connMatrix.h

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#ifndef CONSTELLATION_CONNMATRIX_H
#define CONSTELLATION_CONNMATRIX_H
 
#include <constellation/bundleSet.h>
#include <constellation/tildefs.h>
#include <constellation/connectivities.h>
 
// includes from AIMS
#include <aims/mesh/surface.h>
#include <aims/mesh/texture.h>
 
namespace aims {
  class SparseOrDenseMatrix;
}
 
namespace constel {
  Connectivities *weightedConnMatrix(
    const WeightedFibers &fibers, const AimsSurfaceTriangle &inAimsMesh,
    Motion motion, bool verbose = false);
 
  Connectivities *connMatrix(
    const Fibers &fibers, const AimsSurfaceTriangle &inAimsMesh,
    float distthresh, float wthresh, Motion motion, bool verbose = false);
 
  Connectivity *connMatrixSumRows(
    Connectivities *matrix_ptr, bool verbose = false);
 
  std::vector<double> *connMatrixSumRows(
    const aims::SparseOrDenseMatrix & matrix, bool verbose = false);
 
  Connectivities *connMatrixTargetsRegroup(
    Connectivities *connMatrixToAllMesh,
    const TimeTexture<short> &targetRegionsTexture, int targetRegionsNb,
    bool verbose = false);
 
  Connectivities *connMatrixReducedFromRegion(
    Connectivities *allMeshConnMatrix,
    const TimeTexture<short> &seedRegionsTexture,
    int seedRegionLabel, int seedRegionLabelVertexNb,
    std::vector<std::size_t> **seedVertexIndex = 0, bool verbose = false);
 
  Connectivities *connMatrixRegionExtractTargetsRegroup(
      Connectivities *allMeshConnMatrix,
      const TimeTexture<short> &seedRegionsTexture,
      int seedRegionLabel, const TimeTexture<short> &targetRegionsTexture,
      int targetRegionsNb, std::size_t seedRegionLabelVertexNb,
      std::vector<std::size_t> **seedVertexIndex, bool verbose = false);
 
  void writeAimsFmtConnMatrix(
    Connectivities *connMatrix_ptr, std::string file_name,
    bool verbose = false);
 
  void connMatrixNormalize(
    aims::SparseOrDenseMatrix &connMatrix, bool verbose = false);
 
  Connectivities *connMatrixRegionExtract(
    const aims::SparseOrDenseMatrix &allMeshConnMatrix,
    const TimeTexture<short> &seedRegionsTexture, int seedRegionLabel,
    std::size_t seedRegionLabelVertexNb,
    std::vector<std::size_t> **seedVertexIndex = 0, bool verbose = false);
 
  TimeTexture<float> densityTexture(
    Connectivities *allMeshConnMatrix, std::vector<std::size_t> VertexIndex,
    bool verbose = false);
 
  TimeTexture<float> densityTexture(
    const aims::SparseOrDenseMatrix &allMeshConnMatrix,
    std::vector<std::size_t> VertexIndex, bool verbose = false);
 
  TimeTexture<float> meshDensityTexture(
    Connectivities *connMatrixToAllMesh_ptr, bool verbose = false);
 
  TimeTexture<float> meshDensityTexture(
    const aims::SparseOrDenseMatrix &connMatrixToAllMesh,
    bool verbose = false);
 
  TimeTexture<float> *oneTargetDensityTargetsRegroupTexture(
    const Connectivity *lineMatrixToTargetRegions_ptr,
    const TimeTexture<short> &targetRegionsTex, int timestep);
 
  TimeTexture<float> *oneTargetDensityTargetsRegroupTexture(
    const std::vector<double> *lineMatrixToTargetRegions_ptr,
    const TimeTexture<short> &targetRegionsTex, int timestep);
 
  TimeTexture<float> *connMatrixRow_TO_TimeTexture_FLOAT(
    Connectivity *conn_ptr);
 
  Connectivity *connMatrixToRois(
    const Fibers &fibers, const AimsSurfaceTriangle &inAimsMesh,
    float distthresh, float wthresh, Motion motion, bool verbose = false);
 
  Connectivities *connMatrixSeedMeshToTargetMesh(
    const Fibers &fibers, const AimsSurfaceTriangle &aimsMesh1,
    const AimsSurfaceTriangle &aimsMesh2, float distthresh, float wthresh,
    Motion motion, bool verbose = false);
 
  Connectivities *connMatrixSeedMesh_to_targetMeshTargets_regroup(
    const aims::SparseOrDenseMatrix &connMatrixToAllMesh,
    const TimeTexture<short> &targetRegionsTex, int targetRegionsNb,
    bool verbose = false);
 
  Connectivities *connMatrixSeedMeshRegions_to_targetMeshTargets_regroup(
    Connectivities *connMatrixSeedMeshToTargetMesh_ptr,
    const TimeTexture<short> &seedRegionsTexture,
    const TimeTexture<short> &targetRegionsTex, int targetRegionsNb,
    int seedRegionsNb, bool verbose = false);
 
  aims::SparseOrDenseMatrix* connectivitiesToSparseOrDenseMatrix(
    const Connectivities &);
 
} // namespace constel
 
#endif // ifndef CONSTELLATION_CONNMATRIX_H