diff --git a/CMakeLists.txt b/CMakeLists.txt
index f1b0d6002bd3cb3fd1b8996baec47d89dfa730fd..c31d605bd28213d887e01e20bb954b5bdd8c0342 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -392,6 +392,17 @@ endif()
# Provide an option for generating documentation.
add_subdirectory(Utilities/Doxygen)
+#----------------------------------------------------------------------
+# Provide a target to generate the SuperBuild archive (only for Unix)
+if(UNIX)
+ add_custom_target(SuperBuild-archive
+ COMMAND ./SuperbuildDownloadList.sh
+ ${OTB_BINARY_DIR}/Download
+ ${OTB_BINARY_DIR}
+ WORKING_DIRECTORY ${OTB_SOURCE_DIR}/Utilities/Maintenance
+ )
+endif()
+
# TODO cleanup
# Create target to download data from the OTBData group. This must come after
# all tests have been added that reference the group, so we put it last.
diff --git a/Examples/Projections/test/CMakeLists.txt b/Examples/Projections/test/CMakeLists.txt
index 61c9985d0c46901bb172ebd19613d7871e78a3cd..fad74a593fa3d4bde04cde96b541e4be13827c86 100644
--- a/Examples/Projections/test/CMakeLists.txt
+++ b/Examples/Projections/test/CMakeLists.txt
@@ -88,6 +88,10 @@ otb_add_test(NAME prTeEstimateRPCSensorModelExampleTest COMMAND ${OTB_TEST_DRIVE
2803 1942 -22.958868 -42.808235 0.
980 2734 -22.99534 -43.309672 0.
713 2754 -23.007862 -43.365307 0.
+ 72 2955 -23.012153 -43.541331 0.
+ 2884 1898 -22.954691 -42.786188 0.
+ 2539 47 -22.616041 -42.777877 0.
+ 577 183 -22.551654 -43.271813 0.
)
otb_add_test(NAME prTePlaceNameToLonLatExampleTest COMMAND ${OTB_TEST_DRIVER}
diff --git a/Modules/Applications/AppClassification/app/CMakeLists.txt b/Modules/Applications/AppClassification/app/CMakeLists.txt
index 7613f5a2612a7c62bfe8ecc648dab3f8b0b40436..692aa710eba22f1cf1274dcd08171c063764c9b1 100644
--- a/Modules/Applications/AppClassification/app/CMakeLists.txt
+++ b/Modules/Applications/AppClassification/app/CMakeLists.txt
@@ -65,16 +65,19 @@ otb_create_application(
SOURCES otbKMeansClassification.cxx
LINK_LIBRARIES ${${otb-module}_LIBRARIES})
-set(TrainImagesClassifier_SRC
- otbTrainSVM.cxx otbTrainBoost.cxx otbTrainDecisionTree.cxx
- otbTrainGradientBoostedTree.cxx otbTrainNeuralNetwork.cxx
- otbTrainNormalBayes.cxx otbTrainRandomForests.cxx otbTrainKNN.cxx
- otbTrainLibSVM.cxx
- otbTrainImagesClassifier.cxx)
-
otb_create_application(
NAME TrainImagesClassifier
- SOURCES ${TrainImagesClassifier_SRC}
+ SOURCES otbTrainImagesClassifier.cxx
+ LINK_LIBRARIES ${${otb-module}_LIBRARIES})
+
+otb_create_application(
+ NAME TrainRegression
+ SOURCES otbTrainRegression.cxx
+ LINK_LIBRARIES ${${otb-module}_LIBRARIES})
+
+otb_create_application(
+ NAME PredictRegression
+ SOURCES otbPredictRegression.cxx
LINK_LIBRARIES ${${otb-module}_LIBRARIES})
otb_create_application(
diff --git a/Modules/Applications/AppClassification/app/otbPredictRegression.cxx b/Modules/Applications/AppClassification/app/otbPredictRegression.cxx
new file mode 100644
index 0000000000000000000000000000000000000000..413d70f05d08d50efaef54a0bd38e0c58bd1ca7d
--- /dev/null
+++ b/Modules/Applications/AppClassification/app/otbPredictRegression.cxx
@@ -0,0 +1,275 @@
+/*=========================================================================
+
+ 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.
+
+=========================================================================*/
+#include "otbWrapperApplication.h"
+#include "otbWrapperApplicationFactory.h"
+
+#include "itkUnaryFunctorImageFilter.h"
+#include "otbChangeLabelImageFilter.h"
+#include "otbStandardWriterWatcher.h"
+#include "otbStatisticsXMLFileReader.h"
+#include "otbShiftScaleVectorImageFilter.h"
+#include "otbImageClassificationFilter.h"
+#include "otbMultiToMonoChannelExtractROI.h"
+#include "otbImageToVectorImageCastFilter.h"
+#include "otbMachineLearningModelFactory.h"
+
+namespace otb
+{
+namespace Functor
+{
+/**
+ * simple affine function : y = ax+b
+ */
+template<class TInput, class TOutput>
+class AffineFunctor
+{
+public:
+ typedef double InternalType;
+
+ // constructor
+ AffineFunctor() : m_A(1.0),m_B(0.0) {}
+
+ // destructor
+ virtual ~AffineFunctor() {}
+
+ void SetA(InternalType a)
+ {
+ m_A = a;
+ }
+
+ void SetB(InternalType b)
+ {
+ m_B = b;
+ }
+
+ inline TOutput operator()(const TInput & x) const
+ {
+ return static_cast<TOutput>( static_cast<InternalType>(x)*m_A + m_B);
+ }
+private:
+ InternalType m_A;
+ InternalType m_B;
+};
+
+}
+
+namespace Wrapper
+{
+
+class PredictRegression : public Application
+{
+public:
+ /** Standard class typedefs. */
+ typedef PredictRegression Self;
+ typedef Application Superclass;
+ typedef itk::SmartPointer<Self> Pointer;
+ typedef itk::SmartPointer<const Self> ConstPointer;
+
+ /** Standard macro */
+ itkNewMacro(Self);
+
+ itkTypeMacro(PredictRegression, otb::Application);
+
+ /** Filters typedef */
+ typedef UInt8ImageType MaskImageType;
+ typedef itk::VariableLengthVector<FloatVectorImageType::InternalPixelType> MeasurementType;
+ typedef otb::StatisticsXMLFileReader<MeasurementType> StatisticsReader;
+ typedef otb::ShiftScaleVectorImageFilter<FloatVectorImageType, FloatVectorImageType> RescalerType;
+ typedef itk::UnaryFunctorImageFilter<
+ FloatImageType,
+ FloatImageType,
+ otb::Functor::AffineFunctor<float,float> > OutputRescalerType;
+ typedef otb::ImageClassificationFilter<FloatVectorImageType, FloatImageType, MaskImageType> ClassificationFilterType;
+ typedef ClassificationFilterType::Pointer ClassificationFilterPointerType;
+ typedef ClassificationFilterType::ModelType ModelType;
+ typedef ModelType::Pointer ModelPointerType;
+ typedef ClassificationFilterType::ValueType ValueType;
+ typedef ClassificationFilterType::LabelType LabelType;
+ typedef otb::MachineLearningModelFactory<ValueType, LabelType> MachineLearningModelFactoryType;
+
+private:
+ void DoInit()
+ {
+ SetName("PredictRegression");
+ SetDescription("Performs a prediction of the input image according to a regression model file.");
+
+ // Documentation
+ SetDocName("Predict Regression");
+ SetDocLongDescription("This application predict output values from an input"
+ " image, based on a regression model file produced by"
+ " the TrainRegression application. Pixels of the "
+ "output image will contain the predicted values from"
+ "the regression model (single band). The input pixels"
+ " can be optionally centered and reduced according "
+ "to the statistics file produced by the "
+ "ComputeImagesStatistics application. An optional "
+ "input mask can be provided, in which case only "
+ "input image pixels whose corresponding mask value "
+ "is greater than 0 will be processed. The remaining"
+ " of pixels will be given the value 0 in the output"
+ " image.");
+
+ SetDocLimitations("The input image must contain the feature bands used for"
+ " the model training (without the predicted value). "
+ "If a statistics file was used during training by the "
+ "TrainRegression, it is mandatory to use the same "
+ "statistics file for prediction. If an input mask is "
+ "used, its size must match the input image size.");
+ SetDocAuthors("OTB-Team");
+ SetDocSeeAlso("TrainRegression, ComputeImagesStatistics");
+
+ AddDocTag(Tags::Learning);
+
+ AddParameter(ParameterType_InputImage, "in", "Input Image");
+ SetParameterDescription( "in", "The input image to predict.");
+
+ // TODO : use CSV input/output ?
+
+ AddParameter(ParameterType_InputImage, "mask", "Input Mask");
+ SetParameterDescription( "mask", "The mask allows to restrict "
+ "classification of the input image to the area where mask pixel values "
+ "are greater than 0.");
+ MandatoryOff("mask");
+
+ AddParameter(ParameterType_InputFilename, "model", "Model file");
+ SetParameterDescription("model", "A regression model file (produced by "
+ "TrainRegression application).");
+
+ AddParameter(ParameterType_InputFilename, "imstat", "Statistics file");
+ SetParameterDescription("imstat", "A XML file containing mean and standard"
+ " deviation to center and reduce samples before prediction "
+ "(produced by ComputeImagesStatistics application). If this file contains"
+ "one more band than the sample size, the last stat of last band will be"
+ "applied to expand the output predicted value");
+ MandatoryOff("imstat");
+
+ AddParameter(ParameterType_OutputImage, "out", "Output Image");
+ SetParameterDescription( "out", "Output image containing predicted values");
+
+ AddRAMParameter();
+
+ // Doc example parameter settings
+ SetDocExampleParameterValue("in", "QB_1_ortho.tif");
+ SetDocExampleParameterValue("imstat", "EstimateImageStatisticsQB1.xml");
+ SetDocExampleParameterValue("model", "clsvmModelQB1.svm");
+ SetDocExampleParameterValue("out", "clLabeledImageQB1.tif");
+ }
+
+ void DoUpdateParameters()
+ {
+ // Nothing to do here : all parameters are independent
+ }
+
+ void DoExecute()
+ {
+ // Load input image
+ FloatVectorImageType::Pointer inImage = GetParameterImage("in");
+ inImage->UpdateOutputInformation();
+ unsigned int nbFeatures = inImage->GetNumberOfComponentsPerPixel();
+
+ // Load svm model
+ otbAppLogINFO("Loading model");
+ m_Model = MachineLearningModelFactoryType::CreateMachineLearningModel(GetParameterString("model"),
+ MachineLearningModelFactoryType::ReadMode);
+
+ if (m_Model.IsNull())
+ {
+ otbAppLogFATAL(<< "Error when loading model " << GetParameterString("model") << " : unsupported model type");
+ }
+
+ m_Model->Load(GetParameterString("model"));
+ m_Model->SetRegressionMode(true);
+ otbAppLogINFO("Model loaded");
+
+ // Classify
+ m_ClassificationFilter = ClassificationFilterType::New();
+ m_ClassificationFilter->SetModel(m_Model);
+
+ FloatImageType::Pointer outputImage = m_ClassificationFilter->GetOutput();
+
+ // Normalize input image if asked
+ if(IsParameterEnabled("imstat") )
+ {
+ otbAppLogINFO("Input image normalization activated.");
+ // Normalize input image (optional)
+ StatisticsReader::Pointer statisticsReader = StatisticsReader::New();
+ MeasurementType meanMeasurementVector;
+ MeasurementType stddevMeasurementVector;
+ m_Rescaler = RescalerType::New();
+ // Load input image statistics
+ statisticsReader->SetFileName(GetParameterString("imstat"));
+ meanMeasurementVector = statisticsReader->GetStatisticVectorByName("mean");
+ stddevMeasurementVector = statisticsReader->GetStatisticVectorByName("stddev");
+ otbAppLogINFO( "mean used: " << meanMeasurementVector );
+ otbAppLogINFO( "standard deviation used: " << stddevMeasurementVector );
+ if (meanMeasurementVector.Size() == nbFeatures + 1)
+ {
+ double outMean = meanMeasurementVector[nbFeatures];
+ double outStdDev = stddevMeasurementVector[nbFeatures];
+ meanMeasurementVector.SetSize(nbFeatures,false);
+ stddevMeasurementVector.SetSize(nbFeatures,false);
+ m_OutRescaler = OutputRescalerType::New();
+ m_OutRescaler->SetInput(m_ClassificationFilter->GetOutput());
+ m_OutRescaler->GetFunctor().SetA(outStdDev);
+ m_OutRescaler->GetFunctor().SetB(outMean);
+ outputImage = m_OutRescaler->GetOutput();
+ }
+ else if (meanMeasurementVector.Size() != nbFeatures)
+ {
+ otbAppLogFATAL("Wrong number of components in statistics file : "<<meanMeasurementVector.Size());
+ }
+
+ // Rescale vector image
+ m_Rescaler->SetScale(stddevMeasurementVector);
+ m_Rescaler->SetShift(meanMeasurementVector);
+ m_Rescaler->SetInput(inImage);
+
+ m_ClassificationFilter->SetInput(m_Rescaler->GetOutput());
+ }
+ else
+ {
+ otbAppLogINFO("Input image normalization deactivated.");
+ m_ClassificationFilter->SetInput(inImage);
+ }
+
+
+ if(IsParameterEnabled("mask"))
+ {
+ otbAppLogINFO("Using input mask");
+ // Load mask image and cast into LabeledImageType
+ MaskImageType::Pointer inMask = GetParameterUInt8Image("mask");
+
+ m_ClassificationFilter->SetInputMask(inMask);
+ }
+
+ SetParameterOutputImage<FloatImageType>("out", outputImage);
+
+ }
+
+ ClassificationFilterType::Pointer m_ClassificationFilter;
+ ModelPointerType m_Model;
+ RescalerType::Pointer m_Rescaler;
+ OutputRescalerType::Pointer m_OutRescaler;
+
+};
+
+
+}
+}
+
+OTB_APPLICATION_EXPORT(otb::Wrapper::PredictRegression)
diff --git a/Modules/Applications/AppClassification/app/otbTrainImagesClassifier.cxx b/Modules/Applications/AppClassification/app/otbTrainImagesClassifier.cxx
index 1b9358f04832bed66ec463d1510fbb371ea2a3de..de1520dfca4855e523513f8a4542a95bff1cde84 100644
--- a/Modules/Applications/AppClassification/app/otbTrainImagesClassifier.cxx
+++ b/Modules/Applications/AppClassification/app/otbTrainImagesClassifier.cxx
@@ -14,15 +14,95 @@
PURPOSE. See the above copyright notices for more information.
=========================================================================*/
+#include "otbLearningApplicationBase.h"
+#include "otbWrapperApplicationFactory.h"
-#include "otbTrainImagesClassifier.h"
+#include "otbListSampleGenerator.h"
+
+// Statistic XML Reader
+#include "otbStatisticsXMLFileReader.h"
+
+// Validation
+#include "otbConfusionMatrixCalculator.h"
+
+#include "itkTimeProbe.h"
+#include "otbStandardFilterWatcher.h"
+
+// Normalize the samples
+#include "otbShiftScaleSampleListFilter.h"
+
+// List sample concatenation
+#include "otbConcatenateSampleListFilter.h"
+
+// Balancing ListSample
+#include "otbListSampleToBalancedListSampleFilter.h"
+
+// VectorData projection filter
+
+// Extract a ROI of the vectordata
+#include "otbVectorDataIntoImageProjectionFilter.h"
+
+// Elevation handler
+#include "otbWrapperElevationParametersHandler.h"
namespace otb
{
namespace Wrapper
{
-void TrainImagesClassifier::DoInit()
+class TrainImagesClassifier: public LearningApplicationBase<float,int>
+{
+public:
+ /** Standard class typedefs. */
+ typedef TrainImagesClassifier Self;
+ typedef LearningApplicationBase<float,int> Superclass;
+ typedef itk::SmartPointer<Self> Pointer;
+ typedef itk::SmartPointer<const Self> ConstPointer;
+
+ /** Standard macro */
+ itkNewMacro(Self)
+
+ itkTypeMacro(TrainImagesClassifier, otb::Wrapper::LearningApplicationBase)
+
+ typedef Superclass::SampleType SampleType;
+ typedef Superclass::ListSampleType ListSampleType;
+ typedef Superclass::TargetSampleType TargetSampleType;
+ typedef Superclass::TargetListSampleType TargetListSampleType;
+
+ typedef Superclass::SampleImageType SampleImageType;
+ typedef SampleImageType::PixelType PixelType;
+
+ // SampleList manipulation
+ typedef otb::ListSampleGenerator<SampleImageType, VectorDataType> ListSampleGeneratorType;
+
+ typedef otb::Statistics::ConcatenateSampleListFilter<ListSampleType> ConcatenateListSampleFilterType;
+ typedef otb::Statistics::ConcatenateSampleListFilter<TargetListSampleType> 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;
+
+ // Estimate performance on validation sample
+ typedef otb::ConfusionMatrixCalculator<TargetListSampleType, TargetListSampleType> ConfusionMatrixCalculatorType;
+ typedef ConfusionMatrixCalculatorType::ConfusionMatrixType ConfusionMatrixType;
+ typedef ConfusionMatrixCalculatorType::MapOfIndicesType MapOfIndicesType;
+ typedef ConfusionMatrixCalculatorType::ClassLabelType ClassLabelType;
+
+ // VectorData projection filter
+ typedef otb::VectorDataProjectionFilter<VectorDataType, VectorDataType> VectorDataProjectionFilterType;
+
+ // Extract ROI
+ typedef otb::VectorDataIntoImageProjectionFilter<VectorDataType, SampleImageType> VectorDataReprojectionType;
+
+protected:
+ //using Superclass::AddParameter;
+ //friend void InitSVMParams(TrainImagesClassifier & app);
+
+private:
+
+void DoInit()
{
SetName("TrainImagesClassifier");
SetDescription(
@@ -46,8 +126,6 @@ void TrainImagesClassifier::DoInit()
SetDocAuthors("OTB-Team");
SetDocSeeAlso("OpenCV documentation for machine learning http://docs.opencv.org/modules/ml/doc/ml.html ");
- AddDocTag(Tags::Learning);
-
//Group IO
AddParameter(ParameterType_Group, "io", "Input and output data");
SetParameterDescription("io", "This group of parameters allows to set input and output data.");
@@ -101,24 +179,7 @@ void TrainImagesClassifier::DoInit()
SetParameterDescription("sample.vfn", "Name of the field used to discriminate class labels in the input vector data files.");
SetParameterString("sample.vfn", "Class");
- 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
+ Superclass::DoInit();
AddRANDParameter();
// Doc example parameter settings
@@ -136,15 +197,14 @@ void TrainImagesClassifier::DoInit()
SetDocExampleParameterValue("classifier.libsvm.opt", "false");
SetDocExampleParameterValue("io.out", "svmModelQB1.txt");
SetDocExampleParameterValue("io.confmatout", "svmConfusionMatrixQB1.csv");
-}
+}
-void TrainImagesClassifier::DoUpdateParameters()
+void DoUpdateParameters()
{
// Nothing to do here : all parameters are independent
}
-
-void TrainImagesClassifier::LogConfusionMatrix(ConfusionMatrixCalculatorType* confMatCalc)
+void LogConfusionMatrix(ConfusionMatrixCalculatorType* confMatCalc)
{
ConfusionMatrixCalculatorType::ConfusionMatrixType matrix = confMatCalc->GetConfusionMatrix();
@@ -215,24 +275,7 @@ void TrainImagesClassifier::LogConfusionMatrix(ConfusionMatrixCalculatorType* co
otbAppLogINFO("Confusion matrix (rows = reference labels, columns = produced labels):\n" << os.str());
}
-void TrainImagesClassifier::Classify(ListSampleType::Pointer validationListSample, LabelListSampleType::Pointer predictedList)
-{
- //Classification
- ModelPointerType model = MachineLearningModelFactoryType::CreateMachineLearningModel(GetParameterString("io.out"),
- MachineLearningModelFactoryType::ReadMode);
-
- if (model.IsNull())
- {
- otbAppLogFATAL(<< "Error when loading model " << GetParameterString("io.out"));
- }
-
- model->Load(GetParameterString("io.out"));
- model->SetInputListSample(validationListSample);
- model->SetTargetListSample(predictedList);
- model->PredictAll();
-}
-
-void TrainImagesClassifier::DoExecute()
+void DoExecute()
{
GetLogger()->Debug("Entering DoExecute\n");
//Create training and validation for list samples and label list samples
@@ -243,8 +286,8 @@ void TrainImagesClassifier::DoExecute()
ConcatenateLabelListSampleFilterType::New();
ConcatenateListSampleFilterType::Pointer concatenateValidationSamples = ConcatenateListSampleFilterType::New();
- MeasurementType meanMeasurementVector;
- MeasurementType stddevMeasurementVector;
+ SampleType meanMeasurementVector;
+ SampleType stddevMeasurementVector;
//--------------------------
// Load measurements from images
@@ -358,7 +401,7 @@ void TrainImagesClassifier::DoExecute()
}
ListSampleType::Pointer listSample;
- LabelListSampleType::Pointer labelListSample;
+ TargetListSampleType::Pointer labelListSample;
//--------------------------
// Balancing training sample (if needed)
// if (IsParameterEnabled("sample.b"))
@@ -384,9 +427,9 @@ void TrainImagesClassifier::DoExecute()
//--------------------------
// Split the data set into training/validation set
ListSampleType::Pointer trainingListSample = listSample;
- LabelListSampleType::Pointer trainingLabeledListSample = labelListSample;
+ TargetListSampleType::Pointer trainingLabeledListSample = labelListSample;
- LabelListSampleType::Pointer validationLabeledListSample = concatenateValidationLabels->GetOutput();
+ TargetListSampleType::Pointer validationLabeledListSample = concatenateValidationLabels->GetOutput();
otbAppLogINFO("Size of training set: " << trainingListSample->Size());
otbAppLogINFO("Size of validation set: " << validationListSample->Size());
otbAppLogINFO("Size of labeled training set: " << trainingLabeledListSample->Size());
@@ -395,88 +438,14 @@ void TrainImagesClassifier::DoExecute()
//--------------------------
// Estimate model
//--------------------------
- LabelListSampleType::Pointer predictedList = LabelListSampleType::New();
- const std::string classifierType = GetParameterString("classifier");
-
- if (classifierType == "libsvm")
- {
- #ifdef OTB_USE_LIBSVM
- TrainLibSVM(trainingListSample, trainingLabeledListSample);
- #else
- otbAppLogFATAL("Module LIBSVM is not installed. You should consider turning OTB_USE_LIBSVM on during cmake configuration.");
- #endif
- }
- else if (classifierType == "svm")
- {
- #ifdef OTB_USE_OPENCV
- TrainSVM(trainingListSample, trainingLabeledListSample);
- #else
- otbAppLogFATAL("Module OPENCV is not installed. You should consider turning OTB_USE_OPENCV on during cmake configuration.");
- #endif
- }
- else if (classifierType == "boost")
- {
- #ifdef OTB_USE_OPENCV
- TrainBoost(trainingListSample, trainingLabeledListSample);
- #else
- otbAppLogFATAL("Module OPENCV is not installed. You should consider turning OTB_USE_OPENCV on during cmake configuration.");
- #endif
- }
- else if (classifierType == "dt")
- {
- #ifdef OTB_USE_OPENCV
- TrainDecisionTree(trainingListSample, trainingLabeledListSample);
- #else
- otbAppLogFATAL("Module OPENCV is not installed. You should consider turning OTB_USE_OPENCV on during cmake configuration.");
- #endif
- }
- else if (classifierType == "gbt")
- {
- #ifdef OTB_USE_OPENCV
- TrainGradientBoostedTree(trainingListSample, trainingLabeledListSample);
- #else
- otbAppLogFATAL("Module OPENCV is not installed. You should consider turning OTB_USE_OPENCV on during cmake configuration.");
- #endif
- }
- else if (classifierType == "ann")
- {
- #ifdef OTB_USE_OPENCV
- TrainNeuralNetwork(trainingListSample, trainingLabeledListSample);
- #else
- otbAppLogFATAL("Module OPENCV is not installed. You should consider turning OTB_USE_OPENCV on during cmake configuration.");
- #endif
- }
- else if (classifierType == "bayes")
- {
- #ifdef OTB_USE_OPENCV
- TrainNormalBayes(trainingListSample, trainingLabeledListSample);
- #else
- otbAppLogFATAL("Module OPENCV is not installed. You should consider turning OTB_USE_OPENCV on during cmake configuration.");
- #endif
- }
- else if (classifierType == "rf")
- {
- #ifdef OTB_USE_OPENCV
- TrainRandomForests(trainingListSample, trainingLabeledListSample);
- #else
- otbAppLogFATAL("Module OPENCV is not installed. You should consider turning OTB_USE_OPENCV on during cmake configuration.");
- #endif
- }
- else if (classifierType == "knn")
- {
- #ifdef OTB_USE_OPENCV
- TrainKNN(trainingListSample, trainingLabeledListSample);
- #else
- otbAppLogFATAL("Module OPENCV is not installed. You should consider turning OTB_USE_OPENCV on during cmake configuration.");
- #endif
- }
-
+ this->Train(trainingListSample,trainingLabeledListSample,GetParameterString("io.out"));
//--------------------------
// Performances estimation
//--------------------------
+ TargetListSampleType::Pointer predictedList = TargetListSampleType::New();
ListSampleType::Pointer performanceListSample=ListSampleType::New();
- LabelListSampleType::Pointer performanceLabeledListSample=LabelListSampleType::New();
+ TargetListSampleType::Pointer performanceLabeledListSample=TargetListSampleType::New();
//Test the input validation set size
if(validationLabeledListSample->Size() != 0)
@@ -491,7 +460,7 @@ void TrainImagesClassifier::DoExecute()
performanceLabeledListSample = trainingLabeledListSample;
}
- Classify(performanceListSample, predictedList);
+ this->Classify(performanceListSample, predictedList, GetParameterString("io.out"));
ConfusionMatrixCalculatorType::Pointer confMatCalc = ConfusionMatrixCalculatorType::New();
@@ -605,11 +574,12 @@ void TrainImagesClassifier::DoExecute()
} // END if (this->HasValue("io.confmatout"))
// TODO: implement hyperplane distance classifier and performance validation (cf. object detection) ?
-
}
+ VectorDataReprojectionType::Pointer vdreproj;
+};
-}
-}
+} // end namespace Wrapper
+} // end namespace otb
OTB_APPLICATION_EXPORT(otb::Wrapper::TrainImagesClassifier)
diff --git a/Modules/Applications/AppClassification/app/otbTrainImagesClassifier.h b/Modules/Applications/AppClassification/app/otbTrainImagesClassifier.h
deleted file mode 100644
index 235613fd56eaa5a265dc66f1e60ad26c849e1a27..0000000000000000000000000000000000000000
--- a/Modules/Applications/AppClassification/app/otbTrainImagesClassifier.h
+++ /dev/null
@@ -1,198 +0,0 @@
-/*=========================================================================
- 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.
