diff --git a/Code/Learning/otbCzihoSOMLearningBehaviorFunctor.h b/Code/Learning/otbCzihoSOMLearningBehaviorFunctor.h
index 44260ab8183fb267e4d0ed67362daa3731ea9294..790b397a31950bff9aede8659ef10885c2859b70 100644
--- a/Code/Learning/otbCzihoSOMLearningBehaviorFunctor.h
+++ b/Code/Learning/otbCzihoSOMLearningBehaviorFunctor.h
@@ -68,7 +68,7 @@ namespace Functor {
void SetIterationThreshold ( const itk::Size<VDimension> & sizeInit, unsigned int iterMax )
{
double V0 = static_cast<double>( sizeInit[0] );
- for ( int i = 1; i < VDimension; i++ )
+ for (unsigned int i = 1; i < VDimension; i++ )
{
if ( V0 < static_cast<double>( sizeInit[i] ) )
V0 = static_cast<double>( sizeInit[i] );
diff --git a/Examples/Learning/SOMClassifierExample.cxx b/Examples/Learning/SOMClassifierExample.cxx
index 9283d7d452e219d4a64b88e3e91ab50228f9d6a2..5234423fd5e9412eb6224811de44b3ab98f7efdb 100644
--- a/Examples/Learning/SOMClassifierExample.cxx
+++ b/Examples/Learning/SOMClassifierExample.cxx
@@ -21,12 +21,13 @@
#endif
#include <fstream>
+#include "otbImage.h"
#include "otbVectorImage.h"
#include "otbSOMMap.h"
#include "otbImageFileReader.h"
#include "otbImageFileWriter.h"
#include "itkImageRegionIterator.h"
-#include "itkImageToListAdaptor.h"
+#include "itkListSample.h"
// Software Guide : BeginCommandLineArgs
// INPUTS: {ROI_QB_MUL_1.png}, {ROI_QB_MUL_SOM.png}
@@ -72,7 +73,7 @@ int main(int argc, char* argv[] )
typedef unsigned char LabelPixelType;
const unsigned int Dimension = 2;
- typedef itk::RGBPixel<InputPixelType> PixelType;
+ typedef itk::VariableLengthVector<InputPixelType> PixelType;
// Software Guide : BeginLatex
//
@@ -91,7 +92,7 @@ int main(int argc, char* argv[] )
// Software Guide : EndCodeSnippet
- typedef otb::Image<PixelType,Dimension> InputImageType;
+ typedef otb::VectorImage<InputPixelType,Dimension> InputImageType;
typedef otb::ImageFileReader< InputImageType > ReaderType;
// Software Guide : BeginLatex
@@ -111,7 +112,7 @@ int main(int argc, char* argv[] )
// Software Guide : BeginCodeSnippet
- typedef itk::Statistics::ImageToListAdaptor< InputImageType > SampleType;
+ typedef itk::Statistics::ListSample< PixelType> SampleType;
typedef otb::SOMClassifier<SampleType,SOMMapType,LabelPixelType>
ClassifierType;
@@ -159,7 +160,16 @@ int main(int argc, char* argv[] )
// Software Guide : BeginCodeSnippet
SampleType::Pointer sample = SampleType::New();
- sample->SetImage(reader->GetOutput());
+
+ itk::ImageRegionIterator<InputImageType> it(reader->GetOutput(),reader->GetOutput()->GetLargestPossibleRegion());
+
+ it.GoToBegin();
+
+ while(!it.IsAtEnd())
+ {
+ sample->PushBack(it.Get());
+ ++it;
+ }
// Software Guide : EndCodeSnippet
//
diff --git a/Examples/Learning/SOMExample.cxx b/Examples/Learning/SOMExample.cxx
index a2753335c27ab7e5fbfd4b26a53f3c6d9454d854..fbabb8e4153051b82878b6ec4cc8fac1ef2b95ee 100644
--- a/Examples/Learning/SOMExample.cxx
+++ b/Examples/Learning/SOMExample.cxx
@@ -9,6 +9,8 @@
Copyright (c) Centre National d'Etudes Spatiales. All rights reserved.
See OTBCopyright.txt for details.
