text: /*
   * Copyright (C) 2005-2019 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.
   */
  
  
  #include "otbWrapperApplication.h"
  #include "otbWrapperApplicationFactory.h"
  
  #include "otbScalarImageToTexturesFilter.h"
  #include "otbScalarImageToAdvancedTexturesFilter.h"
  #include "otbScalarImageToHigherOrderTexturesFilter.h"
  
  #include "otbMultiToMonoChannelExtractROI.h"
  #include "otbClampImageFilter.h"
  #include "otbImageList.h"
  #include "otbImageListToVectorImageFilter.h"
  
  namespace otb
  {
  namespace Wrapper
  {
  
  class HaralickTextureExtraction : public Application
  {
  public:
  /** Standard class typedefs. */
  typedef HaralickTextureExtraction     Self;
  typedef Application                   Superclass;
  typedef itk::SmartPointer<Self>       Pointer;
  typedef itk::SmartPointer<const Self> ConstPointer;
  
  typedef MultiToMonoChannelExtractROI<FloatVectorImageType::InternalPixelType,FloatVectorImageType::InternalPixelType>
                                                                                 ExtractorFilterType;
  typedef ClampImageFilter<FloatImageType, FloatImageType>                       ClampFilterType;
  
  typedef ScalarImageToTexturesFilter<FloatImageType, FloatImageType>            HarTexturesFilterType;
  typedef ScalarImageToAdvancedTexturesFilter<FloatImageType, FloatImageType>    AdvTexturesFilterType;
  typedef ScalarImageToHigherOrderTexturesFilter<FloatImageType, FloatImageType> HigTexturesFilterType;
  
  typedef HarTexturesFilterType::SizeType                                        RadiusType;
  typedef HarTexturesFilterType::OffsetType                                      OffsetType;
  
  typedef ImageList<FloatImageType>                                              ImageListType;
  typedef ImageListToVectorImageFilter<ImageListType, FloatVectorImageType>      ImageListToVectorImageFilterType;
  
  
  /** Standard macro */
  itkNewMacro(Self);
  
  itkTypeMacro(HaralickTextureExtraction, otb::Application);
  
  private:
  
  void DoInit() override
  {
  SetName("HaralickTextureExtraction");
  SetDescription("Computes Haralick textural features on the selected channel of the input image");
  
  // Documentation
  SetDocName("Haralick Texture Extraction");
  SetDocLongDescription(
      "This application computes three sets of Haralick features [1][2].\n\n"
  
      "* simple: a set of 8 local Haralick features: Energy (texture uniformity) , "
      "Entropy (measure of randomness of intensity image), Correlation (how "
      "correlated a pixel is to its neighborhood), Inverse Difference Moment (measures "
      "the texture homogeneity), Inertia (intensity contrast between a pixel and its "
      "neighborhood), Cluster Shade, Cluster Prominence, Haralick Correlation;\n\n"
      "* advanced: a set of 10 advanced Haralick features: Mean, Variance (measures the "
      "texture heterogeneity), Dissimilarity, Sum Average, Sum Variance, Sum Entropy, "
      "Difference of Entropies, Difference of Variances, IC1, IC2;\n\n"
      "* higher: a set of 11 higher Haralick features: Short Run Emphasis (measures the "
      "texture sharpness), Long Run Emphasis (measures the texture roughness), Grey-Level "
      "Nonuniformity, Run Length Nonuniformity, Run Percentage (measures the texture "
      "sharpness homogeneity), Low Grey-Level Run Emphasis, High Grey-Level Run Emphasis, "
      "Short Run Low Grey-Level Emphasis, Short Run High Grey-Level Emphasis, Long Run Low "
      "Grey-Level Emphasis and Long Run High Grey-Level Emphasis.\n\n"
      "The documentation of textures (description are formulas) are available in the OTB CookBook (section Textures) and also in corresponding doxygen "
      "documentation of filters (see section *Detailed Description* in doxygen):\n"
      "* **simple**: otbScalarImageToTexturesFilter\n"
      "* **advanced**: otbScalarImageToAdvancedTexturesFilter\n"
      "* **higher**: otbScalarImageToHigherOrderTexturesFilter");
  
  SetDocLimitations("The computation of the features is based on a Gray Level Co-occurrence "
      "matrix (GLCM) from the quantized input image. Consequently the quantization "
      "parameters (min, max, nbbin) must be appropriate to the range of the pixel values.");
  SetDocAuthors("OTB-Team");
  SetDocSeeAlso("[1] HARALICK, Robert M., SHANMUGAM, Karthikeyan, et al. "
      "Textural features for image classification. IEEE Transactions on systems, "
      "man, and cybernetics, 1973, no 6, p. 610-621.\n"
      "[2] otbScalarImageToTexturesFilter, otbScalarImageToAdvancedTexturesFilter and "
      "otbScalarImageToHigherOrderTexturesFilter classes");
  
