[Insight-users] quesition of itkShapeDetectionLevelSetImageFilter
in 3D
kingaza at gmail.com
kingaza at gmail.com
Fri Apr 22 10:55:30 EDT 2005
Hi Luis, itk users
I am thinking about this question these days
the previews pictures are on the condiction where
fastMarching->SetSpeedConstant( 5 );
but even if i set the speed value as 1, or 0.9, 0.8...
nothing improves except the circle region is smaller. so i think it is
not the main cause.
the scale of the data is about 100*100*10, the z grid range and the
others are not within an order of magnitude
so i wonder if the problem is because of poor dimensional scaling. but
i am not sure about it.
Regards,
Kingaza
On 4/18/05, kingaza at gmail.com <kingaza at gmail.com> wrote:
> hi Luis,
>
> thx for your kindly answer
>
> this function is invoked in my mfc application.
> and i get:
> ei = shapeDetection->GetElapsedIterations() = 800;
> RMSChange = shapeDetection->GetRMSChange() = 0.044165259529942602;
>
> while
> shapeDetection->SetMaximumRMSError( 0.02 );
> shapeDetection->SetNumberOfIterations( 800 );
>
> Regards,
> Kingaza
>
> *.h
> int ShapeDetection3D(string input, string output, int seednum, int*
> seed, int iterations=15, double sigma=1.0, double alpha=-0.5, double
> beta=3.0, double curvatureScaling=0.05, double propagationScaling=1.0,
> double initialDistance=5.0);
>
> *.cpp
> int ShapeDetection3D(string input, string output, int seednum, int*
> seed, int iterations, double sigma, double alpha, double beta,
> double curvatureScaling, double propagationScaling, double
> initialDistance)
> {
>
> const unsigned int Dimension = 3;
> typedef itk::Image< InternalPixelType, Dimension > InternalImageType;
>
> typedef itk::Image< BinaryPixelType, Dimension > OutputImageType;
>
> typedef itk::BinaryThresholdImageFilter< InternalImageType, OutputImageType >
> ThresholdingFilterType;
> ThresholdingFilterType::Pointer thresholder = ThresholdingFilterType::New();
>
> thresholder->SetLowerThreshold( -1000.0 );
> thresholder->SetUpperThreshold( 0.0 );
>
> thresholder->SetOutsideValue( 0 );
> thresholder->SetInsideValue( 255 );
>
> typedef itk::ImageFileReader< InternalImageType > ReaderType;
> typedef itk::ImageFileWriter< OutputImageType > WriterType;
>
> ReaderType::Pointer reader = ReaderType::New();
> WriterType::Pointer writer = WriterType::New();
>
> reader->SetFileName( input.c_str() );
> writer->SetFileName( output.c_str() );
>
> reader->Update();
>
> typedef itk::RescaleIntensityImageFilter<InternalImageType, OutputImageType>
> CastFilterType;
>
> typedef itk::CurvatureAnisotropicDiffusionImageFilter<
> InternalImageType,
> InternalImageType > SmoothingFilterType;
>
> SmoothingFilterType::Pointer smoothing = SmoothingFilterType::New();
>
> typedef itk::GradientMagnitudeRecursiveGaussianImageFilter<
> InternalImageType,
> InternalImageType > GradientFilterType;
>
> typedef itk::SigmoidImageFilter<
> InternalImageType,
> InternalImageType > SigmoidFilterType;
>
> GradientFilterType::Pointer gradientMagnitude = GradientFilterType::New();
> SigmoidFilterType::Pointer sigmoid = SigmoidFilterType::New();
>
> sigmoid->SetOutputMinimum( 0.0 );
> sigmoid->SetOutputMaximum( 1.0 );
>
> typedef itk::FastMarchingImageFilter< InternalImageType, InternalImageType >
> FastMarchingFilterType;
>
> FastMarchingFilterType::Pointer fastMarching = FastMarchingFilterType::New();
>
> typedef itk::ShapeDetectionLevelSetImageFilter< InternalImageType,
