DOC: Add all examples for dimension reduction

Examples/DimensionReduction/CMakeLists.txt

@@ -9,6 +9,15 @@ IF(CMAKE_COMPILER_IS_GNUCXX)
   )
 ENDIF(CMAKE_COMPILER_IS_GNUCXX)
 
+ADD_EXECUTABLE(NAPCAExample NAPCAExample.cxx )
+TARGET_LINK_LIBRARIES(NAPCAExample OTBCommon OTBIO OTBBasicFilters)
+
+ADD_EXECUTABLE(MNFExample MNFExample.cxx )
+TARGET_LINK_LIBRARIES(MNFExample OTBCommon OTBIO OTBBasicFilters)
+
+ADD_EXECUTABLE(ICAExample ICAExample.cxx )
+TARGET_LINK_LIBRARIES(ICAExample OTBCommon OTBIO OTBBasicFilters)
+
 ADD_EXECUTABLE(PCAExample PCAExample.cxx )
 TARGET_LINK_LIBRARIES(PCAExample OTBCommon OTBIO OTBBasicFilters)
 

Examples/DimensionReduction/ICAExample.cxx

+/*=========================================================================
+
+  Program:   ORFEO Toolbox
+  Language:  C++
+  Date:      $Date$
+  Version:   $Revision$
+
+
+  Copyright (c) Centre National d'Etudes Spatiales. All rights reserved.
+  See OTBCopyright.txt 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.
+
+=========================================================================*/
+#include "otbImage.h"
+#include "otbVectorImage.h"
+#include "otbImageFileReader.h"
+#include "otbImageFileWriter.h"
+#include "otbPrintableImageFilter.h"
+
+//  Software Guide : BeginCommandLineArgs
+//    INPUTS: {wv2_cannes_8bands.tif}
+//    OUTPUTS: {FastICAOutput.tif}, {InverseFastICAOutput.tif}, {FastICA-input-pretty.png}, {FastICA-output-pretty.png}, {FastICA-invoutput-pretty.png}
+//    8 20 1.
+//  Software Guide : EndCommandLineArgs
+
+// Software Guide : BeginLatex
+//
+// This example illustrates the use of the
+// \doxygen{otb}{FastICAImageFilter}.
+// This filter computes a Principal Component Analysis using an
+// efficient method based on the inner product in order to compute the
+// covariance matrix.
+//
+// The first step required to use this filter is to include its header file.
+//
+// Software Guide : EndLatex
+
+// Software Guide : BeginCodeSnippet
+#include "otbFastICAImageFilter.h"
+// Software Guide : EndCodeSnippet
+
+
+int main(int argc, char* argv[])
+{
+  typedef double PixelType;
+  const unsigned int Dimension = 2;
+  const char *       inputFileName = argv[1];
+  const char *       outputFilename = argv[2];
+  const char *       outputInverseFilename = argv[3];
+  const unsigned int numberOfPrincipalComponentsRequired(atoi(argv[7]));
+  const char *       inpretty = argv[4];
+  const char *       outpretty = argv[5];
+  const char *       invoutpretty = argv[6];
+  unsigned int numIterations = atoi(argv[7]);
+  double mu = atof(argv[8]);
+
+  // Software Guide : BeginLatex
+  //
+  // We start by defining the types for the images and the reader and
+  // the writer. We choose to work with a \doxygen{otb}{VectorImage},
+  // since we will produce a multi-channel image (the principal
+  // components) from a multi-channel input image.
+  //
+  // Software Guide : EndLatex
+
+  // Software Guide : BeginCodeSnippet
+  typedef otb::VectorImage<PixelType, Dimension> ImageType;
+  typedef otb::ImageFileReader<ImageType>        ReaderType;
+  typedef otb::ImageFileWriter<ImageType>        WriterType;
+  // Software Guide : EndCodeSnippet
+  // Software Guide : BeginLatex
+  //
+  // We instantiate now the image reader and we set the image file name.
+  //
+  // Software Guide : EndLatex
+
+  // Software Guide : BeginCodeSnippet
+  ReaderType::Pointer reader     = ReaderType::New();
+  reader->SetFileName(inputFileName);
+  // Software Guide : EndCodeSnippet
+
+  // Software Guide : BeginLatex
+  //
+  // We define the type for the filter. It is templated over the input
+  // and the output image types and also the transformation direction. The
+  // internal structure of this filter is a filter-to-filter like structure.
+  // We can now the instantiate the filter.
+  //
+  // Software Guide : EndLatex
+
+  // Software Guide : BeginCodeSnippet
+  typedef otb::FastICAImageFilter<ImageType, ImageType,
+                                otb::Transform::FORWARD> FastICAFilterType;
+  FastICAFilterType::Pointer FastICAfilter     = FastICAFilterType::New();
+  // Software Guide : EndCodeSnippet
+  
+  // Software Guide : BeginLatex
+  //
+  // We then set the number of principal
+  // components required as output. We can choose to get less PCs than
+  // the number of input bands.
+  //
+  // Software Guide : EndLatex
+
+  // Software Guide : BeginCodeSnippet
+  FastICAfilter->SetNumberOfPrincipalComponentsRequired(
+    numberOfPrincipalComponentsRequired);
+  // Software Guide : EndCodeSnippet
+
+  // Software Guide : BeginLatex
+  //
+  // We set the number of iterations of the ICA algorithm.
+  //
+  // Software Guide : EndLatex
+
+  // Software Guide : BeginCodeSnippet
