From f3c26934f88d4f6ece51b65a42a2bf628b693346 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?C=C3=A9dric=20Traizet?= <traizetc@cesbio.cnes.fr>
Date: Thu, 27 Apr 2017 16:42:02 +0200
Subject: [PATCH] Dimensionality reduction app created (dummy), encode filter
.h and .txx added
---
app/cbDimensionalityReduction.cxx | 31 ++++++
include/encode_filter.h | 53 ++++++++++
include/encode_filter.txx | 160 ++++++++++++++++++++++++++++++
3 files changed, 244 insertions(+)
create mode 100644 app/cbDimensionalityReduction.cxx
create mode 100644 include/encode_filter.h
create mode 100644 include/encode_filter.txx
diff --git a/app/cbDimensionalityReduction.cxx b/app/cbDimensionalityReduction.cxx
new file mode 100644
index 0000000000..5986fd3a74
--- /dev/null
+++ b/app/cbDimensionalityReduction.cxx
@@ -0,0 +1,31 @@
+#include "otbWrapperApplication.h"
+#include "otbWrapperApplicationFactory.h"
+
+class CbDimensionalityReduction : public otb::Wrapper::Application
+{
+public:
+ typedef CbDimensionalityReduction Self;
+ typedef itk::SmartPointer<Self> Pointer;
+ itkNewMacro(Self);
+ itkTypeMacro(CbDimensionalityReduction, otb::Wrapper::Application);
+private:
+ void DoInit()
+ {
+ SetName("CbDimensionalityReduction");
+ SetDescription("Perform dimensionality reduction on the input image");
+ AddRAMParameter();
+ }
+
+ void DoUpdateParameters()
+ {
+ }
+
+ void DoExecute()
+ {
+ std::cout << "Appli !" << std::endl;
+ int ThisDoesNothing = 0;
+ }
+
+};
+
+OTB_APPLICATION_EXPORT(CbDimensionalityReduction)
diff --git a/include/encode_filter.h b/include/encode_filter.h
new file mode 100644
index 0000000000..9a6b70c117
--- /dev/null
+++ b/include/encode_filter.h
@@ -0,0 +1,53 @@
+#ifndef __encode_Filter_h
+#define __encode_Filter_h
+
+#include "itkImageToImageFilter.h"
+#include "itkMacro.h"
+
+
+template< class TImage, class AutoencoderModel, class NormalizerModel>
+class ITK_EXPORT EncodeFilter:public itk::ImageToImageFilter< TImage, TImage >
+{
+ public:
+ /** Standard class typedefs. */
+ typedef EncodeFilter Self;
+ typedef itk::ImageToImageFilter< TImage, TImage > Superclass;
+ typedef itk::SmartPointer< Self > Pointer;
+
+ /** Method for creation through the object factory. */
+ itkNewMacro(Self);
+
+ /** Run-time type information (and related methods). */
+ itkTypeMacro(EncodeFilter, ImageToImageFilter);
+
+ //void SetInputImage(const TImage* image);
+ void SetAutoencoderModel(const std::string encoderPath);
+ void SetNormalizerModel(const std::string NormalizerPath);
+ void SetModels( const AutoencoderModel net, const NormalizerModel normalizer);
+
+ protected:
+ EncodeFilter();
+ ~EncodeFilter(){}
+
+ typename TImage::ConstPointer GetInputImage();
+ AutoencoderModel GetAutoencoderModel();
+ NormalizerModel GetNormalizerModel();
+
+ /** Does the real work. */
+
+ virtual void BeforeThreadedGenerateData();
+ void ThreadedGenerateData(const typename TImage::RegionType &outputRegionForThread, unsigned int threadId) ITK_OVERRIDE;
+
+ private:
+ EncodeFilter(const Self &); //purposely not implemented
+ void operator=(const Self &); //purposely not implemented
+ AutoencoderModel m_net;
+ NormalizerModel m_normalizer;
+};
+
+#ifndef ITK_MANUAL_INSTANTIATION
+#include "encode_filter.txx"
+#endif
+
+
+#endif // __encode_Filter_h
diff --git a/include/encode_filter.txx b/include/encode_filter.txx
new file mode 100644
index 0000000000..adb071854f
--- /dev/null
+++ b/include/encode_filter.txx
@@ -0,0 +1,160 @@
+#ifndef __encode_filter_txx
+#define __encode_filter_txx
+
+#include "encode_filter.h"
+#include <fstream>
+
+
+#include "itkObjectFactory.h"
+#include "itkImageRegionIterator.h"
+#include "itkImageRegionConstIterator.h"
+#include "otbVectorImage.h"
+
+
+#include <shark/Data/Csv.h>
+#include <shark/Data/Pgm.h> //for exporting the learned filters
+#include <shark/Data/SparseData.h>//for reading in the images as sparseData/Libsvm format
+#include <shark/Models/Autoencoder.h>//normal autoencoder model
+#include <shark/Models/TiedAutoencoder.h>//autoencoder with tied weights
+#include <shark/Models/Normalizer.h>
+#include <shark/Algorithms/Trainers/NormalizeComponentsUnitVariance.h>
+
+
+//using namespace shark;
+
