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otbVectorDimensionalityReduction.cxx 16.20 KiB
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/*
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 * Copyright (C) 2005-2017 Centre National d'Etudes Spatiales (CNES)
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 *
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 * This file is part of Orfeo Toolbox
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 *
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 *     https://www.orfeo-toolbox.org/
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 *
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 * Licensed under the Apache License, Version 2.0 (the "License");
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 * you may not use this file except in compliance with the License.
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 * You may obtain a copy of the License at
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 *
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 *     http://www.apache.org/licenses/LICENSE-2.0
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 *
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 * Unless required by applicable law or agreed to in writing, software
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 * distributed under the License is distributed on an "AS IS" BASIS,
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 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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 * See the License for the specific language governing permissions and
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 * limitations under the License.
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 */
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#include "otbWrapperApplication.h"
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#include "otbWrapperApplicationFactory.h"
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#include "otbOGRDataSourceWrapper.h"
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#include "otbOGRFeatureWrapper.h"
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#include "itkVariableLengthVector.h"
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#include "otbStatisticsXMLFileReader.h"
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#include "itkListSample.h"
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#include "otbShiftScaleSampleListFilter.h"
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#include "otbDimensionalityReductionModelFactory.h"
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#include <time.h>
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namespace otb
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{
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namespace Wrapper
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{
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/** Utility function to negate std::isalnum */
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bool IsNotAlphaNum(char c)
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{
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return !std::isalnum(c);
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}
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/**
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 * \class VectorDimensionalityReduction
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 *
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 * Apply a dimensionality reduction model on a vector file
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 */
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class VectorDimensionalityReduction : public Application
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{
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public:
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    /** Standard class typedefs. */
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  typedef VectorDimensionalityReduction Self;
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  typedef Application Superclass;
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  typedef itk::SmartPointer<Self> Pointer;
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  typedef itk::SmartPointer<const Self> ConstPointer;
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  /** Standard macro */
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  itkNewMacro(Self);
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  itkTypeMacro(Self, Application)
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  /** Filters typedef */
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  typedef float                                           ValueType;
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  typedef itk::VariableLengthVector<ValueType>            InputSampleType;
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  typedef itk::Statistics::ListSample<InputSampleType>    ListSampleType;
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  typedef MachineLearningModel<
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    itk::VariableLengthVector<ValueType>,
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    itk::VariableLengthVector<ValueType> >                DimensionalityReductionModelType;
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  typedef DimensionalityReductionModelFactory<
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    ValueType,ValueType>                                  DimensionalityReductionModelFactoryType;
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  typedef DimensionalityReductionModelType::Pointer       ModelPointerType;
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/** Statistics Filters typedef */ typedef itk::VariableLengthVector<ValueType> MeasurementType; typedef otb::StatisticsXMLFileReader<MeasurementType> StatisticsReader; typedef otb::Statistics::ShiftScaleSampleListFilter< ListSampleType, ListSampleType> ShiftScaleFilterType; protected: ~VectorDimensionalityReduction() override { DimensionalityReductionModelFactoryType::CleanFactories(); } private: void DoInit() override { SetName("VectorDimensionalityReduction"); SetDescription("Performs dimensionality reduction of the input vector data " "according to a model file."); SetDocName("Vector Dimensionality Reduction"); SetDocAuthors("OTB-Team"); SetDocLongDescription("This application performs a vector data " "dimensionality reduction based on a model file produced by the " "TrainDimensionalityReduction application."); SetDocSeeAlso("TrainDimensionalityReduction"); SetDocLimitations("None"); AddDocTag(Tags::Learning); AddParameter(ParameterType_InputVectorData, "in", "Name of the input vector data"); SetParameterDescription("in","The input vector data to reduce."); AddParameter(ParameterType_InputFilename, "instat", "Statistics file"); SetParameterDescription("instat", "A XML file containing mean and standard " "deviation to center and reduce samples before dimensionality reduction " "(produced by ComputeImagesStatistics application)."); MandatoryOff("instat"); AddParameter(ParameterType_InputFilename, "model", "Model file"); SetParameterDescription("model", "A model file (produced by the " "TrainDimensionalityReduction application,"); AddParameter(ParameterType_OutputFilename, "out", "Output vector data file " "containing the reduced vector"); SetParameterDescription("out","Output vector data file storing sample " "values (OGR format). If not given, the input vector data file is used. " "In overwrite mode, the original features will be lost."); MandatoryOff("out"); AddParameter(ParameterType_ListView, "feat", "Input features to use for reduction"); SetParameterDescription("feat", "List of field names in the input vector data used as features for reduction."); AddParameter(ParameterType_Choice, "featout", "Output feature"); SetParameterDescription("featout", "Naming of output features"); AddChoice("featout.prefix", "Prefix"); SetParameterDescription("featout.prefix", "Use a name prefix"); AddParameter(ParameterType_String, "featout.prefix.name", "Feature name prefix"); SetParameterDescription("featout.prefix.name","Name prefix for output " "features. This prefix is followed by the numeric index of each output feature."); SetParameterString("featout.prefix.name","reduced_", false); AddChoice("featout.list","List"); SetParameterDescription("featout.list", "Use a list with all names"); AddParameter(ParameterType_StringList, "featout.list.names", "Feature name list"); SetParameterDescription("featout.list.names", "List of field names for the output " "features which result from the reduction."); AddParameter(ParameterType_Int, "pcadim", "Principal component dimension");