+  FastICAfilter->SetNumberOfIterations(numIterations);
+  // Software Guide : EndCodeSnippet
+
+  // Software Guide : BeginLatex
+  //
+  // We also set the $\mu$ parameter.
+  //
+  // Software Guide : EndLatex
+
+  // Software Guide : BeginCodeSnippet
+  FastICAfilter->SetMu( mu );
+  // Software Guide : EndCodeSnippet
+  
+  // Software Guide : BeginLatex
+  //
+  // We now instantiate the writer and set the file name for the
+  // output image.
+  //
+  // Software Guide : EndLatex
+
+  // Software Guide : BeginCodeSnippet
+  WriterType::Pointer writer     = WriterType::New();
+  writer->SetFileName(outputFilename);
+  // Software Guide : EndCodeSnippet
+  // Software Guide : BeginLatex
+  //
+  // We finally plug the pipeline and trigger the PCA computation with
+  // the method \code{Update()} of the writer.
+  //
+  // Software Guide : EndLatex
+
+  // Software Guide : BeginCodeSnippet
+  FastICAfilter->SetInput(reader->GetOutput());
+  writer->SetInput(FastICAfilter->GetOutput());
+
+  writer->Update();
+  // Software Guide : EndCodeSnippet
+
+  // Software Guide : BeginLatex
+  //
+  // \doxygen{otb}{FastICAImageFilter} allows also to compute inverse
+  // transformation from PCA coefficients. In reverse mode, the
+  // covariance matrix or the transformation matrix
+  // (which may not be square) has to be given.
+  //
+  // Software Guide : EndLatex
+  
+  // Software Guide : BeginCodeSnippet
+  typedef otb::FastICAImageFilter< ImageType, ImageType,
+                                 otb::Transform::INVERSE > InvFastICAFilterType;
+  InvFastICAFilterType::Pointer invFilter = InvFastICAFilterType::New();
+  
+  invFilter->SetMeanValues( FastICAfilter->GetMeanValues() );
+  invFilter->SetStdDevValues( FastICAfilter->GetStdDevValues() );
+  invFilter->SetTransformationMatrix( FastICAfilter->GetTransformationMatrix() );
+  invFilter->SetPCATransformationMatrix( FastICAfilter->GetPCATransformationMatrix() );
+  invFilter->SetInput(FastICAfilter->GetOutput());
+    
+  WriterType::Pointer invWriter = WriterType::New();
+  invWriter->SetFileName(outputInverseFilename );
+  invWriter->SetInput(invFilter->GetOutput() );
+
+  invWriter->Update();
+  // Software Guide : EndCodeSnippet
+  
+  //  Software Guide : BeginLatex
+  // Figure~\ref{fig:FastICA_FILTER} shows the result of applying forward
+  // and reverse FastICA transformation to a 8 bands Wordlview2 image.
+  // \begin{figure}
+  // \center
+  // \includegraphics[width=0.32\textwidth]{FastICA-input-pretty.eps}
+  // \includegraphics[width=0.32\textwidth]{FastICA-output-pretty.eps}
+  // \includegraphics[width=0.32\textwidth]{FastICA-invoutput-pretty.eps}
+  // \itkcaption[PCA Filter (forward trasnformation)]{Result of applying the
+  // \doxygen{otb}{FastICAImageFilter} to an image. From left
+  // to right:
+  // original image, color composition with first three principal
+  // components and output of the
+  // inverse mode (the input RGB image).}
+  // \label{fig:FastICA_FILTER}
+  // \end{figure}
+  //
+  //  Software Guide : EndLatex
+
+  // This is for rendering in software guide
+  typedef otb::PrintableImageFilter<ImageType,ImageType> PrintFilterType;
+  typedef PrintFilterType::OutputImageType               VisuImageType;
+  typedef otb::ImageFileWriter<VisuImageType>            VisuWriterType;
+
+  PrintFilterType::Pointer inputPrintFilter = PrintFilterType::New();
+  PrintFilterType::Pointer outputPrintFilter = PrintFilterType::New();
+  PrintFilterType::Pointer invertOutputPrintFilter = PrintFilterType::New();
+  VisuWriterType::Pointer inputVisuWriter = VisuWriterType::New();
+  VisuWriterType::Pointer outputVisuWriter = VisuWriterType::New();
+  VisuWriterType::Pointer invertOutputVisuWriter = VisuWriterType::New();
+
+  inputPrintFilter->SetInput(reader->GetOutput());
+  inputPrintFilter->SetChannel(5);
+  inputPrintFilter->SetChannel(3);
+  inputPrintFilter->SetChannel(2);
+  outputPrintFilter->SetInput(FastICAfilter->GetOutput());
+  outputPrintFilter->SetChannel(1);
+  outputPrintFilter->SetChannel(2);
+  outputPrintFilter->SetChannel(3);
+  invertOutputPrintFilter->SetInput(invFilter->GetOutput());
+  invertOutputPrintFilter->SetChannel(5);
+  invertOutputPrintFilter->SetChannel(3);
+  invertOutputPrintFilter->SetChannel(2);
+
+  inputVisuWriter->SetInput(inputPrintFilter->GetOutput());
+  outputVisuWriter->SetInput(outputPrintFilter->GetOutput());
+  invertOutputVisuWriter->SetInput(invertOutputPrintFilter->GetOutput());
+
+  inputVisuWriter->SetFileName(inpretty);
+  outputVisuWriter->SetFileName(outpretty);
+  invertOutputVisuWriter->SetFileName(invoutpretty);
+
+  inputVisuWriter->Update();
+  outputVisuWriter->Update();
+  invertOutputVisuWriter->Update();
+
+  return EXIT_SUCCESS;
+}

