From fb230dee46a60d3c12c510f53dc467c0469a87d5 Mon Sep 17 00:00:00 2001
From: Julien Michel <julien.michel@c-s.fr>
Date: Mon, 28 Apr 2008 16:13:24 +0000
Subject: [PATCH] =?UTF-8?q?Corrections=20SOM=20gr=C3=A9goire?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit
---
.../otbEuclideanDistanceWithMissingValue.h | 100 +++++++
.../otbEuclideanDistanceWithMissingValue.txx | 149 +++++++++
.../otbCzihoSOMLearningBehaviorFunctor.h | 110 +++++++
.../otbCzihoSOMNeighborhoodBehaviorFunctor.h | 82 +++++
Code/Learning/otbPeriodicSOM.h | 130 ++++++++
Code/Learning/otbPeriodicSOM.txx | 109 +++++++
Code/Learning/otbSOM.h | 40 ++-
Code/Learning/otbSOM.txx | 282 +++++++++++-------
Code/Learning/otbSOMLearningBehaviorFunctor.h | 67 +++++
Code/Learning/otbSOMMap.h | 23 +-
Code/Learning/otbSOMMap.txx | 4 +
Testing/Code/BasicFilters/CMakeLists.txt | 12 +
.../BasicFilters/otbBasicFiltersTests8.cxx | 2 +
.../otbEuclideanDistanceWithMissingValue.cxx | 61 ++++
...tbEuclideanDistanceWithMissingValueNew.cxx | 39 +++
Testing/Code/Learning/CMakeLists.txt | 16 +
Testing/Code/Learning/otbLearningTests2.cxx | 2 +
Testing/Code/Learning/otbPeriodicSOM.cxx | 109 +++++++
Testing/Code/Learning/otbPeriodicSOMNew.cxx | 53 ++++
Testing/Code/Learning/otbSOM.cxx | 30 +-
.../Code/Learning/otbSOMActivationBuilder.cxx | 30 +-
.../Learning/otbSOMActivationBuilderNew.cxx | 15 +-
Testing/Code/Learning/otbSOMClassifier.cxx | 24 +-
Testing/Code/Learning/otbSOMClassifierNew.cxx | 9 +-
Testing/Code/Learning/otbSOMMap.cxx | 11 +-
Testing/Code/Learning/otbSOMNew.cxx | 9 +-
26 files changed, 1354 insertions(+), 164 deletions(-)
create mode 100644 Code/BasicFilters/otbEuclideanDistanceWithMissingValue.h
create mode 100644 Code/BasicFilters/otbEuclideanDistanceWithMissingValue.txx
create mode 100644 Code/Learning/otbCzihoSOMLearningBehaviorFunctor.h
create mode 100644 Code/Learning/otbCzihoSOMNeighborhoodBehaviorFunctor.h
create mode 100644 Code/Learning/otbPeriodicSOM.h
create mode 100644 Code/Learning/otbPeriodicSOM.txx
create mode 100644 Code/Learning/otbSOMLearningBehaviorFunctor.h
create mode 100644 Testing/Code/BasicFilters/otbEuclideanDistanceWithMissingValue.cxx
create mode 100644 Testing/Code/BasicFilters/otbEuclideanDistanceWithMissingValueNew.cxx
create mode 100644 Testing/Code/Learning/otbPeriodicSOM.cxx
create mode 100644 Testing/Code/Learning/otbPeriodicSOMNew.cxx
diff --git a/Code/BasicFilters/otbEuclideanDistanceWithMissingValue.h b/Code/BasicFilters/otbEuclideanDistanceWithMissingValue.h
new file mode 100644
index 0000000000..e4f07d5c65
--- /dev/null
+++ b/Code/BasicFilters/otbEuclideanDistanceWithMissingValue.h
@@ -0,0 +1,100 @@
+/*=========================================================================
+
+ Program: ORFEO Toolbox
+ Language: C++
+ Date: $Date$
+ Version: $Revision$
+
+
+ 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 ITCopyright.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.
+
+=========================================================================*/
+
+#ifndef __otbEuclideanDistanceWithMissingValue_h
+#define __otbEuclideanDistanceWithMissingValue_h
+
+#include <itkEuclideanDistance.h>
+
+namespace otb {
+
+namespace Statistics {
+
+/** \class EuclideanDistanceWithMissingValue
+ * \brief Euclidean distance function facing missing value.
+ *
+ * This class is derived from EuclideanDistance class. In addition
+ * to the initial Evaluate method, the class does not perform calculation
+ * when a component does not contain any data.
+ *
+ * The class can be templated over any container that holds data elements, as
+ * for template of EuclideanDistance.
+ *
+ * The only restriction is that elemnts have to support '\code{NaN}'.
+ *
+ * \sa EuclideanDistance
+ */
+template< class TVector >
+class ITK_EXPORT EuclideanDistanceWithMissingValue :
+ public itk::Statistics::EuclideanDistance< TVector >
+{
+ public:
+ /** Standard "Self" typedef. */
+ typedef EuclideanDistanceWithMissingValue Self;
+ typedef itk::Statistics::EuclideanDistance< TVector > Superclass;
+ typedef itk::SmartPointer< Self > Pointer ;
+ typedef itk::SmartPointer<const Self> ConstPointer;
+ typedef typename Superclass::MeasurementVectorSizeType MeasurementVectorSizeType;
+
+ /** Run-time type information (and related methods). */
+ itkTypeMacro(EuclideanDistanceWithMissingValue, EuclideanDistance);
+
+ /** Method for creation through the object factory. */
+ itkNewMacro(Self) ;
+
+ /** Type of the component of a vector */
+ typedef typename TVector::ValueType ValueType ;
+
+ /** Gets the distance between the origin and x */
+ double Evaluate(const TVector &x) const ;
+
+ /** Gets the distance between x1 and x2 */
+ double Evaluate(const TVector &x1, const TVector &x2) const ;
+
+ /** Gets the cooridnate distance between a and b. NOTE: a and b
+ * should be type of component */
+ double Evaluate(const ValueType &a, const ValueType &b) const ;
+
+ /** Returns true if the distance between x and the origin is less
+ * than radius */
+ bool IsWithinRange(const TVector &x, const double radius) const {
+ return Superclass::IsWithinRange( x, radius ); }
+
+ /** Check if a value is NaN or not */
+ static bool IsMissingValue ( const ValueType & v) ;
+
+ /** Set a value to Nan */
+ static void SetToMissingValue ( ValueType & v );
+
+ protected:
+ EuclideanDistanceWithMissingValue() {}
+ virtual ~EuclideanDistanceWithMissingValue() {}
+} ; // end of class
+
+} // end namespace statistics
+
+} // end namespace otb
+
+#ifndef ITK_MANUAL_INSTANTIATION
+#include "otbEuclideanDistanceWithMissingValue.txx"
+#endif
+
+#endif
+
diff --git a/Code/BasicFilters/otbEuclideanDistanceWithMissingValue.txx b/Code/BasicFilters/otbEuclideanDistanceWithMissingValue.txx
new file mode 100644
index 0000000000..70e7db1f57
--- /dev/null
+++ b/Code/BasicFilters/otbEuclideanDistanceWithMissingValue.txx
@@ -0,0 +1,149 @@
+/*=========================================================================
+
+ Program: ORFEO Toolbox
+ Language: C++
+ Date: $Date$
+ Version: $Revision$
+
+
+ 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 ITCopyright.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.
+
+=========================================================================*/
+
+#ifndef __otbEuclideanDistanceWithMissingValue_txx
+#define __otbEuclideanDistanceWithMissingValue_txx
+
+#include "itkNumericTraits.h"
+
+namespace otb {
+
+namespace Statistics {
+
+template< class TVector >
+inline double
+EuclideanDistanceWithMissingValue< TVector >
+::Evaluate(const TVector &x1, const TVector &x2) const
+{
+ if( itk::MeasurementVectorTraits::GetLength( x1 ) !=
+ itk::MeasurementVectorTraits::GetLength( x2 ) )
+ {
+ itkExceptionMacro( << "Vector lengths must be equal." );
+ }
+
+ double temp, distance = itk::NumericTraits< double >::Zero ;
+
+ for(unsigned int i = 0 ; i < x1.Size(); i++ )
+ {
+ if ( !IsMissingValue( x1[i] ) && !IsMissingValue( x2[i] ) )
+ {
+ temp = x1[i] - x2[i] ;
+ distance += temp * temp ;
+ }
+ }
+
+ return ::vcl_sqrt(distance) ;
+}
+
+template< class TVector >
+inline double
+EuclideanDistanceWithMissingValue< TVector >
+::Evaluate(const TVector &x) const
+{
+ MeasurementVectorSizeType
+ measurementVectorSize = this->GetMeasurementVectorSize();
+ if(measurementVectorSize == 0)
+ {
+ itkExceptionMacro( << "Please set the MeasurementVectorSize first" );
+ }
+ itk::MeasurementVectorTraits::Assert( this->m_Origin, measurementVectorSize,
+ "EuclideanDistance::Evaluate Origin and input vector have different lengths");
+
+ double temp, distance = itk::NumericTraits< double >::Zero ;
+
+ for(unsigned int i = 0 ; i < measurementVectorSize ; i++ )
+ {
+ if ( !IsMissingValue( this->GetOrigin()[i] ) && !IsMissingValue( x[i] ) )
+ {
+ temp = this->GetOrigin()[i] - x[i] ;
+ distance += temp * temp ;
+ }
+ }
+
+ return ::vcl_sqrt(distance) ;
+}
+
+template< class TVector >
+inline double
+EuclideanDistanceWithMissingValue< TVector >
+::Evaluate( const ValueType &a, const ValueType &b ) const
+{
+ // FIXME throw NaN exception ??
