diff --git a/include/lsgrmController.h b/include/lsgrmController.h
index afaba38389be0be222023eb92da2b992f1367f44..5da2eb68079292c37a9878259ca93422930b5212 100644
--- a/include/lsgrmController.h
+++ b/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
diff --git a/include/lsgrmController.txx b/include/lsgrmController.txx
index 052911bf3be7065d4c986afb8dea591b5967ce4a..ec776b6c8eaa63b5fabae45925891e8c1b68f957 100644
--- a/include/lsgrmController.txx
+++ b/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) );
}
diff --git a/include/lsgrmGraphOperations.h b/include/lsgrmGraphOperations.h
index ae7c6ad78f061e305bba66db88197c8d1ae4f5ef..b2e52e9077c9f773f321f57ae750295f741e89d9 100644
--- a/include/lsgrmGraphOperations.h
+++ b/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,
diff --git a/include/lsgrmGraphOperations.txx b/include/lsgrmGraphOperations.txx
index d37e5aa16fa415de38738a469b717bf6a7f10606..c7edae657b9ffc19ff49f4bd4a9e9dd736b7fce6 100644
--- a/include/lsgrmGraphOperations.txx
+++ b/include/lsgrmGraphOperations.txx
@@ -27,7 +27,6 @@ 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,
@@ -36,16 +35,16 @@ MergeAllGraphsAndAchieveSegmentation(
unsigned int numberOfIterations)
{
- // TODO parallelize this ...
+ std::cout << "--- Graph aggregation...\n" << std::endl;
+
+ // TODO parallelize this ?
#ifdef OTB_USE_MPI
if (otb::MPIConfig::Instance()->GetMyRank() != 0)
return;
#endif
TSegmenter segmenter;
- std::string nodesPath, edgesPath;
- std::cout << "--- Graph aggregation...\n" << std::endl;
std::cout << "Reading graphs" << std::endl;
@@ -55,16 +54,7 @@ MergeAllGraphsAndAchieveSegmentation(
{
std::cout << "\tImporting graph of tile " << (row*nbTilesX + col) << " / " << (nbTilesX*nbTilesY) << std::endl;
- typename TSegmenter::GraphType graph;
-
- // Load the graph
- nodesPath = tmpDir + "tile_nodes_" + std::to_string(row) + "_" + std::to_string(col) + ".bin";
- edgesPath = tmpDir + "tile_edges_" + std::to_string(row) + "_" + std::to_string(col) + ".bin";
- ReadGraph<TSegmenter>(graph, nodesPath, edgesPath);
-
- segmenter.m_Graph.m_Nodes.insert(segmenter.m_Graph.m_Nodes.end(),
- graph.m_Nodes.begin(),
- graph.m_Nodes.end());
+ InsertNodesFromTile<TSegmenter>(segmenter.m_Graph, tiles[row*nbTilesX + col], false);
}
}
@@ -95,7 +85,6 @@ MergeAllGraphsAndAchieveSegmentation(
}
}
-
std::cout << "Achieve segmentation process" ;
// Segmentation of the graph
@@ -121,7 +110,6 @@ long long unsigned int RunPartialSegmentation(const typename TSegmenter::Paramet
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,
@@ -130,7 +118,6 @@ long long unsigned int RunPartialSegmentation(const typename TSegmenter::Paramet
bool& isFusion)
{
long long unsigned int accumulatedMemory = 0;
- std::string nodesPath, edgesPath;
isFusion = false;
const unsigned int numberOfNeighborLayers = static_cast<unsigned int>(pow(2, niter + 1) - 2);
@@ -143,28 +130,27 @@ long long unsigned int RunPartialSegmentation(const typename TSegmenter::Paramet
{
if (MyTurn(row*nbTilesX + col))
{
+ // Get the current tile
+ ProcessingTile currentTile = tiles[row*nbTilesX + col];
+
TSegmenter segmenter;
std::cout << "Processing tile " << row << ", " << col << std::endl;
std::cout << "\tLoad graph..." << std::endl;
// Load the graph
- nodesPath = tmpDir + "tile_nodes_" + std::to_string(row) + "_" + std::to_string(col) + ".bin";
- edgesPath = tmpDir + "tile_edges_" + std::to_string(row) + "_" + std::to_string(col) + ".bin";
- ReadGraph<TSegmenter>(segmenter.m_Graph, nodesPath, edgesPath);
-
+ ReadGraph<TSegmenter>(segmenter.m_Graph, currentTile.nodeFileName, currentTile.edgeFileName);