Examples/DimensionReduction/MNFExample.cxx

+/*=========================================================================
+
+  Program:   ORFEO Toolbox
+  Language:  C++
+  Date:      $Date$
+  Version:   $Revision$
+
+
+  Copyright (c) Centre National d'Etudes Spatiales. All rights reserved.
+  See OTBCopyright.txt 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.
+
+=========================================================================*/
+#include "otbImage.h"
+#include "otbVectorImage.h"
+#include "otbImageFileReader.h"
+#include "otbImageFileWriter.h"
+#include "otbPrintableImageFilter.h"
+
+//  Software Guide : BeginCommandLineArgs
+//    INPUTS: {wv2_cannes_8bands.tif}
+//    OUTPUTS: {MNFOutput.tif}, {InverseMNFOutput.tif}, {MNF-input-pretty.png}, {MNF-output-pretty.png}, {MNF-invoutput-pretty.png}
+//    8 1 1
+//  Software Guide : EndCommandLineArgs
+
+// Software Guide : BeginLatex
+//
+// This example illustrates the use of the
+// \doxygen{otb}{MNFImageFilter}.
+// This filter computes a Principal Component Analysis using an
+// efficient method based on the inner product in order to compute the
+// covariance matrix.
+//
+// The first step required to use this filter is to include its header file.
+//
+// Software Guide : EndLatex
+
+// Software Guide : BeginCodeSnippet
+#include "otbMNFImageFilter.h"
+// Software Guide : EndCodeSnippet
+
+// Software Guide : BeginLatex
+//
+// We also need to include the header of the noise filter.
+//
+// SoftwareGuide : EndLatex
+
+// Software Guide : BeginCodeSnippet
+#include "otbLocalActivityVectorImageFilter.h"
+// Software Guide : EndCodeSnippet
+
+
+int main(int argc, char* argv[])
+{
+  typedef double PixelType;
+  const unsigned int Dimension = 2;
+  const char *       inputFileName = argv[1];
+  const char *       outputFilename = argv[2];
+  const char *       outputInverseFilename = argv[3];
+  const unsigned int numberOfPrincipalComponentsRequired(atoi(argv[7]));
+  const char *       inpretty = argv[4];
+  const char *       outpretty = argv[5];
+  const char *       invoutpretty = argv[6];
+  unsigned int vradius = atoi(argv[7]);
+  bool normalization = atoi(argv[8]);
+
+  // Software Guide : BeginLatex
+  //
+  // We start by defining the types for the images and the reader and
+  // the writer. We choose to work with a \doxygen{otb}{VectorImage},
+  // since we will produce a multi-channel image (the principal
+  // components) from a multi-channel input image.
+  //
+  // Software Guide : EndLatex
+
+  // Software Guide : BeginCodeSnippet
+  typedef otb::VectorImage<PixelType, Dimension> ImageType;
+  typedef otb::ImageFileReader<ImageType>        ReaderType;
+  typedef otb::ImageFileWriter<ImageType>        WriterType;
+  // Software Guide : EndCodeSnippet
+  // Software Guide : BeginLatex
+  //
+  // We instantiate now the image reader and we set the image file name.
+  //
+  // Software Guide : EndLatex
+
+  // Software Guide : BeginCodeSnippet
+  ReaderType::Pointer reader     = ReaderType::New();
+  reader->SetFileName(inputFileName);
+  // Software Guide : EndCodeSnippet
+
+  // Software Guide : BeginLatex
+  //
+  // We define the type of the noise filter.
+  //
+  // Software Guide : EndLatex
+
+  // SoftwareGuide : BeginCodeSnippet  
+  typedef otb::LocalActivityVectorImageFilter< ImageType, ImageType > NoiseFilterType;
+  // SoftwareGuide : EndCodeSnippet
+
+
+  // Software Guide : BeginLatex
+  //
+  // We define the type for the filter. It is templated over the input
+  // and the output image types and also the transformation direction. The
+  // internal structure of this filter is a filter-to-filter like structure.
+  // We can now the instantiate the filter.
+  //
+  // Software Guide : EndLatex
+
+  // Software Guide : BeginCodeSnippet
+  typedef otb::MNFImageFilter<ImageType, ImageType,
+                                NoiseFilterType,
+                                otb::Transform::FORWARD> MNFFilterType;
+  MNFFilterType::Pointer MNFfilter     = MNFFilterType::New();
+  // Software Guide : EndCodeSnippet
+  
+  // Software Guide : BeginLatex
+  //
+  // We then set the number of principal
+  // components required as output. We can choose to get less PCs than
+  // the number of input bands.
+  //
+  // Software Guide : EndLatex
+
+  // Software Guide : BeginCodeSnippet
+  MNFfilter->SetNumberOfPrincipalComponentsRequired(
+    numberOfPrincipalComponentsRequired);
+  // Software Guide : EndCodeSnippet
+
+  // Software Guide : BeginLatex
+  //
+  // We set the radius of the sliding window for noise estimation.
+  //
+  // Software Guide : EndLatex
+
+  // Software Guide : BeginCodeSnippet
+  NoiseFilterType::RadiusType radius = {{ vradius, vradius }};
