diff --git a/Examples/Hyperspectral/HyperspectralUnmixing.cxx b/Examples/Hyperspectral/HyperspectralUnmixing.cxx
index e44701971f64389c3336690fd0f62a06c217aa5f..26476ec34b8a20b7165874a9da79d9cb9de6864f 100644
--- a/Examples/Hyperspectral/HyperspectralUnmixing.cxx
+++ b/Examples/Hyperspectral/HyperspectralUnmixing.cxx
@@ -19,118 +19,186 @@
#include "otbImageFileReader.h"
#include "otbImageFileWriter.h"
#include "otbStreamingStatisticsVectorImageFilter.h"
-#include "otbVcaImageFilter.h"
-#include "otbUnConstrainedLeastSquareImageFilter.h"
#include "otbVectorRescaleIntensityImageFilter.h"
#include "otbVectorImageToMatrixImageFilter.h"
#include "itkRescaleIntensityImageFilter.h"
#include "otbVectorRescaleIntensityImageFilter.h"
#include "otbMultiToMonoChannelExtractROI.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: {Indian_pines_corrected.tif}
+// OUTPUTS: {Indian_pines_Unmixing_Output.tif}, {UnmixingbandOutput1.png}, {UnmixingbandOutput2.png}, {UnmixingbandOutput3.png}
+// 16
// Software Guide : EndCommandLineArgs
+
+// Software Guide : BeginLatex
+//
+// This example illustrates the use of the
+// \doxygen{otb}{VcaImageFilter} and \doxygen{otb}{UnConstrainedLeastSquareImageFilter}.
+// The VCA filter computes endmembers using the Vertex Component Analysis
+// and UCLS performs unmixing on the input image using these endmembers.
+//
+// The first step required to use these filters is to include its header files.
+//
+// Software Guide : EndLatex
+
+// Software Guide : BeginCodeSnippet
+#include "otbVcaImageFilter.h"
+#include "otbUnConstrainedLeastSquareImageFilter.h"
+// Software Guide : EndCodeSnippet
int main(int argc, char * argv[])
{
- if (argc != 5)
+ if (argc != 7)
{
std::cerr << "Usage: " << argv[0];
- std::cerr << "inputFileName outputFileName EstimatenumberOfEndmembers outputPrettyFilename1 outputPrettyFilename2 outputPrettyFilename3 " << std::endl;
+ std::cerr << "inputFileName outputFileName outputPrettyFilename1 outputPrettyFilename2 outputPrettyFilename3 EstimatenumberOfEndmembers" << std::endl;
return EXIT_FAILURE;
}
const char * infname = argv[1];
const char * outfname = argv[2];
- const unsigned int estimateNumberOfEndmembers = atoi(argv[3]);
+ const unsigned int estimateNumberOfEndmembers = atoi(argv[6]);
const unsigned int Dimension = 2;
- typedef double PixelType;
- typedef otb::VectorImage<PixelType, Dimension> ImageType;
- typedef otb::VectorImage<unsigned char, 2> OutputPrettyImageType;
+ typedef double PixelType;
+ typedef otb::VectorImage<unsigned char, 2> OutputPrettyImageType;
- typedef otb::ImageFileReader<ImageType> ReaderType;
- typedef otb::ImageFileWriter<ImageType> WriterType;
-
- typedef otb::VectorRescaleIntensityImageFilter<ImageType,ImageType> RescalerType;
- typedef otb::VectorRescaleIntensityImageFilter<ImageType,OutputPrettyImageType> RescalerType2;
-
- typedef otb::StreamingStatisticsVectorImageFilter<ImageType> StreamingStatisticsVectorImageFilterType;
- typedef otb::VCAImageFilter<ImageType> VCAFilterType;
+ // 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
- typedef otb::UnConstrainedLeastSquareImageFilter<ImageType,ImageType,double> UCLSUnmixingFilterType;
-
- typedef otb::VectorImageToMatrixImageFilter<ImageType> VectorImageToMatrixImageFilterType;
+ // Software Guide : BeginCodeSnippet
+ typedef otb::VectorImage<PixelType, Dimension> ImageType;
+ typedef otb::ImageFileReader<ImageType> ReaderType;
+ typedef otb::ImageFileWriter<ImageType> WriterType;
+ // Software Guide : EndCodeSnippet
+
+ typedef otb::VectorRescaleIntensityImageFilter<ImageType,ImageType> RescalerType;
+ typedef otb::StreamingStatisticsVectorImageFilter<ImageType> StreamingStatisticsVectorImageFilterType;
+ typedef otb::VectorImageToMatrixImageFilter<ImageType> VectorImageToMatrixImageFilterType;
typedef vnl_vector<double> VectorType;
typedef vnl_matrix<double> MatrixType;
- /// / Noise filtering
- // typedef otb::LocalActivityVectorImageFilter< ImageType, ImageType > NoiseFilterType;
+ // Software Guide : EndCodeSnippet
+ // Software Guide : BeginLatex
+ //
+ // We instantiate now the image reader and we set the image file name.
