From 82e47317d4465939c1c4f39a7aa283d4c174d703 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?C=C3=A9dric=20Traizet?= <traizetc@cesbio.cnes.fr>
Date: Mon, 29 May 2017 10:53:26 +0200
Subject: [PATCH] some cmments and documentation added
---
include/AutoencoderModel.h | 13 ++--
include/AutoencoderModel.txx | 8 +--
include/DimensionalityReductionModel.h | 64 +++++++------------
.../ImageDimensionalityReductionFilter.txx | 7 +-
4 files changed, 35 insertions(+), 57 deletions(-)
diff --git a/include/AutoencoderModel.h b/include/AutoencoderModel.h
index 81b55a5fbf..ec9b5cdb2b 100644
--- a/include/AutoencoderModel.h
+++ b/include/AutoencoderModel.h
@@ -27,7 +27,7 @@ public:
itkNewMacro(Self);
itkTypeMacro(AutoencoderModel, DimensionalityReductionModel);
- unsigned int GetDimension() {return m_NumberOfHiddenNeurons;};
+ unsigned int GetDimension() {return m_NumberOfHiddenNeurons;}; // Override the Dimensionality Reduction model method, it is used in the dimensionality reduction filter to set the output image size
itkGetMacro(NumberOfHiddenNeurons,unsigned int);
itkSetMacro(NumberOfHiddenNeurons,unsigned int);
@@ -47,9 +47,7 @@ public:
void Load(const std::string & filename, const std::string & name="") ITK_OVERRIDE;
void Train() ITK_OVERRIDE;
- //void Dimensionality_reduction() {}; // Dimensionality reduction is done by DoPredict
-
-
+
protected:
AutoencoderModel();
~AutoencoderModel() ITK_OVERRIDE;
@@ -59,11 +57,14 @@ protected:
private:
+ /** Network attributes */
AutoencoderType m_net;
unsigned int m_NumberOfHiddenNeurons;
+
+ /** Training parameters */
unsigned int m_NumberOfIterations;
- double m_Regularization;
- double m_Noise;
+ double m_Regularization; // L2 Regularization parameter
+ double m_Noise; // probability for an input to be set to 0 (denosing autoencoder)
};
} // end namespace otb
diff --git a/include/AutoencoderModel.txx b/include/AutoencoderModel.txx
index 5c7bc5d97e..4305f805b8 100644
--- a/include/AutoencoderModel.txx
+++ b/include/AutoencoderModel.txx
@@ -6,12 +6,13 @@
#include <shark/Data/Dataset.h>
#include "itkMacro.h"
#include "otbSharkUtils.h"
+
//include train function
#include <shark/ObjectiveFunctions/ErrorFunction.h>
#include <shark/Algorithms/GradientDescent/Rprop.h>// the RProp optimization algorithm
#include <shark/ObjectiveFunctions/Loss/SquaredLoss.h> // squared loss used for regression
#include <shark/ObjectiveFunctions/Regularizer.h> //L2 regulariziation
-#include <shark/Models/ImpulseNoiseModel.h>//noise source to corrupt the inputs
+#include <shark/Models/ImpulseNoiseModel.h> //noise source to corrupt the inputs
#include <shark/Models/ConcatenatedModel.h>//to concatenate the noise with the model
namespace otb
@@ -43,7 +44,7 @@ void AutoencoderModel<TInputValue,AutoencoderType>::Train()
std::size_t inputs = dataDimension(inputSamples);
m_net.setStructure(inputs, m_NumberOfHiddenNeurons);
initRandomUniform(m_net,-0.1*std::sqrt(1.0/inputs),0.1*std::sqrt(1.0/inputs));
- shark::ImpulseNoiseModel noise(m_Noise,0.0);//set an input pixel with probability p to 0
