EMAN::TomoSeg Class Reference

#include <tomoseg.h>

Collaboration diagram for EMAN::TomoSeg:

Public Member Functions
	TomoSeg ()
void	set_verb ()
int	read_bwmap (EMData *map)
int	read_skelmap (EMData *map)
int	generate_objects (int numo, float maxdist, int nowslice)
int	check_neighbors (int x, int y)
void	write_imod (const char *file)

Private Attributes
EMData *	skelmap
EMData *	bwmap
bool	verb
vector< TomoObject >	objs

Detailed Description

Definition at line 55 of file tomoseg.h.

Constructor & Destructor Documentation

TomoSeg()

EMAN::TomoSeg::TomoSeg ( )

inline

Definition at line 58 of file tomoseg.h.

{verb=false;};

References verb.

Member Function Documentation

check_neighbors()

int TomoSeg::check_neighbors	(	int	x,
		int	y
	)

Definition at line 209 of file tomoseg.cpp.

                                       {
        int nb=-1;
        for (int i=-1; i<=1; i++){
                for (int j=-1; j<=1; j++){
                        nb+= (skelmap->get_value_at(x+i,y+j)>0 ? 1 : 0);
                }
        }
        return nb;
}

References skelmap, x, and y.

Referenced by generate_objects().

generate_objects()

int TomoSeg::generate_objects	(	int	numo,
		float	maxdist,
		int	nowslice
	)

Definition at line 145 of file tomoseg.cpp.

                                                                  {
        if (!skelmap){
                printf("No map input.\n");
                return 0;
        }
 
        // Calculate area of each segment       
        EMData *rank=skelmap->process("threshold.notzero");
        rank->process_inplace("morph.object.density",Dict("thresh",0,"more_neighbor",true));
        int nx=rank->get_xsize();
        int ny=rank->get_ysize();
        
        // Take numo largest objects
        for (int i=0; i<numo; i++){
                float max=rank->get_attr("maximum");
                vector <Vec3i> pts;
                float curid=-1;
                bool branch=false;
                if (max<=0)
                        break;
                for (int x=0; x<nx; x++){
                        for (int y=0; y<ny; y++){
                                if (rank->get_value_at(x,y)==max){
                                        if (curid<0)
                                                curid=skelmap->get_value_at(x,y);
                                        if (curid==skelmap->get_value_at(x,y)){
                                                int nb=check_neighbors(x,y);
                                                if (nb>2) branch=true;
                                                pts.push_back(Vec3i(x,y,nb));
                                                rank->set_value_at_fast(x,y,0);
                                        }
                                }
                        }
                }
                if(verb) printf("id=%d,  size=%d",int(curid),int(pts.size()));
                if (branch){
                        if (verb) printf("\n\thave branch, throw out.\n");
                }
                else{
                        objs.push_back(TomoObject(pts,maxdist,nowslice));
                        if (verb) printf("   \t%d points\n",objs.back().get_size() );
                }
                
        }
        
        delete rank;
        return 1;
}

References check_neighbors(), objs, skelmap, verb, x, and y.

read_bwmap()

int EMAN::TomoSeg::read_bwmap

(

EMData *

map

)

read_skelmap()

int TomoSeg::read_skelmap

(

EMData *

map

)

Definition at line 138 of file tomoseg.cpp.

                                    {
        if (!map)
                return 0;
        skelmap=map;
        return 1;
}

References skelmap.

set_verb()

void EMAN::TomoSeg::set_verb ( )

inline

Definition at line 59 of file tomoseg.h.

{verb=!verb;};

References verb.

write_imod()

void TomoSeg::write_imod

(

const char *

file

)

Definition at line 194 of file tomoseg.cpp.

                                        {
        FILE *fp = fopen(file, "w");
        int nx=skelmap->get_xsize();
        int ny=skelmap->get_ysize();
        int nz=skelmap->get_zsize();
        fprintf(fp,"imod %d\n",(int)objs.size());
        fprintf(fp,"max %d %d %d\n",nx,ny,nz);
        for (int i=0; i<(int)objs.size(); i++){
                fprintf(fp,"object %d 1 0\n",i);
                objs[i].write_imod(fp);
                fprintf(fp,"\n");
        }
        fclose(fp);
}

References objs, and skelmap.

Member Data Documentation

bwmap

EMData* EMAN::TomoSeg::bwmap

private

Definition at line 78 of file tomoseg.h.

objs

vector<TomoObject> EMAN::TomoSeg::objs

private

Definition at line 80 of file tomoseg.h.

Referenced by generate_objects(), and write_imod().

skelmap

EMData* EMAN::TomoSeg::skelmap

private

Definition at line 77 of file tomoseg.h.

Referenced by check_neighbors(), generate_objects(), read_skelmap(), and write_imod().

verb

bool EMAN::TomoSeg::verb

private

Definition at line 79 of file tomoseg.h.

Referenced by generate_objects(), set_verb(), and TomoSeg().

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The documentation for this class was generated from the following files:

• tomoseg.h
• tomoseg.cpp