Commit f6fad8b1 authored by remi cresson's avatar remi cresson
Browse files

ENH: implementation of streamed label image writing done

parent d7db5ebb
...@@ -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>
...@@ -108,6 +112,7 @@ private: ...@@ -108,6 +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");
} }
...@@ -163,17 +168,20 @@ private: ...@@ -163,17 +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");
...@@ -220,20 +228,35 @@ private: ...@@ -220,20 +228,35 @@ private:
// 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");
// Switch criterion // Switch criterion
...@@ -243,31 +266,23 @@ private: ...@@ -243,31 +266,23 @@ private:
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!")
} }
std::cout << "Label image size: " << labelImage->GetLargestPossibleRegion() << std::endl;
// 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()
...@@ -291,7 +306,7 @@ private: ...@@ -291,7 +306,7 @@ private:
private: private:
std::vector<std::string> m_TemporaryFilesList; std::vector<std::string> m_TemporaryFilesList;
UInt32ImageType::Pointer labelImage; 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 */
...@@ -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>
...@@ -150,7 +151,7 @@ void Controller<TSegmenter>::RunSegmentation() ...@@ -150,7 +151,7 @@ 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 +196,15 @@ void Controller<TSegmenter>::RunSegmentation() ...@@ -195,14 +196,15 @@ 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
} }
/* /*
...@@ -433,16 +435,16 @@ void Controller<TSegmenter>::SetSpecificParameters(const SegmentationParameterTy ...@@ -433,16 +435,16 @@ 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()
......
...@@ -5,9 +5,6 @@ ...@@ -5,9 +5,6 @@
#include "grmGraphOperations.h" #include "grmGraphOperations.h"
#include "otbVectorImage.h" #include "otbVectorImage.h"
#include "otbMultiChannelExtractROI.h" #include "otbMultiChannelExtractROI.h"
#include "itkGrayscaleFillholeImageFilter.h"
#include "otbStreamingGraphToImageFilter.h"
#include "otbStreamingImageVirtualWriter.h"
namespace lsgrm namespace lsgrm
{ {
...@@ -34,7 +31,7 @@ typename TSegmenter::ImageType::Pointer ReadImageRegion( ...@@ -34,7 +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,
......
...@@ -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,
...@@ -91,86 +91,30 @@ MergeAllGraphsAndAchieveSegmentation( ...@@ -91,86 +91,30 @@ 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 // Sort the nodes top-->down and left-->right
// WriteGraph<TSegmenter>(segmenter.m_Graph, tmpDir, 0, 0); std::sort(segmenter.m_Graph.m_Nodes.begin(), segmenter.m_Graph.m_Nodes.end(),
[imageWidth](const auto & a, const auto & b) -> bool
// TODO: use std::sort to sort the graph (m_Id must be increasing) before the polygon filling
typename TSegmenter::LabelImageType::SizeType outSize;
outSize[0] = imageWidth;
outSize[1] = imageHeight;
typedef StreamingGraphToImageFilter<typename TSegmenter::GraphType,
typename TSegmenter::LabelImageType> GraphToImageFilterType;
typename GraphToImageFilterType::Pointer graphToImageFilter = GraphToImageFilterType::New();
graphToImageFilter->SetGraph(segmenter.m_Graph);
graphToImageFilter->SetOutputSize(outSize);
typedef otb::ImageFileWriter<typename TSegmenter::LabelImageType> VWriterType;
typename VWriterType::Pointer wrt = VWriterType::New();
wrt->SetInput(graphToImageFilter->GetOutput());
wrt->SetNumberOfDivisionsStrippedStreaming(5);
wrt->SetFileName("/homeL/cresson/data/tmp/spot6_surrech_segm2.tif");
wrt->Update();
// 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::CellLists borderPixelsA, borderPixelsB;
lp::ContourOperations::GenerateBorderCells(borderPixels, node->m_Contour, node->m_Id, imageWidth); lp::ContourOperations::GenerateBorderCells(borderPixelsA, a->m_Contour, a->m_Id, imageWidth);
lp::ContourOperations::GenerateBorderCells(borderPixelsB, b->m_Contour, b->m_Id, imageWidth);
for (auto& pix: borderPixels) unsigned int offA = 0;
{ unsigned int offB = 0;
index[0] = pix % imageWidth; for (auto& pix: borderPixelsA)
index[1] = pix / imageWidth; if (pix>offA)
labelImage->SetPixel(index, label); offA=pix;
}
++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 (auto& pix: borderPixelsB)
for(it.GoToBegin();!it.IsAtEnd(); ++it) if (pix>offB)
it.Set(lut[it.Get()]); offB=pix;
// Fill holes return offA > offB;
typedef itk::GrayscaleFillholeImageFilter<typename TSegmenter::LabelImageType, });
typename TSegmenter::LabelImageType> FillholeFilterType;
typename FillholeFilterType::Pointer fillFilter = FillholeFilterType::New();
fillFilter->SetInput(labelImage);
fillFilter->Update();
return fillFilter->GetOutput(); return segmenter.m_Graph;
} }
template<class TSegmenter> template<class TSegmenter>
......