+ if ( IsMissingValue( a ) || IsMissingValue( b ) )
+ return 0.0;
+
+ double temp = a - b ;
+ return ::vcl_sqrt(temp * temp) ;
+}
+
+#if defined(_MSC_VER) /* Microsoft Visual C++ */
+#include <float.h>
+
+template< class TVector >
+/*static */
+bool
+EuclideanDistanceWithMissingValue< TVector >
+::IsMissingValue ( const ValueType & v)
+{
+ return static_cast<bool>( _isnan( const_cast<double>( v ) ) );
+}
+
+#elif HAVE_IEEE_COMPARISONS
+
+template< class TVector >
+/*static */
+bool
+EuclideanDistanceWithMissingValue< TVector >
+::IsMissingValue ( const ValueType & v)
+{
+ return (v!=v);
+}
+
+#else
+
+template< class TVector >
+/*static */
+bool
+EuclideanDistanceWithMissingValue< TVector >
+::IsMissingValue ( const ValueType & v)
+{
+ return static_cast<bool>( isnan(v) );
+}
+
+#endif
+
+template< class TVector >
+/* static */
+void
+EuclideanDistanceWithMissingValue< TVector >
+::SetToMissingValue ( ValueType & v )
+{
+ v = static_cast<ValueType>( 0.0/0.0 );
+}
+
+
+} // end namespace statistics
+
+} // end namespace otb
+
+#endif
+
+
+
diff --git a/Code/Learning/otbCzihoSOMLearningBehaviorFunctor.h b/Code/Learning/otbCzihoSOMLearningBehaviorFunctor.h
new file mode 100644
index 0000000000..44260ab818
--- /dev/null
+++ b/Code/Learning/otbCzihoSOMLearningBehaviorFunctor.h
@@ -0,0 +1,110 @@
+/*=========================================================================
+
+Program: ORFEO Toolbox
+Language: C++
+Date: $Date$
+Version: $Revision$
+
+
+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 ITCopyright.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.
+
+=========================================================================*/
+
+#ifndef __otbCzihoSOMLearningBehaviorFunctor_h
+#define __otbCzihoSOMLearningBehaviorFunctor_h
+
+#include "itkSize.h"
+
+namespace otb {
+
+namespace Functor {
+
+ /** \class CzihoSOMLearningBehaviorFunctor
+ * \brief Beta behavior over SOM training phase
+ *
+ * This class implements an evolution of the \f$ \beta \f$ weightening
+ * coefficient over the SOM training. It is issued from A. Cziho's PhD:
+ * "Compression d'images et analyse de contenu par quantification vectorielle"
+ * PhD dissertation, University of Rennes I, Rennes, France. May 5th, 1999.
+ *
+ * Its behavior is decomposed into two steps depending on the number of iterations:
+ * \f{equation*}
+ \beta = \begn{cases}
+ \beta_0 \left( 1 - \frac{t}{t_0} \right) & \text{ if $t < t_0$} \\
+ \beta_{\text{end}} \left( 1- \frac{t-t_O}{t_{\text{end}}-t_0} \right)
+ & \text{ if $ t_0 \leqslant t < t_{\text{end}}$}
+ \end{cases}
+ \f{equation*}
+ where \f$ t_0 \f$ stands for IterationThreshold.
+ *
+ * CzihoSOMLearningBehaviorFunctor uses some parameters of the SOM class such as:
+ * BetaInit, BetaEnd, NumberOfIterations, but also NeighborhoodSizeInit which may be
+ * (surprisingly) required for the IterationThreshold.
+ *
+ * The functor function uses \code{NumberOfIterations}, \code{BetaInit}, \code{BetaEnd} parameters, that is
+ * why it is necessary to call a specific method for \code{IterationThreshold} intialisation.
+ *
+ * \sa SOM
+ */
+ class CzihoSOMLearningBehaviorFunctor
+ {
+ public :
+ /** Empty constructor / descructor */
+ CzihoSOMLearningBehaviorFunctor () { m_IterationThreshold = 0; }
+ virtual ~CzihoSOMLearningBehaviorFunctor() { }
+
+ /** Accessors */
+ unsigned int GetIterationThreshold () { return this->m_IterationThreshold; }
+
+ template < unsigned int VDimension >
+ void SetIterationThreshold ( const itk::Size<VDimension> & sizeInit, unsigned int iterMax )
+ {
+ double V0 = static_cast<double>( sizeInit[0] );
+ for ( int i = 1; i < VDimension; i++ )
+ {
+ if ( V0 < static_cast<double>( sizeInit[i] ) )
+ V0 = static_cast<double>( sizeInit[i] );
+ }
+
+ m_IterationThreshold = static_cast<unsigned int>(
+ static_cast<double>( iterMax ) * ( 1.0 - 1.0 / ::vcl_sqrt( V0 ) ) );
+ }
+
+ /** Functor */
+ virtual double operator() ( unsigned int currentIteration,
+ unsigned int numberOfIterations,
+ double betaInit, double betaEnd )
+ {
+ if ( currentIteration < m_IterationThreshold )
+ {
+ return betaInit * ( 1.0
+ - static_cast<double>( currentIteration )
+ / static_cast<double>( numberOfIterations ) );
+ }
+ else
+ {
+ return betaEnd * ( 1.0
+ - static_cast<double>( currentIteration - m_IterationThreshold )
+ / static_cast<double>( numberOfIterations - m_IterationThreshold ) );
+ }
+ }
+
+ private:
+ unsigned int m_IterationThreshold;
+
+ }; // end of class CzihoSOMLearningBehaviorFunctor
+
+} // end namespace Functor
+
+} // end namespace otb
+
+#endif
+
diff --git a/Code/Learning/otbCzihoSOMNeighborhoodBehaviorFunctor.h b/Code/Learning/otbCzihoSOMNeighborhoodBehaviorFunctor.h
new file mode 100644
index 0000000000..1d94c90ce9
--- /dev/null
+++ b/Code/Learning/otbCzihoSOMNeighborhoodBehaviorFunctor.h
@@ -0,0 +1,82 @@
+/*=========================================================================
+
+Program: ORFEO Toolbox
+Language: C++
+Date: $Date$
+Version: $Revision$
+
+
+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 ITCopyright.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.
+
+=========================================================================*/
+
+#ifndef __otbCzihoSOMNeighborhoodBehaviorFunctor_h
+#define __otbCzihoSOMNeighborhoodBehaviorFunctor_h
+
+
+namespace otb {
+
+namespace Functor {
+
+ /** \class CzihoSOMNeighborhoodBehaviorFunctor
+ * \brief Neighborhood size behavior over SOM training phase
+ *
+ * This class implements an evolution of the neighborhood size
+ * over the SOM training. It is issued from A. Cziho's PhD:
+ * "Compression d'images et analyse de contenu par quantification vectorielle"
+ * PhD dissertation, University of Rennes I, Rennes, France. May 5th, 1999.
+ *
+ * The behavior of the radius r (\em ie. \code{SizeType} component 0, 1,...) is given by:
+ * \f{equation*}
+ r = r_{\text{init}} \left( 1 - \frac{t}{t_{\text{end}}} \right)^2
+ \f{equation*}
+ *
+ * CzihoSOMNeighborhoodBehaviorFunctor uses some parameters of the SOM class such as:
+ * \code{NeighborhoodSizeInit}, \code{NumberOfIterations} which are parameters of the functor function.
+ * \code{operator()} is templated with the dimension of the neighborhoodSize.
+ *
+ * \sa SOM
+ */
+ class CzihoSOMNeighborhoodBehaviorFunctor
+ {
+ public :
+ /** Empty constructor / descructor */
+ CzihoSOMNeighborhoodBehaviorFunctor () { }
+ virtual ~CzihoSOMNeighborhoodBehaviorFunctor() { }
+
+ /** Functor */
+ template < unsigned int VDimension >
+ itk::Size<VDimension> operator() ( unsigned int currentIteration,
+ unsigned int numberOfIterations,
+ const itk::Size<VDimension> & sizeInit )
+ {
+ itk::Size<VDimension> theSize;
+ double weightening = ::vcl_pow( 1.0
+ - static_cast<double>( currentIteration )
+ / static_cast<double>( numberOfIterations ),
+ 2.0 );
+ for (unsigned int i = 0; i < VDimension; i++ )
+ {
+ theSize[i] = static_cast<typename itk::Size<VDimension>::SizeValueType> (
+ static_cast<double>( sizeInit[i] ) * weightening );
+ }
+
+ return theSize;
+ }
+
+ }; // end of class CzihoSOMNeighborhoodBehaviorFunctor
+
+} // end namespace Functor
+
+} // end namespace otb
+
+#endif
+
diff --git a/Code/Learning/otbPeriodicSOM.h b/Code/Learning/otbPeriodicSOM.h
new file mode 100644
index 0000000000..682c5419be
--- /dev/null
+++ b/Code/Learning/otbPeriodicSOM.h
@@ -0,0 +1,130 @@
+/*=========================================================================
+
+ Program: ORFEO Toolbox
+ Language: C++
+ Date: $Date$
+ Version: $Revision$
+
+
+ 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 ITCopyright.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.
+
+=========================================================================*/
+
+#ifndef __otbPeriodicSOM_h
+#define __otbPeriodicSOM_h
+
+#include "otbSOM.h"
+
+namespace otb {
+
+/**
+ * \class PeriodicSOM
+ * \brief This class is responsible for the learning of a self organizing
+ * map when considered to as a torus.
+ *
+ * This class extends the SOM object which implements the Self
+ * Organizing Map (or Kohonen map) learning.
+ *
+ * The learning process iteratively select the best-response neuron for each input vector,
+ * enhancing its response and the response of its neighbors with respect to a certain radius,
+ * computed from an initial radius, and to a certain learning factor, decreasing at each iteration.
+ *
+ * The behavior of the neighborhood is given by a functor (templated) which parameter is the current
+ * iteration. It returns a neighborhood of type \code{SizeType}.
+ *
+ * The behavior of the learning factor (hold by a beta variable) is given by an other functor
+ * which parameter is the current iteration. It returns a beta value of type \code{double}.
+ *
+ * The SOMMap produced as output can be either initialized with a constant custom value or randomly
+ * generated following a normal law. The seed for the random intialization can be modified.
