Commit 9c4810ec authored by remi cresson's avatar remi cresson

Merge branch 'msbuild_portability'

parents a8984a3b 555fe98c
...@@ -17,6 +17,10 @@ ...@@ -17,6 +17,10 @@
#include "lsgrmFullLambdaScheduleSegmenter.h" #include "lsgrmFullLambdaScheduleSegmenter.h"
#include "lsgrmController.h" #include "lsgrmController.h"
// Graph to label image (streaming version)
#include "otbStreamingGraphToImageFilter.h"
#include "otbStreamingImageVirtualWriter.h"
// system tools // system tools
#include <itksys/SystemTools.hxx> #include <itksys/SystemTools.hxx>
...@@ -65,6 +69,7 @@ private: ...@@ -65,6 +69,7 @@ private:
void DoInit() void DoInit()
{ {
SetName("GenericRegionMerging"); SetName("GenericRegionMerging");
SetDescription("This application allows to use the Large Scale Generic Region Merging library " SetDescription("This application allows to use the Large Scale Generic Region Merging library "
"(LSGRM) and provides currently 3 homogeneity criteria: Euclidean Distance, " "(LSGRM) and provides currently 3 homogeneity criteria: Euclidean Distance, "
...@@ -107,6 +112,7 @@ private: ...@@ -107,6 +112,7 @@ private:
AddChoice("tiling.none", "No tiling layout"); AddChoice("tiling.none", "No tiling layout");
AddParameter(ParameterType_Int, "memory", "Restrict memory use (mb)"); AddParameter(ParameterType_Int, "memory", "Restrict memory use (mb)");
MandatoryOff("memory"); MandatoryOff("memory");
} }
...@@ -128,28 +134,28 @@ private: ...@@ -128,28 +134,28 @@ private:
std::string tmpdir; std::string tmpdir;
if (HasValue("tmpdir")) if (HasValue("tmpdir"))
{ {
tmpdir= GetParameterAsString("tmpdir"); tmpdir= GetParameterAsString("tmpdir");
} }
else else
{ {
tmpdir = itksys::SystemTools::GetFilenamePath(outfname); tmpdir = itksys::SystemTools::GetFilenamePath(outfname);
} }
if (!tmpdir.empty()) if (!tmpdir.empty())
{ {
// A temporary directory is specified: we check that it ends with a POSIX separator // A temporary directory is specified: we check that it ends with a POSIX separator
if (tmpdir[tmpdir.size()-1] != '/') if (tmpdir[tmpdir.size()-1] != '/')
{ {
// If not, we add the separator // If not, we add the separator
tmpdir.append("/"); tmpdir.append("/");
} }
// Check that the directory exists // Check that the directory exists
if (!itksys::SystemTools::FileExists(tmpdir.c_str(),false)) if (!itksys::SystemTools::FileExists(tmpdir.c_str(),false))
{ {
otbAppLogFATAL("The directory " << tmpdir << " does not exist."); otbAppLogFATAL("The directory " << tmpdir << " does not exist.");
} }
otbAppLogINFO("Using temporary directory " << tmpdir); otbAppLogINFO("Using temporary directory " << tmpdir);
} }
...@@ -162,17 +168,20 @@ private: ...@@ -162,17 +168,20 @@ private:
* This function sets the generic parameters of a controller and runs the segmentation * This function sets the generic parameters of a controller and runs the segmentation
*/ */
template<class TSegmenter> template<class TSegmenter>
UInt32ImageType::Pointer SetGenericParametersAndRunSegmentation(const typename TSegmenter::ParamType params){ void
SetGenericParametersAndRunSegmentation(const typename TSegmenter::ParamType params){
// Instantiate the controller // Instantiate the controller
typedef typename lsgrm::Controller<TSegmenter> ControlerType; typedef typename lsgrm::Controller<TSegmenter> ControlerType;
typename ControlerType::Pointer controller = ControlerType::New(); typename ControlerType::Pointer controller = ControlerType::New();
using GraphType = typename ControlerType::GraphType;
// Set specific parameters // Set specific parameters
controller->SetSpecificParameters(params); controller->SetSpecificParameters(params);
// Set input image // Set input image
controller->SetInputImage(GetParameterFloatVectorImage("in")); ImageType::Pointer inputImage = GetParameterFloatVectorImage("in");
controller->SetInputImage(inputImage);
// Set threshold // Set threshold
float thres = GetParameterFloat("threshold"); float thres = GetParameterFloat("threshold");
...@@ -188,86 +197,92 @@ private: ...@@ -188,86 +197,92 @@ private:
int inputTilingMode = GetParameterInt("tiling"); int inputTilingMode = GetParameterInt("tiling");
if (inputTilingMode == TILING_AUTO) if (inputTilingMode == TILING_AUTO)
{ {
// Automatic mode // Automatic mode
