EMAN::TomoCccCmp Class Reference

This implements the technique of Mike Schmid where by the cross correlation is normalized in an effort to remove the effects of the missing wedge. More...

#include <cmp.h>

Inheritance diagram for EMAN::TomoCccCmp:

Collaboration diagram for EMAN::TomoCccCmp:

Public Member Functions
virtual float	cmp (EMData *image, EMData *with) const
	To compare 'image' with another image passed in through its parameters. More...
virtual string	get_name () const
	Get the Cmp's name. More...
virtual string	get_desc () const
TypeDict	get_param_types () const
	Get Cmp parameter information in a dictionary. More...
Public Member Functions inherited from EMAN::Cmp
virtual	~Cmp ()
virtual Dict	get_params () const
	Get the Cmp parameters in a key/value dictionary. More...
virtual void	set_params (const Dict &new_params)
	Set the Cmp parameters using a key/value dictionary. More...

Static Public Member Functions
static Cmp *	NEW ()

Static Public Attributes
static const string	NAME = "ccc.tomo"

Additional Inherited Members
Protected Member Functions inherited from EMAN::Cmp
void	validate_input_args (const EMData *image, const EMData *with) const
Protected Attributes inherited from EMAN::Cmp
Dict	params

Detailed Description

This implements the technique of Mike Schmid where by the cross correlation is normalized in an effort to remove the effects of the missing wedge.

Somewhat of a heuristic solution, but it seems to work. Basiaclly it relies on the observation that 'good' matchs will conentrate the correlation signal in the peak, wheras 'bad' correlations will distribute the signal.

Author

John Flanagan (a port of Mike Schmid's code - Mike Schmid is the intellectual author)

Date

2010-10-18

Parameters

norm	Normalize the ccf (you need to do this if a missing wedge is present)
ccf	Supply your own ccf function (can be used for speedups)
searchx	The maximum acceptable tx from the origin
searchy	The maximum acceptable ty from the origin
searchz	The maximum acceptable tz from the origin

Definition at line 313 of file cmp.h.

Member Function Documentation

cmp()

float TomoCccCmp::cmp ( EMData *  image, EMData *  with  ) const

virtual

To compare 'image' with another image passed in through its parameters.

An optional transformation may be used to transform the 2 images.

Parameters

image	The first image to be compared.
with	The second image to be comppared.

Returns

The comparison result. Smaller better by default

Implements EMAN::Cmp.

Definition at line 643 of file cmp.cpp.

{
        ENTERFUNC;
        EMData* ccf = params.set_default("ccf",(EMData*) NULL);
        bool ccf_ownership = false;
        bool norm = params.set_default("norm",true);
        float negative = (float)params.set_default("negative", 1);
        if (negative) negative=-1.0; else negative=1.0;
        
#ifdef EMAN2_USING_CUDA 
        if(image->getcudarwdata() && with->getcudarwdata()){
                if (!ccf) {
                        ccf = image->calc_ccf(with);
                        ccf_ownership = true;
                }
                //cout << "using CUDA" << endl;
                float2 stats = get_stats_cuda(ccf->getcudarwdata(), ccf->get_xsize(), ccf->get_ysize(), ccf->get_zsize());
                float best_score = get_value_at_wrap_cuda(ccf->getcudarwdata(), 0, 0, 0, ccf->get_xsize(), ccf->get_ysize(), ccf->get_zsize());
                if(norm) {
                        best_score = negative*(best_score - stats.x)/sqrt(stats.y);
                } else {
                        best_score = negative*best_score;
                }
                
                if (ccf_ownership) delete ccf; ccf = 0;
                
                EXITFUNC;
                return best_score;
                
        }
#endif
 
        if (!ccf) {
                ccf = image->calc_ccf(with);
                ccf_ownership = true;
        }
        if (norm) ccf->process_inplace("normalize");
        
        float best_score = ccf->get_value_at_wrap(0,0,0);
        if (ccf_ownership) delete ccf; ccf = 0;
 
        return negative*best_score;
 
}

References EMAN::EMData::calc_ccf(), ENTERFUNC, EXITFUNC, get_stats_cuda(), get_value_at_wrap_cuda(), EMAN::Cmp::params, EMAN::Dict::set_default(), and sqrt().

get_desc()

virtual string EMAN::TomoCccCmp::get_desc ( ) const

inlinevirtual

Implements EMAN::Cmp.

Definition at line 323 of file cmp.h.

                {
                        return "Ccc with consideration given for the missing wedge";
                }

get_name()

virtual string EMAN::TomoCccCmp::get_name ( ) const

inlinevirtual

Get the Cmp's name.

Each Cmp is identified by a unique name.

Returns

The Cmp's name.

Implements EMAN::Cmp.

Definition at line 318 of file cmp.h.

                {
                        return NAME;
                }

References NAME.

get_param_types()

TypeDict EMAN::TomoCccCmp::get_param_types ( ) const

inlinevirtual

Get Cmp 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.

Implements EMAN::Cmp.

Definition at line 333 of file cmp.h.

                {
                        TypeDict d;
                        d.put("norm", EMObject::BOOL,"Whether the cross correlation image should be normalized (should be for normalized images). Default is true.");
                        d.put("ccf", EMObject::EMDATA,"The ccf image, can be provided if it already exists to avoid recalculating it");
                        d.put("normalize", EMObject::EMDATA,"Return the negative value (which is EMAN2 convention), Defalut is true(1)");
                        d.put("searchx", EMObject::INT, "The maximum range of the peak location in the x direction. Default is sizex/4");
                        d.put("searchy", EMObject::INT, "The maximum range of the peak location in the y direction. Default is sizey/4");
                        d.put("searchz", EMObject::INT, "The maximum range of the peak location in the z direction. Default is sizez/4");
                        return d;
                }

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

NEW()

static Cmp * EMAN::TomoCccCmp::NEW ( )

inlinestatic

Definition at line 328 of file cmp.h.

                {
                        return new TomoCccCmp();
                }

Member Data Documentation

NAME

const string TomoCccCmp::NAME = "ccc.tomo"

static

Definition at line 345 of file cmp.h.

Referenced by get_name().

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

• cmp.h
• cmp.cpp