EMAN::PhaseToMassCenterProcessor Class Reference

ToMassCenterProcessor centers image at center of mass, ignores old dx, dy. More...

#include <processor.h>

Inheritance diagram for EMAN::PhaseToMassCenterProcessor:

Collaboration diagram for EMAN::PhaseToMassCenterProcessor:

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 = "xform.phasecenterofmass"

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

ToMassCenterProcessor centers image at center of mass, ignores old dx, dy.

Parameters

int_shift_only

set to 1 only shift by integer, no interpolation

Definition at line 7057 of file processor.h.

Member Function Documentation

get_desc()

virtual string EMAN::PhaseToMassCenterProcessor::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 7072 of file processor.h.

                        {
                                return "centers the image the center of mass, which is calculated using Fourier phases, ignores old dx, dy.";
                        }

get_name()

virtual string EMAN::PhaseToMassCenterProcessor::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 7062 of file processor.h.

                        {
                                return NAME;
                        }

References NAME.

get_param_types()

virtual TypeDict EMAN::PhaseToMassCenterProcessor::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 7077 of file processor.h.

                        {
                                TypeDict d;
                                d.put("int_shift_only", EMObject::INT, "If set, will only shift by integer amounts to avoid interpolation");
                                return d;
                        }

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

NEW()

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

inlinestatic

Definition at line 7067 of file processor.h.

                        {
                                return new PhaseToMassCenterProcessor();
                        }

process_inplace()

void PhaseToMassCenterProcessor::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 7498 of file processor.cpp.

{
        if (!image) {
                LOGWARN("NULL Image");
                return;
        }
 
        int int_shift_only = params.set_default("int_shift_only",1);
 
        vector<float> pcog = image->phase_cog();
 
        int dims = image->get_ndim();
 
        if (int_shift_only) {
                int dx=-int(pcog[0]+0.5f),dy=0,dz=0;
                if ( dims >= 2 ) dy = -int(pcog[1]+0.5);
                if ( dims == 3 ) dz = -int(pcog[2]+0.5);
 
                Transform t;
                t.set_trans((float)dx,(float)dy,(float)dz);
                if (dims == 3) image->set_attr("xform.align3d",&t);
                else if (dims == 2) image->set_attr("xform.align2d",&t);
 
                image->translate(dx,dy,dz);
        } else  {
                float dx=-pcog[0],dy=0.0,dz=0.0;
                if ( dims >= 2 ) dy = -pcog[1];
                if ( dims == 3 ) dz = -pcog[2];
                image->translate(dx,dy,dz);
 
                Transform t;
                t.set_trans(dx,dy,dz);
                if (dims == 3) image->set_attr("xform.align3d",&t);
                else if (dims == 2) image->set_attr("xform.align2d",&t);
        }
}

References LOGWARN, EMAN::Processor::params, EMAN::Dict::set_default(), EMAN::Transform::set_trans(), and EMAN::EMData::translate().

Member Data Documentation

NAME

const string PhaseToMassCenterProcessor::NAME = "xform.phasecenterofmass"

static

Definition at line 7084 of file processor.h.

Referenced by get_name().

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

• processor.h
• processor.cpp