ciftitools.h

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/* This software and supporting documentation are distributed by
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#ifndef AIMS_SPARSEMATRIX_CIFTITOOLS_H
#define AIMS_SPARSEMATRIX_CIFTITOOLS_H

#include <cartobase/smart/rcptr.h>
#include <map>
#include <vector>
#include <string>
#include <list>

template <typename T> class TimeTexture;
class Void;
template <int D, typename T> class AimsTimeSurface;

namespace carto
{
  class Object;
}


namespace aims
{
  class SparseOrDenseMatrix;

  class CiftiTools
  {
  public:
    typedef std::map<std::string, int> BrainStuctureToMeshMap;
    typedef std::vector<carto::rc_ptr<TimeTexture<int> > > RoiTextureList;
    typedef std::vector<carto::rc_ptr<TimeTexture<float> > > TextureList;

    CiftiTools(
      carto::rc_ptr<SparseOrDenseMatrix> matrix,
      const BrainStuctureToMeshMap & smap = BrainStuctureToMeshMap() );
    ~CiftiTools();

    const carto::rc_ptr<SparseOrDenseMatrix> matrix() const
    { return _matrix; }
    carto::rc_ptr<SparseOrDenseMatrix> matrix()
    { return _matrix; }
    void setMatrix( carto::rc_ptr<SparseOrDenseMatrix> matrix );
    const BrainStuctureToMeshMap & brainStructureMap() const
    { return _smap; }
    BrainStuctureToMeshMap & brainStructureMap()
    { return _smap; }
    void setBrainStructureMap( const BrainStuctureToMeshMap & smap )
    { _smap = smap; }
    RoiTextureList *roiTextureFromDimension( int dim ) const;
    TextureList *expandedValueTextureFromDimension(
      int dim,
      const std::vector<int> & dim_indices_pos,
      TextureList* existing_tex_list = 0 ) const;

    // intermediate
    static BrainStuctureToMeshMap defaultBrainStructureToMeshMap();
    int valuesDimNum() const;
    static int valuesDimNum( carto::Object cifti_info );
    static size_t valuesDimSize( const SparseOrDenseMatrix & mat,
                                 int value_dim );
    static std::string dimensionType( carto::Object cifti_info, int dim );
    std::string dimensionType( int dim ) const;

    // lower-level (could probably be private)
    carto::Object getDimensionObject( int dim ) const;

    template <typename T>
    void buildDimensionObjectFromLabelsTexture( int dim,
                                                const TimeTexture<T> & tex );

    static void getLabelsInfo( carto::Object cifti_info, RoiTextureList & );
    static void getSeriesInfo( carto::Object cifti_info, RoiTextureList & );
    void getParcelsInfo( carto::Object cifti_info, RoiTextureList & ) const;
    void getBrainModelsInfo( carto::Object cifti_info,
                             RoiTextureList & ) const;
    void getBrainModelsTexture(
      carto::Object cifti_info, TextureList & texlist, int dim,
      const std::vector<int> & dim_indices_pos ) const;
    void getParcelsTexture(
      carto::Object cifti_info, TextureList & texlist, int dim,
      const std::vector<int> & dim_indices_pos ) const;
    std::list<std::string> getBrainStructures( int dim,
                                               bool keepSurfaces = true,
                                               bool keepVoxels = true ) const;
    std::vector<int> getIndicesForBrainStructure(
      int dim, const std::string & struct_name ) const;
    std::vector<int> getIndicesForSurfaceIndices(
      int dim, int surface_num, const std::vector<int> & roi_indices ) const;
    size_t getBrainStructureMeshNumberOfNodes(
      int dim, const std::string & struct_name ) const;
    bool isMatchingSurface( int dim, const AimsTimeSurface<3, Void> & mesh,
                            std::list<std::string> & brainmodels,
                            int & surf_index, int surf_hint = 0 ) const
    {
      return isMatchingSurfaceOrTexture( dim, mesh, brainmodels, surf_index,
                                         surf_hint );
    }
    template <typename T>
    bool isMatchingTexture( int dim, const TimeTexture<T> & tex,
                            std::list<std::string> & brainmodels,
                            int & surf_index, int surf_hint = 0 ) const
    {
      return isMatchingSurfaceOrTexture( dim, tex, brainmodels, surf_index,
                                         surf_hint );
    }
    bool isMatchingSurfaceOrTexture( int dim, size_t nvertices,
                                     const carto::Object header,
                                     std::list<std::string> & brainmodels,
                                     int & surf_index,
                                     int surf_hint = 0 ) const;

  private:
    template <typename T> bool
      isMatchingSurfaceOrTexture( int dim, const T & mesh,
                                  std::list<std::string> & brainmodels,
                                  int & surf_index, int surf_hint = 0 ) const;
    void getSurfaceModelTexture(
      carto::Object surf, TextureList & texlist,
      const BrainStuctureToMeshMap & smap,
      SparseOrDenseMatrix & mat, int dim,
      const std::vector<int> & dim_indices_pos,
      unsigned  nsurfaces ) const;

    struct Private;

    Private *d;
    mutable carto::rc_ptr<SparseOrDenseMatrix> _matrix;
    BrainStuctureToMeshMap _smap;
  };

}

#endif