+  MNFfilter->GetNoiseImageFilter()->SetRadius(radius);
+  // Software Guide : EndCodeSnippet
+
+  // Software Guide : BeginLatex
+  //
+  // Last, we can activate normalisation.
+  //
+  // Software Guide : EndLatex
+
+  // Software Guide : BeginCodeSnippet
+  MNFfilter->SetUseNormalization( normalization );
+  // Software Guide : EndCodeSnippet
+  
+  // Software Guide : BeginLatex
+  //
+  // We now instantiate the writer and set the file name for the
+  // output image.
+  //
+  // Software Guide : EndLatex
+
+  // Software Guide : BeginCodeSnippet
+  WriterType::Pointer writer     = WriterType::New();
+  writer->SetFileName(outputFilename);
+  // Software Guide : EndCodeSnippet
+  // Software Guide : BeginLatex
+  //
+  // We finally plug the pipeline and trigger the PCA computation with
+  // the method \code{Update()} of the writer.
+  //
+  // Software Guide : EndLatex
+
+  // Software Guide : BeginCodeSnippet
+  MNFfilter->SetInput(reader->GetOutput());
+  writer->SetInput(MNFfilter->GetOutput());
+
+  writer->Update();
+  // Software Guide : EndCodeSnippet
+
+  // Software Guide : BeginLatex
+  //
+  // \doxygen{otb}{MNFImageFilter} allows also to compute inverse
+  // transformation from PCA coefficients. In reverse mode, the
+  // covariance matrix or the transformation matrix
+  // (which may not be square) has to be given.
+  //
+  // Software Guide : EndLatex
+  
+  // Software Guide : BeginCodeSnippet
+  typedef otb::MNFImageFilter< ImageType, ImageType,
+                                 NoiseFilterType,
+                                 otb::Transform::INVERSE > InvMNFFilterType;
+  InvMNFFilterType::Pointer invFilter = InvMNFFilterType::New();
+  
+  invFilter->SetMeanValues( MNFfilter->GetMeanValues() );
+  if ( normalization )
+    invFilter->SetStdDevValues( MNFfilter->GetStdDevValues() );
+  invFilter->SetTransformationMatrix( MNFfilter->GetTransformationMatrix() );
+  invFilter->SetInput(MNFfilter->GetOutput());
+    
+  WriterType::Pointer invWriter = WriterType::New();
+  invWriter->SetFileName(outputInverseFilename );
+  invWriter->SetInput(invFilter->GetOutput() );
+
+  invWriter->Update();
+  // Software Guide : EndCodeSnippet
+  
+  //  Software Guide : BeginLatex
+  // Figure~\ref{fig:MNF_FILTER} shows the result of applying forward
+  // and reverse MNF transformation to a 8 bands Wordlview2 image.
+  // \begin{figure}
+  // \center
+  // \includegraphics[width=0.32\textwidth]{MNF-input-pretty.eps}
+  // \includegraphics[width=0.32\textwidth]{MNF-output-pretty.eps}
+  // \includegraphics[width=0.32\textwidth]{MNF-invoutput-pretty.eps}
+  // \itkcaption[PCA Filter (forward trasnformation)]{Result of applying the
+  // \doxygen{otb}{MNFImageFilter} to an image. From left
+  // to right:
+  // original image, color composition with first three principal
+  // components and output of the
+  // inverse mode (the input RGB image).}
+  // \label{fig:MNF_FILTER}
+  // \end{figure}
+  //
+  //  Software Guide : EndLatex
+
+  // This is for rendering in software guide
+  typedef otb::PrintableImageFilter<ImageType,ImageType> PrintFilterType;
+  typedef PrintFilterType::OutputImageType               VisuImageType;
+  typedef otb::ImageFileWriter<VisuImageType>            VisuWriterType;
+
+  PrintFilterType::Pointer inputPrintFilter = PrintFilterType::New();
+  PrintFilterType::Pointer outputPrintFilter = PrintFilterType::New();
+  PrintFilterType::Pointer invertOutputPrintFilter = PrintFilterType::New();
+  VisuWriterType::Pointer inputVisuWriter = VisuWriterType::New();
+  VisuWriterType::Pointer outputVisuWriter = VisuWriterType::New();
+  VisuWriterType::Pointer invertOutputVisuWriter = VisuWriterType::New();
+
+  inputPrintFilter->SetInput(reader->GetOutput());
+  inputPrintFilter->SetChannel(5);
+  inputPrintFilter->SetChannel(3);
+  inputPrintFilter->SetChannel(2);
+  outputPrintFilter->SetInput(MNFfilter->GetOutput());
+  outputPrintFilter->SetChannel(1);
+  outputPrintFilter->SetChannel(2);
+  outputPrintFilter->SetChannel(3);
+  invertOutputPrintFilter->SetInput(invFilter->GetOutput());
+  invertOutputPrintFilter->SetChannel(5);
+  invertOutputPrintFilter->SetChannel(3);
+  invertOutputPrintFilter->SetChannel(2);
+
+  inputVisuWriter->SetInput(inputPrintFilter->GetOutput());
+  outputVisuWriter->SetInput(outputPrintFilter->GetOutput());
+  invertOutputVisuWriter->SetInput(invertOutputPrintFilter->GetOutput());
+
+  inputVisuWriter->SetFileName(inpretty);
+  outputVisuWriter->SetFileName(outpretty);
+  invertOutputVisuWriter->SetFileName(invoutpretty);
+
+  inputVisuWriter->Update();
+  outputVisuWriter->Update();
+  invertOutputVisuWriter->Update();
+
+  return EXIT_SUCCESS;
+}

