tomoseg.h

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/*
 * This software is issued under a joint BSD/GNU license. You may use the
 * source code in this file under either license. However, note that the
 * complete EMAN2 and SPARX software packages have some GPL dependencies,
 * so you are responsible for compliance with the licenses of these packages
 * if you opt to use BSD licensing. The warranty disclaimer below holds
 * in either instance.
 *
 * This complete copyright notice must be included in any revised version of the
 * source code. Additional authorship citations may be added, but existing
 * author citations must be preserved.
 *
 * This program is free software; you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by.edge
 * the Free Software Foundation; either version 2 of the License, or
 * (at your option) any later version.
 *
 * This program is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
 * GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with this program; if not, write to the Free Software
 * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA 
 */
 
#ifndef eman_tomoseg_h_
#define eman_tomoseg_h_
 
#include "emdata.h"
 
namespace EMAN
{
        class TomoObject{
        public:
                TomoObject(vector<Vec3i> allpt, float md=1, int slice=0);
                void write_imod(FILE *fp);
                int get_size();
                
                /* Starting from connecting two terminis and iteratively bend the polyline by breaking at the 
                 * most distant point from the polyline.*/
                int bend();
                
                /* Enlong the line segments and connect the adjecent objects. */
                void enlong(EMData *bwmap,EMData *skelmap);
                
        public:
                vector<int> ptid;       // ID of the cornor points in the object
                vector<int> segid;      // ID of the segments in the labeled map that are in this object.
                vector<Vec3i> allpoints;// Cooridinates of all points in this object
                float maxdist;          // Max distance to bend the polyline.
                int nowslice;
        };
        class TomoSeg
        {
        public:
                TomoSeg(){verb=false;};
                void set_verb(){verb=!verb;};
                
                /* Read the black-white map. Each segment in the map should be labeled. */
                int read_bwmap(EMData *map);
                
                /* Read the skeleton map. The map should be labeled the same as the bwmap */
                int read_skelmap(EMData *map);
                
                /*  Generate objects from numo largest segments in the skeleton map. */
                int generate_objects(int numo, float maxdist, int nowslice);
                
                /* Check the value of 8 neighbors. Return the number of white neighbors. */
                int check_neighbors(int x,int y);
                
                /* Write objects to imod format */
                void write_imod(const char *file);
                
        private:
                EMData *skelmap;
                EMData *bwmap;
                bool verb;
                vector<TomoObject> objs;
        };
}
 
#endif