Skip to content

LSGRM
LSGRM
Commit 9c4810ec authored by remi cresson's avatar remi cresson
Browse files
Options

Merge branch 'msbuild_portability'

parents a8984a3b 555fe98c
Hide whitespace changes
Inline Side-by-side
Showing with 434 additions and 158 deletions
app/otbLSGRM.cxx
View file @ 9c4810ec
......@@ -17,6 +17,10 @@
#include "lsgrmFullLambdaScheduleSegmenter.h"
#include "lsgrmController.h"
// Graph to label image (streaming version)
#include "otbStreamingGraphToImageFilter.h"
#include "otbStreamingImageVirtualWriter.h"
// system tools
#include <itksys/SystemTools.hxx>
......@@ -65,6 +69,7 @@ private:
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, "
......@@ -107,6 +112,7 @@ private:
AddChoice("tiling.none", "No tiling layout");
AddParameter(ParameterType_Int, "memory", "Restrict memory use (mb)");
MandatoryOff("memory");
}
......@@ -128,28 +134,28 @@ private:
std::string tmpdir;
if (HasValue("tmpdir"))
{
tmpdir= GetParameterAsString("tmpdir");
tmpdir= GetParameterAsString("tmpdir");
}
else
{
tmpdir = itksys::SystemTools::GetFilenamePath(outfname);
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);
// 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);
}
......@@ -162,17 +168,20 @@ private:
* This function sets the generic parameters of a controller and runs the segmentation
*/
template<class TSegmenter>
UInt32ImageType::Pointer SetGenericParametersAndRunSegmentation(const typename TSegmenter::ParamType params){
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
controller->SetInputImage(GetParameterFloatVectorImage("in"));
ImageType::Pointer inputImage = GetParameterFloatVectorImage("in");
controller->SetInputImage(inputImage);
// Set threshold
float thres = GetParameterFloat("threshold");
......@@ -188,86 +197,92 @@ private:
int inputTilingMode = GetParameterInt("tiling");
if (inputTilingMode == TILING_AUTO)
{
// Automatic mode
controller->SetTilingModeAuto();
// 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"));
// User mode
controller->SetTilingModeUser();
controller->SetTileWidth(GetParameterInt("tiling.user.sizex"));
controller->SetTileHeight(GetParameterInt("tiling.user.sizey"));
controller->SetNumberOfFirstIterations(GetParameterInt("tiling.user.nfirstiter"));
}
else if (inputTilingMode == TILING_NONE)
{
// None mode
controller->SetTilingModeNone();
// None mode
controller->SetTilingModeNone();
}
else
{
otbAppLogFATAL("Unknown tiling mode!");
otbAppLogFATAL("Unknown tiling mode!");
}
// Input RAM value?
if (HasValue("memory"))
{
otbAppLogINFO("Setting maximum memory to " << GetParameterInt("memory") << " MBytes");
controller->SetInternalMemoryAvailable(GetParameterInt("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();
// Return the label image
return controller->GetLabeledClusteredOutput();
}
void DoExecute()
{
/*
TODO: the output directory in case the global graph cannot fit in memory (lsgrmController.txx)
*/
// 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);
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;
labelImage = SetGenericParametersAndRunSegmentation<SpringSegmenterType>(params);
grm::SpringParam params;
SetGenericParametersAndRunSegmentation<SpringSegmenterType>(params);
}
else if (inputCriterion == CRITERION_FLS)
{
grm::FLSParam params;
labelImage = SetGenericParametersAndRunSegmentation<FLSSegmenterType>(params);
grm::FLSParam params;
SetGenericParametersAndRunSegmentation<FLSSegmenterType>(params);
}
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()
......@@ -282,15 +297,16 @@ private:
// 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) );
}
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
......
