REFAC: functions use ProcesingTiles instead of many numeric and string variables

include/lsgrmController.h

@@ -49,13 +49,12 @@ public:
   typename LabelImageType::Pointer GetLabeledClusteredOutput();
 
   itkGetMacro(Margin, unsigned int);
-  itkGetMacro(TemporaryFilesList, std::vector<std::string>);
 
-  itkGetMacro(CleanTemporaryDirectory, bool);
-  itkSetMacro(CleanTemporaryDirectory, bool);
+  itkGetMacro(CleanTemporaryFiles, bool);
+  itkSetMacro(CleanTemporaryFiles, bool);
 
-  itkGetMacro(TemporaryDirectory, std::string);
-  itkSetMacro(TemporaryDirectory, std::string);
+  itkGetMacro(TemporaryFilesPrefix, std::string);
+  itkSetMacro(TemporaryFilesPrefix, std::string);
 
   itkGetMacro(Threshold, float);
   itkSetMacro(Threshold, float);
@@ -94,8 +93,8 @@ private:
   long unsigned int GetMaximumNumberOfNodesInMemory();
 
   /* Parameters given by the user */
-  std::string m_TemporaryDirectory;      // Directory used to store intermediate files during the process.
-  bool        m_CleanTemporaryDirectory; // Clean the temporary directory.
+  std::string m_TemporaryFilesPrefix;    // Path used to store intermediate files during the process.
+  bool        m_CleanTemporaryFiles;     // Clean temporary files
   ImageType * m_InputImage;              // Input image
 
   /* Segmentation parameters */
@@ -117,7 +116,6 @@ 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
-  std::vector<std::string>           m_TemporaryFilesList; // list of temporary files
   typename LabelImageType::Pointer   m_LabelImage;         // output label image
 };
 } // end of namespace lsgrm

include/lsgrmController.txx

@@ -14,7 +14,7 @@ Controller<TSegmenter>::Controller()
   m_TileWidth = 0;
   m_NbTilesX = 0;
   m_NbTilesY = 0;
-  m_CleanTemporaryDirectory = true;
+  m_CleanTemporaryFiles = true;
   m_Threshold = 75;
   m_Memory = 0;
 }
@@ -53,8 +53,8 @@ void Controller<TSegmenter>::RunSegmentation()
         "\n\tTiling layout: " << m_NbTilesX << " x " << m_NbTilesY << std::endl;
 
     // Compute the splitting scheme
-    SplitOTBImage<ImageType>(m_InputImage, m_TileWidth, m_TileHeight, m_Margin,
-        m_NbTilesX, m_NbTilesY, m_Tiles);
+    m_Tiles = SplitOTBImage<ImageType>(m_InputImage, m_TileWidth, m_TileHeight, m_Margin,
+        m_NbTilesX, m_NbTilesY, m_TemporaryFilesPrefix);
 
     // Boolean indicating if there are remaining fusions
     bool isFusion = false;
@@ -72,9 +72,7 @@ void Controller<TSegmenter>::RunSegmentation()
         m_NbTilesY,
         m_TileWidth,
         m_TileHeight,
-        m_TemporaryDirectory,
         isFusion);
-    //    long long unsigned int accumulatedMemory = 19373051714;
 
     // Update the given number of iterations
     numberOfIterationsRemaining -= m_NumberOfFirstIterations;
@@ -96,7 +94,6 @@ void Controller<TSegmenter>::RunSegmentation()
           m_Threshold,
           numberOfIterationsForPartialSegmentations,
           m_Tiles,
-          m_TemporaryDirectory,
           m_NbTilesX,
           m_NbTilesY,
           m_InputImage->GetLargestPossibleRegion().GetSize()[0],
@@ -127,7 +124,6 @@ void Controller<TSegmenter>::RunSegmentation()
           m_SpecificParameters,
           m_Threshold,
           m_Tiles,
-          m_TemporaryDirectory,
           m_NbTilesX,
           m_NbTilesY,
           m_InputImage->GetLargestPossibleRegion().GetSize()[0],
@@ -176,7 +172,7 @@ unsigned int Controller<TSegmenter>::GetNodeMemory()
   lsrm::GraphOperations<TSegmenter>::InitNodes(onePixelImage,segmenter,FOUR);
 
   unsigned int memory = segmenter.GetGraphMemory() / (n*n);
-  itkWarningMacro(<<"Size of a node is " << memory);
+  itkDebugMacro(<<"Size of a node is " << memory);
   return memory;
 }
 
