processor radial function: if lowpass > 0, f(x) = exp(-x*x/(lowpass*lowpass)); else f(x) = exp(x*x/(lowpass*lowpass)) More...

#include <processor.h>

Inheritance diagram for EMAN::LowpassAutoBProcessor:

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Collaboration diagram for EMAN::LowpassAutoBProcessor:

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Public Member Functions
string	get_name () const
	Get the processor's name. More...

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::FourierAnlProcessor
void	process_inplace (EMData *image)
	To process an image in-place. 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::FourierAnlProcessor
static string	get_group_desc ()

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.lowpass.autob"

Protected Member Functions
virtual void	preprocess (EMData *image)

void	create_radial_func (vector< float > &radial_mask, EMData *image) const

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 radial function: if lowpass > 0, f(x) = exp(-x*x/(lowpass*lowpass)); else f(x) = exp(x*x/(lowpass*lowpass))

Definition at line 1943 of file processor.h.

Member Function Documentation

◆ create_radial_func()

void LowpassAutoBProcessor::create_radial_func	(	vector< float > &	radial_mask,
		EMData *	image
	)		const

protectedvirtual

Implements EMAN::FourierAnlProcessor.

Definition at line 1143 of file processor.cpp.

                                                                                              {
        float apix=(float)image->get_attr("apix_x");
        int verbose=(int)params["verbose"];
//      int adaptnoise=params.set_default("adaptnoise",0);
        float noisecutoff=(float)params.set_default("noisecutoff",1.0/6.0);
        if (apix<=0 || apix>7.0f) throw ImageFormatException("apix_x > 7.0 or <0");
        float ds=1.0f/(apix*image->get_ysize());        // 0.5 is because radial mask is 2x oversampled
        unsigned int start=(int)floor(1.0/(15.0*ds));
        unsigned int end=radial_mask.size()-2;
        if (noisecutoff>0) end=(int)floor(noisecutoff/ds);
        if (end>radial_mask.size()-2) {
                if (verbose) printf("WARNING: specified noisecutoff too close to Nyquist, reset !");
                end=radial_mask.size()-2;
        }
        if (end<start+2) {
                printf("WARNING: noise cutoff too close to 15 A ! Results will not be good...");
                start=end-5;
        }
 
        FILE *out=NULL;
        if (verbose>2)  {
                printf("Autob -> %d - %d  ds=%g apix=%g rdlmsk=%d\n",start,end,ds,apix,int(radial_mask.size()));
                out=fopen("fitplot.txt","w");
        }
        int N=(radial_mask.size()-start-2);
        float *x=(float *)malloc(N*sizeof(float));
        float *y=(float *)malloc(N*sizeof(float));
        float *dy=(float *)malloc(N*sizeof(float));
        for (unsigned int i=start; i<radial_mask.size()-2; i++ ) {              // -2 is arbitrary because sometimes the last pixel or two have funny values
                x[i-start]=ds*ds*i*i;
                if (radial_mask[i]>0) y[i-start]=log(radial_mask[i]); // ok
                else if (i>start) y[i-start]=y[i-start-1];              // not good
                else y[i-start]=0.0;                                                    // bad
                if (i>start &&i<radial_mask.size()-3) dy[i-start]=y[i-start]-y[i-start-1];      // creates a 'derivative' of sorts, for use in adaptnoise
                if (out) fprintf(out,"%f\t%f\n",x[i-start],y[i-start]);
        }
        if (out) fclose(out);
 
        float slope=0,intercept=0;
        Util::calc_least_square_fit(end-start, x,y,&slope,&intercept,1);
 
        if (verbose) printf("slope=%f  intercept=%f\n",slope,intercept);
 
        float B=(float)params["bfactor"]+slope*4.0f/2.0f;               // *4 is for Henderson definition, 2.0 is for intensity vs amplitude
        float B2=(float)params["bfactor"];
 
        if (verbose) printf("User B = %1.2f      Corrective B = %1.2f  Total B=%1.3f\n",(float)params["bfactor"],slope*2.0,B);
 