include/lsgrmController.h
View file @ 9c4810ec
......@@ -6,6 +6,7 @@
#include "itkObject.h"
#include "itkMacro.h"
namespace lsgrm
{
template<class TSegmenter>
......@@ -30,6 +31,7 @@ public:
using ImageType = typename SegmenterType::ImageType;
using LabelImageType = typename SegmenterType::LabelImageType;
using SegmentationParameterType = typename SegmenterType::ParamType;
using GraphType = typename SegmenterType::GraphType;
/* Default constructor and destructor. */
Controller();
......@@ -48,7 +50,6 @@ public:
void SetTilingModeUser(){m_TilingMode = LSGRM_TILING_USER; Modified();};
void SetTilingModeAuto(){m_TilingMode = LSGRM_TILING_AUTO; Modified();};
typename LabelImageType::Pointer GetLabeledClusteredOutput();
std::vector<std::string> GetTemporaryFilesList();
itkGetMacro(Margin, unsigned int);
......@@ -77,6 +78,8 @@ public:
itkGetMacro(TileHeight, unsigned int);
itkSetMacro(TileHeight, unsigned int);
itkGetMacro(OutputGraph, GraphType);
private:
/** Enum for tiling mode */
......@@ -91,7 +94,7 @@ private:
void ComputeMaximumStabilityMargin(unsigned int width, unsigned int height, unsigned int &iter, unsigned int &margin);
void CheckMemorySize();
unsigned int GetNodeMemory();
long unsigned int GetMaximumNumberOfNodesInMemory();
std::size_t GetMaximumNumberOfNodesInMemory();
/* Parameters given by the user */
std::string m_TemporaryFilesPrefix; // Path used to store intermediate files during the process.
......@@ -116,7 +119,8 @@ private:
LSGRMTilingMode m_TilingMode; // tiling mode (none/user/auto)
unsigned int m_Margin; // stability margin related to m_NumberOfFirstIterations
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
......
include/lsgrmController.txx
View file @ 9c4810ec
......@@ -18,6 +18,7 @@ Controller<TSegmenter>::Controller()
m_NbTilesY = 0;
m_Threshold = 75;
m_Memory = 0;
}
template<class TSegmenter>
......@@ -87,6 +88,7 @@ void Controller<TSegmenter>::RunSegmentation()
// Run first partial segmentation
boost::timer t; t.restart();
auto accumulatedMemory = RunFirstPartialSegmentation<TSegmenter>(
m_InputImage,
m_SpecificParameters,
......@@ -139,7 +141,7 @@ void Controller<TSegmenter>::RunSegmentation()
numberOfIterationsRemaining -= numberOfIterationsForPartialSegmentations;
}
}
#ifdef OTB_USE_MPI
// Only the master process is doing the next part
// TODO: Use the MPI process wich has the largest amount of memory
......@@ -150,7 +152,7 @@ void Controller<TSegmenter>::RunSegmentation()
if(accumulatedMemory <= m_Memory)
{
// Merge all the graphs
m_LabelImage = MergeAllGraphsAndAchieveSegmentation<TSegmenter>(
m_OutputGraph = MergeAllGraphsAndAchieveSegmentation<TSegmenter>(
m_SpecificParameters,
m_Threshold,
m_Tiles,
......@@ -195,14 +197,15 @@ void Controller<TSegmenter>::RunSegmentation()
segmenter.SetInput(m_InputImage);
segmenter.Update();
// Get label image
m_LabelImage = segmenter.GetLabeledClusteredOutput();
m_OutputGraph = segmenter.m_Graph;
}
else
{
itkExceptionMacro(<<"Unknow tiling mode!");
}
// TODO: [MPI] broadcast the graph to other nodes
}
/*
......@@ -264,7 +267,7 @@ void Controller<TSegmenter>::CheckMemorySize()
* Compute the maximum number of nodes which can fit in the memory
*/
template<class TSegmenter>
long unsigned int Controller<TSegmenter>::GetMaximumNumberOfNodesInMemory()
std::size_t Controller<TSegmenter>::GetMaximumNumberOfNodesInMemory()
{
itkDebugMacro(<< "Computing maximum number of nodes in memory");
......@@ -433,16 +436,16 @@ void Controller<TSegmenter>::SetSpecificParameters(const SegmentationParameterTy
m_SpecificParameters = params;
}
template<class TSegmenter>
typename Controller<TSegmenter>::LabelImageType::Pointer
Controller<TSegmenter>::GetLabeledClusteredOutput()
{
#ifdef OTB_USE_MPI
// Get the label image from the master process (the one which achieves segmentation)
BroadcastImage<typename TSegmenter::LabelImageType>(m_LabelImage);
#endif
return m_LabelImage;
}
//template<class TSegmenter>
//typename Controller<TSegmenter>::LabelImageType::Pointer
//Controller<TSegmenter>::GetLabeledClusteredOutput()
//{
//#ifdef OTB_USE_MPI
// // Get the label image from the master process (the one which achieves segmentation)
// BroadcastImage<typename TSegmenter::LabelImageType>(m_LabelImage);
//#endif
// return m_LabelImage;
//}
template <class TSegmenter>
std::vector<std::string> Controller<TSegmenter>::GetTemporaryFilesList()
......