> InternalImageType > ShapeDetectionFilterType;
> ShapeDetectionFilterType::Pointer shapeDetection =
> ShapeDetectionFilterType::New();
>
> smoothing->SetInput( reader->GetOutput() );
> gradientMagnitude->SetInput( smoothing->GetOutput() );
> sigmoid->SetInput( gradientMagnitude->GetOutput() );
>
> shapeDetection->SetInput( fastMarching->GetOutput() );
> shapeDetection->SetFeatureImage( sigmoid->GetOutput() );
>
> thresholder->SetInput( shapeDetection->GetOutput() );
>
> writer->SetInput( thresholder->GetOutput() );
>
> smoothing->SetTimeStep( 0.0625 );//
> smoothing->SetNumberOfIterations( 15 );//5
> smoothing->SetConductanceParameter( 9.0 );
>
> gradientMagnitude->SetSigma( sigma );
> sigmoid->SetAlpha( alpha );
> sigmoid->SetBeta( beta );
>
> typedef FastMarchingFilterType::NodeContainer NodeContainer;
> typedef FastMarchingFilterType::NodeType NodeType;
> NodeContainer::Pointer seeds = NodeContainer::New();
>
> InternalImageType::IndexType seedPosition;
>
> NodeType node;
> const double seedValue = - initialDistance;
>
> node.SetValue( seedValue );
> seeds->Initialize();
> for (int n=0; n< seednum; n++)
> {
> seedPosition[0] = seed[3*n];
> seedPosition[1] = seed[3*n+1];
> seedPosition[2] = seed[3*n+2];
> node.SetIndex( seedPosition );
> seeds->InsertElement( n, node );
> }
>
> fastMarching->SetTrialPoints( seeds );
> fastMarching->SetSpeedConstant( 0.9 );//1.0
>
> CastFilterType::Pointer caster1 = CastFilterType::New();
> CastFilterType::Pointer caster2 = CastFilterType::New();
> CastFilterType::Pointer caster3 = CastFilterType::New();
> CastFilterType::Pointer caster4 = CastFilterType::New();
>
> WriterType::Pointer writer1 = WriterType::New();
> WriterType::Pointer writer2 = WriterType::New();
> WriterType::Pointer writer3 = WriterType::New();
> WriterType::Pointer writer4 = WriterType::New();
>
> caster1->SetInput( smoothing->GetOutput() );
> writer1->SetInput( caster1->GetOutput() );
> writer1->SetFileName("ShapeDetectionLevelSetFilterOutput1.vtk");
> caster1->SetOutputMinimum( 0 );
> caster1->SetOutputMaximum( 255 );
> writer1->Update();
>
> caster2->SetInput( gradientMagnitude->GetOutput() );
> writer2->SetInput( caster2->GetOutput() );
> writer2->SetFileName("ShapeDetectionLevelSetFilterOutput2.vtk");
> caster2->SetOutputMinimum( 0 );
> caster2->SetOutputMaximum( 255 );
> writer2->Update();
>
> caster3->SetInput( sigmoid->GetOutput() );
> writer3->SetInput( caster3->GetOutput() );
> writer3->SetFileName("ShapeDetectionLevelSetFilterOutput3.vtk");
> caster3->SetOutputMinimum( 0 );
> caster3->SetOutputMaximum( 255 );
> writer3->Update();
>
> caster4->SetInput( fastMarching->GetOutput() );
> writer4->SetInput( caster4->GetOutput() );
> writer4->SetFileName("ShapeDetectionLevelSetFilterOutput4.vtk");
> caster4->SetOutputMinimum( 0 );
> caster4->SetOutputMaximum( 255 );
>
>
> fastMarching->SetOutputSize(
> reader->GetOutput()->GetBufferedRegion().GetSize() );
> // fastMarching->SetOutputOrigin(
> // reader->GetOutput()->GetOrigin() );
> // fastMarching->SetOutputSpacing(
> // reader->GetOutput()->GetSpacing() );
>
> shapeDetection->SetPropagationScaling( propagationScaling );
> shapeDetection->SetCurvatureScaling( curvatureScaling );
>
> shapeDetection->SetMaximumRMSError( 0.02 );
> shapeDetection->SetNumberOfIterations( 800 );
>
> try
> {
> writer->Update();
> }
> catch( itk::ExceptionObject & excep )
> {
