EMAN::CtfWtAverager Class Reference

CtfWtAverager. More...

#include <averager.h>

Inheritance diagram for EMAN::CtfWtAverager:

Collaboration diagram for EMAN::CtfWtAverager:

Public Member Functions
	CtfWtAverager ()
void	add_image (EMData *image)
	To add an image to the Averager. More...
EMData *	finish ()
	Finish up the averaging and return the result. More...
string	get_name () const
	Get the Averager's name. More...
string	get_desc () const
void	set_params (const Dict &new_params)
	Set the Averager parameters using a key/value dictionary. More...
Public Member Functions inherited from EMAN::Averager
	Averager ()
virtual	~Averager ()
virtual void	add_image_list (const vector< EMData * > &images)
	To add multiple images to the Averager. More...
virtual void	mult (const float &s)
	Multiply the result image by some floating point constant This is useful when weighting the input images prior to calling add_image - a situation where it is likely you want to divide by the sum of the weights. More...
virtual TypeDict	get_param_types () const
	Get Averager parameter information in a dictionary. More...

Static Public Member Functions
static Averager *	NEW ()

Static Public Attributes
static const string	NAME = "ctf.weight"

Protected Attributes
EMData *	ctfsum
int	nimg
Protected Attributes inherited from EMAN::Averager
Dict	params
EMData *	result

Detailed Description

CtfWtAverager.

Definition at line 486 of file averager.h.

Constructor & Destructor Documentation

CtfWtAverager()

CtfWtAverager::CtfWtAverager

(

)

Definition at line 1255 of file averager.cpp.

        : nimg(0)
{
 
}

Referenced by NEW().

Member Function Documentation

add_image()

void CtfWtAverager::add_image ( EMData *  image )

virtual

To add an image to the Averager.

This image will be averaged in this function.

Parameters

image

The image to be averaged.

Reimplemented from EMAN::Averager.

Definition at line 1262 of file averager.cpp.

{
        if (!image) {
                return;
        }
 
 
 
        EMData *fft=image->do_fft();
 
        if (nimg >= 1 && !EMUtil::is_same_size(fft, result)) {
                LOGERR("%s Averager can only process images of the same size", get_name().c_str());
                return;
        }
 
        nimg++;
        if (nimg == 1) {
                result = fft->copy_head();
                result->to_zero();
        }
 
        Ctf *ctf = (Ctf *)image->get_attr("ctf");
 
        EMData *ctfi = result-> copy();
        float b=ctf->bfactor;
        ctf->bfactor=0;         // no B-factor used in weight
        ctf->compute_2d_complex(ctfi,Ctf::CTF_INTEN);
        ctf->bfactor=b; // return to its original value
 
        float *outd = result->get_data();
        float *ind = fft->get_data();
        float *ctfd = ctfi->get_data();
 
        size_t sz=ctfi->get_xsize()*ctfi->get_ysize();
        for (size_t i = 0; i < sz; i+=2) {
                
                // CTF weight
                outd[i]+=ind[i]*ctfd[i];
                outd[i+1]+=ind[i+1]*ctfd[i];
        }
 
        if (nimg==1) {
                ctfsum=ctfi->copy_head();
                ctfsum->to_zero();
        }
        ctfsum->add(*ctfi);
 
        delete ctf;
        delete fft;
        delete ctfi;
}

References EMAN::Ctf::bfactor, EMAN::Ctf::compute_2d_complex(), copy(), EMAN::Ctf::CTF_INTEN, ctfsum, get_name(), EMAN::EMUtil::is_same_size(), LOGERR, nimg, and EMAN::Averager::result.

finish()

EMData * CtfWtAverager::finish ( )

virtual

Finish up the averaging and return the result.

Returns

The averaged image.

Implements EMAN::Averager.

Definition at line 1314 of file averager.cpp.

{
        int nx=result->get_xsize();
        int ny=result->get_ysize();     
        float *ctfsd=ctfsum->get_data();
        float *outd=result->get_data();
 
        for (int j=0; j<ny; j++) {
                for (int i=0; i<nx; i+=2) {
                        size_t ii=i+j*nx;
                        outd[ii]/=ctfsd[ii];            // snrsd contains total SNR
                        outd[ii+1]/=ctfsd[ii];
                }
        }
        result->update();
        result->set_attr("ptcl_repr",nimg);
//      result->set_attr("ctf_total",ctfsum->calc_radial_dist(ctfsum->get_ysize()/2,0,1,false));
        result->set_attr("ctf_wiener_filtered",0);
        
/*      snrsum->write_image("snr.hdf",-1);
        result->write_image("avg.hdf",-1);*/
        
        delete ctfsum;
        EMData *ret=result->do_ift();
        delete result;
        result=NULL;
        return ret;
}

References ctfsum, nimg, and EMAN::Averager::result.

get_desc()

string EMAN::CtfWtAverager::get_desc ( ) const

inlinevirtual

Implements EMAN::Averager.

Definition at line 499 of file averager.h.

                {
                        return "Average without CTF correction but with CTF weighting. Smoothed SNR can still have large uncertainty, so weighting by envelope-free CTF may provide more uniform results.";
                }

get_name()

string EMAN::CtfWtAverager::get_name ( ) const

inlinevirtual

Get the Averager's name.

Each Averager is identified by a unique name.

Returns

The Averager's name.

Implements EMAN::Averager.

Definition at line 494 of file averager.h.

                {
                        return NAME;
                }

References NAME.

Referenced by add_image().

NEW()

static Averager * EMAN::CtfWtAverager::NEW ( )

inlinestatic

Definition at line 504 of file averager.h.

                {
                        return new CtfWtAverager();
                }

References CtfWtAverager().

set_params()

void EMAN::CtfWtAverager::set_params ( const Dict &  new_params )

inlinevirtual

Set the Averager parameters using a key/value dictionary.

Parameters

new_params

A dictionary containing the new parameters.

Reimplemented from EMAN::Averager.

Definition at line 509 of file averager.h.

                {
                        params = new_params;
//                      outfile = params["outfile"];
                }

References EMAN::Averager::params.

Member Data Documentation

ctfsum

EMData* EMAN::CtfWtAverager::ctfsum

protected

Definition at line 518 of file averager.h.

Referenced by add_image(), and finish().

NAME

const string CtfWtAverager::NAME = "ctf.weight"

static

Definition at line 515 of file averager.h.

Referenced by get_name().

nimg

int EMAN::CtfWtAverager::nimg

protected

Definition at line 519 of file averager.h.

Referenced by add_image(), and finish().

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

• averager.h
• averager.cpp