+ //
+ // Software Guide : EndLatex
- // // Image filtering
- // typedef otb::MNFImageFilter< ImageType, ImageType,
- // NoiseFilterType, otb::Transform::FORWARD > FilterType;
-
- //read image
+ // Software Guide : BeginCodeSnippet
ReaderType::Pointer reader = ReaderType::New();
reader->SetFileName(infname);
+ // Software Guide : EndCodeSnippet
+
reader->UpdateOutputInformation();
+ // Software Guide : BeginLatex
+ //
+ // For now we need to rescale the input image between 0 and 1 to
+ // perform the unmixing algorithm. We use the
+ // \doxygen{otb}{VectorRescaleIntensityImageFilter}.
+ //
+ // Software Guide : EndLatex
//rescale input image between 0 and 1
+
+ // Software Guide : BeginCodeSnippet
RescalerType::Pointer rescaler = RescalerType::New();
rescaler->SetInput(reader->GetOutput());
- rescaler->SetOutputMinimum(0);
- rescaler->SetOutputMaximum(1.);
- /*
- * Estimate Endmembers
- */
- std::cout << "Estimate Endmembers by VCA" << std::endl;
-
+
+ ImageType::PixelType minPixel, maxPixel;
+ minPixel.SetSize(reader->GetOutput()->GetNumberOfComponentsPerPixel());
+ maxPixel.SetSize(reader->GetOutput()->GetNumberOfComponentsPerPixel());
+ minPixel.Fill(0.);
+ maxPixel.Fill(1.);
+
+ rescaler->SetOutputMinimum(minPixel);
+ rescaler->SetOutputMaximum(maxPixel);
+ // Software Guide : EndCodeSnippet
+
+ // Software Guide : BeginLatex
+ //
+ // We define the type for the VCA filter. It is templated over the input
+ // image type. The only parameter is the number of endmembers which
+ // needs to be estimated.
+ // We can now the instantiate the filter.
+ //
+ // Software Guide : EndLatex
+
+ // Software Guide : BeginCodeSnippet
+ typedef otb::VCAImageFilter<ImageType> VCAFilterType;
VCAFilterType::Pointer vca = VCAFilterType::New();
+
vca->SetNumberOfEndmembers(estimateNumberOfEndmembers);
vca->SetInput(rescaler->GetOutput());
+ // Software Guide : EndCodeSnippet
- ImageType::Pointer endmembersImage;
- endmembersImage = vca->GetOutput();
-
- /*
- * Transform Endmembers image to matrix representation
- */
- std::cout << "Endmembers extracted" << std::endl;
- std::cout << "Converting endmembers to matrix" << std::endl;
+
+ // Software Guide : BeginLatex
+ //
+ // We transform the output estimate endmembers to a matrix representation
+ //
+ // Software Guide : EndLatex
+
+ // Software Guide : BeginCodeSnippet
VectorImageToMatrixImageFilterType::Pointer endMember2Matrix = VectorImageToMatrixImageFilterType::New();
- endMember2Matrix->SetInput(endmembersImage);
+ endMember2Matrix->SetInput(vca->GetOutput());
endMember2Matrix->Update();
-
- MatrixType endMembersMatrix = endMember2Matrix->GetMatrix();
- std::cout << "Endmembers matrix : " << endMembersMatrix << std::endl;
-
- /*
- * Unmix
- */
- UCLSUnmixingFilterType::Pointer unmixer =
- UCLSUnmixingFilterType::New();
-
+
+ // Software Guide : EndCodeSnippet
+
+ // Software Guide : BeginLatex
+ //
+ // We can now procedd to the unmixing algorithm.Parameters
+ // needed are the input image and the endmembers matrix.