+ Copyright (c) Institut Telecom ; Telecom Bretagne. All rights reserved.
+ See GETCopyright.txt for details.
This software is distributed WITHOUT ANY WARRANTY; without even
the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
@@ -50,12 +52,15 @@
#include "itkExceptionObject.h"
#include "otbImage.h"
-#include "itkRGBPixel.h"
+#include "otbVectorImage.h"
+#include "itkVariableLengthVector.h"
+
#include "itkVectorExpandImageFilter.h"
#include "itkVectorNearestNeighborInterpolateImageFunction.h"
#include "itkExpandImageFilter.h"
#include "itkNearestNeighborInterpolateImageFunction.h"
+#include "otbPerBandVectorImageFilter.h"
// Software Guide : BeginLatex
// Since the \doxygen{otb}{SOM} class uses a distance, we will need to
@@ -71,30 +76,22 @@
// Software Guide : EndCodeSnippet
#include "otbImageFileReader.h"
#include "otbImageFileWriter.h"
-#include "itkImageToListAdaptor.h"
+#include "itkListSample.h"
int main(int argc, char* argv[])
{
- if(argc!=12)
- {
- std::cout << "Usage: " << argv[0] << "inputImage outputMap activationMap";
- std::cout << "sizeX sizeY neighborX neighborY iterations ";
- std::cout << "beta0 betaEnd initValue" << std::endl;
- return 1;
- }
-
-
- char * inputFileName = argv[1];
- char * outputFileName = argv[2];
- char * actMapFileName = argv[3];
- unsigned int sizeX = atoi(argv[4]);
- unsigned int sizeY = atoi(argv[5]);
- unsigned int neighInitX = atoi(argv[6]);
- unsigned int neighInitY= atoi(argv[7]);
- unsigned int nbIterations= atoi(argv[8]);
- double betaInit = atof(argv[9]);
- double betaEnd= atof(argv[10]);
- float initValue = atof(argv[11]);
+try {
+ const char * inputFileName = argv[1];
+ const char * outputFileName = argv[2];
+ const char * actMapFileName = argv[3];
+ unsigned int sizeX = atoi( argv[4] );
+ unsigned int sizeY = atoi( argv[5] );
+ unsigned int neighInitX = atoi( argv[6] );
+ unsigned int neighInitY= atoi( argv[7] );
+ unsigned int nbIterations = atoi( argv[8] );
+ double betaInit = atof( argv[9] );
+ double betaEnd= atof( argv[10] );
+ double initValue = atof( argv[11] );
// Software Guide : BeginLatex
//
@@ -107,10 +104,10 @@ int main(int argc, char* argv[])
// Software Guide : BeginCodeSnippet
-
const unsigned int Dimension = 2;
- typedef unsigned char ComponentType;
- typedef itk::RGBPixel<ComponentType> PixelType;
+ typedef double PixelType;
+ typedef otb::VectorImage< PixelType, Dimension > ImageType;
+ typedef ImageType::PixelType VectorType;
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
@@ -123,7 +120,7 @@ int main(int argc, char* argv[])
// Software Guide : BeginCodeSnippet
- typedef itk::Statistics::EuclideanDistance<PixelType> DistanceType;
+ typedef itk::Statistics::EuclideanDistance< VectorType > DistanceType;
// Software Guide : EndCodeSnippet
//
@@ -139,8 +136,7 @@ int main(int argc, char* argv[])
// Software Guide : BeginCodeSnippet
-
- typedef otb::SOMMap<PixelType,DistanceType,Dimension> MapType;
+ typedef otb::SOMMap< VectorType, DistanceType, Dimension > MapType;
// Software Guide : EndCodeSnippet
//
@@ -155,8 +151,6 @@ int main(int argc, char* argv[])
// Software Guide : BeginCodeSnippet
-
- typedef otb::Image<PixelType,Dimension> ImageType;
typedef otb::ImageFileReader<ImageType> ReaderType;
// Software Guide : EndCodeSnippet
@@ -171,37 +165,38 @@ int main(int argc, char* argv[])
// Software Guide : BeginCodeSnippet
- typedef itk::Statistics::ImageToListAdaptor<ImageType> ListAdaptorType;
-
+ typedef itk::Statistics::ListSample< VectorType > SampleListType;
+
// Software Guide : EndCodeSnippet
//
// Software Guide : BeginLatex
//
// We can now define the type for the SOM, which is templated over the
-// input sample list and the type of the map to be produced.