// Add stability margin to the graph
{
std::cout << "\tAdd stability margin..." << std::endl;
- AddStabilityMargin<TSegmenter>(segmenter.m_Graph, tmpDir,
+ AddStabilityMargin<TSegmenter>(segmenter.m_Graph, tiles,
row, col, nbTilesX, nbTilesY);
-
std::unordered_map<long unsigned int,
std::vector<typename TSegmenter::NodePointerType> > borderPixelMap;
std::cout << "\tBuild border pixel map..." << std::endl;
- BuildBorderPixelMap<TSegmenter>(segmenter.m_Graph, tiles[row*nbTilesX + col], row, col,
+ BuildBorderPixelMap<TSegmenter>(segmenter.m_Graph, currentTile, row, col,
nbTilesX, nbTilesY, borderPixelMap, imageWidth);
std::cout << "\tRemove duplicated nodes..." << std::endl;
@@ -176,7 +162,7 @@ long long unsigned int RunPartialSegmentation(const typename TSegmenter::Paramet
imageHeight);
std::cout << "\tRemove useless.." << std::endl;
- RemoveUselessNodes<TSegmenter>(tiles[row*nbTilesX + col], segmenter.m_Graph,
+ RemoveUselessNodes<TSegmenter>(currentTile, segmenter.m_Graph,
row, col, nbTilesX, nbTilesY, imageWidth, numberOfNeighborLayers);
}
@@ -198,15 +184,15 @@ long long unsigned int RunPartialSegmentation(const typename TSegmenter::Paramet
// Remove unstable segments
std::cout << "\tRemove unstable segments..." << std::endl;
- RemoveUnstableSegments<TSegmenter>(segmenter.m_Graph, tiles[row*nbTilesX + col], imageWidth);
+ RemoveUnstableSegments<TSegmenter>(segmenter.m_Graph, currentTile, imageWidth);
// Retrieve the amount of memory to store this graph
std::cout << "\tGet graph memory..." << std::endl;
- accumulatedMemory += GetGraphMemory<TSegmenter>(segmenter);
+ accumulatedMemory += segmenter.GetGraphMemory();
- // Write graph to temporay directory (warning specific to Baatz & Schape !!!)
+ // Write graph to temporay directory
std::cout << "\tWrite graph..." << std::endl;
- WriteGraph<TSegmenter>(segmenter.m_Graph, tmpDir, row, col);
+ WriteGraph<TSegmenter>(segmenter.m_Graph, currentTile.nodeFileName, currentTile.edgeFileName);
}
}
}
@@ -224,32 +210,24 @@ long long unsigned int RunPartialSegmentation(const typename TSegmenter::Paramet
{
if (MyTurn(row*nbTilesX + col))
{
- // std::cout << "*" << std::flush;
- typename TSegmenter::GraphType graph;
+ // Get current tile
+ ProcessingTile currentTile = tiles[row*nbTilesX + col];
// Load the graph
- nodesPath = tmpDir + "tile_nodes_" + std::to_string(row) + "_" + std::to_string(col) + ".bin";
- edgesPath = tmpDir + "tile_edges_" + std::to_string(row) + "_" + std::to_string(col) + ".bin";
- ReadGraph<TSegmenter>(graph, nodesPath, edgesPath);
+ typename TSegmenter::GraphType graph;
+ ReadGraph<TSegmenter>(graph, currentTile.nodeFileName, currentTile.edgeFileName);
// Extract stability margin for all borders different from 0 imageWidth-1 et imageHeight -
// and write them to the stability margin
{
std::unordered_map<typename TSegmenter::NodePointerType, unsigned int> borderNodeMap;
- DetectBorderNodes<TSegmenter>(graph, tiles[row*nbTilesX + col],
+ DetectBorderNodes<TSegmenter>(graph, currentTile,
borderNodeMap, imageWidth, imageHeight);
-
ExtractStabilityMargin<TSegmenter>(borderNodeMap, numberOfNeighborLayers);
- std::string nodesPath = tmpDir + "tile_nodes_margin_" +
- std::to_string(row) + "_" + std::to_string(col) + ".bin";
- std::string edgesPath = tmpDir + "tile_edges_margin_" +
- std::to_string(row) + "_" + std::to_string(col) + ".bin";
-
-
- WriteStabilityMargin<TSegmenter>(borderNodeMap, nodesPath, edgesPath);
+ WriteStabilityMargin<TSegmenter>(borderNodeMap, currentTile.nodeMarginFileName, currentTile.edgeMarginFileName);
}
std::cout << "Process finished on tile " << (row*nbTilesX + col) << std::endl;