...@@ -54,6 +54,8 @@ public: ...@@ -54,6 +54,8 @@ public:
typedef typename TLabelImage::RegionType RegionType; typedef typename TLabelImage::RegionType RegionType;
typedef typename TLabelImage::IndexType IndexType; typedef typename TLabelImage::IndexType IndexType;
typedef typename TLabelImage::SizeType SizeType; typedef typename TLabelImage::SizeType SizeType;
typedef typename TLabelImage::SpacingType SpacingType;
typedef typename TLabelImage::PointType PointType;
typedef typename TGraph::NodePointerType NodePointerType; typedef typename TGraph::NodePointerType NodePointerType;
typedef itk::GrayscaleFillholeImageFilter<TLabelImage,TLabelImage> FillholeFilterType; typedef itk::GrayscaleFillholeImageFilter<TLabelImage,TLabelImage> FillholeFilterType;
typedef bg::model::point<float, 2, bg::cs::cartesian> point; typedef bg::model::point<float, 2, bg::cs::cartesian> point;
...@@ -70,9 +72,12 @@ public: ...@@ -70,9 +72,12 @@ public:
virtual void GenerateData(); virtual void GenerateData();
itkSetMacro(OutputSize, SizeType); itkSetMacro(OutputSize, SizeType);
itkSetMacro(OutputOrigin, PointType);
itkSetMacro(OutputSpacing, SpacingType);
itkSetMacro(OutputProjectionRef, std::string);
protected: protected:
StreamingGraphToImageFilter(); StreamingGraphToImageFilter(){};
virtual ~StreamingGraphToImageFilter(){}; virtual ~StreamingGraphToImageFilter(){};
private: private:
...@@ -83,6 +88,9 @@ private: ...@@ -83,6 +88,9 @@ private:
TGraph m_Graph; TGraph m_Graph;
bgi::rtree< value, bgi::quadratic<16> > rtree; bgi::rtree< value, bgi::quadratic<16> > rtree;
SizeType m_OutputSize; SizeType m_OutputSize;
SpacingType m_OutputSpacing;
PointType m_OutputOrigin;
std::string m_OutputProjectionRef;
}; };
} /* namespace lsgrm */ } /* namespace lsgrm */
......
...@@ -13,13 +13,6 @@ ...@@ -13,13 +13,6 @@
namespace lsgrm namespace lsgrm
{ {
template <class TGraph, class TLabelImage>
StreamingGraphToImageFilter<TGraph, TLabelImage>
::StreamingGraphToImageFilter()
{
}
template <class TGraph, class TLabelImage> template <class TGraph, class TLabelImage>
void void
StreamingGraphToImageFilter<TGraph, TLabelImage> StreamingGraphToImageFilter<TGraph, TLabelImage>
...@@ -28,23 +21,27 @@ StreamingGraphToImageFilter<TGraph, TLabelImage> ...@@ -28,23 +21,27 @@ StreamingGraphToImageFilter<TGraph, TLabelImage>
m_Graph = graph; m_Graph = graph;
// Build a R-Tree // Build a R-Tree
std::cout << "Building R-Tree" << std::endl; itkDebugMacro( << "Building R-Tree" );
rtree.clear(); rtree.clear();
unsigned int count = 0; unsigned int count = 0;
for(auto& node : m_Graph.m_Nodes) for(auto& node : m_Graph.m_Nodes)
{ {
// create a box // create a box
box b(point(node->m_Bbox.m_UX, node->m_Bbox.m_UY), box b(
point(node->m_Bbox.m_W, node->m_Bbox.m_UY+node->m_Bbox.m_H)); point(
node->m_Bbox.m_UX,
node->m_Bbox.m_UY),
point(
node->m_Bbox.m_UX + node->m_Bbox.m_W,
node->m_Bbox.m_UY + node->m_Bbox.m_H));
// insert new value // insert new value
rtree.insert(std::make_pair(b, count)); rtree.insert(std::make_pair(b, count));
count++; count++;
} }
std::cout << "Building R-Tree finished" << std::endl; itkDebugMacro( << "Building R-Tree finished" );
// TODO: create a LUT for reordering labels from top-->down and left-->right
} }
...@@ -53,14 +50,19 @@ void ...@@ -53,14 +50,19 @@ void
StreamingGraphToImageFilter<TGraph, TLabelImage> StreamingGraphToImageFilter<TGraph, TLabelImage>
::GenerateOutputInformation() ::GenerateOutputInformation()
{ {
TLabelImage * outputPtr = this->GetOutput(); itkDebugMacro( << "Entering GenerateOutputInformation()" );
// TODO:
// outputPtr->SetOrigin ( m_OutputOrigin ); // Output Largest Possible Region
// outputPtr->SetSpacing ( m_OutputSpacing );
IndexType index; IndexType index;
index.Fill(0); index.Fill(0);
RegionType outputRegion(index, m_OutputSize); RegionType outputRegion(index, m_OutputSize);
// Set output informations
TLabelImage * outputPtr = this->GetOutput();
outputPtr->SetOrigin ( m_OutputOrigin );
outputPtr->SetSpacing ( m_OutputSpacing );
outputPtr->SetLargestPossibleRegion( outputRegion ); outputPtr->SetLargestPossibleRegion( outputRegion );
outputPtr->SetProjectionRef(m_OutputProjectionRef);
} }
...@@ -70,6 +72,8 @@ void ...@@ -70,6 +72,8 @@ void
StreamingGraphToImageFilter<TGraph, TLabelImage> StreamingGraphToImageFilter<TGraph, TLabelImage>
::GenerateData() ::GenerateData()
{ {
itkDebugMacro( << "Entering GenerateData()" );
// Allocate the output buffer // Allocate the output buffer
TLabelImage * outputPtr = this->GetOutput(); TLabelImage * outputPtr = this->GetOutput();
RegionType outReqRegion = outputPtr->GetRequestedRegion();