> std::cerr << "Exception caught !" << std::endl;
> std::cerr << excep << std::endl;
> return -1;
> }
>
> int ni = shapeDetection->GetNumberOfIterations();
> double RMS = shapeDetection->GetMaximumRMSError();
> int ei = shapeDetection->GetElapsedIterations();
> double RMSChange = shapeDetection->GetRMSChange();
>
> std::cout << std::endl;
> std::cout << "Max. no. iterations: " << ni << std::endl;
> std::cout << "Max. RMS error: " << RMS << std::endl;
> std::cout << std::endl;
> std::cout << "No. elpased iterations: " << ei << std::endl;
> std::cout << "RMS change: " << RMSChange << std::endl;
>
> writer4->Update();
>
> /*
> typedef itk::ImageFileWriter< InternalImageType > InternalWriterType;
>
> InternalWriterType::Pointer mapWriter = InternalWriterType::New();
> mapWriter->SetInput( fastMarching->GetOutput() );
> mapWriter->SetFileName("ShapeDetectionLevelSetFilterOutput4.mha");
> mapWriter->Update();
>
> InternalWriterType::Pointer speedWriter = InternalWriterType::New();
> speedWriter->SetInput( sigmoid->GetOutput() );
> speedWriter->SetFileName("ShapeDetectionLevelSetFilterOutput3.mha");
> speedWriter->Update();
>
> InternalWriterType::Pointer gradientWriter = InternalWriterType::New();
> gradientWriter->SetInput( gradientMagnitude->GetOutput() );
> gradientWriter->SetFileName("ShapeDetectionLevelSetFilterOutput2.mha");
> gradientWriter->Update();
> */
> return 0;
> }
>
> On 4/18/05, Luis Ibanez <luis.ibanez at kitware.com> wrote:
> >
> >
> > Hi Kingaza,
> >
> > Thanks for posting the screen shots of your output.
> >
> > It seems that the speed image is not being connected
> > correctly to the FastMarching filter.
> >
> > Your manipulations of origin and spacing may easily
> > be part of the problem....
> >
> > You may also have an problem with the scaling of the
> > speed image. Are you using values from 0.0 to 1.0 ??
> >
> > Please post your code to the list.
> >
> > Thanks
> >
> > Luis
> >
> > -----------------------------
> > kingaza at gmail.com wrote:
> > > hi all,
> > >
> > > I am so terribly puzzled to this problem.
> > > I have tried ShapeDetectionLevelSetFilter in a 3D case. Everything is
> > > ok, but for the last process. It's seems that the feature image out
> > > from sigmoid filter doesn't work at all.
> > >
> > > the attachment pictures are the results out from fastmarching, sigmoid
> > > and shapedetection filters, which i captured from paraview.
> > >
> > > eager for any tip!
> > >
> > > regards,
> > > kingaza
> > >
> > > btw, because of different spacing and origin, i add these codes
> > > fastMarching->SetOutputOrigin(
> > > reader->GetOutput()->GetOrigin() );
> > > fastMarching->SetOutputSpacing(
> > > reader->GetOutput()->GetSpacing() );
> > > after
> > > fastMarching->SetOutputSize(
> > > reader->GetOutput()->GetBufferedRegion().GetSize() );
> > >
> > >
> > > ------------------------------------------------------------------------
> > >
> > >
> > > ------------------------------------------------------------------------
> > >
> > >
> > > ------------------------------------------------------------------------
> > >
> > >
> > > ------------------------------------------------------------------------
> > >
> > > _______________________________________________
> > > Insight-users mailing list
> > > Insight-users at itk.org
> > > http://www.itk.org/mailman/listinfo/insight-users
> >
> >
>
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