+// input sample list and the type of the map to be produced and the two
+// functors that hold the training behavior.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
- typedef otb::SOM<ListAdaptorType,MapType> SOMType;
+ typedef otb::Functor::CzihoSOMLearningBehaviorFunctor
+ LearningBehaviorFunctorType;
+ typedef otb::Functor::CzihoSOMNeighborhoodBehaviorFunctor
+ NeighborhoodBehaviorFunctorType;
+ typedef otb::SOM< SampleListType, MapType,
+ LearningBehaviorFunctorType, NeighborhoodBehaviorFunctorType >
+ SOMType;
// Software Guide : EndCodeSnippet
//
// Software Guide : BeginLatex
//
-// Since the map is itself an image, we can write it to disk with an
-// \doxygen{otb}{ImageFileWriter}.
-//
-// Software Guide : EndLatex
-
-// Software Guide : BeginCodeSnippet
-
- typedef otb::ImageFileWriter<MapType> WriterType;
-
-// Software Guide : EndCodeSnippet
-//
-// Software Guide : BeginLatex
+// As an alternative to standart \code{SOMType}, one can decide to use
+// an \doxygen{otb}{PeriodicSOM}, which behaves like \doxygen{otb}{SOM} but
+// is to be considered to as a torrus instead of a simple map. Hence, the
+// neighborhood behavior of the winning neuron does not depend on its location
+// on the map...
+// \doxygen{otb}{PeriodicSOM} is defined in otbPeriodicSOM.h.
//
// We can now start building the pipeline. The first step is to
// instantiate the reader and pass its output to the adaptor.
@@ -210,13 +205,25 @@ int main(int argc, char* argv[])
// Software Guide : BeginCodeSnippet
-
ReaderType::Pointer reader = ReaderType::New();
reader->SetFileName(inputFileName);
reader->Update();
- ListAdaptorType::Pointer adaptor = ListAdaptorType::New();
- adaptor->SetImage(reader->GetOutput());
+ SampleListType::Pointer sampleList = SampleListType::New();
+ sampleList->SetMeasurementVectorSize( reader->GetOutput()->GetVectorLength() );
+
+ itk::ImageRegionIterator< ImageType > imgIter ( reader->GetOutput(),
+ reader->GetOutput()->GetBufferedRegion() );
+ imgIter.GoToBegin();
+
+ itk::ImageRegionIterator< ImageType > imgIterEnd ( reader->GetOutput(),
+ reader->GetOutput()->GetBufferedRegion() );
+ imgIterEnd.GoToEnd();
+
+ do {
+ sampleList->PushBack( imgIter.Get() );
+ ++imgIter;
+ } while ( imgIter != imgIterEnd );
// Software Guide : EndCodeSnippet
//
@@ -229,7 +236,7 @@ int main(int argc, char* argv[])
// Software Guide : BeginCodeSnippet
SOMType::Pointer som = SOMType::New();
- som->SetListSample(adaptor);
+ som->SetListSample( sampleList );
// Software Guide : EndCodeSnippet
//
@@ -277,11 +284,28 @@ int main(int argc, char* argv[])
// Software Guide : BeginCodeSnippet
-
som->SetNumberOfIterations(nbIterations);
som->SetBetaInit(betaInit);
som->SetBetaEnd(betaEnd);
- som->SetMaxWeight(static_cast<ComponentType>(initValue));
+ som->SetMaxWeight(static_cast<PixelType>(initValue));
+
+// Software Guide : EndCodeSnippet
+//
+// Software Guide : BeginLatex
+//
+// Now comes the intialisation of the functors.
