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LSGRM
Commit bb65d2e0 authored by remicres's avatar remicres
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REFAC: functions use ProcesingTiles instead of many numeric and string variables

parent 69882db5
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Showing with 121 additions and 399 deletions
include/lsgrmController.h
View file @ bb65d2e0
......@@ -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
View file @ bb65d2e0
......@@ -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
View file @ bb65d2e0
......@@ -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,
......
include/lsgrmGraphOperations.txx
View file @ bb65d2e0
......@@ -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];
}