}
@@ -529,156 +507,79 @@ void BuildBorderPixelMap(typename TSegmenter::GraphType& graph,
}
}
+template<class TSegmenter>
+void InsertNodesFromTile(typename TSegmenter::GraphType& graph,
+ ProcessingTile& tile, bool margin = true)
+{
+ typename TSegmenter::GraphType subgraph;
+ if (margin)
+ {
+ ReadGraph<TSegmenter>(subgraph, tile.nodeMarginFileName, tile.edgeMarginFileName);
+ }
+ else
+ {
+ ReadGraph<TSegmenter>(subgraph, tile.nodeFileName, tile.edgeFileName);
+ }
+
+ graph.m_Nodes.insert(graph.m_Nodes.end(), subgraph.m_Nodes.begin(), subgraph.m_Nodes.end());
+
+}
+
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,
const unsigned int nbTilesY)
{
- std::string nodesPath;
- std::string edgesPath;
- unsigned int rowNeigh;
- unsigned int colNeigh;
// Margin to retrieve at top
if(row > 0)
{
- colNeigh = col;
- rowNeigh = row-1;
-
- nodesPath = tmpDir + "tile_nodes_margin_" +
- std::to_string(rowNeigh) + "_" + std::to_string(colNeigh) + ".bin";
-
- edgesPath = tmpDir + "tile_edges_margin_" +
- std::to_string(rowNeigh) + "_" + std::to_string(colNeigh) + ".bin";
-
- typename TSegmenter::GraphType subgraph;
- ReadGraph<TSegmenter>(subgraph, nodesPath, edgesPath);
- graph.m_Nodes.insert(graph.m_Nodes.end(), subgraph.m_Nodes.begin(), subgraph.m_Nodes.end());
+ InsertNodesFromTile<TSegmenter>(graph, tiles[(row-1) * nbTilesX + col]);
}
// Margin to retrieve at right
if(col < nbTilesX - 1)
{
- colNeigh = col + 1;
- rowNeigh = row;
-
- nodesPath = tmpDir + "tile_nodes_margin_" +
- std::to_string(rowNeigh) + "_" + std::to_string(colNeigh) + ".bin";
-
- edgesPath = tmpDir + "tile_edges_margin_" +
- std::to_string(rowNeigh) + "_" + std::to_string(colNeigh) + ".bin";
-
- typename TSegmenter::GraphType subgraph;
- ReadGraph<TSegmenter>(subgraph, nodesPath, edgesPath);
-
- graph.m_Nodes.insert(graph.m_Nodes.end(), subgraph.m_Nodes.begin(), subgraph.m_Nodes.end());
-
+ InsertNodesFromTile<TSegmenter>(graph, tiles[row * nbTilesX + (col+1)]);
}
// Margin to retrieve at bottom
if(row < nbTilesY - 1)
{
- colNeigh = col;
- rowNeigh = row + 1;
-
- nodesPath = tmpDir + "tile_nodes_margin_" +
- std::to_string(rowNeigh) + "_" + std::to_string(colNeigh) + ".bin";
-
- edgesPath = tmpDir + "tile_edges_margin_" +
- std::to_string(rowNeigh) + "_" + std::to_string(colNeigh) + ".bin";
-
- typename TSegmenter::GraphType subgraph;
- ReadGraph<TSegmenter>(subgraph, nodesPath, edgesPath);
- graph.m_Nodes.insert(graph.m_Nodes.end(), subgraph.m_Nodes.begin(), subgraph.m_Nodes.end());
-
+ InsertNodesFromTile<TSegmenter>(graph, tiles[(row+1) * nbTilesX + col]);
}
// Margin to retrieve at left
if(col > 0)
{
- colNeigh = col-1;
- rowNeigh = row;
-
- nodesPath = tmpDir + "tile_nodes_margin_" +
- std::to_string(rowNeigh) + "_" + std::to_string(colNeigh) + ".bin";
-
- edgesPath = tmpDir + "tile_edges_margin_" +
- std::to_string(rowNeigh) + "_" + std::to_string(colNeigh) + ".bin";
-
- typename TSegmenter::GraphType subgraph;
- ReadGraph<TSegmenter>(subgraph, nodesPath, edgesPath);
- graph.m_Nodes.insert(graph.m_Nodes.end(), subgraph.m_Nodes.begin(), subgraph.m_Nodes.end());
+ InsertNodesFromTile<TSegmenter>(graph, tiles[row * nbTilesX + (col-1)]);
}
// Margin to retrieve at top right
if(row > 0 && col < nbTilesX - 1)
{
- colNeigh = col+1;
- rowNeigh = row-1;
-
- nodesPath = tmpDir + "tile_nodes_margin_" +
- std::to_string(rowNeigh) + "_" + std::to_string(colNeigh) + ".bin";
-
- edgesPath = tmpDir + "tile_edges_margin_" +
- std::to_string(rowNeigh) + "_" + std::to_string(colNeigh) + ".bin";
-
- typename TSegmenter::GraphType subgraph;