+ *
+ * \sa SOMMap
+ * \sa SOMActivationBuilder
+ * \sa CzihoSOMLearningBehaviorFunctor
+ * \sa CzihoSOMNeighborhoodBehaviorFunctor
+ */
+template <class TListSample, class TMap,
+ class TSOMLearningBehaviorFunctor = Functor::CzihoSOMLearningBehaviorFunctor,
+ class TSOMNeighborhoodBehaviorFunctor = Functor::CzihoSOMNeighborhoodBehaviorFunctor >
+class ITK_EXPORT PeriodicSOM
+ : public SOM< TListSample, TMap, TSOMLearningBehaviorFunctor, TSOMNeighborhoodBehaviorFunctor >
+{
+public:
+ /** Standard typedefs */
+ typedef PeriodicSOM Self;
+ typedef SOM< TListSample, TMap,
+ TSOMLearningBehaviorFunctor,
+ TSOMNeighborhoodBehaviorFunctor > Superclass;
+ typedef itk::SmartPointer<Self> Pointer;
+ typedef itk::SmartPointer<const Self> ConstPointer;
+
+ /** Creation through object factory macro */
+ itkNewMacro(Self);
+
+ /** Runtime informations macro */
+ itkTypeMacro( PeriodicSOM, SOM );
+
+ typedef TListSample ListSampleType;
+ typedef typename ListSampleType::Pointer ListSamplePointerType;
+ typedef TMap MapType;
+ typedef typename MapType::PixelType NeuronType;
+ typedef typename NeuronType::ValueType ValueType;
+ typedef typename MapType::IndexType IndexType;
+ typedef typename MapType::SizeType SizeType;
+ typedef typename MapType::RegionType RegionType;
+ typedef typename MapType::Pointer MapPointerType;
+
+protected:
+ /** Constructor */
+ PeriodicSOM() {}
+ /** Destructor */
+ virtual ~PeriodicSOM() {}
+ /** Output information redefinition */
+ virtual void GenerateOutputInformation () {
+ Superclass::GenerateOutputInformation (); }
+ /** Output allocation redefinition */
+ virtual void AllocateOutputs() {
+ Superclass::AllocateOutputs(); }
+ /** Main computation method */
+ virtual void GenerateData(void) {
+ Superclass::GenerateData(); }
+ /**
+ * Update the output map with a new sample.
+ * \param sample The new sample to learn,
+ * \param beta The learning coefficient,
+ * \param radius The radius of the nieghbourhood.
+ */
+ virtual void UpdateMap(const NeuronType& sample, double beta, SizeType& radius);
+ /**
+ * Step one iteration.
+ */
+ virtual void Step(unsigned int currentIteration) {
+ Superclass::Step( currentIteration ); }
+ /** PrintSelf method */
+ void PrintSelf(std::ostream& os, itk::Indent indent) const {
+ Superclass::PrintSelf(os,indent); }
+
+private:
+ PeriodicSOM(const Self&); // purposely not implemented
+ void operator=(const Self&); // purposely not implemented
+
+}; // end of class
+
+} // end of namespace otb
+
+#ifndef OTB_MANUAL_INSTANTIATION
+#include "otbPeriodicSOM.txx"
+#endif
+
+#endif
+
+
+
diff --git a/Code/Learning/otbPeriodicSOM.txx b/Code/Learning/otbPeriodicSOM.txx
new file mode 100644
index 0000000000..c4811314d8
--- /dev/null
+++ b/Code/Learning/otbPeriodicSOM.txx
@@ -0,0 +1,109 @@
+/*=========================================================================
+
+ Program: ORFEO Toolbox
+ Language: C++
+ Date: $Date$
+ Version: $Revision$
+
+
+ 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 ITCopyright.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.
+
+=========================================================================*/
+
+#ifndef __otbPeriodicSOM_txx
+#define __otbPeriodicSOM_txx
+
+#include <itkNumericTraits.h>
+#include <itkNeighborhoodIterator.h>
+
+#include "otbPeriodicSOM.h"
+
+
+namespace otb {
+
+/**
+ * Update the output map with a new sample.
+ * \param sample The new sample to learn,
+ * \param beta The learning coefficient,
+ * \param radius The radius of the nieghbourhood.
+ */
+template < class TListSample, class TMap,
+ class TSOMLearningBehaviorFunctor,
+ class TSOMNeighborhoodBehaviorFunctor >
+void
+PeriodicSOM<TListSample,TMap,TSOMLearningBehaviorFunctor,TSOMNeighborhoodBehaviorFunctor>
+::UpdateMap(const NeuronType& sample, double beta, SizeType& radius)
+{
+ unsigned int i,j;
+
+ // output map pointer
+ MapPointerType map = this->GetOutput(0);
+
+ // winner index in the map
+ IndexType position = map->GetWinner(sample);
+ NeuronType winner = map->GetPixel(position);
+
+ // Local neighborhood definition
+ typedef typename MapType::Superclass ImageMapType;
+ typedef itk::NeighborhoodIterator< ImageMapType > NeighborhoodIteratorType;
+ typename MapType::RegionType mapRegion = map->GetLargestPossibleRegion();
+ NeighborhoodIteratorType it ( radius, map, mapRegion );
+
+ // Here, the periodic update is achieved 'by hand' since
+ // PeriodicBoundaryCondition does not allow to modifiy
+ // VectorImage contents
+ SizeType mapSize = mapRegion.GetSize();
+ IndexType positionToUpdate;
+
+ // Iterate over the neighborhood ot the winner neuron
+ it.SetLocation( position );
+
+ for ( i = 0; i < it.Size(); i++ )
+ {
+ typename NeighborhoodIteratorType::OffsetType offset = it.GetOffset(i);
+
+ // The neighborhood is of elliptic shape
+ double theDistance = itk::NumericTraits< double >::Zero;
+ for ( j = 0; j < MapType::ImageDimension; j++ )
+ theDistance += pow( static_cast<double>( offset[j] ), 2.0 )
+ / pow( static_cast<double>( radius[j] ), 2.0 );
+
+ if ( theDistance <= 1.0 )
+ {
+ for ( j = 0; j < MapType::ImageDimension; j++ )
+ {
+ int pos = offset[j] + position[j];
+ positionToUpdate[j] = ( pos >= 0 ) ?
+ pos % mapSize[j] :
+ ( mapSize[j] - ( (-pos) % mapSize[j] ) ) % mapSize[j];
+ }
+
+ NeuronType tempNeuron = it.GetPixel(i);
+ // NeuronType newNeuron ( tempNeuron.Size() );
+ // newNeuron.Fill( 0.0 ); // FIXME
+ NeuronType newNeuron ( tempNeuron );
+
+ double tempBeta = beta / ( 1.0 + theDistance );
+ for( j = 0; j < newNeuron.Size(); j++ )
+ {
+ newNeuron[j] += static_cast<typename NeuronType::ValueType>(
+ ( sample[j] - tempNeuron[j] ) * tempBeta );
+ }
+ map->SetPixel(positionToUpdate,newNeuron);
+ }
+ }
+
+}
+
+} // end of namespace otb
+
+#endif
+
diff --git a/Code/Learning/otbSOM.h b/Code/Learning/otbSOM.h
index 7048ff1302..bcdbcec6f4 100644
--- a/Code/Learning/otbSOM.h
+++ b/Code/Learning/otbSOM.h
@@ -9,6 +9,8 @@ Version: $Revision$
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 ITCopyright.txt for details.
This software is distributed WITHOUT ANY WARRANTY; without even
the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
@@ -21,6 +23,9 @@ PURPOSE. See the above copyright notices for more information.
#include "itkImageToImageFilter.h"
#include "itkEuclideanDistance.h"
+#include "otbCzihoSOMLearningBehaviorFunctor.h"
+#include "otbCzihoSOMNeighborhoodBehaviorFunctor.h"
+
namespace otb
{
/**
@@ -32,13 +37,23 @@ namespace otb
* enhancing its response and the response of its neighbors with respect to a certain radius,
* computed from an initial radius, and to a certain learning factor, decreasing at each iteration.
*
+ * The behavior of the neighborhood is given by a functor (templated) which parameter is the current
+ * iteration. It returns a neighborhood of type \code{SizeType}.
+ *
+ * The behavior of the learning factor (hold by a beta variable) is given by an other functor
+ * which parameter is the current iteration. It returns a beta value of type double.
+ *
* The SOMMap produced as output can be either initialized with a constant custom value or randomly
* generated following a normal law. The seed for the random intialization can be modified.
*
* \sa SOMMap
* \sa SOMActivationBuilder
+ * \sa CzihoSOMLearningBehaviorFunctor
+ * \sa CzihoSOMNeighborhoodBehaviorFunctor
*/
-template <class TListSample,class TMap>
+template < class TListSample, class TMap,
+ class TSOMLearningBehaviorFunctor = Functor::CzihoSOMLearningBehaviorFunctor,
+ class TSOMNeighborhoodBehaviorFunctor = Functor::CzihoSOMNeighborhoodBehaviorFunctor >
class ITK_EXPORT SOM
: public itk::ImageSource<TMap>
{
@@ -64,6 +79,9 @@ class ITK_EXPORT SOM
typedef typename MapType::RegionType RegionType;
typedef typename MapType::Pointer MapPointerType;
+ typedef TSOMLearningBehaviorFunctor SOMLearningBehaviorFunctorType;
+ typedef TSOMNeighborhoodBehaviorFunctor SOMNeighborhoodBehaviorFunctorType;
+
/** Map dimension */
itkStaticConstMacro(MapDimension,unsigned int, MapType::ImageDimension);
@@ -89,24 +107,34 @@ class ITK_EXPORT SOM
itkGetObjectMacro(ListSample,ListSampleType);
itkSetObjectMacro(ListSample,ListSampleType);
+ void SetBetaFunctor ( const SOMLearningBehaviorFunctorType & functor ) {
+ m_BetaFunctor = functor; }
+
+ void SetNeighborhoodSizeFunctor ( const SOMNeighborhoodBehaviorFunctorType & functor ) {
+ m_NeighborhoodSizeFunctor = functor; }
+
protected:
/** Constructor */
SOM();
/** Destructor */
virtual ~SOM();
+ /** Output information redefinition */
+ virtual void GenerateOutputInformation ();
+ /** Output allocation redefinition */
+ virtual void AllocateOutputs();
/** Main computation method */
- void GenerateData(void);
+ virtual void GenerateData(void);
/**
* Update the output map with a new sample.