-
- =========================================================================*/
-#include "otbConfigure.h"
-
-#include "otbWrapperApplicationFactory.h"
-
-#include <iostream>
-
-//Image
-#include "otbVectorImage.h"
-#include "otbVectorData.h"
-#include "otbListSampleGenerator.h"
-
-// ListSample
-#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"
-
-// Validation
-#include "otbConfusionMatrixCalculator.h"
-
-#include "itkTimeProbe.h"
-#include "otbStandardFilterWatcher.h"
-
-// Normalize the samples
-#include "otbShiftScaleSampleListFilter.h"
-
-// List sample concatenation
-#include "otbConcatenateSampleListFilter.h"
-
-// Balancing ListSample
-#include "otbListSampleToBalancedListSampleFilter.h"
-
-// VectorData projection filter
-
-// Extract a ROI of the vectordata
-#include "otbVectorDataIntoImageProjectionFilter.h"
-
-// Elevation handler
-#include "otbWrapperElevationParametersHandler.h"
-
-namespace otb
-{
-namespace Wrapper
-{
-
-class TrainImagesClassifier: public Application
-{
-public:
- /** Standard class typedefs. */
- typedef TrainImagesClassifier Self;
- typedef Application Superclass;
- typedef itk::SmartPointer<Self> Pointer;
- typedef itk::SmartPointer<const Self> ConstPointer;
-
- /** Standard macro */
- itkNewMacro(Self)
-
- itkTypeMacro(TrainImagesClassifier, otb::Application)
-
- typedef FloatVectorImageType::PixelType PixelType;
- typedef FloatVectorImageType::InternalPixelType InternalPixelType;
-
- // Training vectordata
- typedef itk::VariableLengthVector<InternalPixelType> MeasurementType;
-
- // SampleList manipulation
- typedef otb::ListSampleGenerator<FloatVectorImageType, VectorDataType> ListSampleGeneratorType;
-
- typedef ListSampleGeneratorType::ListSampleType ListSampleType;
- 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<MeasurementType> StatisticsReader;
-
- // Enhance List Sample typedef otb::Statistics::ListSampleToBalancedListSampleFilter<ListSampleType, LabelListSampleType> BalancingListSampleFilterType;
- typedef otb::Statistics::ShiftScaleSampleListFilter<ListSampleType, ListSampleType> ShiftScaleFilterType;
-
- // Machine Learning models
- typedef otb::MachineLearningModelFactory<InternalPixelType, ListSampleGeneratorType::ClassLabelType> MachineLearningModelFactoryType;
- typedef MachineLearningModelFactoryType::MachineLearningModelTypePointer ModelPointerType;
-
-#ifdef OTB_USE_OPENCV
- typedef otb::RandomForestsMachineLearningModel<InternalPixelType, ListSampleGeneratorType::ClassLabelType> RandomForestType;
- typedef otb::KNearestNeighborsMachineLearningModel<InternalPixelType, ListSampleGeneratorType::ClassLabelType> KNNType;
- typedef otb::SVMMachineLearningModel<InternalPixelType, ListSampleGeneratorType::ClassLabelType> SVMType;
- typedef otb::BoostMachineLearningModel<InternalPixelType, ListSampleGeneratorType::ClassLabelType> BoostType;
- typedef otb::DecisionTreeMachineLearningModel<InternalPixelType, ListSampleGeneratorType::ClassLabelType> DecisionTreeType;
- typedef otb::GradientBoostedTreeMachineLearningModel<InternalPixelType, ListSampleGeneratorType::ClassLabelType> GradientBoostedTreeType;
- typedef otb::NeuralNetworkMachineLearningModel<InternalPixelType, ListSampleGeneratorType::ClassLabelType> NeuralNetworkType;
- typedef otb::NormalBayesMachineLearningModel<InternalPixelType, ListSampleGeneratorType::ClassLabelType> NormalBayesType;
-#endif
-
-#ifdef OTB_USE_LIBSVM
- typedef otb::LibSVMMachineLearningModel<InternalPixelType, ListSampleGeneratorType::ClassLabelType> LibSVMType;
-#endif
-
- // Estimate performance on validation sample
- typedef otb::ConfusionMatrixCalculator<LabelListSampleType, LabelListSampleType> ConfusionMatrixCalculatorType;
- typedef ConfusionMatrixCalculatorType::ConfusionMatrixType ConfusionMatrixType;
- typedef ConfusionMatrixCalculatorType::MapOfIndicesType MapOfIndicesType;
- typedef ConfusionMatrixCalculatorType::ClassLabelType ClassLabelType;
-
-
- // VectorData projection filter
- typedef otb::VectorDataProjectionFilter<VectorDataType, VectorDataType> VectorDataProjectionFilterType;
-
- // Extract ROI
- typedef otb::VectorDataIntoImageProjectionFilter<VectorDataType, FloatVectorImageType> VectorDataReprojectionType;
-
-protected:
- using Superclass::AddParameter;
- friend void InitSVMParams(TrainImagesClassifier & app);
-
-private:
- void DoInit();
-
- void DoUpdateParameters();
-
- void LogConfusionMatrix(ConfusionMatrixCalculatorType* confMatCalc);
-
-#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, LabelListSampleType::Pointer trainingLabeledListSample);
-#endif
-
-#ifdef OTB_USE_OPENCV
- void TrainBoost(ListSampleType::Pointer trainingListSample, LabelListSampleType::Pointer trainingLabeledListSample);
- void TrainSVM(ListSampleType::Pointer trainingListSample, LabelListSampleType::Pointer trainingLabeledListSample);
- void TrainDecisionTree(ListSampleType::Pointer trainingListSample, LabelListSampleType::Pointer trainingLabeledListSample);
- void TrainGradientBoostedTree(ListSampleType::Pointer trainingListSample, LabelListSampleType::Pointer trainingLabeledListSample);
- void TrainNeuralNetwork(ListSampleType::Pointer trainingListSample, LabelListSampleType::Pointer trainingLabeledListSample);
- void TrainNormalBayes(ListSampleType::Pointer trainingListSample, LabelListSampleType::Pointer trainingLabeledListSample);
- void TrainRandomForests(ListSampleType::Pointer trainingListSample, LabelListSampleType::Pointer trainingLabeledListSample);
- void TrainKNN(ListSampleType::Pointer trainingListSample, LabelListSampleType::Pointer trainingLabeledListSample);
-#endif
-
- void Classify(ListSampleType::Pointer validationListSample, LabelListSampleType::Pointer predictedList);
-
- void DoExecute();
-
- VectorDataReprojectionType::Pointer vdreproj;
-};
-
-}
-}
-
-
diff --git a/Modules/Applications/AppClassification/app/otbTrainKNN.cxx b/Modules/Applications/AppClassification/app/otbTrainKNN.cxx
deleted file mode 100644
index bc31cd4fce6c1c0207570161bd6df033e8fbff45..0000000000000000000000000000000000000000
--- a/Modules/Applications/AppClassification/app/otbTrainKNN.cxx
+++ /dev/null
@@ -1,52 +0,0 @@
-/*=========================================================================
- 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.
-
- =========================================================================*/
-
-#include "otbTrainImagesClassifier.h"
-
-
-namespace otb
-{
-namespace Wrapper
-{
-#ifdef OTB_USE_OPENCV
- void TrainImagesClassifier::InitKNNParams()
- {
- AddChoice("classifier.knn", "KNN classifier");
- SetParameterDescription("classifier.knn", "This group of parameters allows to set KNN classifier parameters. "
- "See complete documentation here \\url{http://docs.opencv.org/modules/ml/doc/k_nearest_neighbors.html}.");
-
- //K parameter
- AddParameter(ParameterType_Int, "classifier.knn.k", "Number of Neighbors");
- SetParameterInt("classifier.knn.k", 32);
- SetParameterDescription("classifier.knn.k","The number of neighbors to use.");
-
- }
-
-
- void TrainImagesClassifier::TrainKNN(ListSampleType::Pointer trainingListSample, LabelListSampleType::Pointer trainingLabeledListSample)
- {
- KNNType::Pointer knnClassifier = KNNType::New();
- knnClassifier->SetInputListSample(trainingListSample);
- knnClassifier->SetTargetListSample(trainingLabeledListSample);
- knnClassifier->SetK(GetParameterInt("classifier.knn.k"));
-
- knnClassifier->Train();
- knnClassifier->Save(GetParameterString("io.out"));
- }
-#endif
-} //end namespace wrapper
-} //end namespace otb
diff --git a/Modules/Applications/AppClassification/app/otbTrainRegression.cxx b/Modules/Applications/AppClassification/app/otbTrainRegression.cxx
new file mode 100644
index 0000000000000000000000000000000000000000..82e865194dd0418e98d04c17550df9919f19ff76
--- /dev/null
+++ b/Modules/Applications/AppClassification/app/otbTrainRegression.cxx
@@ -0,0 +1,543 @@
+/*=========================================================================
+ 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.
+
+ =========================================================================*/
+#include "otbLearningApplicationBase.h"
+#include "otbWrapperApplicationFactory.h"
+
+#include "otbListSampleGenerator.h"
+
+#include "otbImageToEnvelopeVectorDataFilter.h"
+#include "itkPreOrderTreeIterator.h"
+
+// 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"
+
+#include "itkMersenneTwisterRandomVariateGenerator.h"
+
+// Elevation handler
+#include "otbWrapperElevationParametersHandler.h"
+
+namespace otb
+{
+namespace Wrapper
+{
+
+class TrainRegression: public LearningApplicationBase<float,float>
+{
+public:
+ /** Standard class typedefs. */
+ typedef TrainRegression Self;
+ typedef LearningApplicationBase<float,float> Superclass;
+ typedef itk::SmartPointer<Self> Pointer;
+ typedef itk::SmartPointer<const Self> ConstPointer;
+
+ /** Standard macro */
+ itkNewMacro(Self)
+
+ itkTypeMacro(TrainRegression, otb::Wrapper::LearningApplicationBase)
+
+ typedef Superclass::SampleType SampleType;
+ typedef Superclass::ListSampleType ListSampleType;
+ typedef Superclass::TargetSampleType TargetSampleType;
+ typedef Superclass::TargetListSampleType TargetListSampleType;
+
+ typedef Superclass::SampleImageType SampleImageType;
+ typedef SampleImageType::PixelType PixelType;
+
+ // SampleList manipulation
+ typedef otb::ListSampleGenerator<SampleImageType, VectorDataType> ListSampleGeneratorType;
+
+ typedef otb::Statistics::ConcatenateSampleListFilter<ListSampleType> ConcatenateListSampleFilterType;
+ typedef otb::Statistics::ConcatenateSampleListFilter<TargetListSampleType> 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;
+
+ typedef otb::ImageToEnvelopeVectorDataFilter<SampleImageType,VectorDataType> EnvelopeFilterType;
+
+ typedef itk::PreOrderTreeIterator<VectorDataType::DataTreeType> TreeIteratorType;
+
+ typedef itk::Statistics::MersenneTwisterRandomVariateGenerator RandomGeneratorType;
+
+protected:
+ TrainRegression()
+ {
+ this->m_RegressionFlag = true;
+ }
+
+private:
+
+void DoInit()
+{
+ SetName("TrainRegression");
+ SetDescription(
+ "Train a classifier from multiple images to perform regression.");
+
+ // Documentation
+ SetDocName("Train a regression model");
+ SetDocLongDescription(
+ "This application trains a classifier from multiple input images or a csv "
+ "file, in order to perform regression. Predictors are composed of pixel "
+ "values in each band optionally centered and reduced using an XML "
+ "statistics file produced by the ComputeImagesStatistics application.\n "
+ "The output value for each predictor is assumed to be the last band "
+ "(or the last column for CSV files). Training and validation predictor "
+ "lists are built such that their size is inferior to maximum bounds given "
+ "by the user, and the proportion corresponds to the balance parameter. "
+ "Several classifier parameters can be set depending on the chosen "
+ "classifier. In the validation process, the mean square error is computed\n"
+ " This application is based on LibSVM and on OpenCV Machine Learning "
+ "classifiers, and is compatible with OpenCV 2.3.1 and later.");
+ SetDocLimitations("None");
+ SetDocAuthors("OTB-Team");
+ SetDocSeeAlso("OpenCV documentation for machine learning http://docs.opencv.org/modules/ml/doc/ml.html ");
+
+ //Group IO
+ AddParameter(ParameterType_Group, "io", "Input and output data");
+ SetParameterDescription("io", "This group of parameters allows to set input and output data.");
+ AddParameter(ParameterType_InputImageList, "io.il", "Input Image List");
+ SetParameterDescription("io.il", "A list of input images. First (n-1) bands should contain the predictor. The last band should contain the output value to predict.");
+ AddParameter(ParameterType_InputFilename, "io.csv", "Input CSV file");
+ SetParameterDescription("io.csv","Input CSV file containing the predictors, and the output values in last column. Only used when no input image is given");
+ MandatoryOff("io.csv");
+
+ AddParameter(ParameterType_InputFilename, "io.imstat", "Input XML image statistics file");
+ MandatoryOff("io.imstat");
+ SetParameterDescription("io.imstat",
+ "Input XML file containing the mean and the standard deviation of the input images.");
+ AddParameter(ParameterType_OutputFilename, "io.out", "Output regression model");
+ SetParameterDescription("io.out", "Output file containing the model estimated (.txt format).");
+
+ AddParameter(ParameterType_Float,"io.mse","Mean Square Error");
+ SetParameterDescription("io.mse","Mean square error computed with the validation predictors");
+ SetParameterRole("io.mse",Role_Output);
+ DisableParameter("io.mse");
+
+ //Group Sample list
+ AddParameter(ParameterType_Group, "sample", "Training and validation samples parameters");
+ SetParameterDescription("sample",
+ "This group of parameters allows to set training and validation sample lists parameters.");
+
+ AddParameter(ParameterType_Int, "sample.mt", "Maximum training predictors");
+ //MandatoryOff("mt");
+ SetDefaultParameterInt("sample.mt", 1000);
+ SetParameterDescription("sample.mt", "Maximum number of training predictors (default = 1000) (no limit = -1).");
+
+ AddParameter(ParameterType_Int, "sample.mv", "Maximum validation predictors");
+ // MandatoryOff("mv");
+ SetDefaultParameterInt("sample.mv", 1000);
+ SetParameterDescription("sample.mv", "Maximum number of validation predictors (default = 1000) (no limit = -1).");
+
+ AddParameter(ParameterType_Float, "sample.vtr", "Training and validation sample ratio");
+ SetParameterDescription("sample.vtr",
+ "Ratio between training and validation samples (0.0 = all training, 1.0 = all validation) (default = 0.5).");
+ SetParameterFloat("sample.vtr", 0.5);
+
+ Superclass::DoInit();
+
+ AddRANDParameter();
+
+ // Doc example parameter settings
+ SetDocExampleParameterValue("io.il", "training_dataset.tif");
+ SetDocExampleParameterValue("io.out", "regression_model.txt");
+ SetDocExampleParameterValue("io.imstat", "training_statistics.xml");
+ SetDocExampleParameterValue("classifier", "svm");
+}
+
+void DoUpdateParameters()
+{
+ if (HasValue("io.csv") && IsParameterEnabled("io.csv"))
+ {
+ MandatoryOff("io.il");
+ }
+ else
+ {
+ MandatoryOn("io.il");
+ }
+}
+
+void ParseCSVPredictors(std::string path, ListSampleType* outputList)
+{
+ std::ifstream ifs;
+ ifs.open(path.c_str());
+ unsigned int nbCols = 0;
+ char sep = '\t';
+ std::istringstream iss;
+ SampleType elem;
+ while(!ifs.eof())
+ {
+ std::string line;
+ std::getline(ifs,line);
+ // filter current line
+ while (!line.empty() && (line[0] == ' ' || line[0] == '\t'))
+ {
+ line.erase(line.begin());
+ }
+ while (!line.empty() && ( *(line.end()-1) == ' ' || *(line.end()-1) == '\t' || *(line.end()-1) == '\r'))
+ {
+ line.erase(line.end()-1);
+ }
+
+ // Avoid commented lines or too short ones
+ if (!line.empty() && line[0] != '#')
+ {
+ std::vector<itksys::String> words = itksys::SystemTools::SplitString(line.c_str(),sep);
+ if (nbCols == 0)
+ {
+ // detect separator and feature size
+ if (words.size() < 2)
+ {
+ sep = ' ';
+ words = itksys::SystemTools::SplitString(line.c_str(),sep);
+ }
+ if (words.size() < 2)
+ {
+ sep = ';';
+ words = itksys::SystemTools::SplitString(line.c_str(),sep);
+ }
+ if (words.size() < 2)
+ {
+ sep = ',';
+ words = itksys::SystemTools::SplitString(line.c_str(),sep);
+ }
+ if (words.size() < 2)
+ {
+ otbAppLogFATAL(<< "Can't parse CSV file : less than 2 columns or unknonw separator (knowns ones are tab, space, comma and semi-colon)");
+ }
+ nbCols = words.size();
+ elem.SetSize(nbCols,false);
+ outputList->SetMeasurementVectorSize(nbCols);
+ }
+ else if (words.size() != nbCols )
+ {
+ otbAppLogWARNING(<< "Skip CSV line, wrong number of columns : got "<<words.size() << ", expected "<<nbCols);
+ continue;
+ }
+ elem.Fill(0.0);
+ for (unsigned int i=0 ; i<nbCols ; ++i)
+ {
+ iss.str(words[i]);
+ iss >> elem[i];
+ }
+ outputList->PushBack(elem);
+ }
+ }
+ ifs.close();
+}
+
+void DoExecute()
+{
+ GetLogger()->Debug("Entering DoExecute\n");
+ //Create training and validation for list samples and label list samples
+ ConcatenateListSampleFilterType::Pointer concatenateTrainingSamples = ConcatenateListSampleFilterType::New();
+ ConcatenateListSampleFilterType::Pointer concatenateValidationSamples = ConcatenateListSampleFilterType::New();
+
+ SampleType meanMeasurementVector;
+ SampleType stddevMeasurementVector;
+
+ //--------------------------
+ // Load measurements from images
+ unsigned int nbBands = 0;
+ unsigned int nbFeatures = 0;
+ //Iterate over all input images
+
+ FloatVectorImageListType* imageList = GetParameterImageList("io.il");
+
+ //Iterate over all input images
+ for (unsigned int imgIndex = 0; imgIndex < imageList->Size(); ++imgIndex)
+ {
+ FloatVectorImageType::Pointer image = imageList->GetNthElement(imgIndex);
+ image->UpdateOutputInformation();
+
+ if (imgIndex == 0)
+ {
+ nbBands = image->GetNumberOfComponentsPerPixel();
+ nbFeatures = static_cast<unsigned int>(static_cast<int>(nbBands) - 1);
+ if (nbBands < 2)
+ {
+ otbAppLogFATAL(<< "Need at least two bands per image, got "<<nbBands);
+ }
+ else
+ {
+ if (nbBands != image->GetNumberOfComponentsPerPixel())
+ {
+ otbAppLogFATAL(<< "Image has a different number of components than "
+ "the first one, expected "<<nbBands<<", got "<< image->GetNumberOfComponentsPerPixel());
+ }
+ }
+ }
+
+ // Extract image envelope to feed in sampleGenerator
+ EnvelopeFilterType::Pointer envelopeFilter = EnvelopeFilterType::New();
+ envelopeFilter->SetInput(image);
+ envelopeFilter->SetSamplingRate(0);
+ if (!image->GetProjectionRef().empty())
+ {
+ envelopeFilter->SetOutputProjectionRef(image->GetProjectionRef());
+ }
+
+ // Setup the DEM Handler
+ // otb::Wrapper::ElevationParametersHandler::SetupDEMHandlerFromElevationParameters(this,"elev");
+
+ envelopeFilter->Update();
+
+ VectorDataType::Pointer envelope = envelopeFilter->GetOutput();
+
+ TreeIteratorType itVector(envelope->GetDataTree());
+ for (itVector.GoToBegin(); !itVector.IsAtEnd(); ++itVector)
+ {
+ if (itVector.Get()->IsPolygonFeature())
+ {
+ itVector.Get()->SetFieldAsInt(std::string("class"),1);
+ }
+ }
+
+
+ //Sample list generator
+ ListSampleGeneratorType::Pointer sampleGenerator = ListSampleGeneratorType::New();
+
+ sampleGenerator->SetInput(image);
+ sampleGenerator->SetInputVectorData(envelope);
+
+ sampleGenerator->SetClassKey("class");
+ sampleGenerator->SetMaxTrainingSize(GetParameterInt("sample.mt"));
+ sampleGenerator->SetMaxValidationSize(GetParameterInt("sample.mv"));
+ sampleGenerator->SetValidationTrainingProportion(GetParameterFloat("sample.vtr"));
+ sampleGenerator->SetBoundByMin(false);
+ sampleGenerator->SetPolygonEdgeInclusion(true);
+
+ sampleGenerator->Update();
+
+ //Concatenate training and validation samples from the image
+ concatenateTrainingSamples->AddInput(sampleGenerator->GetTrainingListSample());
+ concatenateValidationSamples->AddInput(sampleGenerator->GetValidationListSample());
+ }
+
+ // if no input image, try CSV
+ if (imageList->Size() == 0)
+ {
+ if (HasValue("io.csv") && IsParameterEnabled("io.csv"))
+ {
+ ListSampleType::Pointer csvListSample = ListSampleType::New();
+ this->ParseCSVPredictors(this->GetParameterString("io.csv"), csvListSample);
+ unsigned int totalCSVSize = csvListSample->Size();
+ if (totalCSVSize == 0)
+ {
+ otbAppLogFATAL("No input image and empty CSV file. Missing input data");
+ }
+ nbBands = csvListSample->GetMeasurementVectorSize();
+ nbFeatures = static_cast<unsigned int>(static_cast<int>(nbBands) - 1);
+ ListSampleType::Pointer csvTrainListSample = ListSampleType::New();
+ ListSampleType::Pointer csvValidListSample = ListSampleType::New();
+ csvTrainListSample->SetMeasurementVectorSize(nbBands);
+ csvValidListSample->SetMeasurementVectorSize(nbBands);
+ double ratio = this->GetParameterFloat("sample.vtr");
+ int trainSize = static_cast<int>(static_cast<double>(totalCSVSize)*(1.0-ratio));
+ int validSize = static_cast<int>(static_cast<double>(totalCSVSize)*(ratio));
+ if (trainSize > this->GetParameterInt("sample.mt"))
+ {
+ trainSize = this->GetParameterInt("sample.mt");
+ }
+ if (validSize > this->GetParameterInt("sample.mv"))
+ {
+ validSize = this->GetParameterInt("sample.mv");
+ }
+ double probaTrain = static_cast<double>(trainSize)/static_cast<double>(totalCSVSize);
+ double probaValid = static_cast<double>(validSize)/static_cast<double>(totalCSVSize);
+
+ RandomGeneratorType::Pointer randomGenerator = RandomGeneratorType::GetInstance();
+ for (unsigned int i=0; i<totalCSVSize; ++i)
+ {
+ double random = randomGenerator->GetUniformVariate(0.0, 1.0);
+ if (random < probaTrain)
+ {
+ csvTrainListSample->PushBack(csvListSample->GetMeasurementVector(i));
+ }
+ else if (random < probaTrain + probaValid)
+ {
+ csvValidListSample->PushBack(csvListSample->GetMeasurementVector(i));
+ }
+ }
+ concatenateTrainingSamples->AddInput(csvTrainListSample);
+ concatenateValidationSamples->AddInput(csvValidListSample);
+ }
+ }
+
+ // Update
+ concatenateTrainingSamples->Update();
+ concatenateValidationSamples->Update();
+
+ if (concatenateTrainingSamples->GetOutput()->Size() == 0)
+ {
+ otbAppLogFATAL("No training samples, cannot perform training.");
+ }
+
+ if (concatenateValidationSamples->GetOutput()->Size() == 0)
+ {
+ otbAppLogWARNING("No validation samples.");
+ }
+
+ if (IsParameterEnabled("io.imstat"))
+ {
+ StatisticsReader::Pointer statisticsReader = StatisticsReader::New();
+ statisticsReader->SetFileName(GetParameterString("io.imstat"));
+ meanMeasurementVector = statisticsReader->GetStatisticVectorByName("mean");
+ stddevMeasurementVector = statisticsReader->GetStatisticVectorByName("stddev");
+ // handle stat file without output normalization
+ if (meanMeasurementVector.Size() == nbFeatures)
+ {
+ meanMeasurementVector.SetSize(nbBands,false);
+ meanMeasurementVector[nbFeatures] = 0.0;
+ stddevMeasurementVector.SetSize(nbBands,false);
+ stddevMeasurementVector[nbFeatures] = 1.0;
+ }
+ }
+ else
+ {
+ meanMeasurementVector.SetSize(nbBands);
+ meanMeasurementVector.Fill(0.);
+ stddevMeasurementVector.SetSize(nbBands);
+ stddevMeasurementVector.Fill(1.);
+ }
+
+ // Shift scale the samples
+ ShiftScaleFilterType::Pointer trainingShiftScaleFilter = ShiftScaleFilterType::New();
+ trainingShiftScaleFilter->SetInput(concatenateTrainingSamples->GetOutput());
+ trainingShiftScaleFilter->SetShifts(meanMeasurementVector);
+ trainingShiftScaleFilter->SetScales(stddevMeasurementVector);
+ trainingShiftScaleFilter->Update();
+
+ ListSampleType::Pointer rawValidationListSample=ListSampleType::New();
+
+ //Test if the validation test is empty
+ if ( concatenateValidationSamples->GetOutput()->Size() != 0 )
+ {
+ ShiftScaleFilterType::Pointer validationShiftScaleFilter = ShiftScaleFilterType::New();
+ validationShiftScaleFilter->SetInput(concatenateValidationSamples->GetOutput());
+ validationShiftScaleFilter->SetShifts(meanMeasurementVector);
+ validationShiftScaleFilter->SetScales(stddevMeasurementVector);
+ validationShiftScaleFilter->Update();
+ rawValidationListSample = validationShiftScaleFilter->GetOutput();
+ }
+
+ // Split between predictors and output values
+ ListSampleType::Pointer rawlistSample = trainingShiftScaleFilter->GetOutput();
+ ListSampleType::Pointer listSample = ListSampleType::New();
+ listSample->SetMeasurementVectorSize(nbFeatures);
+ listSample->Resize(rawlistSample->Size());
+ TargetListSampleType::Pointer labelListSample = TargetListSampleType::New();
+ labelListSample->SetMeasurementVectorSize(1);
+ labelListSample->Resize(rawlistSample->Size());
+
+ ListSampleType::Pointer validationListSample = ListSampleType::New();
+ validationListSample->SetMeasurementVectorSize(nbFeatures);
+ validationListSample->Resize(rawValidationListSample->Size());
+ TargetListSampleType::Pointer validationLabeledListSample = TargetListSampleType::New();
+ validationLabeledListSample->SetMeasurementVectorSize(1);
+ validationLabeledListSample->Resize(rawValidationListSample->Size());
+
+ ListSampleType::MeasurementVectorType elem;
+ TargetListSampleType::MeasurementVectorType outElem;
+ for (ListSampleType::InstanceIdentifier i=0; i<rawlistSample->Size() ; ++i)
+ {
+ elem = rawlistSample->GetMeasurementVector(i);
+ outElem[0] = elem[nbFeatures];
+ labelListSample->SetMeasurementVector(i,outElem);
+ elem.SetSize(nbFeatures,false);
+ listSample->SetMeasurementVector(i,elem);
+ }
+ for (ListSampleType::InstanceIdentifier i=0; i<rawValidationListSample->Size() ; ++i)
+ {
+ elem = rawValidationListSample->GetMeasurementVector(i);
+ outElem[0] = elem[nbFeatures];
+ validationLabeledListSample->SetMeasurementVector(i,outElem);
+ elem.SetSize(nbFeatures,false);
+ validationListSample->SetMeasurementVector(i,elem);
+ }
+
+
+ otbAppLogINFO("Number of training samples: " << concatenateTrainingSamples->GetOutput()->Size());
+ //--------------------------
+ // Split the data set into training/validation set
+ ListSampleType::Pointer trainingListSample = listSample;
+ TargetListSampleType::Pointer trainingLabeledListSample = labelListSample;
+
+ otbAppLogINFO("Size of training set: " << trainingListSample->Size());
+ otbAppLogINFO("Size of validation set: " << validationListSample->Size());
+
+ //--------------------------
+ // Estimate model
+ //--------------------------
+ this->Train(trainingListSample,trainingLabeledListSample,GetParameterString("io.out"));
+
+ //--------------------------
+ // Performances estimation
+ //--------------------------
+ ListSampleType::Pointer performanceListSample;
+ TargetListSampleType::Pointer predictedList = TargetListSampleType::New();
+ predictedList->SetMeasurementVectorSize(1);
+ TargetListSampleType::Pointer performanceLabeledListSample;
+
+ //Test the input validation set size
+ if(validationLabeledListSample->Size() != 0)
+ {
+ performanceListSample = validationListSample;
+ performanceLabeledListSample = validationLabeledListSample;
+ }
+ else
+ {
+ otbAppLogWARNING("The validation set is empty. The performance estimation is done using the input training set in this case.");
+ performanceListSample = trainingListSample;
+ performanceLabeledListSample = trainingLabeledListSample;
+ }
+
+ this->Classify(performanceListSample, predictedList, GetParameterString("io.out"));
+
+ otbAppLogINFO("Training performances");
+ double mse=0.0;
+ TargetListSampleType::MeasurementVectorType predictedElem;
+ for (TargetListSampleType::InstanceIdentifier i=0; i<performanceListSample->Size() ; ++i)
+ {
+ outElem = performanceLabeledListSample->GetMeasurementVector(i);
+ predictedElem = predictedList->GetMeasurementVector(i);
+ mse += (outElem[0] - predictedElem[0]) * (outElem[0] - predictedElem[0]);
+ }
+ mse /= static_cast<double>(performanceListSample->Size());
+ otbAppLogINFO("Mean Square Error = "<<mse);
+ this->SetParameterFloat("io.mse",mse);
+}
+
+};
+
+} // end namespace Wrapper
+} // end namespace otb
+
+OTB_APPLICATION_EXPORT(otb::Wrapper::TrainRegression)
diff --git a/Modules/Applications/AppClassification/include/otbLearningApplicationBase.h b/Modules/Applications/AppClassification/include/otbLearningApplicationBase.h
new file mode 100644
index 0000000000000000000000000000000000000000..9af1259c73ff6356d515588f52887db569f63c43
--- /dev/null
+++ b/Modules/Applications/AppClassification/include/otbLearningApplicationBase.h
@@ -0,0 +1,222 @@
+/*=========================================================================
+ 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 "otbWrapperApplication.h"
+
+#include <iostream>
+
+// ListSample
+#include "itkListSample.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
+
+namespace otb
+{
+namespace Wrapper
+{
+
+/** \class LearningApplicationBase
+ * \brief LearningApplicationBase is the base class for application that
+ * use machine learning model.
+ *
+ * This base class offers a DoInit() method to initialize all the parameters
+ * related to machine learning models. They will all be in the choice parameter
+ * named "classifier". The class also offers generic Train() and Classify()
+ * methods. The classes derived from LearningApplicationBase only need these
+ * 3 methods to handle the machine learning model.
+ *
+ * There are multiple machine learning models in OTB, some imported from OpenCV,
+ * and one imported from LibSVM. They all have different parameters. The
+ * purpose of this class is to handle the creation of all parameters related to
+ * machine learning models (in DoInit() ), and to dispatch the calls to
+ * specific train functions in function Train().
+ *
+ * This class is templated over scalar types for input and output values.
+ * Typically, the input value type will be either float of double. The choice
+ * of an output value type depends on the learning mode. This base class
+ * supports both classification and regression modes. For classification
+ * (enabled by default), the output value type corresponds to a class
+ * identifier so integer types suit well. For regression, the output value
+ * should not be an integer type, but rather a floating point type. In addition,
+ * an application deriving this base class for regression should initialize
+ * the m_RegressionFlag to true in their constructor.
+ *
+ * \sa TrainImagesClassifier
+ * \sa TrainRegression
+ *
+ * \ingroup OTBAppClassification
+ */
+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 */
+ 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::MachineLearningModelType ModelType;
+
+ typedef typename ModelType::InputSampleType SampleType;
+ typedef typename ModelType::InputListSampleType ListSampleType;
+
+ typedef typename ModelType::TargetSampleType TargetSampleType;
+ typedef typename ModelType::TargetListSampleType TargetListSampleType;
+ typedef typename ModelType::TargetValueType TargetValueType;
+
+#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:
+ LearningApplicationBase();
+
+ /** Generic method to train and save the machine learning model. This method
+ * uses specific train methods depending on the chosen model.*/
+ void Train(typename ListSampleType::Pointer trainingListSample,
+ typename TargetListSampleType::Pointer trainingLabeledListSample,
+ std::string modelPath);
+
+ /** Generic method to load a model file and use it to classify a sample list*/
+ void Classify(typename ListSampleType::Pointer validationListSample,
+ typename TargetListSampleType::Pointer predictedList,
+ std::string modelPath);
+
+ /** Init method that creates all the parameters for machine learning models */
+ void DoInit();
+
+ /** Flag to switch between classification and regression mode.