- ReadGraph<TSegmenter>(subgraph, nodesPath, edgesPath);
- graph.m_Nodes.insert(graph.m_Nodes.end(), subgraph.m_Nodes.begin(), subgraph.m_Nodes.end());
+ InsertNodesFromTile<TSegmenter>(graph, tiles[(row-1) * nbTilesX + (col+1)]);
}
// Margin to retrieve at bottom right
if(row < nbTilesY - 1 && col < nbTilesX - 1)
{
- colNeigh = col+1;
- rowNeigh = row+1;
-
- nodesPath = tmpDir + "tile_nodes_margin_" +
- std::to_string(rowNeigh) + "_" + std::to_string(colNeigh) + ".bin";
-
- edgesPath = tmpDir + "tile_edges_margin_" +
- std::to_string(rowNeigh) + "_" + std::to_string(colNeigh) + ".bin";
-
- typename TSegmenter::GraphType subgraph;
- ReadGraph<TSegmenter>(subgraph, nodesPath, edgesPath);
- graph.m_Nodes.insert(graph.m_Nodes.end(), subgraph.m_Nodes.begin(), subgraph.m_Nodes.end());
+ InsertNodesFromTile<TSegmenter>(graph, tiles[ (row+1) * nbTilesX + (col+1)]);
}
// Margin to retrieve at bottom left
if(row < nbTilesY - 1 && col > 0)
{
- colNeigh = col-1;
- rowNeigh = row+1;
-
- nodesPath = tmpDir + "tile_nodes_margin_" +
- std::to_string(rowNeigh) + "_" + std::to_string(colNeigh) + ".bin";
-
- edgesPath = tmpDir + "tile_edges_margin_" +
- std::to_string(rowNeigh) + "_" + std::to_string(colNeigh) + ".bin";
-
- typename TSegmenter::GraphType subgraph;
- ReadGraph<TSegmenter>(subgraph, nodesPath, edgesPath);
- graph.m_Nodes.insert(graph.m_Nodes.end(), subgraph.m_Nodes.begin(), subgraph.m_Nodes.end());
+ InsertNodesFromTile<TSegmenter>(graph, tiles[ (row+1) * nbTilesX + (col-1)]);
}
// Margin to retrieve at top left
if(row > 0 && col > 0)
{
- colNeigh = col-1;
- rowNeigh = row-1;
-
- nodesPath = tmpDir + "tile_nodes_margin_" +
- std::to_string(rowNeigh) + "_" + std::to_string(colNeigh) + ".bin";
-
- edgesPath = tmpDir + "tile_edges_margin_" +
- std::to_string(rowNeigh) + "_" + std::to_string(colNeigh) + ".bin";
-
- typename TSegmenter::GraphType subgraph;
- ReadGraph<TSegmenter>(subgraph, nodesPath, edgesPath);
- graph.m_Nodes.insert(graph.m_Nodes.end(), subgraph.m_Nodes.begin(), subgraph.m_Nodes.end());
+ InsertNodesFromTile<TSegmenter>(graph, tiles[ (row-1) * nbTilesX + (col-1)]);
}
}
@@ -694,7 +595,6 @@ long long unsigned int RunFirstPartialSegmentation(
const unsigned int nbTilesY,
const unsigned int tileWidth,
const unsigned int tileHeight,
- const std::string& tmpDir,
bool& isFusion)
{
@@ -717,6 +617,7 @@ long long unsigned int RunFirstPartialSegmentation(
{
// Reading images
ProcessingTile currentTile = tiles[row*nbTilesX + col];
+
std::cout << "Processing tile " << (row*nbTilesX + col) << " / " << (nbTilesX*nbTilesY) <<
" (" << col << ", " << row << ")" <<
" start: [" << currentTile.region.GetIndex()[0] << ", " << currentTile.region.GetIndex()[1] <<
@@ -740,7 +641,7 @@ long long unsigned int RunFirstPartialSegmentation(
// Rescale the graph to be in the reference of the image
std::cout << "\tRescaling graph..." << std::endl;
RescaleGraph<TSegmenter>(segmenter.m_Graph,
- tiles[row*nbTilesX + col],
+ currentTile,
row,
col,
tileWidth,
@@ -749,15 +650,15 @@ long long unsigned int RunFirstPartialSegmentation(
// Remove unstable segments
std::cout << "\tRemoving unstable segments..." << std::endl;
- RemoveUnstableSegments<TSegmenter>(segmenter.m_Graph, tiles[row*nbTilesX + col], imageWidth);
+ RemoveUnstableSegments<TSegmenter>(segmenter.m_Graph, currentTile, imageWidth);
// Retrieve the amount of memory to store this graph
std::cout << "\tRetrieving graph memory..." << std::endl;
- accumulatedMemory += GetGraphMemory<TSegmenter>(segmenter);
+ accumulatedMemory += segmenter.GetGraphMemory();
- // Write graph to temporay directory (warning specific to Baatz & Schape !!!)
