From a30fb6f27767731a488855658600a4772e853692 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?C=C3=A9dric=20Traizet?= <traizetc@cesbio.cnes.fr>
Date: Tue, 20 Jun 2017 10:02:30 +0200
Subject: [PATCH] som is now a machine learning model, ae and pca have been
deactiveted
---
app/cbDimensionalityReductionTrainer.cxx | 2 +-
include/AutoencoderModel.txx | 1 -
include/DimensionalityReductionModelFactory.h | 2 +-
.../DimensionalityReductionModelFactory.txx | 15 +++---
include/SOMModel.h | 52 +++++++++++--------
include/SOMModel.txx | 3 +-
include/cbLearningApplicationBaseDR.h | 25 +++++----
include/cbLearningApplicationBaseDR.txx | 7 +--
otb-module.cmake | 2 +-
9 files changed, 59 insertions(+), 50 deletions(-)
diff --git a/app/cbDimensionalityReductionTrainer.cxx b/app/cbDimensionalityReductionTrainer.cxx
index dd245a44e5..0f085d4c49 100644
--- a/app/cbDimensionalityReductionTrainer.cxx
+++ b/app/cbDimensionalityReductionTrainer.cxx
@@ -9,7 +9,7 @@
#include "otbShiftScaleSampleListFilter.h"
#include "otbStatisticsXMLFileReader.h"
-#include "otbSharkUtils.h"
+//#include "otbSharkUtils.h"
#include <fstream> // write the model file
diff --git a/include/AutoencoderModel.txx b/include/AutoencoderModel.txx
index b415e3d1d0..a23adb9ba2 100644
--- a/include/AutoencoderModel.txx
+++ b/include/AutoencoderModel.txx
@@ -1,4 +1,3 @@
-
#ifndef AutoencoderModel_txx
#define AutoencoderModel_txx
diff --git a/include/DimensionalityReductionModelFactory.h b/include/DimensionalityReductionModelFactory.h
index e7a913cc07..791199b5e8 100644
--- a/include/DimensionalityReductionModelFactory.h
+++ b/include/DimensionalityReductionModelFactory.h
@@ -20,7 +20,7 @@
#include "DimensionalityReductionModel.h"
#include "otbMachineLearningModelFactoryBase.h"
-
+
namespace otb
{
/** \class MachineLearningModelFactory
diff --git a/include/DimensionalityReductionModelFactory.txx b/include/DimensionalityReductionModelFactory.txx
index 5ccf34a388..a546978fb7 100644
--- a/include/DimensionalityReductionModelFactory.txx
+++ b/include/DimensionalityReductionModelFactory.txx
@@ -22,25 +22,25 @@
#include "otbConfigure.h"
#include "SOMModelFactory.h"
-
+/*
#ifdef OTB_USE_SHARK
#include "AutoencoderModelFactory.h"
#include "PCAModelFactory.h"
#endif
-
+*/
#include "itkMutexLockHolder.h"
namespace otb
{
-
+/*
template <class TInputValue, class TTargetValue>
using AutoencoderModelFactory = AutoencoderModelFactoryBase<TInputValue, TTargetValue, shark::Autoencoder<shark::TanhNeuron, shark::LinearNeuron>> ;
template <class TInputValue, class TTargetValue>
using TiedAutoencoderModelFactory = AutoencoderModelFactoryBase<TInputValue, TTargetValue, shark::TiedAutoencoder< shark::TanhNeuron, shark::LinearNeuron>> ;
-
+*/
template <class TInputValue, class TTargetValue>
using SOM2DModelFactory = SOMModelFactory<TInputValue, TTargetValue, 2> ;
@@ -115,13 +115,13 @@ DimensionalityReductionModelFactory<TInputValue,TOutputValue>
RegisterFactory(SOM3DModelFactory<TInputValue,TOutputValue>::New());
RegisterFactory(SOM4DModelFactory<TInputValue,TOutputValue>::New());
RegisterFactory(SOM5DModelFactory<TInputValue,TOutputValue>::New());
-
+ /*
#ifdef OTB_USE_SHARK
RegisterFactory(PCAModelFactory<TInputValue,TOutputValue>::New());
RegisterFactory(AutoencoderModelFactory<TInputValue,TOutputValue>::New());
RegisterFactory(TiedAutoencoderModelFactory<TInputValue,TOutputValue>::New());
#endif
-
+ */
}
template <class TInputValue, class TOutputValue>
@@ -182,6 +182,7 @@ DimensionalityReductionModelFactory<TInputValue,TOutputValue>
itk::ObjectFactoryBase::UnRegisterFactory(som2dFactory);
continue;
}
+ /*
#ifdef OTB_USE_SHARK
// Autoencoder
@@ -210,7 +211,7 @@ DimensionalityReductionModelFactory<TInputValue,TOutputValue>
continue;
}
#endif
-
+*/
}
}
diff --git a/include/SOMModel.h b/include/SOMModel.h
index 290ee45c60..846b0f2a2e 100644
--- a/include/SOMModel.h
+++ b/include/SOMModel.h
@@ -1,7 +1,7 @@
#ifndef SOMModel_h
#define SOMModel_h
-#include "DimensionalityReductionModel.h"
+//#include "DimensionalityReductionModel.h"
#include "otbSOMMap.h"
#include "otbSOM.h"
@@ -11,38 +11,45 @@
