diff --git a/app/cbDimensionalityReduction.cxx b/app/cbDimensionalityReduction.cxx
index c689f7110849e89035c058cb521df46c1605dbda..abe3875264e729e45d343fc032115e1e913fe0fa 100644
--- a/app/cbDimensionalityReduction.cxx
+++ b/app/cbDimensionalityReduction.cxx
@@ -28,6 +28,8 @@
#include "otbImageToVectorImageCastFilter.h"
#include "DimensionalityReductionModelFactory.h"
+#include "PCAModel.h"
+
namespace otb
{
namespace Functor
diff --git a/include/DimensionalityReductionModelFactory.txx b/include/DimensionalityReductionModelFactory.txx
index 4cd8751994904ca076a5cd8fc5810a03b47490a4..51064244036152bdb3d4992370eb50547f2f1cc8 100644
--- a/include/DimensionalityReductionModelFactory.txx
+++ b/include/DimensionalityReductionModelFactory.txx
@@ -24,6 +24,7 @@
#ifdef OTB_USE_SHARK
#include "AutoencoderModelFactory.h"
+#include "PCAModelFactory.h"
#endif
#include "itkMutexLockHolder.h"
@@ -87,6 +88,7 @@ DimensionalityReductionModelFactory<TInputValue,TOutputValue>
#ifdef OTB_USE_SHARK
+ RegisterFactory(PCAModelFactory<TInputValue,TOutputValue>::New());
RegisterFactory(AutoencoderModelFactory<TInputValue,TOutputValue>::New());
RegisterFactory(TiedAutoencoderModelFactory<TInputValue,TOutputValue>::New());
#endif
@@ -137,6 +139,14 @@ DimensionalityReductionModelFactory<TInputValue,TOutputValue>
itk::ObjectFactoryBase::UnRegisterFactory(taeFactory);
continue;
}
+
+ PCAModelFactory<TInputValue,TOutputValue> *pcaFactory =
+ dynamic_cast<PCAModelFactory<TInputValue,TOutputValue> *>(*itFac);
+ if (pcaFactory)
+ {
+ itk::ObjectFactoryBase::UnRegisterFactory(pcaFactory);
+ continue;
+ }
#endif
}
diff --git a/include/PCAModel.h b/include/PCAModel.h
index e7cdafa21b994f4092ae4f81dfbdc3dd4eb47718..529d2fa9bb8ecd2ece54d81e061c25c29e02b899 100644
--- a/include/PCAModel.h
+++ b/include/PCAModel.h
@@ -31,7 +31,7 @@ public:
itkTypeMacro(AutoencoderModel, DimensionalityReductionModel);
unsigned int GetDimension() {return m_Dimension;};
- itkGetMacro(Dimension,unsigned int);
+ //itkGetMacro(Dimension,unsigned int);
bool CanReadFile(const std::string & filename);
bool CanWriteFile(const std::string & filename);
@@ -51,9 +51,9 @@ protected:
virtual void DoPredictBatch(const InputListSampleType *, const unsigned int & startIndex, const unsigned int & size, TargetListSampleType *, ConfidenceListSampleType * = ITK_NULLPTR) const ITK_OVERRIDE;
private:
- LinearModel<> m_encoder
- LinearModel<> m_decoder
- PCA m_pca;
+ shark::LinearModel<> m_encoder;
+ shark::LinearModel<> m_decoder;
+ shark::PCA m_pca;
unsigned int m_Dimension;
};
diff --git a/include/PCAModel.txx b/include/PCAModel.txx
index f0c2c010f9b59488f35db65f7f0d34f702189f8e..329b2558cf77626de248f505844aed3664111f38 100644
--- a/include/PCAModel.txx
+++ b/include/PCAModel.txx
@@ -52,7 +52,7 @@ bool PCAModel<TInputValue>::CanReadFile(const std::string & filename)
try
{
this->Load(filename);
- m_net.name();
+ m_encoder.name();
}
catch(...)