- std::cout << "\tWriting graph..." << std::endl;
- WriteGraph<TSegmenter>(segmenter.m_Graph, tmpDir, row, col);
+ // Write graph to temporay directory
+ std::cout << "\tWriting graph..." << currentTile.nodeFileName << " et " << currentTile.edgeFileName << std::endl;
+ WriteGraph<TSegmenter>(segmenter.m_Graph, currentTile.nodeFileName, currentTile.edgeFileName);
// Extract stability margin for all borders different from 0 imageWidth-1 et imageHeight -1
// and write them to the stability margin
@@ -765,19 +666,12 @@ long long unsigned int RunFirstPartialSegmentation(
{
std::unordered_map<typename TSegmenter::NodePointerType, unsigned int> borderNodeMap;
- DetectBorderNodes<TSegmenter>(segmenter.m_Graph, tiles[row*nbTilesX + col],
+ DetectBorderNodes<TSegmenter>(segmenter.m_Graph, currentTile,
borderNodeMap, imageWidth, imageHeight);
-
ExtractStabilityMargin<TSegmenter>(borderNodeMap, numberOfNeighborLayers);
- std::string nodesPath = tmpDir + "tile_nodes_margin_" +
- std::to_string(row) + "_" + std::to_string(col) + ".bin";
- std::string edgesPath = tmpDir + "tile_edges_margin_" +
- std::to_string(row) + "_" + std::to_string(col) + ".bin";
-
-
- WriteStabilityMargin<TSegmenter>(borderNodeMap, nodesPath, edgesPath);
+ WriteStabilityMargin<TSegmenter>(borderNodeMap, currentTile.nodeMarginFileName, currentTile.edgeMarginFileName);
}
}
} // for each col
@@ -889,96 +783,34 @@ void DetectBorderNodes(typename TSegmenter::GraphType& graph,
}
}
-// Specific to Baatz & Schape (sorry it has to be fast)
+
+// Generic
template<class TSegmenter>
-void ReadGraph(typename TSegmenter::GraphType& graph,
+void ReadGraph(TSegmenter& segmenter,
const std::string& nodesPath,
const std::string& edgesPath)
{
FILE * nodeStream = fopen(nodesPath.c_str(), "r");
assert(nodeStream != NULL);
- std::unordered_map<long unsigned int, typename TSegmenter::NodePointerType> nodeMap;
-
- // Read the size of the graph
- {
- std::size_t graphSize;
- fread(&graphSize, sizeof(graphSize), 1, nodeStream);
- graph.m_Nodes.reserve(graphSize);
-
- // Creation of the nodes
- for(std::size_t i = 0; i < graphSize; i++)
- {
- typename TSegmenter::NodePointerType node(new typename TSegmenter::NodeType());
-
- node->m_Valid = true;
- node->m_Expired = false;
- node->m_IsMerged = true; // force to compute costs for the first iteration
-
- fread(&(node->m_Id), sizeof(node->m_Id), 1, nodeStream);
- fread(&(node->m_Perimeter), sizeof(node->m_Perimeter), 1, nodeStream);
- fread(&(node->m_Area), sizeof(node->m_Area), 1, nodeStream);
- fread(&(node->m_Bbox.m_UX), sizeof(node->m_Bbox.m_UX), 1, nodeStream);
- fread(&(node->m_Bbox.m_UY), sizeof(node->m_Bbox.m_UY), 1, nodeStream);
- fread(&(node->m_Bbox.m_W), sizeof(node->m_Bbox.m_W), 1, nodeStream);
- fread(&(node->m_Bbox.m_H), sizeof(node->m_Bbox.m_H), 1, nodeStream);
-
- std::size_t bands;
- fread(&(bands), sizeof(bands), 1, nodeStream);
- node->m_Means.assign(bands, 0);
- node->m_SquareMeans.assign(bands, 0);
- node->m_SpectralSum.assign(bands, 0);
- node->m_Std.assign(bands, 0);
-
- for(unsigned int b = 0; b < bands; b++)
- {
- fread(&(node->m_Means[b]), sizeof(node->m_Means[b]), 1, nodeStream);
- fread(&(node->m_SquareMeans[b]), sizeof(node->m_SquareMeans[b]), 1, nodeStream);
- fread(&(node->m_SpectralSum[b]), sizeof(node->m_SpectralSum[b]), 1, nodeStream);
- fread(&(node->m_Std[b]), sizeof(node->m_Std[b]), 1, nodeStream);
