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Commit 897ce900 authored by Julien Michel's avatar Julien Michel
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DOC: Add all examples for dimension reduction

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Examples/DimensionReduction/CMakeLists.txt
View file @ 897ce900
......@@ -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 0 → 100644
View file @ 897ce900
/*=========================================================================
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 0 → 100644
View file @ 897ce900
/*=========================================================================
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 0 → 100644
View file @ 897ce900
/*=========================================================================
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