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::CTFCorrProcessor:

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Collaboration diagram for EMAN::CTFCorrProcessor:

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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 = "filter.ctfcorr.simple"

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

defocus	mean defocus in microns
voltage	microscope voltage in Kv
ac	amplitude contrast in %

Definition at line 7239 of file processor.h.

Member Function Documentation

◆ get_desc()

virtual string EMAN::CTFCorrProcessor::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 7254 of file processor.h.

                {
                        return "One of the strongest visual impacts of CTF on a structure is the low resolution high-pass filter effect caused by \
phase contrast. This Processor performs a simple linear filter to roughly correct for this. This is not a substitution or replacement \
for the full CTF correction routine available for single particle work in EMAN, but if you are in a situation where accurate CTF \
correction is not possible, this will allow you to approximate the correction to relieve some of the visual artifacts. Circularly \
symmetric phase flipping can optionally be performed.";
                }

◆ get_name()

virtual string EMAN::CTFCorrProcessor::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 7244 of file processor.h.

                {
                        return NAME;
                }

References NAME.

◆ get_param_types()

virtual TypeDict EMAN::CTFCorrProcessor::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 7263 of file processor.h.

                {
                        TypeDict d;
                        d.put("defocus", EMObject::FLOAT, "Mean defocus to correct for in microns");
                        d.put("ac", EMObject::FLOAT, "Amplitude contrast in % (default 10%)");
                        d.put("cs", EMObject::FLOAT, "Microscope Cs, default 2.7 mm");
                        d.put("voltage", EMObject::FLOAT, "Microscope Voltage in Kv (default 300)");
                        d.put("apix", EMObject::FLOAT, "A/pix (default value from image header)");
                        d.put("hppix", EMObject::FLOAT, "Optional high pass filter radius in pixels to prevent gradient amplification, default disabled");
                        d.put("phaseflip", EMObject::INT, "Also flip phases if set, default false");
                        d.put("useheader", EMObject::INT,"Use CTF header values if present, instead of individual values, default false");
                        return d;
                }

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

◆ NEW()

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

inlinestatic

Definition at line 7249 of file processor.h.

                {
                        return new CTFCorrProcessor();
                }

◆ process_inplace()

void CTFCorrProcessor::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 7710 of file processor.cpp.

{
        if (!image) {
                return;
        }
 
        float defocus = params.set_default("defocus",3.0);
        float ac = params.set_default("ac",10.0);
        float cs = params.set_default("cs",2.7);
        float voltage = params.set_default("voltage",300.0);
        float apix = params.set_default("apix",image->get_attr("apix_x"));
        float hppix = params.set_default("hppix",-1.0f);
        int useheader = params.set_default("useheader",0);
        int phaseflip = params.set_default("phaseflip",0);
 
        int ny = image->get_ysize();
        EMAN2Ctf ctf;
        if (image->has_attr("ctf") && useheader){
                
                ctf.copy_from((Ctf *)(image->get_attr("ctf")));
//              printf("CTF %f\t%f\t%f\t%f\n",ctf.defocus,ctf.ampcont,ctf.voltage,ctf.apix);
        }
        else {
                ctf.defocus=defocus;
                ctf.voltage=voltage;
                ctf.cs=cs;
                
                ctf.ampcont=ac;
                ctf.dfdiff=0;
                ctf.bfactor=200.0;
        }
        ctf.apix=apix;
        ctf.dsbg=1.0/(ctf.apix*ny);
 
        int np=(int)ceil(ny*1.73)+1;
        vector <float> filter = ctf.compute_1d(np,ctf.dsbg,Ctf::CTF_AMP);
 
        // reciprocal until the first CTF maximum, then no filter after that
        int i;
        filter[0]=1.0;
        for (i=1; i<np/2-1; i++) {
                if (filter[i+1]<filter[i]) {
                        filter[i]=1.0/filter[i];
                        break;
                }
                filter[i]=1.0/filter[i];
        }
        int gi=i;
        while (i<np/2) {
                if (phaseflip) filter[i]=filter[gi]*(filter[i]<0?-1.0f:1.0f);
                else filter[i]=filter[gi];
                i++;
        }
        
        if (hppix>0) {
                for (int i=0; i<(int)hppix*3.0; i++) filter[i]*=tanh((float)i/hppix);
        }
 
//      for (i=0; i<np/2; i++) printf("%d\t%1.3g\n",i,filter[i]);
        image->process_inplace("filter.radialtable",Dict("table",filter));
 
}

References EMAN::EMAN2Ctf::ampcont, EMAN::Ctf::apix, EMAN::Ctf::bfactor, EMAN::EMAN2Ctf::compute_1d(), EMAN::EMAN2Ctf::copy_from(), EMAN::Ctf::cs, EMAN::Ctf::CTF_AMP, EMAN::Ctf::defocus, EMAN::EMAN2Ctf::dfdiff, EMAN::EMAN2Ctf::dsbg, EMAN::Processor::params, EMAN::Dict::set_default(), and EMAN::Ctf::voltage.

Member Data Documentation

◆ NAME

const string CTFCorrProcessor::NAME = "filter.ctfcorr.simple"

static

Definition at line 7277 of file processor.h.

Referenced by get_name().

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

Public Member Functions

Static Public Member Functions

Static Public Attributes

Additional Inherited Members

Detailed Description

Member Function Documentation

◆ get_desc()

◆ get_name()

◆ get_param_types()

◆ NEW()

◆ process_inplace()

Member Data Documentation

◆ NAME