#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 5234 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 5249 of file processor.h.
05250 { 05251 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."; 05252 }
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 5239 of file processor.h.
References NAME.
05240 { 05241 return NAME; 05242 }
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 5254 of file processor.h.
References EMAN::EMObject::INT, EMAN::TypeDict::put(), and EMAN::EMObject::STRING.
05255 { 05256 TypeDict d; 05257 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"); 05258 d.put("snrfile", EMObject::STRING, "structure factor file name"); 05259 return d; 05260 }
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 5861 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().
05862 { 05863 if (!image) { 05864 return; 05865 } 05866 05867 int wiener = params["wiener"]; 05868 const char *snrfile = params["snrfile"]; 05869 05870 XYData sf; 05871 int err = sf.read_file(snrfile); 05872 if (err) { 05873 LOGERR("couldn't read structure factor file!"); 05874 return; 05875 } 05876 05877 05878 for (size_t i = 0; i < sf.get_size(); i++) { 05879 if (sf.get_y(i) <= 0) { 05880 sf.set_y(i, -4.0f); 05881 } 05882 else { 05883 sf.set_y(i, log10(sf.get_y(i))); 05884 } 05885 } 05886 sf.update(); 05887 05888 Ctf *image_ctf = image->get_ctf(); 05889 05890 vector < float >ctf; 05891 if (wiener) { 05892 ctf = image_ctf->compute_1d(image->get_ysize(),1.0f/(image_ctf->apix*image->get_ysize()), Ctf::CTF_WIENER_FILTER, &sf); 05893 } 05894 else { 05895 ctf = image_ctf->compute_1d(image->get_ysize(),1.0f/(image_ctf->apix*image->get_ysize()), Ctf::CTF_SNR, &sf); 05896 } 05897 05898 if(image_ctf) {delete image_ctf; image_ctf=0;} 05899 05900 image->process_inplace("normalize.circlemean"); 05901 05902 int nx = image->get_xsize(); 05903 int ny = image->get_ysize(); 05904 05905 Region clip_r(-nx / 2, -ny / 2, nx * 2, ny * 2); 05906 EMData *d3 = image->get_clip(clip_r); 05907 EMData *d2 = d3->do_fft(); 05908 05909 d2->apply_radial_func(0, 2.0f / Ctf::CTFOS, ctf, 0); 05910 05911 if( d3 ) 05912 { 05913 delete d3; 05914 d3 = 0; 05915 } 05916 05917 if( image ) 05918 { 05919 delete image; 05920 image = 0; 05921 } 05922 05923 EMData *d1 = d2->do_ift(); 05924 int d1_nx = d1->get_xsize(); 05925 int d1_ny = d1->get_ysize(); 05926 Region d1_r(d1_nx / 4, d1_ny / 4, d1_nx / 2, d1_ny / 2); 05927 05928 image = d1->get_clip(d1_r); 05929 05930 if( d1 ) 05931 { 05932 delete d1; 05933 d1 = 0; 05934 } 05935 05936 if( d2 ) 05937 { 05938 delete d2; 05939 d2 = 0; 05940 } 05941 }
const string SNRProcessor::NAME = "eman1.filter.snr" [static] |