This processor attempts to remove the low resolution peak present in all cryoEM data. More...

#include <processor.h>

Inheritance diagram for EMAN::HighpassAutoPeakProcessor:

Collaboration diagram for EMAN::HighpassAutoPeakProcessor:

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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...

Public Member Functions inherited from EMAN::FourierAnlProcessor
void	process_inplace (EMData *image)
	To process an image in-place. More...

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::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.highpass.autopeak"

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

virtual void	preprocess (EMData *image)

Protected Attributes
float	highpass

Protected Attributes inherited from EMAN::Processor
Dict	params

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...

Detailed Description

This processor attempts to remove the low resolution peak present in all cryoEM data.

Definition at line 2005 of file processor.h.

Member Function Documentation

◆ create_radial_func()

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

protectedvirtual

Implements EMAN::FourierAnlProcessor.

Definition at line 2148 of file processor.cpp.

{
        unsigned int c;
 
//      for (unsigned int i=0; i<radial_mask.size(); i++) printf("%d\t%f\n",i,radial_mask[i]);
        for (c=2; c<radial_mask.size(); c++) if (radial_mask[c-1]<=radial_mask[c]) break;
        if (c>highpass) c=(unsigned int)highpass;               // the *2 is for the 2x oversampling
 
        radial_mask[0]=0.0;
//      for (int i=1; i<radial_mask.size(); i++) radial_mask[i]=(i<=c?radial_mask[c+1]/radial_mask[i]:1.0);
        for (unsigned int i=1; i<radial_mask.size(); i++) radial_mask[i]=(i<=c?0.0f:1.0f);
 
        printf("%f %d\n",highpass,c);
//      for (unsigned int i=0; i<radial_mask.size(); i++) printf("%d\t%f\n",i,radial_mask[i]);
 
}

References highpass.

◆ get_desc()

string EMAN::HighpassAutoPeakProcessor::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 2017 of file processor.h.

                {
                        return "Attempts to automatically remove the low resolution peak present in virtually all cryoEM data.";
                }

◆ get_name()

string EMAN::HighpassAutoPeakProcessor::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 2008 of file processor.h.

                {
                        return NAME;
                }

References NAME.

◆ NEW()

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

inlinestatic

Definition at line 2012 of file processor.h.

                {
                        return new HighpassAutoPeakProcessor();
                }

◆ preprocess()

void HighpassAutoPeakProcessor::preprocess ( EMData * image )

protectedvirtual

Reimplemented from EMAN::FourierAnlProcessor.

Definition at line 2127 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"]);
        }
 
        const Dict dict = image->get_attr_dict();
 
        if( params.has_key("cutoff_abs") ) {
                highpass = params["cutoff_abs"];
        }
        else if( params.has_key("cutoff_freq") ) {
                highpass = (float)params["cutoff_freq"] * (float)dict["apix_x"] * (float)dict["ny"] / 2.0f;
        }
        else if( params.has_key("cutoff_pixels") ) {
                highpass = (float)params["cutoff_pixels"] / (float)dict["nx"];
        }
}

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

Member Data Documentation

◆ highpass

float EMAN::HighpassAutoPeakProcessor::highpass

protected

Definition at line 2027 of file processor.h.

Referenced by create_radial_func(), and preprocess().

◆ NAME

const string HighpassAutoPeakProcessor::NAME = "filter.highpass.autopeak"

static

Definition at line 2022 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

Protected Attributes

Additional Inherited Members