From dfc3280ce20b3f551c8eae763d06a8e93041f872 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?C=C3=A9dric=20Traizet?= <traizetc@cesbio.cnes.fr>
Date: Thu, 4 May 2017 14:47:26 +0200
Subject: [PATCH] trainer and dimreduc app working for simple autoencoders
---
app/cbDimensionalityReduction.cxx | 44 +++++++++++++-----------
app/cbDimensionalityReductionTrainer.cxx | 17 +++++++--
include/encode_filter.h | 9 ++---
include/encode_filter.txx | 8 ++---
4 files changed, 47 insertions(+), 31 deletions(-)
diff --git a/app/cbDimensionalityReduction.cxx b/app/cbDimensionalityReduction.cxx
index d2b6666079..a539b66c13 100644
--- a/app/cbDimensionalityReduction.cxx
+++ b/app/cbDimensionalityReduction.cxx
@@ -12,6 +12,7 @@
#include "encode_filter.h"
#include "dummy_filter.h"
+#include "otbMultiChannelExtractROI.h"
namespace otb
{
@@ -32,7 +33,7 @@ public:
typedef shark::Autoencoder< shark::TanhNeuron, shark::LinearNeuron> AutoencoderType;
using FilterType = EncodeFilter<image_type, AutoencoderType, shark::Normalizer<shark::RealVector>> ;
-
+ typedef otb::MultiChannelExtractROI<FloatVectorImageType::InternalPixelType, FloatVectorImageType::InternalPixelType> ExtractROIFilterType;
/** Standard macro */
itkNewMacro(Self);
itkTypeMacro(CbDimensionalityReduction, otb::Application);
@@ -51,7 +52,7 @@ private:
AddParameter(ParameterType_InputFilename, "normalizer", "Normalizer model file");
SetParameterDescription("normalizer", "A normalizer model file (produced by the cbDimensionalityReductionTrainer application).");
-
+
AddParameter(ParameterType_OutputImage, "out", "Output Image");
SetParameterDescription("out", "Output image");
@@ -61,36 +62,39 @@ private:
void DoUpdateParameters()
{
}
-
+
void DoExecute()
{
-
std::cout << "Appli" << std::endl;
- FloatVectorImageType::Pointer inImage = GetParameterImage("in");
+ image_type::Pointer inImage = GetParameterImage("in");
std::string encoderPath = GetParameterString("model");
std::string normalizerPath = GetParameterString("normalizer");
- filter = FilterType::New();
- filter->SetAutoencoderModel(encoderPath);
- filter->SetNormalizerModel(normalizerPath);
- filter->SetInput(inImage);
- //filter->Update();
- SetParameterOutputImage("out", filter->GetOutput());
-/*
-
- using DummyFilterType = DummyFilter<image_type> ;
- DummyFilterType::Pointer dummy_filter = DummyFilterType::New(); // this filter simply copies the input image (do not need shark library)
- dummy_filter->SetInput(GetParameterFloatVectorImage("in"));
- dummy_filter->Update();
- SetParameterOutputImage("out", dummy_filter->GetOutput());
-*/
+
+ filter_dim_reduc = FilterType::New();
+ filter_dim_reduc->SetAutoencoderModel(encoderPath);
+ filter_dim_reduc->SetNormalizerModel(normalizerPath);
+ filter_dim_reduc->SetInput(inImage);
+ //SetParameterOutputImage("out", filter_dim_reduc->GetOutput());
+
+ m_ExtractROIFilter = ExtractROIFilterType::New();
+ m_ExtractROIFilter->SetInput(filter_dim_reduc->GetOutput());
+ for (unsigned int idx = 1; idx <= filter_dim_reduc->GetDimension(); ++idx)
+ {
+ m_ExtractROIFilter->SetChannel(idx );
+ }
+
+ SetParameterOutputImage("out", m_ExtractROIFilter->GetOutput());
+
//SetParameterOutputImage("out", inImage); // copy input image
}
- FilterType::Pointer filter;
