Merge keeping the mpised version

Code/lsgrmGraphOperations.h

@@ -2,6 +2,7 @@
 #define __LSGRM_GRAPH_OPERATIONS_H
 #include "lsgrmHeader.h"
 #include "lsrmGraphOperations.h"
+#include "otbImage.h"
 #include "otbImageFileReader.h"
 
 namespace lsgrm

Code/lsgrmGraphOperations.txx

@@ -79,6 +79,7 @@ namespace lsgrm
 			}
 		}
 
+<<<<<<< HEAD
 		if (myrank == 0)
 		  {
 		  std::cout << "\nAchieve segmentation process..." << std::endl;
@@ -106,6 +107,31 @@ namespace lsgrm
 		  clusterWriter->Update();
 		  }
 	    }
+=======
+		std::cout << "\nAchieve segmentation process..." << std::endl;
+		
+		// Segmentation of the graph
+		segmenter.SetImageWidth(imageWidth);
+		segmenter.SetImageHeight(imageHeight);
+		segmenter.SetNumberOfComponentsPerPixel(imageBands);
+		segmenter.SetParam(params);
+		segmenter.SetThreshold(threshold);
+		segmenter.SetDoBFSegmentation(true);
+		segmenter.SetNumberOfIterations(75);
+
+		lsrm::GraphOperations<TSegmenter>::PerfomAllIterationsWithLMBFAndConstThreshold(segmenter);
+
+		// Write output graph to the output graph directory
+		WriteGraph<TSegmenter>(segmenter.m_Graph, outputGraphDirectory, 0, 0);
+				
+		typedef unsigned long int LabelPixelType;
+		typedef otb::Image<LabelPixelType, 2> LabelImageType;
+		typedef otb::ImageFileWriter<LabelImageType> LabelImageWriterType;
+		auto labelWriter = LabelImageWriterType::New();
+		labelWriter->SetFileName("out/labelImage.tiff");
+		labelWriter->SetInput(segmenter.GetLabeledClusteredOutput());
+		labelWriter->Update();
+>>>>>>> upstream/master
 	}
 	
 	template<class TSegmenter>

Code/lsrmBaatzSegmenter.txx

@@ -57,7 +57,7 @@ namespace lsrm
 			std = std::sqrt((square_mean - 2*mean*sum + a_sum * mean* mean) / a_sum);
 			spect_cost += (a_sum * std - a1 * n1->m_Std[b] - a2 * n2->m_Std[b]);
 		}
-		spect_cost *= this->m_Param.m_ShapeWeight;
+		spect_cost *= this->m_Param.m_SpectralWeight;
 
 		if(spect_cost < this->m_Threshold)
 		{
@@ -79,7 +79,7 @@ namespace lsrm
 
 			shape_cost = this->m_Param.m_ShapeWeight * compact_f + (1-this->m_Param.m_ShapeWeight) * smooth_f;
 
-			return (spect_cost + (1-this->m_Param.m_ShapeWeight)*shape_cost);
+			return (spect_cost + (1-this->m_Param.m_SpectralWeight)*shape_cost);
 		}
 		else
 			return spect_cost;

Code/lsrmGraphToOtbImage.h

@@ -26,18 +26,12 @@ namespace lsrm
 		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

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
 {
@@ -45,83 +46,13 @@ 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;
-		}
-		
-		return label_img;
-	}
-
-	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;
-		}
+        // Fill holes
+		typedef itk::GrayscaleFillholeImageFilter<LabelImageType,LabelImageType>  FillholeFilterType;
+		FillholeFilterType::Pointer fillFilter = FillholeFilterType::New();
+		fillFilter->SetInput(label_img);
+		fillFilter->Update();
 		
-		return clusterImg;
+		return fillFilter->GetOutput();
 	}
 		
 } // end of namespace lsrm

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

Code/lsrmSegmenter.h

@@ -24,7 +24,6 @@ namespace lsrm
 		typedef typename GraphOperatorType::NodePointerType NodePointerType;
 		typedef GraphToOtbImage<GraphType> IOType;
 		typedef typename IOType::LabelImageType LabelImageType;
-		typedef typename IOType::ClusteredImageType ClusteredImageType;
 
 		/* Default constructor and destructor */
 		
@@ -81,13 +80,6 @@ namespace lsrm
 				auto labelImg = io.GetLabelImage(this->m_Graph, this->m_ImageWidth, this->m_ImageHeight);
 				return labelImg;
 			}
-
-		inline typename ClusteredImageType::Pointer GetClusteredImageOutput()
-			{
-				IOType io;
-				auto clusteredImg = io.GetClusteredOutput(this->m_Graph, this->m_ImageWidth, this->m_ImageHeight);
-				return clusteredImg;
-			}
 		
 		/* Set methods */
 		SetMacro(bool, DoBFSegmentation);