+ * False by default, child classes may change it in their constructor */
+ bool m_RegressionFlag;
+
+private:
+
+ /** Specific Init and Train methods for each machine learning model */
+ //@{
+#ifdef OTB_USE_LIBSVM
+ void InitLibSVMParams();
+
+ void TrainLibSVM(typename ListSampleType::Pointer trainingListSample,
+ typename TargetListSampleType::Pointer trainingLabeledListSample,
+ std::string modelPath);
+#endif
+
+#ifdef OTB_USE_OPENCV
+ void InitBoostParams();
+ void InitSVMParams();
+ void InitDecisionTreeParams();
+ void InitGradientBoostedTreeParams();
+ void InitNeuralNetworkParams();
+ void InitNormalBayesParams();
+ void InitRandomForestsParams();
+ void InitKNNParams();
+
+ void TrainBoost(typename ListSampleType::Pointer trainingListSample,
+ typename TargetListSampleType::Pointer trainingLabeledListSample,
+ std::string modelPath);
+ void TrainSVM(typename ListSampleType::Pointer trainingListSample,
+ typename TargetListSampleType::Pointer trainingLabeledListSample,
+ std::string modelPath);
+ void TrainDecisionTree(typename ListSampleType::Pointer trainingListSample,
+ typename TargetListSampleType::Pointer trainingLabeledListSample,
+ std::string modelPath);
+ void TrainGradientBoostedTree(typename ListSampleType::Pointer trainingListSample,
+ typename TargetListSampleType::Pointer trainingLabeledListSample,
+ std::string modelPath);
+ void TrainNeuralNetwork(typename ListSampleType::Pointer trainingListSample,
+ typename TargetListSampleType::Pointer trainingLabeledListSample,
+ std::string modelPath);
+ void TrainNormalBayes(typename ListSampleType::Pointer trainingListSample,
+ typename TargetListSampleType::Pointer trainingLabeledListSample,
+ std::string modelPath);
+ void TrainRandomForests(typename ListSampleType::Pointer trainingListSample,
+ typename TargetListSampleType::Pointer trainingLabeledListSample,
+ std::string modelPath);
+ void TrainKNN(typename ListSampleType::Pointer trainingListSample,
+ typename TargetListSampleType::Pointer trainingLabeledListSample,
+ std::string modelPath);
+#endif
+ //@}
+};
+
+}
+}
+
+#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.txx"
+#endif
+#ifdef OTB_USE_LIBSVM
+#include "otbTrainLibSVM.txx"
+#endif
+#endif
+
+#endif
diff --git a/Modules/Applications/AppClassification/include/otbLearningApplicationBase.txx b/Modules/Applications/AppClassification/include/otbLearningApplicationBase.txx
new file mode 100644
index 0000000000000000000000000000000000000000..a545538656efbafd98fa520944b09a183ef87fcb
--- /dev/null
+++ b/Modules/Applications/AppClassification/include/otbLearningApplicationBase.txx
@@ -0,0 +1,177 @@
+/*=========================================================================
+ 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);
+
+ // main choice parameter that will contain all machine learning options
+ 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();
+ if (!m_RegressionFlag)
+ {
+ InitBoostParams(); // Regression not supported
+ }
+ InitDecisionTreeParams();
+ InitGradientBoostedTreeParams();
+ InitNeuralNetworkParams();
+ if (!m_RegressionFlag)
+ {
+ InitNormalBayesParams(); // Regression not supported
+ }
+ InitRandomForestsParams();
+ InitKNNParams();
+#endif
+}
+
+template <class TInputValue, class TOutputValue>
+void
+LearningApplicationBase<TInputValue,TOutputValue>
+::Classify(typename ListSampleType::Pointer validationListSample,
+ typename TargetListSampleType::Pointer predictedList,
+ std::string modelPath)
+{
+ // load a machine learning model from file and predict the input sample list
+ ModelPointerType model = ModelFactoryType::CreateMachineLearningModel(modelPath,
+ ModelFactoryType::ReadMode);
+
+ if (model.IsNull())
+ {
+ otbAppLogFATAL(<< "Error when loading model " << modelPath);
+ }
+
+ model->Load(modelPath);
+ model->SetRegressionMode(this->m_RegressionFlag);
+ model->SetInputListSample(validationListSample);
+ model->SetTargetListSample(predictedList);
+ model->PredictAll();
+}
+
+template <class TInputValue, class TOutputValue>
+void
+LearningApplicationBase<TInputValue,TOutputValue>
+::Train(typename ListSampleType::Pointer trainingListSample,
+ typename TargetListSampleType::Pointer trainingLabeledListSample,
+ std::string modelPath)
+{
+ // get the name of the chosen machine learning model
+ const std::string modelName = GetParameterString("classifier");
+ // call specific train function
+ 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
diff --git a/Modules/Applications/AppClassification/app/otbTrainBoost.cxx b/Modules/Applications/AppClassification/include/otbTrainBoost.txx
similarity index 82%
rename from Modules/Applications/AppClassification/app/otbTrainBoost.cxx
rename to Modules/Applications/AppClassification/include/otbTrainBoost.txx
index c107f8016ea1bdecaf2ca9a68c8af259184715c2..23e666bfc1d877072b41312ce0478a8a41036500 100644
--- a/Modules/Applications/AppClassification/app/otbTrainBoost.cxx
+++ b/Modules/Applications/AppClassification/include/otbTrainBoost.txx
@@ -14,16 +14,19 @@
PURPOSE. See the above copyright notices for more information.
=========================================================================*/
-
-#include "otbTrainImagesClassifier.h"
-
+#ifndef __otbTrainBoost_txx
+#define __otbTrainBoost_txx
+#include "otbLearningApplicationBase.h"
namespace otb
{
namespace Wrapper
{
-#ifdef OTB_USE_OPENCV
- void TrainImagesClassifier::InitBoostParams()
+
+ template <class TInputValue, class TOutputValue>
+ void
+ LearningApplicationBase<TInputValue,TOutputValue>
+ ::InitBoostParams()
{
AddChoice("classifier.boost", "Boost classifier");
SetParameterDescription("classifier.boost", "This group of parameters allows to set Boost classifier parameters. "
@@ -55,10 +58,15 @@ namespace Wrapper
SetParameterDescription("classifier.boost.m","Maximum depth of the tree.");
}
-
- void TrainImagesClassifier::TrainBoost(ListSampleType::Pointer trainingListSample, LabelListSampleType::Pointer trainingLabeledListSample)
+ template <class TInputValue, class TOutputValue>
+ void
+ LearningApplicationBase<TInputValue,TOutputValue>
+ ::TrainBoost(typename ListSampleType::Pointer trainingListSample,
+ typename TargetListSampleType::Pointer trainingLabeledListSample,
+ std::string modelPath)
{
- BoostType::Pointer boostClassifier = BoostType::New();
+ typename BoostType::Pointer boostClassifier = BoostType::New();
+ boostClassifier->SetRegressionMode(this->m_RegressionFlag);
boostClassifier->SetInputListSample(trainingListSample);
boostClassifier->SetTargetListSample(trainingLabeledListSample);
boostClassifier->SetBoostType(GetParameterInt("classifier.boost.t"));
@@ -67,9 +75,10 @@ namespace Wrapper
boostClassifier->SetMaxDepth(GetParameterInt("classifier.boost.m"));
boostClassifier->Train();
- boostClassifier->Save(GetParameterString("io.out"));
+ boostClassifier->Save(modelPath);
}
-#endif
} //end namespace wrapper
} //end namespace otb
+
+#endif
diff --git a/Modules/Applications/AppClassification/app/otbTrainDecisionTree.cxx b/Modules/Applications/AppClassification/include/otbTrainDecisionTree.txx
similarity index 86%
rename from Modules/Applications/AppClassification/app/otbTrainDecisionTree.cxx
rename to Modules/Applications/AppClassification/include/otbTrainDecisionTree.txx
index 9f94a7fc6050bb13a2169242619e8232f32d47c3..04df9380caacca8975caf05f8bb0b6b8237d0ff5 100644
--- a/Modules/Applications/AppClassification/app/otbTrainDecisionTree.cxx
+++ b/Modules/Applications/AppClassification/include/otbTrainDecisionTree.txx
@@ -14,15 +14,19 @@
PURPOSE. See the above copyright notices for more information.
=========================================================================*/
-
-#include "otbTrainImagesClassifier.h"
+#ifndef __otbTrainDecisionTree_txx
+#define __otbTrainDecisionTree_txx
+#include "otbLearningApplicationBase.h"
namespace otb
{
namespace Wrapper
{
-#ifdef OTB_USE_OPENCV
-void TrainImagesClassifier::InitDecisionTreeParams()
+
+template <class TInputValue, class TOutputValue>
+void
+LearningApplicationBase<TInputValue,TOutputValue>
+::InitDecisionTreeParams()
{
AddChoice("classifier.dt", "Decision Tree classifier");
SetParameterDescription("classifier.dt",
@@ -81,10 +85,15 @@ void TrainImagesClassifier::InitDecisionTreeParams()
}
-void TrainImagesClassifier::TrainDecisionTree(ListSampleType::Pointer trainingListSample,
- LabelListSampleType::Pointer trainingLabeledListSample)
+template <class TInputValue, class TOutputValue>
+void
+LearningApplicationBase<TInputValue,TOutputValue>
+::TrainDecisionTree(typename ListSampleType::Pointer trainingListSample,
+ typename TargetListSampleType::Pointer trainingLabeledListSample,
+ std::string modelPath)
{
- DecisionTreeType::Pointer classifier = DecisionTreeType::New();
+ typename DecisionTreeType::Pointer classifier = DecisionTreeType::New();
+ classifier->SetRegressionMode(this->m_RegressionFlag);
classifier->SetInputListSample(trainingListSample);
classifier->SetTargetListSample(trainingLabeledListSample);
classifier->SetMaxDepth(GetParameterInt("classifier.dt.max"));
@@ -101,8 +110,10 @@ void TrainImagesClassifier::TrainDecisionTree(ListSampleType::Pointer trainingLi
classifier->SetTruncatePrunedTree(false);
}
classifier->Train();
- classifier->Save(GetParameterString("io.out"));
+ classifier->Save(modelPath);
}
-#endif
+
} //end namespace wrapper
} //end namespace otb
+
+#endif
diff --git a/Modules/Applications/AppClassification/app/otbTrainGradientBoostedTree.cxx b/Modules/Applications/AppClassification/include/otbTrainGradientBoostedTree.txx
similarity index 63%
rename from Modules/Applications/AppClassification/app/otbTrainGradientBoostedTree.cxx
rename to Modules/Applications/AppClassification/include/otbTrainGradientBoostedTree.txx
index c703ad4c57a0d8efb8103dadc64a92701a16d162..b55612581cd1140185ae53eab3ae407c51536b6b 100644
--- a/Modules/Applications/AppClassification/app/otbTrainGradientBoostedTree.cxx
+++ b/Modules/Applications/AppClassification/include/otbTrainGradientBoostedTree.txx
@@ -14,23 +14,34 @@
PURPOSE. See the above copyright notices for more information.
=========================================================================*/
-
-#include "otbTrainImagesClassifier.h"
+#ifndef __otbTrainGradientBoostedTree_txx
+#define __otbTrainGradientBoostedTree_txx
+#include "otbLearningApplicationBase.h"
namespace otb
{
namespace Wrapper
{
-#ifdef OTB_USE_OPENCV
-void TrainImagesClassifier::InitGradientBoostedTreeParams()
+
+template <class TInputValue, class TOutputValue>
+void
+LearningApplicationBase<TInputValue,TOutputValue>
+::InitGradientBoostedTreeParams()
{
AddChoice("classifier.gbt", "Gradient Boosted Tree classifier");
SetParameterDescription(
"classifier.gbt",
"This group of parameters allows to set Gradient Boosted Tree classifier parameters. "
"See complete documentation here \\url{http://docs.opencv.org/modules/ml/doc/gradient_boosted_trees.html}.");
- //LossFunctionType : not exposed, as only one type is used for Classification,
- // the other three are used for regression.
+
+ if (m_RegressionFlag)
+ {
+ AddParameter(ParameterType_Choice, "classifier.gbt.t", "Loss Function Type");
+ SetParameterDescription("classifier.gbt.t","Type of loss functionused for training.");
+ AddChoice("classifier.gbt.t.sqr","Squared Loss");
+ AddChoice("classifier.gbt.t.abs","Absolute Loss");
+ AddChoice("classifier.gbt.t.hub","Huber Loss");
+ }
//WeakCount
AddParameter(ParameterType_Int, "classifier.gbt.w", "Number of boosting algorithm iterations");
@@ -67,10 +78,15 @@ void TrainImagesClassifier::InitGradientBoostedTreeParams()
}
-void TrainImagesClassifier::TrainGradientBoostedTree(
- ListSampleType::Pointer trainingListSample, LabelListSampleType::Pointer trainingLabeledListSample)
+template <class TInputValue, class TOutputValue>
+void
+LearningApplicationBase<TInputValue,TOutputValue>
+::TrainGradientBoostedTree(typename ListSampleType::Pointer trainingListSample,
+ typename TargetListSampleType::Pointer trainingLabeledListSample,
+ std::string modelPath)
{
- GradientBoostedTreeType::Pointer classifier = GradientBoostedTreeType::New();
+ typename GradientBoostedTreeType::Pointer classifier = GradientBoostedTreeType::New();
+ classifier->SetRegressionMode(this->m_RegressionFlag);
classifier->SetInputListSample(trainingListSample);
classifier->SetTargetListSample(trainingLabeledListSample);
classifier->SetWeakCount(GetParameterInt("classifier.gbt.w"));
@@ -78,9 +94,34 @@ void TrainImagesClassifier::TrainGradientBoostedTree(
classifier->SetSubSamplePortion(GetParameterFloat("classifier.gbt.p"));
classifier->SetMaxDepth(GetParameterInt("classifier.gbt.max"));
+ if (m_RegressionFlag)
+ {
+ switch (GetParameterInt("classifier.gbt.t"))
+ {
+ case 0: // SQUARED_LOSS
+ classifier->SetLossFunctionType(CvGBTrees::SQUARED_LOSS);
+ break;
+ case 1: // ABSOLUTE_LOSS
+ classifier->SetLossFunctionType(CvGBTrees::ABSOLUTE_LOSS);
+ break;
+ case 2: // HUBER_LOSS
+ classifier->SetLossFunctionType(CvGBTrees::HUBER_LOSS);
+ break;
+ default:
+ classifier->SetLossFunctionType(CvGBTrees::SQUARED_LOSS);
+ break;
+ }
+ }
+ else
+ {
+ classifier->SetLossFunctionType(CvGBTrees::DEVIANCE_LOSS);
+ }
+
classifier->Train();
- classifier->Save(GetParameterString("io.out"));
+ classifier->Save(modelPath);
}
-#endif
+
} //end namespace wrapper
} //end namespace otb
+
+#endif
diff --git a/Modules/Applications/AppClassification/include/otbTrainKNN.txx b/Modules/Applications/AppClassification/include/otbTrainKNN.txx
new file mode 100644
index 0000000000000000000000000000000000000000..93656003a1b24e601a630393983934bb65b5e797
--- /dev/null
+++ b/Modules/Applications/AppClassification/include/otbTrainKNN.txx
@@ -0,0 +1,86 @@
+/*=========================================================================
+ 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 __otbTrainKNN_txx
+#define __otbTrainKNN_txx
+#include "otbLearningApplicationBase.h"
+
+namespace otb
+{
+namespace Wrapper
+{
+
+ template <class TInputValue, class TOutputValue>
+ void
+ LearningApplicationBase<TInputValue,TOutputValue>
+ ::InitKNNParams()
+ {
+ AddChoice("classifier.knn", "KNN classifier");
+ SetParameterDescription("classifier.knn", "This group of parameters allows to set KNN classifier parameters. "
+ "See complete documentation here \\url{http://docs.opencv.org/modules/ml/doc/k_nearest_neighbors.html}.");
+
+ //K parameter
+ AddParameter(ParameterType_Int, "classifier.knn.k", "Number of Neighbors");
+ SetParameterInt("classifier.knn.k", 32);
+ SetParameterDescription("classifier.knn.k","The number of neighbors to use.");
+
+ if (this->m_RegressionFlag)
+ {
+ // Decision rule : mean / median
+ AddParameter(ParameterType_Choice, "classifier.knn.rule", "Decision rule");
+ SetParameterDescription("classifier.knn.rule", "Decision rule for regression output");
+
+ AddChoice("classifier.knn.rule.mean", "Mean of neighbors values");
+ SetParameterDescription("classifier.knn.rule.mean","Returns the mean of neighbors values");
+
+ AddChoice("classifier.knn.rule.median", "Median of neighbors values");
+ SetParameterDescription("classifier.knn.rule.median","Returns the median of neighbors values");
+ }
+ }
+
+ template <class TInputValue, class TOutputValue>
+ void
+ LearningApplicationBase<TInputValue,TOutputValue>
+ ::TrainKNN(typename ListSampleType::Pointer trainingListSample,
+ typename TargetListSampleType::Pointer trainingLabeledListSample,
+ std::string modelPath)
+ {
+ typename KNNType::Pointer knnClassifier = KNNType::New();
+ knnClassifier->SetRegressionMode(this->m_RegressionFlag);
+ knnClassifier->SetInputListSample(trainingListSample);
+ knnClassifier->SetTargetListSample(trainingLabeledListSample);
+ knnClassifier->SetK(GetParameterInt("classifier.knn.k"));
+ if (this->m_RegressionFlag)
+ {
+ std::string decision = this->GetParameterString("classifier.knn.rule");
+ if (decision == "mean")
+ {
+ knnClassifier->SetDecisionRule(KNNType::KNN_MEAN);
+ }
+ else if (decision == "median")
+ {
+ knnClassifier->SetDecisionRule(KNNType::KNN_MEDIAN);
+ }
+ }
+
+ knnClassifier->Train();
+ knnClassifier->Save(modelPath);
+ }
+
+} //end namespace wrapper
+} //end namespace otb
+
+#endif
diff --git a/Modules/Applications/AppClassification/app/otbTrainLibSVM.cxx b/Modules/Applications/AppClassification/include/otbTrainLibSVM.txx
similarity index 52%
rename from Modules/Applications/AppClassification/app/otbTrainLibSVM.cxx
rename to Modules/Applications/AppClassification/include/otbTrainLibSVM.txx
index e117337708d3effd267a462a1d24f8b2f6736e18..928245655fd30d983c970947feef81dbd0c8304f 100644
--- a/Modules/Applications/AppClassification/app/otbTrainLibSVM.cxx
+++ b/Modules/Applications/AppClassification/include/otbTrainLibSVM.txx
@@ -14,16 +14,19 @@
PURPOSE. See the above copyright notices for more information.
=========================================================================*/
-
-#include "otbTrainImagesClassifier.h"
-
+#ifndef __otbTrainLibSVM_txx
+#define __otbTrainLibSVM_txx
+#include "otbLearningApplicationBase.h"
namespace otb
{
namespace Wrapper
{
-#ifdef OTB_USE_LIBSVM
- void TrainImagesClassifier::InitLibSVMParams()
+
+ template <class TInputValue, class TOutputValue>
+ void
+ LearningApplicationBase<TInputValue,TOutputValue>
+ ::InitLibSVMParams()
{
AddChoice("classifier.libsvm", "LibSVM classifier");
SetParameterDescription("classifier.libsvm", "This group of parameters allows to set SVM classifier parameters.");
@@ -34,6 +37,21 @@ namespace Wrapper
AddChoice("classifier.libsvm.k.sigmoid", "Sigmoid");
SetParameterString("classifier.libsvm.k", "linear");
SetParameterDescription("classifier.libsvm.k", "SVM Kernel Type.");
+ AddParameter(ParameterType_Choice, "classifier.libsvm.m", "SVM Model Type");
+ SetParameterDescription("classifier.libsvm.m", "Type of SVM formulation.");
+ if (this->m_RegressionFlag)
+ {
+ AddChoice("classifier.libsvm.m.epssvr", "Epsilon Support Vector Regression");
+ AddChoice("classifier.libsvm.m.nusvr", "Nu Support Vector Regression");
+ SetParameterString("classifier.libsvm.m", "epssvr");
+ }
+ else
+ {
+ AddChoice("classifier.libsvm.m.csvc", "C support vector classification");
+ AddChoice("classifier.libsvm.m.nusvc", "Nu support vector classification");
+ AddChoice("classifier.libsvm.m.oneclass", "Distribution estimation (One Class SVM)");
+ SetParameterString("classifier.libsvm.m", "csvc");
+ }
AddParameter(ParameterType_Float, "classifier.libsvm.c", "Cost parameter C");
SetParameterFloat("classifier.libsvm.c", 1.0);
SetParameterDescription(
@@ -45,12 +63,25 @@ namespace Wrapper
AddParameter(ParameterType_Empty, "classifier.libsvm.prob", "Probability estimation");
MandatoryOff("classifier.libsvm.prob");
SetParameterDescription("classifier.libsvm.prob", "Probability estimation flag.");
- }
+ if (this->m_RegressionFlag)
+ {
+ AddParameter(ParameterType_Float, "classifier.libsvm.eps", "Epsilon");
+ SetParameterFloat("classifier.libsvm.eps", 1e-3);
+ AddParameter(ParameterType_Float, "classifier.libsvm.nu", "Nu");
+ SetParameterFloat("classifier.libsvm.nu", 0.5);
+ }
+ }
- void TrainImagesClassifier::TrainLibSVM(ListSampleType::Pointer trainingListSample, LabelListSampleType::Pointer trainingLabeledListSample)
+ template <class TInputValue, class TOutputValue>
+ void
+ LearningApplicationBase<TInputValue,TOutputValue>
+ ::TrainLibSVM(typename ListSampleType::Pointer trainingListSample,
+ typename TargetListSampleType::Pointer trainingLabeledListSample,
+ std::string modelPath)
{
- LibSVMType::Pointer libSVMClassifier = LibSVMType::New();
+ typename LibSVMType::Pointer libSVMClassifier = LibSVMType::New();
+ libSVMClassifier->SetRegressionMode(this->m_RegressionFlag);
libSVMClassifier->SetInputListSample(trainingListSample);
libSVMClassifier->SetTargetListSample(trainingLabeledListSample);
//SVM Option
@@ -83,9 +114,47 @@ namespace Wrapper
libSVMClassifier->SetKernelType(LINEAR);
break;
}
+ if (this->m_RegressionFlag)
+ {
+ switch (GetParameterInt("classifier.libsvm.m"))
+ {
+ case 0: // EPSILON_SVR
+ libSVMClassifier->SetSVMType(EPSILON_SVR);
+ break;
+ case 1: // NU_SVR
+ libSVMClassifier->SetSVMType(NU_SVR);
+ break;
+ default:
+ libSVMClassifier->SetSVMType(EPSILON_SVR);
+ break;
+ }
+ libSVMClassifier->SetEpsilon(GetParameterFloat("classifier.libsvm.eps"));
+ libSVMClassifier->SetNu(GetParameterFloat("classifier.libsvm.nu"));
+ }
+ else
+ {
+ switch (GetParameterInt("classifier.libsvm.m"))
+ {
+ case 0: // C_SVC
+ libSVMClassifier->SetSVMType(C_SVC);
+ break;
+ case 1: // NU_SVC
+ libSVMClassifier->SetSVMType(NU_SVC);
+ break;
+ case 2: // ONE_CLASS
+ libSVMClassifier->SetSVMType(ONE_CLASS);
+ break;
+ default:
+ libSVMClassifier->SetSVMType(C_SVC);
+ break;
+ }
+ }
+
libSVMClassifier->Train();
- libSVMClassifier->Save(GetParameterString("io.out"));
+ libSVMClassifier->Save(modelPath);
}
-#endif
+
} //end namespace wrapper
} //end namespace otb
+
+#endif
diff --git a/Modules/Applications/AppClassification/app/otbTrainNeuralNetwork.cxx b/Modules/Applications/AppClassification/include/otbTrainNeuralNetwork.txx
similarity index 87%
rename from Modules/Applications/AppClassification/app/otbTrainNeuralNetwork.cxx
rename to Modules/Applications/AppClassification/include/otbTrainNeuralNetwork.txx
index 29b3657ad2ef612a89a83f923cf370c3a9bbbc5c..40f120f69bcaa1df15454070d63e38feda46e960 100644
--- a/Modules/Applications/AppClassification/app/otbTrainNeuralNetwork.cxx
+++ b/Modules/Applications/AppClassification/include/otbTrainNeuralNetwork.txx
@@ -14,16 +14,20 @@
PURPOSE. See the above copyright notices for more information.
=========================================================================*/
-
+#ifndef __otbTrainNeuralNetwork_txx
+#define __otbTrainNeuralNetwork_txx
#include <boost/lexical_cast.hpp>
-#include "otbTrainImagesClassifier.h"
+#include "otbLearningApplicationBase.h"
namespace otb
{
namespace Wrapper
{
-#ifdef OTB_USE_OPENCV
-void TrainImagesClassifier::InitNeuralNetworkParams()
+
+template <class TInputValue, class TOutputValue>
+void
+LearningApplicationBase<TInputValue,TOutputValue>
+::InitNeuralNetworkParams()
{
AddChoice("classifier.ann", "Artificial Neural Network classifier");
SetParameterDescription("classifier.ann",
@@ -119,10 +123,15 @@ void TrainImagesClassifier::InitNeuralNetworkParams()
}
-void TrainImagesClassifier::TrainNeuralNetwork(ListSampleType::Pointer trainingListSample,
- LabelListSampleType::Pointer trainingLabeledListSample)
+template <class TInputValue, class TOutputValue>
+void
+LearningApplicationBase<TInputValue,TOutputValue>
+::TrainNeuralNetwork(typename ListSampleType::Pointer trainingListSample,
+ typename TargetListSampleType::Pointer trainingLabeledListSample,
+ std::string modelPath)
{
- NeuralNetworkType::Pointer classifier = NeuralNetworkType::New();
+ typename NeuralNetworkType::Pointer classifier = NeuralNetworkType::New();
+ classifier->SetRegressionMode(this->m_RegressionFlag);
classifier->SetInputListSample(trainingListSample);
classifier->SetTargetListSample(trainingLabeledListSample);
@@ -153,18 +162,23 @@ void TrainImagesClassifier::TrainNeuralNetwork(ListSampleType::Pointer trainingL
unsigned int nbClasses = 0;
- LabelType currentLabel = 0, prevLabel = 0;
- for (unsigned int itLab = 0; itLab < trainingLabeledListSample->Size(); ++itLab)
+ if (this->m_RegressionFlag)
+ {
+ layerSizes.push_back(1);
+ }
+ else
{
- currentLabel = trainingLabeledListSample->GetMeasurementVector(itLab);
- if ((currentLabel != prevLabel) || (itLab == 0))
+ std::set<TargetValueType> labelSet;
+ TargetSampleType currentLabel;
+ for (unsigned int itLab = 0; itLab < trainingLabeledListSample->Size(); ++itLab)
{
- ++nbClasses;
+ currentLabel = trainingLabeledListSample->GetMeasurementVector(itLab);
+ labelSet.insert(currentLabel[0]);
}
- prevLabel = currentLabel;
+ nbClasses = labelSet.size();
+ layerSizes.push_back(nbClasses);
}
- layerSizes.push_back(nbClasses);
classifier->SetLayerSizes(layerSizes);
switch (GetParameterInt("classifier.ann.f"))
@@ -208,8 +222,10 @@ void TrainImagesClassifier::TrainNeuralNetwork(ListSampleType::Pointer trainingL
classifier->SetEpsilon(GetParameterFloat("classifier.ann.eps"));
classifier->SetMaxIter(GetParameterInt("classifier.ann.iter"));
classifier->Train();
- classifier->Save(GetParameterString("io.out"));
+ classifier->Save(modelPath);
}
-#endif
+
} //end namespace wrapper
} //end namespace otb
+
+#endif
diff --git a/Modules/Applications/AppClassification/app/otbTrainNormalBayes.cxx b/Modules/Applications/AppClassification/include/otbTrainNormalBayes.txx
similarity index 59%
rename from Modules/Applications/AppClassification/app/otbTrainNormalBayes.cxx
rename to Modules/Applications/AppClassification/include/otbTrainNormalBayes.txx
index d33e6eaf9cd79a99120a5176b096a94fb98b190c..d5f3cce8e3ef2ae3fbe02a2b21e99d0004df3944 100644
--- a/Modules/Applications/AppClassification/app/otbTrainNormalBayes.cxx
+++ b/Modules/Applications/AppClassification/include/otbTrainNormalBayes.txx
@@ -14,16 +14,19 @@
PURPOSE. See the above copyright notices for more information.
=========================================================================*/
-
-#include "otbTrainImagesClassifier.h"
-
+#ifndef __otbTrainNormalBayes_txx
+#define __otbTrainNormalBayes_txx
+#include "otbLearningApplicationBase.h"
namespace otb
{
namespace Wrapper
{
-#ifdef OTB_USE_OPENCV
- void TrainImagesClassifier::InitNormalBayesParams()
+
+ template <class TInputValue, class TOutputValue>
+ void
+ LearningApplicationBase<TInputValue,TOutputValue>
+ ::InitNormalBayesParams()
{
AddChoice("classifier.bayes", "Normal Bayes classifier");
SetParameterDescription("classifier.bayes", "Use a Normal Bayes Classifier. "
@@ -31,15 +34,22 @@ namespace Wrapper
}
-
- void TrainImagesClassifier::TrainNormalBayes(ListSampleType::Pointer trainingListSample, LabelListSampleType::Pointer trainingLabeledListSample)
+ template <class TInputValue, class TOutputValue>
+ void
+ LearningApplicationBase<TInputValue,TOutputValue>
+ ::TrainNormalBayes(typename ListSampleType::Pointer trainingListSample,
+ typename TargetListSampleType::Pointer trainingLabeledListSample,
+ std::string modelPath)
{
- NormalBayesType::Pointer classifier = NormalBayesType::New();
+ typename NormalBayesType::Pointer classifier = NormalBayesType::New();
+ classifier->SetRegressionMode(this->m_RegressionFlag);
classifier->SetInputListSample(trainingListSample);
classifier->SetTargetListSample(trainingLabeledListSample);
classifier->Train();
- classifier->Save(GetParameterString("io.out"));
+ classifier->Save(modelPath);
}
-#endif
+
} //end namespace wrapper
} //end namespace otb
+
+#endif
diff --git a/Modules/Applications/AppClassification/app/otbTrainRandomForests.cxx b/Modules/Applications/AppClassification/include/otbTrainRandomForests.txx
similarity index 87%
rename from Modules/Applications/AppClassification/app/otbTrainRandomForests.cxx
rename to Modules/Applications/AppClassification/include/otbTrainRandomForests.txx
index 1798b9d9b59b7ffa2323936084736b6b423a3cb5..a856243a300dfc35d559e683aef21268d8c25a12 100644
--- a/Modules/Applications/AppClassification/app/otbTrainRandomForests.cxx
+++ b/Modules/Applications/AppClassification/include/otbTrainRandomForests.txx
@@ -14,15 +14,19 @@
PURPOSE. See the above copyright notices for more information.
