otbLSGRM.cxx

#include "itkFixedArray.h"
#include "itkObjectFactory.h"

// Elevation handler
#include "otbWrapperElevationParametersHandler.h"
#include "otbWrapperApplicationFactory.h"

// Application engine
#include "otbStandardFilterWatcher.h"
#include "itkFixedArray.h"
#include "itkImageSource.h"

// LSGRM
#include <iostream>
#include "lsgrmBaatzSegmenter.h"
#include "lsgrmSpringSegmenter.h"
#include "lsgrmFullLambdaScheduleSegmenter.h"
#include "lsgrmController.h"

// system tools
#include <itksys/SystemTools.hxx>

namespace otb
{

namespace Wrapper
{

class LSGRM : public Application
{
public:
  /** Standard class typedefs. */
  typedef LSGRM                         Self;
  typedef Application                   Superclass;
  typedef itk::SmartPointer<Self>       Pointer;
  typedef itk::SmartPointer<const Self> ConstPointer;

  /** Standard macro */
  itkNewMacro(Self);
  itkTypeMacro(LSGRM, Application);

  /** Useful typedefs */
  typedef otb::VectorImage<float, 2>                    ImageType;
  typedef lsgrm::BaatzSegmenter<ImageType>              BaatzSegmenterType;
  typedef lsgrm::SpringSegmenter<ImageType>             SpringSegmenterType;
  typedef lsgrm::FullLambdaScheduleSegmenter<ImageType> FLSSegmenterType;

private:

  /* Tiling mode choice */
  enum TilingMode
  {
    TILING_AUTO,
    TILING_USER,
    TILING_NONE
  };

  /* Criterion choice */
  enum Criterion
  {
    CRITERION_BAATZ,
    CRITERION_SPRING,
    CRITERION_FLS
  };

  void DoInit()
  {
    SetName("GenericRegionMerging");
    SetDescription("This application allows to use the Large Scale Generic Region Merging library "
        "(LSGRM) and provides currently 3 homogeneity criteria: Euclidean Distance, "
        "Full Lambda Schedule and Baatz & Schape criterion.");

    // Input and Output images
    AddParameter(ParameterType_InputImage, "in", "Input Image");
    AddParameter(ParameterType_OutputImage, "out", "Ouput Label Image");
    SetDefaultOutputPixelType("out", ImagePixelType_uint32);

    // Criterion choice
    AddParameter(ParameterType_Choice, "criterion", "Homogeneity criterion to use");
    AddChoice("criterion.bs", "Baatz & Schape");
    AddChoice("criterion.ed", "Euclidean Distance");
    AddChoice("criterion.fls", "Full Lambda Schedule");

    // Generic parameters
    AddParameter(ParameterType_Float, "threshold", "Threshold for the criterion");
    AddParameter(ParameterType_Int, "niter", "Maximum number of iterations");
    SetDefaultParameterInt("niter", 75);
    MandatoryOff("niter");

    // Specific parameters for Baatz & Schape
    AddParameter(ParameterType_Float, "criterion.bs.cw", "Weight for the spectral homogeneity");
    SetDefaultParameterFloat("criterion.bs.cw", 0.5);
    MandatoryOff("criterion.bs.cw");
    AddParameter(ParameterType_Float, "criterion.bs.sw", "Weight for the spatial homogeneity");
    SetDefaultParameterFloat("criterion.bs.sw", 0.5);
    MandatoryOff("criterion.bs.sw");

    // For large scale
    AddParameter(ParameterType_Directory, "tmpdir", "Directory for temporary files");
    AddParameter(ParameterType_Choice, "tiling", "Tiling layout for the large scale segmentation");
    AddChoice("tiling.auto", "Automatic tiling layout");
    AddChoice("tiling.user", "User tiling layout");
    AddParameter(ParameterType_Int, "tiling.user.sizex", "Tiles width");
    AddParameter(ParameterType_Int, "tiling.user.sizey", "Tiles height");
    AddParameter(ParameterType_Int, "tiling.user.nfirstiter", "Number of first iterations");
    AddParameter(ParameterType_Int, "tiling.user.memory", "Available memory");
    AddChoice("tiling.none", "No tiling layout");
  }

  void DoUpdateParameters()
  {
  }

  /*
   * Return a prefix for temporary files
   */
  std::string GetTemporaryFilesPrefix()
  {

    // Get output filename (without extension)
    std::string outfname = GetParameterString("out");
    std::string outbfname = itksys::SystemTools::GetFilenameWithoutExtension(outfname.c_str());

    // Get specified temporary directory
    std::string tmpdir = GetParameterAsString("tmpdir");
    if (!tmpdir.empty())
      {
      // A temporary directory is specified: we check that it ends with a POSIX separator
      if (tmpdir[tmpdir.size()-1] != '/')
        {
        // If not, we add the separator
        tmpdir.append("/");
        }
      }