controller->SetTilingModeAuto(); controller->SetTilingModeAuto();
} }
else if (inputTilingMode == TILING_USER) else if (inputTilingMode == TILING_USER)
{ {
// User mode // User mode
controller->SetTilingModeUser(); controller->SetTilingModeUser();
controller->SetTileWidth(GetParameterInt("tiling.user.sizex")); controller->SetTileWidth(GetParameterInt("tiling.user.sizex"));
controller->SetTileHeight(GetParameterInt("tiling.user.sizey")); controller->SetTileHeight(GetParameterInt("tiling.user.sizey"));
controller->SetNumberOfFirstIterations(GetParameterInt("tiling.user.nfirstiter")); controller->SetNumberOfFirstIterations(GetParameterInt("tiling.user.nfirstiter"));
} }
else if (inputTilingMode == TILING_NONE) else if (inputTilingMode == TILING_NONE)
{ {
// None mode // None mode
controller->SetTilingModeNone(); controller->SetTilingModeNone();
} }
else else
{ {
otbAppLogFATAL("Unknown tiling mode!"); otbAppLogFATAL("Unknown tiling mode!");
} }
// Input RAM value? // Input RAM value?
if (HasValue("memory")) if (HasValue("memory"))
{ {
otbAppLogINFO("Setting maximum memory to " << GetParameterInt("memory") << " MBytes"); otbAppLogINFO("Setting maximum memory to " << GetParameterInt("memory") << " MBytes");
controller->SetInternalMemoryAvailable(GetParameterInt("memory")); controller->SetInternalMemoryAvailable(GetParameterInt("memory"));
} }
// Run the segmentation // Run the segmentation
controller->RunSegmentation(); 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 // Get temporary files list
m_TemporaryFilesList = controller->GetTemporaryFilesList(); m_TemporaryFilesList = controller->GetTemporaryFilesList();
// Return the label image
return controller->GetLabeledClusteredOutput();
} }
void DoExecute() void DoExecute()
{ {
/*
TODO: the output directory in case the global graph cannot fit in memory (lsgrmController.txx)
*/
// Input image
ImageType::Pointer inputImage = GetParameterFloatVectorImage("in"); ImageType::Pointer inputImage = GetParameterFloatVectorImage("in");
// Output image
UInt32ImageType::Pointer labelImage = UInt32ImageType::New();
// Switch criterion // Switch criterion
int inputCriterion = GetParameterInt("criterion"); int inputCriterion = GetParameterInt("criterion");
if (inputCriterion == CRITERION_BAATZ) if (inputCriterion == CRITERION_BAATZ)
{ {
grm::BaatzParam params; grm::BaatzParam params;
params.m_SpectralWeight = GetParameterFloat("criterion.bs.cw"); params.m_SpectralWeight = GetParameterFloat("criterion.bs.cw");
params.m_ShapeWeight = GetParameterFloat("criterion.bs.sw"); params.m_ShapeWeight = GetParameterFloat("criterion.bs.sw");
labelImage = SetGenericParametersAndRunSegmentation<BaatzSegmenterType>(params); SetGenericParametersAndRunSegmentation<BaatzSegmenterType>(params);
} }
else if (inputCriterion == CRITERION_SPRING) else if (inputCriterion == CRITERION_SPRING)
{ {
grm::SpringParam params; grm::SpringParam params;
labelImage = SetGenericParametersAndRunSegmentation<SpringSegmenterType>(params); SetGenericParametersAndRunSegmentation<SpringSegmenterType>(params);
} }
else if (inputCriterion == CRITERION_FLS) else if (inputCriterion == CRITERION_FLS)
{ {
grm::FLSParam params; grm::FLSParam params;
labelImage = SetGenericParametersAndRunSegmentation<FLSSegmenterType>(params); SetGenericParametersAndRunSegmentation<FLSSegmenterType>(params);
} }
else else
{ {
otbAppLogFATAL("Unknow criterion!") 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() void AfterExecuteAndWriteOutputs()
...@@ -282,15 +297,16 @@ private: ...@@ -282,15 +297,16 @@ private:
// Delete temporary files // Delete temporary files
for (unsigned int i = 0 ; i < m_TemporaryFilesList.size() ; i++) for (unsigned int i = 0 ; i < m_TemporaryFilesList.size() ; i++)
{ {
if( remove(m_TemporaryFilesList.at(i).c_str() ) != 0 ) if( remove(m_TemporaryFilesList.at(i).c_str() ) != 0 )
{ {
otbAppLogWARNING( "Error deleting file " << m_TemporaryFilesList.at(i) ); otbAppLogWARNING( "Error deleting file " << m_TemporaryFilesList.at(i) );
} }
} }
} }
private: private:
std::vector<std::string> m_TemporaryFilesList; std::vector<std::string> m_TemporaryFilesList;
itk::ImageSource<UInt32ImageType>::Pointer m_LabelImageSource;
}; // app class }; // app class
} // end of namespace wrapper } // end of namespace wrapper
......