{
@@ -72,9 +72,9 @@ template <class TInputValue>
void PCAModel<TInputValue>::Save(const std::string & filename, const std::string & name)
{
std::ofstream ofs(filename);
- ofs << m_net.name() << std::endl; //first line
+ ofs << m_encoder.name() << std::endl; //first line
boost::archive::polymorphic_text_oarchive oa(ofs);
- m_net.write(oa);
+ m_encoder.write(oa);
ofs.close();
}
@@ -82,17 +82,17 @@ template <class TInputValue>
void PCAModel<TInputValue>::Load(const std::string & filename, const std::string & name)
{
std::ifstream ifs(filename);
- char autoencoder[256];
- ifs.getline(autoencoder,256);
- std::string autoencoderstr(autoencoder);
+ char encoder[256];
+ ifs.getline(encoder,256);
+ std::string encoderstr(encoder);
- if (autoencoderstr != m_net.name()){
+ if (autoencoderstr != m_encoder.name()){
itkExceptionMacro(<< "Error opening " << filename.c_str() );
}
boost::archive::polymorphic_text_iarchive ia(ifs);
m_net.read(ia);
ifs.close();
- m_NumberOfHiddenNeurons = m_net.numberOfHiddenNeurons();
+ m_Dimension = m_encoder.outputSize();
//this->m_Size = m_NumberOfHiddenNeurons;
}
@@ -108,14 +108,18 @@ PCAModel<TInputValue>::DoPredict(const InputSampleType & value, ConfidenceValueT
}
shark::Data<shark::RealVector> data;
data.element(0)=samples;
- data = m_net.encode(data);
+ data = m_encoder(data);
TargetSampleType target;
//target.SetSize(m_NumberOfHiddenNeurons);
+
for(unsigned int a = 0; a < m_NumberOfHiddenNeurons; ++a){
- //target[a]=data.element(0)[a];
- target=data.element(0)[a];
+ target[a]=p[a];
+
+ //target.SetElement(a,p[a]);
+
+
}
return target;
}
@@ -130,7 +134,7 @@ void PCAModel<TInputValue>
Shark::ListSampleRangeToSharkVector(input, features,startIndex,size);
shark::Data<shark::RealVector> data = shark::createDataFromRange(features);
TargetSampleType target;
- data = m_net.encode(data);
+ data = m_encoder(data);
unsigned int id = startIndex;
target.SetSize(m_NumberOfHiddenNeurons);
for(const auto& p : data.elements()){
diff --git a/include/PCAModelFactory.h b/include/PCAModelFactory.h
new file mode 100644
index 0000000000000000000000000000000000000000..56c0b88c6c3d85414d8f0d95b93f64047d2fbd06
--- /dev/null
+++ b/include/PCAModelFactory.h
@@ -0,0 +1,59 @@
+#ifndef PCAModelFactory_h
+#define PCAModelFactory_h
+
+
+#include "itkObjectFactoryBase.h"
+#include "itkImageIOBase.h"
+
+namespace otb
+{
+
+template <class TInputValue, class TTargetValue>
+class ITK_EXPORT PCAModelFactory : public itk::ObjectFactoryBase
+{
+public:
+ /** Standard class typedefs. */
+ typedef PCAModelFactory Self;
+ typedef itk::ObjectFactoryBase Superclass;
+ typedef itk::SmartPointer<Self> Pointer;
+ typedef itk::SmartPointer<const Self> ConstPointer;
+
+ /** Class methods used to interface with the registered factories. */
+ const char* GetITKSourceVersion(void) const ITK_OVERRIDE;
+ const char* GetDescription(void) const ITK_OVERRIDE;
+
+ /** Method for class instantiation. */
+ itkFactorylessNewMacro(Self);
+
+ /** Run-time type information (and related methods). */
+ itkTypeMacro(PCAModelFactory, itk::ObjectFactoryBase);
+
+ /** Register one factory of this type */
+ static void RegisterOneFactory(void)
+ {
+ Pointer PCAFactory = PCAModelFactory::New();
+ itk::ObjectFactoryBase::RegisterFactory(PCAFactory);
+ }
+
+protected:
+ PCAModelFactory();
+ ~PCAModelFactory() ITK_OVERRIDE;
+
+private:
+ PCAModelFactory(const Self &); //purposely not implemented
+ void operator =(const Self&); //purposely not implemented
+
+};
+
+
+
+} //namespace otb
+
+
+#ifndef OTB_MANUAL_INSTANTIATION
+#include "PCAModelFactory.txx"
+#endif
+
+#endif
+
+
diff --git a/include/PCAModelFactory.txx b/include/PCAModelFactory.txx
new file mode 100644
index 0000000000000000000000000000000000000000..2a0ff98b44a2f9a352be9eb2018dba75180ffce8
--- /dev/null
+++ b/include/PCAModelFactory.txx
@@ -0,0 +1,65 @@
+/*=========================================================================
+
+ 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.
+
+=========================================================================*/
+#ifndef AutoencoderModelFactory_txx
+#define AutoencoderModelFactory_txx
+
+
+#include "AutoencoderModelFactory.h"
+
+#include "itkCreateObjectFunction.h"
+#include "AutoencoderModel.h"
+#include <shark/Algorithms/Trainers/PCA.h>
+#include "itkVersion.h"
+
+namespace otb
+{
+template <class TInputValue, class TOutputValue>
+PCAModelFactory<TInputValue,TOutputValue>::PCAModelFactory()
+{
+
+ std::string classOverride = std::string("DimensionalityReductionModel");
+ std::string subclass = std::string("PCAModel");
+
+ this->RegisterOverride(classOverride.c_str(),
+ subclass.c_str(),
+ "Shark PCA ML Model",
+ 1,
+ // itk::CreateObjectFunction<AutoencoderModel<TInputValue,TOutputValue> >::New());
+ itk::CreateObjectFunction<PCAModel<TInputValue,shark::LinearModel<> > >::New());
+}
+
+template <class TInputValue, class TOutputValue>
+PCAModelFactory<TInputValue,TOutputValue>::~PCAModelFactory()
+{
+}
+
+template <class TInputValue, class TOutputValue>
+const char* PCAModelFactory<TInputValue,TOutputValue>::GetITKSourceVersion(void) const
+{
+ return ITK_SOURCE_VERSION;
+}
+
+template <class TInputValue, class TOutputValue>
+const char* PCAModelFactory<TInputValue,TOutputValue>::GetDescription() const
+{
+ return "PCA model factory";
+}
+
+} // end namespace otb
+
+#endif
diff --git a/include/cbLearningApplicationBaseDR.h b/include/cbLearningApplicationBaseDR.h
index da6311c263a0e391e8e4dc4dcdda3217972a96ac..abd8cfc55f801a69747ec1e9f143e6cf36ff6ebd 100644
--- a/include/cbLearningApplicationBaseDR.h
+++ b/include/cbLearningApplicationBaseDR.h
@@ -16,6 +16,7 @@
#ifdef OTB_USE_SHARK
#include "AutoencoderModel.h"
+#include "PCAModel.h"
#endif
namespace otb