* \param sample The new sample to learn,
* \param beta The learning coefficient,
* \param radius The radius of the nieghbourhood.
*/
- void UpdateMap(const NeuronType& sample, double beta, SizeType& radius);
+ virtual void UpdateMap(const NeuronType& sample, double beta, SizeType& radius);
/**
* Step one iteration.
*/
- void Step(unsigned int currentIteration);
+ virtual void Step(unsigned int currentIteration);
/** PrintSelf method */
void PrintSelf(std::ostream& os, itk::Indent indent) const;
@@ -133,6 +161,10 @@ class ITK_EXPORT SOM
unsigned int m_Seed;
/** The input list sample */
ListSamplePointerType m_ListSample;
+ /** Behavior of the Learning weightening (link to the beta coefficient) */
+ SOMLearningBehaviorFunctorType m_BetaFunctor;
+ /** Behavior of the Neighborhood extent */
+ SOMNeighborhoodBehaviorFunctorType m_NeighborhoodSizeFunctor;
};
} // end namespace otb
diff --git a/Code/Learning/otbSOM.txx b/Code/Learning/otbSOM.txx
index abbed6dd10..177fe1ea2f 100644
--- a/Code/Learning/otbSOM.txx
+++ b/Code/Learning/otbSOM.txx
@@ -9,6 +9,9 @@ Version: $Revision$
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 ITCopyright.txt for details.
+
This software is distributed WITHOUT ANY WARRANTY; without even
the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
@@ -31,8 +34,10 @@ namespace otb
/**
* Constructor
*/
-template <class TListSample,class TMap>
-SOM<TListSample,TMap>
+template < class TListSample, class TMap,
+ class TSOMLearningBehaviorFunctor,
+ class TSOMNeighborhoodBehaviorFunctor >
+SOM<TListSample,TMap,TSOMLearningBehaviorFunctor,TSOMNeighborhoodBehaviorFunctor>
::SOM()
{
this->SetNumberOfRequiredInputs(0);
@@ -51,8 +56,10 @@ SOM<TListSample,TMap>
/**
* Destructor
*/
-template <class TListSample,class TMap>
-SOM<TListSample,TMap>
+template < class TListSample, class TMap,
+ class TSOMLearningBehaviorFunctor,
+ class TSOMNeighborhoodBehaviorFunctor >
+SOM<TListSample,TMap,TSOMLearningBehaviorFunctor,TSOMNeighborhoodBehaviorFunctor>
::~SOM()
{
}
@@ -62,138 +69,195 @@ SOM<TListSample,TMap>
* \param beta The learning coefficient,
* \param radius The radius of the nieghbourhood.
*/
-template <class TListSample,class TMap>
+template < class TListSample, class TMap,
+ class TSOMLearningBehaviorFunctor,
+ class TSOMNeighborhoodBehaviorFunctor >
void
-SOM<TListSample,TMap>
-::UpdateMap(const NeuronType& sample, double beta, SizeType& radius)
+SOM<TListSample,TMap,TSOMLearningBehaviorFunctor,TSOMNeighborhoodBehaviorFunctor>
+::UpdateMap( const NeuronType& sample, double beta, SizeType& radius )
{
- // output map pointer
- MapPointerType map = this->GetOutput();
-
- // typedefs
- typedef itk::ImageRegionIteratorWithIndex<MapType> IteratorType;
- typedef itk::ContinuousIndex<double,MapType::ImageDimension> ContinuousIndexType;
- typedef itk::Statistics::EuclideanDistance<ContinuousIndexType> DistanceType;
- typename DistanceType::Pointer distance = DistanceType::New();
-
- // winner index in the map
- IndexType position = map->GetWinner(sample);
- NeuronType winner = map->GetPixel(position);
-
- // Local neighborhood definition
- RegionType localRegion;
- IndexType localIndex = position-radius;
- SizeType localSize;
- for(unsigned int i=0;i<MapType::ImageDimension;++i)
- {
- localSize[i]= 2*radius[i]+1;
- }
- localRegion.SetIndex(localIndex);
- localRegion.SetSize(localSize);
- localRegion.Crop(map->GetLargestPossibleRegion());
- IteratorType it(map,localRegion);
-
- // Walk through the map, and evolve each neuron depending on its
- // distance to the winner.
- for(it.GoToBegin();!it.IsAtEnd();++it)
- {
- NeuronType tempNeuron = it.Get();
- NeuronType newNeuron;
- double tempBeta = beta/(1+distance->Evaluate(ContinuousIndexType(position),ContinuousIndexType(it.GetIndex())));
- for(unsigned int i = 0; i<NeuronType::Length;++i)
+ // output map pointer
+ MapPointerType map = this->GetOutput(0);
+
+ // typedefs
+ typedef itk::ImageRegionIteratorWithIndex<MapType> IteratorType;
+ typedef itk::ContinuousIndex<double,MapType::ImageDimension> ContinuousIndexType;
+ typedef itk::Statistics::EuclideanDistance<ContinuousIndexType> DistanceType;
+ typename DistanceType::Pointer distance = DistanceType::New();
+
+ // winner index in the map
+ IndexType position = map->GetWinner(sample);
+ NeuronType winner = map->GetPixel(position);
+
+ // Local neighborhood definition
+ RegionType localRegion;
+ IndexType localIndex = position-radius;
+ SizeType localSize;
+ for(unsigned int i=0;i<MapType::ImageDimension;++i)
+ {
+ localSize[i]= 2*radius[i]+1;
+ }
+ localRegion.SetIndex(localIndex);
+ localRegion.SetSize(localSize);
+ localRegion.Crop( map->GetLargestPossibleRegion() );
+ IteratorType it ( map, localRegion );
+
+ // Walk through the map, and evolve each neuron depending on its
+ // distance to the winner.
+ for(it.GoToBegin();!it.IsAtEnd();++it)
{
- newNeuron[i] = tempNeuron[i]+static_cast<typename NeuronType::ValueType>((sample[i]-tempNeuron[i])*tempBeta);
+ NeuronType tempNeuron = it.Get();
+ NeuronType newNeuron ( tempNeuron.Size() );
+ double tempBeta = beta
+ / ( 1 +
+ distance->Evaluate( ContinuousIndexType(position),
+ ContinuousIndexType(it.GetIndex()) ) );
+
+ for(unsigned int i = 0; i < newNeuron.Size();++i)
+ {
+ newNeuron[i] = tempNeuron[i]
+ +static_cast<typename NeuronType::ValueType>(
+ ( sample[i] - tempNeuron[i] ) * tempBeta );
+ }
+
+ it.Set(newNeuron);
}
- it.Set(newNeuron);
- }
}
/**
* Step one iteration.
*/
-template <class TListSample,class TMap>
+template < class TListSample, class TMap,
+ class TSOMLearningBehaviorFunctor,
+ class TSOMNeighborhoodBehaviorFunctor >
void
-SOM<TListSample,TMap>
+SOM<TListSample,TMap,TSOMLearningBehaviorFunctor,TSOMNeighborhoodBehaviorFunctor>
::Step(unsigned int currentIteration)
{
- // Compute the new learning coefficient
- double newBeta = (m_BetaEnd-m_BetaInit)/static_cast<double>(m_NumberOfIterations)
- *static_cast<double>(currentIteration)+m_BetaInit;
-
- // Compute the new neighborhood size
- SizeType newSize;
- newSize[0]=m_NeighborhoodSizeInit[0]-static_cast<int>((static_cast<float>(currentIteration)
- /static_cast<float>(m_NumberOfIterations))*static_cast<float>(m_NeighborhoodSizeInit[0]-2));
-
- newSize[1]=m_NeighborhoodSizeInit[1]-static_cast<int>((static_cast<float>(currentIteration)
- /static_cast<float>(m_NumberOfIterations))*static_cast<float>(m_NeighborhoodSizeInit[1]-2));
-
- // update the neurons map with each example of the training set.
- otbMsgDebugMacro(<<"Beta: "<<newBeta<<", radius: "<<newSize);
- for(typename ListSampleType::Iterator it=m_ListSample->Begin();it!=m_ListSample->End();++it)
- {
- UpdateMap(it.GetMeasurementVector(),newBeta,newSize);
- }
+ // Compute the new learning coefficient
+ double newBeta = m_BetaFunctor(
+ currentIteration, m_NumberOfIterations, m_BetaInit, m_BetaEnd );
+
+ // Compute the new neighborhood size
+ SizeType newSize = m_NeighborhoodSizeFunctor(
+ currentIteration, m_NumberOfIterations, m_NeighborhoodSizeInit );
+
+ // update the neurons map with each example of the training set.