  AddDocTag(Tags::FeatureExtraction);
  AddDocTag("Textures");
  
  AddParameter(ParameterType_InputImage, "in",  "Input Image");
  SetParameterDescription("in", "The input image to compute the features on.");
  
  AddParameter(ParameterType_Int,  "channel",  "Selected Channel");
  SetParameterDescription("channel", "The selected channel index");
  SetDefaultParameterInt("channel", 1);
  SetMinimumParameterIntValue("channel", 1);
  
  AddParameter(ParameterType_Int, "step", "Computation step");
  SetParameterDescription("step", "Step (in pixels) to compute output texture values."
    " The first computed pixel position is shifted by (step-1)/2 in both directions.");
  SetDefaultParameterInt("step", 1);
  SetMinimumParameterIntValue("step", 1);
  MandatoryOff("step");
  
  AddParameter(ParameterType_Group, "parameters", "Texture feature parameters");
  SetParameterDescription("parameters","This group of parameters allows one to define "
      "texture parameters.");
  
  AddParameter(ParameterType_Int,"parameters.xrad","X Radius");
  SetParameterDescription("parameters.xrad", "X Radius");
  SetDefaultParameterInt("parameters.xrad", 2);
  
  AddParameter(ParameterType_Int,"parameters.yrad","Y Radius");
  SetParameterDescription("parameters.yrad", "Y Radius");
  SetDefaultParameterInt("parameters.yrad", 2);
  
  AddParameter(ParameterType_Int,"parameters.xoff","X Offset");
  SetParameterDescription("parameters.xoff", "X Offset");
  SetDefaultParameterInt("parameters.xoff", 1);
  
  AddParameter(ParameterType_Int,"parameters.yoff","Y Offset");
  SetParameterDescription("parameters.yoff", "Y Offset");
  SetDefaultParameterInt("parameters.yoff", 1);
  
  AddParameter(ParameterType_Float,"parameters.min","Image Minimum");
  SetParameterDescription("parameters.min", "Image Minimum");
  SetDefaultParameterFloat("parameters.min", 0);
  
  AddParameter(ParameterType_Float,"parameters.max","Image Maximum");
  SetParameterDescription("parameters.max", "Image Maximum");
  SetDefaultParameterFloat("parameters.max", 255);
  
  AddParameter(ParameterType_Int,"parameters.nbbin","Histogram number of bin");
  SetParameterDescription("parameters.nbbin", "Histogram number of bin");
  SetDefaultParameterInt("parameters.nbbin", 8);
  
  AddParameter(ParameterType_Choice, "texture", "Texture Set Selection");
  SetParameterDescription("texture", "Choice of The Texture Set");
  
  AddChoice("texture.simple", "Simple Haralick Texture Features");
  SetParameterDescription("texture.simple", "This group of parameters defines "
      "the 8 local Haralick texture feature output image. The image channels are: "
      "Energy, Entropy, Correlation, Inverse Difference Moment, Inertia, Cluster "
      "Shade, Cluster Prominence and Haralick Correlation");
  
  AddChoice("texture.advanced", "Advanced Texture Features");
  SetParameterDescription("texture.advanced", "This group of parameters defines "
      "the 10 advanced texture feature output image. The image channels are: Mean, "
      "Variance, Dissimilarity, Sum Average, Sum Variance, Sum Entropy, Difference "
      "of Entropies, Difference of Variances, IC1 and IC2");
  
  AddChoice("texture.higher", "Higher Order Texture Features");
  SetParameterDescription("texture.higher", "This group of parameters defines the "
      "11 higher order texture feature output image. The image channels are: "
      "Short Run Emphasis, Long Run Emphasis, Grey-Level Nonuniformity, "
      "Run Length Nonuniformity, Run Percentage, Low Grey-Level Run Emphasis, "
      "High Grey-Level Run Emphasis, Short Run Low Grey-Level Emphasis, "
      "Short Run High Grey-Level Emphasis, Long Run Low Grey-Level Emphasis and "
      "Long Run High Grey-Level Emphasis");
  
  AddParameter(ParameterType_OutputImage, "out", "Output Image");
  SetParameterDescription("out", "Output image containing the selected texture features.");
  MandatoryOff("out");
  EnableParameter("out");
  
  AddRAMParameter();
  