=========================================================================*/
-
-#include "otbTrainImagesClassifier.h"
+#ifndef __otbTrainRandomForests_txx
+#define __otbTrainRandomForests_txx
+#include "otbLearningApplicationBase.h"
namespace otb
{
namespace Wrapper
{
-#ifdef OTB_USE_OPENCV
-void TrainImagesClassifier::InitRandomForestsParams()
+
+template <class TInputValue, class TOutputValue>
+void
+LearningApplicationBase<TInputValue,TOutputValue>
+::InitRandomForestsParams()
{
AddChoice("classifier.rf", "Random forests classifier");
SetParameterDescription("classifier.rf",
@@ -95,10 +99,15 @@ void TrainImagesClassifier::InitRandomForestsParams()
//TerminationCriteria not exposed
}
-void TrainImagesClassifier::TrainRandomForests(ListSampleType::Pointer trainingListSample,
- LabelListSampleType::Pointer trainingLabeledListSample)
+template <class TInputValue, class TOutputValue>
+void
+LearningApplicationBase<TInputValue,TOutputValue>
+::TrainRandomForests(typename ListSampleType::Pointer trainingListSample,
+ typename TargetListSampleType::Pointer trainingLabeledListSample,
+ std::string modelPath)
{
- RandomForestType::Pointer classifier = RandomForestType::New();
+ typename RandomForestType::Pointer classifier = RandomForestType::New();
+ classifier->SetRegressionMode(this->m_RegressionFlag);
classifier->SetInputListSample(trainingListSample);
classifier->SetTargetListSample(trainingLabeledListSample);
classifier->SetMaxDepth(GetParameterInt("classifier.rf.max"));
@@ -110,8 +119,10 @@ void TrainImagesClassifier::TrainRandomForests(ListSampleType::Pointer trainingL
classifier->SetForestAccuracy(GetParameterFloat("classifier.rf.acc"));
classifier->Train();
- classifier->Save(GetParameterString("io.out"));
+ classifier->Save(modelPath);
}
-#endif
+
} //end namespace wrapper
} //end namespace otb
+
+#endif
diff --git a/Modules/Applications/AppClassification/app/otbTrainSVM.cxx b/Modules/Applications/AppClassification/include/otbTrainSVM.txx
similarity index 57%
rename from Modules/Applications/AppClassification/app/otbTrainSVM.cxx
rename to Modules/Applications/AppClassification/include/otbTrainSVM.txx
index a41e103746f5f5d7968f26220791436232caac74..ac0f153ed4f78df8c5a7d838c3e32beed62ddd9f 100644
--- a/Modules/Applications/AppClassification/app/otbTrainSVM.cxx
+++ b/Modules/Applications/AppClassification/include/otbTrainSVM.txx
@@ -14,28 +14,38 @@
PURPOSE. See the above copyright notices for more information.
=========================================================================*/
-
-#include "otbTrainImagesClassifier.h"
-
+#ifndef __otbTrainSVM_txx
+#define __otbTrainSVM_txx
+#include "otbLearningApplicationBase.h"
namespace otb
{
namespace Wrapper
{
-#ifdef OTB_USE_OPENCV
- void TrainImagesClassifier::InitSVMParams()
+
+ template <class TInputValue, class TOutputValue>
+ void
+ LearningApplicationBase<TInputValue,TOutputValue>
+ ::InitSVMParams()
{
AddChoice("classifier.svm", "SVM classifier (OpenCV)");
SetParameterDescription("classifier.svm", "This group of parameters allows to set SVM classifier parameters. "
"See complete documentation here \\url{http://docs.opencv.org/modules/ml/doc/support_vector_machines.html}.");
AddParameter(ParameterType_Choice, "classifier.svm.m", "SVM Model Type");
- AddChoice("classifier.svm.m.csvc", "C support vector classification");
- AddChoice("classifier.svm.m.nusvc", "Nu support vector classification");
- AddChoice("classifier.svm.m.oneclass", "Distribution estimation (One Class SVM)");
- //AddChoice("classifier.svm.m.epssvr", "Epsilon Support Vector Regression");
- //AddChoice("classifier.svm.m.nusvr", "Nu Support Vector Regression");
- SetParameterString("classifier.svm.m", "csvc");
SetParameterDescription("classifier.svm.m", "Type of SVM formulation.");
+ if (this->m_RegressionFlag)
+ {
+ AddChoice("classifier.svm.m.epssvr", "Epsilon Support Vector Regression");
+ AddChoice("classifier.svm.m.nusvr", "Nu Support Vector Regression");
+ SetParameterString("classifier.svm.m", "epssvr");
+ }
+ else
+ {
+ AddChoice("classifier.svm.m.csvc", "C support vector classification");
+ AddChoice("classifier.svm.m.nusvc", "Nu support vector classification");
+ AddChoice("classifier.svm.m.oneclass", "Distribution estimation (One Class SVM)");
+ SetParameterString("classifier.svm.m", "csvc");
+ }
AddParameter(ParameterType_Choice, "classifier.svm.k", "SVM Kernel Type");
AddChoice("classifier.svm.k.linear", "Linear");
AddChoice("classifier.svm.k.rbf", "Gaussian radial basis function");
@@ -52,9 +62,26 @@ namespace Wrapper
"Parameter nu of a SVM optimization problem (NU_SVC / ONE_CLASS)");
SetParameterFloat("classifier.svm.nu", 0.0);
SetParameterDescription("classifier.svm.nu", "Parameter nu of a SVM optimization problem.");
- //AddParameter(ParameterType_Float, "classifier.svm.p", "Parameter epsilon of a SVM optimization problem (EPS_SVR)");
- //SetParameterFloat("classifier.svm.p", 0.0);
- //SetParameterDescription("classifier.svm.p", "Parameter epsilon of a SVM optimization problem (EPS_SVR).");
+ if (this->m_RegressionFlag)
+ {
+ AddParameter(ParameterType_Float, "classifier.svm.p", "Parameter epsilon of a SVM optimization problem (EPS_SVR)");
+ SetParameterFloat("classifier.svm.p", 1.0);
+ SetParameterDescription("classifier.svm.p", "Parameter epsilon of a SVM optimization problem (EPS_SVR).");
+
+ AddParameter(ParameterType_Choice, "classifier.svm.term", "Termination criteria");
+ SetParameterDescription("classifier.svm.term","Termination criteria for iterative algorithm");
+ AddChoice("classifier.svm.term.iter", "Stops when maximum iteration is reached.");
+ AddChoice("classifier.svm.term.eps", "Stops when accuracy is lower than epsilon.");
+ AddChoice("classifier.svm.term.all", "Stops when either iteration or epsilon criteria is true");
+
+ AddParameter(ParameterType_Float, "classifier.svm.iter", "Maximum iteration");
+ SetParameterFloat("classifier.svm.iter", 1000);
+ SetParameterDescription("classifier.svm.iter", "Maximum number of iterations (corresponds to the termination criteria 'iter').");
+
+ AddParameter(ParameterType_Float, "classifier.svm.eps", "Epsilon accuracy threshold");
+ SetParameterFloat("classifier.svm.eps", FLT_EPSILON);
+ SetParameterDescription("classifier.svm.eps", "Epsilon accuracy (corresponds to the termination criteria 'eps').");
+ }
AddParameter(ParameterType_Float, "classifier.svm.coef0", "Parameter coef0 of a kernel function (POLY / SIGMOID)");
SetParameterFloat("classifier.svm.coef0", 0.0);
SetParameterDescription("classifier.svm.coef0", "Parameter coef0 of a kernel function (POLY / SIGMOID).");
@@ -76,9 +103,15 @@ namespace Wrapper
"because the samples are not identically processed within OpenCV.");
}
- void TrainImagesClassifier::TrainSVM(ListSampleType::Pointer trainingListSample, LabelListSampleType::Pointer trainingLabeledListSample)
+ template <class TInputValue, class TOutputValue>
+ void
+ LearningApplicationBase<TInputValue,TOutputValue>
+ ::TrainSVM(typename ListSampleType::Pointer trainingListSample,
+ typename TargetListSampleType::Pointer trainingLabeledListSample,
+ std::string modelPath)
{
- SVMType::Pointer SVMClassifier = SVMType::New();
+ typename SVMType::Pointer SVMClassifier = SVMType::New();
+ SVMClassifier->SetRegressionMode(this->m_RegressionFlag);
SVMClassifier->SetInputListSample(trainingListSample);
SVMClassifier->SetTargetListSample(trainingLabeledListSample);
switch (GetParameterInt("classifier.svm.k"))
@@ -104,36 +137,69 @@ namespace Wrapper
std::cout << "CvSVM::LINEAR = " << CvSVM::LINEAR << std::endl;
break;
}
- switch (GetParameterInt("classifier.svm.m"))
+ if (this->m_RegressionFlag)
{
- case 0: // C_SVC
- SVMClassifier->SetSVMType(CvSVM::C_SVC);
- std::cout << "CvSVM::C_SVC = " << CvSVM::C_SVC << std::endl;
- break;
- case 1: // NU_SVC
- SVMClassifier->SetSVMType(CvSVM::NU_SVC);
- std::cout << "CvSVM::NU_SVC = " << CvSVM::NU_SVC << std::endl;
- break;
- case 2: // ONE_CLASS
- SVMClassifier->SetSVMType(CvSVM::ONE_CLASS);
- std::cout << "CvSVM::ONE_CLASS = " << CvSVM::ONE_CLASS << std::endl;
- break;
- /*case 3: // EPS_SVR
- SVMClassifier->SetSVMType(CvSVM::EPS_SVR);
- std::cout<<"CvSVM::EPS_SVR = "<<CvSVM::EPS_SVR<<std::endl;
- break;
- case 4: // NU_SVR
- SVMClassifier->SetSVMType(CvSVM::NU_SVR);
- std::cout<<"CvSVM::NU_SVR = "<<CvSVM::NU_SVR<<std::endl;
- break; */
- default: // DEFAULT = C_SVC
- SVMClassifier->SetSVMType(CvSVM::C_SVC);
- std::cout << "CvSVM::C_SVC = " << CvSVM::C_SVC << std::endl;
- break;
+ switch (GetParameterInt("classifier.svm.m"))
+ {
+ case 0: // EPS_SVR
+ SVMClassifier->SetSVMType(CvSVM::EPS_SVR);
+ std::cout<<"CvSVM::EPS_SVR = "<<CvSVM::EPS_SVR<<std::endl;
+ break;
+ case 1: // NU_SVR
+ SVMClassifier->SetSVMType(CvSVM::NU_SVR);
+ std::cout<<"CvSVM::NU_SVR = "<<CvSVM::NU_SVR<<std::endl;
+ break;
+ default: // DEFAULT = EPS_SVR
+ SVMClassifier->SetSVMType(CvSVM::EPS_SVR);
+ std::cout << "CvSVM::EPS_SVR = " << CvSVM::EPS_SVR << std::endl;
+ break;
+ }
+ }
+ else
+ {
+ switch (GetParameterInt("classifier.svm.m"))
+ {
+ case 0: // C_SVC
+ SVMClassifier->SetSVMType(CvSVM::C_SVC);
+ std::cout << "CvSVM::C_SVC = " << CvSVM::C_SVC << std::endl;
+ break;
+ case 1: // NU_SVC
+ SVMClassifier->SetSVMType(CvSVM::NU_SVC);
+ std::cout << "CvSVM::NU_SVC = " << CvSVM::NU_SVC << std::endl;
+ break;
+ case 2: // ONE_CLASS
+ SVMClassifier->SetSVMType(CvSVM::ONE_CLASS);
+ std::cout << "CvSVM::ONE_CLASS = " << CvSVM::ONE_CLASS << std::endl;
+ break;
+ default: // DEFAULT = C_SVC
+ SVMClassifier->SetSVMType(CvSVM::C_SVC);
+ std::cout << "CvSVM::C_SVC = " << CvSVM::C_SVC << std::endl;
+ break;
+ }
}
SVMClassifier->SetC(GetParameterFloat("classifier.svm.c"));
SVMClassifier->SetNu(GetParameterFloat("classifier.svm.nu"));
- //SVMClassifier->SetP(GetParameterFloat("classifier.svm.p"));
+ if (this->m_RegressionFlag)
+ {
+ SVMClassifier->SetP(GetParameterFloat("classifier.svm.p"));
+ switch (GetParameterInt("classifier.svm.term"))
+ {
+ case 0: // ITER
+ SVMClassifier->SetTermCriteriaType(CV_TERMCRIT_ITER);
+ break;
+ case 1: // EPS
+ SVMClassifier->SetTermCriteriaType(CV_TERMCRIT_EPS);
+ break;
+ case 2: // ITER+EPS
+ SVMClassifier->SetTermCriteriaType(CV_TERMCRIT_ITER+CV_TERMCRIT_EPS);
+ break;
+ default:
+ SVMClassifier->SetTermCriteriaType(CV_TERMCRIT_ITER);
+ break;
+ }
+ SVMClassifier->SetMaxIter(GetParameterInt("classifier.svm.iter"));
+ SVMClassifier->SetEpsilon(GetParameterFloat("classifier.svm.eps"));
+ }
SVMClassifier->SetCoef0(GetParameterFloat("classifier.svm.coef0"));
SVMClassifier->SetGamma(GetParameterFloat("classifier.svm.gamma"));
SVMClassifier->SetDegree(GetParameterFloat("classifier.svm.degree"));
@@ -142,17 +208,21 @@ namespace Wrapper
SVMClassifier->SetParameterOptimization(true);
}
SVMClassifier->Train();
- SVMClassifier->Save(GetParameterString("io.out"));
+ SVMClassifier->Save(modelPath);
// Update the displayed parameters in the GUI after the training process, for further use of them
SetParameterFloat("classifier.svm.c", static_cast<float> (SVMClassifier->GetOutputC()));
SetParameterFloat("classifier.svm.nu", static_cast<float> (SVMClassifier->GetOutputNu()));
- //SetParameterFloat("classifier.svm.p", static_cast<float> (SVMClassifier->GetOutputP()));
+ if (this->m_RegressionFlag)
+ {
+ SetParameterFloat("classifier.svm.p", static_cast<float> (SVMClassifier->GetOutputP()));
+ }
SetParameterFloat("classifier.svm.coef0", static_cast<float> (SVMClassifier->GetOutputCoef0()));
SetParameterFloat("classifier.svm.gamma", static_cast<float> (SVMClassifier->GetOutputGamma()));
SetParameterFloat("classifier.svm.degree", static_cast<float> (SVMClassifier->GetOutputDegree()));
}
-#endif
} //end namespace wrapper
} //end namespace otb
+
+#endif
diff --git a/Modules/Applications/AppClassification/test/CMakeLists.txt b/Modules/Applications/AppClassification/test/CMakeLists.txt
index c4e275fe5a33fc8e629a13c9016a5584c8a4b0a3..63a5c0918f5df9138ab25e78968b8305743f2409 100644
--- a/Modules/Applications/AppClassification/test/CMakeLists.txt
+++ b/Modules/Applications/AppClassification/test/CMakeLists.txt
@@ -841,3 +841,36 @@ otb_test_application(NAME cdbTvVectorDataDSValidationWrongRoads_LI
${OTBAPP_BASELINE_FILES}/cdbTvVectorDataDSValidationOutpout_LI_wr.shp
${TEMP}/cdbTvVectorDataDSValidationOutpout_LI_wr.shp)
+if(OTB_USE_OPENCV)
+#----------- TrainRegression TESTS ----------------
+# y = 0.01*x^2 + 1.5*x - 300
+otb_test_application(NAME apTvClTrainRegressionTest_monovar
+ APP TrainRegression
+ OPTIONS -io.il ${INPUTDATA}/QB_Toulouse_Ortho_regression.tif
+ -io.imstat ${INPUTDATA}/QB_Toulouse_Ortho_regression.xml
+ -io.out ${TEMP}/apTvClTrainRegressionTest_monovar.rf
+ -sample.mt 20000
+ -sample.mv 20000
+ -sample.vtr 0.5
+ -rand 121212
+ -classifier rf
+ -classifier.rf.ra 0.0001
+ -classifier.rf.max 6
+ -classifier.rf.acc 0.0005
+ VALID --compare-ascii ${NOTOL}
+ ${OTBAPP_BASELINE_FILES}/apTvClTrainRegressionTest_monovar.rf
+ ${TEMP}/apTvClTrainRegressionTest_monovar.rf)
+
+#----------- PredictRegression TESTS ----------------
+otb_test_application(NAME apTvClPredictRegressionTest_monovar
+ APP PredictRegression
+ OPTIONS -in ${INPUTDATA}/QB_Toulouse_Ortho_PAN.tif
+ -model ${OTBAPP_BASELINE_FILES}/apTvClTrainRegressionTest_monovar.rf
+ -imstat ${INPUTDATA}/QB_Toulouse_Ortho_regression.xml
+ -out ${TEMP}/apTvClPredictRegressionTest_monovar.tif
+ VALID --compare-image 1
+ ${OTBAPP_BASELINE}/apTvClPredictRegressionTest_monovar.tif
+ ${TEMP}/apTvClPredictRegressionTest_monovar.tif)
+
+endif()
+
diff --git a/Modules/Applications/AppFiltering/test/CMakeLists.txt b/Modules/Applications/AppFiltering/test/CMakeLists.txt
index d497c9bf8e1b6d51f5668b4ce2ee4be134d91078..984c1830c277999af835fefc934ffcf6bbb2ef8d 100644
--- a/Modules/Applications/AppFiltering/test/CMakeLists.txt
+++ b/Modules/Applications/AppFiltering/test/CMakeLists.txt
@@ -51,8 +51,8 @@ otb_test_application(NAME apTvDespeckleFrost
-filter.frost.rad 5
-filter.frost.deramp 0.1
VALID --compare-image ${EPSILON_7}
- ${BASELINE}/bfFiltreLee_05_05_12.tif
- ${TEMP}/bfFiltreLee_05_05_12_app.tif)
+ ${BASELINE}/bfFiltreFrost_05_05_12_app.tif
+ ${TEMP}/bfFiltreFrost_05_05_12_app.tif)
otb_test_application(NAME apTvDespeckleGammaMAP
APP Despeckle
diff --git a/Modules/Filtering/ImageManipulation/test/otbImageToNoDataMaskFilter.cxx b/Modules/Filtering/ImageManipulation/test/otbImageToNoDataMaskFilter.cxx
index 109a2ec7d44c4ad2ff420337613260d64ba66b8a..d5c2b4283635847be4947e15791e785ec1924d9d 100644
--- a/Modules/Filtering/ImageManipulation/test/otbImageToNoDataMaskFilter.cxx
+++ b/Modules/Filtering/ImageManipulation/test/otbImageToNoDataMaskFilter.cxx
@@ -69,12 +69,12 @@ int otbImageToNoDataMaskFilter(int itkNotUsed(argc),char * itkNotUsed(argv) [])
for(it.GoToBegin();!it.IsAtEnd();++it,++count)
{
- if (count%2 == 0 and it.Get()!=0)
+ if (count%2 == 0 && it.Get()!=0)
{
std::cerr<<"Pixel should be masked"<<std::endl;
failed = true;
}
- else if(count%2 == 1 and it.Get()!=255)
+ else if(count%2 == 1 && it.Get()!=255)
{
std::cerr<<"Pixel should not be masked"<<std::endl;
failed = true;
diff --git a/Modules/Filtering/Polarimetry/include/otbReciprocalHAlphaImageFilter.h b/Modules/Filtering/Polarimetry/include/otbReciprocalHAlphaImageFilter.h
index f1747c595c0ad69b2f819cec9376e9b79634e1e3..06a7a949d5ae59d1090521a4a914c50627362a5c 100644
--- a/Modules/Filtering/Polarimetry/include/otbReciprocalHAlphaImageFilter.h
+++ b/Modules/Filtering/Polarimetry/include/otbReciprocalHAlphaImageFilter.h
@@ -78,13 +78,13 @@ public:
VNLMatrixType vnlMat(3, 3, 0.);
vnlMat[0][0] = ComplexType(T0, 0.);
- vnlMat[0][1] = std::conj(ComplexType(Coherency[1]));
- vnlMat[0][2] = std::conj(ComplexType(Coherency[2]));
- vnlMat[1][0] = ComplexType(Coherency[1]);
+ vnlMat[0][1] = ComplexType(Coherency[1]);
+ vnlMat[0][2] = ComplexType(Coherency[2]);
+ vnlMat[1][0] = std::conj(ComplexType(Coherency[1]));
vnlMat[1][1] = ComplexType(T1, 0.);
- vnlMat[1][2] = std::conj(ComplexType(Coherency[4]));
- vnlMat[2][0] = ComplexType(Coherency[2]);
- vnlMat[2][1] = ComplexType(Coherency[4]);
+ vnlMat[1][2] = ComplexType(Coherency[4]);
+ vnlMat[2][0] = std::conj(ComplexType(Coherency[2]));
+ vnlMat[2][1] = std::conj(ComplexType(Coherency[4]));
vnlMat[2][2] = ComplexType(T2, 0.);
// Only compute the left symetry to respect the previous Hermitian Analisys code
@@ -95,6 +95,7 @@ public:
// Entropy estimation
double totalEigenValues(0.0);
double p[3];
+ double plog[3];
double entropy;
double alpha;
double anisotropy;
@@ -120,46 +121,32 @@ public:
}
}
- totalEigenValues = sortedRealEigenValues[0] + sortedRealEigenValues[1] + sortedRealEigenValues[2];
- if (totalEigenValues <m_Epsilon)
+ totalEigenValues = 0.0;
+ for (unsigned int k = 0; k < 3; ++k)
{
- totalEigenValues = m_Epsilon;
+ sortedRealEigenValues[k] = std::max(sortedRealEigenValues[k], 0.);
+ totalEigenValues += sortedRealEigenValues[k];
}
+
for (unsigned int k = 0; k < 3; ++k)
{
- p[k] = std::max(sortedRealEigenValues[k], 0.) / totalEigenValues;
+ p[k] = sortedRealEigenValues[k] / totalEigenValues;
+
+ if (p[k]<m_Epsilon) //n=log(n)-->0 when n-->0
+ plog[k]=0.0;
+ else
+ plog[k]=-p[k]*log(p[k])/log(3.0);
}
- if ( (p[0] < m_Epsilon) || (p[1] < m_Epsilon) || (p[2] < m_Epsilon) )
- {
- entropy =0.0;
- }
- else
- {
- entropy = p[0]*log(p[0]) + p[1]*log(p[1]) + p[2]*log(p[2]);
- entropy /= -log(3.);
- }
+ entropy = 0.0;
+ for (unsigned int k = 0; k < 3; ++k)
+ entropy += plog[k];
// alpha estimation
double val0, val1, val2;
double a0, a1, a2;
- for(unsigned int k = 0; k < 3; ++k)
- {
- p[k] = sortedRealEigenValues[k] / totalEigenValues;
-
- if (p[k] < 0.)
- {
- p[k] = 0.;
- }
-
- if (p[k] > 1.)
