[Insight-users] quesition of itkShapeDetectionLevelSetImageFilter
in 3D
kingaza at gmail.com
kingaza at gmail.com
Mon May 2 09:04:50 EDT 2005
Hi Luis,
Thanks for your suggestion, and I will try it.
Regrads,
Kingaza
On 4/28/05, Luis Ibanez <luis.ibanez at kitware.com> wrote:
>
>
> Hi Kingaza,
>
> Please read the chapter on LevelSet methods from the
> ITK Software Guide
>
> http://www.itk.org/ItkSoftwareGuide.pdf
>
> it explains in detail how to compute speed images.
>
> If you look at the code of the most recent CVS version of the LevelSet
> examples in InsightApplications, all of them are using the Speed image
> as input to the FastMarching preprocessing filter.
>
>
> Regards,
>
> Luis
>
> --------------------------
> kingaza at gmail.com wrote:
>
> > Hi Luis,
> >
> > Thanks for your answer.
> >
> > but i have still question
> > 1) I don't know how to generate such a speed image you mentioned. I
> > think the image from fastMarching filter is just the speed image, and
> > what i do is only to set the seeds and the constant speed.
> >
> > 2)I know the Origin and the Spcing is very important, and in my first
> > letter I have mentioned that the codes for origin and spacing are
> > added by myself.
> > fastMarching->SetOutputOrigin( reader->GetOutput()->GetOrigin() );
> > fastMarching->SetOutputSpacing(
> > reader->GetOutput()->GetSpacing() );
> > but even if i did so, i could not get the correct result.
> >
> > how should i do?
> > now i am reading ShapeDetectionLevelSet in InsightApplications, and it
> > works some acceptable. but i am so unfamiliar with fltk... :(
> >
> > any help is appreciated.
> >
> >
> > Regards,
> > Kingaza
> >
> > On 4/24/05, Luis Ibanez <luis.ibanez at kitware.com> wrote:
> >
> >>
> >>Hi Kingaza,
> >>
> >>Thanks for posting your code.
> >>
> >>1) The FastMarching will give better results if you
> >> feed it with the speed image instead of using
> >> the constant speed:
> >>
> >> fastMarching->SetSpeedConstant( 0.9 );
> >>
> >> Examples on how to connect the speed image as input
> >> to the FastMarching filter are available in
> >>
> >> Insight/Examples/Segmentation
> >>
> >>2) The Origin and Spacing parameters in FastMarcing
> >> are *VERY* important for this filter. You have
> >> them commented out in your code.
> >>
> >>Regards,
> >>
> >>
> >> Luis
> >>
> >>------------------------
> >>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
> >>>>
> >>>>
> >>>_______________________________________________
> >>>Insight-users mailing list
> >>>Insight-users at itk.org
> >>>http://www.itk.org/mailman/listinfo/insight-users
> >>>
> >>>
> >>
> >>
> > _______________________________________________
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> >
> >
>
>
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