EMAN::SNRProcessor Class Reference

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. More...

#include <processor.h>

Inheritance diagram for EMAN::SNRProcessor:

Collaboration diagram for EMAN::SNRProcessor:

Public Member Functions
virtual void	process_inplace (EMData *image)
	To process an image in-place. More...
virtual string	get_name () const
	Get the processor's name. More...
virtual string	get_desc () const
	Get the descrition of this specific processor. More...
virtual TypeDict	get_param_types () const
	Get processor parameter information in a dictionary. More...
Public Member Functions inherited from EMAN::Processor
virtual	~Processor ()
virtual EMData *	process (const EMData *const image)
	To proccess an image out-of-place. More...
virtual void	process_list_inplace (vector< EMData * > &images)
	To process multiple images using the same algorithm. More...
virtual Dict	get_params () const
	Get the processor parameters in a key/value dictionary. More...
virtual void	set_params (const Dict &new_params)
	Set the processor parameters using a key/value dictionary. More...

Static Public Member Functions
static Processor *	NEW ()
Static Public Member Functions inherited from EMAN::Processor
static string	get_group_desc ()
	Get the description of this group of processors. More...
static void	EMFourierFilterInPlace (EMData *fimage, Dict params)
	Compute a Fourier-filter processed image in place. More...
static EMData *	EMFourierFilter (EMData *fimage, Dict params)
	Compute a Fourier-processor processed image without altering the original image. More...

Static Public Attributes
static const string	NAME = "eman1.filter.snr"

Additional Inherited Members
Public Types inherited from EMAN::Processor
enum	fourier_filter_types {   TOP_HAT_LOW_PASS , TOP_HAT_HIGH_PASS , TOP_HAT_BAND_PASS , TOP_HOMOMORPHIC ,   GAUSS_LOW_PASS , GAUSS_HIGH_PASS , GAUSS_BAND_PASS , GAUSS_INVERSE ,   GAUSS_HOMOMORPHIC , BUTTERWORTH_LOW_PASS , BUTTERWORTH_HIGH_PASS , BUTTERWORTH_HOMOMORPHIC ,   KAISER_I0 , KAISER_SINH , KAISER_I0_INVERSE , KAISER_SINH_INVERSE ,   SHIFT , TANH_LOW_PASS , TANH_HIGH_PASS , TANH_HOMOMORPHIC ,   TANH_BAND_PASS , RADIAL_TABLE , CTF_ }
	Fourier filter Processor type enum. More...
Protected Attributes inherited from EMAN::Processor
Dict	params

Detailed Description

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.

Parameters

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 7285 of file processor.h.

Member Function Documentation

get_desc()

virtual string EMAN::SNRProcessor::get_desc ( ) const

inlinevirtual

Get the descrition of this specific processor.

This function must be overwritten by a subclass.

Returns

The description of this processor.

Implements EMAN::Processor.

Definition at line 7300 of file processor.h.

                {
                        return "Process 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.";
                }

get_name()

virtual string EMAN::SNRProcessor::get_name ( ) const

inlinevirtual

Get the processor's name.

Each processor is identified by a unique name.

Returns

The processor's name.

Implements EMAN::Processor.

Definition at line 7290 of file processor.h.

                {
                        return NAME;
                }

References NAME.

get_param_types()

virtual TypeDict EMAN::SNRProcessor::get_param_types ( ) const

inlinevirtual

Get processor parameter information in a dictionary.

Each parameter has one record in the dictionary. Each record contains its name, data-type, and description.

Returns

A dictionary containing the parameter info.

Reimplemented from EMAN::Processor.

Definition at line 7305 of file processor.h.

                {
                        TypeDict d;
                        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");
                        d.put("snrfile", EMObject::STRING, "structure factor file name");
                        return d;
                }

References EMAN::EMObject::INT, EMAN::TypeDict::put(), and EMAN::EMObject::STRING.

NEW()

static Processor * EMAN::SNRProcessor::NEW ( )

inlinestatic

Definition at line 7295 of file processor.h.

                {
                        return new SNRProcessor();
                }

process_inplace()

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.

Parameters

image

The image to be processed.

Implements EMAN::Processor.

Definition at line 7627 of file processor.cpp.

{
        if (!image) {
                return;
        }
 
        int wiener = params["wiener"];
        const char *snrfile = params["snrfile"];
 
        XYData sf;
        int err = sf.read_file(snrfile);
        if (err) {
                LOGERR("couldn't read structure factor file!");
                return;
        }
 
 
        for (size_t i = 0; i < sf.get_size(); i++) {
                if (sf.get_y(i) <= 0) {
                        sf.set_y(i, -4.0f);
                }
                else {
                        sf.set_y(i, log10(sf.get_y(i)));
                }
        }
        sf.update();
 
        Ctf *image_ctf = image->get_ctf();
 
        vector < float >ctf;
        if (wiener) {
                ctf = image_ctf->compute_1d(image->get_ysize(),1.0f/(image_ctf->apix*image->get_ysize()), Ctf::CTF_WIENER_FILTER, &sf);
        }
        else {
                ctf = image_ctf->compute_1d(image->get_ysize(),1.0f/(image_ctf->apix*image->get_ysize()), Ctf::CTF_SNR, &sf);
        }
 
        if(image_ctf) {delete image_ctf; image_ctf=0;}
 
        image->process_inplace("normalize.circlemean");
 
        int nx = image->get_xsize();
        int ny = image->get_ysize();
 
        Region clip_r(-nx / 2, -ny / 2, nx * 2, ny * 2);
        EMData *d3 = image->get_clip(clip_r);
        EMData *d2 = d3->do_fft();
 
//      d2->apply_radial_func(0, 2.0f / Ctf::CTFOS, ctf, 0);    // this is troubling! only EMAN1 CTF used CTFOS, and then, not correctly...
        d2->apply_radial_func(0, 2.0f, ctf, 0);
 
        if( d3 )
        {
                delete d3;
                d3 = 0;
        }
 
        if( image )
        {
                delete image;
                image = 0;
        }
 
        EMData *d1 = d2->do_ift();
        int d1_nx = d1->get_xsize();
        int d1_ny = d1->get_ysize();
        Region d1_r(d1_nx / 4, d1_ny / 4, d1_nx / 2, d1_ny / 2);
 
        image = d1->get_clip(d1_r);
 
        if( d1 )
        {
                delete d1;
                d1 = 0;
        }
 
        if( d2 )
        {
                delete d2;
                d2 = 0;
        }
}

References EMAN::Ctf::apix, EMAN::EMData::apply_radial_func(), EMAN::Ctf::compute_1d(), EMAN::Ctf::CTF_SNR, EMAN::Ctf::CTF_WIENER_FILTER, EMAN::EMData::get_clip(), EMAN::XYData::get_size(), EMAN::XYData::get_y(), log10(), LOGERR, EMAN::Processor::params, EMAN::XYData::read_file(), EMAN::XYData::set_y(), and EMAN::XYData::update().

Member Data Documentation

NAME

const string SNRProcessor::NAME = "eman1.filter.snr"

static

Definition at line 7313 of file processor.h.

Referenced by get_name().

---

The documentation for this class was generated from the following files:

• processor.h
• processor.cpp