include/lsgrmGraphOperations.h
View file @ 9c4810ec
......@@ -5,7 +5,6 @@
#include "grmGraphOperations.h"
#include "otbVectorImage.h"
#include "otbMultiChannelExtractROI.h"
#include "itkGrayscaleFillholeImageFilter.h"
namespace lsgrm
{
......@@ -32,7 +31,7 @@ typename TSegmenter::ImageType::Pointer ReadImageRegion(
typename TSegmenter::ImageType::RegionType region);
template<class TSegmenter>
typename TSegmenter::LabelImageType::Pointer
typename TSegmenter::GraphType
MergeAllGraphsAndAchieveSegmentation(
const typename TSegmenter::ParamType& params,
const float& threshold,
......@@ -79,13 +78,13 @@ void RemoveUselessNodes(ProcessingTile& tile,
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,
const unsigned int imageWidth,
const unsigned int imageHeight);
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,
typename TSegmenter::GraphType& graph,
const unsigned int imageWidth);
......@@ -97,9 +96,10 @@ void BuildBorderPixelMap(typename TSegmenter::GraphType& graph,
const unsigned int colTile,
const unsigned int nbTilesX,
const unsigned int nbTilesY,
std::unordered_map<long unsigned int,
std::unordered_map<std::size_t,
std::vector<typename TSegmenter::NodePointerType> >& borderPixelMap,
const unsigned int imageWidth);
const unsigned int imageWidth,
bool merging = false);
template<class TSegmenter>
void InsertNodesFromTile(typename TSegmenter::GraphType& graph,
......
include/lsgrmGraphOperations.txx
View file @ 9c4810ec
......@@ -25,7 +25,7 @@ typename TSegmenter::ImageType::Pointer ReadImageRegion(
}
template<class TSegmenter>
typename TSegmenter::LabelImageType::Pointer
typename TSegmenter::GraphType
MergeAllGraphsAndAchieveSegmentation(
const typename TSegmenter::ParamType& params,
const float& threshold,
......@@ -63,13 +63,13 @@ MergeAllGraphsAndAchieveSegmentation(
{
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::cout << "\tBuildBorderPixelMap..." << std::endl;
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;
......@@ -91,69 +91,42 @@ MergeAllGraphsAndAchieveSegmentation(
segmenter.SetThreshold(threshold);
segmenter.SetDoFastSegmentation(false); // was true
segmenter.SetNumberOfIterations(numberOfIterations);
grm::GraphOperations<TSegmenter>::PerfomAllIterationsWithLMBFAndConstThreshold(segmenter);
// // Write output graph to the output graph directory
// WriteGraph<TSegmenter>(segmenter.m_Graph, tmpDir, 0, 0);
// Generate the label image
typename TSegmenter::LabelImageType::IndexType index;
index.Fill(0);
typename TSegmenter::LabelImageType::SizeType size;
size[0] = imageWidth;
size[1] = imageHeight;
typename TSegmenter::LabelImageType::RegionType region(index, size);
const typename TSegmenter::LabelImageType::InternalPixelType noDataLabel = 0;
typename TSegmenter::LabelImageType::Pointer labelImage = TSegmenter::LabelImageType::New();
labelImage->SetRegions(region);
labelImage->Allocate();
labelImage->FillBuffer(noDataLabel);
