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remi cresson authoredf6fad8b1
#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"// Graph to label image (streaming version)#include "otbStreamingGraphToImageFilter.h"#include "otbStreamingImageVirtualWriter.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()7172737475767778798081828384858687888990919293949596979899100101102103104105106107108109110111112113114115116117118119120121122123124125126127128129130131132133134135136137138139140
{
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");
MandatoryOff("tmpdir");
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");
AddChoice("tiling.none", "No tiling layout");
AddParameter(ParameterType_Int, "memory", "Restrict memory use (mb)");
MandatoryOff("memory");
}
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;
if (HasValue("tmpdir"))
{
tmpdir= GetParameterAsString("tmpdir");
}
else
{
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tmpdir = itksys::SystemTools::GetFilenamePath(outfname);
}
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.");
}
otbAppLogINFO("Using temporary directory " << tmpdir);
}
// 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>
void
SetGenericParametersAndRunSegmentation(const typename TSegmenter::ParamType params){
// Instantiate the controller
typedef typename lsgrm::Controller<TSegmenter> ControlerType;
typename ControlerType::Pointer controller = ControlerType::New();
using GraphType = typename ControlerType::GraphType;
// Set specific parameters
controller->SetSpecificParameters(params);
// Set input image
ImageType::Pointer inputImage = GetParameterFloatVectorImage("in");
controller->SetInputImage(inputImage);
// 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"));
}
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else if (inputTilingMode == TILING_NONE)
{
// None mode
controller->SetTilingModeNone();
}
else
{
otbAppLogFATAL("Unknown tiling mode!");
}
// Input RAM value?
if (HasValue("memory"))
{
otbAppLogINFO("Setting maximum memory to " << GetParameterInt("memory") << " MBytes");
controller->SetInternalMemoryAvailable(GetParameterInt("memory"));
}
// Run the segmentation
controller->RunSegmentation();
// Prepare the label image source
typedef lsgrm::StreamingGraphToImageFilter<GraphType, UInt32ImageType> LabelImageSourceType;
typename LabelImageSourceType::Pointer labelImageSource = LabelImageSourceType::New();
labelImageSource->SetGraph(controller->GetOutputGraph());
labelImageSource->SetOutputSize(inputImage->GetLargestPossibleRegion().GetSize());
labelImageSource->SetOutputOrigin(inputImage->GetOrigin());
labelImageSource->SetOutputSpacing(inputImage->GetSpacing());
labelImageSource->SetOutputProjectionRef(inputImage->GetProjectionRef());
labelImageSource->GenerateOutputInformation();
m_LabelImageSource = static_cast<itk::ImageSource<UInt32ImageType>*>(labelImageSource);
SetParameterOutputImage<UInt32ImageType>("out", m_LabelImageSource->GetOutput());
// TODO: find an intelligent value of RAM
if (dynamic_cast<OutputImageParameter*>(GetParameterByKey("out")))
{
OutputImageParameter* paramDown = dynamic_cast<OutputImageParameter*>(GetParameterByKey("out"));
paramDown->SetRAMValue(256);
}
// Get temporary files list
m_TemporaryFilesList = controller->GetTemporaryFilesList();
}
void DoExecute()
{
ImageType::Pointer inputImage = GetParameterFloatVectorImage("in");
// 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");
SetGenericParametersAndRunSegmentation<BaatzSegmenterType>(params);
}
else if (inputCriterion == CRITERION_SPRING)
{
grm::SpringParam params;
SetGenericParametersAndRunSegmentation<SpringSegmenterType>(params);
}
else if (inputCriterion == CRITERION_FLS)
{
grm::FLSParam params;
SetGenericParametersAndRunSegmentation<FLSSegmenterType>(params);
}
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else
{
otbAppLogFATAL("Unknow criterion!")
}
}
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;
itk::ImageSource<UInt32ImageType>::Pointer m_LabelImageSource;
}; // app class
} // end of namespace wrapper
} // end of namespace otb
OTB_APPLICATION_EXPORT(otb::Wrapper::LSGRM)