ciftitools.h

Go to the documentation of this file.

/* This software and supporting documentation are distributed by
 *     Institut Federatif de Recherche 49
 *     CEA/NeuroSpin, Batiment 145,
 *     91191 Gif-sur-Yvette cedex
 *     France
 *
 * This software is governed by the CeCILL-B license under
 * French law and abiding by the rules of distribution of free software.
 * You can  use, modify and/or redistribute the software under the
 * terms of the CeCILL-B license as circulated by CEA, CNRS
 * and INRIA at the following URL "http://www.cecill.info".
 *
 * As a counterpart to the access to the source code and  rights to copy,
 * modify and redistribute granted by the license, users are provided only
 * with a limited warranty  and the software's author,  the holder of the
 * economic rights,  and the successive licensors  have only  limited
 * liability.
 *
 * In this respect, the user's attention is drawn to the risks associated
 * with loading,  using,  modifying and/or developing or reproducing the
 * software by the user in light of its specific status of free software,
 * that may mean  that it is complicated to manipulate,  and  that  also
 * therefore means  that it is reserved for developers  and  experienced
 * professionals having in-depth computer knowledge. Users are therefore
 * encouraged to load and test the software's suitability as regards their
 * requirements in conditions enabling the security of their systems and/or
 * data to be ensured and,  more generally, to use and operate it in the
 * same conditions as regards security.
 *
 * The fact that you are presently reading this means that you have had
 * knowledge of the CeCILL-B license and that you accept its terms.
 */
 
#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