#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 | |
Processor * | NEW () |
Static Public Attributes | |
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 5118 of file processor.h.
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Get the descrition of this specific processor. This function must be overwritten by a subclass.
Implements EMAN::Processor. Definition at line 5133 of file processor.h. 05134 { 05135 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."; 05136 }
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Get the processor's name. Each processor is identified by a unique name.
Implements EMAN::Processor. Definition at line 5123 of file processor.h. 05124 {
05125 return NAME;
05126 }
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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 5138 of file processor.h. References EMAN::TypeDict::put(). 05139 { 05140 TypeDict d; 05141 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"); 05142 d.put("snrfile", EMObject::STRING, "structure factor file name"); 05143 return d; 05144 }
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Definition at line 5128 of file processor.h. 05129 { 05130 return new SNRProcessor(); 05131 }
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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.
Implements EMAN::Processor. Definition at line 5671 of file processor.cpp. References EMAN::Ctf::apix, EMAN::EMData::apply_radial_func(), EMAN::Ctf::compute_1d(), 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, nx, ny, EMAN::EMData::process_inplace(), EMAN::XYData::read_file(), EMAN::XYData::set_y(), and EMAN::XYData::update(). 05672 { 05673 if (!image) { 05674 return; 05675 } 05676 05677 int wiener = params["wiener"]; 05678 const char *snrfile = params["snrfile"]; 05679 05680 XYData sf; 05681 int err = sf.read_file(snrfile); 05682 if (err) { 05683 LOGERR("couldn't read structure factor file!"); 05684 return; 05685 } 05686 05687 05688 for (size_t i = 0; i < sf.get_size(); i++) { 05689 if (sf.get_y(i) <= 0) { 05690 sf.set_y(i, -4.0f); 05691 } 05692 else { 05693 sf.set_y(i, log10(sf.get_y(i))); 05694 } 05695 } 05696 sf.update(); 05697 05698 Ctf *image_ctf = image->get_ctf(); 05699 05700 vector < float >ctf; 05701 if (wiener) { 05702 ctf = image_ctf->compute_1d(image->get_ysize(),1.0f/(image_ctf->apix*image->get_ysize()), Ctf::CTF_WIENER_FILTER, &sf); 05703 } 05704 else { 05705 ctf = image_ctf->compute_1d(image->get_ysize(),1.0f/(image_ctf->apix*image->get_ysize()), Ctf::CTF_SNR, &sf); 05706 } 05707 05708 if(image_ctf) {delete image_ctf; image_ctf=0;} 05709 05710 image->process_inplace("normalize.circlemean"); 05711 05712 int nx = image->get_xsize(); 05713 int ny = image->get_ysize(); 05714 05715 Region clip_r(-nx / 2, -ny / 2, nx * 2, ny * 2); 05716 EMData *d3 = image->get_clip(clip_r); 05717 EMData *d2 = d3->do_fft(); 05718 05719 d2->apply_radial_func(0, 2.0f / Ctf::CTFOS, ctf, 0); 05720 05721 if( d3 ) 05722 { 05723 delete d3; 05724 d3 = 0; 05725 } 05726 05727 if( image ) 05728 { 05729 delete image; 05730 image = 0; 05731 } 05732 05733 EMData *d1 = d2->do_ift(); 05734 int d1_nx = d1->get_xsize(); 05735 int d1_ny = d1->get_ysize(); 05736 Region d1_r(d1_nx / 4, d1_ny / 4, d1_nx / 2, d1_ny / 2); 05737 05738 image = d1->get_clip(d1_r); 05739 05740 if( d1 ) 05741 { 05742 delete d1; 05743 d1 = 0; 05744 } 05745 05746 if( d2 ) 05747 { 05748 delete d2; 05749 d2 = 0; 05750 } 05751 }
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Definition at line 173 of file processor.cpp. |