BUG: Use grm::GraphToOTBImage, and fix polygon re-ordering

include/lsgrmController.txx

@@ -75,7 +75,7 @@ void Controller<TSegmenter>::RunSegmentation()
 
   if (m_TilingMode == LSGRM_TILING_AUTO || m_TilingMode == LSGRM_TILING_USER)
     {
-    unsigned int numberOfIterationsForPartialSegmentations = 3; // TODO: find a smart value
+    const unsigned int numberOfIterationsForPartialSegmentations = 3; // TODO: find a smart value
     unsigned int numberOfIterationsRemaining = m_NumberOfIterations;
 
     // Boolean indicating if there are remaining fusions

include/lsgrmGraphOperations.txx

@@ -94,8 +94,28 @@ MergeAllGraphsAndAchieveSegmentation(
   //  // Write output graph to the output graph directory
   //  WriteGraph<TSegmenter>(segmenter.m_Graph, tmpDir, 0, 0);
 
-  return segmenter.GetLabeledClusteredOutput();
+  // Convert graph to label image
+  typename TSegmenter::LabelImageType::Pointer labelImage = segmenter.GetLabeledClusteredOutput();
+
+  // Re-order nodes labels (left->right to top->bottom)
+  using LabelImageIterator = itk::ImageRegionIterator<typename TSegmenter::LabelImageType>;
+  LabelImageIterator it(labelImage, labelImage->GetLargestPossibleRegion());
+  const typename TSegmenter::LabelImageType::InternalPixelType noDataLabel = 0;
+  typename TSegmenter::LabelImageType::InternalPixelType label = 1;
+  vnl_vector<typename TSegmenter::LabelImageType::InternalPixelType> lut(label,noDataLabel);
+  for(it.GoToBegin();!it.IsAtEnd(); ++it)
+    {
+    unsigned int inputLabel = it.Get();
+    if (lut[ inputLabel ] == noDataLabel)
+      {
+      lut[ inputLabel ] = label;
+      label++;
+      }
+    }
+  for(it.GoToBegin();!it.IsAtEnd(); ++it)
+    it.Set(lut[it.Get()]);
 
+  return labelImage;
 }
 
 template<class TSegmenter>

include/lsgrmGraphToOtbImage.h

-#ifndef __LSRM_GRAPH_TO_OTBIMAGE_H
-#define __LSRM_GRAPH_TO_OTBIMAGE_H
-#include <itkRGBPixel.h>
-#include <itkImageRegion.h>
-#include <otbImage.h>
-#include <otbVectorImage.h>
-#include <otbImageFileReader.h>
-#include <otbImageFileWriter.h>
-#include "grmGraph.h"
-#include <string>
-#include <stdlib.h>
-#include <time.h>
-#include "lpContour.h"
-
-namespace lsgrm
-{
-template<class TGraph>
-class GraphToOtbImage
-{
-public:
-
-  /* Some convenient typedefs */
-  typedef TGraph GraphType;
-  typedef typename GraphType::NodeType NodeType;
-  typedef std::vector< std::shared_ptr<NodeType> > NodeList;
-  typedef typename NodeList::const_iterator NodeConstIterator;
-  typedef unsigned int LabelPixelType;
-  typedef otb::Image<LabelPixelType, 2> LabelImageType;
-  using ContourOperator = lp::ContourOperations;
-
-
-  LabelImageType::Pointer GetLabelImage(const GraphType& graph,
-      const unsigned int width,
-      const unsigned int height);
-};
-
-} // end of namespace lsrm
-#include "lsgrmGraphToOtbImage.txx"
-#endif

include/lsgrmGraphToOtbImage.txx

-#ifndef __LSRM_GRAPH_TO_OTBIMAGE_TXX
-#define __LSRM_GRAPH_TO_OTBIMAGE_TXX
-#include "lsgrmGraphToOtbImage.h"
-#include "itkImageRegionIterator.h"
-#include "itkGrayscaleFillholeImageFilter.h"
-
-namespace lsgrm
-{
-template<class TGraph>
-typename GraphToOtbImage<TGraph>::LabelImageType::Pointer
-GraphToOtbImage<TGraph>::GetLabelImage(const GraphType& graph,
-    const unsigned int width,
-    const unsigned int height)
-    {
-  LabelImageType::IndexType labelImageRegionStart;
-  LabelImageType::SizeType labelImageRegionSize;
-  LabelImageType::RegionType labelImageRegion;
-
-  labelImageRegionStart[0] = 0; labelImageRegionStart[1] = 0;
-  labelImageRegionSize[0] = width; labelImageRegionSize[1] = height;
-  labelImageRegion.SetIndex(labelImageRegionStart);
-  labelImageRegion.SetSize(labelImageRegionSize);
-
-  LabelImageType::Pointer label_img = LabelImageType::New();
-  label_img->SetRegions(labelImageRegion);
-  label_img->Allocate();
-
-  using LabelImageIterator = itk::ImageRegionIterator<LabelImageType>;
-  LabelImageIterator it(label_img, label_img->GetLargestPossibleRegion());
-  for(it.GoToBegin();!it.IsAtEnd(); ++it)
-    it.Set(0);
-
-  // Start at 1 (value 0 can be used for invalid pixels)
-  LabelImageType::InternalPixelType label = 1;
-  for(auto& region : graph.m_Nodes)
-    {
-    lp::CellLists borderPixels;
-    ContourOperator::GenerateBorderCells(borderPixels, region->m_Contour, region->m_Id, width);
-
-    for (auto& pix: borderPixels)
-      {
-      labelImageRegionStart[0] = pix % width;
-      labelImageRegionStart[1] = pix / width;
-      label_img->SetPixel(labelImageRegionStart, label);
-      }
-    ++label;
-    }
-
-  // Sort labels in their appearance order from left->right to top->bottom
-  const LabelImageType::InternalPixelType noDataLabel = 0;
-  vnl_vector<LabelImageType::InternalPixelType> lut(label,noDataLabel);
-  label=1;
-  for(it.GoToBegin();!it.IsAtEnd(); ++it)
-    {
-    unsigned int inputLabel = it.Get();
-    if (lut[ inputLabel ] == noDataLabel)
-      {
-      lut[ inputLabel ] = label;
-      label++;
-      }
-    }
-  for(it.GoToBegin();!it.IsAtEnd(); ++it)
-    it.Set(lut[it.Get()]);
-
-  // Fill holes
-  typedef itk::GrayscaleFillholeImageFilter<LabelImageType,LabelImageType>  FillholeFilterType;
-  FillholeFilterType::Pointer fillFilter = FillholeFilterType::New();
-  fillFilter->SetInput(label_img);
-  fillFilter->Update();
-
-  return fillFilter->GetOutput();
-    }
-
-} // end of namespace lsrm
-#endif

include/lsgrmSegmenter.h

@@ -39,7 +39,7 @@ public:
   typedef typename GraphType::EdgeListType EdgeListType;
   typedef typename grm::GraphOperations<TSegmenterType> GraphOperatorType;
   typedef typename GraphOperatorType::NodePointerType NodePointerType;
-  typedef GraphToOtbImage<GraphType> IOType;
+  typedef grm::GraphToOtbImage<GraphType> IOType;
   typedef typename IOType::LabelImageType LabelImageType;
 
   ~Segmenter(){};