTerm diffusionIterations=20
>> lowerThreshold outputScaleLevel gradientMode " << std::endl;
>>
>> diffusion->SetNumberOfIterations( 5 ); // 5 typically
>> diffusion->SetConductanceParameter( 3.0 ); // 3.0 typically
>> diffusion->SetTimeStep(0.125);
>>
>> watershed->SetLevel( 0.001 ); // 0->1 en %
>> watershed->SetThreshold( 0.001 ); // 0->1 en %
>>
>> diffusion->SetInput(itkImporter->GetOutput());
>> gradient->SetInput(diffusion->GetOutput());
>> watershed->SetInput(gradient->GetOutput());
>>
>> try
>> {
>> watershed->Update();
>> }
>> catch (itk::ExceptionObject &e)
>> {
>> std::cerr << e << std::endl;
>> }
>> caster->SetInput(watershed->GetOutput());
>> itkExporter->SetInput(caster->GetOutput());
>> }
>>
>> ------------------------------------
>>
>> Maybe can you help me?
>> Thanks again,
>>
>> Regards,
>>
>> Laurent
>>
>>
>>
>> Miller, James V (Research) wrote:
>>
>>> Watershed can be run on grayscale images. The example
>>> (WatershedSegmentation1.cxx) is set up to process RGB pixels. But=20
>>> you can
>>> easily run watershed on a grayscale image.
>>>
>>> You'll want to create a similar program to=20
>>> WatershedSegmentation1.cxx that
>>> reads a scalar image, produces a gradient magnitude image
>>> (GradientMagnitudeImageFilter or=20
>>> RecursiveGradientMagnitudeImageFilter), and
>>> runs watershed on the gradient magnitude image.
>>>
>>> So you just need to change the pixel type, delete the word "Vector"=20
>>> from any
>>> class type in example, and change the CastType to a CastImageFilter=20
>>> that
>>> converts a scalar image into an image of floating point pixels=20
>>> (alternative,
>>> you can remove the cast filter altogether and have the reader return =
an
>>> image of floating point pixels. Here is a quick stab at it (haven't =
>>> tried
>>> to compile it....)
>>>
>>> #ifdef _MSC_VER
>>> #pragma warning ( disable : 4786 )
>>> #endif
>>>
>>> #include <iostream>
>>>
>>> #include "itkGradientAnisotropicDiffusionImageFilter.h"
>>> #include "itkGradientMagnitudeImageFilter.h"
>>> #include "itkWatershedImageFilter.h"
>>>
>>> #include "itkImageFileReader.h"
>>> #include "itkImageFileWriter.h"
>>> #include "itkUnaryFunctorImageFilter.h"
>>> #include "itkScalarToRGBPixelFunctor.h"
>>>
>>> int main( int argc, char *argv[] )
>>> {
>>> if (argc < 8 )
>>> {
>>> std::cerr << "Missing Parameters " << std::endl;
>>> std::cerr << "Usage: " << argv[0];
>>> std::cerr << " inputImage outputImage conductanceTerm
>>> diffusionIterations lowerThreshold outputScaleLevel gradientMode " <<=
>>> std::endl;
>>> return 1;
>>> }
>>> =20
>>> typedef itk::RGBPixel<unsigned char> RGBPixelType;
>>> typedef itk::Image<RGBPixelType, 2> RGBImageType;
>>> typedef itk::Image<unsigned long, 2> LabeledImageType;
>>> typedef itk::Image<float, 2> ScalarImageType;
>>>
>>> typedef itk::ImageFileReader<ScalarImageType> FileReaderType;
>>> typedef itk::GradientAnisotropicDiffusionImageFilter<ScalarImageType=
,
>>> ScalarImageType> DiffusionFilterType;
>>> typedef itk::GradientMagnitudeImageFilter<ScalarImageType>
>>> ScalarMagnitudeFilterType; typedef=20
>>> itk::WatershedImageFilter<ScalarImageType> WatershedFilterType;
>>> // Software Guide : EndCodeSnippet
>>>
>>> typedef itk::ImageFileWriter<RGBImageType> FileWriterType;
>>>
>>> FileReaderType::Pointer reader =3D FileReaderType::New();
>>> reader->SetFileName(argv[1]);
>>> =20
>>> DiffusionFilterType::Pointer diffusion =3D DiffusionFilterType::New(=
);
>>> diffusion->SetNumberOfIterations( atoi(argv[4]) );
>>> diffusion->SetConductanceParameter( atof(argv[3]) );
>>> diffusion->SetTimeStep(0.125);
>>>
>>>
>>> GradientMagnitudeFilterType::Pointer gradient =3D
>>> GradientMagnitudeFilterType::New();
>>> gradient->SetUsePrincipleComponents(atoi(argv[7]));
>>>
>>>
>>> WatershedFilterType::Pointer watershed =3D WatershedFilterType::New(=
);
>>> watershed->SetLevel( atof(argv[6]) );
>>> watershed->SetThreshold( atof(argv[5]) );
>>>
>>>
>>> typedef itk::Functor::ScalarToRGBPixelFunctor<unsigned long>
>>> ColorMapFunctorType;
>>> typedef itk::UnaryFunctorImageFilter<LabeledImageType,
>>> RGBImageType, ColorMapFunctorType> ColorMapFilterType;
>>> ColorMapFilterType::Pointer colormapper =3D ColorMapFilterType::New(=
);
>>> =20
>>> FileWriterType::Pointer writer =3D FileWriterType::New();
>>> writer->SetFileName(argv[2]);
>>>
>>> diffusion->SetInput(reader->GetOutput());
>>> gradient->SetInput(diffusion->GetOutput());
>>> watershed->SetInput(gradient->GetOutput());
>>> colormapper->SetInput(watershed->GetOutput());
>>> writer->SetInput(colormapper->GetOutput());
>>>
>>> try {
>>> writer->Update();
>>> }
>>> catch (itk::ExceptionObject &e)
>>> {
>>> std::cerr << e << std::endl;
>>> }
>>> return 0;
>>> }
>>>
>>>
>>>
>>>
>>>
>>> -----Original Message-----
>>> From: Laurent Mundeleer [mailto:lmundele@ulb.ac.be]
>>> Sent: Thursday, April 29, 2004 6:10 AM
>>> To: insight-users@itk.org
>>> Subject: [Insight-users] watershed segmentation without RGB?
>>>
>>>
>>> Hi all,
>>>
>>> I'd like to apply the watershed filter to CT images, is it possible? =
>>> In the documentation, it 's specified that RGB values are required...=
>>> How can I do?
>>>
>>> Thanks in advance
>>>
>>> Regards,
>>>
>>> Laurent
>>>
>>> =20
>>>
>>
>
>
>
>
--=20
********************************************
Laurent Mundeleer
Universit=E9 Libre de Bruxelles (ULB)
Service des Syst=E8mes Logiques et Num=E9riques (SLN) CP165/57
50, Av. F.Roosevelt
1050 Bruxelles
Belgium
tel : ++32.2.650.22.97
fax : ++32.2.650.22.98
e-mail : lmundele@ulb.ac.be
********************************************
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