...@@ -6,6 +6,7 @@ ...@@ -6,6 +6,7 @@
#include "itkObject.h" #include "itkObject.h"
#include "itkMacro.h" #include "itkMacro.h"
namespace lsgrm namespace lsgrm
{ {
template<class TSegmenter> template<class TSegmenter>
...@@ -30,6 +31,7 @@ public: ...@@ -30,6 +31,7 @@ public:
using ImageType = typename SegmenterType::ImageType; using ImageType = typename SegmenterType::ImageType;
using LabelImageType = typename SegmenterType::LabelImageType; using LabelImageType = typename SegmenterType::LabelImageType;
using SegmentationParameterType = typename SegmenterType::ParamType; using SegmentationParameterType = typename SegmenterType::ParamType;
using GraphType = typename SegmenterType::GraphType;
/* Default constructor and destructor. */ /* Default constructor and destructor. */
Controller(); Controller();
...@@ -48,7 +50,6 @@ public: ...@@ -48,7 +50,6 @@ public:
void SetTilingModeUser(){m_TilingMode = LSGRM_TILING_USER; Modified();}; void SetTilingModeUser(){m_TilingMode = LSGRM_TILING_USER; Modified();};
void SetTilingModeAuto(){m_TilingMode = LSGRM_TILING_AUTO; Modified();}; void SetTilingModeAuto(){m_TilingMode = LSGRM_TILING_AUTO; Modified();};
typename LabelImageType::Pointer GetLabeledClusteredOutput();
std::vector<std::string> GetTemporaryFilesList(); std::vector<std::string> GetTemporaryFilesList();
itkGetMacro(Margin, unsigned int); itkGetMacro(Margin, unsigned int);
...@@ -77,6 +78,8 @@ public: ...@@ -77,6 +78,8 @@ public:
itkGetMacro(TileHeight, unsigned int); itkGetMacro(TileHeight, unsigned int);
itkSetMacro(TileHeight, unsigned int); itkSetMacro(TileHeight, unsigned int);
itkGetMacro(OutputGraph, GraphType);
private: private:
/** Enum for tiling mode */ /** Enum for tiling mode */
...@@ -91,7 +94,7 @@ private: ...@@ -91,7 +94,7 @@ private:
void ComputeMaximumStabilityMargin(unsigned int width, unsigned int height, unsigned int &iter, unsigned int &margin); void ComputeMaximumStabilityMargin(unsigned int width, unsigned int height, unsigned int &iter, unsigned int &margin);
void CheckMemorySize(); void CheckMemorySize();
unsigned int GetNodeMemory(); unsigned int GetNodeMemory();
long unsigned int GetMaximumNumberOfNodesInMemory(); std::size_t GetMaximumNumberOfNodesInMemory();
/* Parameters given by the user */ /* Parameters given by the user */
std::string m_TemporaryFilesPrefix; // Path used to store intermediate files during the process. std::string m_TemporaryFilesPrefix; // Path used to store intermediate files during the process.