        float cutval=exp(-B*pow(end*ds,2.0f)/4.0f)/exp(-B2*pow(end*ds,2.0f)/4.0f);
        for (unsigned int i=0; i<radial_mask.size(); i++) {
                if (i<=end) radial_mask[i]=exp(-B*pow(i*ds,2.0f)/4.0f);
                else radial_mask[i]=cutval*exp(-B2*pow(i*ds,2.0f)/4.0f);
        }
        if (verbose>1) Util::save_data(0,ds,radial_mask,"filter.txt");
 
        free(x);
        free(y);
        free(dy);
 }

References EMAN::Util::calc_least_square_fit(), ImageFormatException, log(), EMAN::Processor::params, EMAN::Util::save_data(), EMAN::Dict::set_default(), x, and y.

◆ get_desc()

string EMAN::LowpassAutoBProcessor::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 1956 of file processor.h.

                {
                        return "This processor sharpens a map based on the concept that the power spectrum should be roughly flat over the ~15 A-Nyquist resolution range, then combines this inverse B-factor with the specified low-pass Gaussian filter parameters to produce a single aggregate Gaussian filter.";
                }

◆ get_name()

string EMAN::LowpassAutoBProcessor::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 1946 of file processor.h.

                {
                        return NAME;
                }

References NAME.

◆ get_param_types()

virtual TypeDict EMAN::LowpassAutoBProcessor::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::FourierAnlProcessor.

Definition at line 1963 of file processor.h.

                {
                        TypeDict d = FourierAnlProcessor::get_param_types();
                        d.put("bfactor", EMObject::FLOAT, "B-factor in terms of e^-(B s^2/4)");
                        d.put("noisecutoff", EMObject::FLOAT, "Spatial frequency past which inverse-B will not be applied, default=1/6A");
//                      d.put("adaptnoise", EMObject::INT, "Dual linear fit separating lower resolution signal from higher resolution noise. Noise region not upweighted.");
                        d.put("return_radial", EMObject::BOOL, "Return the radial filter function as an attribute (filter_curve)");
                        d.put("verbose", EMObject::INT, "Print information about the determined B-factor");
                        return d;
                }

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

◆ NEW()

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

inlinestatic

Definition at line 1951 of file processor.h.

                {
                        return new LowpassAutoBProcessor();
                }

◆ preprocess()

virtual void EMAN::LowpassAutoBProcessor::preprocess ( EMData * image )

inlineprotectedvirtual

Reimplemented from EMAN::FourierAnlProcessor.

Definition at line 1975 of file processor.h.

                                                        {
                        if(params.has_key("apix")) {
                                image->set_attr("apix_x", (float)params["apix"]);
                                image->set_attr("apix_y", (float)params["apix"]);
                                image->set_attr("apix_z", (float)params["apix"]);
                        }
                        float apix=(float)image->get_attr("apix_x");
                        params["bfactor"] = pow(apix/(float)params["cutoff_abs"],0.0f);
 
                        const Dict dict = image->get_attr_dict();
                        if (params.has_key("cutoff_abs")) {
                                params["bfactor"] = pow(apix/(float)params["cutoff_abs"],2.0f);
                        }
                        else if( params.has_key("cutoff_freq") ) {
                                float val =  (float)params["cutoff_freq"] * apix;
                                params["cutoff_abs"] = val;
                                params["bfactor"] = pow(apix/(float)params["cutoff_abs"],2.0f);
                        }
                        else if( params.has_key("cutoff_pixels") ) {
                                float val = (float)params["cutoff_pixels"] / (float)dict["nx"];
                                params["cutoff_abs"] = val;
                                params["bfactor"] = pow(apix/(float)params["cutoff_abs"],2.0f);
                        }
                }

References EMAN::Dict::has_key(), and EMAN::Processor::params.

Member Data Documentation

◆ NAME

const string LowpassAutoBProcessor::NAME ="filter.lowpass.autob"

static

Definition at line 1961 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

Protected Member Functions

Additional Inherited Members

Detailed Description

Member Function Documentation

◆ create_radial_func()

◆ get_desc()

◆ get_name()

◆ get_param_types()

◆ NEW()

◆ preprocess()

Member Data Documentation

◆ NAME