  // Doc example parameter settings
  SetDocExampleParameterValue("in", "qb_RoadExtract.tif");
  SetDocExampleParameterValue("channel", "2");
  SetDocExampleParameterValue("parameters.xrad", "3");
  SetDocExampleParameterValue("parameters.yrad", "3");
  SetDocExampleParameterValue("texture", "simple");
  SetDocExampleParameterValue("out", "HaralickTextures.tif");
  
  SetOfficialDocLink();
  }
  
  void DoUpdateParameters() override
  {
    // Nothing to do here : all parameters are independent
  }
  
  void DoExecute() override
  {
    FloatVectorImageType::Pointer inImage = GetParameterImage("in");
    inImage->UpdateOutputInformation();
    int nBComp = inImage->GetNumberOfComponentsPerPixel();
  
    if( GetParameterInt("channel") > nBComp )
      {
      itkExceptionMacro(<< "The specified channel index is invalid.");
      }
  
    const std::string texType = GetParameterString("texture");
  
    RadiusType radius;
    radius[0] = GetParameterInt("parameters.xrad");
    radius[1] = GetParameterInt("parameters.yrad");
  
    OffsetType offset;
    offset[0] = GetParameterInt("parameters.xoff");
    offset[1] = GetParameterInt("parameters.yoff");
  
    RadiusType stepping;
    stepping.Fill(GetParameterInt("step"));
  
    OffsetType stepOffset;
    stepOffset.Fill((GetParameterInt("step") - 1) / 2);
  
    m_ExtractorFilter = ExtractorFilterType::New();
    m_ExtractorFilter->SetInput(inImage);
    m_ExtractorFilter->SetStartX(inImage->GetLargestPossibleRegion().GetIndex(0));
    m_ExtractorFilter->SetStartY(inImage->GetLargestPossibleRegion().GetIndex(1));
    m_ExtractorFilter->SetSizeX(inImage->GetLargestPossibleRegion().GetSize(0));
    m_ExtractorFilter->SetSizeY(inImage->GetLargestPossibleRegion().GetSize(1));
    m_ExtractorFilter->SetChannel(GetParameterInt("channel"));
    m_ExtractorFilter->UpdateOutputInformation();
  
    m_ClampFilter = ClampFilterType::New();
    m_ClampFilter->SetInput(m_ExtractorFilter->GetOutput());
    m_ClampFilter->SetLower(GetParameterFloat("parameters.min"));
    m_ClampFilter->SetUpper(GetParameterFloat("parameters.max"));
  
    m_HarTexFilter    = HarTexturesFilterType::New();
    m_HarImageList    = ImageListType::New();
    m_HarConcatener   = ImageListToVectorImageFilterType::New();
  
    m_AdvTexFilter  = AdvTexturesFilterType::New();
    m_AdvImageList  = ImageListType::New();
    m_AdvConcatener = ImageListToVectorImageFilterType::New();
  
    m_HigTexFilter  = HigTexturesFilterType::New();
    m_HigImageList  = ImageListType::New();
    m_HigConcatener = ImageListToVectorImageFilterType::New();
  
    if( texType == "simple" )
      {
      m_HarTexFilter->SetInput(const_cast<FloatImageType*>(m_ClampFilter->GetOutput()));
      m_HarTexFilter->SetRadius(radius);
      m_HarTexFilter->SetOffset(offset);
      m_HarTexFilter->SetInputImageMinimum(GetParameterFloat("parameters.min"));
      m_HarTexFilter->SetInputImageMaximum(GetParameterFloat("parameters.max"));
      m_HarTexFilter->SetNumberOfBinsPerAxis(GetParameterInt("parameters.nbbin"));
      m_HarTexFilter->SetSubsampleFactor(stepping);
      m_HarTexFilter->SetSubsampleOffset(stepOffset);
      m_HarTexFilter->UpdateOutputInformation();
      m_HarImageList->PushBack(m_HarTexFilter->GetEnergyOutput());
      m_HarImageList->PushBack(m_HarTexFilter->GetEntropyOutput());
      m_HarImageList->PushBack(m_HarTexFilter->GetCorrelationOutput());
      m_HarImageList->PushBack(m_HarTexFilter->GetInverseDifferenceMomentOutput());
      m_HarImageList->PushBack(m_HarTexFilter->GetInertiaOutput());
      m_HarImageList->PushBack(m_HarTexFilter->GetClusterShadeOutput());
      m_HarImageList->PushBack(m_HarTexFilter->GetClusterProminenceOutput());
      m_HarImageList->PushBack(m_HarTexFilter->GetHaralickCorrelationOutput());
      m_HarConcatener->SetInput(m_HarImageList);
      SetParameterOutputImage("out", m_HarConcatener->GetOutput());
      }
  