+//
+// Software Guide : EndLatex
+
+// Software Guide : BeginCodeSnippet
+
+ LearningBehaviorFunctorType learningFunctor;
+ learningFunctor.SetIterationThreshold( radius, nbIterations );
+ som->SetBetaFunctor( learningFunctor );
+
+ NeighborhoodBehaviorFunctorType neighborFunctor;
+ som->SetNeighborhoodSizeFunctor( neighborFunctor );
+
// Software Guide : EndCodeSnippet
//
// Software Guide : BeginLatex
@@ -289,39 +313,35 @@ int main(int argc, char* argv[])
// Finally, we set up the las part of the pipeline where the plug the
// output of the SOM into the writer. The learning procedure is
// triggered by calling the \code{Update()} method on the writer.
+// Since the map is itself an image, we can write it to disk with an
+// \doxygen{otb}{ImageFileWriter}.
//
// Software Guide : EndLatex
-// Software Guide : BeginCodeSnippet
-
+// Software Guide : BeginCodeSnippet
+ typedef otb::ImageFileWriter< ImageType > WriterType;
WriterType::Pointer writer = WriterType::New();
writer->SetFileName(outputFileName);
- writer->SetInput(som->GetOutput());
- writer->Update();
// Software Guide : EndCodeSnippet
//Just for visualization purposes, we zoom the image.
- typedef itk::VectorExpandImageFilter< MapType, MapType > ExpandType;
- typedef itk::VectorNearestNeighborInterpolateImageFunction< MapType,
+ typedef otb::Image<PixelType,2> SingleImageType;
+ typedef itk::ExpandImageFilter< SingleImageType, SingleImageType > ExpandType;
+ typedef otb::PerBandVectorImageFilter<MapType,MapType,ExpandType> VectorExpandType;
+ typedef itk::NearestNeighborInterpolateImageFunction< SingleImageType,
double > InterpolatorType;
InterpolatorType::Pointer interpolator = InterpolatorType::New();
- ExpandType::Pointer expand = ExpandType::New();
+ VectorExpandType::Pointer expand = VectorExpandType::New();
expand->SetInput(som->GetOutput());
- expand->SetExpandFactors( 40 );
- expand->SetInterpolator( interpolator );
- PixelType pix;
- pix[0]= 255;
- pix[1]= 255;
- pix[2]= 255;
- expand->SetEdgePaddingValue(pix);
+ expand->GetFilter()->SetExpandFactors( 40 );
+ expand->GetFilter()->SetInterpolator( interpolator );
+ expand->GetFilter()->SetEdgePaddingValue(255);
writer->SetInput(expand->GetOutput());
writer->Update();
-
-
// Software Guide : BeginLatex
// Figure \ref{fig:SOMMAP} shows the result of the SOM learning. Since
// we have performed a learning on RGB pixel values, the produced SOM
@@ -374,7 +394,7 @@ int main(int argc, char* argv[])
// Software Guide : BeginCodeSnippet
- typedef otb::SOMActivationBuilder<ListAdaptorType,MapType,
+ typedef otb::SOMActivationBuilder< SampleListType, MapType,
OutputImageType> SOMActivationBuilderType;
// Software Guide : EndCodeSnippet
@@ -390,7 +410,7 @@ int main(int argc, char* argv[])
SOMActivationBuilderType::Pointer somAct
= SOMActivationBuilderType::New();
somAct->SetInput(som->GetOutput());
- somAct->SetListSample(adaptor);
+ somAct->SetListSample( sampleList );
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
@@ -402,10 +422,11 @@ int main(int argc, char* argv[])
// Software Guide : BeginCodeSnippet
- ActivationWriterType::Pointer actWriter = ActivationWriterType::New();
- actWriter->SetFileName(actMapFileName);
- actWriter->SetInput(somAct->GetOutput());
- actWriter->Update();
+ if ( actMapFileName != NULL )
+ {
+ ActivationWriterType::Pointer actWriter = ActivationWriterType::New();
+ actWriter->SetFileName(actMapFileName);
+
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
@@ -414,20 +435,24 @@ int main(int argc, char* argv[])
//
// Software Guide : EndLatex
- //Just for visualization purposes, we zoom the image.
- typedef itk::ExpandImageFilter< OutputImageType, OutputImageType > ExpandType2;
- typedef itk::NearestNeighborInterpolateImageFunction< OutputImageType, double > InterpolatorType2;
+ //Just for visualization purposes, we zoom the image.
