EMAN::CtfCWautoAverager Class Reference

CtfCWautoAverager averages the images with CTF correction with a Wiener filter. More...

#include <averager.h>

Inheritance diagram for EMAN::CtfCWautoAverager:

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Collaboration diagram for EMAN::CtfCWautoAverager:

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List of all members.

Public Member Functions
	CtfCWautoAverager ()
void	add_image (EMData *image)
	To add an image to the Averager.
EMData *	finish ()
	Finish up the averaging and return the result.
string	get_name () const
	Get the Averager's name.
string	get_desc () const
void	set_params (const Dict &new_params)
	Set the Averager parameters using a key/value dictionary.
Static Public Member Functions
static Averager *	NEW ()
Protected Attributes
EMData *	snrsum
int	nimg

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Detailed Description

CtfCWautoAverager averages the images with CTF correction with a Wiener filter.

The Weiner filter is estimated directly from the data.

Definition at line 413 of file averager.h.

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Constructor & Destructor Documentation

CtfCWautoAverager::CtfCWautoAverager

(

)

Definition at line 463 of file averager.cpp.

Referenced by NEW().

        : nimg(0)
{

}

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Member Function Documentation

void CtfCWautoAverager::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.

Implements EMAN::Averager.

Definition at line 470 of file averager.cpp.

References EMAN::EMData::add(), b, EMAN::Ctf::bfactor, EMAN::Ctf::compute_2d_complex(), copy(), EMAN::EMData::copy_head(), EMAN::Ctf::CTF_AMP, EMAN::Ctf::CTF_SNR, EMAN::EMData::do_fft(), EMAN::EMData::get_attr(), EMAN::EMData::get_data(), get_name(), EMAN::EMData::get_xsize(), EMAN::EMData::get_ysize(), EMAN::EMUtil::is_same_size(), LOGERR, nimg, snrsum, and EMAN::EMData::to_zero().

{
        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");
        float b=ctf->bfactor;
        ctf->bfactor=100.0;                     // FIXME - this is a temporary fixed B-factor which does a (very) little sharpening

        EMData *snr = result -> copy();
        ctf->compute_2d_complex(snr,Ctf::CTF_SNR);
        EMData *ctfi = result-> copy();
        ctf->compute_2d_complex(ctfi,Ctf::CTF_AMP);

        ctf->bfactor=b; // return to its original value

        float *outd = result->get_data();
        float *ind = fft->get_data();
        float *snrd = snr->get_data();
        float *ctfd = ctfi->get_data();

        size_t sz=snr->get_xsize()*snr->get_ysize();
        for (size_t i = 0; i < sz; i+=2) {
                if (snrd[i]<0) snrd[i]=0;
                ctfd[i]=fabs(ctfd[i]);
                if (ctfd[i]<.05) {
                        if (snrd[i]<=0) ctfd[i]=.05f;
                        else ctfd[i]=snrd[i]*10.0f;
                }
                outd[i]+=ind[i]*snrd[i]/ctfd[i];
                outd[i+1]+=ind[i+1]*snrd[i]/ctfd[i];
        }

        if (nimg==1) {
                snrsum=snr->copy_head();
                float *ssnrd=snrsum->get_data();
                // we're only using the real component, and we need to start with 1.0
                for (size_t i = 0; i < sz; i+=2) { ssnrd[i]=1.0; ssnrd[i+1]=0.0; }
        }
        snrsum->add(*snr);

        delete ctf;
        delete fft;
        delete snr;
        delete ctfi;
}

EMData * CtfCWautoAverager::finish

(

)

[virtual]

Finish up the averaging and return the result.

Returns:

The averaged image.

Implements EMAN::Averager.

Definition at line 533 of file averager.cpp.

References EMAN::EMData::do_ift(), EMAN::EMData::get_data(), EMAN::EMData::get_xsize(), EMAN::EMData::get_ysize(), nimg, EMAN::EMData::set_attr(), snrsum, and EMAN::EMData::update().

{
/*      EMData *tmp=result->do_ift();
        tmp->write_image("ctfcw.hdf",0);
        delete tmp;

        tmp=snrsum->do_ift();
        tmp->write_image("ctfcw.hdf",1);
        delete tmp;*/

//      snrsum->write_image("snrsum.hdf",-1);
        size_t sz=result->get_xsize()*result->get_ysize();
        float *snrsd=snrsum->get_data();
        float *outd=result->get_data();

        for (size_t i=0; i<sz; i+=2) {
                outd[i]/=snrsd[i];              // snrsd contains total SNR+1
                outd[i+1]/=snrsd[i];
        }
        result->update();
        result->set_attr("ptcl_repr",nimg);

        delete snrsum;
        EMData *ret=result->do_ift();
        delete result;
        result=NULL;
        return ret;
}

string EMAN::CtfCWautoAverager::get_name

(

)

const [inline, virtual]

Get the Averager's name.

Each Averager is identified by a unique name.

Returns:

The Averager's name.

Implements EMAN::Averager.

Definition at line 421 of file averager.h.

Referenced by add_image().

                {
                        return "ctf.auto";
                }

string EMAN::CtfCWautoAverager::get_desc

(

)

const [inline, virtual]

Implements EMAN::Averager.

Definition at line 426 of file averager.h.

                {
                        return "Averaging with autmatic CTF correction. Does not require a structure factor, but only works with EMAN2's CTF model";
                }

static Averager* EMAN::CtfCWautoAverager::NEW

(

)

[inline, static]

Definition at line 431 of file averager.h.

References CtfCWautoAverager().

                {
                        return new CtfCWautoAverager();
                }

void EMAN::CtfCWautoAverager::set_params

(

const Dict &

new_params

)

[inline, virtual]

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 436 of file averager.h.

References EMAN::Averager::params.

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

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Member Data Documentation

EMData* EMAN::CtfCWautoAverager::snrsum [protected]

Definition at line 442 of file averager.h.

Referenced by add_image(), and finish().

int EMAN::CtfCWautoAverager::nimg [protected]

Definition at line 443 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