#include "otbCzihoSOMLearningBehaviorFunctor.h"
#include "otbCzihoSOMNeighborhoodBehaviorFunctor.h"
-
+#include "otbMachineLearningModelTraits.h"
+#include "otbMachineLearningModel.h"
namespace otb
{
template <class TInputValue, unsigned int MapDimension>
-class ITK_EXPORT SOMModel: public DimensionalityReductionModel<TInputValue,TInputValue>
+class ITK_EXPORT SOMModel: public MachineLearningModel<itk::VariableLengthVector< TInputValue> , itk::VariableLengthVector< TInputValue>>
{
public:
typedef SOMModel Self;
- typedef DimensionalityReductionModel<TInputValue,TInputValue> Superclass;
+ typedef MachineLearningModel<itk::VariableLengthVector< TInputValue> , itk::VariableLengthVector< TInputValue>> Superclass;
typedef itk::SmartPointer<Self> Pointer;
typedef itk::SmartPointer<const Self> ConstPointer;
- typedef typename Superclass::InputValueType InputValueType;
- typedef typename Superclass::InputSampleType InputSampleType;
- typedef typename Superclass::InputListSampleType InputListSampleType;
- typedef typename InputListSampleType::Pointer ListSamplePointerType;
- typedef typename Superclass::TargetValueType TargetValueType;
- typedef typename Superclass::TargetSampleType TargetSampleType;
- typedef typename Superclass::TargetListSampleType TargetListSampleType;
+ typedef typename Superclass::InputValueType InputValueType;
+ typedef typename Superclass::InputSampleType InputSampleType;
+ typedef typename Superclass::InputListSampleType InputListSampleType;
+ typedef typename InputListSampleType::Pointer ListSamplePointerType;
+ typedef typename Superclass::TargetValueType TargetValueType;
+ typedef typename Superclass::TargetSampleType TargetSampleType;
+ typedef typename Superclass::TargetListSampleType TargetListSampleType;
- typedef SOMMap<itk::VariableLengthVector<TInputValue>,itk::Statistics::EuclideanDistanceMetric<itk::VariableLengthVector<TInputValue>>, MapDimension> MapType;
- typedef typename MapType::SizeType SizeType;
- typedef typename MapType::SpacingType SpacingType;
+ /// Confidence map related typedefs
- typedef otb::SOM<InputListSampleType, MapType> EstimatorType;
+ typedef typename Superclass::ConfidenceValueType ConfidenceValueType;
+ typedef typename Superclass::ConfidenceSampleType ConfidenceSampleType;
+ typedef typename Superclass::ConfidenceListSampleType ConfidenceListSampleType;
-
- typedef Functor::CzihoSOMLearningBehaviorFunctor SOMLearningBehaviorFunctorType;
- typedef Functor::CzihoSOMNeighborhoodBehaviorFunctor SOMNeighborhoodBehaviorFunctorType;
+
+
+ typedef SOMMap<itk::VariableLengthVector<TInputValue>,itk::Statistics::EuclideanDistanceMetric<itk::VariableLengthVector<TInputValue>>, MapDimension> MapType;
+ typedef typename MapType::SizeType SizeType;
+ typedef typename MapType::SpacingType SpacingType;
+ typedef otb::SOM<InputListSampleType, MapType> EstimatorType;
+
+ typedef Functor::CzihoSOMLearningBehaviorFunctor SOMLearningBehaviorFunctorType;
+ typedef Functor::CzihoSOMNeighborhoodBehaviorFunctor SOMNeighborhoodBehaviorFunctorType;
itkNewMacro(Self);
itkTypeMacro(SOMModel, DimensionalityReductionModel);
@@ -72,8 +79,8 @@ public:
bool CanReadFile(const std::string & filename);
bool CanWriteFile(const std::string & filename);
- void Save(const std::string & filename, const std::string & name="") ITK_OVERRIDE;
- void Load(const std::string & filename, const std::string & name="") ITK_OVERRIDE;
+ void Save(const std::string & filename, const std::string & name="") ;
+ void Load(const std::string & filename, const std::string & name="") ;
void Train() ITK_OVERRIDE;
//void Dimensionality_reduction() {}; // Dimensionality reduction is done by DoPredict
@@ -83,11 +90,10 @@ protected:
SOMModel();
~SOMModel() ITK_OVERRIDE;
- virtual TargetSampleType DoPredict(const InputSampleType& input) const ITK_OVERRIDE;
-
private:
typename MapType::Pointer m_SOMMap;
-
+
+ virtual TargetSampleType DoPredict(const InputSampleType& input, ConfidenceValueType * quality = ITK_NULLPTR) const;
/** Map Parameters used for training */
diff --git a/include/SOMModel.txx b/include/SOMModel.txx
