#include <averager.h>
Inheritance diagram for EMAN::CtfCAutoAverager:
Public Member Functions | |
CtfCAutoAverager () | |
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 | |
Averager * | NEW () |
Static Public Attributes | |
const string | NAME = "ctf.auto" |
Protected Attributes | |
EMData * | snrsum |
int | nimg |
The Weiner filter is estimated directly from the data.
Definition at line 426 of file averager.h.
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Definition at line 598 of file averager.cpp. 00599 : nimg(0) 00600 { 00601 00602 }
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To add an image to the Averager. This image will be averaged in this function.
Implements EMAN::Averager. Definition at line 605 of file averager.cpp. References EMAN::EMData::add(), b, EMAN::Ctf::bfactor, EMAN::Ctf::compute_2d_complex(), copy(), EMAN::EMData::copy_head(), 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, EMAN::EMData::process_inplace(), snrsum, and EMAN::EMData::to_zero(). 00606 { 00607 if (!image) { 00608 return; 00609 } 00610 00611 00612 00613 EMData *fft=image->do_fft(); 00614 00615 if (nimg >= 1 && !EMUtil::is_same_size(fft, result)) { 00616 LOGERR("%s Averager can only process images of the same size", get_name().c_str()); 00617 return; 00618 } 00619 00620 nimg++; 00621 if (nimg == 1) { 00622 result = fft->copy_head(); 00623 result->to_zero(); 00624 } 00625 00626 Ctf *ctf = (Ctf *)image->get_attr("ctf"); 00627 float b=ctf->bfactor; 00628 ctf->bfactor=0; // NO B-FACTOR CORRECTION ! 00629 00630 EMData *snr = result -> copy(); 00631 ctf->compute_2d_complex(snr,Ctf::CTF_SNR); 00632 EMData *ctfi = result-> copy(); 00633 ctf->compute_2d_complex(ctfi,Ctf::CTF_AMP); 00634 00635 ctf->bfactor=b; // return to its original value 00636 00637 float *outd = result->get_data(); 00638 float *ind = fft->get_data(); 00639 float *snrd = snr->get_data(); 00640 float *ctfd = ctfi->get_data(); 00641 00642 size_t sz=snr->get_xsize()*snr->get_ysize(); 00643 for (size_t i = 0; i < sz; i+=2) { 00644 if (snrd[i]<0) snrd[i]=0; 00645 ctfd[i]=fabs(ctfd[i]); 00646 00647 // This limits the maximum possible amplification in CTF correction to 10x 00648 if (ctfd[i]<.05) ctfd[i]=0.05f; 00649 // { 00650 // if (snrd[i]<=0) ctfd[i]=.05f; 00651 // else ctfd[i]=snrd[i]*10.0f; 00652 // } 00653 00654 // SNR weight and CTF correction 00655 outd[i]+=ind[i]*snrd[i]/ctfd[i]; 00656 outd[i+1]+=ind[i+1]*snrd[i]/ctfd[i]; 00657 } 00658 00659 if (nimg==1) { 00660 snrsum=snr->copy_head(); 00661 float *ssnrd=snrsum->get_data(); 00662 // we're only using the real component, for Wiener filter we put 1.0 in R, but for just SNR weight we use 0 00663 for (size_t i = 0; i < sz; i+=2) { ssnrd[i]=0.0; ssnrd[i+1]=0.0; } 00664 } 00665 snr->process_inplace("math.absvalue"); 00666 snrsum->add(*snr); 00667 00668 delete ctf; 00669 delete fft; 00670 delete snr; 00671 delete ctfi; 00672 }
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Finish up the averaging and return the result.
Implements EMAN::Averager. Definition at line 674 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, nx, ny, EMAN::EMData::set_attr(), snrsum, and EMAN::EMData::update(). 00675 { 00676 /* EMData *tmp=result->do_ift(); 00677 tmp->write_image("ctfcw.hdf",0); 00678 delete tmp; 00679 00680 tmp=snrsum->do_ift(); 00681 tmp->write_image("ctfcw.hdf",1); 00682 delete tmp;*/ 00683 00684 // snrsum->write_image("snrsum.hdf",-1); 00685 //size_t sz=result->get_xsize()*result->get_ysize(); 00686 int nx=result->get_xsize(); 00687 int ny=result->get_ysize(); 00688 float *snrsd=snrsum->get_data(); 00689 float *outd=result->get_data(); 00690 00691 int rm=(ny-2)*(ny-2)/4; 00692 for (int j=0; j<ny; j++) { 00693 for (int i=0; i<nx; i+=2) { 00694 size_t ii=i+j*nx; 00695 if ((j<ny/2 && i*i/4+j*j>rm) ||(j>=ny/2 && i*i/4+(ny-j)*(ny-j)>rm) || snrsd[ii]==0) { outd[ii]=outd[ii+1]=0; continue; } 00696 // we aren't wiener filtering, but if the total SNR is too low, we don't want TOO much exaggeration of noise 00697 if (snrsd[ii]<.05) { 00698 outd[ii]*=20.0; // 1/0.05 00699 outd[ii+1]*=20.0; 00700 } 00701 else { 00702 outd[ii]/=snrsd[ii]; // snrsd contains total SNR 00703 outd[ii+1]/=snrsd[ii]; 00704 } 00705 } 00706 } 00707 result->update(); 00708 result->set_attr("ptcl_repr",nimg); 00709 result->set_attr("ctf_snr_total",snrsum->calc_radial_dist(snrsum->get_ysize()/2,0,1,false)); 00710 result->set_attr("ctf_wiener_filtered",0); 00711 00712 /* snrsum->write_image("snr.hdf",-1); 00713 result->write_image("avg.hdf",-1);*/ 00714 00715 delete snrsum; 00716 EMData *ret=result->do_ift(); 00717 delete result; 00718 result=NULL; 00719 return ret; 00720 }
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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 }
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Get the Averager's name. Each Averager is identified by a unique name.
Implements EMAN::Averager. Definition at line 434 of file averager.h. Referenced by add_image(). 00435 {
00436 return NAME;
00437 }
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Definition at line 444 of file averager.h. 00445 { 00446 return new CtfCAutoAverager(); 00447 }
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Set the Averager parameters using a key/value dictionary.
Reimplemented from EMAN::Averager. Definition at line 449 of file averager.h. 00450 { 00451 params = new_params; 00452 // outfile = params["outfile"]; 00453 }
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Definition at line 52 of file averager.cpp. |
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Definition at line 459 of file averager.h. Referenced by add_image(), and finish(). |
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Definition at line 458 of file averager.h. Referenced by add_image(), and finish(). |