- }
-
- {
- std::size_t contourSize;
- fread(&(contourSize), sizeof(contourSize), 1, nodeStream);
- short moves[contourSize];
- fread(&moves, sizeof(short), contourSize, nodeStream);
- for(unsigned int b = 0; b < contourSize; b++)
- {
- node->m_Contour.push_back(moves[b]);
- }
- }
- nodeMap[node->m_Id] = node;
- graph.m_Nodes.push_back(node);
- }
- }
- fclose(nodeStream);
-
- // Build edges with nodeMap
FILE * edgeStream = fopen(edgesPath.c_str(), "r");
assert(edgeStream != NULL);
- for(auto& node: graph.m_Nodes)
- {
- long unsigned int nodeId;
- fread(&(nodeId), sizeof(nodeId), 1, edgeStream);
- assert(nodeId == node->m_Id);
-
- std::size_t edgeSize;
- fread(&(edgeSize), sizeof(edgeSize), 1, edgeStream);
- node->m_Edges.reserve(edgeSize);
- for(unsigned int b = 0; b < edgeSize; b++)
- {
- long unsigned int targetId;
- unsigned int boundary;
- fread(&(targetId), sizeof(targetId), 1, edgeStream);
- fread(&(boundary), sizeof(boundary), 1, edgeStream);
- node->m_Edges.push_back(typename TSegmenter::EdgeType(nodeMap[targetId], 0, boundary));
- }
- }
+ segmenter.ReadGraph(nodeStream, edgeStream);
+ fclose(nodeStream);
fclose(edgeStream);
}
+template<class TSegmenter>
+void ReadGraph(typename TSegmenter::GraphType& graph,
+ const std::string& nodesPath,
+ const std::string& edgesPath)
+{
+ TSegmenter segmenter;
+ ReadGraph<TSegmenter>(segmenter, nodesPath, edgesPath);
+ graph = segmenter.m_Graph;
+}
+
// Write stability margin
template<class TSegmenter>
void WriteStabilityMargin(std::unordered_map<
@@ -992,52 +824,19 @@ void WriteStabilityMargin(std::unordered_map<
FILE * edgeStream = fopen(edgesPath.c_str(), "wb");
assert(edgeStream != NULL);
- // Write size of the graph
- {
- // Write number of nodes
- std::size_t size = stabilityMargin.size();
- fwrite(&size, sizeof(size), 1, nodeStream);
- }
+ // Write number of nodes
+ std::size_t size = stabilityMargin.size();
+ fwrite(&size, sizeof(size), 1, nodeStream);
+ TSegmenter seg;
for(auto& kv : stabilityMargin)
{
auto node = kv.first;
-
- fwrite(&(node->m_Id), sizeof(node->m_Id), 1, nodeStream);
- fwrite(&(node->m_Perimeter), sizeof(node->m_Perimeter), 1, nodeStream);
- fwrite(&(node->m_Area), sizeof(node->m_Area), 1, nodeStream);
- fwrite(&(node->m_Bbox.m_UX), sizeof(node->m_Bbox.m_UX), 1, nodeStream);
- fwrite(&(node->m_Bbox.m_UY), sizeof(node->m_Bbox.m_UY), 1, nodeStream);
- fwrite(&(node->m_Bbox.m_W), sizeof(node->m_Bbox.m_W), 1, nodeStream);
- fwrite(&(node->m_Bbox.m_H), sizeof(node->m_Bbox.m_H), 1, nodeStream);
-
- std::size_t bands = node->m_Means.size();
- fwrite(&(bands), sizeof(bands), 1, nodeStream);
-
- for(unsigned int b = 0; b < node->m_Means.size(); b++)
- {
- fwrite(&(node->m_Means[b]), sizeof(node->m_Means[b]), 1, nodeStream);
- fwrite(&(node->m_SquareMeans[b]), sizeof(node->m_SquareMeans[b]), 1, nodeStream);
- fwrite(&(node->m_SpectralSum[b]), sizeof(node->m_SpectralSum[b]), 1, nodeStream);
- fwrite(&(node->m_Std[b]), sizeof(node->m_Std[b]), 1, nodeStream);
- }
-
- {
- std::size_t contourSize = node->m_Contour.size();
- fwrite(&(contourSize), sizeof(contourSize), 1, nodeStream);
- short moves[contourSize];
- for(unsigned int b = 0; b < contourSize; b++)
- {
- moves[b] = node->m_Contour[b];
- }
- fwrite(moves, sizeof(short), contourSize, nodeStream);
- }
+ seg.WriteNode(node, nodeStream);
// Write only edges pointing to nodes which are in the stability margin.