+ otbMsgDebugMacro(<<"Beta: "<<newBeta<<", radius: "<<newSize);
+ for ( typename ListSampleType::Iterator it = m_ListSample->Begin();
+ it != m_ListSample->End();
+ ++it )
+ {
+ UpdateMap( it.GetMeasurementVector(), newBeta, newSize );
+ }
+}
+/**
+ * Output information redefinition
+ */
+template < class TListSample, class TMap,
+ class TSOMLearningBehaviorFunctor,
+ class TSOMNeighborhoodBehaviorFunctor >
+void
+SOM<TListSample,TMap,TSOMLearningBehaviorFunctor,TSOMNeighborhoodBehaviorFunctor>
+::GenerateOutputInformation ()
+{
+ Superclass::GenerateOutputInformation();
+ this->GetOutput()->SetNumberOfComponentsPerPixel(
+ m_ListSample->GetMeasurementVectorSize() );
+
+ IndexType index;
+ index.Fill(0);
+
+ RegionType region;
+ region.SetIndex(index);
+ region.SetSize( this->GetMapSize() );
+ this->GetOutput()->SetRegions( region );
+
}
+/**
+ * Output redefinition
+ */
+template < class TListSample, class TMap,
+ class TSOMLearningBehaviorFunctor,
+ class TSOMNeighborhoodBehaviorFunctor >
+void
+SOM<TListSample,TMap,TSOMLearningBehaviorFunctor,TSOMNeighborhoodBehaviorFunctor>
+::AllocateOutputs()
+{
+ if ( this->GetNumberOfOutputs() != 1 )
+ itkExceptionMacro( << "Number of output image should be 1" );
+
+ // output neuron map fill
+ MapPointerType map = this->GetOutput(0);
+ map->Allocate();
+}
+
/**
* Main computation method
*/
-template <class TListSample,class TMap>
+template < class TListSample, class TMap,
+ class TSOMLearningBehaviorFunctor,
+ class TSOMNeighborhoodBehaviorFunctor >
void
-SOM<TListSample,TMap>
+SOM<TListSample,TMap,TSOMLearningBehaviorFunctor,TSOMNeighborhoodBehaviorFunctor>
::GenerateData(void)
{
- // output neuron map fill
- MapPointerType map = this->GetOutput();
- RegionType region;
- IndexType index;
- index.Fill(0);
- region.SetIndex(index);
- region.SetSize(m_MapSize);
- map->SetRegions(region);
- map->Allocate();
-
- if(m_RandomInit)
- {
- typedef itk::Statistics::MersenneTwisterRandomVariateGenerator GeneratorType;
- typedef itk::ImageRegionIterator<MapType> IteratorType;
- GeneratorType::Pointer generator = GeneratorType::New();
- generator->Initialize(m_Seed);
- NeuronType neuronInit;
- IteratorType it(map,map->GetLargestPossibleRegion());
-
- for(it.GoToBegin();!it.IsAtEnd();++it)
+ this->AllocateOutputs();
+ this->BeforeThreadedGenerateData();
+
+ MapPointerType map = this->GetOutput(0);
+
+ if ( m_RandomInit )
{
- for(int i=0;i<NeuronType::Length;++i)
- {
- neuronInit[i]=static_cast<typename NeuronType::ValueType>(
- generator->GetUniformVariate(static_cast<double>(m_MinWeight),static_cast<double>(m_MaxWeight)));
- }
- it.Set(neuronInit);
+ typedef itk::Statistics::MersenneTwisterRandomVariateGenerator GeneratorType;
+ typedef itk::ImageRegionIterator<MapType> IteratorType;
+ GeneratorType::Pointer generator = GeneratorType::New();
+ generator->Initialize(m_Seed);
+
+ NeuronType neuronInit ( m_ListSample->GetMeasurementVectorSize() );
+ IteratorType it ( map, map->GetLargestPossibleRegion() );
+
+ for ( it.GoToBegin(); !it.IsAtEnd(); ++it )
+ {
+ for(unsigned int i=0;i< neuronInit.Size();++i)
+ {
+ neuronInit[i]=static_cast<typename NeuronType::ValueType>(
+ generator->GetUniformVariate(static_cast<double>(m_MinWeight),
+ static_cast<double>(m_MaxWeight)) );
+ }
+ it.Set(neuronInit);
+ }
+ }
+ else
+ {
+ NeuronType neuronInit ( m_ListSample->GetMeasurementVectorSize() );
+ neuronInit.Fill(m_MaxWeight);
+ map->FillBuffer(neuronInit);
+ }
+
+ // Step through the iterations
+ for(unsigned int i = 0;i<m_NumberOfIterations;++i)
+ {
+ //otbMsgDebugMacro(<<"Step "<<i+1<<" / "<<m_NumberOfIterations);
+ std::cerr << "Step "<< i+1 <<" / "<<m_NumberOfIterations << " \r";
+ Step(i);
}
- }
- else
- {
- NeuronType neuronInit;
- neuronInit.Fill(m_MaxWeight);
- map->FillBuffer(neuronInit);
- }
-
- // Step through the iterations
- for(unsigned int i = 0;i<m_NumberOfIterations;++i)
- {
- otbMsgDebugMacro(<<"Step "<<i+1<<" / "<<m_NumberOfIterations);
- Step(i);
- }
+
+ this->AfterThreadedGenerateData();
}
/**
*PrintSelf method
*/
-template <class TListSample,class TMap>
+template < class TListSample, class TMap,
+ class TSOMLearningBehaviorFunctor,
+ class TSOMNeighborhoodBehaviorFunctor >
void
-SOM<TListSample,TMap>
+SOM<TListSample,TMap,TSOMLearningBehaviorFunctor,TSOMNeighborhoodBehaviorFunctor>
::PrintSelf(std::ostream& os, itk::Indent indent) const
{
- Superclass::PrintSelf(os,indent);
+ Superclass::PrintSelf(os,indent);
}
+
} // end namespace otb
+
#endif
+
diff --git a/Code/Learning/otbSOMLearningBehaviorFunctor.h b/Code/Learning/otbSOMLearningBehaviorFunctor.h
new file mode 100644
index 0000000000..17e7073847
--- /dev/null
+++ b/Code/Learning/otbSOMLearningBehaviorFunctor.h
@@ -0,0 +1,67 @@
+/*=========================================================================
+
+Program: ORFEO Toolbox
+Language: C++
+Date: $Date$
+Version: $Revision$
+
+
+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 ITCopyright.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.
+
+=========================================================================*/
+
+#ifndef __otbSOMLearningBehaviorFunctor_h
+#define __otbSOMLearningBehaviorFunctor_h
+
+
+namespace otb {
+
+namespace Functor {
+
+ /** \class SOMLearningBehaviorFunctor
+ * \brief Classical Beta behavior over SOM training phase
+ *
+ * This class implements an standart evolution of the $\beta$ weightening
+ * coefficient over the SOM training.
+ *
+ * \f{equation*}
+ \beta = \beta_0 + \left( \beta_{\text{end}} - \beta_0 \right)
+ \frac{t}{t_{\text{end}}}
+ \f{equation*}
+ *
+ * \sa SOM
+ */
+ class SOMLearningBehaviorFunctor
+ {
+ public :
+ /** Empty constructor / descructor */
+ CzihoSOMLearningBehaviorFunctor () { }
+ virtual ~CzihoSOMLearningBehaviorFunctor() { }
+
+ /** Functor */
+ virtual double operator() ( unsigned int currentIteration,
+ unsigned int numberOfIterations,
+ double betaInit, double betaEnd )
+ {
+ return betaInit + ( betaEnd - betaInit )
+ * static_cast<double>( currentIteration )
+ / static_cast<double>( numberOfIterations );
+ }
+
+ }; // end of class SOMLearningBehaviorFunctor
+
+} // end namespace Functor
+
+} // end namespace otb
+
+#endif
+
+
diff --git a/Code/Learning/otbSOMMap.h b/Code/Learning/otbSOMMap.h
index 173f9c26ed..a826d8e7b7 100644
--- a/Code/Learning/otbSOMMap.h
+++ b/Code/Learning/otbSOMMap.h
@@ -9,6 +9,9 @@ Version: $Revision$
Copyright (c) Centre National d'Etudes Spatiales. All rights reserved.
See OTBCopyright.txt for details.
+Copyright (c) Institut Telecom ; Telecom Bretagne. All right 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
@@ -18,9 +21,9 @@ PURPOSE. See the above copyright notices for more information.
#ifndef _otbSOMMap_h
#define _otbSOMMap_h
-#include "itkFixedArray.h"
+#include "itkVariableLengthVector.h"
#include "itkEuclideanDistance.h"
-#include "otbImage.h"
+#include "otbVectorImage.h"
namespace otb
{
@@ -42,22 +45,26 @@ namespace otb
* \sa SOM
* \sa SOMActivationBuilder
*/
-template <class TNeuron=itk::FixedArray<float,3>,
- class TDistance=itk::Statistics::EuclideanDistance<TNeuron>,unsigned int VMapDimension=2>
+template <class TNeuron=itk::VariableLengthVector<double>,
+ class TDistance=itk::Statistics::EuclideanDistance<TNeuron>,
+ unsigned int VMapDimension=2>
class ITK_EXPORT SOMMap
-: public Image<TNeuron,VMapDimension>
+: public otb::VectorImage<typename TNeuron::ComponentType,VMapDimension>
{
public:
/** Standard typedefs */
typedef SOMMap Self;
- typedef Image<TNeuron,VMapDimension> Superclass;
+ typedef otb::VectorImage<typename TNeuron::ComponentType,VMapDimension> Superclass;
typedef itk::SmartPointer<Self> Pointer;
typedef itk::SmartPointer<const Self> ConstPointer;
/** Creation through object factory macro */
itkNewMacro(Self);
- /** Runtime informations macro */
- itkTypeMacro(SOMMap,Image);
+ /**
+ * There is no runtime informations macro since
+ * this class has to be considered to as a simple VectorImage
+ * // itkTypeMacro(SOMMap,VectorImage);
+ * */
/** Template parameters related typedefs */
typedef TNeuron NeuronType;
diff --git a/Code/Learning/otbSOMMap.txx b/Code/Learning/otbSOMMap.txx
index 288a5ffee4..a008f1f950 100644
--- a/Code/Learning/otbSOMMap.txx
+++ b/Code/Learning/otbSOMMap.txx
@@ -9,6 +9,9 @@ Version: $Revision$
Copyright (c) Centre National d'Etudes Spatiales. All rights reserved.
See OTBCopyright.txt for details.
