From f6fad8b1ce9af1bd75d543d73a50e93cf2826435 Mon Sep 17 00:00:00 2001
From: remi cresson <remi.cresson@teledetection.fr>
Date: Tue, 7 Nov 2017 11:12:35 +0000
Subject: [PATCH] ENH: implementation of streamed label image writing done
---
app/otbLSGRM.cxx | 129 ++++++++++++---------
include/lsgrmController.h | 8 +-
include/lsgrmController.txx | 28 ++---
include/lsgrmGraphOperations.h | 5 +-
include/lsgrmGraphOperations.txx | 94 +++------------
include/otbStreamingGraphToImageFilter.h | 14 ++-
include/otbStreamingGraphToImageFilter.txx | 95 +++++++--------
7 files changed, 164 insertions(+), 209 deletions(-)
diff --git a/app/otbLSGRM.cxx b/app/otbLSGRM.cxx
index b056e67..20e9330 100644
--- a/app/otbLSGRM.cxx
+++ b/app/otbLSGRM.cxx
@@ -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>
@@ -108,6 +112,7 @@ private:
AddChoice("tiling.none", "No tiling layout");
AddParameter(ParameterType_Int, "memory", "Restrict memory use (mb)");
+
MandatoryOff("memory");
}
@@ -129,28 +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);
}
@@ -163,17 +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");
@@ -189,85 +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");
// 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!")
}
- 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()
@@ -282,16 +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;
- UInt32ImageType::Pointer labelImage;
+ itk::ImageSource<UInt32ImageType>::Pointer m_LabelImageSource;
}; // app class
} // end of namespace wrapper
diff --git a/include/lsgrmController.h b/include/lsgrmController.h
index 9550c32..ac8e649 100644
--- a/include/lsgrmController.h
+++ b/include/lsgrmController.h
@@ -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 */
@@ -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
diff --git a/include/lsgrmController.txx b/include/lsgrmController.txx
index 2d2ee41..7f423a2 100644
--- a/include/lsgrmController.txx
+++ b/include/lsgrmController.txx
@@ -18,6 +18,7 @@ Controller<TSegmenter>::Controller()
m_NbTilesY = 0;
m_Threshold = 75;
m_Memory = 0;
+
}
template<class TSegmenter>
@@ -150,7 +151,7 @@ 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 +196,15 @@ 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
+
}
/*
@@ -433,16 +435,16 @@ 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()
diff --git a/include/lsgrmGraphOperations.h b/include/lsgrmGraphOperations.h
index 24d2c2a..28c2111 100644
--- a/include/lsgrmGraphOperations.h
+++ b/include/lsgrmGraphOperations.h
@@ -5,9 +5,6 @@
#include "grmGraphOperations.h"
#include "otbVectorImage.h"
#include "otbMultiChannelExtractROI.h"
-#include "itkGrayscaleFillholeImageFilter.h"
-#include "otbStreamingGraphToImageFilter.h"
-#include "otbStreamingImageVirtualWriter.h"
namespace lsgrm
{
@@ -34,7 +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,
diff --git a/include/lsgrmGraphOperations.txx b/include/lsgrmGraphOperations.txx
index 15c9b80..6e587ab 100644
--- a/include/lsgrmGraphOperations.txx
+++ b/include/lsgrmGraphOperations.txx
@@ -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,
@@ -91,86 +91,30 @@ 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);
-
- // 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::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;
- }
+ // 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);
- // 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++;
- }
- }
+ unsigned int offA = 0;
+ unsigned int offB = 0;
+ for (auto& pix: borderPixelsA)
+ if (pix>offA)
+ offA=pix;
- // Apply LUT
- for(it.GoToBegin();!it.IsAtEnd(); ++it)
- it.Set(lut[it.Get()]);
+ for (auto& pix: borderPixelsB)
+ if (pix>offB)
+ offB=pix;
- // Fill holes
