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EMAN::CtfCAutoAverager Class Reference

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

#include <averager.h>

Inheritance diagram for EMAN::CtfCAutoAverager:

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Collaboration diagram for EMAN::CtfCAutoAverager:

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List of all members.

Public Member Functions

 CtfCAutoAverager ()
void add_image (EMData *image)
 To add an image to the Averager.
EMDatafinish ()
 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 AveragerNEW ()

Static Public Attributes

static const string NAME = "ctf.auto"

Protected Attributes

EMDatasnrsum
int nimg

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 426 of file averager.h.


Constructor & Destructor Documentation

CtfCAutoAverager::CtfCAutoAverager  ) 
 

Definition at line 576 of file averager.cpp.

Referenced by NEW().

00577         : nimg(0)
00578 {
00579 
00580 }


Member Function Documentation

void CtfCAutoAverager::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 583 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().

00584 {
00585         if (!image) {
00586                 return;
00587         }
00588 
00589 
00590 
00591         EMData *fft=image->do_fft();
00592 
00593         if (nimg >= 1 && !EMUtil::is_same_size(fft, result)) {
00594                 LOGERR("%s Averager can only process images of the same size", get_name().c_str());
00595                 return;
00596         }
00597 
00598         nimg++;
00599         if (nimg == 1) {
00600                 result = fft->copy_head();
00601                 result->to_zero();
00602         }
00603 
00604         Ctf *ctf = (Ctf *)image->get_attr("ctf");
00605         float b=ctf->bfactor;
00606         ctf->bfactor=0;                 // NO B-FACTOR CORRECTION !
00607 
00608         EMData *snr = result -> copy();
00609         ctf->compute_2d_complex(snr,Ctf::CTF_SNR);
00610         EMData *ctfi = result-> copy();
00611         ctf->compute_2d_complex(ctfi,Ctf::CTF_AMP);
00612 
00613         ctf->bfactor=b; // return to its original value
00614 
00615         float *outd = result->get_data();
00616         float *ind = fft->get_data();
00617         float *snrd = snr->get_data();
00618         float *ctfd = ctfi->get_data();
00619 
00620         size_t sz=snr->get_xsize()*snr->get_ysize();
00621         for (size_t i = 0; i < sz; i+=2) {
00622                 if (snrd[i]<0) snrd[i]=0;
00623                 ctfd[i]=fabs(ctfd[i]);
00624                 
00625                 // This limits the maximum possible amplification in CTF correction to 10x
00626                 if (ctfd[i]<.05) {
00627                         if (snrd[i]<=0) ctfd[i]=.05f;
00628                         else ctfd[i]=snrd[i]*10.0f;
00629                 }
00630                 
00631                 // SNR weight and CTF correction
00632                 outd[i]+=ind[i]*snrd[i]/ctfd[i];
00633                 outd[i+1]+=ind[i+1]*snrd[i]/ctfd[i];
00634         }
00635 
00636         if (nimg==1) {
00637                 snrsum=snr->copy_head();
00638                 float *ssnrd=snrsum->get_data();
00639                 // we're only using the real component, for Wiener filter we put 1.0 in R, but for just SNR weight we use 0
00640                 for (size_t i = 0; i < sz; i+=2) { ssnrd[i]=0.0; ssnrd[i+1]=0.0; }
00641         }
00642         snrsum->add(*snr);
00643 
00644         delete ctf;
00645         delete fft;
00646         delete snr;
00647         delete ctfi;
00648 }

EMData * CtfCAutoAverager::finish  )  [virtual]
 

Finish up the averaging and return the result.

Returns:
The averaged image.

Implements EMAN::Averager.

Definition at line 650 of file averager.cpp.

References EMAN::EMData::calc_radial_dist(), 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().

00651 {
00652 /*      EMData *tmp=result->do_ift();
00653         tmp->write_image("ctfcw.hdf",0);
00654         delete tmp;
00655 
00656         tmp=snrsum->do_ift();
00657         tmp->write_image("ctfcw.hdf",1);
00658         delete tmp;*/
00659 
00660 //      snrsum->write_image("snrsum.hdf",-1);
00661         size_t sz=result->get_xsize()*result->get_ysize();
00662         float *snrsd=snrsum->get_data();
00663         float *outd=result->get_data();
00664 
00665         for (size_t i=0; i<sz; i+=2) {
00666                 if (snrsd[i]==0) outd[i]=outd[i+1]=0;
00667                 // we aren't wiener filtering, but if the total SNR is too low, we don't want TOO much exaggeration of noise
00668                 if (snrsd[i]<.05) {             
00669                         outd[i]*=20.0;          // 1/0.05
00670                         outd[i+1]*=20.0;
00671                 }
00672                 else {
00673                         outd[i]/=snrsd[i];              // snrsd contains total SNR
00674                         outd[i+1]/=snrsd[i];
00675                 }
00676         }
00677         result->update();
00678         result->set_attr("ptcl_repr",nimg);
00679         result->set_attr("ctf_snr_total",snrsum->calc_radial_dist(snrsum->get_ysize()/2,0,1,false));
00680         result->set_attr("ctf_wiener_filtered",0);
00681         
00682 /*      snrsum->write_image("snr.hdf",-1);
00683         result->write_image("avg.hdf",-1);*/
00684         
00685         delete snrsum;
00686         EMData *ret=result->do_ift();
00687         delete result;
00688         result=NULL;
00689         return ret;
00690 }

string EMAN::CtfCAutoAverager::get_desc  )  const [inline, virtual]
 

Implements EMAN::Averager.

Definition at line 439 of file averager.h.

00440                 {
00441                         return "Averaging with automatic CTF correction and SNR weight. No B-factor correction (as this is best done in 3-D). Does not require a structure factor, but only works with EMAN2's CTF model";
00442                 }

string EMAN::CtfCAutoAverager::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 434 of file averager.h.

References NAME.

Referenced by add_image().

00435                 {
00436                         return NAME;
00437                 }

static Averager* EMAN::CtfCAutoAverager::NEW  )  [inline, static]
 

Definition at line 444 of file averager.h.

References CtfCAutoAverager().

00445                 {
00446                         return new CtfCAutoAverager();
00447                 }

void EMAN::CtfCAutoAverager::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 449 of file averager.h.

References EMAN::Averager::params.

00450                 {
00451                         params = new_params;
00452 //                      outfile = params["outfile"];
00453                 }


Member Data Documentation

const string CtfCAutoAverager::NAME = "ctf.auto" [static]
 

Definition at line 455 of file averager.h.

Referenced by get_name().

int EMAN::CtfCAutoAverager::nimg [protected]
 

Definition at line 459 of file averager.h.

Referenced by add_image(), and finish().

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

Definition at line 458 of file averager.h.

Referenced by add_image(), and finish().


The documentation for this class was generated from the following files:
Generated on Mon Jul 19 13:05:54 2010 for EMAN2 by  doxygen 1.4.4