+Copyright (c) Institut Telecom ; Telecom Bretagne. All right 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
@@ -59,6 +62,7 @@ SOMMap<TNeuron,TDistance,VMapDimension>
// Define the minimum distance and position
IndexType minPos = it.GetIndex();
+
double minDistance = activation->Evaluate(sample,it.Get());
// Iterate through the map to get the minimum distance position
diff --git a/Testing/Code/BasicFilters/CMakeLists.txt b/Testing/Code/BasicFilters/CMakeLists.txt
index f65f5025a2..3a4cbb79ca 100755
--- a/Testing/Code/BasicFilters/CMakeLists.txt
+++ b/Testing/Code/BasicFilters/CMakeLists.txt
@@ -774,6 +774,16 @@ ADD_TEST(bfTvRationalQuotientResampleImageFilter ${BASICFILTERS_TESTS7}
80 80
)
+# ------- otb::EuclideanDistanceWithMissingValue ----------------------------
+
+ ADD_TEST(bfTuEuclideanDistanceWithMissingValueNew ${BASICFILTERS_TESTS8}
+ otbEuclideanDistanceWithMissingValueNew)
+
+ADD_TEST(bfTvEuclideanDistanceWithMissingValue ${BASICFILTERS_TESTS8}
+ otbEuclideanDistanceWithMissingValue)
+
+
+=======
# ------- otb::LabelizeNeighborhoodConnectedImageFilter ----------------------------
ADD_TEST(bfTuLabelizeNeighborhoodConnectedImageFilterNew ${BASICFILTERS_TESTS8}
@@ -919,6 +929,8 @@ otbLabelizeNeighborhoodConnectedImageFilterNew.cxx
otbLabelizeNeighborhoodConnectedImageFilter.cxx
otbLabelizeConfidenceConnectedImageFilterNew.cxx
otbLabelizeConfidenceConnectedImageFilter.cxx
+otbEuclideanDistanceWithMissingValueNew.cxx
+otbEuclideanDistanceWithMissingValue.cxx
)
INCLUDE_DIRECTORIES("${OTBTesting_BINARY_DIR}")
diff --git a/Testing/Code/BasicFilters/otbBasicFiltersTests8.cxx b/Testing/Code/BasicFilters/otbBasicFiltersTests8.cxx
index f4e4171f88..abf982d8af 100644
--- a/Testing/Code/BasicFilters/otbBasicFiltersTests8.cxx
+++ b/Testing/Code/BasicFilters/otbBasicFiltersTests8.cxx
@@ -33,4 +33,6 @@ void RegisterTests()
REGISTER_TEST(otbLabelizeNeighborhoodConnectedImageFilter);
REGISTER_TEST(otbLabelizeConfidenceConnectedImageFilterNew);
REGISTER_TEST(otbLabelizeConfidenceConnectedImageFilter);
+ REGISTER_TEST(otbEuclideanDistanceWithMissingValueNew);
+ REGISTER_TEST(otbEuclideanDistanceWithMissingValue);
}
diff --git a/Testing/Code/BasicFilters/otbEuclideanDistanceWithMissingValue.cxx b/Testing/Code/BasicFilters/otbEuclideanDistanceWithMissingValue.cxx
new file mode 100644
index 0000000000..b88fdfa4a3
--- /dev/null
+++ b/Testing/Code/BasicFilters/otbEuclideanDistanceWithMissingValue.cxx
@@ -0,0 +1,61 @@
+/*=========================================================================
+
+Program: ORFEO Toolbox
+Language: C++
+Date: $Date$
+Version: $Revision$
+
+
+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 ITCopyright.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 <iostream>
+
+#include "itkVariableLengthVector.h"
+#include "otbEuclideanDistanceWithMissingValue.h"
+
+int otbEuclideanDistanceWithMissingValue( int argc, char * argv[] )
+{
+
+ typedef itk::VariableLengthVector< double > VectorType;
+ typedef otb::Statistics::EuclideanDistanceWithMissingValue< VectorType > DistanceType;
+
+ DistanceType::Pointer dist = DistanceType::New();
+
+ if ( dist->IsMissingValue( 0.0 ) )
+ return EXIT_FAILURE;
+
+ if ( dist->IsMissingValue( 1.0 ) )
+ return EXIT_FAILURE;
+
+ if ( dist->IsMissingValue( -1.0 ) )
+ return EXIT_FAILURE;
+
+ /*
+ std::cerr << "Is O Nan ?? -> " << dist->IsMissingValue( 0.0 ) << "\n";
+ std::cerr << "Is 1 Nan ?? -> " << dist->IsMissingValue( 1.0 ) << "\n";
+ std::cerr << "Is -1 Nan ?? -> " << dist->IsMissingValue( -1.0 ) << "\n";
+ */
+
+ double x = 0.0;
+
+ dist->SetToMissingValue(x);
+ if ( !dist->IsMissingValue( x ) )
+ return EXIT_FAILURE;
+ // std::cerr << "Is x (=" << x << ") Nan ?? -> " << dist->IsMissingValue( x ) << "\n";
+
+ return EXIT_SUCCESS;
+}
+
+
+
diff --git a/Testing/Code/BasicFilters/otbEuclideanDistanceWithMissingValueNew.cxx b/Testing/Code/BasicFilters/otbEuclideanDistanceWithMissingValueNew.cxx
new file mode 100644
index 0000000000..063cdccfc3
--- /dev/null
+++ b/Testing/Code/BasicFilters/otbEuclideanDistanceWithMissingValueNew.cxx
@@ -0,0 +1,39 @@
+/*=========================================================================
+
+Program: ORFEO Toolbox
+Language: C++
+Date: $Date$
+Version: $Revision$
+
+
+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 ITCopyright.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 <iostream>
+
+#include "itkVariableLengthVector.h"
+#include "otbEuclideanDistanceWithMissingValue.h"
+
+int otbEuclideanDistanceWithMissingValueNew( int argc, char * argv[] )
+{
+
+ typedef itk::VariableLengthVector< double > VectorType;
+ typedef otb::Statistics::EuclideanDistanceWithMissingValue< VectorType > DistanceType;
+
+ DistanceType::Pointer dist = DistanceType::New();
+
+ return EXIT_SUCCESS;
+}
+
+
+
diff --git a/Testing/Code/Learning/CMakeLists.txt b/Testing/Code/Learning/CMakeLists.txt
index 05aff8bbc7..1730b07384 100644
--- a/Testing/Code/Learning/CMakeLists.txt
+++ b/Testing/Code/Learning/CMakeLists.txt
@@ -161,6 +161,20 @@ ADD_TEST(leTvSOM ${LEARNING_TESTS2}
${TEMP}/leSOMPoupeesSubOutputMap1.hdr
32 32 10 10 5 1.0 0.1 0)
+# ------- otb::PeriodicSOM -----------------------------
+
+ADD_TEST(leTuPeriodicSOMNew ${LEARNING_TESTS2}
+ otbPeriodicSOMNew)
+
+ADD_TEST(leTvPeriodicSOM ${LEARNING_TESTS2}
+ --compare-image ${EPSILON}
+ ${BASELINE}/lePeriodicSOMPoupeesSubOutputMap1.hdr
+ ${TEMP}/lePeriodicSOMPoupeesSubOutputMap1.hdr
+ otbSOM
+ ${INPUTDATA}/poupees_sub.png
+ ${TEMP}/lePeriodicSOMPoupeesSubOutputMap1.hdr
+ 32 32 10 10 5 1.0 0.1 0)
+
# ------- otb::SOMActivationBuilder -----------------------------
ADD_TEST(leTuSOMActivationBuilderNew ${LEARNING_TESTS2}
@@ -267,6 +281,8 @@ otbSOMMapNew.cxx
otbSOMMap.cxx
otbSOMNew.cxx
otbSOM.cxx
+otbPeriodicSOMNew.cxx
+otbPeriodicSOM.cxx
otbSOMActivationBuilderNew.cxx
otbSOMActivationBuilder.cxx
)
diff --git a/Testing/Code/Learning/otbLearningTests2.cxx b/Testing/Code/Learning/otbLearningTests2.cxx
index d7c0956f34..cc1f0e7232 100644
--- a/Testing/Code/Learning/otbLearningTests2.cxx
+++ b/Testing/Code/Learning/otbLearningTests2.cxx
@@ -37,6 +37,8 @@ REGISTER_TEST(otbSOMMapNew);
REGISTER_TEST(otbSOMMap);
REGISTER_TEST(otbSOMNew);
REGISTER_TEST(otbSOM);
+REGISTER_TEST(otbPeriodicSOMNew);
+REGISTER_TEST(otbPeriodicSOM);
REGISTER_TEST(otbSOMActivationBuilderNew);
REGISTER_TEST(otbSOMActivationBuilder);
}
diff --git a/Testing/Code/Learning/otbPeriodicSOM.cxx b/Testing/Code/Learning/otbPeriodicSOM.cxx
new file mode 100644
index 0000000000..05b8a2c836
--- /dev/null
+++ b/Testing/Code/Learning/otbPeriodicSOM.cxx
@@ -0,0 +1,109 @@
+/*=========================================================================
+
+ 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 "itkExceptionObject.h"
+#include "otbVectorImage.h"
+#include "otbSOMMap.h"
+#include "otbPeriodicSOM.h"
+#include "itkRGBPixel.h"
+#include "itkEuclideanDistance.h"
+#include "otbImageFileReader.h"
+#include "otbImageFileWriter.h"
+#include "itkListSample.h"
+#include "itkImageRegionIterator.h"
+
+int otbPeriodicSOM(int argc, char* argv[])
+{
+try
+ {
+ const unsigned int Dimension = 2;
+ char * inputFileName = argv[1];
+ char * outputFileName = argv[2];
+ unsigned int sizeX = atoi(argv[3]);
+ unsigned int sizeY = atoi(argv[4]);
+ unsigned int neighInitX = atoi(argv[5]);
+ unsigned int neighInitY= atoi(argv[6]);
+ unsigned int nbIterations= atoi(argv[7]);
+ double betaInit = atof(argv[8]);
+ double betaEnd= atof(argv[9]);
+ double initValue = atof(argv[10]);
+
+
+ typedef double ComponentType;
+ typedef itk::VariableLengthVector<ComponentType> PixelType;
+ typedef itk::Statistics::EuclideanDistance<PixelType> DistanceType;
+ typedef otb::SOMMap<PixelType,DistanceType,Dimension> MapType;
+ typedef otb::VectorImage<ComponentType,Dimension> ImageType;
