otbTrainSharkKMeans.hxx

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/*
 * Copyright (C) 2005-2022 Centre National d'Etudes Spatiales (CNES)
 *
 * This file is part of Orfeo Toolbox
 *
 *     https://www.orfeo-toolbox.org/
 *
 * Licensed under the Apache License, Version 2.0 (the "License");
 * you may not use this file except in compliance with the License.
 * You may obtain a copy of the License at
 *
 *     http://www.apache.org/licenses/LICENSE-2.0
 *
 * Unless required by applicable law or agreed to in writing, software
 * distributed under the License is distributed on an "AS IS" BASIS,
 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 * See the License for the specific language governing permissions and
 * limitations under the License.
 */
#ifndef otbTrainSharkKMeans_hxx
#define otbTrainSharkKMeans_hxx
 
#include "otbLearningApplicationBase.h"
#include "otbSharkKMeansMachineLearningModel.h"
#include "otbStatisticsXMLFileReader.h"
 
namespace otb
{
namespace Wrapper
{
template <class TInputValue, class TOutputValue>
void LearningApplicationBase<TInputValue, TOutputValue>::InitSharkKMeansParams()
{
  AddChoice("classifier.sharkkm", "Shark kmeans classifier");
  SetParameterDescription("classifier.sharkkm", "http://image.diku.dk/shark/sphinx_pages/build/html/rest_sources/tutorials/algorithms/kmeans.html ");
 
  // MaxNumberOfIterations
  AddParameter(ParameterType_Int, "classifier.sharkkm.maxiter", "Maximum number of iterations for the kmeans algorithm");
  SetParameterInt("classifier.sharkkm.maxiter", 10);
  SetMinimumParameterIntValue("classifier.sharkkm.maxiter", 0);
  SetParameterDescription("classifier.sharkkm.maxiter", "The maximum number of iterations for the kmeans algorithm. 0=unlimited");
 
  // Number of classes
  AddParameter(ParameterType_Int, "classifier.sharkkm.k", "Number of classes for the kmeans algorithm");
  SetParameterInt("classifier.sharkkm.k", 2);
  SetParameterDescription("classifier.sharkkm.k", "The number of classes used for the kmeans algorithm. Default set to 2 class");
  SetMinimumParameterIntValue("classifier.sharkkm.k", 2);
 
  // Input centroids
  AddParameter(ParameterType_InputFilename, "classifier.sharkkm.incentroids", "User defined input centroids");
  SetParameterDescription("classifier.sharkkm.incentroids",
                          "Input text file containing centroid posistions used to initialize the algorithm. "
                          "Each centroid must be described by p parameters, p being the number of features in "
                          "the input vector data, and the number of centroids must be equal to the number of classes "
                          "(one centroid per line with values separated by spaces).");
  MandatoryOff("classifier.sharkkm.incentroids");
 
  // Centroid statistics
  AddParameter(ParameterType_InputFilename, "classifier.sharkkm.cstats", "Statistics file");
  SetParameterDescription("classifier.sharkkm.cstats",
                          "A XML file containing mean and standard deviation to center"
                          "and reduce the input centroids before the KMeans algorithm, produced by ComputeImagesStatistics application.");
  MandatoryOff("classifier.sharkkm.cstats");
 
  // Output centroids
  AddParameter(ParameterType_OutputFilename, "classifier.sharkkm.outcentroids", "Output centroids text file");
  SetParameterDescription("classifier.sharkkm.outcentroids", "Output text file containing centroids after the kmean algorithm.");
  MandatoryOff("classifier.sharkkm.outcentroids");
}
 
template <class TInputValue, class TOutputValue>
void LearningApplicationBase<TInputValue, TOutputValue>::TrainSharkKMeans(typename ListSampleType::Pointer trainingListSample,
                                                                          typename TargetListSampleType::Pointer trainingLabeledListSample,
                                                                          std::string                            modelPath)
{
  unsigned int nbMaxIter = static_cast<unsigned int>(abs(GetParameterInt("classifier.sharkkm.maxiter")));
  unsigned int k         = static_cast<unsigned int>(abs(GetParameterInt("classifier.sharkkm.k")));
 
  typedef otb::SharkKMeansMachineLearningModel<InputValueType, OutputValueType> SharkKMeansType;
  typename SharkKMeansType::Pointer classifier = SharkKMeansType::New();
  classifier->SetRegressionMode(this->m_RegressionFlag);
  classifier->SetInputListSample(trainingListSample);
  classifier->SetTargetListSample(trainingLabeledListSample);
  classifier->SetK(k);
 
  // Initialize centroids from file
  if (IsParameterEnabled("classifier.sharkkm.incentroids") && HasValue("classifier.sharkkm.incentroids"))
  {
    shark::Data<shark::RealVector> centroidData;
    shark::importCSV(centroidData, GetParameterString("classifier.sharkkm.incentroids"), ' ');
    if (HasValue("classifier.sharkkm.cstats"))
    {
      auto statisticsReader = otb::StatisticsXMLFileReader<itk::VariableLengthVector<float>>::New();
      statisticsReader->SetFileName(GetParameterString("classifier.sharkkm.cstats"));
      auto meanMeasurementVector   = statisticsReader->GetStatisticVectorByName("mean");
      auto stddevMeasurementVector = statisticsReader->GetStatisticVectorByName("stddev");
 
      // Convert itk Variable Length Vector to shark Real Vector
      shark::RealVector offsetRV(meanMeasurementVector.Size());
      shark::RealVector scaleRV(stddevMeasurementVector.Size());
 
      assert(meanMeasurementVector.Size() == stddevMeasurementVector.Size());
      for (unsigned int i = 0; i < meanMeasurementVector.Size(); ++i)
      {
        scaleRV[i] = 1 / stddevMeasurementVector[i];
        // Subtract the normalized mean
        offsetRV[i] = -meanMeasurementVector[i] / stddevMeasurementVector[i];
      }
 
      shark::Normalizer<> normalizer(scaleRV, offsetRV);
      centroidData = normalizer(centroidData);
    }
 
    if (centroidData.numberOfElements() != k)
      otbAppLogWARNING("The input centroid file will not be used because it contains "
                       << centroidData.numberOfElements() << " points, which is different than from the requested number of class: " << k << ".");
 
    classifier->SetCentroidsFromData(centroidData);
  }
 
  classifier->SetMaximumNumberOfIterations(nbMaxIter);
  classifier->Train();
  classifier->Save(modelPath);
 
  if (HasValue("classifier.sharkkm.outcentroids"))
    classifier->ExportCentroids(GetParameterString("classifier.sharkkm.outcentroids"));
}
 
} // end namespace wrapper
} // end namespace otb
 
#endif