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| ==EstimatePCAModel.cxx== | | {{warning|1=The media wiki content on this page is no longer maintained.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