-
fwrite(&(node->m_Id), sizeof(node->m_Id), 1, edgeStream);
std::size_t edgeSize = node->m_Edges.size();
-
for(auto& edg : node->m_Edges)
{
if(stabilityMargin.find(edg.GetRegion()) == stabilityMargin.end())
@@ -1048,8 +847,7 @@ void WriteStabilityMargin(std::unordered_map<
{
if(stabilityMargin.find(edg.GetRegion()) != stabilityMargin.end())
{
- fwrite(&(edg.GetRegion()->m_Id), sizeof(edg.GetRegion()->m_Id), 1, edgeStream);
- fwrite(&(edg.m_Boundary), sizeof(edg.m_Boundary), 1, edgeStream);
+ seg.WriteEdge(edg, edgeStream);
}
}
}
@@ -1058,65 +856,26 @@ void WriteStabilityMargin(std::unordered_map<
fclose(edgeStream);
}
-// Specific to Baatz & Schape (sorry it has to be fast)
+// Write the graph
template<class TSegmenter>
void WriteGraph(typename TSegmenter::GraphType& graph,
- const std::string& tmpDir,
- const unsigned int row,
- const unsigned int col)
+ const std::string& nodeFile,
+ const std::string& edgeFile)
{
- // One file for the nodes
- std::string nodeFile = tmpDir + "tile_nodes_" +
- std::to_string(row) + "_" + std::to_string(col) + ".bin";
- // One file for the edges
- std::string edgeFile = tmpDir + "tile_edges_" +
- std::to_string(row) + "_" + std::to_string(col) + ".bin";
FILE * nodeStream = fopen(nodeFile.c_str(), "wb");
assert(nodeStream != NULL);
FILE * edgeStream = fopen(edgeFile.c_str(), "wb");
assert(edgeStream != NULL);
- // Write size of the graph
- {
- // Write number of nodes
- std::size_t size = graph.m_Nodes.size();
- fwrite(&size, sizeof(size), 1, nodeStream);
- }
-
+ // Write number of nodes
+ std::size_t size = graph.m_Nodes.size();
+ fwrite(&size, sizeof(size), 1, nodeStream);
+ TSegmenter seg;
for(auto& node : graph.m_Nodes)
{
-
- fwrite(&(node->m_Id), sizeof(node->m_Id), 1, nodeStream);
- fwrite(&(node->m_Perimeter), sizeof(node->m_Perimeter), 1, nodeStream);
- fwrite(&(node->m_Area), sizeof(node->m_Area), 1, nodeStream);
- fwrite(&(node->m_Bbox.m_UX), sizeof(node->m_Bbox.m_UX), 1, nodeStream);
- fwrite(&(node->m_Bbox.m_UY), sizeof(node->m_Bbox.m_UY), 1, nodeStream);
- fwrite(&(node->m_Bbox.m_W), sizeof(node->m_Bbox.m_W), 1, nodeStream);
- fwrite(&(node->m_Bbox.m_H), sizeof(node->m_Bbox.m_H), 1, nodeStream);
-
- std::size_t bands = node->m_Means.size();
- fwrite(&(bands), sizeof(bands), 1, nodeStream);
-
- for(unsigned int b = 0; b < node->m_Means.size(); b++)
- {
- fwrite(&(node->m_Means[b]), sizeof(node->m_Means[b]), 1, nodeStream);
- fwrite(&(node->m_SquareMeans[b]), sizeof(node->m_SquareMeans[b]), 1, nodeStream);
- fwrite(&(node->m_SpectralSum[b]), sizeof(node->m_SpectralSum[b]), 1, nodeStream);
- fwrite(&(node->m_Std[b]), sizeof(node->m_Std[b]), 1, nodeStream);
- }
-
- {
- std::size_t contourSize = node->m_Contour.size();
- fwrite(&(contourSize), sizeof(contourSize), 1, nodeStream);
- short moves[contourSize];
- for(unsigned int b = 0; b < contourSize; b++)