- {
- p[k] = 1.;
- }
- }
-
val0 = std::abs(sortedGreaterEigenVector[0]);
a0=acos(vcl_abs(val0)) * CONST_180_PI;
@@ -171,14 +158,10 @@ public:
alpha=p[0]*a0 + p[1]*a1 + p[2]*a2;
- if (alpha>90)
- {
- alpha=0.;
- }
-
// Anisotropy estimation
anisotropy=(sortedRealEigenValues[1] - sortedRealEigenValues[2])/(sortedRealEigenValues[1] + sortedRealEigenValues[2] + m_Epsilon);
+
result[0] = static_cast<OutputValueType>(entropy);
result[1] = static_cast<OutputValueType>(alpha);
result[2] = static_cast<OutputValueType>(anisotropy);
diff --git a/Modules/Filtering/Polarimetry/test/CMakeLists.txt b/Modules/Filtering/Polarimetry/test/CMakeLists.txt
index c3825403977252f806d4e27ec4fa085eefcdbb5e..4d7a2a42b78f04c19a89665141b71f17dd4c4cf7 100644
--- a/Modules/Filtering/Polarimetry/test/CMakeLists.txt
+++ b/Modules/Filtering/Polarimetry/test/CMakeLists.txt
@@ -40,7 +40,7 @@ otb_module_target_label(otbPolarimetryTestDriver)
# Tests Declaration
otb_add_test(NAME saTvMuellerToPolarisationDegreeAndPowerImageFilter COMMAND otbPolarimetryTestDriver
- --compare-image ${EPSILON_12} ${BASELINE}/saTvMuellerToPolarisationDegreeAndPowerImageFilter.tif
+ --compare-image ${EPSILON_7} ${BASELINE}/saTvMuellerToPolarisationDegreeAndPowerImageFilter.tif
${TEMP}/saTvMuellerToPolarisationDegreeAndPowerImageFilter.tif
otbMuellerToPolarisationDegreeAndPowerImageFilter
${BASELINE}/saTvSinclairImageFilter_SinclairToMueller.tif
@@ -48,7 +48,7 @@ otb_add_test(NAME saTvMuellerToPolarisationDegreeAndPowerImageFilter COMMAND otb
)
otb_add_test(NAME saTvVectorMultiChannelsPolarimetricSynthesisFilter COMMAND otbPolarimetryTestDriver
- --compare-image ${EPSILON_12} ${BASELINE}/saTvMultiPolarimetricSynthesis1.tif
+ --compare-image ${EPSILON_7} ${BASELINE}/saTvMultiPolarimetricSynthesis1.tif
${TEMP}/resMultiPolarimetricSynthesis1.tif
otbVectorMultiChannelsPolarimetricSynthesisFilter
${INPUTDATA}/RSAT2_AltonaExtract_1000_1000_100_100.hdr
@@ -60,10 +60,13 @@ otb_add_test(NAME saTvVectorMultiChannelsPolarimetricSynthesisFilter COMMAND otb
)
otb_add_test(NAME saTvReciprocalHAlphaImageFilter COMMAND otbPolarimetryTestDriver
- --compare-image ${EPSILON_12} ${BASELINE}/saTvReciprocalHAlphaImageFilter.tif
+ --compare-image ${EPSILON_7} ${BASELINE}/saTvReciprocalHAlphaImageFilter.tif
${TEMP}/saTvReciprocalHAlphaImageFilter.tif
otbReciprocalHAlphaImageFilter
- ${BASELINE}/saTvSinclairImageFilter_SinclairToReciprocalCoherency.tif
+ ${INPUTDATA}/RSAT_imagery_HH.tif
+ ${INPUTDATA}/RSAT_imagery_HV.tif
+ ${INPUTDATA}/RSAT_imagery_VV.tif
+ 5
${TEMP}/saTvReciprocalHAlphaImageFilter.tif
)
@@ -72,7 +75,7 @@ otb_add_test(NAME saTuReciprocalLinearCovarianceToReciprocalCircularCovarianceIm
)
otb_add_test(NAME saTvReciprocalCovarianceToReciprocalCoherencyImageFilter COMMAND otbPolarimetryTestDriver
- --compare-image ${EPSILON_12} ${BASELINE}/saTvSinclairImageFilter_SinclairToReciprocalCoherency.tif
+ --compare-image ${EPSILON_7} ${BASELINE}/saTvSinclairImageFilter_SinclairToReciprocalCoherency.tif
${TEMP}/saTvMLCToCoherencyImageFilter.tif
otbReciprocalCovarianceToReciprocalCoherencyImageFilter
${BASELINE}/saTvSinclairImageFilter_SinclairToReciprocalCovariance.tif
@@ -91,7 +94,7 @@ otb_add_test(NAME saTuPolarimetricSynthesisFunctor COMMAND otbPolarimetryTestDri
otbPolarimetricSynthesisFunctor )
otb_add_test(NAME saTvMultiChannelsPolarimetricSynthesisFilter COMMAND otbPolarimetryTestDriver
- --compare-image ${EPSILON_12} ${BASELINE}/saTvMultiPolarimetricSynthesis2.tif
+ --compare-image ${EPSILON_7} ${BASELINE}/saTvMultiPolarimetricSynthesis2.tif
${TEMP}/resMultiPolarimetricSynthesis2.tif
otbMultiChannelsPolarimetricSynthesisFilter
${INPUTDATA}/RSAT_imagery_HH.tif
@@ -105,7 +108,7 @@ otb_add_test(NAME saTvMultiChannelsPolarimetricSynthesisFilter COMMAND otbPolari
)
otb_add_test(NAME saTvMultiChannelsPolarimetricSynthesisFilter_C COMMAND otbPolarimetryTestDriver
- --compare-image ${EPSILON_12} ${BASELINE}/saTvMultiPolarimetricSynthesis2.tif
+ --compare-image ${EPSILON_7} ${BASELINE}/saTvMultiPolarimetricSynthesis2.tif
${TEMP}/resMultiPolarimetricSynthesis2.tif
otbMultiChannelsPolarimetricSynthesisFilter
${INPUTDATA}/RSAT_imageryC_HH.tif
@@ -119,7 +122,7 @@ otb_add_test(NAME saTvMultiChannelsPolarimetricSynthesisFilter_C COMMAND otbPola
)
otb_add_test(NAME saTvSinclairImageFilter_SinclairToMueller COMMAND otbPolarimetryTestDriver
- --compare-image ${EPSILON_12} ${BASELINE}/saTvSinclairImageFilter_SinclairToMueller.tif
+ --compare-image ${EPSILON_7} ${BASELINE}/saTvSinclairImageFilter_SinclairToMueller.tif
${TEMP}/saTvSinclairImageFilter_SinclairToMueller.tif
otbSinclairImageFilter
SinclairToMuellerMatrix
@@ -130,7 +133,7 @@ otb_add_test(NAME saTvSinclairImageFilter_SinclairToMueller COMMAND otbPolarimet
)
otb_add_test(NAME saTvSinclairImageFilter_SinclairToMueller_C COMMAND otbPolarimetryTestDriver
- --compare-image ${EPSILON_12} ${BASELINE}/saTvSinclairImageFilter_SinclairToMueller.tif
+ --compare-image ${EPSILON_7} ${BASELINE}/saTvSinclairImageFilter_SinclairToMueller.tif
${TEMP}/saTvSinclairImageFilter_SinclairToMueller.tif
otbSinclairImageFilter
SinclairToMuellerMatrix
@@ -141,7 +144,7 @@ otb_add_test(NAME saTvSinclairImageFilter_SinclairToMueller_C COMMAND otbPolarim
)
otb_add_test(NAME saTvSinclairImageFilter_SinclairToCovariance COMMAND otbPolarimetryTestDriver
- --compare-image ${EPSILON_12} ${BASELINE}/saTvSinclairImageFilter_SinclairToCovariance.tif
+ --compare-image ${EPSILON_7} ${BASELINE}/saTvSinclairImageFilter_SinclairToCovariance.tif
${TEMP}/saTvSinclairImageFilter_SinclairToCovariance.tif
otbSinclairImageFilter
SinclairToCovarianceMatrix
@@ -152,7 +155,7 @@ otb_add_test(NAME saTvSinclairImageFilter_SinclairToCovariance COMMAND otbPolari
)
otb_add_test(NAME saTvSinclairImageFilter_SinclairToCovariance_C COMMAND otbPolarimetryTestDriver
- --compare-image ${EPSILON_12} ${BASELINE}/saTvSinclairImageFilter_SinclairToCovariance.tif
+ --compare-image ${EPSILON_7} ${BASELINE}/saTvSinclairImageFilter_SinclairToCovariance.tif
${TEMP}/saTvSinclairImageFilter_SinclairToCovariance.tif
otbSinclairImageFilter
SinclairToCovarianceMatrix
@@ -167,7 +170,7 @@ otb_add_test(NAME saTuSinclairImageFilterNew COMMAND otbPolarimetryTestDriver
)
otb_add_test(NAME saTvSinclairImageFilter_SinclairToCircularCovarianceMatrix COMMAND otbPolarimetryTestDriver
- --compare-image ${EPSILON_12} ${BASELINE}/saTvSinclairImageFilter_SinclairToCircularCovarianceMatrix.tif
+ --compare-image ${EPSILON_7} ${BASELINE}/saTvSinclairImageFilter_SinclairToCircularCovarianceMatrix.tif
${TEMP}/saTvSinclairImageFilter_SinclairToCircularCovarianceMatrix.tif
otbSinclairImageFilter
SinclairToCircularCovarianceMatrix
@@ -178,7 +181,7 @@ otb_add_test(NAME saTvSinclairImageFilter_SinclairToCircularCovarianceMatrix COM
)
otb_add_test(NAME saTvSinclairImageFilter_SinclairToCircularCovarianceMatrix_C COMMAND otbPolarimetryTestDriver
- --compare-image ${EPSILON_12} ${BASELINE}/saTvSinclairImageFilter_SinclairToCircularCovarianceMatrix.tif
+ --compare-image ${EPSILON_7} ${BASELINE}/saTvSinclairImageFilter_SinclairToCircularCovarianceMatrix.tif
${TEMP}/saTvSinclairImageFilter_SinclairToCircularCovarianceMatrix.tif
otbSinclairImageFilter
SinclairToCircularCovarianceMatrix
@@ -189,7 +192,7 @@ otb_add_test(NAME saTvSinclairImageFilter_SinclairToCircularCovarianceMatrix_C C
)
otb_add_test(NAME saTvSinclairImageFilter_SinclairToCoherency COMMAND otbPolarimetryTestDriver
- --compare-image ${EPSILON_12} ${BASELINE}/saTvSinclairImageFilter_SinclairToCoherency.tif
+ --compare-image ${EPSILON_7} ${BASELINE}/saTvSinclairImageFilter_SinclairToCoherency.tif
${TEMP}/saTvSinclairImageFilter_SinclairToCoherency.tif
otbSinclairImageFilter
SinclairToCoherencyMatrix
@@ -200,7 +203,7 @@ otb_add_test(NAME saTvSinclairImageFilter_SinclairToCoherency COMMAND otbPolarim
)
otb_add_test(NAME saTvSinclairImageFilter_SinclairToCoherency_C COMMAND otbPolarimetryTestDriver
- --compare-image ${EPSILON_12} ${BASELINE}/saTvSinclairImageFilter_SinclairToCoherency.tif
+ --compare-image ${EPSILON_7} ${BASELINE}/saTvSinclairImageFilter_SinclairToCoherency.tif
${TEMP}/saTvSinclairImageFilter_SinclairToCoherency.tif
otbSinclairImageFilter
SinclairToCoherencyMatrix
@@ -223,7 +226,7 @@ otb_add_test(NAME saTuSinclairReciprocalImageFilterNew COMMAND otbPolarimetryTes
)
otb_add_test(NAME saTvSinclairReciprocalImageFilter_SinclairToReciprocalCovariance COMMAND otbPolarimetryTestDriver
- --compare-image ${EPSILON_12} ${BASELINE}/saTvSinclairImageFilter_SinclairToReciprocalCovariance.tif
+ --compare-image ${EPSILON_7} ${BASELINE}/saTvSinclairImageFilter_SinclairToReciprocalCovariance.tif
${TEMP}/saTvSinclairImageFilter_SinclairToReciprocalCovariance.tif
otbSinclairReciprocalImageFilter
SinclairToReciprocalCovarianceMatrix
@@ -234,7 +237,7 @@ otb_add_test(NAME saTvSinclairReciprocalImageFilter_SinclairToReciprocalCovarian
)
otb_add_test(NAME saTvSinclairReciprocalImageFilter_SinclairToReciprocalCovariance_C COMMAND otbPolarimetryTestDriver
- --compare-image ${EPSILON_12} ${BASELINE}/saTvSinclairImageFilter_SinclairToReciprocalCovariance.tif
+ --compare-image ${EPSILON_7} ${BASELINE}/saTvSinclairImageFilter_SinclairToReciprocalCovariance.tif
${TEMP}/saTvSinclairImageFilter_SinclairToReciprocalCovariance.tif
otbSinclairReciprocalImageFilter
SinclairToReciprocalCovarianceMatrix
@@ -245,7 +248,7 @@ otb_add_test(NAME saTvSinclairReciprocalImageFilter_SinclairToReciprocalCovarian
)
otb_add_test(NAME saTvSinclairReciprocalImageFilter_SinclairToReciprocalCircularCovarianceMatrix COMMAND otbPolarimetryTestDriver
- --compare-image ${EPSILON_12} ${BASELINE}/saTvSinclairImageFilter_SinclairToReciprocalCircularCovarianceMatrix.tif
+ --compare-image ${EPSILON_7} ${BASELINE}/saTvSinclairImageFilter_SinclairToReciprocalCircularCovarianceMatrix.tif
${TEMP}/saTvSinclairImageFilter_SinclairToReciprocalCircularCovarianceMatrix.tif
otbSinclairReciprocalImageFilter
SinclairToReciprocalCircularCovarianceMatrix
@@ -257,7 +260,7 @@ otb_add_test(NAME saTvSinclairReciprocalImageFilter_SinclairToReciprocalCircular
otb_add_test(NAME saTvSinclairReciprocalImageFilter_SinclairToReciprocalCircularCovarianceMatrix_C COMMAND otbPolarimetryTestDriver
- --compare-image ${EPSILON_12} ${BASELINE}/saTvSinclairImageFilter_SinclairToReciprocalCircularCovarianceMatrix.tif
+ --compare-image ${EPSILON_7} ${BASELINE}/saTvSinclairImageFilter_SinclairToReciprocalCircularCovarianceMatrix.tif
${TEMP}/saTvSinclairImageFilter_SinclairToReciprocalCircularCovarianceMatrix.tif
otbSinclairReciprocalImageFilter
SinclairToReciprocalCircularCovarianceMatrix
@@ -268,7 +271,7 @@ otb_add_test(NAME saTvSinclairReciprocalImageFilter_SinclairToReciprocalCircular
)
otb_add_test(NAME saTvSinclairReciprocalImageFilter_SinclairToReciprocalCoherency COMMAND otbPolarimetryTestDriver
- --compare-image ${EPSILON_12} ${BASELINE}/saTvSinclairImageFilter_SinclairToReciprocalCoherency.tif
+ --compare-image ${EPSILON_7} ${BASELINE}/saTvSinclairImageFilter_SinclairToReciprocalCoherency.tif
${TEMP}/saTvSinclairImageFilter_SinclairToReciprocalCoherency.tif
otbSinclairReciprocalImageFilter
SinclairToReciprocalCoherencyMatrix
@@ -279,7 +282,7 @@ otb_add_test(NAME saTvSinclairReciprocalImageFilter_SinclairToReciprocalCoherenc
)
otb_add_test(NAME saTvSinclairReciprocalImageFilter_SinclairToReciprocalCoherency_C COMMAND otbPolarimetryTestDriver
- --compare-image ${EPSILON_12} ${BASELINE}/saTvSinclairImageFilter_SinclairToReciprocalCoherency.tif
+ --compare-image ${EPSILON_7} ${BASELINE}/saTvSinclairImageFilter_SinclairToReciprocalCoherency.tif
${TEMP}/saTvSinclairImageFilter_SinclairToReciprocalCoherency.tif
otbSinclairReciprocalImageFilter
SinclairToReciprocalCoherencyMatrix
@@ -291,7 +294,7 @@ otb_add_test(NAME saTvSinclairReciprocalImageFilter_SinclairToReciprocalCoherenc
otb_add_test(NAME saTvReciprocalLinearCovarianceToReciprocalCircularCovarianceImageFilter COMMAND otbPolarimetryTestDriver
- --compare-image ${EPSILON_12} ${BASELINE}/saTvSinclairImageFilter_SinclairToReciprocalCircularCovarianceMatrix.tif
+ --compare-image ${EPSILON_7} ${BASELINE}/saTvSinclairImageFilter_SinclairToReciprocalCircularCovarianceMatrix.tif
${TEMP}/saTvMLCToCircularCoherencyDegreeImageFilter.tif
otbReciprocalLinearCovarianceToReciprocalCircularCovarianceImageFilter
${BASELINE}/saTvSinclairImageFilter_SinclairToReciprocalCovariance.tif
@@ -299,7 +302,7 @@ otb_add_test(NAME saTvReciprocalLinearCovarianceToReciprocalCircularCovarianceIm
)
otb_add_test(NAME saTvReciprocalCoherencyToReciprocalMuellerImageFilter COMMAND otbPolarimetryTestDriver
- --compare-image ${EPSILON_12} ${BASELINE}/saTvSinclairImageFilter_SinclairToMueller.tif
+ --compare-image ${EPSILON_7} ${BASELINE}/saTvSinclairImageFilter_SinclairToMueller.tif
${TEMP}/saTvReciprocalCoherencyToMuellerImageFilter.tif
otbReciprocalCoherencyToReciprocalMuellerImageFilter
${BASELINE}/saTvSinclairImageFilter_SinclairToReciprocalCoherency.tif
@@ -315,7 +318,7 @@ otb_add_test(NAME saTuReciprocalCovarianceToCoherencyDegreeImageFilterNew COMMAN
)
otb_add_test(NAME saTvMuellerToReciprocalCovarianceImageFilter COMMAND otbPolarimetryTestDriver
- --compare-image ${EPSILON_12} ${BASELINE}/saTvSinclairImageFilter_SinclairToReciprocalCovariance.tif
+ --compare-image ${EPSILON_7} ${BASELINE}/saTvSinclairImageFilter_SinclairToReciprocalCovariance.tif
${TEMP}/saTvMuellerToMLCImageFilter.tif
otbMuellerToReciprocalCovarianceImageFilter
${BASELINE}/saTvSinclairImageFilter_SinclairToMueller.tif
@@ -363,7 +366,7 @@ otb_add_test(NAME saTuSinclairToCovarianceMatrixFunctor COMMAND otbPolarimetryTe
)
otb_add_test(NAME saTvReciprocalCovarianceToCoherencyDegreeImageFilter COMMAND otbPolarimetryTestDriver
- --compare-image ${EPSILON_12} ${BASELINE}/saTvMLCToCoherencyDegreeImageFilter.tif
+ --compare-image ${EPSILON_7} ${BASELINE}/saTvMLCToCoherencyDegreeImageFilter.tif
${TEMP}/saTvMLCToCoherencyDegreeImageFilter.tif
otbReciprocalCovarianceToCoherencyDegreeImageFilter
${BASELINE}/saTvSinclairImageFilter_SinclairToReciprocalCovariance.tif
diff --git a/Modules/Filtering/Polarimetry/test/otbReciprocalHAlphaImageFilter.cxx b/Modules/Filtering/Polarimetry/test/otbReciprocalHAlphaImageFilter.cxx
index 702a2dab4d74aab3d005d39f3f60996cf48e20d5..8855b9d3c022c750079f67820a67df0bbfb5002e 100644
--- a/Modules/Filtering/Polarimetry/test/otbReciprocalHAlphaImageFilter.cxx
+++ b/Modules/Filtering/Polarimetry/test/otbReciprocalHAlphaImageFilter.cxx
@@ -24,35 +24,80 @@
#include "otbImageFileReader.h"
#include "otbImageFileWriter.h"
#include "otbReciprocalHAlphaImageFilter.h"
+#include "itkMeanImageFilter.h"
+#include "otbPerBandVectorImageFilter.h"
+#include "otbSinclairReciprocalImageFilter.h"
+#include "otbSinclairToReciprocalCoherencyMatrixFunctor.h"
+
int otbReciprocalHAlphaImageFilter(int itkNotUsed(argc), char * argv[])
{
- const char * inputFilename = argv[1];
- const char * outputFilename = argv[2];
-
- typedef double PixelType;
- typedef std::complex<PixelType> InputPixelType;
- const unsigned int Dimension = 2;
+ const char * inputFilenameHH = argv[1];
+ const char * inputFilenameHV = argv[2];
+ const char * inputFilenameVV = argv[3];
+ int size = atoi(argv[4]);
+ const char * outputFilename = argv[5];
- typedef otb::VectorImage<InputPixelType, Dimension> ImageType;
- typedef otb::VectorImage<PixelType, Dimension> RealImageType;
-
- typedef otb::ReciprocalHAlphaImageFilter<ImageType, RealImageType> FilterType;
+ typedef std::complex<double> ComplexPixelType;
+ const unsigned int Dimension = 2;
- typedef otb::ImageFileReader<ImageType> ReaderType;
- typedef otb::ImageFileWriter<RealImageType> WriterType;
- ReaderType::Pointer reader = ReaderType::New();
+ typedef otb::Image<ComplexPixelType, Dimension> ComplexImageType;
+ typedef otb::VectorImage<ComplexPixelType, Dimension> ComplexVectorImageType;
+ typedef otb::VectorImage<double, Dimension> RealVectorImageType;
+
+
+
+ typedef otb::ImageFileReader<ComplexImageType> ReaderType;
+ typedef otb::ImageFileWriter<RealVectorImageType> WriterType;
+
+
+ typedef otb::SinclairReciprocalImageFilter<ComplexImageType, ComplexImageType, ComplexImageType, ComplexVectorImageType,
+ otb::Functor::SinclairToReciprocalCovarianceMatrixFunctor<ComplexImageType::PixelType,
+ ComplexImageType::PixelType,
+ ComplexImageType::PixelType,
+ ComplexVectorImageType::PixelType> > SinclaireToC3FilterType;
+
+
+ typedef itk::MeanImageFilter<ComplexImageType, ComplexImageType> MeanFilterType;
+ typedef otb::PerBandVectorImageFilter<ComplexVectorImageType, ComplexVectorImageType, MeanFilterType> PerBandMeanFilterType;
+
+
+ typedef otb::ReciprocalHAlphaImageFilter<ComplexVectorImageType, RealVectorImageType> HAlphaFilterType;
+
+
+
+ ReaderType::Pointer readerHH = ReaderType::New();
+ ReaderType::Pointer readerHV = ReaderType::New();
+ ReaderType::Pointer readerVV = ReaderType::New();
+
WriterType::Pointer writer = WriterType::New();
- reader->SetFileName(inputFilename);
-
- FilterType::Pointer filter = FilterType::New();
- filter->SetInput(reader->GetOutput());
+ SinclaireToC3FilterType::Pointer sinclairtoc3 = SinclaireToC3FilterType::New();
+ PerBandMeanFilterType::Pointer perBand = PerBandMeanFilterType::New();
+ HAlphaFilterType::Pointer haafilter = HAlphaFilterType::New();
+
+
+ MeanFilterType::InputSizeType radius;
+ radius.Fill( size );
+ perBand->GetFilter()->SetRadius(radius);
+
+
+ readerHH->SetFileName(inputFilenameHH);
+ readerHV->SetFileName(inputFilenameHV);
+ readerVV->SetFileName(inputFilenameVV);
+
+ sinclairtoc3->SetInputHH(readerHH->GetOutput());
+ sinclairtoc3->SetInputHV_VH(readerHV->GetOutput());
+ sinclairtoc3->SetInputVV(readerVV->GetOutput());
+
+ perBand->SetInput(sinclairtoc3->GetOutput());
+
+ haafilter->SetInput(perBand->GetOutput());
writer->SetFileName(outputFilename);
- writer->SetInput(filter->GetOutput());
+ writer->SetInput(haafilter->GetOutput());
writer->Update();
return EXIT_SUCCESS;
diff --git a/Modules/Learning/Supervised/include/otbBoostMachineLearningModel.h b/Modules/Learning/Supervised/include/otbBoostMachineLearningModel.h
index 185d10ba44bf26db0a9444c5eb61025ef4f2899a..a812eca2b8f36708b19e186d7221a0a23cc07f4f 100644
--- a/Modules/Learning/Supervised/include/otbBoostMachineLearningModel.h
+++ b/Modules/Learning/Supervised/include/otbBoostMachineLearningModel.h
@@ -92,6 +92,11 @@ public:
itkGetMacro(MaxDepth, int);
itkSetMacro(MaxDepth, int);
+ /** Train the machine learning model */
+ virtual void Train();
+ /** Predict values using the model */
+ virtual TargetSampleType Predict(const InputSampleType& input, ConfidenceValueType *quality=NULL) const;
+
/** Save the model to file */
virtual void Save(const std::string & filename, const std::string & name="");
@@ -117,11 +122,6 @@ protected:
/** PrintSelf method */
void PrintSelf(std::ostream& os, itk::Indent indent) const;
- /** Train the machine learning model */
- virtual void TrainClassification();
- /** Predict values using the model */
- virtual TargetSampleType PredictClassification(const InputSampleType& input, ConfidenceValueType *quality=NULL) const;
-
private:
BoostMachineLearningModel(const Self &); //purposely not implemented
void operator =(const Self&); //purposely not implemented
diff --git a/Modules/Learning/Supervised/include/otbBoostMachineLearningModel.txx b/Modules/Learning/Supervised/include/otbBoostMachineLearningModel.txx
index 493107f9ff2b8da6c652fc67bc31376664eed1cc..15a9d5c293b8fa61a87b2f714aef15d0379a0686 100644
--- a/Modules/Learning/Supervised/include/otbBoostMachineLearningModel.txx
+++ b/Modules/Learning/Supervised/include/otbBoostMachineLearningModel.txx
@@ -52,7 +52,7 @@ BoostMachineLearningModel<TInputValue,TOutputValue>
template <class TInputValue, class TOutputValue>
void
BoostMachineLearningModel<TInputValue,TOutputValue>
-::TrainClassification()
+::Train()
{
//convert listsample to opencv matrix
cv::Mat samples;
@@ -77,7 +77,7 @@ template <class TInputValue, class TOutputValue>
typename BoostMachineLearningModel<TInputValue,TOutputValue>
::TargetSampleType
BoostMachineLearningModel<TInputValue,TOutputValue>
-::PredictClassification(const InputSampleType & input, ConfidenceValueType *quality) const
+::Predict(const InputSampleType & input, ConfidenceValueType *quality) const
{
//convert listsample to Mat
cv::Mat sample;
diff --git a/Modules/Learning/Supervised/include/otbDecisionTreeMachineLearningModel.h b/Modules/Learning/Supervised/include/otbDecisionTreeMachineLearningModel.h
index 6415fa940e273e5d9074a130ba95a8d8105a4978..651a48f6ee319e2c4171f15741df7e9615205c2d 100644
--- a/Modules/Learning/Supervised/include/otbDecisionTreeMachineLearningModel.h
+++ b/Modules/Learning/Supervised/include/otbDecisionTreeMachineLearningModel.h
@@ -147,11 +147,10 @@ public:
return m_Priors;
}
- /** Setters/Getters to IsRegression flag
- * Default is False
- */
- itkGetMacro(IsRegression, bool);
- itkSetMacro(IsRegression, bool);
+ /** Train the machine learning model */
+ virtual void Train();
+ /** Predict values using the model */
+ virtual TargetSampleType Predict(const InputSampleType& input, ConfidenceValueType *quality=NULL) const;
/** Save the model to file */
virtual void Save(const std::string & filename, const std::string & name="");
@@ -178,11 +177,6 @@ protected:
/** PrintSelf method */
void PrintSelf(std::ostream& os, itk::Indent indent) const;
- /** Train the machine learning model */
- virtual void TrainClassification();
- /** Predict values using the model */
- virtual TargetSampleType PredictClassification(const InputSampleType& input, ConfidenceValueType *quality=NULL) const;
-
private:
DecisionTreeMachineLearningModel(const Self &); //purposely not implemented
void operator =(const Self&); //purposely not implemented
@@ -196,7 +190,6 @@ private:
int m_MaxCategories;
int m_CVFolds;
bool m_Use1seRule;
- bool m_IsRegression;
bool m_TruncatePrunedTree;
std::vector<float> m_Priors;
diff --git a/Modules/Learning/Supervised/include/otbDecisionTreeMachineLearningModel.txx b/Modules/Learning/Supervised/include/otbDecisionTreeMachineLearningModel.txx
index ada456e94c35ff1467e97b8301a5e4a315fa35f6..283fb039c35fd04aea4cc2a63c580ee665014ab4 100644
--- a/Modules/Learning/Supervised/include/otbDecisionTreeMachineLearningModel.txx
+++ b/Modules/Learning/Supervised/include/otbDecisionTreeMachineLearningModel.txx
@@ -38,9 +38,9 @@ DecisionTreeMachineLearningModel<TInputValue,TOutputValue>
m_MaxCategories(10),
m_CVFolds(10),
m_Use1seRule(true),
- m_IsRegression(false),
m_TruncatePrunedTree(true)
{
+ this->m_IsRegressionSupported = true;
}
@@ -55,7 +55,7 @@ DecisionTreeMachineLearningModel<TInputValue,TOutputValue>
template <class TInputValue, class TOutputValue>
void
DecisionTreeMachineLearningModel<TInputValue,TOutputValue>
-::TrainClassification()
+::Train()
{
//convert listsample to opencv matrix
cv::Mat samples;
@@ -73,7 +73,7 @@ DecisionTreeMachineLearningModel<TInputValue,TOutputValue>
cv::Mat var_type = cv::Mat(this->GetInputListSample()->GetMeasurementVectorSize() + 1, 1, CV_8U );
var_type.setTo(cv::Scalar(CV_VAR_NUMERICAL) ); // all inputs are numerical
- if (!m_IsRegression) //Classification
+ if (!this->m_RegressionMode) //Classification
var_type.at<uchar>(this->GetInputListSample()->GetMeasurementVectorSize(), 0) = CV_VAR_CATEGORICAL;
m_DTreeModel->train(samples,CV_ROW_SAMPLE,labels,cv::Mat(),cv::Mat(),var_type,cv::Mat(),params);
@@ -83,7 +83,7 @@ template <class TInputValue, class TOutputValue>
typename DecisionTreeMachineLearningModel<TInputValue,TOutputValue>
::TargetSampleType
DecisionTreeMachineLearningModel<TInputValue,TOutputValue>
-::PredictClassification(const InputSampleType & input, ConfidenceValueType *quality) const
+::Predict(const InputSampleType & input, ConfidenceValueType *quality) const
{
//convert listsample to Mat
cv::Mat sample;
diff --git a/Modules/Learning/Supervised/include/otbGradientBoostedTreeMachineLearningModel.h b/Modules/Learning/Supervised/include/otbGradientBoostedTreeMachineLearningModel.h
index 3126f44c0ff7073def41f025df615e74013b590b..f10a89c68066f8ee6bbacc252b4088fa057157be 100644
--- a/Modules/Learning/Supervised/include/otbGradientBoostedTreeMachineLearningModel.h
+++ b/Modules/Learning/Supervised/include/otbGradientBoostedTreeMachineLearningModel.h
@@ -100,6 +100,11 @@ public:
itkGetMacro(UseSurrogates, bool);
itkSetMacro(UseSurrogates, bool);
+ /** Train the machine learning model */
+ virtual void Train();
+ /** Predict values using the model */
+ virtual TargetSampleType Predict(const InputSampleType& input, ConfidenceValueType *quality=NULL) const;
+
/** Save the model to file */
virtual void Save(const std::string & filename, const std::string & name="");
@@ -125,11 +130,6 @@ protected:
/** PrintSelf method */
void PrintSelf(std::ostream& os, itk::Indent indent) const;
- /** Train the machine learning model */
- virtual void TrainClassification();
- /** Predict values using the model */
- virtual TargetSampleType PredictClassification(const InputSampleType& input, ConfidenceValueType *quality=NULL) const;
-
private:
GradientBoostedTreeMachineLearningModel(const Self &); //purposely not implemented
void operator =(const Self&); //purposely not implemented
@@ -142,7 +142,6 @@ private:
double m_SubSamplePortion;
int m_MaxDepth;
bool m_UseSurrogates;
- bool m_IsRegression;
};
diff --git a/Modules/Learning/Supervised/include/otbGradientBoostedTreeMachineLearningModel.txx b/Modules/Learning/Supervised/include/otbGradientBoostedTreeMachineLearningModel.txx
index 595f1bb060b8ffbcb533352915f41b69c2bd1458..d08abec0290776a5d6a7ddfd3df27e6b5216d620 100644
--- a/Modules/Learning/Supervised/include/otbGradientBoostedTreeMachineLearningModel.txx
+++ b/Modules/Learning/Supervised/include/otbGradientBoostedTreeMachineLearningModel.txx
@@ -36,9 +36,9 @@ GradientBoostedTreeMachineLearningModel<TInputValue,TOutputValue>
m_Shrinkage(0.01),
m_SubSamplePortion(0.8),
m_MaxDepth(3),
- m_UseSurrogates(false),
- m_IsRegression(false)
+ m_UseSurrogates(false)
{
+ this->m_IsRegressionSupported = true;
}
@@ -53,7 +53,7 @@ GradientBoostedTreeMachineLearningModel<TInputValue,TOutputValue>
template <class TInputValue, class TOutputValue>
void
GradientBoostedTreeMachineLearningModel<TInputValue,TOutputValue>
-::TrainClassification()
+::Train()
{
//convert listsample to opencv matrix
cv::Mat samples;
@@ -62,7 +62,6 @@ GradientBoostedTreeMachineLearningModel<TInputValue,TOutputValue>
cv::Mat labels;
otb::ListSampleToMat<TargetListSampleType>(this->GetTargetListSample(),labels);
-
CvGBTreesParams params = CvGBTreesParams(m_LossFunctionType, m_WeakCount, m_Shrinkage, m_SubSamplePortion,
m_MaxDepth, m_UseSurrogates);
@@ -70,7 +69,7 @@ GradientBoostedTreeMachineLearningModel<TInputValue,TOutputValue>
cv::Mat var_type = cv::Mat(this->GetInputListSample()->GetMeasurementVectorSize() + 1, 1, CV_8U );
var_type.setTo(cv::Scalar(CV_VAR_NUMERICAL) ); // all inputs are numerical
- if (!m_IsRegression) //Classification
+ if (!this->m_RegressionMode) //Classification
var_type.at<uchar>(this->GetInputListSample()->GetMeasurementVectorSize(), 0) = CV_VAR_CATEGORICAL;
m_GBTreeModel->train(samples,CV_ROW_SAMPLE,labels,cv::Mat(),cv::Mat(),var_type,cv::Mat(),params, false);
@@ -80,7 +79,7 @@ template <class TInputValue, class TOutputValue>
typename GradientBoostedTreeMachineLearningModel<TInputValue,TOutputValue>
::TargetSampleType
GradientBoostedTreeMachineLearningModel<TInputValue,TOutputValue>
-::PredictClassification(const InputSampleType & input, ConfidenceValueType *quality) const
+::Predict(const InputSampleType & input, ConfidenceValueType *quality) const
{
//convert listsample to Mat
cv::Mat sample;
diff --git a/Modules/Learning/Supervised/include/otbImageClassificationFilter.txx b/Modules/Learning/Supervised/include/otbImageClassificationFilter.txx
index 88d2ad012441455cc2c2d221e79e175731b3e31f..b0a5d5e3e842ec986dfc2400736b84e2a405bb53 100644
--- a/Modules/Learning/Supervised/include/otbImageClassificationFilter.txx
+++ b/Modules/Learning/Supervised/include/otbImageClassificationFilter.txx
@@ -118,7 +118,7 @@ ImageClassificationFilter<TInputImage, TOutputImage, TMaskImage>
}
// setup iterator for confidence map
- bool computeConfidenceMap(m_UseConfidenceMap && m_Model->HasConfidenceIndex());
+ bool computeConfidenceMap(m_UseConfidenceMap && m_Model->HasConfidenceIndex() && !m_Model->GetRegressionMode());
ConfidenceMapIteratorType confidenceIt;
if (computeConfidenceMap)
{
diff --git a/Modules/Learning/Supervised/include/otbKNearestNeighborsMachineLearningModel.h b/Modules/Learning/Supervised/include/otbKNearestNeighborsMachineLearningModel.h
index b8524b7fb677aff35b706a54b87b6a917251754b..3f29a10af3ed6b46d700684eddeab80a5076c17a 100644
--- a/Modules/Learning/Supervised/include/otbKNearestNeighborsMachineLearningModel.h
+++ b/Modules/Learning/Supervised/include/otbKNearestNeighborsMachineLearningModel.h
@@ -58,12 +58,23 @@ public:
itkGetMacro(K, int);
itkSetMacro(K, int);
- /** Setters/Getters to IsRegression flag
- * Default is False
- * \see http://docs.opencv.org/modules/ml/doc/k_nearest_neighbors.html
+ /** Decision rule once the KNN are found :
+ * [for classification]
+ * - KNN_VOTING : output value with maximum occurences (for classification)
+ * [for regression]
+ * - KNN_MEAN : output mean value of neighbors
+ * - KNN_MEDIAN : output median value of neighbors
*/
- itkGetMacro(IsRegression, bool);
- itkSetMacro(IsRegression, bool);
+ enum {KNN_VOTING, KNN_MEAN, KNN_MEDIAN};
+
+ /** Setters/Getters to the decision rule */
+ itkGetMacro(DecisionRule, int);
+ itkSetMacro(DecisionRule, int);
+
+ /** Train the machine learning model */
+ virtual void Train();
+ /** Predict values using the model */
+ virtual TargetSampleType Predict(const InputSampleType& input, ConfidenceValueType *quality=NULL) const;
/** Save the model to file */
virtual void Save(const std::string & filename, const std::string & name="");
@@ -90,18 +101,14 @@ protected:
/** PrintSelf method */
void PrintSelf(std::ostream& os, itk::Indent indent) const;
- /** Train the machine learning model */
- virtual void TrainClassification();
- /** Predict values using the model */
- virtual TargetSampleType PredictClassification(const InputSampleType& input, ConfidenceValueType *quality=NULL) const;
-
private:
KNearestNeighborsMachineLearningModel(const Self &); //purposely not implemented
void operator =(const Self&); //purposely not implemented
CvKNearest * m_KNearestModel;
int m_K;
- bool m_IsRegression;
+
+ int m_DecisionRule;
};
} // end namespace otb
diff --git a/Modules/Learning/Supervised/include/otbKNearestNeighborsMachineLearningModel.txx b/Modules/Learning/Supervised/include/otbKNearestNeighborsMachineLearningModel.txx
index e890b9137ac284848eda3c10885bfd736a4c28ac..fd33b7c9061fc3ce66c70cf9ea5c4c7780c42dc8 100644
--- a/Modules/Learning/Supervised/include/otbKNearestNeighborsMachineLearningModel.txx
+++ b/Modules/Learning/Supervised/include/otbKNearestNeighborsMachineLearningModel.txx
@@ -23,6 +23,7 @@
#include "otbOpenCVUtils.h"
#include <fstream>
+#include <set>
#include "itkMacro.h"
namespace otb
@@ -33,9 +34,10 @@ KNearestNeighborsMachineLearningModel<TInputValue,TTargetValue>
::KNearestNeighborsMachineLearningModel() :
m_KNearestModel (new CvKNearest),
m_K(32),
- m_IsRegression(false)
+ m_DecisionRule(KNN_VOTING)
{
this->m_ConfidenceIndex = true;
+ this->m_IsRegressionSupported = true;
}
@@ -50,7 +52,7 @@ KNearestNeighborsMachineLearningModel<TInputValue,TTargetValue>
template <class TInputValue, class TTargetValue>
void
KNearestNeighborsMachineLearningModel<TInputValue,TTargetValue>
-::TrainClassification()
+::Train()
{
//convert listsample to opencv matrix
cv::Mat samples;
@@ -59,26 +61,44 @@ KNearestNeighborsMachineLearningModel<TInputValue,TTargetValue>
cv::Mat labels;
otb::ListSampleToMat<TargetListSampleType>(this->GetTargetListSample(), labels);
+ // update decision rule if needed
+ if (this->m_RegressionMode)
+ {
+ if (this->m_DecisionRule == KNN_VOTING)
+ {
+ this->SetDecisionRule(KNN_MEAN);
+ }
+ }
+ else
+ {
+ if (this->m_DecisionRule != KNN_VOTING)
+ {
+ this->SetDecisionRule(KNN_VOTING);
+ }
+ }
+
//train the KNN model
- m_KNearestModel->train(samples, labels, cv::Mat(), m_IsRegression, m_K, false);
+ m_KNearestModel->train(samples, labels, cv::Mat(), this->m_RegressionMode, m_K, false);
}
template <class TInputValue, class TTargetValue>
typename KNearestNeighborsMachineLearningModel<TInputValue,TTargetValue>
::TargetSampleType
KNearestNeighborsMachineLearningModel<TInputValue,TTargetValue>
-::PredictClassification(const InputSampleType & input, ConfidenceValueType *quality) const
+::Predict(const InputSampleType & input, ConfidenceValueType *quality) const
{
//convert listsample to Mat
cv::Mat sample;
otb::SampleToMat<InputSampleType>(input, sample);
float result;
+ cv::Mat nearest(1,m_K,CV_32FC1);
+ result = m_KNearestModel->find_nearest(sample, m_K,0,0,&nearest,0);
+ // compute quality if asked (only happens in classification mode)
if (quality != NULL)
{
- cv::Mat nearest(1,m_K,CV_32FC1);
- result = m_KNearestModel->find_nearest(sample, m_K,0,0,&nearest,0);
+ assert(!this->m_RegressionMode);
unsigned int accuracy = 0;
for (int k=0 ; k < m_K ; ++k)
{
@@ -89,9 +109,22 @@ KNearestNeighborsMachineLearningModel<TInputValue,TTargetValue>
}
(*quality) = static_cast<ConfidenceValueType>(accuracy);
}
- else
+
+ // Decision rule :
+ // VOTING is OpenCV default behaviour for classification
+ // MEAN is OpenCV default behaviour for regression
+ // MEDIAN : only case that must be handled here
+ if (this->m_DecisionRule == KNN_MEDIAN)
{
- result = m_KNearestModel->find_nearest(sample, m_K);
+ std::multiset<float> values;
+ for (int k=0 ; k < m_K ; ++k)
+ {
+ values.insert(nearest.at<float>(0,k));
+ }
+ std::multiset<float>::iterator median = values.begin();
+ int pos = (m_K >> 1);
+ for (int k=0 ; k < pos ; ++k , ++median) {}
+ result = *median;
}
TargetSampleType target;
@@ -106,12 +139,17 @@ KNearestNeighborsMachineLearningModel<TInputValue,TTargetValue>
::Save(const std::string & filename, const std::string & itkNotUsed(name))
{
//there is no m_KNearestModel->save(filename.c_str(), name.c_str()).