- typedef itk::GrayscaleFillholeImageFilter<typename TSegmenter::LabelImageType,
- typename TSegmenter::LabelImageType> FillholeFilterType;
- typename FillholeFilterType::Pointer fillFilter = FillholeFilterType::New();
- fillFilter->SetInput(labelImage);
- fillFilter->Update();
+ return offA > offB;
+ });
- return fillFilter->GetOutput();
+ return segmenter.m_Graph;
}
template<class TSegmenter>
diff --git a/include/otbStreamingGraphToImageFilter.h b/include/otbStreamingGraphToImageFilter.h
index d79a92f..1bd3bb4 100644
--- a/include/otbStreamingGraphToImageFilter.h
+++ b/include/otbStreamingGraphToImageFilter.h
@@ -54,6 +54,8 @@ public:
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;
@@ -70,9 +72,12 @@ public:
virtual void GenerateData();
itkSetMacro(OutputSize, SizeType);
+ itkSetMacro(OutputOrigin, PointType);
+ itkSetMacro(OutputSpacing, SpacingType);
+ itkSetMacro(OutputProjectionRef, std::string);
protected:
- StreamingGraphToImageFilter();
+ StreamingGraphToImageFilter(){};
virtual ~StreamingGraphToImageFilter(){};
private:
@@ -80,9 +85,12 @@ private:
StreamingGraphToImageFilter(const Self &); //purposely not implemented
void operator =(const Self&); //purposely not implemented
- TGraph m_Graph;
+ TGraph m_Graph;
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 */
diff --git a/include/otbStreamingGraphToImageFilter.txx b/include/otbStreamingGraphToImageFilter.txx
index 0e984f1..26ef5d0 100644
--- a/include/otbStreamingGraphToImageFilter.txx
+++ b/include/otbStreamingGraphToImageFilter.txx
@@ -13,13 +13,6 @@
namespace lsgrm
{
-template <class TGraph, class TLabelImage>
-StreamingGraphToImageFilter<TGraph, TLabelImage>
-::StreamingGraphToImageFilter()
- {
-
- }
-
template <class TGraph, class TLabelImage>
void
StreamingGraphToImageFilter<TGraph, TLabelImage>
@@ -28,23 +21,27 @@ StreamingGraphToImageFilter<TGraph, TLabelImage>
m_Graph = graph;
// Build a R-Tree
- std::cout << "Building R-Tree" << std::endl;
+ itkDebugMacro( << "Building R-Tree" );
+
rtree.clear();
unsigned int count = 0;
for(auto& node : m_Graph.m_Nodes)
{
// create a box
- box b(point(node->m_Bbox.m_UX, node->m_Bbox.m_UY),
- point(node->m_Bbox.m_W, node->m_Bbox.m_UY+node->m_Bbox.m_H));
+ box b(
+ 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
rtree.insert(std::make_pair(b, count));
count++;
}
- std::cout << "Building R-Tree finished" << std::endl;
-
- // TODO: create a LUT for reordering labels from top-->down and left-->right
+ itkDebugMacro( << "Building R-Tree finished" );
}
@@ -53,14 +50,19 @@ void
StreamingGraphToImageFilter<TGraph, TLabelImage>
::GenerateOutputInformation()
{
- TLabelImage * outputPtr = this->GetOutput();
- // TODO:
- // outputPtr->SetOrigin ( m_OutputOrigin );
- // outputPtr->SetSpacing ( m_OutputSpacing );
+ itkDebugMacro( << "Entering GenerateOutputInformation()" );
+
+ // Output Largest Possible Region
IndexType index;
index.Fill(0);
RegionType outputRegion(index, m_OutputSize);
+
+ // Set output informations
+ TLabelImage * outputPtr = this->GetOutput();
+ outputPtr->SetOrigin ( m_OutputOrigin );
+ outputPtr->SetSpacing ( m_OutputSpacing );
outputPtr->SetLargestPossibleRegion( outputRegion );
+ outputPtr->SetProjectionRef(m_OutputProjectionRef);
}
@@ -70,6 +72,8 @@ void
StreamingGraphToImageFilter<TGraph, TLabelImage>
::GenerateData()
{
+ itkDebugMacro( << "Entering GenerateData()" );
+
// Allocate the output buffer
TLabelImage * outputPtr = this->GetOutput();
RegionType outReqRegion = outputPtr->GetRequestedRegion();
@@ -77,12 +81,17 @@ StreamingGraphToImageFilter<TGraph, TLabelImage>
outputPtr->Allocate();
// Find nodes intersecting find the output requested region
- box query_box(point(outReqRegion.GetIndex(0), outReqRegion.GetIndex(1)),
