[Insight-users] watershed segmentation without RGB?
Laurent Mundeleer
lmundele at ulb.ac.be
Fri, 30 Apr 2004 14:38:06 +0200
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;
=20
typedef itk::CastImageFilter<ImageTypeOut, ImageType> CastFilterType;=
typedef itk::GradientAnisotropicDiffusionImageFilter<ImageType, =20
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->GetUpdateInformationCall=
back());
=20
importer->SetPipelineModifiedCallback(exporter->GetPipelineModifiedCallba=
ck());
importer->SetWholeExtentCallback(exporter->GetWholeExtentCallback());
importer->SetSpacingCallback(exporter->GetSpacingCallback());
importer->SetOriginCallback(exporter->GetOriginCallback());
importer->SetScalarTypeCallback(exporter->GetScalarTypeCallback());
=20
importer->SetNumberOfComponentsCallback(exporter->GetNumberOfComponentsCa=
llback());
=20
importer->SetPropagateUpdateExtentCallback(exporter->GetPropagateUpdateEx=
tentCallback());
importer->SetUpdateDataCallback(exporter->GetUpdateDataCallback());
importer->SetDataExtentCallback(exporter->GetDataExtentCallback());
importer->SetBufferPointerCallback(exporter->GetBufferPointerCallback()=
);
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->GetUpdateInformationCall=
back());
=20
importer->SetPipelineModifiedCallback(exporter->GetPipelineModifiedCallba=
ck());
importer->SetWholeExtentCallback(exporter->GetWholeExtentCallback());
importer->SetSpacingCallback(exporter->GetSpacingCallback());
importer->SetOriginCallback(exporter->GetOriginCallback());
importer->SetScalarTypeCallback(exporter->GetScalarTypeCallback());
=20
importer->SetNumberOfComponentsCallback(exporter->GetNumberOfComponentsCa=
llback());
=20
importer->SetPropagateUpdateExtentCallback(exporter->GetPropagateUpdateEx=
tentCallback());
importer->SetUpdateDataCallback(exporter->GetUpdateDataCallback());
importer->SetDataExtentCallback(exporter->GetDataExtentCallback());
importer->SetBufferPointerCallback(exporter->GetBufferPointerCallback()=
);
importer->SetCallbackUserData(exporter->GetCallbackUserData());
}
//-----------------------------------------------------------------
///contructeur initialisant le pipeline ITK
tumorFilterITK::tumorFilterITK(vtkImageImport* vtkImporter,=20
vtkImageExport *vtkExporter)
{ =20
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();
=20
ConnectPipelines(vtkExporter, itkImporter);
ConnectPipelines(itkExporter, vtkImporter); =20
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 you ca=
n
>easily run watershed on a grayscale image.
>
>You'll want to create a similar program to WatershedSegmentation1.cxx th=
at
>reads a scalar image, produces a gradient magnitude image
>(GradientMagnitudeImageFilter or RecursiveGradientMagnitudeImageFilter),=
and
>runs watershed on the gradient magnitude image.
>
>So you just need to change the pixel type, delete the word "Vector" from=
any
>class type in example, and change the CastType to a CastImageFilter that=
>converts a scalar image into an image of floating point pixels (alternat=
ive,
>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 tri=
ed
>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;=20
> typedef 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=20
> {
> writer->Update();
> }
> catch (itk::ExceptionObject &e)
> {
> std::cerr << e << std::endl;
> }
> =20
> return 0;
>}
>
>
>
>
>
>-----Original Message-----
>From: Laurent Mundeleer [mailto:lmundele at ulb.ac.be]
>Sent: Thursday, April 29, 2004 6:10 AM
>To: insight-users at 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 at ulb.ac.be
********************************************