- //We need to save the K parameter and IsRegression flag used and the samples.
+ //We need to save the K parameter, IsRegression flag, DecisionRule and the samples.
std::ofstream ofs(filename.c_str());
//Save K parameter and IsRegression flag.
ofs << "K=" << m_K << "\n";
- ofs << "IsRegression=" << m_IsRegression << "\n";
+ ofs << "IsRegression=" << this->m_RegressionMode << "\n";
+ // Save the DecisionRule if regression
+ if (this->m_RegressionMode)
+ {
+ ofs << "DecisionRule=" << m_DecisionRule << "\n";
+ }
//Save the samples. First column is the Label and other columns are the sample data.
typename InputListSampleType::ConstIterator sampleIt = this->GetInputListSample()->Begin();
@@ -154,8 +192,15 @@ KNearestNeighborsMachineLearningModel<TInputValue,TTargetValue>
std::getline(ifs, line);
pos = line.find_first_of("=", 0);
nextpos = line.find_first_of(" \n\r", pos+1);
- this->SetIsRegression(boost::lexical_cast<bool>(line.substr(pos+1, nextpos-pos-1)));
-
+ this->SetRegressionMode(boost::lexical_cast<bool>(line.substr(pos+1, nextpos-pos-1)));
+ //third line is the DecisionRule parameter (only for regression)
+ if (this->m_RegressionMode)
+ {
+ std::getline(ifs, line);
+ pos = line.find_first_of("=", 0);
+ nextpos = line.find_first_of(" \n\r", pos+1);
+ this->SetDecisionRule(boost::lexical_cast<int>(line.substr(pos+1, nextpos-pos-1)));
+ }
//Clear previous listSample (if any)
typename InputListSampleType::Pointer samples = InputListSampleType::New();
typename TargetListSampleType::Pointer labels = TargetListSampleType::New();
diff --git a/Modules/Learning/Supervised/include/otbLibSVMMachineLearningModel.h b/Modules/Learning/Supervised/include/otbLibSVMMachineLearningModel.h
index 18eba7fbb28d336967ac669d05cda51bc5ebdc4c..622923753e37d1216de669a9724c72b979015f83 100644
--- a/Modules/Learning/Supervised/include/otbLibSVMMachineLearningModel.h
+++ b/Modules/Learning/Supervised/include/otbLibSVMMachineLearningModel.h
@@ -59,6 +59,11 @@ public:
itkNewMacro(Self);
itkTypeMacro(SVMMachineLearningModel, MachineLearningModel);
+ /** Train the machine learning model */
+ virtual void Train();
+ /** Predict values using the model */
+ virtual TargetSampleType Predict(const InputSampleType& input, ConfidenceValueType *quality=NULL) const;
+
/** Save the model to file */
virtual void Save(const std::string &filename, const std::string & name="");
@@ -75,23 +80,40 @@ public:
//@}
//Setters/Getters to SVM model
- // itkGetMacro(SVMType, int);
- // itkSetMacro(SVMType, int);
+ otbGetObjectMemberMacro(SVMestimator, SVMType, int);
+ otbSetObjectMemberMacro(SVMestimator, SVMType, int);
+
+ otbGetObjectMemberMacro(SVMestimator, KernelType, int);
+ otbSetObjectMemberMacro(SVMestimator, KernelType, int);
+
+ otbGetObjectMemberMacro(SVMestimator, C, double);
+ otbSetObjectMemberMacro(SVMestimator, C, double);
- itkGetMacro(KernelType, int);
- itkSetMacro(KernelType, int);
+ // TODO : we should harmonize this parameter name : ParameterOptimization -> ParametersOptimization
+ bool GetParameterOptimization()
+ {
+ return this->m_SVMestimator->GetParametersOptimization();
+ }
+ void SetParameterOptimization(bool value)
+ {
+ this->m_SVMestimator->SetParametersOptimization(value);
+ this->Modified();
+ }
- itkGetMacro(C, float);
- itkSetMacro(C, float);
+ otbGetObjectMemberMacro(SVMestimator, DoProbabilityEstimates, bool);
+ void SetDoProbabilityEstimates(bool value)
+ {
+ this->m_SVMestimator->DoProbabilityEstimates(value);
+ }
- itkGetMacro(ParameterOptimization, bool);
- itkSetMacro(ParameterOptimization, bool);
-
- itkGetMacro(DoProbabilityEstimates, bool);
- itkSetMacro(DoProbabilityEstimates, bool);
+ otbGetObjectMemberMacro(SVMestimator, Epsilon, double);
+ otbSetObjectMemberMacro(SVMestimator, Epsilon, double);
- // itkGetMacro(Epsilon, int);
- // itkSetMacro(Epsilon, int);
+ otbGetObjectMemberMacro(SVMestimator, P, double);
+ otbSetObjectMemberMacro(SVMestimator, P, double);
+
+ otbGetObjectMemberMacro(SVMestimator, Nu, double);
+ otbSetObjectMemberMacro(SVMestimator, Nu, double);
protected:
/** Constructor */
@@ -103,19 +125,10 @@ protected:
/** PrintSelf method */
void PrintSelf(std::ostream& os, itk::Indent indent) const;
- /** Train the machine learning model */
- virtual void TrainClassification();
- /** Predict values using the model */
- virtual TargetSampleType PredictClassification(const InputSampleType& input, ConfidenceValueType *quality=NULL) const;
-
private:
LibSVMMachineLearningModel(const Self &); //purposely not implemented
void operator =(const Self&); //purposely not implemented
- int m_KernelType;
- float m_C;
- bool m_ParameterOptimization;
- bool m_DoProbabilityEstimates;
typename SVMEstimatorType::Pointer m_SVMestimator;
};
} // end namespace otb
diff --git a/Modules/Learning/Supervised/include/otbLibSVMMachineLearningModel.txx b/Modules/Learning/Supervised/include/otbLibSVMMachineLearningModel.txx
index 24e91e54a25406d100a8cae8f4b09741f124e80f..e95e97543d3a67537c848c8933165d5907370400 100644
--- a/Modules/Learning/Supervised/include/otbLibSVMMachineLearningModel.txx
+++ b/Modules/Learning/Supervised/include/otbLibSVMMachineLearningModel.txx
@@ -20,10 +20,6 @@
#include <fstream>
#include "otbLibSVMMachineLearningModel.h"
-//#include "otbOpenCVUtils.h"
-
-// SVM estimator
-//#include "otbSVMSampleListModelEstimator.h"
namespace otb
{
@@ -32,15 +28,14 @@ template <class TInputValue, class TOutputValue>
LibSVMMachineLearningModel<TInputValue,TOutputValue>
::LibSVMMachineLearningModel()
{
- // m_SVMModel = new CvSVM;
- // m_SVMType = CvSVM::C_SVC;
- m_KernelType = LINEAR;
- // m_TermCriteriaType = CV_TERMCRIT_ITER;
- m_C = 1.0;
- // m_Epsilon = 1e-6;
- m_ParameterOptimization = false;
- m_DoProbabilityEstimates = false;
m_SVMestimator = SVMEstimatorType::New();
+ m_SVMestimator->SetSVMType(C_SVC);
+ m_SVMestimator->SetC(1.0);
+ m_SVMestimator->SetKernelType(LINEAR);
+ m_SVMestimator->SetParametersOptimization(false);
+ m_SVMestimator->DoProbabilityEstimates(false);
+ //m_SVMestimator->SetEpsilon(1e-6);
+ this->m_IsRegressionSupported = true;
}
@@ -55,7 +50,7 @@ LibSVMMachineLearningModel<TInputValue,TOutputValue>
template <class TInputValue, class TOutputValue>
void
LibSVMMachineLearningModel<TInputValue,TOutputValue>
-::TrainClassification()
+::Train()
{
// Set up SVM's parameters
// CvSVMParams params;
@@ -64,25 +59,19 @@ LibSVMMachineLearningModel<TInputValue,TOutputValue>
// params.term_crit = cvTermCriteria(m_TermCriteriaType, m_MaxIter, m_Epsilon);
// // Train the SVM
-
- m_SVMestimator->SetC(m_C);
- m_SVMestimator->SetKernelType(m_KernelType);
- m_SVMestimator->SetParametersOptimization(m_ParameterOptimization);
- m_SVMestimator->DoProbabilityEstimates(m_DoProbabilityEstimates);
-
m_SVMestimator->SetInputSampleList(this->GetInputListSample());
m_SVMestimator->SetTrainingSampleList(this->GetTargetListSample());
m_SVMestimator->Update();
- this->m_ConfidenceIndex = m_DoProbabilityEstimates;
+ this->m_ConfidenceIndex = this->GetDoProbabilityEstimates();
}
template <class TInputValue, class TOutputValue>
typename LibSVMMachineLearningModel<TInputValue,TOutputValue>
::TargetSampleType
LibSVMMachineLearningModel<TInputValue,TOutputValue>
-::PredictClassification(const InputSampleType & input, ConfidenceValueType *quality) const
+::Predict(const InputSampleType & input, ConfidenceValueType *quality) const
{
TargetSampleType target;
diff --git a/Modules/Learning/Supervised/include/otbMachineLearningModel.h b/Modules/Learning/Supervised/include/otbMachineLearningModel.h
index ba0ca60d224fa138fe5a9e8e702993555394559b..b18e39e15c89fabff9ff2c640122740e710972f5 100644
--- a/Modules/Learning/Supervised/include/otbMachineLearningModel.h
+++ b/Modules/Learning/Supervised/include/otbMachineLearningModel.h
@@ -97,10 +97,10 @@ public:
//@}
/** Train the machine learning model */
- void Train();
+ virtual void Train() =0;
/** Predict values using the model */
- TargetSampleType Predict(const InputSampleType& input, ConfidenceValueType *quality = NULL) const;
+ virtual TargetSampleType Predict(const InputSampleType& input, ConfidenceValueType *quality = NULL) const = 0;
/** Classify all samples in InputListSample and fill TargetListSample with the associated label */
void PredictAll();
@@ -140,6 +140,12 @@ public:
itkGetObjectMacro(TargetListSample,TargetListSampleType);
//@}
+ /**\name Use model in regression mode */
+ //@{
+ itkGetMacro(RegressionMode,bool);
+ void SetRegressionMode(bool flag);
+ //@}
+
protected:
/** Constructor */
MachineLearningModel();
@@ -156,22 +162,14 @@ protected:
/** Target list sample */
typename TargetListSampleType::Pointer m_TargetListSample;
- /** Train the machine learning model */
- virtual void TrainRegression()
- {
- itkGenericExceptionMacro(<< "Regression mode not implemented.");
- }
- virtual void TrainClassification() = 0;
- /** Predict values using the model */
- virtual TargetSampleType PredictRegression(const InputSampleType& itkNotUsed(input)) const
- {
- itkGenericExceptionMacro(<< "Regression mode not implemented.");
- }
-
- virtual TargetSampleType PredictClassification(const InputSampleType& input, ConfidenceValueType *quality = NULL) const = 0;
-
+ /** flag to choose between classification and regression modes */
bool m_RegressionMode;
+ /** flag that indicates if the model supports regression, child
+ * classes should modify it in their constructor if they support
+ * regression mode */
+ bool m_IsRegressionSupported;
+
/** flag that tells if the model support confidence index output */
bool m_ConfidenceIndex;
private:
diff --git a/Modules/Learning/Supervised/include/otbMachineLearningModel.txx b/Modules/Learning/Supervised/include/otbMachineLearningModel.txx
index b4b6127c11c252c3d5a73d0a50716d48da6e7a49..8cc82055fe1a7a08594a01f3d9aeba6dfc12d927 100644
--- a/Modules/Learning/Supervised/include/otbMachineLearningModel.txx
+++ b/Modules/Learning/Supervised/include/otbMachineLearningModel.txx
@@ -25,7 +25,10 @@ namespace otb
template <class TInputValue, class TOutputValue, class TConfidenceValue>
MachineLearningModel<TInputValue,TOutputValue,TConfidenceValue>
-::MachineLearningModel() : m_RegressionMode(false),m_ConfidenceIndex(false)
+::MachineLearningModel() :
+ m_RegressionMode(false),
+ m_IsRegressionSupported(false),
+ m_ConfidenceIndex(false)
{}
@@ -37,23 +40,17 @@ MachineLearningModel<TInputValue,TOutputValue,TConfidenceValue>
template <class TInputValue, class TOutputValue, class TConfidenceValue>
void
MachineLearningModel<TInputValue,TOutputValue,TConfidenceValue>
-::Train()
+::SetRegressionMode(bool flag)
{
- if(m_RegressionMode)
- return this->TrainRegression();
- else
- return this->TrainClassification();
-}
-
-template <class TInputValue, class TOutputValue, class TConfidenceValue>
-typename MachineLearningModel<TInputValue,TOutputValue,TConfidenceValue>::TargetSampleType
-MachineLearningModel<TInputValue,TOutputValue,TConfidenceValue>
-::Predict(const InputSampleType& input, ConfidenceValueType *quality) const
-{
- if(m_RegressionMode)
- return this->PredictRegression(input);
- else
- return this->PredictClassification(input,quality);
+ if (flag && !m_IsRegressionSupported)
+ {
+ itkGenericExceptionMacro(<< "Regression mode not implemented.");
+ }
+ if (m_RegressionMode != flag)
+ {
+ m_RegressionMode = flag;
+ this->Modified();
+ }
}
template <class TInputValue, class TOutputValue, class TConfidenceValue>
diff --git a/Modules/Learning/Supervised/include/otbNeuralNetworkMachineLearningModel.h b/Modules/Learning/Supervised/include/otbNeuralNetworkMachineLearningModel.h
index 2eab72042d9ff5b3228df2d628ee0618127b01f4..fa1abade18cce80abb493406fabbcebbe97c9ddc 100644
--- a/Modules/Learning/Supervised/include/otbNeuralNetworkMachineLearningModel.h
+++ b/Modules/Learning/Supervised/include/otbNeuralNetworkMachineLearningModel.h
@@ -151,6 +151,11 @@ public:
itkGetMacro(Epsilon, double);
itkSetMacro(Epsilon, double);
+ /** Train the machine learning model */
+ virtual void Train();
+ /** Predict values using the model */
+ virtual TargetSampleType Predict(const InputSampleType& input, ConfidenceValueType *quality=NULL) const;
+
/** Save the model to file */
virtual void Save(const std::string & filename, const std::string & name="");
@@ -178,15 +183,14 @@ protected:
/** PrintSelf method */
void PrintSelf(std::ostream& os, itk::Indent indent) const;
- /** Train the machine learning model */
- virtual void TrainClassification();
- /** Predict values using the model */
- virtual TargetSampleType PredictClassification(const InputSampleType& input, ConfidenceValueType *quality=NULL) const;
-
private:
NeuralNetworkMachineLearningModel(const Self &); //purposely not implemented
void operator =(const Self&); //purposely not implemented
+ void CreateNetwork();
+ CvANN_MLP_TrainParams SetNetworkParameters();
+ void SetupNetworkAndTrain(cv::Mat& labels);
+
CvANN_MLP * m_ANNModel;
int m_TrainMethod;
int m_ActivateFunction;
diff --git a/Modules/Learning/Supervised/include/otbNeuralNetworkMachineLearningModel.txx b/Modules/Learning/Supervised/include/otbNeuralNetworkMachineLearningModel.txx
index 01c31811d7c793630dfcfe5f0026cc6b7be73356..b76e6dd70d3f57741ac83ef9ce448362d9e942fc 100644
--- a/Modules/Learning/Supervised/include/otbNeuralNetworkMachineLearningModel.txx
+++ b/Modules/Learning/Supervised/include/otbNeuralNetworkMachineLearningModel.txx
@@ -43,6 +43,7 @@ NeuralNetworkMachineLearningModel<TInputValue, TOutputValue>::NeuralNetworkMachi
m_CvMatOfLabels(0)
{
this->m_ConfidenceIndex = true;
+ this->m_IsRegressionSupported = true;
}
template<class TInputValue, class TOutputValue>
@@ -52,7 +53,7 @@ NeuralNetworkMachineLearningModel<TInputValue, TOutputValue>::~NeuralNetworkMach
cvReleaseMat(&m_CvMatOfLabels);
}
-/** Train the machine learning model */
+/** Sets the topology of the NN */
template<class TInputValue, class TOutputValue>
void NeuralNetworkMachineLearningModel<TInputValue, TOutputValue>::SetLayerSizes(const std::vector<unsigned int> layers)
{
@@ -72,10 +73,14 @@ template<class TInputValue, class TOutputValue>
void NeuralNetworkMachineLearningModel<TInputValue, TOutputValue>::LabelsToMat(const TargetListSampleType * labels,
cv::Mat & output)
{
- unsigned int nbSamples = labels->Size();
+ unsigned int nbSamples = 0;
+ if (labels != NULL)
+ {
+ nbSamples = labels->Size();
+ }
// Check for valid listSample
- if (labels != NULL && nbSamples > 0)
+ if (nbSamples > 0)
{
// Build an iterator
typename TargetListSampleType::ConstIterator labelSampleIt = labels->Begin();
@@ -130,9 +135,8 @@ void NeuralNetworkMachineLearningModel<TInputValue, TOutputValue>::LabelsToMat(c
}
}
-/** Train the machine learning model */
template<class TInputValue, class TOutputValue>
-void NeuralNetworkMachineLearningModel<TInputValue, TOutputValue>::TrainClassification()
+void NeuralNetworkMachineLearningModel<TInputValue, TOutputValue>::CreateNetwork()
{
//Create the neural network
const unsigned int nbLayers = m_LayerSizes.size();
@@ -147,14 +151,11 @@ void NeuralNetworkMachineLearningModel<TInputValue, TOutputValue>::TrainClassifi
}
m_ANNModel->create(layers, m_ActivateFunction, m_Alpha, m_Beta);
+}
- //convert listsample to opencv matrix
- cv::Mat samples;
- otb::ListSampleToMat<InputListSampleType>(this->GetInputListSample(), samples);
-
- cv::Mat matOutputANN;
- LabelsToMat(this->GetTargetListSample(), matOutputANN);
-
+template<class TInputValue, class TOutputValue>
+CvANN_MLP_TrainParams NeuralNetworkMachineLearningModel<TInputValue, TOutputValue>::SetNetworkParameters()
+{
CvANN_MLP_TrainParams params;
params.train_method = m_TrainMethod;
params.bp_dw_scale = m_BackPropDWScale;
@@ -163,14 +164,43 @@ void NeuralNetworkMachineLearningModel<TInputValue, TOutputValue>::TrainClassifi
params.rp_dw_min = m_RegPropDWMin;
CvTermCriteria term_crit = cvTermCriteria(m_TermCriteriaType, m_MaxIter, m_Epsilon);
params.term_crit = term_crit;
+ return params;
+}
+template<class TInputValue, class TOutputValue>
+void NeuralNetworkMachineLearningModel<TInputValue, TOutputValue>::SetupNetworkAndTrain(cv::Mat& labels)
+{
+ //convert listsample to opencv matrix
+ cv::Mat samples;
+ otb::ListSampleToMat<InputListSampleType>(this->GetInputListSample(), samples);
+ this->CreateNetwork();
+ CvANN_MLP_TrainParams params = this->SetNetworkParameters();
//train the Neural network model
- m_ANNModel->train(samples, matOutputANN, cv::Mat(), cv::Mat(), params);
+ m_ANNModel->train(samples, labels, cv::Mat(), cv::Mat(), params);
+}
+
+/** Train the machine learning model for classification*/
+template<class TInputValue, class TOutputValue>
+void NeuralNetworkMachineLearningModel<TInputValue, TOutputValue>::Train()
+{
+ //Transform the targets into a matrix of labels
+ cv::Mat matOutputANN;
+ if (this->m_RegressionMode)
+ {
+ // MODE REGRESSION
+ otb::ListSampleToMat<TargetListSampleType>(this->GetTargetListSample(), matOutputANN);
+ }
+ else
+ {
+ // MODE CLASSIFICATION : store the map between internal labels and output labels
+ LabelsToMat(this->GetTargetListSample(), matOutputANN);
+ }
+ this->SetupNetworkAndTrain(matOutputANN);
}
template<class TInputValue, class TOutputValue>
typename NeuralNetworkMachineLearningModel<TInputValue, TOutputValue>::TargetSampleType NeuralNetworkMachineLearningModel<
- TInputValue, TOutputValue>::PredictClassification(const InputSampleType & input, ConfidenceValueType *quality) const
+ TInputValue, TOutputValue>::Predict(const InputSampleType & input, ConfidenceValueType *quality) const
{
//convert listsample to Mat
cv::Mat sample;
@@ -183,6 +213,15 @@ typename NeuralNetworkMachineLearningModel<TInputValue, TOutputValue>::TargetSam
TargetSampleType target;
float currentResponse = 0;
float maxResponse = response.at<float> (0, 0);
+
+ if (this->m_RegressionMode)
+ {
+ // MODE REGRESSION : only output first response
+ target[0] = maxResponse;
+ return target;
+ }
+
+ // MODE CLASSIFICATION : find the highest response
float secondResponse = -1e10;
target[0] = m_CvMatOfLabels->data.i[0];
diff --git a/Modules/Learning/Supervised/include/otbNormalBayesMachineLearningModel.h b/Modules/Learning/Supervised/include/otbNormalBayesMachineLearningModel.h
index 31b5373ce16510512aa90065e151408a764898ed..8ecfcd2b51d607169b30dcc86dd59d2096d728f4 100644
--- a/Modules/Learning/Supervised/include/otbNormalBayesMachineLearningModel.h
+++ b/Modules/Learning/Supervised/include/otbNormalBayesMachineLearningModel.h
@@ -52,6 +52,11 @@ public:
itkNewMacro(Self);
itkTypeMacro(NormalBayesMachineLearningModel, MachineLearningModel);
+ /** Train the machine learning model */
+ virtual void Train();
+ /** Predict values using the model */
+ virtual TargetSampleType Predict(const InputSampleType& input, ConfidenceValueType *quality=NULL) const;
+
/** Save the model to file */
virtual void Save(const std::string & filename, const std::string & name="");
@@ -77,11 +82,6 @@ protected:
/** PrintSelf method */
void PrintSelf(std::ostream& os, itk::Indent indent) const;
- /** Train the machine learning model */
- virtual void TrainClassification();
- /** Predict values using the model */
- virtual TargetSampleType PredictClassification(const InputSampleType& input, ConfidenceValueType *quality=NULL) const;
-
private:
NormalBayesMachineLearningModel(const Self &); //purposely not implemented
void operator =(const Self&); //purposely not implemented
diff --git a/Modules/Learning/Supervised/include/otbNormalBayesMachineLearningModel.txx b/Modules/Learning/Supervised/include/otbNormalBayesMachineLearningModel.txx
index bfc163553ddb58eb7e3e9f2150fc9cb63dbfaca2..7538f02c8818fcd07851f26044724992d4747af5 100644
--- a/Modules/Learning/Supervised/include/otbNormalBayesMachineLearningModel.txx
+++ b/Modules/Learning/Supervised/include/otbNormalBayesMachineLearningModel.txx
@@ -45,7 +45,7 @@ NormalBayesMachineLearningModel<TInputValue,TOutputValue>
template <class TInputValue, class TOutputValue>
void
NormalBayesMachineLearningModel<TInputValue,TOutputValue>
-::TrainClassification()
+::Train()
{
//convert listsample to opencv matrix
cv::Mat samples;
@@ -61,7 +61,7 @@ template <class TInputValue, class TOutputValue>
typename NormalBayesMachineLearningModel<TInputValue,TOutputValue>
::TargetSampleType
NormalBayesMachineLearningModel<TInputValue,TOutputValue>
-::PredictClassification(const InputSampleType & input, ConfidenceValueType *quality) const
+::Predict(const InputSampleType & input, ConfidenceValueType *quality) const
{
//convert listsample to Mat
cv::Mat sample;
diff --git a/Modules/Learning/Supervised/include/otbRandomForestsMachineLearningModel.h b/Modules/Learning/Supervised/include/otbRandomForestsMachineLearningModel.h
index 20aff52a7e200f47f9127005addc442d25fd5799..ec62b761358634daa8e268c1488770bb801d3543 100644
--- a/Modules/Learning/Supervised/include/otbRandomForestsMachineLearningModel.h
+++ b/Modules/Learning/Supervised/include/otbRandomForestsMachineLearningModel.h
@@ -59,6 +59,11 @@ public:
itkNewMacro(Self);
itkTypeMacro(RandomForestsMachineLearningModel, MachineLearningModel);
+ /** Train the machine learning model */
+ virtual void Train();
+ /** Predict values using the model */
+ virtual TargetSampleType Predict(const InputSampleType& input, ConfidenceValueType *quality=NULL) const;
+
/** Save the model to file */
virtual void Save(const std::string & filename, const std::string & name="");
@@ -115,9 +120,6 @@ public:
itkGetMacro(TerminationCriteria, int);
itkSetMacro(TerminationCriteria, int);
- itkGetMacro(RegressionMode, bool);
- itkSetMacro(RegressionMode, bool);
-
/** Returns a matrix containing variable importance */
VariableImportanceMatrixType GetVariableImportance();
@@ -139,11 +141,6 @@ protected:
/* /\** Target list sample *\/ */
/* typename TargetListSampleType::Pointer m_TargetListSample; */
- /** Train the machine learning model */
- virtual void TrainClassification();
- /** Predict values using the model */
- virtual TargetSampleType PredictClassification(const InputSampleType& input, ConfidenceValueType *quality=NULL) const;
-
private:
RandomForestsMachineLearningModel(const Self &); //purposely not implemented
void operator =(const Self&); //purposely not implemented
@@ -208,8 +205,6 @@ private:
float m_ForestAccuracy;
/** The type of the termination criteria */
int m_TerminationCriteria;
- /** Perform regression instead of classification */
- bool m_RegressionMode;
};
} // end namespace otb
diff --git a/Modules/Learning/Supervised/include/otbRandomForestsMachineLearningModel.txx b/Modules/Learning/Supervised/include/otbRandomForestsMachineLearningModel.txx
index 0797c2fabf18077612470b70604d8a3492a64446..78642f1212ac9d75dc75d3bd9e9482d73bc948dc 100644
--- a/Modules/Learning/Supervised/include/otbRandomForestsMachineLearningModel.txx
+++ b/Modules/Learning/Supervised/include/otbRandomForestsMachineLearningModel.txx
@@ -32,17 +32,17 @@ RandomForestsMachineLearningModel<TInputValue,TOutputValue>
m_RFModel (new CvRTrees),
m_MaxDepth(5),
m_MinSampleCount(10),
- m_RegressionAccuracy(0),
+ m_RegressionAccuracy(0.01),
m_ComputeSurrogateSplit(false),
m_MaxNumberOfCategories(10),
m_CalculateVariableImportance(false),
m_MaxNumberOfVariables(0),
m_MaxNumberOfTrees(100),
m_ForestAccuracy(0.01),
- m_TerminationCriteria(CV_TERMCRIT_ITER | CV_TERMCRIT_EPS),
- m_RegressionMode(false)
+ m_TerminationCriteria(CV_TERMCRIT_ITER | CV_TERMCRIT_EPS)
{
this->m_ConfidenceIndex = true;
+ this->m_IsRegressionSupported = true;
}
@@ -65,7 +65,7 @@ RandomForestsMachineLearningModel<TInputValue,TOutputValue>
template <class TInputValue, class TOutputValue>
void
RandomForestsMachineLearningModel<TInputValue,TOutputValue>
-::TrainClassification()
+::Train()
{
//convert listsample to opencv matrix
cv::Mat samples;
@@ -96,7 +96,7 @@ RandomForestsMachineLearningModel<TInputValue,TOutputValue>
cv::Mat var_type = cv::Mat(this->GetInputListSample()->GetMeasurementVectorSize() + 1, 1, CV_8U );
var_type.setTo(cv::Scalar(CV_VAR_NUMERICAL) ); // all inputs are numerical
- if(m_RegressionMode)
+ if(this->m_RegressionMode)
var_type.at<uchar>(this->GetInputListSample()->GetMeasurementVectorSize(), 0) = CV_VAR_NUMERICAL;
else
var_type.at<uchar>(this->GetInputListSample()->GetMeasurementVectorSize(), 0) = CV_VAR_CATEGORICAL;
@@ -110,7 +110,7 @@ template <class TInputValue, class TOutputValue>
typename RandomForestsMachineLearningModel<TInputValue,TOutputValue>
::TargetSampleType
RandomForestsMachineLearningModel<TInputValue,TOutputValue>
-::PredictClassification(const InputSampleType & value, ConfidenceValueType *quality) const
+::Predict(const InputSampleType & value, ConfidenceValueType *quality) const
{
//convert listsample to Mat
cv::Mat sample;
diff --git a/Modules/Learning/Supervised/include/otbSVMMachineLearningModel.h b/Modules/Learning/Supervised/include/otbSVMMachineLearningModel.h
index 406bdd10e6b04a808fbd2be168e0f7504aa79578..569ab321427925e1e662d941d2be1a398fda54cc 100644
--- a/Modules/Learning/Supervised/include/otbSVMMachineLearningModel.h
+++ b/Modules/Learning/Supervised/include/otbSVMMachineLearningModel.h
@@ -51,6 +51,11 @@ public:
itkNewMacro(Self);
itkTypeMacro(SVMMachineLearningModel, MachineLearningModel);
+ /** Train the machine learning model */
+ virtual void Train();
+ /** Predict values using the model */
+ virtual TargetSampleType Predict(const InputSampleType& input, ConfidenceValueType *quality=NULL) const;
+
/** Save the model to file */
virtual void Save(const std::string & filename, const std::string & name="");
@@ -126,11 +131,6 @@ protected:
/** PrintSelf method */
void PrintSelf(std::ostream& os, itk::Indent indent) const;
- /** Train the machine learning model */
- virtual void TrainClassification();
- /** Predict values using the model */
- virtual TargetSampleType PredictClassification(const InputSampleType& input, ConfidenceValueType *quality=NULL) const;
-
private:
SVMMachineLearningModel(const Self &); //purposely not implemented
void operator =(const Self&); //purposely not implemented
diff --git a/Modules/Learning/Supervised/include/otbSVMMachineLearningModel.txx b/Modules/Learning/Supervised/include/otbSVMMachineLearningModel.txx
index 064db060d1670146d4b618d94fa529017475758e..9d0b7d685948ebf67b070c6a16fcc9e6f760ea34 100644
--- a/Modules/Learning/Supervised/include/otbSVMMachineLearningModel.txx
+++ b/Modules/Learning/Supervised/include/otbSVMMachineLearningModel.txx
@@ -50,6 +50,7 @@ SVMMachineLearningModel<TInputValue,TOutputValue>
m_OutputP(0)
{
this->m_ConfidenceIndex = true;
+ this->m_IsRegressionSupported = true;
}
@@ -64,8 +65,16 @@ SVMMachineLearningModel<TInputValue,TOutputValue>
template <class TInputValue, class TOutputValue>
void
SVMMachineLearningModel<TInputValue,TOutputValue>
-::TrainClassification()
+::Train()
{
+ // Check that the SVM type is compatible with the chosen mode (classif/regression)
+ if ( bool(m_SVMType == CvSVM::NU_SVR || m_SVMType == CvSVM::EPS_SVR) != this->m_RegressionMode)
+ {
+ itkGenericExceptionMacro("SVM type incompatible with chosen mode (classification or regression."