...@@ -116,7 +119,8 @@ private: ...@@ -116,7 +119,8 @@ private:
LSGRMTilingMode m_TilingMode; // tiling mode (none/user/auto) LSGRMTilingMode m_TilingMode; // tiling mode (none/user/auto)
unsigned int m_Margin; // stability margin related to m_NumberOfFirstIterations unsigned int m_Margin; // stability margin related to m_NumberOfFirstIterations
std::vector<ProcessingTile> m_Tiles; // list of tiles std::vector<ProcessingTile> m_Tiles; // list of tiles
typename LabelImageType::Pointer m_LabelImage; // output label image GraphType m_OutputGraph; // Output graph
}; };
} // end of namespace lsgrm } // end of namespace lsgrm
......
...@@ -18,6 +18,7 @@ Controller<TSegmenter>::Controller() ...@@ -18,6 +18,7 @@ Controller<TSegmenter>::Controller()
m_NbTilesY = 0; m_NbTilesY = 0;
m_Threshold = 75; m_Threshold = 75;
m_Memory = 0; m_Memory = 0;
} }
template<class TSegmenter> template<class TSegmenter>
...@@ -87,6 +88,7 @@ void Controller<TSegmenter>::RunSegmentation() ...@@ -87,6 +88,7 @@ void Controller<TSegmenter>::RunSegmentation()
// Run first partial segmentation // Run first partial segmentation
boost::timer t; t.restart(); boost::timer t; t.restart();
auto accumulatedMemory = RunFirstPartialSegmentation<TSegmenter>( auto accumulatedMemory = RunFirstPartialSegmentation<TSegmenter>(
m_InputImage, m_InputImage,
m_SpecificParameters, m_SpecificParameters,
...@@ -139,7 +141,7 @@ void Controller<TSegmenter>::RunSegmentation() ...@@ -139,7 +141,7 @@ void Controller<TSegmenter>::RunSegmentation()
numberOfIterationsRemaining -= numberOfIterationsForPartialSegmentations; numberOfIterationsRemaining -= numberOfIterationsForPartialSegmentations;
} }
} }
#ifdef OTB_USE_MPI #ifdef OTB_USE_MPI
// Only the master process is doing the next part // Only the master process is doing the next part
// TODO: Use the MPI process wich has the largest amount of memory // TODO: Use the MPI process wich has the largest amount of memory
...@@ -150,7 +152,7 @@ void Controller<TSegmenter>::RunSegmentation() ...@@ -150,7 +152,7 @@ void Controller<TSegmenter>::RunSegmentation()
if(accumulatedMemory <= m_Memory) if(accumulatedMemory <= m_Memory)
{ {
// Merge all the graphs // Merge all the graphs
m_LabelImage = MergeAllGraphsAndAchieveSegmentation<TSegmenter>( m_OutputGraph = MergeAllGraphsAndAchieveSegmentation<TSegmenter>(
m_SpecificParameters, m_SpecificParameters,
m_Threshold, m_Threshold,
m_Tiles, m_Tiles,
...@@ -195,14 +197,15 @@ void Controller<TSegmenter>::RunSegmentation() ...@@ -195,14 +197,15 @@ void Controller<TSegmenter>::RunSegmentation()
segmenter.SetInput(m_InputImage); segmenter.SetInput(m_InputImage);
segmenter.Update(); segmenter.Update();
// Get label image m_OutputGraph = segmenter.m_Graph;
m_LabelImage = segmenter.GetLabeledClusteredOutput();
} }
else else
{ {
itkExceptionMacro(<<"Unknow tiling mode!"); itkExceptionMacro(<<"Unknow tiling mode!");
} }
// TODO: [MPI] broadcast the graph to other nodes
} }
/* /*
...@@ -264,7 +267,7 @@ void Controller<TSegmenter>::CheckMemorySize() ...@@ -264,7 +267,7 @@ void Controller<TSegmenter>::CheckMemorySize()
* Compute the maximum number of nodes which can fit in the memory * Compute the maximum number of nodes which can fit in the memory
*/ */
template<class TSegmenter> template<class TSegmenter>
long unsigned int Controller<TSegmenter>::GetMaximumNumberOfNodesInMemory() std::size_t Controller<TSegmenter>::GetMaximumNumberOfNodesInMemory()
{ {
itkDebugMacro(<< "Computing maximum number of nodes in memory"); itkDebugMacro(<< "Computing maximum number of nodes in memory");
...@@ -433,16 +436,16 @@ void Controller<TSegmenter>::SetSpecificParameters(const SegmentationParameterTy ...@@ -433,16 +436,16 @@ void Controller<TSegmenter>::SetSpecificParameters(const SegmentationParameterTy
m_SpecificParameters = params; m_SpecificParameters = params;
} }
template<class TSegmenter> //template<class TSegmenter>
typename Controller<TSegmenter>::LabelImageType::Pointer //typename Controller<TSegmenter>::LabelImageType::Pointer
Controller<TSegmenter>::GetLabeledClusteredOutput() //Controller<TSegmenter>::GetLabeledClusteredOutput()
{ //{
#ifdef OTB_USE_MPI //#ifdef OTB_USE_MPI
// Get the label image from the master process (the one which achieves segmentation) // // Get the label image from the master process (the one which achieves segmentation)
BroadcastImage<typename TSegmenter::LabelImageType>(m_LabelImage); // BroadcastImage<typename TSegmenter::LabelImageType>(m_LabelImage);
#endif //#endif
return m_LabelImage; // return m_LabelImage;
} //}
template <class TSegmenter> template <class TSegmenter>
std::vector<std::string> Controller<TSegmenter>::GetTemporaryFilesList() std::vector<std::string> Controller<TSegmenter>::GetTemporaryFilesList()
......