+ FilterType::Pointer filter_dim_reduc;
+ ExtractROIFilterType::Pointer m_ExtractROIFilter;
+
};
}
}
diff --git a/app/cbDimensionalityReductionTrainer.cxx b/app/cbDimensionalityReductionTrainer.cxx
index 7250e35ddd..2ceb73d902 100644
--- a/app/cbDimensionalityReductionTrainer.cxx
+++ b/app/cbDimensionalityReductionTrainer.cxx
@@ -99,7 +99,18 @@ private:
AddParameter(ParameterType_StringList, "feat", "Field names to be calculated."); //
SetParameterDescription("feat","List of field names in the input vector data used as features for training."); //
+
+ AddParameter(ParameterType_Int, "k","target dimension");
+ SetParameterDescription("k", "Dimension of the output feature vectors");
+
+ /*
+ AddParameter(ParameterType_InputFilename, "model", "Dimensionality Reduction model file");
+ SetParameterDescription("model", "A model file (produced by cbDimensionalityReduction application.");
+ AddParameter(ParameterType_InputFilename, "normalizer", "normalizer model file");
+ SetParameterDescription("normalizer", "A model file (produced by cbDimensionalityReduction application.");
+*/
+
/*
AddParameter(ParameterType_InputVectorData, "val", "Name of the input validation vector data");
SetParameterDescription("val","The vector data used for validation.");
@@ -141,9 +152,9 @@ private:
otb::Shark::ListSampleToSharkVector<ListSampleType>( input, features);
shark::Data<shark::RealVector> inputSamples = shark::createDataFromRange( features );
- std::size_t numHidden= 5; // stoi convert string to int
- std::size_t iterations = 10;
- double regularisation = 0; // stod convert string to double
+ std::size_t numHidden= GetParameterInt("k");
+ std::size_t iterations = 100;
+ double regularisation = 0;
shark::Normalizer<shark::RealVector> normalizer = trainNormalizer(inputSamples);
diff --git a/include/encode_filter.h b/include/encode_filter.h
index 9a6b70c117..6b5e361fb3 100644
--- a/include/encode_filter.h
+++ b/include/encode_filter.h
@@ -24,15 +24,15 @@ class ITK_EXPORT EncodeFilter:public itk::ImageToImageFilter< TImage, TImage >
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 BeforeThreadedGenerateData();
@@ -42,7 +42,8 @@ class ITK_EXPORT EncodeFilter:public itk::ImageToImageFilter< TImage, TImage >
EncodeFilter(const Self &); //purposely not implemented
void operator=(const Self &); //purposely not implemented
AutoencoderModel m_net;
- NormalizerModel m_normalizer;
+ NormalizerModel m_normalizer;
+ std::size_t m_hidden_neuron;
};
#ifndef ITK_MANUAL_INSTANTIATION
diff --git a/include/encode_filter.txx b/include/encode_filter.txx
index adb071854f..8e7b334a9a 100644
--- a/include/encode_filter.txx
+++ b/include/encode_filter.txx
@@ -37,6 +37,7 @@ void EncodeFilter<TImage, AutoencoderModel, NormalizerModel>::SetAutoencoderMode
boost::archive::polymorphic_text_iarchive ia(ifs);
m_net.read(ia);
ifs.close();
+ m_hidden_neuron = m_net.numberOfHiddenNeurons();
}
@@ -101,15 +102,13 @@ this->SetNumberOfThreads(1);
}
-/*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();
@@ -149,11 +148,12 @@ void EncodeFilter<TImage, AutoencoderModel, NormalizerModel>::ThreadedGenerateDa
for(unsigned int a = 0; a < numHidden; ++a){
pixelValue[a]=vect_out[a];
}
-
+
imageIteratorOut.Set(pixelValue);
++imageIteratorOut;
++vect_it;
}
+
}
--
GitLab