From be00abcdf8e47254335fa359ebc329d9a39c2aaf Mon Sep 17 00:00:00 2001
From: Thomas Feuvrier <thomas.feuvrier@c-s.fr>
Date: Thu, 29 Jan 2009 14:20:42 +0100
Subject: [PATCH] ENH: Add PCA new testing as example to study PCA capability
in OTB
---
Testing/Code/BasicFilters/CMakeLists.txt | 13 ++
.../BasicFilters/otbBasicFiltersTests11.cxx | 1 +
.../otbImagePCAShapeModelEstimatorTest.cxx | 205 ++++++++++++++++++
3 files changed, 219 insertions(+)
create mode 100755 Testing/Code/BasicFilters/otbImagePCAShapeModelEstimatorTest.cxx
diff --git a/Testing/Code/BasicFilters/CMakeLists.txt b/Testing/Code/BasicFilters/CMakeLists.txt
index 1a3bc72a13..8b6e9da752 100644
--- a/Testing/Code/BasicFilters/CMakeLists.txt
+++ b/Testing/Code/BasicFilters/CMakeLists.txt
@@ -1120,6 +1120,18 @@ ADD_TEST(bfTuPointSetFunctionNew ${BASICFILTERS_TESTS11}
otbPointSetFunctionNew
)
+
+# ------- otbPCAShapeModelEstimatorTest ----------------------------
+ADD_TEST(bfTvImagePCAShapeModelEstimatorTest ${BASICFILTERS_TESTS11}
+ otbImagePCAShapeModelEstimatorTest
+ ${INPUTDATA}/poupees_sub_c1.png
+ ${INPUTDATA}/poupees_sub_c2.png
+ ${INPUTDATA}/poupees_sub_c3.png
+ ${TEMP}/imagePCAShapeModelEstimatorTest_mean.tif
+ ${TEMP}/imagePCAShapeModelEstimatorTest_eigen_vectors1.tif
+ ${TEMP}/imagePCAShapeModelEstimatorTest_eigen_vectors2.tif
+ )
+
#
#ADD_TEST(bfTvCountImageFunction ${BASICFILTERS_TESTS11}
#--compare-ascii ${TOL}
@@ -1309,6 +1321,7 @@ otbPointSetFunctionNew.cxx
#otbCountImageFunctionTest.cxx
#otbCountImageFilterNew.cxx
#otbCountImageFilterTest.cxx
+otbImagePCAShapeModelEstimatorTest.cxx
)
diff --git a/Testing/Code/BasicFilters/otbBasicFiltersTests11.cxx b/Testing/Code/BasicFilters/otbBasicFiltersTests11.cxx
index 2a21aea6f2..7d4000c022 100644
--- a/Testing/Code/BasicFilters/otbBasicFiltersTests11.cxx
+++ b/Testing/Code/BasicFilters/otbBasicFiltersTests11.cxx
@@ -32,4 +32,5 @@ REGISTER_TEST(otbPointSetFunctionNew);
//REGISTER_TEST(otbCountImageFunctionTest);
//REGISTER_TEST(otbCountImageFilterNew);
//REGISTER_TEST(otbCountImageFilterTest);
+REGISTER_TEST(otbImagePCAShapeModelEstimatorTest);
}
diff --git a/Testing/Code/BasicFilters/otbImagePCAShapeModelEstimatorTest.cxx b/Testing/Code/BasicFilters/otbImagePCAShapeModelEstimatorTest.cxx
new file mode 100755
index 0000000000..ac640603ba
--- /dev/null
+++ b/Testing/Code/BasicFilters/otbImagePCAShapeModelEstimatorTest.cxx
@@ -0,0 +1,205 @@
+/*=========================================================================
+
+ Program: Insight Segmentation & Registration Toolkit
+ Module: $RCSfile: itkImagePCAShapeModelEstimatorTest.cxx,v $
+ Language: C++
+ Date: $Date: 2008-02-03 04:05:34 $
+ Version: $Revision: 1.11 $
+
+ Copyright (c) Insight Software Consortium. All rights reserved.