+ typedef otb::ImageFileReader<ImageType> ReaderType;
+ typedef itk::Statistics::ListSample<PixelType> ListSampleType;
+
+ typedef otb::PeriodicSOM<ListSampleType,MapType> SOMType;
+ typedef otb::ImageFileWriter<MapType> WriterType;
+
+ ReaderType::Pointer reader = ReaderType::New();
+ reader->SetFileName(inputFileName);
+ reader->Update();
+
+ ListSampleType::Pointer listSample = ListSampleType::New();
+
+ itk::ImageRegionIterator<ImageType> it(reader->GetOutput(),reader->GetOutput()->GetLargestPossibleRegion());
+
+ it.GoToBegin();
+
+ while(!it.IsAtEnd())
+ {
+ listSample->PushBack(it.Get());
+ ++it;
+ }
+
+ std::cout<<"LIST SAMPLE SIZE: "<<listSample->GetMeasurementVectorSize()<<std::endl;
+
+ // Instantiation
+ SOMType::Pointer som = SOMType::New();
+ som->SetListSample(listSample);
+ SOMType::SizeType size;
+ size[0]=sizeX;
+ size[1]=sizeY;
+ som->SetMapSize(size);
+ SOMType::SizeType radius;
+ radius[0] = neighInitX;
+ radius[1] = neighInitY;
+ som->SetNeighborhoodSizeInit(radius);
+ som->SetNumberOfIterations(nbIterations);
+ som->SetBetaInit(betaInit);
+ som->SetBetaEnd(betaEnd);
+ som->SetMaxWeight(initValue);
+ som->SetRandomInit(false);
+
+ WriterType::Pointer writer = WriterType::New();
+ writer->SetFileName(outputFileName);
+ writer->SetInput(som->GetOutput());
+ writer->Update();
+ }
+catch( itk::ExceptionObject & err )
+ {
+ std::cout << "Exception itk::ExceptionObject thrown !" << std::endl;
+ std::cout << err << std::endl;
+ return EXIT_FAILURE;
+ }
+catch( ... )
+ {
+ std::cout << "Unknown exception thrown !" << std::endl;
+ return EXIT_FAILURE;
+ }
+ return EXIT_SUCCESS;
+}
diff --git a/Testing/Code/Learning/otbPeriodicSOMNew.cxx b/Testing/Code/Learning/otbPeriodicSOMNew.cxx
new file mode 100644
index 0000000000..3f8d35e9e2
--- /dev/null
+++ b/Testing/Code/Learning/otbPeriodicSOMNew.cxx
@@ -0,0 +1,53 @@
+/*=========================================================================
+
+ 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 "itkExceptionObject.h"
+#include "otbSOMMap.h"
+#include "otbPeriodicSOM.h"
+#include "itkRGBPixel.h"
+#include "itkEuclideanDistance.h"
+#include "itkListSample.h"
+
+int otbPeriodicSOMNew(int argc, char* argv[])
+{
+try
+ {
+ const unsigned int Dimension = 2;
+ typedef float ComponentType;
+ typedef itk::VariableLengthVector<ComponentType> PixelType;
+ typedef itk::Statistics::EuclideanDistance<PixelType> DistanceType;
+ typedef otb::SOMMap<PixelType,DistanceType,Dimension> SOMMapType;
+// typedef itk::Statistics::ImageToListAdaptor<SOMMapType> AdaptorType;
+ typedef itk::Statistics::ListSample<PixelType> ListSampleType;
+ typedef otb::PeriodicSOM<ListSampleType,SOMMapType> SOMType;
+
+ // Instantiation
+ SOMType::Pointer som = SOMType::New();
+ }
+catch( itk::ExceptionObject & err )
+ {
+ std::cout << "Exception itk::ExceptionObject thrown !" << std::endl;
+ std::cout << err << std::endl;
+ return EXIT_FAILURE;
+ }
+catch( ... )
+ {
+ std::cout << "Unknown exception thrown !" << std::endl;
+ return EXIT_FAILURE;
+ }
+ return EXIT_SUCCESS;
+}
diff --git a/Testing/Code/Learning/otbSOM.cxx b/Testing/Code/Learning/otbSOM.cxx
index 71367c1d4f..03b1474f39 100644
--- a/Testing/Code/Learning/otbSOM.cxx
+++ b/Testing/Code/Learning/otbSOM.cxx
@@ -16,14 +16,15 @@
=========================================================================*/
#include "itkExceptionObject.h"
-#include "otbImage.h"
+#include "otbVectorImage.h"
#include "otbSOMMap.h"
#include "otbSOM.h"
#include "itkRGBPixel.h"
#include "itkEuclideanDistance.h"
#include "otbImageFileReader.h"
#include "otbImageFileWriter.h"
-#include "itkImageToListAdaptor.h"
+#include "itkListSample.h"
+#include "itkImageRegionIterator.h"
int otbSOM(int argc, char* argv[])
{
@@ -43,26 +44,37 @@ try
typedef double ComponentType;
- typedef itk::RGBPixel<ComponentType> PixelType;
+ typedef itk::VariableLengthVector<ComponentType> PixelType;
typedef itk::Statistics::EuclideanDistance<PixelType> DistanceType;
typedef otb::SOMMap<PixelType,DistanceType,Dimension> MapType;
- typedef otb::Image<PixelType,Dimension> ImageType;
+ typedef otb::VectorImage<ComponentType,Dimension> ImageType;
typedef otb::ImageFileReader<ImageType> ReaderType;
- typedef itk::Statistics::ImageToListAdaptor<ImageType> ListAdaptorType;
+ typedef itk::Statistics::ListSample<PixelType> ListSampleType;
- typedef otb::SOM<ListAdaptorType,MapType> SOMType;
+ typedef otb::SOM<ListSampleType,MapType> SOMType;
typedef otb::ImageFileWriter<MapType> WriterType;
ReaderType::Pointer reader = ReaderType::New();
reader->SetFileName(inputFileName);
reader->Update();
- ListAdaptorType::Pointer adaptor = ListAdaptorType::New();
- adaptor->SetImage(reader->GetOutput());
+ ListSampleType::Pointer listSample = ListSampleType::New();
+
+ itk::ImageRegionIterator<ImageType> it(reader->GetOutput(),reader->GetOutput()->GetLargestPossibleRegion());
+
+ it.GoToBegin();
+ while(!it.IsAtEnd())
+ {
+ listSample->PushBack(it.Get());
+ ++it;
+ }
+
+ std::cout<<"LIST SAMPLE SIZE: "<<listSample->GetMeasurementVectorSize()<<std::endl;
+
// Instantiation
SOMType::Pointer som = SOMType::New();
- som->SetListSample(adaptor);
+ som->SetListSample(listSample);
SOMType::SizeType size;
size[0]=sizeX;
size[1]=sizeY;
diff --git a/Testing/Code/Learning/otbSOMActivationBuilder.cxx b/Testing/Code/Learning/otbSOMActivationBuilder.cxx
index c3a6494858..7eb60a3e41 100644
--- a/Testing/Code/Learning/otbSOMActivationBuilder.cxx
+++ b/Testing/Code/Learning/otbSOMActivationBuilder.cxx
@@ -19,11 +19,13 @@
#include "otbImage.h"
#include "otbSOMMap.h"
#include "otbSOMActivationBuilder.h"
-#include "itkRGBPixel.h"
+#include "itkVariableLengthVector.h"
#include "itkEuclideanDistance.h"
#include "otbImageFileReader.h"
#include "otbImageFileWriter.h"
-#include "itkImageToListAdaptor.h"
+#include "itkListSample.h"
+#include "otbVectorImage.h"
+#include "itkImageRegionIterator.h"
int otbSOMActivationBuilder(int argc, char* argv[])
{
@@ -36,33 +38,43 @@ try
typedef float ComponentType;
typedef unsigned char OutputPixelType;
- typedef itk::RGBPixel<ComponentType> PixelType;
+ typedef itk::VariableLengthVector<ComponentType> PixelType;
typedef itk::Statistics::EuclideanDistance<PixelType> DistanceType;
typedef otb::SOMMap<PixelType,DistanceType,Dimension> MapType;
typedef otb::ImageFileReader<MapType> MapReaderType;
- typedef otb::Image<PixelType,Dimension> InputImageType;
+ typedef otb::VectorImage<ComponentType,Dimension> InputImageType;
typedef otb::ImageFileReader<InputImageType> ReaderType;
- typedef itk::Statistics::ImageToListAdaptor<InputImageType> AdaptorType;
+ typedef itk::Statistics::ListSample<PixelType> ListSampleType;
typedef otb::Image<OutputPixelType,Dimension> OutputImageType;
typedef otb::ImageFileWriter<OutputImageType> WriterType;
- typedef otb::SOMActivationBuilder<AdaptorType,MapType,OutputImageType> SOMActivationBuilderType;
+ typedef otb::SOMActivationBuilder<ListSampleType,MapType,OutputImageType> SOMActivationBuilderType;
ReaderType::Pointer reader = ReaderType::New();
reader->SetFileName(vectorSetFileName);
reader->Update();
- AdaptorType::Pointer adaptor = AdaptorType::New();
- adaptor->SetImage(reader->GetOutput());
+
+ ListSampleType::Pointer listSample = ListSampleType::New();
+
+ itk::ImageRegionIterator<InputImageType> it(reader->GetOutput(),reader->GetOutput()->GetLargestPossibleRegion());
+
+ it.GoToBegin();
+
+ while(!it.IsAtEnd())
+ {
+ listSample->PushBack(it.Get());
+ ++it;
+ }
MapReaderType::Pointer mapReader = MapReaderType::New();
mapReader->SetFileName(mapFileName);
SOMActivationBuilderType::Pointer somAct = SOMActivationBuilderType::New();
somAct->SetInput(mapReader->GetOutput());
- somAct->SetListSample(adaptor);
+ somAct->SetListSample(listSample);
