#include <processor.h>
Inheritance diagram for EMAN::SNRProcessor:
Public Member Functions | |
virtual void | process_inplace (EMData *image) |
To process an image in-place. | |
virtual string | get_name () const |
Get the processor's name. | |
virtual string | get_desc () const |
Get the descrition of this specific processor. | |
virtual TypeDict | get_param_types () const |
Get processor parameter information in a dictionary. | |
Static Public Member Functions | |
static Processor * | NEW () |
Static Public Attributes | |
static const string | NAME = "eman1.filter.snr" |
wiener | if set to 1, then use wiener processor to process the images using the estimated SNR with CTF amplitude correction | |
snrfile | structure factor file name |
Definition at line 5062 of file processor.h.
virtual string EMAN::SNRProcessor::get_desc | ( | ) | const [inline, virtual] |
Get the descrition of this specific processor.
This function must be overwritten by a subclass.
Implements EMAN::Processor.
Definition at line 5077 of file processor.h.
05078 { 05079 return "Processor the images by the estimated SNR in each image.if parameter 'wiener' is 1, then wiener processor the images using the estimated SNR with CTF amplitude correction."; 05080 }
virtual string EMAN::SNRProcessor::get_name | ( | ) | const [inline, virtual] |
Get the processor's name.
Each processor is identified by a unique name.
Implements EMAN::Processor.
Definition at line 5067 of file processor.h.
References NAME.
05068 { 05069 return NAME; 05070 }
virtual TypeDict EMAN::SNRProcessor::get_param_types | ( | ) | const [inline, virtual] |
Get processor parameter information in a dictionary.
Each parameter has one record in the dictionary. Each record contains its name, data-type, and description.
Reimplemented from EMAN::Processor.
Definition at line 5082 of file processor.h.
References EMAN::EMObject::INT, EMAN::TypeDict::put(), and EMAN::EMObject::STRING.
05083 { 05084 TypeDict d; 05085 d.put("wiener", EMObject::INT, "if set to 1, then use wiener processor to process the images using the estimated SNR with CTF amplitude correction"); 05086 d.put("snrfile", EMObject::STRING, "structure factor file name"); 05087 return d; 05088 }
static Processor* EMAN::SNRProcessor::NEW | ( | ) | [inline, static] |
void SNRProcessor::process_inplace | ( | EMData * | image | ) | [virtual] |
To process an image in-place.
For those processors which can only be processed out-of-place, override this function to just print out some error message to remind user call the out-of-place version.
image | The image to be processed. |
Implements EMAN::Processor.
Definition at line 5669 of file processor.cpp.
References EMAN::Ctf::apix, EMAN::EMData::apply_radial_func(), EMAN::Ctf::compute_1d(), EMAN::Ctf::CTF_SNR, EMAN::Ctf::CTF_WIENER_FILTER, EMAN::Ctf::CTFOS, EMAN::EMData::do_fft(), EMAN::EMData::do_ift(), EMAN::EMData::get_clip(), EMAN::EMData::get_ctf(), EMAN::XYData::get_size(), EMAN::EMData::get_xsize(), EMAN::XYData::get_y(), EMAN::EMData::get_ysize(), log10(), LOGERR, EMAN::Processor::params, EMAN::EMData::process_inplace(), EMAN::XYData::read_file(), EMAN::XYData::set_y(), and EMAN::XYData::update().
05670 { 05671 if (!image) { 05672 return; 05673 } 05674 05675 int wiener = params["wiener"]; 05676 const char *snrfile = params["snrfile"]; 05677 05678 XYData sf; 05679 int err = sf.read_file(snrfile); 05680 if (err) { 05681 LOGERR("couldn't read structure factor file!"); 05682 return; 05683 } 05684 05685 05686 for (size_t i = 0; i < sf.get_size(); i++) { 05687 if (sf.get_y(i) <= 0) { 05688 sf.set_y(i, -4.0f); 05689 } 05690 else { 05691 sf.set_y(i, log10(sf.get_y(i))); 05692 } 05693 } 05694 sf.update(); 05695 05696 Ctf *image_ctf = image->get_ctf(); 05697 05698 vector < float >ctf; 05699 if (wiener) { 05700 ctf = image_ctf->compute_1d(image->get_ysize(),1.0f/(image_ctf->apix*image->get_ysize()), Ctf::CTF_WIENER_FILTER, &sf); 05701 } 05702 else { 05703 ctf = image_ctf->compute_1d(image->get_ysize(),1.0f/(image_ctf->apix*image->get_ysize()), Ctf::CTF_SNR, &sf); 05704 } 05705 05706 if(image_ctf) {delete image_ctf; image_ctf=0;} 05707 05708 image->process_inplace("normalize.circlemean"); 05709 05710 int nx = image->get_xsize(); 05711 int ny = image->get_ysize(); 05712 05713 Region clip_r(-nx / 2, -ny / 2, nx * 2, ny * 2); 05714 EMData *d3 = image->get_clip(clip_r); 05715 EMData *d2 = d3->do_fft(); 05716 05717 d2->apply_radial_func(0, 2.0f / Ctf::CTFOS, ctf, 0); 05718 05719 if( d3 ) 05720 { 05721 delete d3; 05722 d3 = 0; 05723 } 05724 05725 if( image ) 05726 { 05727 delete image; 05728 image = 0; 05729 } 05730 05731 EMData *d1 = d2->do_ift(); 05732 int d1_nx = d1->get_xsize(); 05733 int d1_ny = d1->get_ysize(); 05734 Region d1_r(d1_nx / 4, d1_ny / 4, d1_nx / 2, d1_ny / 2); 05735 05736 image = d1->get_clip(d1_r); 05737 05738 if( d1 ) 05739 { 05740 delete d1; 05741 d1 = 0; 05742 } 05743 05744 if( d2 ) 05745 { 05746 delete d2; 05747 d2 = 0; 05748 } 05749 }
const string SNRProcessor::NAME = "eman1.filter.snr" [static] |