+ "SVM types for classification are C_SVC, NU_SVC, ONE_CLASS. "
+ "SVM types for regression are NU_SVR, EPS_SVR");
+ }
+
//convert listsample to opencv matrix
cv::Mat samples;
otb::ListSampleToMat<InputListSampleType>(this->GetInputListSample(), samples);
@@ -109,7 +118,7 @@ template <class TInputValue, class TOutputValue>
typename SVMMachineLearningModel<TInputValue,TOutputValue>
::TargetSampleType
SVMMachineLearningModel<TInputValue,TOutputValue>
-::PredictClassification(const InputSampleType & input, ConfidenceValueType *quality) const
+::Predict(const InputSampleType & input, ConfidenceValueType *quality) const
{
//convert listsample to Mat
cv::Mat sample;
@@ -135,10 +144,10 @@ void
SVMMachineLearningModel<TInputValue,TOutputValue>
::Save(const std::string & filename, const std::string & name)
{
- if (name == "")
- m_SVMModel->save(filename.c_str(), 0);
- else
- m_SVMModel->save(filename.c_str(), name.c_str());
+ if (name == "")
+ m_SVMModel->save(filename.c_str(), 0);
+ else
+ m_SVMModel->save(filename.c_str(), name.c_str());
}
template <class TInputValue, class TOutputValue>
@@ -147,9 +156,9 @@ SVMMachineLearningModel<TInputValue,TOutputValue>
::Load(const std::string & filename, const std::string & name)
{
if (name == "")
- m_SVMModel->load(filename.c_str(), 0);
+ m_SVMModel->load(filename.c_str(), 0);
else
- m_SVMModel->load(filename.c_str(), name.c_str());
+ m_SVMModel->load(filename.c_str(), name.c_str());
}
template <class TInputValue, class TOutputValue>
@@ -157,29 +166,29 @@ bool
SVMMachineLearningModel<TInputValue,TOutputValue>
::CanReadFile(const std::string & file)
{
- std::ifstream ifs;
- ifs.open(file.c_str());
-
- if(!ifs)
- {
- std::cerr<<"Could not read file "<<file<<std::endl;
- return false;
- }
-
- while (!ifs.eof())
- {
- std::string line;
- std::getline(ifs, line);
-
- //if (line.find(m_SVMModel->getName()) != std::string::npos)
- if (line.find(CV_TYPE_NAME_ML_SVM) != std::string::npos)
+ std::ifstream ifs;
+ ifs.open(file.c_str());
+
+ if(!ifs)
+ {
+ std::cerr<<"Could not read file "<<file<<std::endl;
+ return false;
+ }
+
+ while (!ifs.eof())
+ {
+ std::string line;
+ std::getline(ifs, line);
+
+ //if (line.find(m_SVMModel->getName()) != std::string::npos)
+ if (line.find(CV_TYPE_NAME_ML_SVM) != std::string::npos)
{
- //std::cout<<"Reading a "<<CV_TYPE_NAME_ML_SVM<<" model"<<std::endl;
- return true;
+ //std::cout<<"Reading a "<<CV_TYPE_NAME_ML_SVM<<" model"<<std::endl;
+ return true;
}
- }
- ifs.close();
- return false;
+ }
+ ifs.close();
+ return false;
}
template <class TInputValue, class TOutputValue>
diff --git a/Modules/Learning/Supervised/test/CMakeLists.txt b/Modules/Learning/Supervised/test/CMakeLists.txt
index 7ffe8757b490c64081ffb6fe424a582d382d4df5..abca168f4f7794ea1a9133370c65555593b9bf19 100644
--- a/Modules/Learning/Supervised/test/CMakeLists.txt
+++ b/Modules/Learning/Supervised/test/CMakeLists.txt
@@ -7,6 +7,7 @@ otbConfusionMatrixMeasurementsTest.cxx
otbMachineLearningModelCanRead.cxx
otbTrainMachineLearningModel.cxx
otbImageClassificationFilter.cxx
+otbMachineLearningRegressionTests.cxx
)
add_executable(otbSupervisedTestDriver ${OTBSupervisedTests})
diff --git a/Modules/Learning/Supervised/test/otbMachineLearningRegressionTests.cxx b/Modules/Learning/Supervised/test/otbMachineLearningRegressionTests.cxx
new file mode 100644
index 0000000000000000000000000000000000000000..f54a9a96adc5a60f18f2a2411ff0e078ad5aba6d
--- /dev/null
+++ b/Modules/Learning/Supervised/test/otbMachineLearningRegressionTests.cxx
@@ -0,0 +1,669 @@
+/*=========================================================================
+
+ 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.
+
+ =========================================================================*/
+
+#include "otbConfigure.h"
+
+#include "itkMersenneTwisterRandomVariateGenerator.h"
+
+#ifdef OTB_USE_OPENCV
+#include "otbNeuralNetworkMachineLearningModel.h"
+#include "otbSVMMachineLearningModel.h"
+#include "otbBoostMachineLearningModel.h"
+#include "otbDecisionTreeMachineLearningModel.h"
+#include "otbGradientBoostedTreeMachineLearningModel.h"
+#include "otbKNearestNeighborsMachineLearningModel.h"
+#include "otbRandomForestsMachineLearningModel.h"
+#endif
+
+#ifdef OTB_USE_LIBSVM
+#include "otbLibSVMMachineLearningModel.h"
+#endif
+
+typedef float PrecisionType;
+typedef otb::MachineLearningModel<PrecisionType,PrecisionType> MachineLearningModelRegressionType;
+typedef MachineLearningModelRegressionType::InputValueType InputValueRegressionType;
+typedef MachineLearningModelRegressionType::InputSampleType InputSampleRegressionType;
+typedef MachineLearningModelRegressionType::InputListSampleType InputListSampleRegressionType;
+typedef MachineLearningModelRegressionType::TargetValueType TargetValueRegressionType;
+typedef MachineLearningModelRegressionType::TargetSampleType TargetSampleRegressionType;
+typedef MachineLearningModelRegressionType::TargetListSampleType TargetListSampleRegressionType;
+typedef itk::Statistics::MersenneTwisterRandomVariateGenerator RandomGeneratorType;
+
+const double epsilon = 0.1;
+
+typedef struct RegressionTestParamStruct
+{
+ double vMin;
+ double vMax;
+ size_t count;
+ double eps;
+} RegressionTestParam;
+
+template <typename TPrecision>
+struct LinearFunctionSampleGenerator
+{
+ typedef TPrecision PrecisionType;
+ LinearFunctionSampleGenerator(TPrecision a, TPrecision b)
+ : m_a(a), m_b(b), m_NbInputVars(1), m_NbOutputVars(1) {
+ m_isl = InputListSampleRegressionType::New();
+ m_tsl = TargetListSampleRegressionType::New();
+ };
+ void GenerateSamples(TPrecision sMin, TPrecision sMax, size_t nbSamples)
+ {
+ m_isl->Clear();
+ m_tsl->Clear();
+ m_isl->SetMeasurementVectorSize(m_NbInputVars);
+ m_tsl->SetMeasurementVectorSize(m_NbOutputVars);
+
+ RandomGeneratorType::Pointer randomGenerator = RandomGeneratorType::GetInstance();
+ InputSampleRegressionType inputSample;
+ inputSample.SetSize(m_NbInputVars);
+ TargetSampleRegressionType outputSample;
+
+ TPrecision sampleStep = (sMax-sMin)/nbSamples;
+ for(size_t i=0; i<nbSamples; ++i)
+ {
+ TPrecision x = randomGenerator->GetUniformVariate(0.0, 1.0) * static_cast<TPrecision>(nbSamples);
+ TPrecision inputValue = sMin+ x*sampleStep;
+ inputSample[0] = inputValue;
+ outputSample[0] = m_a*inputValue+m_b;
+ m_isl->PushBack(inputSample);
+ m_tsl->PushBack(outputSample);
+ }
+ }
+
+ TPrecision m_a;
+ TPrecision m_b;
+ const size_t m_NbInputVars;
+ const size_t m_NbOutputVars;
+ InputListSampleRegressionType::Pointer m_isl;
+ TargetListSampleRegressionType::Pointer m_tsl;
+};
+
+template <typename TPrecision>
+struct BilinearFunctionSampleGenerator
+{
+ typedef TPrecision PrecisionType;
+ BilinearFunctionSampleGenerator(TPrecision a, TPrecision b, TPrecision c)
+ : m_a(a), m_b(b), m_c(c), m_NbInputVars(2), m_NbOutputVars(1) {
+ m_isl = InputListSampleRegressionType::New();
+ m_tsl = TargetListSampleRegressionType::New();
+ };
+ void GenerateSamples(TPrecision sMin, TPrecision sMax, size_t nbSamples)
+ {
+ m_isl->Clear();
+ m_tsl->Clear();
+ m_isl->SetMeasurementVectorSize(m_NbInputVars);
+ m_tsl->SetMeasurementVectorSize(m_NbOutputVars);
+
+ RandomGeneratorType::Pointer randomGenerator = RandomGeneratorType::GetInstance();
+ InputSampleRegressionType inputSample;
+ inputSample.SetSize(m_NbInputVars);
+ TargetSampleRegressionType outputSample;
+
+ TPrecision sampleStep = (sMax-sMin)/nbSamples;
+ for(size_t i=0; i<nbSamples; ++i)
+ {
+ TPrecision x = randomGenerator->GetUniformVariate(0.0, 1.0) * static_cast<TPrecision>(nbSamples);
+ TPrecision inputValue1 = sMin+ x*sampleStep;
+ x = randomGenerator->GetUniformVariate(0.0, 1.0) * static_cast<TPrecision>(nbSamples);
+ TPrecision inputValue2 = sMin+ x*sampleStep;
+ inputSample[0] = inputValue1;
+ inputSample[1] = inputValue2;
+ outputSample[0] = m_a*inputValue1+m_b*inputValue2+m_c;
+ m_isl->PushBack(inputSample);
+ m_tsl->PushBack(outputSample);
+ }
+ }
+
+ TPrecision m_a;
+ TPrecision m_b;
+ TPrecision m_c;
+ const size_t m_NbInputVars;
+ const size_t m_NbOutputVars;
+ InputListSampleRegressionType::Pointer m_isl;
+ TargetListSampleRegressionType::Pointer m_tsl;
+};
+
+template <typename TPrecision>
+struct PolynomialFunctionSampleGenerator
+{
+ typedef TPrecision PrecisionType;
+ PolynomialFunctionSampleGenerator(std::vector<TPrecision> c)
+ : m_c(c), m_NbInputVars(1), m_NbOutputVars(1) {
+ m_isl = InputListSampleRegressionType::New();
+ m_tsl = TargetListSampleRegressionType::New();
+ };
+ void GenerateSamples(TPrecision sMin, TPrecision sMax, size_t nbSamples)
+ {
+ m_isl->Clear();
+ m_tsl->Clear();
+ m_isl->SetMeasurementVectorSize(m_NbInputVars);
+ m_tsl->SetMeasurementVectorSize(m_NbOutputVars);
+
+ RandomGeneratorType::Pointer randomGenerator = RandomGeneratorType::GetInstance();
+ InputSampleRegressionType inputSample;
+ inputSample.SetSize(m_NbInputVars);
+ TargetSampleRegressionType outputSample;
+
+ TPrecision sampleStep = (sMax-sMin)/nbSamples;
+ for(size_t i=0; i<nbSamples; ++i)
+ {
+ TPrecision x = randomGenerator->GetUniformVariate(0.0, 1.0) * static_cast<TPrecision>(nbSamples);
+ TPrecision inputValue = sMin+ x*sampleStep;
+ inputSample[0] = inputValue;
+ TPrecision y = 0.0;
+ for (unsigned int j=0; j<m_c.size() ; ++j)
+ {
+ y += m_c[j] * pow(static_cast<double>(inputValue), static_cast<double>(j));
+ }
+ outputSample[0] = y;
+ m_isl->PushBack(inputSample);
+ m_tsl->PushBack(outputSample);
+ }
+ }
+
+ std::vector<TPrecision> m_c;
+ const size_t m_NbInputVars;
+ const size_t m_NbOutputVars;
+ InputListSampleRegressionType::Pointer m_isl;
+ TargetListSampleRegressionType::Pointer m_tsl;
+};
+
+template <typename SampleGeneratorType, typename RegressionType>
+int testRegression(SampleGeneratorType& sg, RegressionType& rgrsn, RegressionTestParam param)
+{
+ std::cout << "Generating training samples" << std::endl;
+ sg.GenerateSamples(param.vMin, param.vMax, param.count);
+
+ rgrsn->SetInputListSample(sg.m_isl);
+ rgrsn->SetTargetListSample(sg.m_tsl);
+ std::cout << "Training" << std::endl;
+ rgrsn->Train();
+
+ std::cout << "Generate validation samples"<<std::endl;
+ sg.GenerateSamples(param.vMin, param.vMax, param.count);
+
+ std::cout << "Validation" << std::endl;
+ //Check the prediction accuracy
+ typename InputListSampleRegressionType::Iterator sampleIt = sg.m_isl->Begin();
+ typename TargetListSampleRegressionType::Iterator resultIt = sg.m_tsl->Begin();
+ typename InputListSampleRegressionType::Iterator sampleLast = sg.m_isl->End();
+ typename TargetListSampleRegressionType::Iterator resultLast = sg.m_tsl->End();
+ typename SampleGeneratorType::PrecisionType rmse = 0.0;
+ while(sampleIt != sampleLast && resultIt != resultLast)
+ {
+ //typename SampleGeneratorType::PrecisionType invalue = sampleIt.GetMeasurementVector()[0];
+ typename SampleGeneratorType::PrecisionType prediction = rgrsn->Predict(sampleIt.GetMeasurementVector())[0];
+ typename SampleGeneratorType::PrecisionType expected = resultIt.GetMeasurementVector()[0];
+ rmse += std::pow(prediction - expected, static_cast<PrecisionType>(2.0));
+ ++sampleIt;
+ ++resultIt;
+ }
+
+ rmse = sqrt( rmse / static_cast<double>(param.count) );
+ std::cout << "RMSE = "<< rmse << std::endl;
+ if(rmse > param.eps)
+ {
+ std::cout << "Failed : RMSE above expected precision !" << std::endl;
+ return EXIT_FAILURE;
+ }
+
+ return EXIT_SUCCESS;
+}
+
+#ifdef OTB_USE_LIBSVM
+MachineLearningModelRegressionType::Pointer getLibSVMRegressionModel()
+{
+ typedef otb::LibSVMMachineLearningModel<InputValueRegressionType,
+ TargetValueRegressionType>
+ libsvmType;
+ libsvmType::Pointer regression = libsvmType::New();
+ regression->SetRegressionMode(true);
+ regression->SetSVMType(EPSILON_SVR);
+ regression->SetKernelType(RBF);
+ regression->SetEpsilon(1e-5);
+ regression->SetParameterOptimization(true);
+ return regression.GetPointer();
+}
+
+int otbLibSVMRegressionTests(int itkNotUsed(argc),
+ char * itkNotUsed(argv) [])
+{
+ int status = EXIT_SUCCESS;
+ int ret;
+ MachineLearningModelRegressionType::Pointer regression;
+
+ RegressionTestParam param;
+ param.vMin = -0.5;
+ param.vMax = 0.5;
+ param.count = 200;
+ param.eps = 0.1;
+
+ std::cout << "Testing regression on a linear monovariate function" << std::endl;
+ LinearFunctionSampleGenerator<PrecisionType> lfsg(2.0, 1.0);
+ regression = getLibSVMRegressionModel();
+ ret = testRegression(lfsg,regression,param);
+ if (ret == EXIT_FAILURE)
+ {
+ status = EXIT_FAILURE;
+ }
+ std::cout << "Testing regression on a bilinear function" << std::endl;
+ BilinearFunctionSampleGenerator<PrecisionType> bfsg(2.0,-1.0,1.0);
+ regression = getLibSVMRegressionModel();
+ ret = testRegression(bfsg,regression,param);
+ if (ret == EXIT_FAILURE)
+ {
+ status = EXIT_FAILURE;
+ }
+ std::cout << "Testing regression on a polynomial function" << std::endl;
+ std::vector<PrecisionType> coeffs;
+ coeffs.push_back(0.0);
+ coeffs.push_back(-1.0);
+ coeffs.push_back(0.0);
+ coeffs.push_back(4.0);
+ PolynomialFunctionSampleGenerator<PrecisionType> pfsg(coeffs);
+ regression = getLibSVMRegressionModel();
+ ret = testRegression(pfsg,regression,param);
+ if (ret == EXIT_FAILURE)
+ {
+ status = EXIT_FAILURE;
+ }
+ return status;
+}
+
+#endif
+
+#ifdef OTB_USE_OPENCV
+MachineLearningModelRegressionType::Pointer getNeuralNetworkRegressionModel(unsigned int nbInputVar)
+{
+ typedef otb::NeuralNetworkMachineLearningModel<InputValueRegressionType,
+ TargetValueRegressionType>
+ NeuralNetworkType;
+ NeuralNetworkType::Pointer regression = NeuralNetworkType::New();
+
+ regression->SetRegressionMode(1);
+ regression->SetTrainMethod(CvANN_MLP_TrainParams::BACKPROP);
+ std::vector<unsigned int> layerSizes;
+ layerSizes.push_back(nbInputVar);
+ layerSizes.push_back(5);
+ layerSizes.push_back(1);
+ regression->SetLayerSizes(layerSizes);
+ regression->SetActivateFunction(CvANN_MLP::SIGMOID_SYM);
+ regression->SetAlpha(1.0);
+ regression->SetBeta(1.0);
+ regression->SetBackPropDWScale(0.1);
+ regression->SetBackPropMomentScale(0.1);
+ regression->SetRegPropDW0(0.1);
+ regression->SetRegPropDWMin(1e-7);
+ regression->SetTermCriteriaType(CV_TERMCRIT_EPS);
+ regression->SetEpsilon(1e-5);
+ regression->SetMaxIter(1e4);
+ return regression.GetPointer();
+}
+
+int otbNeuralNetworkRegressionTests(int itkNotUsed(argc),
+ char * itkNotUsed(argv) [])
+{
+ int status = EXIT_SUCCESS;
+ int ret;
+ MachineLearningModelRegressionType::Pointer regression;
+
+ RegressionTestParam param;
+ param.vMin = -0.5;
+ param.vMax = 0.5;
+ param.count = 20000;
+ param.eps = 0.1;
+
+ std::cout << "Testing regression on a linear monovariate function" << std::endl;
+ LinearFunctionSampleGenerator<PrecisionType> lfsg(2.0, 1.0);
+ regression = getNeuralNetworkRegressionModel(1);
+ ret = testRegression(lfsg,regression,param);
+ if (ret == EXIT_FAILURE)
+ {
+ status = EXIT_FAILURE;
+ }
+ std::cout << "Testing regression on a bilinear function" << std::endl;
+ BilinearFunctionSampleGenerator<PrecisionType> bfsg(2.0,-1.0,1.0);
+ regression = getNeuralNetworkRegressionModel(2);
+ ret = testRegression(bfsg,regression,param);
+ if (ret == EXIT_FAILURE)
+ {
+ status = EXIT_FAILURE;
+ }
+ std::cout << "Testing regression on a polynomial function" << std::endl;
+ std::vector<PrecisionType> coeffs;
+ coeffs.push_back(0.0);
+ coeffs.push_back(-1.0);
+ coeffs.push_back(0.0);
+ coeffs.push_back(4.0);
+ PolynomialFunctionSampleGenerator<PrecisionType> pfsg(coeffs);
+ regression = getNeuralNetworkRegressionModel(1);
+ ret = testRegression(pfsg,regression,param);
+ if (ret == EXIT_FAILURE)
+ {
+ status = EXIT_FAILURE;
+ }
+ return status;
+}
+
+
+MachineLearningModelRegressionType::Pointer getSVMRegressionModel()
+{
+ typedef otb::SVMMachineLearningModel<InputValueRegressionType,
+ TargetValueRegressionType>
+ SVMType;
+ SVMType::Pointer regression = SVMType::New();
+
+ regression->SetRegressionMode(1);
+ regression->SetSVMType(CvSVM::NU_SVR);
+ regression->SetNu(0.5);
+ regression->SetKernelType(CvSVM::RBF);
+ regression->SetTermCriteriaType(CV_TERMCRIT_ITER+CV_TERMCRIT_EPS);
+ regression->SetMaxIter(100000);
+ regression->SetEpsilon(1e-5);
+ regression->SetParameterOptimization(true);
+ return regression.GetPointer();
+}
+
+int otbSVMRegressionTests(int itkNotUsed(argc),
+ char * itkNotUsed(argv) [])
+{
+ int status = EXIT_SUCCESS;
+ int ret;
+ MachineLearningModelRegressionType::Pointer regression;
+
+ RegressionTestParam param;
+ param.vMin = -0.5;
+ param.vMax = 0.5;
+ param.count = 200;
+ param.eps = 0.1;
+
+ std::cout << "Testing regression on a linear monovariate function" << std::endl;
+ LinearFunctionSampleGenerator<PrecisionType> lfsg(2.0, 1.0);
+ regression = getSVMRegressionModel();
+ ret = testRegression(lfsg,regression,param);
+ if (ret == EXIT_FAILURE)
+ {
+ status = EXIT_FAILURE;
+ }
+ std::cout << "Testing regression on a bilinear function" << std::endl;
+ BilinearFunctionSampleGenerator<PrecisionType> bfsg(2.0,-1.0,1.0);
+ regression = getSVMRegressionModel();
+ ret = testRegression(bfsg,regression,param);
+ if (ret == EXIT_FAILURE)
+ {
+ status = EXIT_FAILURE;
+ }
+ std::cout << "Testing regression on a polynomial function" << std::endl;
+ std::vector<PrecisionType> coeffs;
+ coeffs.push_back(0.0);
+ coeffs.push_back(-1.0);
+ coeffs.push_back(0.0);
+ coeffs.push_back(4.0);
+ PolynomialFunctionSampleGenerator<PrecisionType> pfsg(coeffs);
+ regression = getSVMRegressionModel();
+ ret = testRegression(pfsg,regression,param);
+ if (ret == EXIT_FAILURE)
+ {
+ status = EXIT_FAILURE;
+ }
+ return status;
+}
+
+
+MachineLearningModelRegressionType::Pointer getDecisionTreeRegressionModel()
+{
+ typedef otb::DecisionTreeMachineLearningModel<InputValueRegressionType,
+ TargetValueRegressionType>
+ DTreeType;
+ DTreeType::Pointer regression = DTreeType::New();
+ regression->SetRegressionMode(true);
+ regression->SetRegressionAccuracy(0.005);
+ return regression.GetPointer();
+}
+
+int otbDecisionTreeRegressionTests(int itkNotUsed(argc),
+ char * itkNotUsed(argv) [])
+{
+ int status = EXIT_SUCCESS;
+ int ret;
+ MachineLearningModelRegressionType::Pointer regression;
+
+ RegressionTestParam param;
+ param.vMin = -0.5;
+ param.vMax = 0.5;
+ param.count = 200;
+ param.eps = 0.1;
+
+ std::cout << "Testing regression on a linear monovariate function" << std::endl;
+ LinearFunctionSampleGenerator<PrecisionType> lfsg(2.0, 1.0);
+ regression = getDecisionTreeRegressionModel();
+ ret = testRegression(lfsg,regression,param);
+ if (ret == EXIT_FAILURE)
+ {
+ status = EXIT_FAILURE;
+ }
+ std::cout << "Testing regression on a bilinear function" << std::endl;
+ BilinearFunctionSampleGenerator<PrecisionType> bfsg(2.0,-1.0,1.0);
+ regression = getDecisionTreeRegressionModel();
+ // increase the number of training samples for bilinear function
+ param.count = 1000;
+ ret = testRegression(bfsg,regression,param);
+ if (ret == EXIT_FAILURE)
+ {
+ status = EXIT_FAILURE;
+ }
+ std::cout << "Testing regression on a polynomial function" << std::endl;
+ std::vector<PrecisionType> coeffs;
+ coeffs.push_back(0.0);
+ coeffs.push_back(-1.0);
+ coeffs.push_back(0.0);
+ coeffs.push_back(4.0);
+ PolynomialFunctionSampleGenerator<PrecisionType> pfsg(coeffs);
+ param.count = 200;
+ regression = getDecisionTreeRegressionModel();
+ ret = testRegression(pfsg,regression,param);
+ if (ret == EXIT_FAILURE)
+ {
+ status = EXIT_FAILURE;
+ }
+ return status;
+}
+
+
+MachineLearningModelRegressionType::Pointer getGradientBoostedTreeRegressionModel()
+{
+ typedef otb::GradientBoostedTreeMachineLearningModel<InputValueRegressionType,
+ TargetValueRegressionType>
+ GBTreeType;
+ GBTreeType::Pointer regression = GBTreeType::New();
+ regression->SetRegressionMode(true);
+ regression->SetShrinkage(0.1);
+ regression->SetSubSamplePortion(0.8);
+ regression->SetLossFunctionType(CvGBTrees::SQUARED_LOSS);
+ return regression.GetPointer();
+}
+