using LabelImageIterator = itk::ImageRegionIterator<typename TSegmenter::LabelImageType>;
LabelImageIterator it(labelImage, labelImage->GetLargestPossibleRegion());
// Start at 1 (value 0 can be used for invalid pixels)
unsigned int label = 1;
for(auto& node : segmenter.m_Graph.m_Nodes)
{
lp::CellLists borderPixels;
lp::ContourOperations::GenerateBorderCells(borderPixels, node->m_Contour, node->m_Id, imageWidth);
for (auto& pix: borderPixels)
{
index[0] = pix % imageWidth;
index[1] = pix / imageWidth;
labelImage->SetPixel(index, label);
}
++label;
}
// Re-order nodes labels (left->right to top->bottom)
vnl_vector<typename TSegmenter::LabelImageType::InternalPixelType> lut(label,noDataLabel);
label = 1;
for(it.GoToBegin();!it.IsAtEnd(); ++it)
{
unsigned int inputLabel = it.Get();
if (lut[ inputLabel ] == noDataLabel && inputLabel != noDataLabel)
{
lut[ inputLabel ] = label;
label++;
}
}
// Apply LUT
for(it.GoToBegin();!it.IsAtEnd(); ++it)
it.Set(lut[it.Get()]);
// Fill holes
typedef itk::GrayscaleFillholeImageFilter<typename TSegmenter::LabelImageType,
typename TSegmenter::LabelImageType> FillholeFilterType;
typename FillholeFilterType::Pointer fillFilter = FillholeFilterType::New();
fillFilter->SetInput(labelImage);
fillFilter->Update();
return fillFilter->GetOutput();}
// patch raf (sort using node id directly --> seems ok)
// Sort the nodes top-->down and left-->right
/*
std::sort(segmenter.m_Graph.m_Nodes.begin(), segmenter.m_Graph.m_Nodes.end(),
[imageWidth](const auto & a, const auto & b) -> bool
{
lp::CellLists borderPixelsA, borderPixelsB;
lp::ContourOperations::GenerateBorderCells(borderPixelsA, a->m_Contour, a->m_Id, imageWidth);
lp::ContourOperations::GenerateBorderCells(borderPixelsB, b->m_Contour, b->m_Id, imageWidth);
// patch raf (were unsigned int)
std::size_t offA = 0;
std::size_t offB = 0;
// end patch
for (auto& pix: borderPixelsA)
if (pix>offA)
offA=pix;
for (auto& pix: borderPixelsB)
if (pix>offB)
offB=pix;
return offA > offB;
});
*/
std::sort(segmenter.m_Graph.m_Nodes.begin(), segmenter.m_Graph.m_Nodes.end(),
[](const auto & a, const auto & b) -> bool
{
return a->m_Id < b->m_Id;
});
// end patch
return segmenter.m_Graph;
}
template<class TSegmenter>
long long unsigned int RunPartialSegmentation(const typename TSegmenter::ParamType& params,
......@@ -198,7 +171,7 @@ long long unsigned int RunPartialSegmentation(const typename TSegmenter::ParamTy
row, col, nbTilesX, nbTilesY);
std::cout << "\tBuild border pixel map..." << std::endl;
std::unordered_map<long unsigned int, std::vector<typename TSegmenter::NodePointerType> > borderPixelMap;
std::unordered_map<std::size_t, std::vector<typename TSegmenter::NodePointerType> > borderPixelMap;
BuildBorderPixelMap<TSegmenter>(segmenter.m_Graph, currentTile, row, col,
nbTilesX, nbTilesY, borderPixelMap, imageWidth);
......@@ -366,7 +339,7 @@ void RemoveUselessNodes(ProcessingTile& tile,
}
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,
