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| ==EstimatePCAModel.cxx== | | {{warning|1=The media wiki content on this page is no longer maintained. The examples presented on the https://itk.org/Wiki/* pages likely require ITK version 4.13 or earlier releases. In many cases, the examples on this page no longer conform to the best practices for modern ITK versions.}} |
| <source lang="cpp">
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| /*
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| Author: Juan Cardelino <juan dot cardelino at gmail dot com>
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| */
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| | |
| // ITK | |
| #include "itkBinaryThresholdImageFilter.h"
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| #include "itkBoundedReciprocalImageFilter.h"
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| #include "itkChangeInformationImageFilter.h"
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| #include "itkCommand.h"
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| #include "itkCurvatureAnisotropicDiffusionImageFilter.h"
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| #include "itkEuler2DTransform.h"
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| #include "itkFastMarchingImageFilter.h"
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| #include "itkGeodesicActiveContourShapePriorLevelSetImageFilter.h"
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| #include "itkGradientMagnitudeRecursiveGaussianImageFilter.h"
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| #include "itkImage.h"
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| #include "itkImageFileReader.h"
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| #include "itkImageFileWriter.h"
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| #include "itkImagePCAShapeModelEstimator.h"
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| #include "itkMultiplyImageFilter.h"
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| #include "itkNumericSeriesFileNames.h"
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| #include "itkNormalVariateGenerator.h"
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| #include "itkOnePlusOneEvolutionaryOptimizer.h"
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| #include "itkPCAShapeSignedDistanceFunction.h"
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| #include "itkRescaleIntensityImageFilter.h"
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| #include "itkShapePriorMAPCostFunction.h"
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| #include "itkSpatialFunctionImageEvaluatorFilter.h"
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| | |
| // VNL
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| #include "vnl/vnl_sample.h"
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| | |
| int main( int argc, char *argv[] )
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| {
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| if( argc < 5 )
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| {
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| std::cerr << "Missing Parameters " << std::endl;
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| std::cerr << "Usage: " << argv[0];
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| std::cerr << " nbTrain trainFilePattern";
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| std::cerr << " nbModes modeFilePattern";
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| std::cerr << std::endl;
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| return 1;
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| }
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| | |
| for(int i=0; i<argc;i++)
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| {
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| std::cout << "id: " << i << " arg: " << argv[i] << std::endl;
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| }
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| const unsigned int Dimension = 2;
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| typedef float my_PixelType;
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| typedef itk::Image< my_PixelType, Dimension > ImageType;
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| | |
| typedef itk::ImageFileReader< ImageType > ReaderType;
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| typedef itk::ImageFileWriter< ImageType > WriterType;
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| typedef itk::MultiplyImageFilter < ImageType , ImageType ,ImageType > ScaleType;
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| | |
| unsigned int nb_train=atoi(argv[1]);
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| itk::NumericSeriesFileNames::Pointer fileNamesCreator =
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| itk::NumericSeriesFileNames::New();
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| std::vector<ImageType::Pointer> trainingImages( nb_train );
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| fileNamesCreator->SetStartIndex( 0 );
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| fileNamesCreator->SetEndIndex( nb_train - 1 );
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| fileNamesCreator->SetSeriesFormat( argv[2] );
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| const std::vector<std::string> & shapeModeFileNames =
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| fileNamesCreator->GetFileNames();
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| | |
| for ( unsigned int k = 0; k < nb_train; k++ )
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| {
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| ReaderType::Pointer reader = ReaderType::New();
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| reader->SetFileName( shapeModeFileNames[k].c_str() );
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| reader->Update();
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| trainingImages[k] = reader->GetOutput();
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| }
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| | |
| typedef itk::ImagePCAShapeModelEstimator<ImageType, ImageType > my_Estimatortype; | |
| my_Estimatortype::Pointer filter = my_Estimatortype::New();
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| filter->SetNumberOfTrainingImages(nb_train);
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| filter->SetNumberOfPrincipalComponentsRequired(2);
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| | |
| for ( unsigned int k = 0; k < nb_train; k++ )
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| {
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| filter->SetInput(k, trainingImages[k] );
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| }
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| | |
| unsigned int nb_modes=atoi(argv[3]);
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| itk::NumericSeriesFileNames::Pointer fileNamesOutCreator =
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| itk::NumericSeriesFileNames::New();
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| fileNamesOutCreator->SetStartIndex( 0 );
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| fileNamesOutCreator->SetEndIndex( nb_modes-1 );
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| fileNamesOutCreator->SetSeriesFormat( argv[4] );
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| const std::vector<std::string> & outFileNames = fileNamesOutCreator->GetFileNames();
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| ScaleType::Pointer scaler = ScaleType::New();
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| filter->Update();
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| my_Estimatortype::VectorOfDoubleType v=filter->GetEigenValues();
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| double sv_mean=sqrt(v[0]);
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| for ( unsigned int k = 0; k < nb_modes; k++ )
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| {
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| double sv=sqrt(v[k]);
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| double sv_n=sv/sv_mean;
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| //double sv_n=sv;
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| std::cout << "writing: " << outFileNames[k] << std::endl;
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| std::cout << "svd[" << k << "]: " << sv << " norm: " << sv_n << std::endl;
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| WriterType::Pointer writer = WriterType::New();
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| writer->SetFileName( outFileNames[k].c_str() );
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| scaler->SetInput(filter->GetOutput(k));
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| scaler->SetConstant(sv_n);
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| writer->SetInput( scaler->GetOutput() );
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| writer->Update();
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| }
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| | |
| return EXIT_SUCCESS;
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| }
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| </source>
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| {{ITKCMakeLists|EstimatePCAModel}}
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