Examples/DimensionReduction/NAPCAExample.cxx

+/*=========================================================================
+
+  Program:   ORFEO Toolbox
+  Language:  C++
+  Date:      $Date$
+  Version:   $Revision$
+
+
+  Copyright (c) Centre National d'Etudes Spatiales. All rights reserved.
+  See OTBCopyright.txt 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.
+
+=========================================================================*/
+#include "otbImage.h"
+#include "otbVectorImage.h"
+#include "otbImageFileReader.h"
+#include "otbImageFileWriter.h"
+#include "otbPrintableImageFilter.h"
+
+//  Software Guide : BeginCommandLineArgs
+//    INPUTS: {wv2_cannes_8bands.tif}
+//    OUTPUTS: {NAPCAOutput.tif}, {InverseNAPCAOutput.tif}, {napca-input-pretty.png}, {napca-output-pretty.png}, {napca-invoutput-pretty.png}
+//    8 1 1
+//  Software Guide : EndCommandLineArgs
+
+// Software Guide : BeginLatex
+//
+// This example illustrates the use of the
+// \doxygen{otb}{NAPCAImageFilter}.
+// This filter computes a Principal Component Analysis using an
+// efficient method based on the inner product in order to compute the
+// covariance matrix.
+//
+// The first step required to use this filter is to include its header file.
+//
+// Software Guide : EndLatex
+
+// Software Guide : BeginCodeSnippet
+#include "otbNAPCAImageFilter.h"
+// Software Guide : EndCodeSnippet
+
+// Software Guide : BeginLatex
+//
+// We also need to include the header of the noise filter.
+//
+// SoftwareGuide : EndLatex
+
+// Software Guide : BeginCodeSnippet
+#include "otbLocalActivityVectorImageFilter.h"
+// Software Guide : EndCodeSnippet
+
+
+int main(int argc, char* argv[])
+{
+  typedef double PixelType;
+  const unsigned int Dimension = 2;
+  const char *       inputFileName = argv[1];
+  const char *       outputFilename = argv[2];
+  const char *       outputInverseFilename = argv[3];
+  const unsigned int numberOfPrincipalComponentsRequired(atoi(argv[7]));
+  const char *       inpretty = argv[4];
+  const char *       outpretty = argv[5];
+  const char *       invoutpretty = argv[6];
+  unsigned int vradius = atoi(argv[7]);
+  bool normalization = atoi(argv[8]);
+
+  // Software Guide : BeginLatex
+  //
+  // We start by defining the types for the images and the reader and
+  // the writer. We choose to work with a \doxygen{otb}{VectorImage},
+  // since we will produce a multi-channel image (the principal
+  // components) from a multi-channel input image.
+  //
+  // Software Guide : EndLatex
+
+  // Software Guide : BeginCodeSnippet
+  typedef otb::VectorImage<PixelType, Dimension> ImageType;
+  typedef otb::ImageFileReader<ImageType>        ReaderType;
+  typedef otb::ImageFileWriter<ImageType>        WriterType;
+  // Software Guide : EndCodeSnippet
+  // Software Guide : BeginLatex
+  //
+  // We instantiate now the image reader and we set the image file name.
+  //
+  // Software Guide : EndLatex
+
+  // Software Guide : BeginCodeSnippet
+  ReaderType::Pointer reader     = ReaderType::New();
+  reader->SetFileName(inputFileName);
+  // Software Guide : EndCodeSnippet
+
+  // Software Guide : BeginLatex
+  //
+  // We define the type of the noise filter.
+  //
+  // Software Guide : EndLatex
+
+  // SoftwareGuide : BeginCodeSnippet  
+  typedef otb::LocalActivityVectorImageFilter< ImageType, ImageType > NoiseFilterType;
+  // SoftwareGuide : EndCodeSnippet
+
+
+  // Software Guide : BeginLatex
+  //
+  // We define the type for the filter. It is templated over the input
+  // and the output image types and also the transformation direction. The
+  // internal structure of this filter is a filter-to-filter like structure.
+  // We can now the instantiate the filter.
+  //
+  // Software Guide : EndLatex
+
+  // Software Guide : BeginCodeSnippet
+  typedef otb::NAPCAImageFilter<ImageType, ImageType,
+                                NoiseFilterType,
+                                otb::Transform::FORWARD> NAPCAFilterType;
+  NAPCAFilterType::Pointer napcafilter     = NAPCAFilterType::New();
+  // Software Guide : EndCodeSnippet
+  
+  // Software Guide : BeginLatex
+  //
+  // We then set the number of principal
+  // components required as output. We can choose to get less PCs than
+  // the number of input bands.
+  //
+  // Software Guide : EndLatex
+
+  // Software Guide : BeginCodeSnippet
+  napcafilter->SetNumberOfPrincipalComponentsRequired(
+    numberOfPrincipalComponentsRequired);
+  // Software Guide : EndCodeSnippet
+
+  // Software Guide : BeginLatex
+  //
+  // We set the radius of the sliding window for noise estimation.
+  //
+  // Software Guide : EndLatex
+
+  // Software Guide : BeginCodeSnippet
+  NoiseFilterType::RadiusType radius = {{ vradius, vradius }};