+ shark::ImpulseNoiseModel noise(m_Noise,0.0); //set an input pixel with probability m_Noise to 0
shark::ConcatenatedModel<shark::RealVector,shark::RealVector> model = noise>> m_net;
shark::LabeledData<shark::RealVector,shark::RealVector> trainSet(inputSamples,inputSamples);//labels identical to inputs
@@ -92,7 +93,7 @@ template <class TInputValue, class AutoencoderType>
void AutoencoderModel<TInputValue,AutoencoderType>::Save(const std::string & filename, const std::string & name)
{
std::ofstream ofs(filename);
- ofs << m_net.name() << std::endl; //first line
+ ofs << m_net.name() << std::endl; // the first line of the model file contains a key
boost::archive::polymorphic_text_oarchive oa(ofs);
m_net.write(oa);
ofs.close();
@@ -163,6 +164,5 @@ void AutoencoderModel<TInputValue,AutoencoderType>
}
}
-
} // namespace otb
#endif
diff --git a/include/DimensionalityReductionModel.h b/include/DimensionalityReductionModel.h
index 23ffad38bf..c5026551ee 100644
--- a/include/DimensionalityReductionModel.h
+++ b/include/DimensionalityReductionModel.h
@@ -25,42 +25,32 @@
namespace otb
{
-/** \class MachineLearningModel
- * \brief MachineLearningModel is the base class for all classifier objects (SVM, KNN,
- * Random Forests, Artificial Neural Network, ...) implemented in the supervised classification framework of the OTB.
+/** \class DimensionalityReductionModel
+ * \brief DimensionalityReductionModel is the base class for all dimensionality Reduction objects (PCA, autoencoders and SOM) implemented in the dimensionality Reduction framework of the OTB.
*
- * MachineLearningModel is an abstract object that specifies behavior and
- * interface of supervised classifiers (SVM, KNN, Random Forests, Artificial
- * Neural Network, ...) in the generic supervised classification framework of the OTB.
- * The main generic virtual methods specifically implemented in each classifier
- * derived from the MachineLearningModel class are two learning-related methods:
- * Train() and Save(), and three classification-related methods: Load(),
+ * DimensionalityReductionModel is an abstract object that specifies behavior and
+ * interface of dimensionality reduction algorithms (PCA, autoencoders and SOM) in the generic dimensionality Reduction framework of the OTB.
+ * The main generic virtual methods specifically implemented in each model
+ * derived from the DimensionalityReductionModel class are two learning-related methods:
+ * Train() and Save(), and three dimensionality reduction related methods: Load(),
* DoPredict() and optionnaly DoPredictBatch().
*
* Thus, each classifier derived from the MachineLearningModel class
* computes its corresponding model with Train() and exports it with
* the help of the Save() method.
*
- * It is also possible to classify any input sample composed of several
+ * It is also possible to reduce the dimensionality of any input sample composed of several
* features (or any number of bands in the case of a pixel extracted
* from a multi-band image) with the help of the Predict() method which
* needs a previous loading of the classification model with the Load() method.