+ See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details.
+
+ This software is distributed WITHOUT ANY WARRANTY; without even
+ the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE. See the above copyright notices for more information.
+
+=========================================================================*/
+#if defined(_MSC_VER)
+#pragma warning ( disable : 4786 )
+#endif
+// Insight classes
+#include "itkImage.h"
+#include "itkVector.h"
+#include "vnl/vnl_matrix_fixed.h"
+#include "vnl/vnl_math.h"
+#include "itkImageRegionIterator.h"
+#include "itkLightProcessObject.h"
+#include "itkTextOutput.h"
+
+#include "otbImageFileReader.h"
+#include "otbImageFileWriter.h"
+
+#include "itkImagePCAShapeModelEstimator.h"
+
+//Data definitions
+#define IMGWIDTH 2
+#define IMGHEIGHT 2
+#define NDIMENSION 2
+#define NUMTRAINIMAGES 3
+#define NUMLARGESTPC 2
+
+// class to support progress feeback
+
+
+class ShowProgressObject
+{
+public:
+ ShowProgressObject(itk::LightProcessObject * o)
+ {m_Process = o;}
+ void ShowProgress()
+ {std::cout << "Progress " << m_Process->GetProgress() << std::endl;}
+ itk::LightProcessObject::Pointer m_Process;
+};
+
+
+int otbImagePCAShapeModelEstimatorTest(int argc, char* argv[] )
+{
+/* const unsigned int numberOfPrincipalComponentsRequired(atoi(argv[1]));
+ const unsigned int numberOfTrainingImages(atoi(argv[2]));
+ std::vector<std::string> imagesfilenames;
+ std::vector<std::string> outputimagesfilenames;
+ int cpt(3);
+ for(; cpt<(numberOfTrainingImages+3) ; cpt++)
+ {
+ imagesfilenames.push_back(argv[cpt]);
+ }
+ int cpt2(cpt);
+ for(; cpt<(numberOfPrincipalComponentsRequired+cpt2) ; cpt++)
+ {
+ outputimagesfilenames.push_back(argv[cpt]);
+ }
+*/
+
+
+ itk::OutputWindow::SetInstance(itk::TextOutput::New().GetPointer());
+
+
+ //------------------------------------------------------
+ //Create 3 simple test images with
+ //------------------------------------------------------
+ typedef itk::Image<double,NDIMENSION> InputImageType;
+ typedef itk::Image<double,NDIMENSION> OutputImageType;
+ typedef
+ itk::ImageRegionIterator< InputImageType > InputImageIterator;
+
+ typedef
+ itk::ImageRegionIterator< OutputImageType > OutputImageIterator;
+
+ typedef otb::ImageFileReader<InputImageType> ReaderType;
+ typedef otb::ImageFileWriter<OutputImageType> WriterType;
+
+ // Instantiating object
+ ReaderType::Pointer reader1 = ReaderType::New();
+ ReaderType::Pointer reader2 = ReaderType::New();
+ ReaderType::Pointer reader3 = ReaderType::New();
+
+ WriterType::Pointer writer1 = WriterType::New();
+ WriterType::Pointer writer2 = WriterType::New();
+ WriterType::Pointer writer3 = WriterType::New();
+
+ reader1->SetFileName(argv[1]);
+ reader2->SetFileName(argv[2]);
+ reader3->SetFileName(argv[3]);
+
+ writer1->SetFileName(argv[4]);
+ writer2->SetFileName(argv[5]);
+ writer3->SetFileName(argv[6]);
+
+ //----------------------------------------------------------------------
+ // Test code for the Shape model estimator
+ //----------------------------------------------------------------------
+
+ //----------------------------------------------------------------------
+ //Set the image model estimator
+ //----------------------------------------------------------------------
+ typedef itk::ImagePCAShapeModelEstimator<InputImageType, OutputImageType>
