ENH: new base application for classif and regression

Modules/Applications/AppClassification/include/otbLearningApplicationBase.h

+/*=========================================================================
+ 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 __otbLearningApplicationBase_h
+#define __otbLearningApplicationBase_h
+
+#include "otbConfigure.h"
+
+#include "otbWrapperApplicationFactory.h"
+
+#include <iostream>
+
+// ListSample
+#include "otbListSampleGenerator.h"
+#include "itkVariableLengthVector.h"
+
+//Estimator
+#include "otbMachineLearningModelFactory.h"
+
+#ifdef OTB_USE_OPENCV
+# include "otbKNearestNeighborsMachineLearningModel.h"
+# include "otbRandomForestsMachineLearningModel.h"
+# include "otbSVMMachineLearningModel.h"
+# include "otbBoostMachineLearningModel.h"
+# include "otbDecisionTreeMachineLearningModel.h"
+# include "otbGradientBoostedTreeMachineLearningModel.h"
+# include "otbNormalBayesMachineLearningModel.h"
+# include "otbNeuralNetworkMachineLearningModel.h"
+#endif
+
+#ifdef OTB_USE_LIBSVM 
+#include "otbLibSVMMachineLearningModel.h"
+#endif
+
+// Statistic XML Reader
+#include "otbStatisticsXMLFileReader.h"
+
+#include "itkTimeProbe.h"
+#include "otbStandardFilterWatcher.h"
+
+// Normalize the samples
+#include "otbShiftScaleSampleListFilter.h"
+
+// List sample concatenation
+#include "otbConcatenateSampleListFilter.h"
+
+// Balancing ListSample
+#include "otbListSampleToBalancedListSampleFilter.h"
+
+namespace otb
+{
+namespace Wrapper
+{
+
+template <class TInputValue, class TOutputValue>
+class LearningApplicationBase: public Application
+{
+public:
+  /** Standard class typedefs. */
+  typedef LearningApplicationBase Self;
+  typedef Application             Superclass;
+  typedef itk::SmartPointer<Self> Pointer;
+  typedef itk::SmartPointer<const Self> ConstPointer;
+
+  /** Standard macro */
+  itkNewMacro(Self)
+
+  itkTypeMacro(LearningApplicationBase, otb::Application)
+
+  typedef TInputValue                             InputValueType;
+  typedef TOutputValue                            OutputValueType;
+
+  typedef otb::VectorImage<InputValueType>        SampleImageType;
+  typedef typename SampleImageType::PixelType     PixelType;
+
+  // Machine Learning models
+  typedef otb::MachineLearningModelFactory<
+            InputValueType, OutputValueType>             ModelFactoryType;
+  typedef typename ModelFactoryType::MachineLearningModelTypePointer ModelPointerType;
+  typedef typename ModelFactoryType::MachineLearningModel            ModelType;
+  
+  typedef typename ModelType::InputSampleType     SampleType;
+  typedef typename ModelType::InputListSampleType ListSampleType;
+  
+  typedef typename ModelType::TargetSampleType      TargetSampleType;
+  typedef typename ModelType::TargetListSampleType  TargetListSampleType;
+
+  // SampleList manipulation
+  typedef otb::ListSampleGenerator<SampleImageType, VectorDataType> ListSampleGeneratorType;
+
+  typedef ListSampleGeneratorType::LabelType LabelType;
+  typedef ListSampleGeneratorType::ListLabelType LabelListSampleType;
+  typedef otb::Statistics::ConcatenateSampleListFilter<ListSampleType> ConcatenateListSampleFilterType;
+  typedef otb::Statistics::ConcatenateSampleListFilter<LabelListSampleType> ConcatenateLabelListSampleFilterType;
+
+  // Statistic XML file Reader
+  typedef otb::StatisticsXMLFileReader<SampleType> StatisticsReader;
+
+  // Enhance List Sample  typedef otb::Statistics::ListSampleToBalancedListSampleFilter<ListSampleType, LabelListSampleType>      BalancingListSampleFilterType;
+  typedef otb::Statistics::ShiftScaleSampleListFilter<ListSampleType, ListSampleType> ShiftScaleFilterType;
+
+  
+#ifdef OTB_USE_OPENCV
+  typedef otb::RandomForestsMachineLearningModel<InputValueType, OutputValueType> RandomForestType;
+  typedef otb::KNearestNeighborsMachineLearningModel<InputValueType, OutputValueType> KNNType;
+  typedef otb::SVMMachineLearningModel<InputValueType, OutputValueType> SVMType;
+  typedef otb::BoostMachineLearningModel<InputValueType, OutputValueType> BoostType;
