Fix bug generation of labels

Code/lsrmGraphToOtbImage.h

@@ -35,9 +35,9 @@ namespace lsrm
 											  const unsigned int width,
 											  const unsigned int height);
 
-		ClusteredImageType::Pointer GetClusteredOutput(const GraphType& graph,
+		/*ClusteredImageType::Pointer GetClusteredOutput(const GraphType& graph,
 													   const unsigned int width,
-													   const unsigned int height);	
+													   const unsigned int height);*/	
 	};
 	
 } // end of namespace lsrm

Code/lsrmGraphToOtbImage.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 "lsrmGraph.h"
+#include <string>
+#include <stdlib.h>
+#include <time.h>
+#include "lpContour.h"
+
+namespace lsrm
+{
+	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 long int LabelPixelType;
+		typedef otb::Image<LabelPixelType, 2> LabelImageType;
+		typedef unsigned char ClusterPixelType;
+		typedef otb::VectorImage<ClusterPixelType, 2> ClusteredImageType;
+		using ContourOperator = lp::ContourOperations;
+		
+
+		LabelImageType::Pointer GetLabelImage(const GraphType& graph,
+											  const unsigned int width,
+											  const unsigned int height);
+
+		ClusteredImageType::Pointer GetClusteredOutput(const GraphType& graph,
+													   const unsigned int width,
+													   const unsigned int height);	
+	};
+	
+} // end of namespace lsrm
+#include "lsrmGraphToOtbImage.txx"
+#endif

Code/lsrmGraphToOtbImage.txx

@@ -2,6 +2,7 @@
 #define __LSRM_GRAPH_TO_OTBIMAGE_TXX
 #include "lsrmGraphToOtbImage.h"
 #include "itkImageRegionIterator.h"
+#include "itkGrayscaleFillholeImageFilter.h"
 
 namespace lsrm
 {
@@ -45,20 +46,16 @@ namespace lsrm
 			++label;
 		}
 
-		long unsigned int pixelValue = 0;
-		for(it.GoToBegin(); !it.IsAtEnd(); ++it)
-		{
-			auto pixel = it.Get();
-			if(pixel == 0)
-				it.Set(pixelValue);
-			else
-				pixelValue = pixel;
-		}
+        // Fill holes
+		typedef itk::GrayscaleFillholeImageFilter<LabelImageType,LabelImageType>  FillholeFilterType;
+		FillholeFilterType::Pointer fillFilter = FillholeFilterType::New();
+		fillFilter->SetInput(label_img);
+		fillFilter->Update();
 		
-		return label_img;
+		return fillFilter->GetOutput();
 	}
 
-	template<class TGraph>
+	/*template<class TGraph>
 	typename GraphToOtbImage<TGraph>::ClusteredImageType::Pointer
 	GraphToOtbImage<TGraph>::GetClusteredOutput(const GraphType& graph,
 												const unsigned int width,
@@ -122,7 +119,7 @@ namespace lsrm
 		}
 		
 		return clusterImg;
-	}
+	}*/
 		
 } // end of namespace lsrm
 #endif

Code/lsrmGraphToOtbImage.txx~

+#ifndef __LSRM_GRAPH_TO_OTBIMAGE_TXX
+#define __LSRM_GRAPH_TO_OTBIMAGE_TXX
+#include "lsrmGraphToOtbImage.h"
+#include "itkImageRegionIterator.h"
+#include "itkGrayscaleFillholeImageFilter.h"
+
+namespace lsrm
+{
+	template<class TGraph>
+	typename GraphToOtbImage<TGraph>::LabelImageType::Pointer
+	GraphToOtbImage<TGraph>::GetLabelImage(const GraphType& graph,
+										   const unsigned int width,
+										   const unsigned int height)
+	{
+		LabelImageType::IndexType index;
+		LabelImageType::SizeType size;
+		LabelImageType::RegionType region;
+
+		index[0] = 0; index[1] = 0;
+		size[0] = width; size[1] = height;
+		region.SetIndex(index);
+		region.SetSize(size);
+
+		LabelImageType::Pointer label_img = LabelImageType::New();
+		label_img->SetRegions(region);
+		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)
+		long unsigned int 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)
+			{
+				index[0] = pix % width;
+				index[1] = pix / width;
+				label_img->SetPixel(index, label);
+			}
+			++label;
+		}
+
+        // Fill holes
+		typedef itk::GrayscaleFillholeImageFilter<LabelImageType,LabelImageType>  FillholeFilterType;
+		FillholeFilterType::Pointer fillFilter = FillholeFilterType::New();
+		fillFilter->SetInput(label_img);
+		fillFilter->Update();
+		
+		return fillFilter->GetOutput();
+	}
+
+	template<class TGraph>
+	typename GraphToOtbImage<TGraph>::ClusteredImageType::Pointer
+	GraphToOtbImage<TGraph>::GetClusteredOutput(const GraphType& graph,
+												const unsigned int width,
+												const unsigned int height)
+	{
+		ClusteredImageType::IndexType index;
+		ClusteredImageType::SizeType size;
+		ClusteredImageType::RegionType region;
+
+		index[0] = 0; index[1] = 0;
+		size[0] = width; size[1] = height;
+		region.SetIndex(index);
+		region.SetSize(size);
+
+		ClusteredImageType::Pointer clusterImg = ClusteredImageType::New();
+		clusterImg->SetRegions(region);
+		clusterImg->SetNumberOfComponentsPerPixel(3);
+		clusterImg->Allocate();
+
+		ClusteredImageType::PixelType pixelValue;
+		pixelValue.Reserve(3);
+		pixelValue[0] = 0;
+		pixelValue[1] = 0;
+		pixelValue[2] = 0;
+
+		using ClusterImageIterator = itk::ImageRegionIterator<ClusteredImageType>;
+		ClusterImageIterator it(clusterImg, clusterImg->GetLargestPossibleRegion());
+		for(it.GoToBegin();!it.IsAtEnd(); ++it)
+			it.Set(pixelValue);
+
+		srand(time(NULL));
+		unsigned char c1, c2, c3;
+		for(auto& region : graph.m_Nodes)
+		{
+			c1 = rand() % 256;
+			c2 = rand() % 256;
+			c3 = rand() % 256;
+
+			lp::CellLists borderPixels;
+			ContourOperator::GenerateBorderCells(borderPixels, region->m_Contour, region->m_Id, width);
+			
+			for (auto& pix : borderPixels)
+			{
+				index[0] = pix % width;
+				index[1] = pix / width;
+				pixelValue[0] = c1;
+				pixelValue[1] = c2;
+				pixelValue[2] = c3;
+				clusterImg->SetPixel(index, pixelValue);
+			}
+		}
+
+		
+		for(it.GoToBegin(); !it.IsAtEnd(); ++it)
+		{
+			auto pixel = it.Get();
+			if(pixel[0] == 0 && pixel[1] == 0 && pixel[2] == 0)
+				it.Set(pixelValue);
+			else
+				pixelValue = pixel;
+		}
+		
+		return clusterImg;
+	}
+		
+} // end of namespace lsrm
+#endif