...@@ -5,7 +5,6 @@ ...@@ -5,7 +5,6 @@
#include "grmGraphOperations.h" #include "grmGraphOperations.h"
#include "otbVectorImage.h" #include "otbVectorImage.h"
#include "otbMultiChannelExtractROI.h" #include "otbMultiChannelExtractROI.h"
#include "itkGrayscaleFillholeImageFilter.h"
namespace lsgrm namespace lsgrm
{ {
...@@ -32,7 +31,7 @@ typename TSegmenter::ImageType::Pointer ReadImageRegion( ...@@ -32,7 +31,7 @@ typename TSegmenter::ImageType::Pointer ReadImageRegion(
typename TSegmenter::ImageType::RegionType region); typename TSegmenter::ImageType::RegionType region);
template<class TSegmenter> template<class TSegmenter>
typename TSegmenter::LabelImageType::Pointer typename TSegmenter::GraphType
MergeAllGraphsAndAchieveSegmentation( MergeAllGraphsAndAchieveSegmentation(
const typename TSegmenter::ParamType& params, const typename TSegmenter::ParamType& params,
const float& threshold, const float& threshold,
...@@ -79,13 +78,13 @@ void RemoveUselessNodes(ProcessingTile& tile, ...@@ -79,13 +78,13 @@ void RemoveUselessNodes(ProcessingTile& tile,
template<class TSegmenter> template<class TSegmenter>
void UpdateNeighborsOfNoneDuplicatedNodes(std::unordered_map<long unsigned int, void UpdateNeighborsOfNoneDuplicatedNodes(std::unordered_map<std::size_t,
std::vector<typename TSegmenter::NodePointerType> >& borderPixelMap, std::vector<typename TSegmenter::NodePointerType> >& borderPixelMap,
const unsigned int imageWidth, const unsigned int imageWidth,
const unsigned int imageHeight); const unsigned int imageHeight);
template<class TSegmenter> template<class TSegmenter>
void RemoveDuplicatedNodes(std::unordered_map<long unsigned int, void RemoveDuplicatedNodes(std::unordered_map<std::size_t,
std::vector<typename TSegmenter::NodePointerType> >& borderPixelMap, std::vector<typename TSegmenter::NodePointerType> >& borderPixelMap,
typename TSegmenter::GraphType& graph, typename TSegmenter::GraphType& graph,
const unsigned int imageWidth); const unsigned int imageWidth);
...@@ -97,9 +96,10 @@ void BuildBorderPixelMap(typename TSegmenter::GraphType& graph, ...@@ -97,9 +96,10 @@ void BuildBorderPixelMap(typename TSegmenter::GraphType& graph,
const unsigned int colTile, const unsigned int colTile,
const unsigned int nbTilesX, const unsigned int nbTilesX,
const unsigned int nbTilesY, const unsigned int nbTilesY,
std::unordered_map<long unsigned int, std::unordered_map<std::size_t,
std::vector<typename TSegmenter::NodePointerType> >& borderPixelMap, std::vector<typename TSegmenter::NodePointerType> >& borderPixelMap,
const unsigned int imageWidth); const unsigned int imageWidth,
bool merging = false);
template<class TSegmenter> template<class TSegmenter>
void InsertNodesFromTile(typename TSegmenter::GraphType& graph, void InsertNodesFromTile(typename TSegmenter::GraphType& graph,
......
