Binarize an image based on the circular average around each pixel in real space. More...

#include <processor.h>

Inheritance diagram for EMAN::CircularAverageBinarizeProcessor:

Collaboration diagram for EMAN::CircularAverageBinarizeProcessor:

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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 = "threshold.binary.circularmean"

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

Binarize an image based on the circular average around each pixel in real space.

The pixel is set to 1 when the ring average around the pixel keeps decreasing for n pixels as the radius of the ring increases. Here n is the threshold. This essentially picks out the local maximum pixels with some noise tolerance.

Author: : Muyuan Chen

Date: : 03/2015

Definition at line 9444 of file processor.h.

Member Function Documentation

◆ get_desc()

string EMAN::CircularAverageBinarizeProcessor::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 9458 of file processor.h.

                {
                        return "Binarize an image based on the circular average around each pixel in real space.";
                }

◆ get_name()

virtual string EMAN::CircularAverageBinarizeProcessor::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 9450 of file processor.h.

                {
                        return NAME;
                }

References NAME.

◆ get_param_types()

virtual TypeDict EMAN::CircularAverageBinarizeProcessor::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 9462 of file processor.h.

                {
                        TypeDict d;
                        d.put("thresh", EMObject::INT, "The radius threshold that the circular average of density keep dropping.");
                        return d;
                }

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

◆ NEW()

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

inlinestatic

Definition at line 9454 of file processor.h.

                {
                        return new CircularAverageBinarizeProcessor( );
                }

◆ process()

EMData * CircularAverageBinarizeProcessor::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 14438 of file processor.cpp.

{
        int thr=params.set_default("thresh",5);
 
        EMData* bwmap= image -> copy();
        int x_size = image->get_xsize();
        int y_size = image->get_ysize();
        int z_size = image->get_zsize();
 
        int ix,iy,iz,it,count,ic;
        int *dx=new int[thr*8],*dy=new int[thr*8];
        for (it=1; it<=thr; it++){
                // calculate the indexes
                count=0;
                for (ix=-thr-1; ix<=thr+1; ix++){
                        for (iy=-thr-1; iy<=thr+1; iy++){
                                int d2=ix*ix+iy*iy;
                                if (d2>=it*it && d2<(it+1)*(it+1)){
                                        dx[count]=ix;
                                        dy[count]=iy;
                                        count++;
                                }
                        }
                }
                // for each pixel
                for (iz=0; iz<z_size; iz++){
                        for (ix=0; ix<x_size; ix++){
                                for (iy=0; iy<y_size; iy++){
                                        // circular average on each ring
                                        float mn=0;
                                        if (bwmap->get_value_at(ix,iy,iz)==0)
                                                continue;
                                        for (ic=0; ic<count; ic++){
                                                mn+=image->sget_value_at(ix+dx[ic],iy+dy[ic],iz);
                                        }
                                        mn/=count;
                                        if (mn>bwmap->get_value_at(ix,iy,iz))
                                                mn=0;
                                        bwmap->set_value_at(ix,iy,iz,mn);
                                }
                        }
                }
        }
        // binarize image
        for (iz=0; iz<z_size; iz++){
                for (ix=0; ix<x_size; ix++){
                        for (iy=0; iy<y_size; iy++){
                                if (bwmap->get_value_at(ix,iy,iz)>0)
                                        bwmap->set_value_at(ix,iy,iz,1);
                                else
                                        bwmap->set_value_at(ix,iy,iz,0);
                        }
                }
        }
        delete[] dx;
        delete[] dy;
        return bwmap;
 
 
}

References copy(), EMAN::Processor::params, and EMAN::Dict::set_default().

Referenced by process_inplace().

◆ process_inplace()

void CircularAverageBinarizeProcessor::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 14498 of file processor.cpp.

{
        EMData *tmp=process(image);
        memcpy(image->get_data(),tmp->get_data(),(size_t)image->get_xsize()*image->get_ysize()*image->get_zsize()*sizeof(float));
        delete tmp;
        image->update();
        return;
 
}

References process().

Member Data Documentation

◆ NAME

const string CircularAverageBinarizeProcessor::NAME = "threshold.binary.circularmean"

static

Definition at line 9468 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