- point(outReqRegion.GetIndex(0)+outReqRegion.GetSize(0), outReqRegion.GetIndex(1)+outReqRegion.GetSize(1)));
+ box query_box(
+ point(
+ outReqRegion.GetIndex(0),
+ outReqRegion.GetIndex(1)),
+ point(
+ outReqRegion.GetIndex(0)+outReqRegion.GetSize(0),
+ outReqRegion.GetIndex(1)+outReqRegion.GetSize(1)));
std::vector<value> result_s;
- std::cout << "R-Tree query on output requested region " << outReqRegion << std::endl;
+ itkDebugMacro( << "R-Tree query on output requested region " << outReqRegion );
rtree.query(bgi::intersects(query_box), std::back_inserter(result_s));
- std::cout << "R-Tree query done. Number of nodes: " << result_s.size() << std::endl;
+ itkDebugMacro( << "R-Tree query done. Number of nodes: " << result_s.size() );
// Retrieve the bounding box of the intersecting nodes (a kind of "Input requested region")
box realBBox(query_box);
@@ -97,23 +106,22 @@ StreamingGraphToImageFilter<TGraph, TLabelImage>
size[0] = realBBox.max_corner().get<0>() - realBBox.min_corner().get<0>();
size[1] = realBBox.max_corner().get<1>() - realBBox.min_corner().get<1>();
RegionType inputRequestedRegion(index, size);
- std::cout << "Input Requested region: " << inputRequestedRegion << std::endl;
+ itkDebugMacro( << "Input Requested region: " << inputRequestedRegion );
// Generate the label image
- std::cout << "Allocate " << std::endl;
+ itkDebugMacro( << "Allocate buffered region ");
const typename TLabelImage::InternalPixelType noDataLabel = 0;
typename TLabelImage::Pointer labelImage = TLabelImage::New();
labelImage->SetRegions(inputRequestedRegion);
labelImage->Allocate();
labelImage->FillBuffer(noDataLabel);
- std::cout << "Allocate ok" << std::endl;
+ itkDebugMacro( << "Allocate buffered region ok" );
using LabelImageIterator = itk::ImageRegionIterator<TLabelImage>;
LabelImageIterator it(labelImage, inputRequestedRegion);
- // Start at 1 (value 0 can be used for invalid pixels)
- std::cout << "Iterate " << std::endl;
- unsigned int label = 1 ;
+ // Burn boundaries
+ itkDebugMacro( << "Burning boundaries " );
for(auto& res : result_s)
{
NodePointerType node = m_Graph.m_Nodes[res.second];
@@ -125,43 +133,20 @@ StreamingGraphToImageFilter<TGraph, TLabelImage>
{
index[0] = pix % m_OutputSize[0];
index[1] = pix / m_OutputSize[0];
- labelImage->SetPixel(index, label);
- }
- ++label;
- }
- std::cout << "Iterate ok " << std::endl;
-
- // Re-order nodes labels (left->right to top->bottom)
- std::cout << "re-order " << std::endl;
- vnl_vector<typename TLabelImage::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++;
+ labelImage->SetPixel(index, res.second);
}
}
- std::cout << "re-order ok" << std::endl;
-
- // Apply LUT
- std::cout << "apply LUT" << std::endl;
- for(it.GoToBegin();!it.IsAtEnd(); ++it)
- it.Set(lut[it.Get()]);
- std::cout << "apply LUT ok" << std::endl;
+ itkDebugMacro( << "Burning boundaries ok ");
// Fill holes
- std::cout << "fill Hole filter" << std::endl;
+ itkDebugMacro( << "fill Hole filter" );
typename FillholeFilterType::Pointer fillFilter = FillholeFilterType::New();
fillFilter->SetInput(labelImage);
fillFilter->Update();
- std::cout << "Fill Hole filter OutputLargestPossibleRegion:" << fillFilter->GetOutput()->GetLargestPossibleRegion() << std::endl;
- std::cout << "fill Hole filter ok" << std::endl;
+ itkDebugMacro( << "Fill Hole filter OutputLargestPossibleRegion:" << fillFilter->GetOutput()->GetLargestPossibleRegion() );
+ itkDebugMacro( << "fill Hole filter ok" );
// Extract the stable region
-
LabelImageIterator outIt(outputPtr, outReqRegion);
LabelImageIterator inIt (fillFilter->GetOutput(), outReqRegion);
for (inIt.GoToBegin(), outIt.GoToBegin(); !outIt.IsAtEnd(); ++outIt, ++inIt)
--
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