Zeroes the values on the X=0 and y=0 Fourier axes (except x=y=0) More...

#include <processor.h>

Inheritance diagram for EMAN::GaussZFourierProcessor:

Collaboration diagram for EMAN::GaussZFourierProcessor:

[legend]

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

void	process_inplace (EMData *image)
	To process an image in-place. More...

void	set_params (const Dict &new_params)
	Set the processor parameters using a key/value dictionary. More...

TypeDict	get_param_types () const
	Get processor parameter information in a dictionary. More...

string	get_desc () const
	Get the descrition of this specific processor. 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...

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.lowpass.gaussz"

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

Zeroes the values on the X=0 and y=0 Fourier axes (except x=y=0)

Definition at line 542 of file processor.h.

Member Function Documentation

◆ get_desc()

string EMAN::GaussZFourierProcessor::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 575 of file processor.h.

                {
                        return "Applies a Gaussian lowpass filter (or its inverse), but only along the Z axis (or X-Y). May be useful in anisotropic filtering of tomograms.";
                }

◆ get_name()

string EMAN::GaussZFourierProcessor::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 545 of file processor.h.

                {
                        return NAME;
                }

References NAME.

◆ get_param_types()

TypeDict EMAN::GaussZFourierProcessor::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 557 of file processor.h.

                {
                        TypeDict d;
                        d.put("cutoff_abs", EMObject::FLOAT, "Processor radius in terms of Nyquist (0-.5)");
                        d.put("cutoff_pixels", EMObject::FLOAT, " Width in Fourier pixels (0 - size()/2)");
                        d.put("cutoff_freq", EMObject::FLOAT, "1/Resolution in 1/A (0 - 1 / 2*apix). eg - a 20 A filter is cutoff_freq=0.05");
                        d.put("hppix", EMObject::FLOAT, "If specified will also apply a high pass filter with the specified radius in pixels");
                        d.put("apix", EMObject::FLOAT, " Override A/pix in the image header (changes x,y and z)");
                        d.put("centerfreq", EMObject::FLOAT, "center of filter frequency at z");
                        d.put("xynoz", EMObject::INT, "If set, filters the X-Y plane instead of Z");
                        return d;
                }

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

◆ NEW()

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

inlinestatic

Definition at line 570 of file processor.h.

                {
                        return new GaussZFourierProcessor();
                }

◆ process_inplace()

void GaussZFourierProcessor::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 1300 of file processor.cpp.

{
        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"]);
        }
        
        int xynoz = params.set_default("xynoz",0);
 
        const Dict dict = image->get_attr_dict();
        if( params.has_key("cutoff_freq") ) {
                float val =  (float)params["cutoff_freq"] * (float)dict["apix_x"];
                params["cutoff_abs"] = val;
        }
        else if( params.has_key("cutoff_pixels") ) {
                float val = ((float)params["cutoff_pixels"] / (float)dict["nx"]);
                params["cutoff_abs"] = val;
        }
 
        float omega = params["cutoff_abs"];
        float zcenter=params.set_default("centerfreq",0.0f);
        float hppix = params.set_default("hppix",-1.0f);
        
        omega = (omega<0?-1.0:1.0)*0.5f/omega/omega;
 
        EMData *fft;
        int f=0;
 
        if (!image) {
                LOGWARN("NULL Image");
                return;
        }
 
        if (!image->is_complex()) {
                fft = image->do_fft();
                f=1;
        }
        else {
                fft=image;
        }
 
        int nx=fft->get_xsize();
        int ny=fft->get_ysize();
        int nz=fft->get_ysize();
        omega /=(nz*nz)/4;
        zcenter=zcenter*(float)dict["apix_x"]*nz;
 
        if (xynoz) {
                for (int x=0; x<nx/2; x++) {
                        for (int z=(x==0?0:-nz/2); z<nz/2; z++) {
                                for (int y=(x==0&&z==0?0:-ny/2); y<ny/2; y++) {
                                        std::complex <float> v=fft->get_complex_at(x,y,z);
                                        float r=Util::hypot_fast(x,y);
                                        fft->set_complex_at(x,y,z,v*exp(-omega*(r-zcenter)*(r-zcenter))*(r>hppix?1.0f:Util::hypot3(x,y,z)/hppix));
                                }
                        }
                }
        }
        else {
                for (int z=-nz/2; z<nz/2; z++) {
                        for (int y=-ny/2; y<ny/2; y++) {
                                for (int x=0; x<nx/2; x++) {
                                        std::complex <float> v=fft->get_complex_at(x,y,z);
                                        fft->set_complex_at(x,y,z,v*exp(-omega*(abs(z)-zcenter)*(abs(z)-zcenter))*(fabs(z)>hppix?1.0f:Util::hypot3(x,y,z)/hppix));
                                }
                        }
                }
        }
 
        if (f) {
                EMData *ift=fft->do_ift();
                memcpy(image->get_data(),ift->get_data(),(nx-2)*ny*nz*sizeof(float));
                delete fft;
                delete ift;
        }
 
}

References EMAN::Dict::has_key(), EMAN::Util::hypot3(), EMAN::Util::hypot_fast(), LOGWARN, EMAN::Processor::params, EMAN::Dict::set_default(), x, and y.

◆ set_params()

void EMAN::GaussZFourierProcessor::set_params ( const Dict & new_params )

inlinevirtual

Set the processor parameters using a key/value dictionary.

Parameters

new_params A dictionary containing the new parameters.

Reimplemented from EMAN::Processor.

Definition at line 552 of file processor.h.

                {
                        params = new_params;
                }

References EMAN::Processor::params.

Member Data Documentation

◆ NAME

const string GaussZFourierProcessor::NAME = "filter.lowpass.gaussz"

static

Definition at line 580 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()

◆ set_params()

Member Data Documentation

◆ NAME