- {
- moves[b] = node->m_Contour[b];
- }
- fwrite(moves, sizeof(short), contourSize, nodeStream);
- }
+ seg.WriteNode(node, nodeStream);
// Write edges
fwrite(&(node->m_Id), sizeof(node->m_Id), 1, edgeStream);
@@ -1124,8 +883,7 @@ void WriteGraph(typename TSegmenter::GraphType& graph,
fwrite(&(edgeSize), sizeof(edgeSize), 1, edgeStream);
for(auto& edg : node->m_Edges)
{
- fwrite(&(edg.GetRegion()->m_Id), sizeof(edg.GetRegion()->m_Id), 1, edgeStream);
- fwrite(&(edg.m_Boundary), sizeof(edg.m_Boundary), 1, edgeStream);
+ seg.WriteEdge(edg, edgeStream);
}
}
@@ -1133,29 +891,6 @@ void WriteGraph(typename TSegmenter::GraphType& graph,
fclose(edgeStream);
}
-template<class TSegmenter>
-long long unsigned int GetGraphMemory(TSegmenter segmenter)
-{
-// TSegmenter::GraphType graph = segmenter.graph;
-// long long unsigned int memory = 0;
-// long unsigned int numberOfMoves = 0;
-//
-// // Amount of memory needed to store the nodes
-// memory += graph.m_Nodes.size() * (sizeof(*graph.m_Nodes.begin()) + sizeof(graph.m_Nodes.begin()) + 4 * sizeof(float));
-//
-// for(auto& node : graph.m_Nodes)
-// {
-// memory += node->m_Edges.size() * (sizeof(*node->m_Edges.begin()) + sizeof(node->m_Edges.begin()));
-// numberOfMoves += node->m_Contour.size();
-// }
-//
-// memory += std::ceil(numberOfMoves / 4);
-//
-// return memory;
-
- return segmenter.GetGraphMemory();
-}
-
template<class TSegmenter>
void RemoveUnstableSegments(typename TSegmenter::GraphType& graph,
ProcessingTile& tile,
@@ -1236,29 +971,13 @@ void RescaleGraph(typename TSegmenter::GraphType& graph,
unsigned int rowNodeTile, colNodeTile;
unsigned int rowNodeImg, colNodeImg;
-// unsigned int currTileWidth = tile.columns[1] - tile.columns[0] + 1;
-// currTileWidth += tile.margin[1];
-// currTileWidth += tile.margin[3];
-// unsigned int diffHeightMargin = tile.margin[0];
-// unsigned int diffWidthMargin = tile.margin[3];
-
for(auto& node : graph.m_Nodes)
{
-
-// // Row of the start pixel of the node
-// rowNodeTile = node->m_Id / currTileWidth;
-// // Col of the start pixel of the node
-// colNodeTile = node->m_Id % currTileWidth;
-//
-// // Row of the start pixel of the node in the image
-// rowNodeImg = rowTile * tileHeight + rowNodeTile - diffHeightMargin;
-// // Col of the start pixel of the node in the image
-// colNodeImg = colTile * tileWidth + colNodeTile - diffWidthMargin;
-//
-// node->m_Id = rowNodeImg * imageWidth + colNodeImg;
-
+ // Start pixel index of the node (in the tile)
rowNodeTile = node->m_Id / tile.region.GetSize()[0];
colNodeTile = node->m_Id % tile.region.GetSize()[0];
+
+ // Start pixel index of the node (in the image)
rowNodeImg = rowTile * tileHeight + rowNodeTile - tile.margin[0];
colNodeImg = colTile * tileWidth + colNodeTile - tile.margin[3];
node->m_Id = rowNodeImg * imageWidth + colNodeImg;