    // Check that the directory exists
    if (!itksys::SystemTools::FileExists(tmpdir.c_str(),false))
      {
      otbAppLogFATAL("The directory " << tmpdir << " does not exist.");
      }

    // Return the prefix
    std::string prefix = tmpdir + outbfname;
    return prefix;
  }

  /*
   * This function sets the generic parameters of a controller and runs the segmentation
   */
  template<class TSegmenter>
  UInt32ImageType::Pointer SetGenericParametersAndRunSegmentation(const typename TSegmenter::ParamType params){

    // Instantiate the controller
    typedef typename lsgrm::Controller<TSegmenter> ControlerType;
    typename ControlerType::Pointer controller = ControlerType::New();

    // Set specific parameters
    controller->SetSpecificParameters(params);

    // Set input image
    controller->SetInputImage(GetParameterFloatVectorImage("in"));

    // Set threshold
    float thres = GetParameterFloat("threshold");
    controller->SetThreshold(thres*thres);

    // Set number of iterations
    controller->SetNumberOfIterations(GetParameterInt("niter"));

    // Set temporary files prefix
    controller->SetTemporaryFilesPrefix(this->GetTemporaryFilesPrefix());

    // Switch tiling mode
    int inputTilingMode = GetParameterInt("tiling");
    if (inputTilingMode == TILING_AUTO)
      {
      // Automatic mode
      controller->SetTilingModeAuto();
      }
    else if (inputTilingMode == TILING_USER)
      {
      // User mode
      controller->SetTilingModeUser();
      controller->SetTileWidth(GetParameterInt("tiling.user.sizex"));
      controller->SetTileHeight(GetParameterInt("tiling.user.sizey"));
      controller->SetNumberOfFirstIterations(GetParameterInt("tiling.user.nfirstiter"));
      controller->SetInternalMemoryAvailable(GetParameterInt("tiling.user.memory"));
      }
    else if (inputTilingMode == TILING_NONE)
      {
      // None mode
      controller->SetTilingModeNone();
      }
    else
      {
      otbAppLogFATAL("Unknow tiling mode!");
      }

    // Run the segmentation
    controller->RunSegmentation();

    // Get temporary files list
    m_TemporaryFilesList = controller->GetTemporaryFilesList();

    // Return the label image
    return controller->GetLabeledClusteredOutput();
  }

  void DoExecute()
  {
    /*
        To add:
        the output directory in case the global graph cannot fit in memory
        TODO: It seems to be a cast-related bug when changing the output pixel type (e.g. uint16) !
     */

    // Input image
    ImageType::Pointer inputImage = GetParameterFloatVectorImage("in");

    // Output image
    UInt32ImageType::Pointer labelImage = UInt32ImageType::New();

    // Switch criterion
    int inputCriterion = GetParameterInt("criterion");
    if (inputCriterion == CRITERION_BAATZ)
      {
      grm::BaatzParam params;
      params.m_SpectralWeight = GetParameterFloat("criterion.bs.cw");
      params.m_ShapeWeight = GetParameterFloat("criterion.bs.sw");
      labelImage = SetGenericParametersAndRunSegmentation<BaatzSegmenterType>(params);
      }
    else if (inputCriterion == CRITERION_SPRING)
      {
      grm::SpringParam params;
      labelImage = SetGenericParametersAndRunSegmentation<SpringSegmenterType>(params);
      }
    else if (inputCriterion == CRITERION_FLS)
      {
      grm::FLSParam params;
      labelImage = SetGenericParametersAndRunSegmentation<FLSSegmenterType>(params);
      }
    else
      {
      otbAppLogFATAL("Unknow criterion!")
      }

    // Set output image projection, origin and spacing for labelImage
    labelImage->SetProjectionRef(inputImage->GetProjectionRef());
    labelImage->SetOrigin(inputImage->GetOrigin());
    labelImage->SetSpacing(inputImage->GetSpacing());
    SetParameterOutputImage<UInt32ImageType>("out", labelImage);

  }

  void AfterExecuteAndWriteOutputs()
  {

#ifdef OTB_USE_MPI
    // When MPI is activated, only the master thread proceed
    if (otb::MPIConfig::Instance()->GetMyRank() != 0)
      return;
#endif

    // Delete temporary files
    for (unsigned int i = 0 ; i < m_TemporaryFilesList.size() ; i++)
      {
      if( remove(m_TemporaryFilesList.at(i).c_str() ) != 0  )
        {
        otbAppLogWARNING( "Error deleting file " << m_TemporaryFilesList.at(i) );
        }
      }
  }

private:
  std::vector<std::string> m_TemporaryFilesList;

}; // app class
} // end of namespace wrapper
} // end of namespace otb

OTB_APPLICATION_EXPORT(otb::Wrapper::LSGRM)