Label each object in a black-white image. More...

#include <processor.h>

Inheritance diagram for EMAN::ObjLabelProcessor:

Collaboration diagram for EMAN::ObjLabelProcessor:

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Public Member Functions
virtual void	process_inplace (EMData *image)
	To process an image in-place. More...

virtual EMData *	process (const EMData *const image)
	To proccess an image out-of-place. More...

virtual string	get_name () const
	Get the processor's name. More...

string	get_desc () const
	Get the descrition of this specific processor. More...

virtual TypeDict	get_param_types () const
	Get processor parameter information in a dictionary. More...

Public Member Functions inherited from EMAN::Processor
virtual	~Processor ()

virtual void	process_list_inplace (vector< EMData * > &images)
	To process multiple images using the same algorithm. More...

virtual Dict	get_params () const
	Get the processor parameters in a key/value dictionary. More...

virtual void	set_params (const Dict &new_params)
	Set the processor parameters using a key/value dictionary. More...

Static Public Member Functions
static Processor *	NEW ()

Static Public Member Functions inherited from EMAN::Processor
static string	get_group_desc ()
	Get the description of this group of processors. More...

static void	EMFourierFilterInPlace (EMData *fimage, Dict params)
	Compute a Fourier-filter processed image in place. More...

static EMData *	EMFourierFilter (EMData *fimage, Dict params)
	Compute a Fourier-processor processed image without altering the original image. More...

Static Public Attributes
static const string	NAME = "morph.object.label"

Additional Inherited Members
Public Types inherited from EMAN::Processor
enum	fourier_filter_types { TOP_HAT_LOW_PASS , TOP_HAT_HIGH_PASS , TOP_HAT_BAND_PASS , TOP_HOMOMORPHIC , GAUSS_LOW_PASS , GAUSS_HIGH_PASS , GAUSS_BAND_PASS , GAUSS_INVERSE , GAUSS_HOMOMORPHIC , BUTTERWORTH_LOW_PASS , BUTTERWORTH_HIGH_PASS , BUTTERWORTH_HOMOMORPHIC , KAISER_I0 , KAISER_SINH , KAISER_I0_INVERSE , KAISER_SINH_INVERSE , SHIFT , TANH_LOW_PASS , TANH_HIGH_PASS , TANH_HOMOMORPHIC , TANH_BAND_PASS , RADIAL_TABLE , CTF_ }
	Fourier filter Processor type enum. More...

Protected Attributes inherited from EMAN::Processor
Dict	params

Detailed Description

Label each object in a black-white image.

Also return the center of each object.

Author: : Muyuan Chen

Date: : 03/2015

Definition at line 9507 of file processor.h.

Member Function Documentation

◆ get_desc()

string EMAN::ObjLabelProcessor::get_desc ( ) const

inlinevirtual

Get the descrition of this specific processor.

This function must be overwritten by a subclass.

Returns: The description of this processor.

Implements EMAN::Processor.

Definition at line 9521 of file processor.h.

                {
                        return "Label each object above threshold. Also return the center of each object. Treats a 3D volume as 2D slices.";
                }

◆ get_name()

virtual string EMAN::ObjLabelProcessor::get_name ( ) const

inlinevirtual

Get the processor's name.

Each processor is identified by a unique name.

Returns: The processor's name.

Implements EMAN::Processor.

Definition at line 9513 of file processor.h.

                {
                        return NAME;
                }

References NAME.

◆ get_param_types()

virtual TypeDict EMAN::ObjLabelProcessor::get_param_types ( ) const

inlinevirtual

Get processor parameter information in a dictionary.

Each parameter has one record in the dictionary. Each record contains its name, data-type, and description.

Returns: A dictionary containing the parameter info.

Reimplemented from EMAN::Processor.

Definition at line 9525 of file processor.h.

                {
                        TypeDict d;
                        d.put("write_centers", EMObject::BOOL, "Write the center of each object in the attribute obj_centers.");
                        return d;
                }

References EMAN::EMObject::BOOL, and EMAN::TypeDict::put().

◆ NEW()

static Processor * EMAN::ObjLabelProcessor::NEW ( )

inlinestatic

Definition at line 9517 of file processor.h.

                {
                        return new ObjLabelProcessor();
                }

◆ process()

EMData * ObjLabelProcessor::process ( const EMData *const image )

virtual

To proccess an image out-of-place.

