#include <averager.h>
Inheritance diagram for EMAN::CtfCWautoAverager:
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 () |
Static Public Attributes | |
static const string | NAME = "ctfw.auto" |
Protected Attributes | |
EMData * | snrsum |
int | nimg |
The Weiner filter is estimated directly from the data.
Definition at line 551 of file averager.h.
CtfCWautoAverager::CtfCWautoAverager | ( | ) |
Definition at line 637 of file averager.cpp.
Referenced by NEW().
00638 : nimg(0) 00639 { 00640 00641 }
void CtfCWautoAverager::add_image | ( | EMData * | image | ) | [virtual] |
To add an image to the Averager.
This image will be averaged in this function.
image | The image to be averaged. |
Implements EMAN::Averager.
Definition at line 644 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, EMAN::EMData::process_inplace(), EMAN::Averager::result, snrsum, and EMAN::EMData::to_zero().
00645 { 00646 if (!image) { 00647 return; 00648 } 00649 00650 00651 00652 EMData *fft=image->do_fft(); 00653 00654 if (nimg >= 1 && !EMUtil::is_same_size(fft, result)) { 00655 LOGERR("%s Averager can only process images of the same size", get_name().c_str()); 00656 return; 00657 } 00658 00659 nimg++; 00660 if (nimg == 1) { 00661 result = fft->copy_head(); 00662 result->to_zero(); 00663 } 00664 00665 Ctf *ctf = (Ctf *)image->get_attr("ctf"); 00666 //string cc=ctf->to_string(); 00667 //FILE *out=fopen("ctf.txt","a"); 00668 //fprintf(out,"%s\n",cc.c_str()); 00669 //fclose(out); 00670 float b=ctf->bfactor; 00671 ctf->bfactor=100.0; // FIXME - this is a temporary fixed B-factor which does a (very) little sharpening 00672 00673 // if (nimg==1) unlink("snr.hdf"); 00674 00675 EMData *snr = result -> copy(); 00676 ctf->compute_2d_complex(snr,Ctf::CTF_SNR); 00677 // snr->write_image("snr.hdf",-1); 00678 EMData *ctfi = result-> copy(); 00679 ctf->compute_2d_complex(ctfi,Ctf::CTF_AMP); 00680 00681 ctf->bfactor=b; // return to its original value 00682 00683 float *outd = result->get_data(); 00684 float *ind = fft->get_data(); 00685 float *snrd = snr->get_data(); 00686 float *ctfd = ctfi->get_data(); 00687 00688 size_t sz=snr->get_xsize()*snr->get_ysize(); 00689 for (size_t i = 0; i < sz; i+=2) { 00690 if (snrd[i]<0) snrd[i]=0; 00691 ctfd[i]=fabs(ctfd[i]); 00692 if (ctfd[i]<.05) ctfd[i]=0.05f; 00693 // { 00694 // if (snrd[i]<=0) ctfd[i]=.05f; 00695 // else ctfd[i]=snrd[i]*10.0f; 00696 // } 00697 outd[i]+=ind[i]*snrd[i]/ctfd[i]; 00698 outd[i+1]+=ind[i+1]*snrd[i]/ctfd[i]; 00699 } 00700 00701 if (nimg==1) { 00702 snrsum=snr->copy_head(); 00703 float *ssnrd=snrsum->get_data(); 00704 // we're only using the real component, and we need to start with 1.0 00705 for (size_t i = 0; i < sz; i+=2) { ssnrd[i]=1.0; ssnrd[i+1]=0.0; } 00706 } 00707 // snr->write_image("snr.hdf",-1); 00708 snr->process_inplace("math.absvalue"); 00709 snrsum->add(*snr); 00710 00711 delete ctf; 00712 delete fft; 00713 delete snr; 00714 delete ctfi; 00715 }
EMData * CtfCWautoAverager::finish | ( | ) | [virtual] |
Finish up the averaging and return the result.
Implements EMAN::Averager.
Definition at line 717 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::Averager::result, EMAN::EMData::set_attr(), snrsum, and EMAN::EMData::update().
00718 { 00719 /* EMData *tmp=result->do_ift(); 00720 tmp->write_image("ctfcw.hdf",0); 00721 delete tmp; 00722 00723 tmp=snrsum->do_ift(); 00724 tmp->write_image("ctfcw.hdf",1); 00725 delete tmp;*/ 00726 00727 //snrsum->write_image("snrsum.hdf",-1); 00728 //size_t sz=result->get_xsize()*result->get_ysize(); 00729 int nx=result->get_xsize(); 00730 int ny=result->get_ysize(); 00731 float *snrsd=snrsum->get_data(); 00732 float *outd=result->get_data(); 00733 00734 int rm=(ny-2)*(ny-2)/4; 00735 for (int j=0; j<ny; j++) { 00736 for (int i=0; i<nx; i+=2) { 00737 size_t ii=i+j*nx; 00738 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; } 00739 outd[ii]/=snrsd[ii]; // snrsd contains total SNR 00740 outd[ii+1]/=snrsd[ii]; 00741 } 00742 } 00743 00744 result->update(); 00745 result->set_attr("ptcl_repr",nimg); 00746 result->set_attr("ctf_snr_total",snrsum->calc_radial_dist(snrsum->get_ysize()/2,0,1,false)); 00747 result->set_attr("ctf_wiener_filtered",1); 00748 00749 delete snrsum; 00750 EMData *ret=result->do_ift(); 00751 delete result; 00752 result=NULL; 00753 return ret; 00754 }
string EMAN::CtfCWautoAverager::get_desc | ( | ) | const [inline, virtual] |
Implements EMAN::Averager.
Definition at line 564 of file averager.h.
00565 { 00566 return "Averaging with autmatic CTF correction. Does not require a structure factor, but only works with EMAN2's CTF model"; 00567 }
string EMAN::CtfCWautoAverager::get_name | ( | ) | const [inline, virtual] |
Get the Averager's name.
Each Averager is identified by a unique name.
Implements EMAN::Averager.
Definition at line 559 of file averager.h.
References NAME.
Referenced by add_image().
00560 { 00561 return NAME; 00562 }
static Averager* EMAN::CtfCWautoAverager::NEW | ( | ) | [inline, static] |
Definition at line 569 of file averager.h.
References CtfCWautoAverager().
00570 { 00571 return new CtfCWautoAverager(); 00572 }
void EMAN::CtfCWautoAverager::set_params | ( | const Dict & | new_params | ) | [inline, virtual] |
Set the Averager parameters using a key/value dictionary.
new_params | A dictionary containing the new parameters. |
Reimplemented from EMAN::Averager.
Definition at line 574 of file averager.h.
References EMAN::Averager::params.
00575 { 00576 params = new_params; 00577 // outfile = params["outfile"]; 00578 }
const string CtfCWautoAverager::NAME = "ctfw.auto" [static] |
int EMAN::CtfCWautoAverager::nimg [protected] |
EMData* EMAN::CtfCWautoAverager::snrsum [protected] |