From c9051b5447296495d798e718f39810351cc0851d Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?C=C3=A9dric=20Traizet?= <traizetc@cesbio.cnes.fr>
Date: Thu, 11 May 2017 15:23:19 +0200
Subject: [PATCH] encode_filter and dummy_filter have been removed, as they are
not used in the applications anymore.
---
include/dummy_filter.h | 47 -----------
include/dummy_filter.txx | 79 ------------------
include/encode_filter.h | 54 -------------
include/encode_filter.txx | 165 --------------------------------------
4 files changed, 345 deletions(-)
delete mode 100644 include/dummy_filter.h
delete mode 100644 include/dummy_filter.txx
delete mode 100644 include/encode_filter.h
delete mode 100644 include/encode_filter.txx
diff --git a/include/dummy_filter.h b/include/dummy_filter.h
deleted file mode 100644
index ea6dd8d21a..0000000000
--- a/include/dummy_filter.h
+++ /dev/null
@@ -1,47 +0,0 @@
-#ifndef __dummy_Filter_h
-#define __dummy_Filter_h
-
-#include "itkImageToImageFilter.h"
-#include "itkMacro.h"
-
-
-template< class TImage>
-class ITK_EXPORT DummyFilter:public itk::ImageToImageFilter< TImage, TImage >
-{
- public:
- /** Standard class typedefs. */
- typedef DummyFilter 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(DummyFilter, ImageToImageFilter);
-
- //void SetInputImage(const TImage* image);
-
-
- protected:
- DummyFilter();
- ~DummyFilter(){}
-
- typename TImage::ConstPointer GetInputImage();
-
- /** Does the real work. */
-
- virtual void BeforeThreadedGenerateData();
- void ThreadedGenerateData(const typename TImage::RegionType &outputRegionForThread, unsigned int threadId) ITK_OVERRIDE;
-
- private:
- DummyFilter(const Self &); //purposely not implemented
- void operator=(const Self &); //purposely not implemented
-};
-
-#ifndef ITK_MANUAL_INSTANTIATION
-#include "dummy_filter.txx"
-#endif
-
-
-#endif // __dummy_Filter_h
diff --git a/include/dummy_filter.txx b/include/dummy_filter.txx
deleted file mode 100644
index 2ec1ced9e8..0000000000
--- a/include/dummy_filter.txx
+++ /dev/null
@@ -1,79 +0,0 @@
-#ifndef __dummy_filter_txx
-#define __dummy_filter_txx
-
-#include "dummy_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>
-DummyFilter<TImage>::DummyFilter()
-{
- this->SetNumberOfRequiredInputs(1);
-}
-
-
-
-template< class TImage>
-typename TImage::ConstPointer DummyFilter<TImage>::GetInputImage()
-{
- return static_cast< const TImage * >
- ( this->itk::ProcessObject::GetInput(0) );
-}
-
-
-
-
-
-template< class TImage>
-void DummyFilter<TImage>::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>
-void DummyFilter<TImage>::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);
- itk::ImageRegionIterator<TImage> imageIteratorOut(output,outputRegionForThread);
-
- typename TImage::PixelType pixelValue;
- while(!inputIterator.IsAtEnd()){
- imageIteratorOut.Set(inputIterator.Get());
- ++inputIterator;
- ++imageIteratorOut;
- }
-
-}
-
-
-#endif
diff --git a/include/encode_filter.h b/include/encode_filter.h
deleted file mode 100644
index 903912be28..0000000000
--- a/include/encode_filter.h
+++ /dev/null
@@ -1,54 +0,0 @@
-#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);
- std::size_t GetDimension(){return m_hidden_neuron;};
- protected:
- EncodeFilter();
- ~EncodeFilter(){}
-
- typename TImage::ConstPointer GetInputImage();
- AutoencoderModel GetAutoencoderModel();
- NormalizerModel GetNormalizerModel();
-
- // Does the real work.
- virtual void GenerateOutputInformation();
- 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;
- std::size_t m_hidden_neuron;
-};
-
-#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
deleted file mode 100644
index a96b048f33..0000000000
--- a/include/encode_filter.txx
+++ /dev/null
@@ -1,165 +0,0 @@
-#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();
- m_hidden_neuron = m_net.numberOfHiddenNeurons();
-}
-
-
-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>::GenerateOutputInformation()
-{
- Superclass::GenerateOutputInformation();
- this->GetOutput()->SetNumberOfComponentsPerPixel( m_hidden_neuron );
-}
-
-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
--
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