#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 5236 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 5251 of file processor.h.
05252 { 05253 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."; 05254 }
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 5241 of file processor.h.
References NAME.
05242 { 05243 return NAME; 05244 }
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 5256 of file processor.h.
References EMAN::EMObject::INT, EMAN::TypeDict::put(), and EMAN::EMObject::STRING.
05257 { 05258 TypeDict d; 05259 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"); 05260 d.put("snrfile", EMObject::STRING, "structure factor file name"); 05261 return d; 05262 }
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 5873 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().
05874 { 05875 if (!image) { 05876 return; 05877 } 05878 05879 int wiener = params["wiener"]; 05880 const char *snrfile = params["snrfile"]; 05881 05882 XYData sf; 05883 int err = sf.read_file(snrfile); 05884 if (err) { 05885 LOGERR("couldn't read structure factor file!"); 05886 return; 05887 } 05888 05889 05890 for (size_t i = 0; i < sf.get_size(); i++) { 05891 if (sf.get_y(i) <= 0) { 05892 sf.set_y(i, -4.0f); 05893 } 05894 else { 05895 sf.set_y(i, log10(sf.get_y(i))); 05896 } 05897 } 05898 sf.update(); 05899 05900 Ctf *image_ctf = image->get_ctf(); 05901 05902 vector < float >ctf; 05903 if (wiener) { 05904 ctf = image_ctf->compute_1d(image->get_ysize(),1.0f/(image_ctf->apix*image->get_ysize()), Ctf::CTF_WIENER_FILTER, &sf); 05905 } 05906 else { 05907 ctf = image_ctf->compute_1d(image->get_ysize(),1.0f/(image_ctf->apix*image->get_ysize()), Ctf::CTF_SNR, &sf); 05908 } 05909 05910 if(image_ctf) {delete image_ctf; image_ctf=0;} 05911 05912 image->process_inplace("normalize.circlemean"); 05913 05914 int nx = image->get_xsize(); 05915 int ny = image->get_ysize(); 05916 05917 Region clip_r(-nx / 2, -ny / 2, nx * 2, ny * 2); 05918 EMData *d3 = image->get_clip(clip_r); 05919 EMData *d2 = d3->do_fft(); 05920 05921 d2->apply_radial_func(0, 2.0f / Ctf::CTFOS, ctf, 0); 05922 05923 if( d3 ) 05924 { 05925 delete d3; 05926 d3 = 0; 05927 } 05928 05929 if( image ) 05930 { 05931 delete image; 05932 image = 0; 05933 } 05934 05935 EMData *d1 = d2->do_ift(); 05936 int d1_nx = d1->get_xsize(); 05937 int d1_ny = d1->get_ysize(); 05938 Region d1_r(d1_nx / 4, d1_ny / 4, d1_nx / 2, d1_ny / 2); 05939 05940 image = d1->get_clip(d1_r); 05941 05942 if( d1 ) 05943 { 05944 delete d1; 05945 d1 = 0; 05946 } 05947 05948 if( d2 ) 05949 { 05950 delete d2; 05951 d2 = 0; 05952 } 05953 }
const string SNRProcessor::NAME = "eman1.filter.snr" [static] |