    if( texType == "advanced" )
      {
      m_AdvTexFilter->SetInput(const_cast<FloatImageType*>(m_ClampFilter->GetOutput()));
      m_AdvTexFilter->SetRadius(radius);
      m_AdvTexFilter->SetOffset(offset);
      m_AdvTexFilter->SetInputImageMinimum(GetParameterFloat("parameters.min"));
      m_AdvTexFilter->SetInputImageMaximum(GetParameterFloat("parameters.max"));
      m_AdvTexFilter->SetNumberOfBinsPerAxis(GetParameterInt("parameters.nbbin"));
      m_AdvTexFilter->SetSubsampleFactor(stepping);
      m_AdvTexFilter->SetSubsampleOffset(stepOffset);
      m_AdvImageList->PushBack(m_AdvTexFilter->GetMeanOutput());
      m_AdvImageList->PushBack(m_AdvTexFilter->GetVarianceOutput());
      m_AdvImageList->PushBack(m_AdvTexFilter->GetDissimilarityOutput());
      m_AdvImageList->PushBack(m_AdvTexFilter->GetSumAverageOutput());
      m_AdvImageList->PushBack(m_AdvTexFilter->GetSumVarianceOutput());
      m_AdvImageList->PushBack(m_AdvTexFilter->GetSumEntropyOutput());
      m_AdvImageList->PushBack(m_AdvTexFilter->GetDifferenceEntropyOutput());
      m_AdvImageList->PushBack(m_AdvTexFilter->GetDifferenceVarianceOutput());
      m_AdvImageList->PushBack(m_AdvTexFilter->GetIC1Output());
      m_AdvImageList->PushBack(m_AdvTexFilter->GetIC2Output());
      m_AdvConcatener->SetInput(m_AdvImageList);
      SetParameterOutputImage("out", m_AdvConcatener->GetOutput());
      }
  
    if( texType == "higher" )
      {
      m_HigTexFilter->SetInput(const_cast<FloatImageType*>(m_ClampFilter->GetOutput()));
      m_HigTexFilter->SetRadius(radius);
      m_HigTexFilter->SetOffset(offset);
      m_HigTexFilter->SetInputImageMinimum(GetParameterFloat("parameters.min"));
      m_HigTexFilter->SetInputImageMaximum(GetParameterFloat("parameters.max"));
      m_HigTexFilter->SetNumberOfBinsPerAxis(GetParameterInt("parameters.nbbin"));
      m_HigTexFilter->SetSubsampleFactor(stepping);
      m_HigTexFilter->SetSubsampleOffset(stepOffset);
      m_HigImageList->PushBack(m_HigTexFilter->GetShortRunEmphasisOutput());
      m_HigImageList->PushBack(m_HigTexFilter->GetLongRunEmphasisOutput());
      m_HigImageList->PushBack(m_HigTexFilter->GetGreyLevelNonuniformityOutput());
      m_HigImageList->PushBack(m_HigTexFilter->GetRunLengthNonuniformityOutput());
      m_HigImageList->PushBack(m_HigTexFilter->GetLowGreyLevelRunEmphasisOutput());
      m_HigImageList->PushBack(m_HigTexFilter->GetHighGreyLevelRunEmphasisOutput());
      m_HigImageList->PushBack(m_HigTexFilter->GetShortRunLowGreyLevelEmphasisOutput());
      m_HigImageList->PushBack(m_HigTexFilter->GetShortRunHighGreyLevelEmphasisOutput());
      m_HigImageList->PushBack(m_HigTexFilter->GetLongRunLowGreyLevelEmphasisOutput());
      m_HigImageList->PushBack(m_HigTexFilter->GetLongRunHighGreyLevelEmphasisOutput());
      m_HigConcatener->SetInput(m_HigImageList);
      SetParameterOutputImage("out", m_HigConcatener->GetOutput());
      }
  
  }
  ExtractorFilterType::Pointer m_ExtractorFilter;
  ClampFilterType::Pointer     m_ClampFilter;
  
  HarTexturesFilterType::Pointer            m_HarTexFilter;
  ImageListType::Pointer                    m_HarImageList;
  ImageListToVectorImageFilterType::Pointer m_HarConcatener;
  AdvTexturesFilterType::Pointer            m_AdvTexFilter;
  ImageListType::Pointer                    m_AdvImageList;
  ImageListToVectorImageFilterType::Pointer m_AdvConcatener;
  HigTexturesFilterType::Pointer            m_HigTexFilter;
  ImageListType::Pointer                    m_HigImageList;
  ImageListToVectorImageFilterType::Pointer m_HigConcatener;
  };
  }
  }
  
  OTB_APPLICATION_EXPORT(otb::Wrapper::HaralickTextureExtraction)
  