+  napcafilter->GetNoiseImageFilter()->SetRadius(radius);
+  // Software Guide : EndCodeSnippet
+
+  // Software Guide : BeginLatex
+  //
+  // Last, we can activate normalisation.
+  //
+  // Software Guide : EndLatex
+
+  // Software Guide : BeginCodeSnippet
+  napcafilter->SetUseNormalization( normalization );
+  // Software Guide : EndCodeSnippet
+  
+  // Software Guide : BeginLatex
+  //
+  // We now instantiate the writer and set the file name for the
+  // output image.
+  //
+  // Software Guide : EndLatex
+
+  // Software Guide : BeginCodeSnippet
+  WriterType::Pointer writer     = WriterType::New();
+  writer->SetFileName(outputFilename);
+  // Software Guide : EndCodeSnippet
+  // Software Guide : BeginLatex
+  //
+  // We finally plug the pipeline and trigger the PCA computation with
+  // the method \code{Update()} of the writer.
+  //
+  // Software Guide : EndLatex
+
+  // Software Guide : BeginCodeSnippet
+  napcafilter->SetInput(reader->GetOutput());
+  writer->SetInput(napcafilter->GetOutput());
+
+  writer->Update();
+  // Software Guide : EndCodeSnippet
+
+  // Software Guide : BeginLatex
+  //
+  // \doxygen{otb}{NAPCAImageFilter} allows also to compute inverse
+  // transformation from PCA coefficients. In reverse mode, the
+  // covariance matrix or the transformation matrix
+  // (which may not be square) has to be given.
+  //
+  // Software Guide : EndLatex
+  
+  // Software Guide : BeginCodeSnippet
+  typedef otb::NAPCAImageFilter< ImageType, ImageType,
+                                 NoiseFilterType,
+                                 otb::Transform::INVERSE > InvNAPCAFilterType;
+  InvNAPCAFilterType::Pointer invFilter = InvNAPCAFilterType::New();
+  
+  invFilter->SetMeanValues( napcafilter->GetMeanValues() );
+  if ( normalization )
+    invFilter->SetStdDevValues( napcafilter->GetStdDevValues() );
+  invFilter->SetTransformationMatrix( napcafilter->GetTransformationMatrix() );
+  invFilter->SetInput(napcafilter->GetOutput());
+    
+  WriterType::Pointer invWriter = WriterType::New();
+  invWriter->SetFileName(outputInverseFilename );
+  invWriter->SetInput(invFilter->GetOutput() );
+
+  invWriter->Update();
+  // Software Guide : EndCodeSnippet
+  
+  //  Software Guide : BeginLatex
+  // Figure~\ref{fig:NAPCA_FILTER} shows the result of applying forward
+  // and reverse NAPCA transformation to a 8 bands Wordlview2 image.
+  // \begin{figure}
+  // \center
+  // \includegraphics[width=0.32\textwidth]{napca-input-pretty.eps}
+  // \includegraphics[width=0.32\textwidth]{napca-output-pretty.eps}
+  // \includegraphics[width=0.32\textwidth]{napca-invoutput-pretty.eps}
+  // \itkcaption[PCA Filter (forward trasnformation)]{Result of applying the
+  // \doxygen{otb}{NAPCAImageFilter} to an image. From left
+  // to right:
+  // original image, color composition with first three principal
+  // components and output of the
+  // inverse mode (the input RGB image).}
+  // \label{fig:PCNAA_FILTER}
+  // \end{figure}
+  //
+  //  Software Guide : EndLatex
+
+  // This is for rendering in software guide
+  typedef otb::PrintableImageFilter<ImageType,ImageType> PrintFilterType;
+  typedef PrintFilterType::OutputImageType               VisuImageType;
+  typedef otb::ImageFileWriter<VisuImageType>            VisuWriterType;
+
+  PrintFilterType::Pointer inputPrintFilter = PrintFilterType::New();
+  PrintFilterType::Pointer outputPrintFilter = PrintFilterType::New();
+  PrintFilterType::Pointer invertOutputPrintFilter = PrintFilterType::New();
+  VisuWriterType::Pointer inputVisuWriter = VisuWriterType::New();
+  VisuWriterType::Pointer outputVisuWriter = VisuWriterType::New();
+  VisuWriterType::Pointer invertOutputVisuWriter = VisuWriterType::New();
+
+  inputPrintFilter->SetInput(reader->GetOutput());
+  inputPrintFilter->SetChannel(5);
+  inputPrintFilter->SetChannel(3);
+  inputPrintFilter->SetChannel(2);
+  outputPrintFilter->SetInput(napcafilter->GetOutput());
+  outputPrintFilter->SetChannel(1);
+  outputPrintFilter->SetChannel(2);
+  outputPrintFilter->SetChannel(3);
+  invertOutputPrintFilter->SetInput(invFilter->GetOutput());
+  invertOutputPrintFilter->SetChannel(5);
+  invertOutputPrintFilter->SetChannel(3);
+  invertOutputPrintFilter->SetChannel(2);
+
+  inputVisuWriter->SetInput(inputPrintFilter->GetOutput());
+  outputVisuWriter->SetInput(outputPrintFilter->GetOutput());
+  invertOutputVisuWriter->SetInput(invertOutputPrintFilter->GetOutput());
+
+  inputVisuWriter->SetFileName(inpretty);
+  outputVisuWriter->SetFileName(outpretty);
+  invertOutputVisuWriter->SetFileName(invoutpretty);
+
+  inputVisuWriter->Update();
+  outputVisuWriter->Update();
+  invertOutputVisuWriter->Update();
+
+  return EXIT_SUCCESS;
+}

