#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 = "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 473 of file averager.cpp. Referenced by NEW(). 00474 : nimg(0) 00475 { 00476 00477 }
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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 480 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(). 00481 { 00482 if (!image) { 00483 return; 00484 } 00485 00486 00487 00488 EMData *fft=image->do_fft(); 00489 00490 if (nimg >= 1 && !EMUtil::is_same_size(fft, result)) { 00491 LOGERR("%s Averager can only process images of the same size", get_name().c_str()); 00492 return; 00493 } 00494 00495 nimg++; 00496 if (nimg == 1) { 00497 result = fft->copy_head(); 00498 result->to_zero(); 00499 } 00500 00501 Ctf *ctf = (Ctf *)image->get_attr("ctf"); 00502 float b=ctf->bfactor; 00503 ctf->bfactor=100.0; // FIXME - this is a temporary fixed B-factor which does a (very) little sharpening 00504 00505 EMData *snr = result -> copy(); 00506 ctf->compute_2d_complex(snr,Ctf::CTF_SNR); 00507 EMData *ctfi = result-> copy(); 00508 ctf->compute_2d_complex(ctfi,Ctf::CTF_AMP); 00509 00510 ctf->bfactor=b; // return to its original value 00511 00512 float *outd = result->get_data(); 00513 float *ind = fft->get_data(); 00514 float *snrd = snr->get_data(); 00515 float *ctfd = ctfi->get_data(); 00516 00517 size_t sz=snr->get_xsize()*snr->get_ysize(); 00518 for (size_t i = 0; i < sz; i+=2) { 00519 if (snrd[i]<0) snrd[i]=0; 00520 ctfd[i]=fabs(ctfd[i]); 00521 if (ctfd[i]<.05) { 00522 if (snrd[i]<=0) ctfd[i]=.05f; 00523 else ctfd[i]=snrd[i]*10.0f; 00524 } 00525 outd[i]+=ind[i]*snrd[i]/ctfd[i]; 00526 outd[i+1]+=ind[i+1]*snrd[i]/ctfd[i]; 00527 } 00528 00529 if (nimg==1) { 00530 snrsum=snr->copy_head(); 00531 float *ssnrd=snrsum->get_data(); 00532 // we're only using the real component, and we need to start with 1.0 00533 for (size_t i = 0; i < sz; i+=2) { ssnrd[i]=1.0; ssnrd[i+1]=0.0; } 00534 } 00535 snrsum->add(*snr); 00536 00537 delete ctf; 00538 delete fft; 00539 delete snr; 00540 delete ctfi; 00541 }
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Finish up the averaging and return the result.
Implements EMAN::Averager. Definition at line 543 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(). 00544 { 00545 /* EMData *tmp=result->do_ift(); 00546 tmp->write_image("ctfcw.hdf",0); 00547 delete tmp; 00548 00549 tmp=snrsum->do_ift(); 00550 tmp->write_image("ctfcw.hdf",1); 00551 delete tmp;*/ 00552 00553 // snrsum->write_image("snrsum.hdf",-1); 00554 size_t sz=result->get_xsize()*result->get_ysize(); 00555 float *snrsd=snrsum->get_data(); 00556 float *outd=result->get_data(); 00557 00558 for (size_t i=0; i<sz; i+=2) { 00559 outd[i]/=snrsd[i]; // snrsd contains total SNR+1 00560 outd[i+1]/=snrsd[i]; 00561 } 00562 result->update(); 00563 result->set_attr("ptcl_repr",nimg); 00564 00565 delete snrsum; 00566 EMData *ret=result->do_ift(); 00567 delete result; 00568 result=NULL; 00569 return ret; 00570 }
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Implements EMAN::Averager. Definition at line 439 of file averager.h. 00440 { 00441 return "Averaging with autmatic CTF correction. 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. References NAME. Referenced by add_image(). 00435 { 00436 return NAME; 00437 }
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Definition at line 444 of file averager.h. References CtfCWautoAverager(). 00445 { 00446 return new CtfCWautoAverager(); 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. References EMAN::Averager::params. 00450 { 00451 params = new_params; 00452 // outfile = params["outfile"]; 00453 }
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Definition at line 455 of file averager.h. Referenced by get_name(). |
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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(). |