corticalReferential.h

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/*
 *  Copyright (C) 2000-2004 CEA
 *
 *  This software and supporting documentation were developed by
 *      CEA/DSV/SHFJ
 *      4 place du General Leclerc
 *      91401 Orsay cedex
 *      France
 */


/**************** BRAND NEW DEV VERSION YEAH!!!!****************/


#ifndef AIMS_CORTICALREFERENTIAL_H
#define AIMS_CORTICALREFERENTIAL_H


#include <aims/mesh/texture.h>
#include <aims/io/reader.h>
#include <aims/io/writer.h>

#include <cortical_surface/surfacereferential/corticalTools.h>
#include <cortical_surface/surfacereferential/corticalConstraints.h>
#include <cortical_surface/surfacereferential/sulcusCleaner.h>

namespace aims
{

        class CorticalReferential
        {
        
                public:
        
                        AimsSurfaceTriangle mesh;
                        AimsSurface<3, Void> mesh_base;
                        std::map<unsigned, std::set< std::pair<unsigned,float> > >  weightLapl;
                //Liste de voisinage
                        std::vector<std::set<uint> > neigh;
                //Surface vector
                        std::vector<Point3df> vert;
        
                //Poles Index and size (=vertex numbers)
                        int size, nord, sud, ind_min;
                        std::pair<int,int> poles_points;
        
                //Parametres pour l'execution
                        std::string adr;
                        std::string adr_par;
                        std::string adr_mer;
                        std::string adr_call;
                        std::string adr_poles;
                
                //Condition d'arret des iterations (difference avec la moy du laplacien 1000 iter. avant
                        float criterium;
        
                //Reglage du pas pour le calcul iteratif
                        float _dt;
                
                //Si on doit faire les cotes du sillon central inverses
                        int context;
                
                //Ce que l'on effectue
                        int choice_process;                     
        
                //Reglage du terme d'attache aux donn�s
                        float _Beta;
                
                //Type d'attache aux données
                        int typeBeta;
                
        //Adresse des outputs
                        std::string adr_lat;
                        std::string adr_lon;
        
                //Textures de contraintes
                
                        TimeTexture<float> constraint_lat;
                        TimeTexture<float> constraint_lat_cleaned;
                        TimeTexture<float> constraint_lat_read;
                        TimeTexture<float> constraint_long;
                        TimeTexture<float> constraint_long_cleaned;
                        TimeTexture<float> constraint_long_read;
                        TimeTexture<short> cercle_polaire;
        
                        TimeTexture<float> pole_call;
                        TimeTexture<float> pole_insula;
                        TimeTexture<float> poles;
                
                        std::vector<unsigned> forb_list;
        
                // indique si on a deja trouve les poles
                        bool poles_found;
                        
                // indique si on doit parametriser l'insula ou non
                        bool doInsulaParameterization;
        
                //A voir pour le reste
                        TimeTexture<float> diff_meridian_origine;
                        TimeTexture<float> distance_poles;
                        float diametre;
        
                //Constructor
                        CorticalReferential ( ) {}
                        CorticalReferential ( std::string & adr_param, 
                                              std::string & adr_parallele, 
                                              std::string & adr_meridien, 
                                              std::string & adr_calleux, 
                                              std::string & _adr_poles, 
                                              float criter, 
                                              float dt, 
                                              int c, 
                                              int choice, 
                                              float Beta, 
                                              int tBeta, 
                                              std::string & adrlat, 
                                              std::string & adrlon,
                                              bool _doInsulaParam = true ) : 
                                                  adr(adr_param), 
                                                  adr_par(adr_parallele), 
                                                  adr_mer(adr_meridien), 
                                                  adr_call(adr_calleux), 
                                                  adr_poles(_adr_poles), 
                                                  criterium(criter), 
                                                  _dt(dt), 
                                                  context(c), 
                                                  choice_process(choice), 
                                                  _Beta(Beta), 
                                                  typeBeta(tBeta), 
                                                  adr_lat(adrlat), 
                                                  adr_lon(adrlon),
                                                  doInsulaParameterization(_doInsulaParam)
                        {
                            
                                std::cout << "constructeur" << std::endl;
                                std::cout << "mesh adress : " << adr << std::endl;
                                std::cout << "adr_par : " << adr_par << std::endl;
                                std::cout << "adr_mer : " << adr_mer << std::endl;
                                std::cout << "adr_call : " << adr_call << std::endl;
                                std::cout << "adr_poles : " << adr_poles << std::endl;
                                std::cout << "_dt : "<< _dt  << std::endl;
                                std::cout << "criterium : " << criterium  << std::endl;
                                std::cout << "context : " << context  << std::endl;
                                std::cout << "choice : " << choice_process  << std::endl;
                                std::cout << "Beta : " << _Beta  << std::endl;
        
                        //Opening brain mesh
                                Reader < AimsSurfaceTriangle > r(adr);
                                r.read( mesh );
                                std::cout << "reader mesh ok" << std::endl;
                        
                        //Mesh version AimsSurface
                                mesh_base = mesh[0];
                                std::cout << "mesh_base ok" << std::endl;
                        //Surface vector
                                vert = mesh_base.vertex();
                                std::cout << "vert ok!" << std::endl;
        
                        //Computing neighbourhood
                neigh = SurfaceManip::surfaceNeighbours ( mesh );
        
                                std::cout << "neigh ok" << std::endl;
                                weightLapl = AimsMeshWeightFiniteElementLaplacian ( mesh_base, 0.98 );
        
                                std::cout << "weightlaplacian ok" << std::endl;
                                size = vert.size();
                                std::cout << "size :" << size << std::endl;
        
                        //LECTURE DES POLES (A INTEGRER PAR LA SUITE AUX CONTRAINTES)
        
                                Reader < TimeTexture<float> > lp1 ( adr_call );
                                lp1.read( pole_call );
        
                                Reader < TimeTexture<float> > lp2 ( adr_poles );
                                lp2.read( poles );
        
                                poles_found = false;
                                std::cout << "Constructeur fini!!" << std::endl;
                        }
                        
        
                //Main methods
                        void process();
                        void constraintPreprocess();
                        void latitudePropagation();
                        void longitudePropagation();
                
                
                //Diffusion methods
                        void cingularPoint();
                        TimeTexture<float> diffusionLatitudeRelax ( TimeTexture<float> & tex );
                        TimeTexture<float> diffusionLatitude ( TimeTexture<float> &);
                        TimeTexture<float> diffusionLongitudeRelax ( TimeTexture<float> & tex, TimeTexture<float> & side);
                        TimeTexture<float> diffusionLongitude ( TimeTexture<float> & tex, TimeTexture<float> & side, TimeTexture<float> & poleSave, int ind);
                        Texture<float> AimsMeshLaplacian_meridian ( const Texture<float> &smooth, TimeTexture<float> &source, const std::map<unsigned, std::set< std::pair<unsigned,float> > > &lapl, TimeTexture<float> & side);
                
        };



}

#endif