+ ImagePCAShapeModelEstimatorType;
+
+ ImagePCAShapeModelEstimatorType::Pointer
+ applyPCAShapeEstimator = ImagePCAShapeModelEstimatorType::New();
+
+ //----------------------------------------------------------------------
+ //Set the parameters of the clusterer
+ //----------------------------------------------------------------------
+ applyPCAShapeEstimator->SetNumberOfTrainingImages( NUMTRAINIMAGES );
+ applyPCAShapeEstimator->SetNumberOfPrincipalComponentsRequired( NUMLARGESTPC + 1 );
+ applyPCAShapeEstimator->SetNumberOfPrincipalComponentsRequired( NUMLARGESTPC );
+ applyPCAShapeEstimator->SetInput(0, reader1->GetOutput() );
+ applyPCAShapeEstimator->SetInput(1, reader2->GetOutput() );
+ applyPCAShapeEstimator->SetInput(2, reader3->GetOutput() );
+
+ applyPCAShapeEstimator->Update();
+
+ writer1->SetInput(applyPCAShapeEstimator->GetOutput( 0 ));
+ writer1->Update();
+ writer2->SetInput(applyPCAShapeEstimator->GetOutput( 1 ));
+ writer2->Update();
+ writer3->SetInput(applyPCAShapeEstimator->GetOutput( 2 ));
+ writer3->Update();
+
+ //Test the printself function to increase coverage
+ applyPCAShapeEstimator->Print(std::cout);
+
+ //Exercise TypeMacro in superclass
+ typedef ImagePCAShapeModelEstimatorType::Superclass GenericEstimatorType;
+ std::cout << applyPCAShapeEstimator->GenericEstimatorType::GetNameOfClass() << std::endl;
+
+ //Print out the number of training images and the number of principal
+ //components
+ std::cout << "The number of training images are: " <<
+ applyPCAShapeEstimator->GetNumberOfTrainingImages() << std::endl;
+
+ std::cout << "The number of principal components desired are: " <<
+ applyPCAShapeEstimator->GetNumberOfPrincipalComponentsRequired() << std::endl;
+
+ //Print the eigen vectors
+ vnl_vector<double> eigenValues =
+ applyPCAShapeEstimator->GetEigenValues();
+ unsigned int numEigVal = eigenValues.size();
+ std::cout << "Number of returned eign-values: " << numEigVal << std::endl;
+
+ std::cout << "The " <<
+ applyPCAShapeEstimator->GetNumberOfPrincipalComponentsRequired() <<
+ " largest eigen values are:" << std::endl;
+
+ for(unsigned int i= 0; i< vnl_math_min( numEigVal, (unsigned int)NUMLARGESTPC ); i++ )
+ {
+ std::cout << eigenValues[ i ] << std::endl;
+ }
+ std::cout << "" << std::endl;
+ std::cout << "" << std::endl;
+
+
+ //Print the MeanImage
+ OutputImageType::Pointer outImage = applyPCAShapeEstimator->GetOutput( 0 );
+ OutputImageIterator outImageIt( outImage, outImage->GetBufferedRegion() );
+ outImageIt.GoToBegin();
+
+ std::cout << "The mean image is:" << std::endl;
+ while(!outImageIt.IsAtEnd() )
+ {
+ std::cout << (double)(outImageIt.Get()) << ";" << std::endl;
+ ++outImageIt;
+ }
+ std::cout << " " << std::endl;
+
+ //Print the largest two eigen vectors
+ for (unsigned int j=1; j< NUMLARGESTPC + 1; j++ )
+ {
+ OutputImageType::Pointer outImage2 = applyPCAShapeEstimator->GetOutput( j );
+ OutputImageIterator outImage2It( outImage2, outImage2->GetBufferedRegion() );
+ outImage2It.GoToBegin();
+
+ std::cout << "" << std::endl;
+ std::cout << "The eigen vector number: " << j << " is:" << std::endl;
+ while(!outImage2It.IsAtEnd() )
+ {
+ std::cout << (double) (outImage2It.Get()) << ";" << std::endl;
+ ++outImage2It;
+ }
+ std::cout << " " << std::endl;
+
+ }
+
+ return EXIT_SUCCESS;
+}
--
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