const unsigned int imageWidth,
const unsigned int imageHeight)
......@@ -376,7 +349,7 @@ void UpdateNeighborsOfNoneDuplicatedNodes(std::unordered_map<long unsigned int,
for(auto& pn : borderPixelMap)
{
long int neighborhood[4];
NeighIDType neighborhood[4];
grm::FOURNeighborhood(neighborhood, pn.first, imageWidth, imageHeight);
for(short j = 0; j < 4; ++j)
......@@ -404,7 +377,7 @@ void UpdateNeighborsOfNoneDuplicatedNodes(std::unordered_map<long unsigned int,
{
if(borderPixelMap.find(pix) != borderPixelMap.end())
{
long int pixNeighborhood[4];
NeighIDType pixNeighborhood[4];
grm::FOURNeighborhood(pixNeighborhood, pix, imageWidth, imageHeight);
for(short k = 0; k < 4; k++)
......@@ -431,7 +404,7 @@ void UpdateNeighborsOfNoneDuplicatedNodes(std::unordered_map<long unsigned int,
}
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,
typename TSegmenter::GraphType& graph,
const unsigned int imageWidth)
......@@ -502,9 +475,10 @@ void BuildBorderPixelMap(typename TSegmenter::GraphType& graph,
const unsigned int colTile,
const unsigned int nbTilesX,
const unsigned int nbTilesY,
std::unordered_map<long unsigned int,
std::unordered_map<std::size_t,
std::vector<typename TSegmenter::NodePointerType> >& borderPixelMap,
const unsigned int imageWidth)
const unsigned int imageWidth,
bool merging)
{
unsigned int rowPixel, colPixel;
unsigned int rowMin = (tile.rows[0] > 0) ? tile.rows[0] - 1 : tile.rows[0];
......@@ -521,6 +495,15 @@ void BuildBorderPixelMap(typename TSegmenter::GraphType& graph,
{
continue;
}
// patch raf (exclude nodes all outside tiles - on merging stage only)
else if(merging && (node->m_Bbox.m_UX > tile.columns[1] ||
node->m_Bbox.m_UY > tile.rows[1] ||
node->m_Bbox.m_UX + node->m_Bbox.m_W - 1 < tile.columns[0] ||
node->m_Bbox.m_UY + node->m_Bbox.m_H - 1 < tile.rows[0]))
{
continue;
}
// end patch
else
{
lp::CellLists borderPixels;
......@@ -683,7 +666,7 @@ long long unsigned int RunFirstPartialSegmentation(
segmenter.SetNumberOfIterations(niter);
segmenter.SetInput(imageTile);
segmenter.Update();
if(segmenter.GetComplete() == false)
isFusion = true;
......@@ -696,7 +679,7 @@ long long unsigned int RunFirstPartialSegmentation(
tileWidth,
tileHeight,
imageWidth);
// Remove unstable segments
std::cout << "\tRemoving unstable segments..." << std::endl;
RemoveUnstableSegments<TSegmenter>(segmenter.m_Graph, currentTile, imageWidth);
......@@ -1029,7 +1012,7 @@ void RescaleGraph(typename TSegmenter::GraphType& graph,
// Start pixel index of the node (in the image)
rowNodeImg = rowTile * tileHeight + rowNodeTile - tile.margin[0];
colNodeImg = colTile * tileWidth + colNodeTile - tile.margin[3];
node->m_Id = rowNodeImg * imageWidth + colNodeImg;
node->m_Id = (std::size_t)rowNodeImg * (std::size_t)imageWidth + (std::size_t)colNodeImg;
// Change also its bounding box
node->m_Bbox.m_UX = colTile * tileWidth + node->m_Bbox.m_UX - tile.margin[3];
......