Examples/DimensionReduction/PCAExample.cxx

@@ -19,14 +19,12 @@
 #include "otbVectorImage.h"
 #include "otbImageFileReader.h"
 #include "otbImageFileWriter.h"
-#include "otbMultiToMonoChannelExtractROI.h"
-#include "itkRescaleIntensityImageFilter.h"
-#include "otbVectorRescaleIntensityImageFilter.h"
+#include "otbPrintableImageFilter.h"
 
 //  Software Guide : BeginCommandLineArgs
-//    INPUTS: {ROI_QB_MUL_1.png}
-//    OUTPUTS: {PCAOutput.tif}, {InversePCAOutput.tif}, {InversePCAOutput1.png}, {PCAOutput1.png}, {PCAOutput2.png}, {PCAOutput3.png}
-//    3
+//    INPUTS: {wv2_cannes_8bands.tif}
+//    OUTPUTS: {PCAOutput.tif}, {InversePCAOutput.tif}, {input-pretty.png}, {output-pretty.png}, {invoutput-pretty.png}
+//    8
 //  Software Guide : EndCommandLineArgs
 
 // Software Guide : BeginLatex
@@ -52,7 +50,11 @@ int main(int argc, char* argv[])
   const char *       inputFileName = argv[1];
   const char *       outputFilename = argv[2];
   const char *       outputInverseFilename = argv[3];
-  const unsigned int numberOfPrincipalComponentsRequired(atoi(argv[8]));
+  const unsigned int numberOfPrincipalComponentsRequired(atoi(argv[7]));
+  const char *       inpretty = argv[4];
+  const char *       outpretty = argv[5];
+  const char *       invoutpretty = argv[6];
+
 
   // Software Guide : BeginLatex
   //
@@ -155,75 +157,59 @@ int main(int argc, char* argv[])
   
   //  Software Guide : BeginLatex
   // Figure~\ref{fig:PCA_FILTER} shows the result of applying forward
-  // and reverse PCA transformation to a 3 band RGB image.
+  // and reverse PCA transformation to a 8 bands Wordlview2 image.
   // \begin{figure}
   // \center
-  // \includegraphics[width=0.25\textwidth]{ROI_QB_MUL_1.eps}
-  // \includegraphics[width=0.25\textwidth]{PCAOutput1.eps}
-  // \includegraphics[width=0.25\textwidth]{PCAOutput2.eps}
-  // \includegraphics[width=0.25\textwidth]{PCAOutput3.eps}
-  // \includegraphics[width=0.25\textwidth]{InversePCAOutput1.eps}
+  // \includegraphics[width=0.32\textwidth]{input-pretty.eps}
+  // \includegraphics[width=0.32\textwidth]{output-pretty.eps}
+  // \includegraphics[width=0.32\textwidth]{invoutput-pretty.eps}
   // \itkcaption[PCA Filter (forward trasnformation)]{Result of applying the
   // \doxygen{otb}{PCAImageFilter} to an image. From left
-  // to right and top to bottom:
-  // original image, first PC, second PC, third PC and output of the
+  // to right:
+  // original image, color composition with first three principal
+  // components and output of the
   // inverse mode (the input RGB image).}
   // \label{fig:PCA_FILTER}
   // \end{figure}
   //
   //  Software Guide : EndLatex
 