+int otbGradientBoostedTreeRegressionTests(int itkNotUsed(argc),
+ char * itkNotUsed(argv) [])
+{
+ int status = EXIT_SUCCESS;
+ int ret;
+ MachineLearningModelRegressionType::Pointer regression;
+
+ RegressionTestParam param;
+ param.vMin = -0.5;
+ param.vMax = 0.5;
+ param.count = 200;
+ param.eps = 0.1;
+
+ std::cout << "Testing regression on a linear monovariate function" << std::endl;
+ LinearFunctionSampleGenerator<PrecisionType> lfsg(2.0, 1.0);
+ regression = getGradientBoostedTreeRegressionModel();
+ ret = testRegression(lfsg,regression,param);
+ if (ret == EXIT_FAILURE)
+ {
+ status = EXIT_FAILURE;
+ }
+ std::cout << "Testing regression on a bilinear function" << std::endl;
+ BilinearFunctionSampleGenerator<PrecisionType> bfsg(2.0,-1.0,1.0);
+ // increase number of training samples for bilinear function
+ param.count = 1000;
+ regression = getGradientBoostedTreeRegressionModel();
+ ret = testRegression(bfsg,regression,param);
+ if (ret == EXIT_FAILURE)
+ {
+ status = EXIT_FAILURE;
+ }
+ std::cout << "Testing regression on a polynomial function" << std::endl;
+ std::vector<PrecisionType> coeffs;
+ coeffs.push_back(0.0);
+ coeffs.push_back(-1.0);
+ coeffs.push_back(0.0);
+ coeffs.push_back(4.0);
+ PolynomialFunctionSampleGenerator<PrecisionType> pfsg(coeffs);
+ param.count = 200;
+ regression = getGradientBoostedTreeRegressionModel();
+ ret = testRegression(pfsg,regression,param);
+ if (ret == EXIT_FAILURE)
+ {
+ status = EXIT_FAILURE;
+ }
+ return status;
+}
+
+
+MachineLearningModelRegressionType::Pointer getKNearestNeighborsRegressionModel()
+{
+ typedef otb::KNearestNeighborsMachineLearningModel<InputValueRegressionType,
+ TargetValueRegressionType>
+ KNNType;
+ KNNType::Pointer regression = KNNType::New();
+ regression->SetRegressionMode(true);
+ regression->SetK(5);
+ regression->SetDecisionRule(KNNType::KNN_MEDIAN);
+ return regression.GetPointer();
+}
+
+int otbKNearestNeighborsRegressionTests(int itkNotUsed(argc),
+ char * itkNotUsed(argv) [])
+{
+ int status = EXIT_SUCCESS;
+ int ret;
+ MachineLearningModelRegressionType::Pointer regression;
+
+ RegressionTestParam param;
+ param.vMin = -0.5;
+ param.vMax = 0.5;
+ param.count = 200;
+ param.eps = 0.1;
+
+ std::cout << "Testing regression on a linear monovariate function" << std::endl;
+ LinearFunctionSampleGenerator<PrecisionType> lfsg(2.0, 1.0);
+ regression = getKNearestNeighborsRegressionModel();
+ ret = testRegression(lfsg,regression,param);
+ if (ret == EXIT_FAILURE)
+ {
+ status = EXIT_FAILURE;
+ }
+ std::cout << "Testing regression on a bilinear function" << std::endl;
+ BilinearFunctionSampleGenerator<PrecisionType> bfsg(2.0,-1.0,1.0);
+ regression = getKNearestNeighborsRegressionModel();
+ ret = testRegression(bfsg,regression,param);
+ if (ret == EXIT_FAILURE)
+ {
+ status = EXIT_FAILURE;
+ }
+ std::cout << "Testing regression on a polynomial function" << std::endl;
+ std::vector<PrecisionType> coeffs;
+ coeffs.push_back(0.0);
+ coeffs.push_back(-1.0);
+ coeffs.push_back(0.0);
+ coeffs.push_back(4.0);
+ PolynomialFunctionSampleGenerator<PrecisionType> pfsg(coeffs);
+ regression = getKNearestNeighborsRegressionModel();
+ ret = testRegression(pfsg,regression,param);
+ if (ret == EXIT_FAILURE)
+ {
+ status = EXIT_FAILURE;
+ }
+ return status;
+}
+
+
+MachineLearningModelRegressionType::Pointer getRandomForestsRegressionModel()
+{
+ typedef otb::RandomForestsMachineLearningModel<InputValueRegressionType,
+ TargetValueRegressionType>
+ RFType;
+ RFType::Pointer regression = RFType::New();
+ regression->SetRegressionMode(true);
+ regression->SetRegressionAccuracy(0.005);
+ return regression.GetPointer();
+}
+
+
+int otbRandomForestsRegressionTests(int itkNotUsed(argc),
+ char * itkNotUsed(argv) [])
+{
+ int status = EXIT_SUCCESS;
+ int ret;
+ MachineLearningModelRegressionType::Pointer regression;
+
+ RegressionTestParam param;
+ param.vMin = -0.5;
+ param.vMax = 0.5;
+ param.count = 200;
+ param.eps = 0.1;
+
+ std::cout << "Testing regression on a linear monovariate function" << std::endl;
+ LinearFunctionSampleGenerator<PrecisionType> lfsg(2.0, 1.0);
+ regression = getRandomForestsRegressionModel();
+ ret = testRegression(lfsg,regression,param);
+ if (ret == EXIT_FAILURE)
+ {
+ status = EXIT_FAILURE;
+ }
+ std::cout << "Testing regression on a bilinear function" << std::endl;
+ BilinearFunctionSampleGenerator<PrecisionType> bfsg(2.0,-1.0,1.0);
+ // increase number of training samples for bilinear function
+ param.count = 1000;
+ regression = getRandomForestsRegressionModel();
+ ret = testRegression(bfsg,regression,param);
+ if (ret == EXIT_FAILURE)
+ {
+ status = EXIT_FAILURE;
+ }
+ std::cout << "Testing regression on a polynomial function" << std::endl;
+ std::vector<PrecisionType> coeffs;
+ coeffs.push_back(0.0);
+ coeffs.push_back(-1.0);
+ coeffs.push_back(0.0);
+ coeffs.push_back(4.0);
+ PolynomialFunctionSampleGenerator<PrecisionType> pfsg(coeffs);
+ param.count = 200;
+ regression = getRandomForestsRegressionModel();
+ ret = testRegression(pfsg,regression,param);
+ if (ret == EXIT_FAILURE)
+ {
+ status = EXIT_FAILURE;
+ }
+ return status;
+}
+#endif
diff --git a/Modules/Learning/Supervised/test/otbSupervisedTestDriver.cxx b/Modules/Learning/Supervised/test/otbSupervisedTestDriver.cxx
index e498bd082ed53ec2862ea5b99913b6b7de897b38..2bf373c87f9f0579df333951b83ae818739d25c2 100644
--- a/Modules/Learning/Supervised/test/otbSupervisedTestDriver.cxx
+++ b/Modules/Learning/Supervised/test/otbSupervisedTestDriver.cxx
@@ -28,6 +28,7 @@ void RegisterTests()
#ifdef OTB_USE_LIBSVM
REGISTER_TEST(otbLibSVMMachineLearningModelNew);
REGISTER_TEST(otbLibSVMMachineLearningModel);
+ REGISTER_TEST(otbLibSVMRegressionTests);
#endif
#ifdef OTB_USE_OPENCV
@@ -48,8 +49,14 @@ void RegisterTests()
REGISTER_TEST(otbDecisionTreeMachineLearningModel);
REGISTER_TEST(otbGradientBoostedTreeMachineLearningModelNew);
REGISTER_TEST(otbGradientBoostedTreeMachineLearningModel);
- #endif
+ REGISTER_TEST(otbNeuralNetworkRegressionTests);
+ REGISTER_TEST(otbSVMRegressionTests);
+ REGISTER_TEST(otbDecisionTreeRegressionTests);
+ REGISTER_TEST(otbGradientBoostedTreeRegressionTests);
+ REGISTER_TEST(otbKNearestNeighborsRegressionTests);
+ REGISTER_TEST(otbRandomForestsRegressionTests);
+#endif
- REGISTER_TEST(otbImageClassificationFilterNew);
+ REGISTER_TEST(otbImageClassificationFilterNew);
REGISTER_TEST(otbImageClassificationFilter);
}
diff --git a/Modules/Learning/Supervised/test/otbTrainMachineLearningModel.cxx b/Modules/Learning/Supervised/test/otbTrainMachineLearningModel.cxx
index 39a2a2f7628c98aca338093af70d1d75d35badee..64d69a120a2dd2cd8e3418ef248ff8c12324f6ed 100644
--- a/Modules/Learning/Supervised/test/otbTrainMachineLearningModel.cxx
+++ b/Modules/Learning/Supervised/test/otbTrainMachineLearningModel.cxx
@@ -381,20 +381,12 @@ int otbSVMMachineLearningRegressionModel(int argc, char * argv[])
SVMType::Pointer classifier = SVMType::New();
//Init SVM type in regression mode
- //Available mode for regression in openCV are eps_svr and nu_svr
+ classifier->SetRegressionMode(1);
classifier->SetSVMType(CvSVM::EPS_SVR);
- //classifier->SetSVMType(CvSVM::NU_SVR);
-
- //P should be >0. Increasing value give better result. Need to investigate why.
classifier->SetP(10);
-
- //IN case you're using nu_svr you should set nu to a positive value between 0
- //and 1.
- //classifier->SetNu(0.9);
-
- //Use RBF kernel.Don't know what is recommended in case of svm regression
classifier->SetKernelType(CvSVM::RBF);
+
classifier->SetInputListSample(samples);
classifier->SetTargetListSample(labels);
classifier->Train();
@@ -432,6 +424,7 @@ int otbSVMMachineLearningRegressionModel(int argc, char * argv[])
}
else
{
+ std::cout << age << "\t" << predicted->GetMeasurementVector(0)[0] << "\n";
return EXIT_FAILURE;
}
}
@@ -447,9 +440,9 @@ int otbKNearestNeighborsMachineLearningModel(int argc, char * argv[])
{
if (argc != 3 )
{
- std::cout<<"Wrong number of arguments "<<std::endl;
- std::cout<<"Usage : sample file, output file"<<std::endl;
- return EXIT_FAILURE;
+ std::cout<<"Wrong number of arguments "<<std::endl;
+ std::cout<<"Usage : sample file, output file"<<std::endl;
+ return EXIT_FAILURE;
}
typedef otb::KNearestNeighborsMachineLearningModel<InputValueType,TargetValueType> KNearestNeighborsType;
@@ -528,11 +521,11 @@ int otbRandomForestsMachineLearningModelNew(int itkNotUsed(argc), char * itkNotU
int otbRandomForestsMachineLearningModel(int argc, char * argv[])
{
if (argc != 3 )
- {
+ {
std::cout<<"Wrong number of arguments "<<std::endl;
std::cout<<"Usage : sample file, output file "<<std::endl;
return EXIT_FAILURE;
- }
+ }
typedef otb::RandomForestsMachineLearningModel<InputValueType,TargetValueType> RandomForestType;
InputListSampleType::Pointer samples = InputListSampleType::New();
@@ -620,9 +613,9 @@ int otbBoostMachineLearningModel(int argc, char * argv[])
{
if (argc != 3 )
{
- std::cout<<"Wrong number of arguments "<<std::endl;
- std::cout<<"Usage : sample file, output file "<<std::endl;
- return EXIT_FAILURE;
+ std::cout<<"Wrong number of arguments "<<std::endl;
+ std::cout<<"Usage : sample file, output file "<<std::endl;
+ return EXIT_FAILURE;
}
typedef otb::BoostMachineLearningModel<InputValueType, TargetValueType> BoostType;
diff --git a/Modules/Learning/Supervised/test/tests-libsvm.cmake b/Modules/Learning/Supervised/test/tests-libsvm.cmake
index 04764df301cb2b2fa7f1951d023495ddf93b5b4b..30dc7eec130d6baa87a8fd37296ce7501548dc7c 100644
--- a/Modules/Learning/Supervised/test/tests-libsvm.cmake
+++ b/Modules/Learning/Supervised/test/tests-libsvm.cmake
@@ -22,3 +22,7 @@ otb_add_test(NAME leTuLibSVMMachineLearningModelCanRead COMMAND otbSupervisedTes
${TEMP}/libsvm_model.txt
)
set_property(TEST leTuLibSVMMachineLearningModelCanRead PROPERTY DEPENDS leTvLibSVMMachineLearningModel)
+
+otb_add_test(NAME leTvLibSVMMachineLearningModelReg COMMAND otbSupervisedTestDriver
+ otbLibSVMRegressionTests
+ )
diff --git a/Modules/Learning/Supervised/test/tests-opencv.cmake b/Modules/Learning/Supervised/test/tests-opencv.cmake
index 55855a4aa912a3b3497bb9b8d9f2bc69d6dccea4..3be269fe8d8e7f17f85f9e4d11c944feb2dc3e02 100644
--- a/Modules/Learning/Supervised/test/tests-opencv.cmake
+++ b/Modules/Learning/Supervised/test/tests-opencv.cmake
@@ -10,6 +10,32 @@ otb_add_test(NAME leTvANNMachineLearningModel COMMAND otbSupervisedTestDriver
${TEMP}/ann_model.txt
)
+# ------------------ Regression tests --------------------
+otb_add_test(NAME leTvANNMachineLearningModelReg COMMAND otbSupervisedTestDriver
+ otbNeuralNetworkRegressionTests
+ )
+
+otb_add_test(NAME leTvSVMMachineLearningModelReg COMMAND otbSupervisedTestDriver
+ otbSVMRegressionTests
+ )
+
+otb_add_test(NAME leTvDecisionTreeMachineLearningModelReg COMMAND otbSupervisedTestDriver
+ otbDecisionTreeRegressionTests
+ )
+
+otb_add_test(NAME leTvGradientBoostedTreeMachineLearningModelReg COMMAND otbSupervisedTestDriver
+ otbGradientBoostedTreeRegressionTests
+ )
+
+otb_add_test(NAME leTvKNearestNeighborsMachineLearningModelReg COMMAND otbSupervisedTestDriver
+ otbKNearestNeighborsRegressionTests
+ )
+
+otb_add_test(NAME leTvRandomForestsMachineLearningModelReg COMMAND otbSupervisedTestDriver
+ otbRandomForestsRegressionTests
+ )
+# --------------------------------------------------------------
+
otb_add_test(NAME leTuSVMMachineLearningModelNew COMMAND otbSupervisedTestDriver
otbSVMMachineLearningModelNew)
diff --git a/SuperBuild/CMake/External_gdal.cmake b/SuperBuild/CMake/External_gdal.cmake
index a76075af1adfc2996686a606df020c750f99f151..61ce0d3b757c83b8f1755191f190832a650110ec 100644
--- a/SuperBuild/CMake/External_gdal.cmake
+++ b/SuperBuild/CMake/External_gdal.cmake
@@ -51,9 +51,9 @@ else()
INSTALL_DIR ${SB_INSTALL_PREFIX}
DOWNLOAD_DIR ${DOWNLOAD_LOCATION}
DEPENDS ${${proj}_DEPENDENCIES}
- UPDATE_COMMAND ${CMAKE_COMMAND} -E copy_directory ${GDAL_SB_SRC} ${GDAL_SB_BUILD_DIR}
- PATCH_COMMAND ${CMAKE_COMMAND} -E touch ${GDAL_SB_SRC}/config.rpath
- CONFIGURE_COMMAND
+ UPDATE_COMMAND ${CMAKE_COMMAND} -E copy_directory ${GDAL_SB_SRC} ${GDAL_SB_BUILD_DIR}
+ PATCH_COMMAND ${CMAKE_COMMAND} -E touch ${GDAL_SB_SRC}/config.rpath COMMAND ${CMAKE_COMMAND} -E copy ${CMAKE_SOURCE_DIR}/patches/GDAL/GNUmakefile ${GDAL_SB_SRC}/swig/python/GNUmakefile
+ CONFIGURE_COMMAND
# use 'env' because CTest launcher doesn't perform shell interpretation
${SB_ENV_CONFIGURE_CMD}
${GDAL_SB_BUILD_DIR}/configure
@@ -86,7 +86,7 @@ else()
INSTALL_DIR ${SB_INSTALL_PREFIX}
DOWNLOAD_DIR ${DOWNLOAD_LOCATION}
DEPENDS ${${proj}_DEPENDENCIES}
- PATCH_COMMAND ${CMAKE_COMMAND} -E copy_directory ${GDAL_SB_SRC} ${GDAL_SB_BUILD_DIR}
+ PATCH_COMMAND ${CMAKE_COMMAND} -E copy_directory ${GDAL_SB_SRC} ${GDAL_SB_BUILD_DIR} COMMAND ${CMAKE_COMMAND} -E copy ${CMAKE_SOURCE_DIR}/patches/GDAL/GNUmakefile ${GDAL_SB_SRC}/swig/python/GNUmakefile
CONFIGURE_COMMAND ${CMAKE_COMMAND} -E copy ${CMAKE_SOURCE_DIR}/patches/${proj}/ogrsqlitevirtualogr.cpp
${GDAL_SB_BUILD_DIR}/ogr/ogrsf_frmts/sqlite/ogrsqlitevirtualogr.cpp
BUILD_COMMAND nmake /f ${GDAL_SB_BUILD_DIR}/makefile.vc MSVC_VER=${MSVC_VERSION} EXT_NMAKE_OPT=${CMAKE_BINARY_DIR}/nmake_gdal_extra.opt
diff --git a/SuperBuild/patches/GDAL/GNUmakefile b/SuperBuild/patches/GDAL/GNUmakefile
new file mode 100644
index 0000000000000000000000000000000000000000..71f029d8726dbf9cda8644471ceee789f1e279cf
--- /dev/null
+++ b/SuperBuild/patches/GDAL/GNUmakefile
@@ -0,0 +1,95 @@
+
+
+include ../../GDALmake.opt
+
+ifndef PYTHON
+ PYTHON=python
+endif
+
+all: build
+
+BINDING = python
+include ../SWIGmake.base
+
+PACKAGE_DIR=osgeo
+SWIGOUTPUTDIR=extensions/
+
+SCRIPTS = `ls ./scripts`
+PY_COMMANDS = epsg_tr.py gdalchksum.py gdal2xyz.py gcps2wld.py \
+ gdalimport.py gdal_merge.py pct2rgb.py rgb2pct.py \
+ gcps2vec.py
+PY_MODULES = ${PACKAGE_DIR}/gdal.py ${PACKAGE_DIR}/ogr.py ${PACKAGE_DIR}/osr.py ${PACKAGE_DIR}/gdalconst.py ${PACKAGE_DIR}/gdal_array.py
+
+clean:
+ -rm -f ${PACKAGE_DIR}/*.pyc
+ -rm -rf build
+ -rm -f *.pyc
+ -rm -rf *.egg-info
+ -rm -f *.so ./osgeo/*.so
+ -rm -rf dist
+
+SWIGARGS += -outdir "${PACKAGE_DIR}"
+
+
+veryclean: clean
+ -rm -f ${WRAPPERS} ${PY_MODULES}
+ -rm -f ${SWIGOUTPUTDIR}/gdal_wrap.cpp
+ -rm -f ${SWIGOUTPUTDIR}/gdalconst_wrap.c
+ -rm -f ${SWIGOUTPUTDIR}/ogr_wrap.cpp
+ -rm -f ${SWIGOUTPUTDIR}/osr_wrap.cpp
+ -rm -f ${SWIGOUTPUTDIR}/gdal_array_wrap.cpp
+
+gdal_wrap.cpp: ../include/python/gdal_python.i
+
+ogr_wrap.cpp: ../include/python/ogr_python.i
+
+osr_wrap.cpp: ../include/python/osr_python.i
+
+gdal_array_wrap.cpp: ../include/gdal_array.i ../include/python/typemaps_python.i
+ $(SWIG) $(SWIGARGS) $(SWIGDEFINES) -I$(GDAL_ROOT) -c++ -$(BINDING) -o $(SWIGOUTPUTDIR)$@ gdal_array.i
+
+# A few hacks (cat, mv) : the first one for SWIG < 1.3.36 and the second one for SWIG <= 1.3.39 python 3.X on 64bit platforms
+# The python3.2.patch is from https://sourceforge.net/tracker/?func=detail&aid=3057804&group_id=1645&atid=101645
+# and is no longer necessary with swig 2.0.4
+generate: ${WRAPPERS} gdal_array_wrap.cpp
+ for i in gdal_wrap.cpp gdalconst_wrap.c ogr_wrap.cpp osr_wrap.cpp gdal_array_wrap.cpp; do sed "s/PyErr_Format(PyExc_RuntimeError, mesg)/PyErr_SetString(PyExc_RuntimeError, mesg)/" ${SWIGOUTPUTDIR}/$$i | sed "s/int len;/Py_ssize_t len;/" > ${SWIGOUTPUTDIR}/$$i.tmp; mv -f ${SWIGOUTPUTDIR}/$$i.tmp ${SWIGOUTPUTDIR}/$$i; done
+ -grep "1\.3\.40" extensions/gdal_wrap.cpp >/dev/null && patch -p0 < python3.2.patch
+ -grep "1\.3\.40" extensions/gdal_wrap.cpp >/dev/null && cat python3.2.patch | sed "s/gdal_wrap/ogr_wrap/" | patch -p0
+ -grep "1\.3\.40" extensions/gdal_wrap.cpp >/dev/null && cat python3.2.patch | sed "s/gdal_wrap/osr_wrap/" | patch -p0
+ -grep "1\.3\.40" extensions/gdal_wrap.cpp >/dev/null && cat python3.2.patch | sed "s/gdal_wrap\.cpp/gdalconst_wrap\.c/" | patch -p0
+ -grep "1\.3\.40" extensions/gdal_wrap.cpp >/dev/null && cat python3.2.patch | sed "s/gdal_wrap/gdal_array_wrap/" | patch -p0
+
+build:
+ $(PYTHON) setup.py build
+
+egg:
+ $(PYTHON) setup.py bdist_egg
+
+install:
+
+ifeq ($(PY_HAVE_SETUPTOOLS),1)
+ $(PYTHON) setup.py install --prefix=$(DESTDIR)$(prefix) --install-purelib=$(prefix)/lib --install-scripts=$(prefix)/bin --install-platlib=$(prefix)/lib
+else
+ $(PYTHON) setup.py install --prefix=$(DESTDIR)$(prefix)
+endif
+
+ for f in $(SCRIPTS) ; do $(INSTALL) ./scripts/$$f $(DESTDIR)$(INST_BIN) ; done
+
+docs:
+ $(PYTHON) ../include/python/docs/doxy2swig.py ../../ogr/xml/ogrlayer_8cpp.xml ../include/python/docs/ogr_layer_docs.i OGRLayerShadow OGR_L_
+
+ $(PYTHON) ../include/python/docs/doxy2swig.py ../../ogr/xml/ogrgeometry_8cpp.xml ../include/python/docs/ogr_geometry_docs.i OGRGeometryShadow OGR_G_
+
+ $(PYTHON) ../include/python/docs/doxy2swig.py ../../ogr/xml/ogrdatasource_8cpp.xml ../include/python/docs/ogr_datasource_docs.i OGRDataSourceShadow OGR_DS_
+
+
+ $(PYTHON) ../include/python/docs/doxy2swig.py ../../ogr/xml/ogrsfdriver_8cpp.xml ../include/python/docs/ogr_driver_docs.i OGRDriverShadow OGR_Dr_
+
+ $(PYTHON) ../include/python/docs/doxy2swig.py ../../ogr/xml/ogrfeature_8cpp.xml ../include/python/docs/ogr_feature_docs.i OGRFeatureShadow OGR_F_
+
+ $(PYTHON) ../include/python/docs/doxy2swig.py ../../ogr/xml/ogrfeaturedefn_8cpp.xml ../include/python/docs/ogr_featuredef_docs.i OGRFeatureDefnShadow OGR_FD_
+
+ $(PYTHON) ../include/python/docs/doxy2swig.py ../../ogr/xml/ogrfielddefn_8cpp.xml ../include/python/docs/ogr_fielddef_docs.i OGRFieldDefnShadow OGR_Fld_
+
+epydoc: generate
+ epydoc --config epydoc.conf
diff --git a/Utilities/Maintenance/SuperbuildDownloadList.sh b/Utilities/Maintenance/SuperbuildDownloadList.sh
index e0cc7033b1933fc5d8943747184a249d51d01f5c..2cb32210b12d8d28a5c985047956271ad4e970e2 100755
--- a/Utilities/Maintenance/SuperbuildDownloadList.sh
+++ b/Utilities/Maintenance/SuperbuildDownloadList.sh
@@ -1,2 +1,62 @@
#/bin/bash
-grep -h -E "^[^#]*\"https?://.*(\.tar\.gz|\.tar\.bz2|\.tgz|\.tar\.xz|\.zip|export=download).*\"" ../../SuperBuild/CMake/*.cmake | grep -o -E "https?://[^\"]*" | sed "s/\/download$//" | sort | uniq
+
+if [ $# -eq 2 ]; then
+DOWNLOAD_DIR=$(readlink -f $1)
+OUTPUT_DIR=$(readlink -f $2)
+else
+echo 'Usage: '$0' <download_directory> <archive_output_directory>'
+exit 1
+fi
+
+SB_CMAKE_DIR_REL=$(dirname $0)/../../SuperBuild/CMake
+SB_CMAKE_DIR=$(readlink -f ${SB_CMAKE_DIR_REL})
+
+DOWNLOAD_LIST=$(grep -h -E "^[^#]*\"https?://.*(\.tar\.gz|\.tar\.bz2|\.tgz|\.tar\.xz|\.zip|export=download).*\"" ${SB_CMAKE_DIR}/*.cmake | grep -o -E "https?://[^\"]*" | sed "s/\/\(download\)\?$//" | sort | uniq)
+
+DOWNLOAD_NAMES=
+
+mkdir -p ${DOWNLOAD_DIR}
+cd ${DOWNLOAD_DIR}
+
+echo "Start downloads..."
+
+for url in ${DOWNLOAD_LIST}; do
+ # clean log file
+ echo "" >download.log
+
+ file_name=$(echo "${url}" | grep -o -E "[^\/]+$")
+ docs_google=$(echo "${file_name}" | grep -F "export=download")
+ if [ "${docs_google}" = "" ]; then
+ echo "Download ${file_name}..."
+ wget -N ${url} -o download.log
+ else
+ # look into the original file for a valid download name
+ file_name=$(grep -h -A 3 -B 3 -F "${url}" ${SB_CMAKE_DIR}/*.cmake | grep -E "^[^#]*DOWNLOAD_NAME" | grep -o -E "[^ ]*\.(tar\.gz|tar\.bz2|tar\.xz|zip)" | uniq)
+ if [ -z "$file_name" ]; then
+ echo "Can't find correct filename for url ${url} : skip download"
+ else
+ echo "Download ${file_name}..."
+ wget -O ${file_name} ${url} -o download.log
+ fi
+ fi
+
+ download_errors=$(grep "ERROR" download.log)
+ if [ "$download_errors" != "" ]; then
+ echo "=== Error downloading ${file_name} ==="
+ cat download.log
+ else
+ if [ "$file_name" != "" ]; then
+ DOWNLOAD_NAMES="${DOWNLOAD_NAMES} ${file_name}"
+ fi
+ fi
+done
+
+rm download.log
+
+echo "Create archive..."
+
+cd ${OUTPUT_DIR}
+tar -cjf SuperBuild-archives.tar.bz2 -C ${DOWNLOAD_DIR} ${DOWNLOAD_NAMES}
+
+echo "Compute md5sum..."
+md5sum SuperBuild-archives.tar.bz2 >SuperBuild-archives.md5