...@@ -25,7 +25,7 @@ typename TSegmenter::ImageType::Pointer ReadImageRegion( ...@@ -25,7 +25,7 @@ typename TSegmenter::ImageType::Pointer ReadImageRegion(
} }
template<class TSegmenter> template<class TSegmenter>
typename TSegmenter::LabelImageType::Pointer typename TSegmenter::GraphType
MergeAllGraphsAndAchieveSegmentation( MergeAllGraphsAndAchieveSegmentation(
const typename TSegmenter::ParamType& params, const typename TSegmenter::ParamType& params,
const float& threshold, const float& threshold,
...@@ -63,13 +63,13 @@ MergeAllGraphsAndAchieveSegmentation( ...@@ -63,13 +63,13 @@ MergeAllGraphsAndAchieveSegmentation(
{ {
std::cout << "Cleaning nodes of tile " << (row*nbTilesX + col) << " / " << (nbTilesX*nbTilesY) << std::endl; std::cout << "Cleaning nodes of tile " << (row*nbTilesX + col) << " / " << (nbTilesX*nbTilesY) << std::endl;
std::unordered_map<long unsigned int, std::unordered_map<std::size_t,
std::vector<typename TSegmenter::NodePointerType> > borderPixelMap; std::vector<typename TSegmenter::NodePointerType> > borderPixelMap;
std::cout << "\tBuildBorderPixelMap..." << std::endl; std::cout << "\tBuildBorderPixelMap..." << std::endl;
BuildBorderPixelMap<TSegmenter>(segmenter.m_Graph, tiles[row*nbTilesX + col], row, col, BuildBorderPixelMap<TSegmenter>(segmenter.m_Graph, tiles[row*nbTilesX + col], row, col,
nbTilesX, nbTilesY, borderPixelMap, imageWidth); nbTilesX, nbTilesY, borderPixelMap, imageWidth, true);
std::cout << "\tRemoveDuplicatedNodes..." << std::endl; std::cout << "\tRemoveDuplicatedNodes..." << std::endl;
...@@ -91,69 +91,42 @@ MergeAllGraphsAndAchieveSegmentation( ...@@ -91,69 +91,42 @@ MergeAllGraphsAndAchieveSegmentation(
segmenter.SetThreshold(threshold); segmenter.SetThreshold(threshold);
segmenter.SetDoFastSegmentation(false); // was true segmenter.SetDoFastSegmentation(false); // was true
segmenter.SetNumberOfIterations(numberOfIterations); segmenter.SetNumberOfIterations(numberOfIterations);
grm::GraphOperations<TSegmenter>::PerfomAllIterationsWithLMBFAndConstThreshold(segmenter); grm::GraphOperations<TSegmenter>::PerfomAllIterationsWithLMBFAndConstThreshold(segmenter);
// // Write output graph to the output graph directory // patch raf (sort using node id directly --> seems ok)
// WriteGraph<TSegmenter>(segmenter.m_Graph, tmpDir, 0, 0); // Sort the nodes top-->down and left-->right
/*
// Generate the label image std::sort(segmenter.m_Graph.m_Nodes.begin(), segmenter.m_Graph.m_Nodes.end(),
typename TSegmenter::LabelImageType::IndexType index; [imageWidth](const auto & a, const auto & b) -> bool
index.Fill(0); {
typename TSegmenter::LabelImageType::SizeType size; lp::CellLists borderPixelsA, borderPixelsB;
size[0] = imageWidth; lp::ContourOperations::GenerateBorderCells(borderPixelsA, a->m_Contour, a->m_Id, imageWidth);
size[1] = imageHeight; lp::ContourOperations::GenerateBorderCells(borderPixelsB, b->m_Contour, b->m_Id, imageWidth);
typename TSegmenter::LabelImageType::RegionType region(index, size);
const typename TSegmenter::LabelImageType::InternalPixelType noDataLabel = 0; // patch raf (were unsigned int)
typename TSegmenter::LabelImageType::Pointer labelImage = TSegmenter::LabelImageType::New(); std::size_t offA = 0;
labelImage->SetRegions(region); std::size_t offB = 0;
labelImage->Allocate();