+ typedef itk::ExpandImageFilter< OutputImageType, OutputImageType > ExpandType2;
+ typedef itk::NearestNeighborInterpolateImageFunction< OutputImageType,double > InterpolatorType2;
- InterpolatorType2::Pointer interpolator2 = InterpolatorType2::New();
- ExpandType2::Pointer expand2 = ExpandType2::New();
- expand2->SetInput(somAct->GetOutput());
- expand2->SetExpandFactors( 20 );
- expand2->SetInterpolator( interpolator2 );
- expand2->SetEdgePaddingValue(255);
- actWriter->SetInput(expand2->GetOutput());
- actWriter->Update();
+ InterpolatorType2::Pointer interpolator2 = InterpolatorType2::New();
+ ExpandType2::Pointer expand2 = ExpandType2::New();
+ expand2->SetInput(somAct->GetOutput());
+ expand2->SetExpandFactors( 20 );
+ expand2->SetInterpolator( interpolator2 );
+ expand2->SetEdgePaddingValue(255);
+ actWriter->SetInput(expand2->GetOutput());
+ actWriter->Update();
+ }
- return EXIT_SUCCESS;
+ } catch ( ... ) {
+ return EXIT_FAILURE;
+ }
+ return EXIT_SUCCESS;
}
diff --git a/Testing/Fa/CMakeLists.txt b/Testing/Fa/CMakeLists.txt
index d726410a717b26842215d4bc6b21fa23860a392b..7f010bd8465574be1c30af4040f3c8cd143c1472 100755
--- a/Testing/Fa/CMakeLists.txt
+++ b/Testing/Fa/CMakeLists.txt
@@ -170,11 +170,9 @@ ADD_TEST(FA-00060-le_Map_Activation ${CXX_TEST_PATH}/MapActivation
0.1
128
1
- ${TEMP}/FA-00013-le-som.hd
- ${TEMP}/FA-00013-le-som-zoom.mhd
+ ${TEMP}/FA-00013-le-som.hdr
${TEMP}/FA-00013-le-actMap.png
- ${TEMP}/FA-00013-le-actMap-zoom.png
- ${TEMP}/FA-00013-le-som.mhd
+ ${TEMP}/FA-00013-le-som.hdr
)
# ------- Fin des FAs traitees -----------------------------------
diff --git a/Testing/Fa/MapActivation.cxx b/Testing/Fa/MapActivation.cxx
index 9e288c5cbc07238f00a08fa78430a61811504287..32e00c3c9918b825beb7fb84a96f16df092ffa63 100755
--- a/Testing/Fa/MapActivation.cxx
+++ b/Testing/Fa/MapActivation.cxx
@@ -52,14 +52,12 @@
int main(int argc, char* argv[] )
{
- if (argc < 14)
+ if (argc < 12)
{
- std::cout << "Usage : " << argv[0] << " inputTabImage size radius NumberOfIterations BetaInit BetaEnd MaxWeight MinWeight som som-zoom actMap actMap-zoom som" << std::endl ;
+ std::cout << "Usage : " << argv[0] << " inputTabImage size radius NumberOfIterations BetaInit BetaEnd MaxWeight MinWeight som actMap som" << std::endl ;
return EXIT_FAILURE;
}
-
- const int nbparam= 9;
typedef otb::Image<double, 2 > ListImageType;
@@ -67,14 +65,13 @@ int main(int argc, char* argv[] )
TabReaderType::Pointer Tabreader = TabReaderType::New();
Tabreader->SetFileName(argv[1]);
Tabreader->Update();
- ListImageType::Pointer tabreadImage = ListImageType::New();
- tabreadImage = Tabreader->GetOutput();
+ ListImageType::Pointer tabreadImage = Tabreader->GetOutput();
typedef itk::ImageRegionIterator< ListImageType > IteratorType;
IteratorType It1( tabreadImage, tabreadImage->GetLargestPossibleRegion() );
- const int nblines=591; // (const int)(tabreadImage->GetLargestPossibleRegion().GetSize()[1]);
+ const int nblines= (const int)(tabreadImage->GetLargestPossibleRegion().GetSize()[1]);
- const int nbcolonnes=9;//tabreadImage->GetLargestPossibleRegion().GetSize()[0];