+  typedef otb::DecisionTreeMachineLearningModel<InputValueType, OutputValueType> DecisionTreeType;
+  typedef otb::GradientBoostedTreeMachineLearningModel<InputValueType, OutputValueType> GradientBoostedTreeType;
+  typedef otb::NeuralNetworkMachineLearningModel<InputValueType, OutputValueType> NeuralNetworkType;
+  typedef otb::NormalBayesMachineLearningModel<InputValueType, OutputValueType> NormalBayesType;
+#endif
+
+#ifdef OTB_USE_LIBSVM 
+  typedef otb::LibSVMMachineLearningModel<InputValueType, OutputValueType> LibSVMType;
+#endif
+ 
+protected:
+  using Superclass::AddParameter;
+  friend void InitSVMParams(LearningApplicationBase & app);
+
+private:
+  void DoInit();
+
+#ifdef OTB_USE_LIBSVM 
+  void InitLibSVMParams();
+#endif  
+  
+#ifdef OTB_USE_OPENCV
+  void InitBoostParams();
+  void InitSVMParams();
+  void InitDecisionTreeParams();
+  void InitGradientBoostedTreeParams();
+  void InitNeuralNetworkParams();
+  void InitNormalBayesParams();
+  void InitRandomForestsParams();
+  void InitKNNParams();
+#endif
+
+#ifdef OTB_USE_LIBSVM 
+  void TrainLibSVM(ListSampleType::Pointer trainingListSample, TargetListSampleType::Pointer trainingLabeledListSample);
+#endif 
+  
+#ifdef OTB_USE_OPENCV
+  void TrainBoost(ListSampleType::Pointer trainingListSample, TargetListSampleType::Pointer trainingLabeledListSample, std::string modelPath);
+  void TrainSVM(ListSampleType::Pointer trainingListSample, TargetListSampleType::Pointer trainingLabeledListSample, std::string modelPath);
+  void TrainDecisionTree(ListSampleType::Pointer trainingListSample, TargetListSampleType::Pointer trainingLabeledListSample, std::string modelPath);
+  void TrainGradientBoostedTree(ListSampleType::Pointer trainingListSample, TargetListSampleType::Pointer trainingLabeledListSample, std::string modelPath);
+  void TrainNeuralNetwork(ListSampleType::Pointer trainingListSample, TargetListSampleType::Pointer trainingLabeledListSample, std::string modelPath);
+  void TrainNormalBayes(ListSampleType::Pointer trainingListSample, TargetListSampleType::Pointer trainingLabeledListSample, std::string modelPath);
+  void TrainRandomForests(ListSampleType::Pointer trainingListSample, TargetListSampleType::Pointer trainingLabeledListSample, std::string modelPath);
+  void TrainKNN(ListSampleType::Pointer trainingListSample, TargetListSampleType::Pointer trainingLabeledListSample, std::string modelPath);
+#endif
+
+  void Train(ListSampleType::Pointer trainingListSample, TargetListSampleType::Pointer trainingLabeledListSample, std::string modelPath, std::string modelName);
+
+  void Classify(ListSampleType::Pointer validationListSample, TargetListSampleType::Pointer predictedList, std::string modelPath);
+
+  bool m_RegressionFlag;
+
+};
+
+}
+}
+
+#ifndef OTB_MANUAL_INSTANTIATION
+#include "otbLearningApplicationBase.txx"
+#ifdef OTB_USE_OPENCV
+#include "otbTrainBoost.txx"
+#include "otbTrainDecisionTree.txx"
+#include "otbTrainGradientBoostedTree.txx"
+#include "otbTrainKNN.txx"
+#include "otbTrainNeuralNetwork.txx"
+#include "otbTrainNormalBayes.txx"
+#include "otbTrainRandomForests.txx"
+#include "otbTrainSVM.cxx"
+#endif
+#ifdef OTB_USE_LIBSVM
+#include "otbTrainLibSVM.txx"
+#endif
+#endif
+
+#endif

Modules/Applications/AppClassification/include/otbLearningApplicationBase.txx

+/*=========================================================================
+ 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 __otbLearningApplicationBase_txx
+#define __otbLearningApplicationBase_txx
+
+#include "otbLearningApplicationBase.h"
+
+namespace otb
+{
+namespace Wrapper
+{
+
+template <class TInputValue, class TOutputValue>
+LearningApplicationBase<TInputValue,TOutputValue>
+::LearningApplicationBase() : m_RegressionFlag(false)
+{
+} 
+
+template <class TInputValue, class TOutputValue>
+void
+LearningApplicationBase<TInputValue,TOutputValue>
+::DoInit()
+{
+  AddDocTag(Tags::Learning);
+
+  AddParameter(ParameterType_Choice, "classifier", "Classifier to use for the training");
+  SetParameterDescription("classifier", "Choice of the classifier to use for the training.");
+
+  //Group LibSVM