include/lsgrmSegmenter.h
View file @ 9c4810ec
......@@ -106,7 +106,7 @@ public:
void ReadGraph(FILE * nodeStream, FILE * edgeStream)
{
std::unordered_map<long unsigned int, NodePointerType> nodeMap;
std::unordered_map<std::size_t, NodePointerType> nodeMap;
// Read the size of the graph
{
......@@ -151,7 +151,7 @@ public:
for(auto& node: this->m_Graph.m_Nodes)
{
long unsigned int nodeId;
std::size_t nodeId;
fread(&(nodeId), sizeof(nodeId), 1, edgeStream);
assert(nodeId == node->m_Id);
......@@ -160,7 +160,7 @@ public:
node->m_Edges.reserve(edgeSize);
for(unsigned int b = 0; b < edgeSize; b++)
{
long unsigned int targetId;
std::size_t targetId;
unsigned int boundary;
fread(&(targetId), sizeof(targetId), 1, edgeStream);
fread(&(boundary), sizeof(boundary), 1, edgeStream);
......
include/otbStreamingGraphToImageFilter.h 0 → 100644
View file @ 9c4810ec
/*
* otbStreamingGraphToImageFilter.h
*
* Created on: 6 nov. 2017
* Author: cresson
*/
#ifndef MODULES_REMOTE_LSGRM_INCLUDE_OTBSTREAMINGGRAPHTOIMAGEFILTER_H_
#define MODULES_REMOTE_LSGRM_INCLUDE_OTBSTREAMINGGRAPHTOIMAGEFILTER_H_
#include "itkImageSource.h"
#include "itkExceptionObject.h"
#include "itkImageRegion.h"
#include "itkGrayscaleFillholeImageFilter.h"
#include "grmGraphOperations.h"
// Boost R-Tree
#include <boost/geometry.hpp>
#include <boost/geometry/geometries/point.hpp>
#include <boost/geometry/geometries/box.hpp>
#include <boost/geometry/index/rtree.hpp>
// to store queries results
#include <vector>
// just for output
#include <iostream>
#include <boost/foreach.hpp>
namespace bg = boost::geometry;
namespace bgi = boost::geometry::index;
namespace lsgrm
{
template <class TGraph, class TLabelImage>
class ITK_EXPORT StreamingGraphToImageFilter : public itk::ImageSource<TLabelImage>
{
public:
/** Standard class typedefs. */
typedef StreamingGraphToImageFilter Self;
typedef itk::ImageSource<TLabelImage> Superclass;
typedef itk::SmartPointer<Self> Pointer;
/** Method for creation through the object factory. */
itkNewMacro(Self);
/** Run-time type information (and related methods). */
itkTypeMacro(StreamingGraphToImageFilter, ImageSource);
/** Typedefs for processing */
typedef typename TLabelImage::RegionType RegionType;
typedef typename TLabelImage::IndexType IndexType;
typedef typename TLabelImage::SizeType SizeType;
typedef typename TLabelImage::SpacingType SpacingType;
typedef typename TLabelImage::PointType PointType;
typedef typename TGraph::NodePointerType NodePointerType;
typedef itk::GrayscaleFillholeImageFilter<TLabelImage,TLabelImage> FillholeFilterType;
typedef bg::model::point<float, 2, bg::cs::cartesian> point;
typedef bg::model::box<point> box;
typedef std::pair<box, unsigned> value;
/** Set the input graph and build the R-Tree */
void SetGraph(const TGraph graph);
/** Prepare image allocation at the first call of the pipeline processing */
virtual void GenerateOutputInformation(void);
/** Does the real work. */
virtual void GenerateData();
itkSetMacro(OutputSize, SizeType);
itkSetMacro(OutputOrigin, PointType);
itkSetMacro(OutputSpacing, SpacingType);
itkSetMacro(OutputProjectionRef, std::string);
protected:
StreamingGraphToImageFilter(){};
virtual ~StreamingGraphToImageFilter(){};
private:
StreamingGraphToImageFilter(const Self &); //purposely not implemented
void operator =(const Self&); //purposely not implemented