index 13765ccbfb..29e226f4da 100644
--- a/include/SOMModel.txx
+++ b/include/SOMModel.txx
@@ -1,4 +1,3 @@
-
#ifndef SOMModel_txx
#define SOMModel_txx
@@ -177,7 +176,7 @@ void SOMModel<TInputValue, MapDimension>::Load(const std::string & filename, con
template <class TInputValue, unsigned int MapDimension>
typename SOMModel<TInputValue, MapDimension>::TargetSampleType
-SOMModel<TInputValue, MapDimension>::DoPredict(const InputSampleType & value) const
+SOMModel<TInputValue, MapDimension>::DoPredict(const InputSampleType & value, ConfidenceValueType * quality) const
{
unsigned int dimension =MapType::ImageDimension;
TargetSampleType target;
diff --git a/include/cbLearningApplicationBaseDR.h b/include/cbLearningApplicationBaseDR.h
index a45024aa47..71c31f40fe 100644
--- a/include/cbLearningApplicationBaseDR.h
+++ b/include/cbLearningApplicationBaseDR.h
@@ -15,12 +15,12 @@
#include "DimensionalityReductionModelFactory.h"
#include "SOMModel.h"
-
+/*
#ifdef OTB_USE_SHARK
#include "AutoencoderModel.h"
#include "PCAModel.h"
#endif
-
+*/
namespace otb
{
namespace Wrapper
@@ -99,7 +99,7 @@ public:
typedef SOMMap<itk::VariableLengthVector<TInputValue>,itk::Statistics::EuclideanDistanceMetric<itk::VariableLengthVector<TInputValue>>, 5> Map5DType;
typedef otb::SOMModel<InputValueType, 5> SOM5DModelType;
-
+/*
#ifdef OTB_USE_SHARK
typedef shark::Autoencoder< shark::TanhNeuron, shark::LinearNeuron> AutoencoderType;
typedef otb::AutoencoderModel<InputValueType, AutoencoderType> AutoencoderModelType;
@@ -109,7 +109,7 @@ public:
typedef otb::PCAModel<InputValueType> PCAModelType;
#endif
-
+ */
protected:
cbLearningApplicationBaseDR();
@@ -131,11 +131,15 @@ private:
/** Specific Init and Train methods for each machine learning model */
//@{
-
+
+ void InitSOMParams();
+ template <class somchoice>
+ void TrainSOM(typename ListSampleType::Pointer trainingListSample, std::string modelPath);
+ void BeforeTrainSOM(typename ListSampleType::Pointer trainingListSample, std::string modelPath);
+/*
#ifdef OTB_USE_SHARK
void InitAutoencoderParams();
void InitPCAParams();
- void InitSOMParams();
void BeforeTrainAutoencoder(typename ListSampleType::Pointer trainingListSample, std::string modelPath);
template <class autoencoderchoice>
@@ -143,10 +147,8 @@ private:
void TrainPCA(typename ListSampleType::Pointer trainingListSample, std::string modelPath);
- template <class somchoice>
- void TrainSOM(typename ListSampleType::Pointer trainingListSample, std::string modelPath);
- void BeforeTrainSOM(typename ListSampleType::Pointer trainingListSample, std::string modelPath);
-#endif
+
+#endif */
//@}
};
@@ -156,10 +158,11 @@ private:
#ifndef OTB_MANUAL_INSTANTIATION
#include "cbLearningApplicationBaseDR.txx"
#include "cbTrainSOM.txx"
+/*
#ifdef OTB_USE_SHARK
#include "cbTrainAutoencoder.txx"
#include "cbTrainPCA.txx"
-#endif
+#endif*/
#endif
#endif
diff --git a/include/cbLearningApplicationBaseDR.txx b/include/cbLearningApplicationBaseDR.txx
index 5603cca4f6..2befe3e396 100644
--- a/include/cbLearningApplicationBaseDR.txx
+++ b/include/cbLearningApplicationBaseDR.txx
@@ -50,11 +50,12 @@ cbLearningApplicationBaseDR<TInputValue,TOutputValue>
InitSOMParams();
+ /*
#ifdef OTB_USE_SHARK
InitAutoencoderParams();
InitPCAParams();
#endif
-
+ */
}
template <class TInputValue, class TOutputValue>
@@ -79,7 +80,7 @@ cbLearningApplicationBaseDR<TInputValue,TOutputValue>
{
BeforeTrainSOM(trainingListSample,modelPath);
}
-
+ /*
if(modelName == "autoencoder")
{
#ifdef OTB_USE_SHARK
@@ -104,7 +105,7 @@ cbLearningApplicationBaseDR<TInputValue,TOutputValue>
#else
otbAppLogFATAL("Module SharkLearning is not installed. You should consider turning OTB_USE_SHARK on during cmake configuration.");
#endif
- }
+ }*/
}
}
diff --git a/otb-module.cmake b/otb-module.cmake
index f4a7c8f8ca..258fdf1c44 100644
--- a/otb-module.cmake
+++ b/otb-module.cmake
@@ -6,9 +6,9 @@ otb_module(CbDimensionalityReduction
OTBITK
OTBShark
OTBBoost
- OTBSupervised
OTBAppClassification
OTBSOM
+ OTBLearningBase
DESCRIPTION
"${DOCUMENTATION}"
)
--
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