For those processors which can only be processed out-of-place, override this function to give the right behavior.

Parameters

image The image will be copied, actual process happen on copy of image.

Returns: the image processing result, may or may not be the same size of the input image

Reimplemented from EMAN::Processor.

Definition at line 14557 of file processor.cpp.

{
 
        EMData* imageCp= image -> copy();
        process_inplace(imageCp);
 
        return imageCp;
}

References copy(), and process_inplace().

◆ process_inplace()

void ObjLabelProcessor::process_inplace ( EMData * image )

virtual

To process an image in-place.

For those processors which can only be processed out-of-place, override this function to just print out some error message to remind user call the out-of-place version.

Parameters

image The image to be processed.

Implements EMAN::Processor.

Definition at line 14566 of file processor.cpp.

{
        // Now treats 3d volume as 2d slices
        bool writecenter=params.set_default("write_centers",false);
        int nx = image->get_xsize();
        int ny = image->get_ysize();
        int nz = image->get_zsize();
 
        int y1;
        bool spanLeft, spanRight;
        vector<Vec3i> pvec;
        float cx,cy;
        int npx;
        int count=0;
        vector<float> centers(2);
        for (int zz = 0; zz < nz; zz++) {
 
                for (int yy = 0; yy < ny; yy++) {
                        for (int xx = 0; xx < nx; xx++) {
                                if (image->get_value_at(xx,yy,zz)>0){
                                        pvec.push_back(Vec3i(xx,yy,zz));
                                        if (writecenter && count<0){
                                                cx/=npx;cy/=npx;
                                                centers.push_back(cx);
                                                centers.push_back(cy);
                                                cx=cy=0;npx=0;
                                        }
                                        count--;
                                }
                                while(!pvec.empty())
                                {
                                        Vec3i v=pvec.back();
                                        int x=v[0],y=v[1],z=v[2];
//                                      printf("%d\t%d\t%d\n",x,y,z);
                                        pvec.pop_back();
                                        y1 = y;
                                        while(y1 > 0 && image->get_value_at(x,y1,zz)>0) y1--;
//                                      y1++;
                                        spanLeft = spanRight = 0;
                                        bool nowstop=0;
                                        while(1)
                                        {
                                                if(image->get_value_at(x,y1,zz)>0){
                                                        image->set_value_at(x,y1,zz,count);
                                                        if (writecenter){
                                                                cx+=x;cy+=y1;npx++;
                                                        }
                                                }
 
//                                              printf("\t %d\t%d\t%d\n",x,y1,z);
                                                if(!spanLeft && x > 0 && image->get_value_at(x-1,y1,zz)>0)
                                                {
                                                        pvec.push_back(Vec3i(x-1,y1,zz));
                                                        spanLeft = 1;
                                                }
                                                else if(spanLeft && x > 0 && image->get_value_at(x-1,y1,zz)<=0)
                                                {
                                                        spanLeft = 0;
                                                }
                                                if(!spanRight && x < nx - 1 && image->get_value_at(x+1,y1,zz)>0)
                                                {
                                                        pvec.push_back(Vec3i(x+1,y1,zz));
                                                        spanRight = 1;
                                                }
                                                else if(spanRight && x < nx - 1 && image->get_value_at(x+1,y1,zz)<=0)
                                                {
                                                        spanRight = 0;
                                                }
                                                y1++;
                                                if (nowstop)
                                                        break;
                                                if (y1 >= ny-1 || image->get_value_at(x,y1,zz)<=0)
                                                        nowstop=1;
                                        }
                                }
 
 
                        }
                }
        }
        printf("%d objects.\n",-count);
        image->mult(-1);
        if (writecenter) image->set_attr("obj_centers",centers);
}

References get_value_at(), EMAN::Processor::params, EMAN::Dict::set_default(), x, and y.

Referenced by process().

Member Data Documentation

◆ NAME

const string ObjLabelProcessor::NAME = "morph.object.label"

static

Definition at line 9531 of file processor.h.

Referenced by get_name().

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

Public Member Functions

Static Public Member Functions

Static Public Attributes

Additional Inherited Members

Detailed Description

Member Function Documentation

◆ get_desc()

◆ get_name()

◆ get_param_types()

◆ NEW()

◆ process()

◆ process_inplace()

Member Data Documentation

◆ NAME