+ const int nbcolonnes= (const int)tabreadImage->GetLargestPossibleRegion().GetSize()[0];
double vectTab[nblines][nbcolonnes];
std::cout<<"lignes = "<<nblines<<" colonnes = "<<nbcolonnes<<std::endl;
@@ -83,15 +80,14 @@ int main(int argc, char* argv[] )
vectTab[It1.GetIndex()[1]][It1.GetIndex()[0]]=It1.Get();
}
- typedef itk::Vector< double, nbparam > MeasurementVectorType ;
- //typedef itk::VariableLengthVector< double > MeasurementVectorType ;
+ typedef itk::VariableLengthVector< double > MeasurementVectorType ;
typedef itk::Statistics::ListSample< MeasurementVectorType > SampleType ;
SampleType::Pointer liste = SampleType::New() ;
- MeasurementVectorType tab;
-
for(int j=0;j<nblines;j++)
{
+ MeasurementVectorType tab;
+ tab.SetSize(nbcolonnes);
for(int i=0;i<nbcolonnes;i++)
{
tab[i] = vectTab[j][i];
@@ -131,29 +127,6 @@ int main(int argc, char* argv[] )
somwriter->SetInput(som->GetOutput());
somwriter->Update();
-
- //Just for visualization purposes, we zoom the image.
- typedef itk::VectorExpandImageFilter< MapType, MapType > ExpandType;
- typedef itk::VectorNearestNeighborInterpolateImageFunction< MapType, double > InterpolatorType;
-
- InterpolatorType::Pointer interpolator = InterpolatorType::New();
- ExpandType::Pointer expand = ExpandType::New();
- expand->SetInput(som->GetOutput());
- expand->SetExpandFactors( 40 );
- expand->SetInterpolator( interpolator );
- MeasurementVectorType pix;
- for(int j=0;j<nbcolonnes;j++)
- {
- pix[j]= 255;
- }
-
-
- expand->SetEdgePaddingValue(pix);
- somwriter->SetInput(expand->GetOutput());
- somwriter->SetFileName(argv[10]/*"som-zoom.mhd"*/);
- somwriter->Update();
-
-
typedef unsigned char OutputPixelType;
typedef otb::Image<OutputPixelType,2> OutputImageType;
@@ -164,31 +137,17 @@ int main(int argc, char* argv[] )
somAct->SetListSample(liste);
ActivationWriterType::Pointer actWriter = ActivationWriterType::New();
- actWriter->SetFileName(argv[11]/*"actMap.png"*/);
+ actWriter->SetFileName(argv[10]/*"actMap.png"*/);
actWriter->SetInput(somAct->GetOutput());
actWriter->Update();
- //Just for visualization purposes, we zoom the image.
- typedef itk::ExpandImageFilter< OutputImageType, OutputImageType > ExpandType2;
- typedef itk::NearestNeighborInterpolateImageFunction< OutputImageType,double > InterpolatorType2;
-
- InterpolatorType2::Pointer interpolator2 = InterpolatorType2::New();
- ExpandType2::Pointer expand2 = ExpandType2::New();
- expand2->SetInput(somAct->GetOutput());
- expand2->SetExpandFactors( 40 );
- expand2->SetInterpolator( interpolator2 );
- expand2->SetEdgePaddingValue(255);
- actWriter->SetInput(expand2->GetOutput());
- actWriter->SetFileName(argv[12]/*"actMap-zoom.png"*/);
- actWriter->Update();
-
-
+
//Classifier :
typedef otb::ImageFileReader<MapType> SOMReaderType;
typedef otb::SOMClassifier<SampleType,MapType,unsigned char> ClassifierType;
SOMReaderType::Pointer somreader = SOMReaderType::New();
- somreader->SetFileName(argv[13]/*"som.mhd"*/);
+ somreader->SetFileName(argv[11]/*"som.mhd"*/);
somreader->Update();
ClassifierType::Pointer classifier = ClassifierType::New() ;