+template< class TImage, class AutoencoderModel, class NormalizerModel>
+EncodeFilter<TImage, AutoencoderModel, NormalizerModel>::EncodeFilter()
+{
+ this->SetNumberOfRequiredInputs(1);
+}
+
+
+template< class TImage, class AutoencoderModel, class NormalizerModel>
+void EncodeFilter<TImage, AutoencoderModel, NormalizerModel>::SetAutoencoderModel(const std::string encoderPath)
+{
+ //m_net = net;
+ std::ifstream ifs(encoderPath);
+ boost::archive::polymorphic_text_iarchive ia(ifs);
+ m_net.read(ia);
+ ifs.close();
+}
+
+
+template< class TImage, class AutoencoderModel, class NormalizerModel>
+void EncodeFilter<TImage, AutoencoderModel, NormalizerModel>::SetNormalizerModel(const std::string NormalizerPath)
+{
+ //m_normalizer = normalizer;
+ std::ifstream ifs(NormalizerPath);
+ boost::archive::polymorphic_text_iarchive ia(ifs);
+ m_normalizer.read(ia);
+ ifs.close();
+}
+
+
+template< class TImage, class AutoencoderModel, class NormalizerModel>
+void EncodeFilter<TImage, AutoencoderModel, NormalizerModel>::SetModels(const AutoencoderModel net, const NormalizerModel normalizer)
+{
+ m_net = net;
+ m_normalizer = normalizer;
+}
+
+
+template< class TImage, class AutoencoderModel, class NormalizerModel>
+typename TImage::ConstPointer EncodeFilter<TImage, AutoencoderModel, NormalizerModel>::GetInputImage()
+{
+ return static_cast< const TImage * >
+ ( this->itk::ProcessObject::GetInput(0) );
+}
+
+
+
+template< class TImage, class AutoencoderModel, class NormalizerModel>
+AutoencoderModel EncodeFilter<TImage, AutoencoderModel, NormalizerModel>::GetAutoencoderModel()
+{
+ return m_net;
+}
+
+
+template< class TImage, class AutoencoderModel, class NormalizerModel>
+NormalizerModel EncodeFilter<TImage, AutoencoderModel, NormalizerModel>::GetNormalizerModel()
+{
+ return m_normalizer;
+}
+
+
+
+struct Data_with_info {
+ shark::Data<shark::RealVector> data; // This file format can be used to do Machine Learning with the Shark ML library
+ otb::VectorImage<double, 2>::RegionType region;
+ otb::VectorImage<double, 2>::PointType origin;
+ otb::VectorImage<double, 2>::SpacingType spacing;
+};
+
+
+template< class TImage, class AutoencoderModel, class NormalizerModel>
+void EncodeFilter<TImage, AutoencoderModel, NormalizerModel>::BeforeThreadedGenerateData()
+{
+#ifdef _OPENMP
+// OpenMP will take care of threading
+this->SetNumberOfThreads(1);
+#endif
+}
+
+
+/*template< class TImage, class AutoencoderModel, class NormalizerModel>
+void EncodeFilter<TImage, AutoencoderModel, NormalizerModel>::GenerateData()*/
+template< class TImage, class AutoencoderModel, class NormalizerModel>
+void EncodeFilter<TImage, AutoencoderModel, NormalizerModel>::ThreadedGenerateData(const typename TImage::RegionType &outputRegionForThread, unsigned int threadId)
+{
+ //Data_with_info info;
+ typename TImage::ConstPointer input = this->GetInput();
+ typename TImage::Pointer output = this->GetOutput();
+
+ // Image to vector
+ const unsigned int img_bands = input->GetNumberOfComponentsPerPixel();
+
+ itk::ImageRegionConstIterator<TImage> inputIterator(input,outputRegionForThread);
+
+ std::vector<shark::RealVector> image_vect;
+
+ typename TImage::PixelType pixelValue;
+ while(!inputIterator.IsAtEnd()){
+ shark::RealVector vect;
+ pixelValue = inputIterator.Get();
+ for(unsigned int a = 0; a < img_bands; ++a){
+ vect.push_back(pixelValue[a]);
+ }
+ image_vect.push_back(vect);
+ ++inputIterator;
+ }
+ shark::Data<shark::RealVector> data = shark::createDataFromRange(image_vect);
+ image_vect.clear();
+
+ /** Normalize the data */
+
+ data= transform(data, m_normalizer);
+ /** Encode the data */
+
+ data = m_net.encode(data);
+
+ /** vector to image */
+
+ std::size_t numHidden = data.element(1).size();
+ output->SetVectorLength(numHidden);
+ itk::ImageRegionIterator<TImage> imageIteratorOut(output,outputRegionForThread);
+ auto vect_it = data.elements().begin();
+ while(!imageIteratorOut.IsAtEnd() && vect_it!=data.elements().end()){
+ pixelValue.SetSize(numHidden);
+ shark::RealVector vect_out=(*vect_it);
+ for(unsigned int a = 0; a < numHidden; ++a){
+ pixelValue[a]=vect_out[a];
+ }
+
+ imageIteratorOut.Set(pixelValue);
+ ++imageIteratorOut;
+ ++vect_it;
+ }
+}
+
+
+#endif
--
GitLab