connMatrixTools.h

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#ifndef CONSTELLATION_CONNMATRIXTOOLS_H
#define CONSTELLATION_CONNMATRIXTOOLS_H
 
#include <aims/sparsematrix/sparseMatrix.h>
#include <constellation/connectivities.h>
#include <constellation/bundleSet.h>
#include <aims/mesh/surface.h>
#include <aims/mesh/texture.h>
 
namespace constel {
 
  void fillconnMatrix(
      Connectivities *conn, QuickMap &fiberExtremity1NeighMeshVertex,
      QuickMap &fiberExtremity2NeighMeshVertex, double connectivityThreshold,
      double distanceThreshold, unsigned connectionLength = 1);
 
  void fillconnMatrixNoSmoothing(
      Connectivities *conn_ptr, QuickMap &fiberExtremity1NeighMeshVertex,
      QuickMap &fiberExtremity2NeighMeshVertex);
 
  void fillconnMatrix(
      aims::SparseMatrix *conn_ptr, QuickMap &fiberExtremity1NeighMeshVertex,
      QuickMap &fiberExtremity2NeighMeshVertex, double connectivityThreshold,
      double distanceThreshold, unsigned connectionLength = 1);
 
  void fillconnMatrix(
      aims::SparseMatrix *conn_ptr, aims::SparseMatrix *conn_ptr2,
      QuickMap &fiberExtremity1NeighMeshVertex,
      QuickMap &fiberExtremity2NeighMeshVertex, double connectivityThreshold,
      double distanceThreshold, std::size_t rowIndex_min,
      std::size_t rowIndex_max = 0, unsigned connectionLength = 1);
 
  void fillNonSymetricConnMatrix(
      Connectivities *conn_ptr, QuickMap &fiberExtremity1NeighMeshVertex_rows,
      QuickMap &fiberExtremity2NeighMeshVertex_cols,
      double connectivityThreshold, double distanceThreshold);
 
  void fillconnMatrixWithConnections(
      Connectivities *conn_ptr, const BundleConnections &connections,
      std::vector< double > cortexConnectionsWeights,
      double connectivityThreshold, double distanceThreshold);
 
  void fillconnMatrixWithConnections(
      aims::SparseMatrix *conn_ptr, const BundleConnections &connections,
      double connectivityThreshold, double distanceThreshold,
      std::size_t rowIndex_min = 0, std::size_t rowIndex_max = 0,
      aims::SparseMatrix *conn_ptr2 = 0);
 
  void fillconnMatrixWithConnectionsPlusLength(
      Connectivities *conn_ptr, const BundleConnections &connections,
      double connectivityThreshold, double distanceThreshold,
      unsigned length_min, unsigned length_max,
      ConnectionsLength &connectionsLength);
 
  void fillconnMatrixWithConnectionsPlusLengthWeight(
      Connectivities *conn_ptr, const BundleConnections &connections,
      double connectivityThreshold, double distanceThreshold,
      unsigned length_min, unsigned length_max,
      ConnectionsLength &connectionsLength);
 
  void fillconnMatrixWithConnectionsPlusFloatLengthWeight(
      Connectivities *conn_ptr, const BundleConnections &connections,
      double connectivityThreshold, double distanceThreshold,
      float length_min, float length_max,
      ConnectionsFloatLength &connectionsLength);
 
  void fillNonSymetricConnMatrixWithConnections(
      Connectivities *conn_ptr, const BundleConnections &connections,
      double connectivityThreshold, double distanceThreshold);
 
  template<int D, class T> bool
  computeIntersectionPointFiberSegmentAndMesh(
      const AimsTimeSurface<D, T> &aimsMesh,
      const std::vector<std::set<unsigned> > &polygonsByVertex_Index,
      Point3df fiberPoint1, Point3df fiberPoint2, unsigned meshClosestPoint,
      QuickMap **polygonVerticesDistMap = 0);
 
  template<int D, class T> bool
  computeIntersectionPointFiberSegmentAndMesh2(
      const AimsTimeSurface<D, T> &aimsMesh,
      const std::vector<std::set<unsigned> > &polygonsByVertex_Index,
      Point3df fiberPoint1, Point3df fiberPoint2, unsigned meshClosestPoint,
      QuickMap **polygonVerticesDistMap = 0);
 
  template<int D, class T> bool
  computeIntersectionPointNeighborhoodFiberSegmentAndMesh(
      const AimsTimeSurface<D, T> &aimsMesh,
      const std::vector<std::set<unsigned> > &polygonsByVertex_Index,
      Point3df fiberPoint1, Point3df fiberPoint2, unsigned meshClosestPoint,
      std::vector<QuickMap> &distanceThresholdNeighborhoodByVertex,
      QuickMap **polygonVerticesDistMap_2ptr);
 
  void connMatrixTargetsToTargets(
      const Fibers &fibers, const AimsSurfaceTriangle &inAimsMesh,
      Motion motion, const TimeTexture<short> &targetRegionsTex,
      std::string filename);
 
  void connMatrixSeedRegion(
      const Fibers &fibers, const AimsSurfaceTriangle &inAimsMesh,
      Motion motion, const TimeTexture<short> &seedRegionsTex,
      std::size_t seedRegionLabel, std::string connmatrix_filename,
      std::string connTexture_filename);
 
  void connMatrixSeedRegionSmoothed(
      const Fibers &fibers, const AimsSurfaceTriangle &inAimsMesh,
      Motion motion, const TimeTexture<short> &seedRegionsTex,
      std::size_t seedRegionLabel, float distthresh, float wthresh,
      std::string connmatrix_filename, std::string connTexture_filename = "",
      bool logOption = false);
 
} // namespace constel
 
#endif // ifndef CONSTELLATION_CONNMATRIXTOOLS_H