WriterType::Pointer writer = WriterType::New();
writer->SetFileName(outputFileName);
diff --git a/Testing/Code/Learning/otbSOMActivationBuilderNew.cxx b/Testing/Code/Learning/otbSOMActivationBuilderNew.cxx
index 85d704ee54..1e75883dfe 100644
--- a/Testing/Code/Learning/otbSOMActivationBuilderNew.cxx
+++ b/Testing/Code/Learning/otbSOMActivationBuilderNew.cxx
@@ -19,10 +19,11 @@
#include "otbSOMMap.h"
#include "otbSOM.h"
#include "otbSOMActivationBuilder.h"
-#include "itkRGBPixel.h"
#include "itkEuclideanDistance.h"
-#include "itkImageToListAdaptor.h"
-
+#include "itkListSample.h"
+#include "itkVariableLengthVector.h"
+#include "otbImage.h"
+#include "otbVectorImage.h"
int otbSOMActivationBuilderNew(int argc, char* argv[])
{
@@ -31,14 +32,14 @@ try
const unsigned int Dimension =2;
typedef float ComponentType;
typedef unsigned char OutputPixelType;
- typedef itk::RGBPixel<ComponentType> PixelType;
+ typedef itk::VariableLengthVector<ComponentType> PixelType;
typedef itk::Statistics::EuclideanDistance<PixelType> DistanceType;
typedef otb::SOMMap<PixelType,DistanceType,Dimension> MapType;
- typedef otb::Image<PixelType,Dimension> InputImageType;
- typedef itk::Statistics::ImageToListAdaptor<InputImageType> AdaptorType;
+ typedef otb::VectorImage<ComponentType,Dimension> InputImageType;
+ typedef itk::Statistics::ListSample<PixelType> ListSampleType;
typedef otb::Image<OutputPixelType,Dimension> OutputImageType;
- typedef otb::SOMActivationBuilder<AdaptorType,MapType,OutputImageType> SOMActivationBuilderType;
+ typedef otb::SOMActivationBuilder<ListSampleType,MapType,OutputImageType> SOMActivationBuilderType;
// Instantiation
SOMActivationBuilderType::Pointer somAct = SOMActivationBuilderType::New();
diff --git a/Testing/Code/Learning/otbSOMClassifier.cxx b/Testing/Code/Learning/otbSOMClassifier.cxx
index 838d09cee1..a7045c1012 100644
--- a/Testing/Code/Learning/otbSOMClassifier.cxx
+++ b/Testing/Code/Learning/otbSOMClassifier.cxx
@@ -22,12 +22,13 @@
#include <fstream>
#include "otbVectorImage.h"
+#include "otbImage.h"
#include "otbSOMMap.h"
#include "otbSOMClassifier.h"
#include "otbImageFileReader.h"
#include "otbImageFileWriter.h"
#include "itkImageRegionIterator.h"
-#include "itkImageToListAdaptor.h"
+#include "itkListSample.h"
int otbSOMClassifier(int argc, char* argv[] )
{
@@ -48,13 +49,13 @@ int otbSOMClassifier(int argc, char* argv[] )
typedef int LabelPixelType;
const unsigned int Dimension = 2;
- typedef itk::RGBPixel<InputPixelType> PixelType;
+ typedef itk::VariableLengthVector<InputPixelType> PixelType;
typedef itk::Statistics::EuclideanDistance<PixelType> DistanceType;
typedef otb::SOMMap<PixelType,DistanceType,Dimension> SOMMapType;
- typedef otb::Image<PixelType,Dimension> InputImageType;
+ typedef otb::VectorImage<InputPixelType,Dimension> InputImageType;
typedef otb::ImageFileReader< InputImageType > ReaderType;
typedef otb::ImageFileReader<SOMMapType> SOMReaderType;
- typedef itk::Statistics::ImageToListAdaptor< InputImageType > SampleType;
+ typedef itk::Statistics::ListSample< PixelType > SampleType;
typedef otb::SOMClassifier<SampleType,SOMMapType,LabelPixelType> ClassifierType;
typedef otb::Image<LabelPixelType, Dimension > OutputImageType;
typedef itk::ImageRegionIterator< OutputImageType> OutputIteratorType;
@@ -70,11 +71,20 @@ int otbSOMClassifier(int argc, char* argv[] )
somreader->Update();
std::cout<<"SOM map read"<<std::endl;
- SampleType::Pointer sample = SampleType::New();
- sample->SetImage(reader->GetOutput());
+ SampleType::Pointer listSample = SampleType::New();
+
+ itk::ImageRegionIterator<InputImageType> it(reader->GetOutput(),reader->GetOutput()->GetLargestPossibleRegion());
+
+ it.GoToBegin();
+
+ while(!it.IsAtEnd())
+ {
+ listSample->PushBack(it.Get());
+ ++it;
+ }
ClassifierType::Pointer classifier = ClassifierType::New() ;
- classifier->SetSample(sample.GetPointer());
+ classifier->SetSample(listSample.GetPointer());
classifier->SetMap(somreader->GetOutput());
classifier->Update() ;
diff --git a/Testing/Code/Learning/otbSOMClassifierNew.cxx b/Testing/Code/Learning/otbSOMClassifierNew.cxx
index 0e53d63797..ec95897e89 100644
--- a/Testing/Code/Learning/otbSOMClassifierNew.cxx
+++ b/Testing/Code/Learning/otbSOMClassifierNew.cxx
@@ -23,7 +23,8 @@
#include <fstream>
#include "otbSOMMap.h"
#include "otbSOMClassifier.h"
-#include "itkImageToListAdaptor.h"
+#include "itkListSample.h"
+#include "otbVectorImage.h"
int otbSOMClassifierNew(int argc, char* argv[] )
{
@@ -33,11 +34,11 @@ int otbSOMClassifierNew(int argc, char* argv[] )
typedef int LabelPixelType;
const unsigned int Dimension = 2;
- typedef itk::RGBPixel<InputPixelType> PixelType;
+ typedef itk::VariableLengthVector<InputPixelType> PixelType;
typedef itk::Statistics::EuclideanDistance<PixelType> DistanceType;
typedef otb::SOMMap<PixelType,DistanceType,Dimension> SOMMapType;
- typedef otb::Image<PixelType,Dimension> InputImageType;
- typedef itk::Statistics::ImageToListAdaptor< InputImageType > SampleType;
+ typedef otb::VectorImage<InputPixelType,Dimension> InputImageType;
+ typedef itk::Statistics::ListSample< PixelType > SampleType;
typedef otb::SOMClassifier<SampleType,SOMMapType,LabelPixelType> ClassifierType;
ClassifierType::Pointer classifier = ClassifierType::New() ;
diff --git a/Testing/Code/Learning/otbSOMMap.cxx b/Testing/Code/Learning/otbSOMMap.cxx
index 5fa01dcfde..f85fbe17eb 100644
--- a/Testing/Code/Learning/otbSOMMap.cxx
+++ b/Testing/Code/Learning/otbSOMMap.cxx
@@ -19,17 +19,19 @@
#include "otbSOMMap.h"
#include "itkRGBPixel.h"
#include "itkEuclideanDistance.h"
+#include "itkVariableLengthVector.h"
int otbSOMMap(int argc, char* argv[])
{
try
{
const unsigned int Dimension = 2;
- typedef float ComponentType;
- typedef itk::RGBPixel<ComponentType> PixelType;
- typedef itk::Statistics::EuclideanDistance<PixelType> DistanceType;
+ typedef float InternalPixelType;
+ typedef itk::VariableLengthVector<InternalPixelType> PixelType;
+ typedef itk::Statistics::EuclideanDistance<PixelType> DistanceType;
typedef otb::SOMMap<PixelType,DistanceType,Dimension> SOMMapType;
+
// Instantiation
SOMMapType::Pointer somMap = SOMMapType::New();
@@ -42,15 +44,18 @@ try
region.SetIndex(index);
region.SetSize(size);
somMap->SetRegions(region);
+ somMap->SetNumberOfComponentsPerPixel(3);
somMap->Allocate();
// Filling with null pixels
PixelType nullPixel;
+ nullPixel.SetSize(3);
nullPixel.Fill(0);
somMap->FillBuffer(nullPixel);
// Definition of a non-null pixel
PixelType winner;
+ winner.SetSize(3);
winner.Fill(1);
index.Fill(32);
somMap->SetPixel(index,winner);
diff --git a/Testing/Code/Learning/otbSOMNew.cxx b/Testing/Code/Learning/otbSOMNew.cxx
index 4a24a778a8..326ff6bd79 100644
--- a/Testing/Code/Learning/otbSOMNew.cxx
+++ b/Testing/Code/Learning/otbSOMNew.cxx
@@ -20,7 +20,7 @@
#include "otbSOM.h"
#include "itkRGBPixel.h"
#include "itkEuclideanDistance.h"
-#include "itkImageToListAdaptor.h"
+#include "itkListSample.h"
int otbSOMNew(int argc, char* argv[])
{
@@ -28,11 +28,12 @@ try
{
const unsigned int Dimension = 2;
typedef float ComponentType;
- typedef itk::RGBPixel<ComponentType> PixelType;
+ typedef itk::VariableLengthVector<ComponentType> PixelType;
typedef itk::Statistics::EuclideanDistance<PixelType> DistanceType;
typedef otb::SOMMap<PixelType,DistanceType,Dimension> SOMMapType;
- typedef itk::Statistics::ImageToListAdaptor<SOMMapType> AdaptorType;
- typedef otb::SOM<AdaptorType,SOMMapType> SOMType;
+// typedef itk::Statistics::ImageToListAdaptor<SOMMapType> AdaptorType;
+ typedef itk::Statistics::ListSample<PixelType> ListSampleType;
+ typedef otb::SOM<ListSampleType,SOMMapType> SOMType;
// Instantiation
SOMType::Pointer som = SOMType::New();
--
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