+#ifdef OTB_USE_LIBSVM 
+  InitLibSVMParams();
+#endif
+
+#ifdef OTB_USE_OPENCV
+  InitSVMParams();
+  InitBoostParams();
+  InitDecisionTreeParams();
+  InitGradientBoostedTreeParams();
+  InitNeuralNetworkParams();
+  InitNormalBayesParams();
+  InitRandomForestsParams();
+  InitKNNParams();
+#endif
+
+  AddRANDParameter();
+}
+
+template <class TInputValue, class TOutputValue>
+void
+LearningApplicationBase<TInputValue,TOutputValue>
+::Classify(ListSampleType::Pointer validationListSample,
+           TargetListSampleType::Pointer predictedList,
+           std::string modelPath)
+{
+  //Classification
+  ModelPointerType model = ModelFactoryType::CreateMachineLearningModel(modelPath,
+                                                                        ModelFactoryType::ReadMode);
+
+  if (model.IsNull())
+    {
+    otbAppLogFATAL(<< "Error when loading model " << modelPath);
+    }
+
+  model->Load(modelPath);
+  model->SetInputListSample(validationListSample);
+  model->SetTargetListSample(predictedList);
+  model->PredictAll();
+}
+
+template <class TInputValue, class TOutputValue>
+void
+LearningApplicationBase<TInputValue,TOutputValue>
+::Train(ListSampleType::Pointer trainingListSample,
+        TargetListSampleType::Pointer trainingLabeledListSample,
+        std::string modelPath,
+        std::string modelName)
+{
+  if (modelName == "libsvm")
+    {
+	#ifdef OTB_USE_LIBSVM
+    TrainLibSVM(trainingListSample, trainingLabeledListSample, modelPath);
+    #else
+    otbAppLogFATAL("Module LIBSVM is not installed. You should consider turning OTB_USE_LIBSVM on during cmake configuration.");
+    #endif
+    }
+  else if (modelName == "svm")
+    {
+	#ifdef OTB_USE_OPENCV
+    TrainSVM(trainingListSample, trainingLabeledListSample, modelPath);
+    #else
+    otbAppLogFATAL("Module OPENCV is not installed. You should consider turning OTB_USE_OPENCV on during cmake configuration.");
+    #endif
+    }
+  else if (modelName == "boost")
+    {
+	#ifdef OTB_USE_OPENCV
+    TrainBoost(trainingListSample, trainingLabeledListSample, modelPath);
+    #else
+    otbAppLogFATAL("Module OPENCV is not installed. You should consider turning OTB_USE_OPENCV on during cmake configuration.");
+    #endif
+    }
+  else if (modelName == "dt")
+    {
+	#ifdef OTB_USE_OPENCV
+    TrainDecisionTree(trainingListSample, trainingLabeledListSample, modelPath);
+    #else
+    otbAppLogFATAL("Module OPENCV is not installed. You should consider turning OTB_USE_OPENCV on during cmake configuration.");
+    #endif
+    }
+  else if (modelName == "gbt")
+    {
+	#ifdef OTB_USE_OPENCV
+    TrainGradientBoostedTree(trainingListSample, trainingLabeledListSample, modelPath);
+    #else
+    otbAppLogFATAL("Module OPENCV is not installed. You should consider turning OTB_USE_OPENCV on during cmake configuration.");
+    #endif
+    }
+  else if (modelName == "ann")
+    {
+	#ifdef OTB_USE_OPENCV
+    TrainNeuralNetwork(trainingListSample, trainingLabeledListSample, modelPath);
+    #else
+    otbAppLogFATAL("Module OPENCV is not installed. You should consider turning OTB_USE_OPENCV on during cmake configuration.");
+    #endif
+    }
+  else if (modelName == "bayes")
+    {
+	#ifdef OTB_USE_OPENCV
+    TrainNormalBayes(trainingListSample, trainingLabeledListSample, modelPath);
+    #else
+    otbAppLogFATAL("Module OPENCV is not installed. You should consider turning OTB_USE_OPENCV on during cmake configuration.");
+    #endif
+    }
+  else if (modelName == "rf")
+    {
+	#ifdef OTB_USE_OPENCV
+    TrainRandomForests(trainingListSample, trainingLabeledListSample, modelPath);
+    #else
+    otbAppLogFATAL("Module OPENCV is not installed. You should consider turning OTB_USE_OPENCV on during cmake configuration.");
+    #endif
+    }
+  else if (modelName == "knn")
+    {
+	#ifdef OTB_USE_OPENCV
+    TrainKNN(trainingListSample, trainingLabeledListSample, modelPath);
+    #else
+    otbAppLogFATAL("Module OPENCV is not installed. You should consider turning OTB_USE_OPENCV on during cmake configuration.");
+    #endif
+    }
+}
+
+}
+}
+
+#endif