-  typedef otb::Image<PixelType, Dimension> MonoImageType;
-
-  typedef otb::MultiToMonoChannelExtractROI<PixelType, PixelType>
-  ExtractROIFilterType;
-
-  typedef otb::Image<unsigned char, 2>                OutputImageType;
-  typedef otb::VectorImage<unsigned char, 2>          OutputPrettyImageType;
-  typedef otb::ImageFileWriter<OutputImageType>       WriterType2;
-  typedef otb::ImageFileWriter<OutputPrettyImageType> WriterType3;
-  
-  typedef itk::RescaleIntensityImageFilter<MonoImageType,
-                                           OutputImageType> RescalerType;
-  
-  typedef otb::VectorRescaleIntensityImageFilter<ImageType,
-                                                 OutputPrettyImageType> RescalerType2;
-  
-  typedef ImageType::PixelType                  VectorPixelType;
-
-  for (unsigned int cpt = 0; cpt < numberOfPrincipalComponentsRequired; cpt++)
-    {
-    ExtractROIFilterType::Pointer extractROIFilter = ExtractROIFilterType::New();
-    RescalerType::Pointer         rescaler = RescalerType::New();
-    WriterType2::Pointer          writer2 = WriterType2::New();
-
-    extractROIFilter->SetInput(pcafilter->GetOutput());
-    extractROIFilter->SetChannel(cpt + 1);
-
-    rescaler->SetInput(extractROIFilter->GetOutput());
-    rescaler->SetOutputMinimum(0);
-    rescaler->SetOutputMaximum(255);
-
-    writer2->SetInput(rescaler->GetOutput());
-    writer2->SetFileName(argv[cpt + 5]);
-    writer2->Update();
-    }
-
-  WriterType3::Pointer          writerInverse = WriterType3::New();
-  RescalerType2::Pointer        rescalerInverse = RescalerType2::New();
-  rescalerInverse->SetInput(invFilter->GetOutput());
-  
-  VectorPixelType minimum, maximum;
-  minimum.SetSize(3);
-  maximum.SetSize(3);
-  minimum.Fill(0);
-  maximum.Fill(255);
-  rescalerInverse->SetOutputMinimum(minimum);
-  rescalerInverse->SetOutputMaximum(maximum);
-
-  writerInverse->SetInput(rescalerInverse->GetOutput());
-  writerInverse->SetFileName(argv[4]);
-  writerInverse->Update();
+  // This is for rendering in software guide
+  typedef otb::PrintableImageFilter<ImageType,ImageType> PrintFilterType;
+  typedef PrintFilterType::OutputImageType               VisuImageType;
+  typedef otb::ImageFileWriter<VisuImageType>            VisuWriterType;
+
+  PrintFilterType::Pointer inputPrintFilter = PrintFilterType::New();
+  PrintFilterType::Pointer outputPrintFilter = PrintFilterType::New();
+  PrintFilterType::Pointer invertOutputPrintFilter = PrintFilterType::New();
+  VisuWriterType::Pointer inputVisuWriter = VisuWriterType::New();
+  VisuWriterType::Pointer outputVisuWriter = VisuWriterType::New();
+  VisuWriterType::Pointer invertOutputVisuWriter = VisuWriterType::New();
+
+  inputPrintFilter->SetInput(reader->GetOutput());
+  inputPrintFilter->SetChannel(5);
+  inputPrintFilter->SetChannel(3);
+  inputPrintFilter->SetChannel(2);
+  outputPrintFilter->SetInput(pcafilter->GetOutput());
+  outputPrintFilter->SetChannel(1);
+  outputPrintFilter->SetChannel(2);
+  outputPrintFilter->SetChannel(3);
+  invertOutputPrintFilter->SetInput(invFilter->GetOutput());
+  invertOutputPrintFilter->SetChannel(5);
+  invertOutputPrintFilter->SetChannel(3);
+  invertOutputPrintFilter->SetChannel(2);
+
+  inputVisuWriter->SetInput(inputPrintFilter->GetOutput());
+  outputVisuWriter->SetInput(outputPrintFilter->GetOutput());
+  invertOutputVisuWriter->SetInput(invertOutputPrintFilter->GetOutput());
+
+  inputVisuWriter->SetFileName(inpretty);
+  outputVisuWriter->SetFileName(outpretty);
+  invertOutputVisuWriter->SetFileName(invoutpretty);
+
+  inputVisuWriter->Update();
+  outputVisuWriter->Update();
+  invertOutputVisuWriter->Update();
 
   return EXIT_SUCCESS;
 }