+ //
+ // Software Guide : EndLatex
+
+ // Software Guide : BeginCodeSnippet
+ typedef otb::UnConstrainedLeastSquareImageFilter<ImageType,ImageType,double> UCLSUnmixingFilterType;
+ UCLSUnmixingFilterType::Pointer unmixer = UCLSUnmixingFilterType::New();
unmixer->SetInput(rescaler->GetOutput());
- unmixer->SetMatrix(endMembersMatrix);
- unmixer->SetNumberOfThreads(1); // FIXME : currently buggy
-
- ImageType::Pointer abundanceMap;
- abundanceMap = unmixer->GetOutput();
-
- /*
- * Write abundance map
- */
- std::cout << "Write abundance map " << outfname << std::endl;
+ unmixer->SetMatrix(endMember2Matrix->GetMatrix());
+ // Software Guide : EndCodeSnippet
+ unmixer->SetNumberOfThreads(1); // FIXME : currently buggy
+
+ // Software Guide : BeginLatex
+ //
+ // We now instantiate the writer and set the file name for the
+ // output image and trigger the unmixing computation with the \code{Update()} of the writer.
+ //
+ // Software Guide : EndLatex
+
+ // Software Guide : BeginCodeSnippet
WriterType::Pointer writer = WriterType::New();
- writer->SetInput(abundanceMap);
+ writer->SetInput(unmixer->GetOutput());
writer->SetFileName(outfname);
-
writer->Update();
+ // Software Guide : EndCodeSnippet
+ // Software Guide : BeginLatex
+ // Figure~\ref{fig:UNMIXING_FILTER} shows the result of applying unmixing
+ // to a 220 band AVIRIS image.
+ // \begin{figure}
+ // \center
+ // \includegraphics[width=0.25\textwidth]{UnmixingbandOutput1.eps}
+ // \includegraphics[width=0.25\textwidth]{UnmixingbandOutput2.eps}
+ // \includegraphics[width=0.25\textwidth]{UnmixingbandOutput3.eps}
+ // \itkcaption[Unmixing Filter]{Result of applying the
+ // \doxygen{otb}{VcaImageFilter} and \doxygen{otb}{UnConstrainedLeastSquareImageFilter} to an image. From left
+ // to right and top to bottom:
+ // first abundance map band, second abundance map band, third abundance map band.}
+ // \label{fig:UNMIXING_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;
@@ -144,7 +212,7 @@ int main(int argc, char * argv[])
PrettyRescalerType::Pointer prettyRescaler = PrettyRescalerType::New();
WriterType2::Pointer writer2 = WriterType2::New();
- extractROIFilter->SetInput(abundanceMap);
+ extractROIFilter->SetInput(unmixer->GetOutput());
extractROIFilter->SetChannel(cpt + 1);
prettyRescaler->SetInput(extractROIFilter->GetOutput());
@@ -152,7 +220,7 @@ int main(int argc, char * argv[])
prettyRescaler->SetOutputMaximum(255);
writer2->SetInput(prettyRescaler->GetOutput());
- writer2->SetFileName(argv[cpt + 4]);
+ writer2->SetFileName(argv[cpt + 3]);
writer2->Update();
}