@@ -198,7 +194,8 @@ long unsigned int Controller<TSegmenter>::GetMaximumNumberOfNodesInMemory()
 }
 
 template<class TSegmenter>
-void Controller<TSegmenter>::ComputeMaximumStabilityMargin(unsigned int width,
+void
+Controller<TSegmenter>::ComputeMaximumStabilityMargin(unsigned int width,
     unsigned int height, unsigned int &niter, unsigned int &margin)
     {
   itkDebugMacro(<< "Computing maximum stability margin");
@@ -331,7 +328,7 @@ void Controller<TSegmenter>::GetAutomaticConfiguration()
   long long unsigned int memoryUsed = GetNodeMemory();
   memoryUsed *= static_cast<long long unsigned int>(m_TileHeight + 2*m_Margin);
   memoryUsed *= static_cast<long long unsigned int>(m_TileWidth + 2*m_Margin);
-  itkWarningMacro(<< "An amount of " << memoryUsed/(1024.0*1024.0) << " Mbytes of RAM will be used for regular tiles of size "
+  itkDebugMacro(<< "An amount of " << memoryUsed/(1024.0*1024.0) << " Mbytes of RAM will be used for regular tiles of size "
       << (m_TileWidth + 2*m_Margin) << "x" << (m_TileHeight + 2*m_Margin) );
 
 }

include/lsgrmGraphOperations.h

@@ -16,6 +16,12 @@ struct ProcessingTile
   long int tileNeighbors[8]; // tile Neighbors at (top, top right, right, bottom right, bottom, bottom left, left, top left)
   long int margin[4]; // Is there a margin at top, left, bottom or right
   otb::VectorImage<double>::RegionType region; // The image region
+
+  // Temporary files
+  std::string nodeFileName;
+  std::string edgeFileName;
+  std::string nodeMarginFileName;
+  std::string edgeMarginFileName;
 };
 
 // Read an image region
@@ -30,7 +36,6 @@ MergeAllGraphsAndAchieveSegmentation(
     const typename TSegmenter::ParameterType& params,
     const float& threshold,
     std::vector<ProcessingTile>& tiles,
-    const std::string& tmpDir,
     const unsigned int nbTilesX,
     const unsigned int nbTilesY,
     const unsigned int imageWidth,
@@ -50,7 +55,6 @@ long long unsigned int RunFirstPartialSegmentation(
     const unsigned int nbTilesY,
     const unsigned int tileWidth,
     const unsigned int tileHeight,
-    const std::string& tmpDir,
     bool& isFusion);
 
 template<class TSegmenter>
@@ -59,7 +63,6 @@ long long unsigned int RunPartialSegmentation(
     const float& threshold,
     const unsigned int niter,
     std::vector<ProcessingTile>& tiles,
-    const std::string& tmpDir,
     const unsigned int nbTilesX,
     const unsigned int nbTilesY,
     const unsigned int imageWidth,
@@ -101,9 +104,13 @@ void BuildBorderPixelMap(typename TSegmenter::GraphType& graph,
     std::vector<typename TSegmenter::NodePointerType> >& borderPixelMap,
     const unsigned int imageWidth);
 
+template<class TSegmenter>
+void InsertNodesFromTile(typename TSegmenter::GraphType& graph,
+    ProcessingTile& tile, bool margin = true);
+
 template<class TSegmenter>
 void AddStabilityMargin(typename TSegmenter::GraphType& graph,
-    const std::string& tmpDir,
+    std::vector<ProcessingTile>& tiles,
     const unsigned int row,
     const unsigned int col,
     const unsigned int nbTilesX,
@@ -134,18 +141,19 @@ void DetectBorderNodes(typename TSegmenter::GraphType& graph,
     const unsigned int imageHeight);
 
 template<class TSegmenter>
-void ReadGraph(typename TSegmenter::GraphType& graph,
+void ReadGraph(TSegmenter& segmenter,
     const std::string& nodesPath,
     const std::string& edgesPath);
 
 template<class TSegmenter>
-void WriteGraph(typename TSegmenter::GraphType& graph,
-    const std::string& tmpDir,
-    const unsigned int row,
-    const unsigned int col);
+void ReadGraph(typename TSegmenter::GraphType& graph,
+    const std::string& nodesPath,
+    const std::string& edgesPath);
 
 template<class TSegmenter>
-long long unsigned int GetGraphMemory(TSegmenter segmenter);
+void WriteGraph(typename TSegmenter::GraphType& graph,
+    const std::string& nodesFile,
+    const std::string& edgesFile);
 
 template<class TSegmenter>
 void RemoveUnstableSegments(typename TSegmenter::GraphType& graph,