*
- * \sa MachineLearningModelFactory
- * \sa LibSVMMachineLearningModel
- * \sa SVMMachineLearningModel
- * \sa BoostMachineLearningModel
- * \sa KNearestNeighborsMachineLearningModel
- * \sa DecisionTreeMachineLearningModel
- * \sa RandomForestsMachineLearningModel
- * \sa GradientBoostedTreeMachineLearningModel
- * \sa NormalBayesMachineLearningModel
- * \sa NeuralNetworkMachineLearningModel
- * \sa SharkRandomForestsMachineLearningModel
- * \sa ImageClassificationFilter
+ * \sa DimensionalityReductionModelFactory
+ * \sa SOMModel
+ * \sa PCAModel
+ * \sa AutoencderModel
+ * \sa ImageDimensionalityReductionFilter
*
- *
- * \ingroup OTBSupervised
+ * \ingroup cbDimensionalityReduction
*/
template <class TInputValue, class TTargetValue>
class ITK_EXPORT DimensionalityReductionModel
@@ -121,7 +111,7 @@ public:
/** Get the size of the output after dimensionality reduction */
virtual unsigned int GetDimension() = 0;
- /**\name Classification model file manipulation */
+ /**\name Dimensionality Reduction model file manipulation */
//@{
/** Save the model to file */
virtual void Save(const std::string & filename, const std::string & name="") = 0;
@@ -132,10 +122,10 @@ public:
/**\name Classification model file compatibility tests */
//@{
- /** Is the input model file readable and compatible with the corresponding classifier ? */
+ /** Is the input model file readable and compatible with the corresponding model ? */
virtual bool CanReadFile(const std::string &) = 0;
- /** Is the input model file writable and compatible with the corresponding classifier ? */
+ /** Is the input model file writable and compatible with the corresponding model ? */
virtual bool CanWriteFile(const std::string &) = 0;
//@}
@@ -165,19 +155,13 @@ protected:
/** Is DoPredictBatch multi-threaded ? */
bool m_IsDoPredictBatchMultiThreaded;
-
-
-
-
private:
/** Actual implementation of BatchPredicition
* Default implementation will call DoPredict iteratively
* \param input The input batch
- * \param startIndex Index of the first sample to predict
- * \param size Number of samples to predict
- * \param target Pointer to the list of produced labels
- * \param quality Pointer to the list of produced confidence
- * values, or NULL
+ * \param startIndex Index of the first sample to reduce
+ * \param size Number of samples to reduce
+ * \param target Pointer to the list of reduced samples
*
* Override me if internal implementation allows for batch
* prediction.
@@ -187,11 +171,9 @@ private:
*/
virtual void DoPredictBatch(const InputListSampleType * input, const unsigned int & startIndex, const unsigned int & size, TargetListSampleType * target) const;
- /** Actual implementation of single sample prediction
- * \param input sample to predict
- * \param quality Pointer to a variable to store confidence value,
- * or NULL
- * \return The predicted label
+ /** Actual implementation of single sample reduction
+ * \param input sample to reduce
+ * \return The reduced sample
*/
virtual TargetSampleType DoPredict(const InputSampleType& input) const = 0;
diff --git a/include/ImageDimensionalityReductionFilter.txx b/include/ImageDimensionalityReductionFilter.txx
index 3dbfd16bfe..4eee4d3c9f 100644
--- a/include/ImageDimensionalityReductionFilter.txx
+++ b/include/ImageDimensionalityReductionFilter.txx
@@ -163,14 +163,10 @@ ImageDimensionalityReductionFilter<TInputImage, TOutputImage, TMaskImage>
InputIteratorType inIt(inputPtr, outputRegionForThread);
OutputIteratorType outIt(outputPtr, outputRegionForThread);
- // typedef typename ModelType::InputValueType InputValueType;
typedef typename ModelType::InputSampleType InputSampleType;
typedef typename ModelType::InputListSampleType InputListSampleType;
typedef typename ModelType::TargetValueType TargetValueType;
- // typedef typename ModelType::TargetSampleType TargetSampleType;
typedef typename ModelType::TargetListSampleType TargetListSampleType;
- // typedef typename ModelType::ConfidenceValueType ConfidenceValueType;
- // typedef typename ModelType::ConfidenceSampleType ConfidenceSampleType;
typename InputListSampleType::Pointer samples = InputListSampleType::New();
unsigned int num_features = inputPtr->GetNumberOfComponentsPerPixel();
@@ -193,11 +189,10 @@ ImageDimensionalityReductionFilter<TInputImage, TOutputImage, TMaskImage>
typename TargetListSampleType::Pointer labels;
// This call is threadsafe
- //labels = m_Model->PredictBatch(samples,confidences);
labels = m_Model->PredictBatch(samples);
+
// Set the output values
-
typename TargetListSampleType::ConstIterator labIt = labels->Begin();
for (outIt.GoToBegin(); !outIt.IsAtEnd(); ++outIt)
--
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