EMAN::TomoWedgeCccCmp Class Reference

Both images should be FFTs. More...

#include <cmp.h>

Inheritance diagram for EMAN::TomoWedgeCccCmp:

Collaboration diagram for EMAN::TomoWedgeCccCmp:

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.thresh"

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

Both images should be FFTs.

Computes a CCC excluding pixels with very small value (assumes they are missing wedge) Returns overlap amount as "fft_overlap" in "image"

Date

2010-10-18

Definition at line 352 of file cmp.h.

Member Function Documentation

cmp()

float TomoWedgeCccCmp::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 691 of file cmp.cpp.

{
        ENTERFUNC;
        EMData *imageo=image;
        EMData *witho=with;
        if (!image->is_complex()) image=image->do_fft();
        if (!with ->is_complex()) with =with ->do_fft();
        if (image->get_xsize()!=with->get_xsize() || image->get_ysize()!=with->get_ysize() || image->get_zsize()!=with->get_zsize())  throw InvalidCallException("Error: TomoWedgeCccCmp requires same sized images");
 
        float sigmaimg = params.set_default("sigmaimg",0.5f);
        float sigmawith = params.set_default("sigmawith",0.5f);
        int negative = params.set_default("negative",1);
 
        // Note 'sigma' is the STD of real and imag values treated independently
        // s1 and s2 are threshold values squared (for speed)
        float s1=pow((float)image->get_attr("sigma")*sigmaimg,(float)2.0);              
        float s2=pow((float)with->get_attr("sigma")*sigmawith,(float)2.0);
        
        
        double sum=0;
        double sumsq1=0;
        double sumsq2=0;
        double norm=0;
        for (int z=0; z<image->get_zsize(); z++) {
                for (int y=0; y<image->get_ysize(); y++) {
                        for (int x=0; x<image->get_xsize(); x+=2) {
                                float v1r=image->get_value_at(x,y,z);
                                float v1i=image->get_value_at(x+1,y,z);
                                float v1=Util::square_sum(v1r,v1i);
                                if (v1<s1) continue;
                                
                                float v2r=with->get_value_at(x,y,z);
                                float v2i=with->get_value_at(x+1,y,z);
                                float v2=Util::square_sum(v2r,v2i);
                                if (v2<s2) continue;
                                
                                sum+=v1r*v2r+v1i*v2i;
                                sumsq1+=v1;
                                if (Util::is_nan(sumsq1)) { printf("TomoWedgeCccCmp: NaN encountered: %d %d %d %f %f %f\n",x,y,z,v1r,v1i,v1); }
                                sumsq2+=v2;
                                norm+=1.0;
                        }
                }
        }
        imageo->set_attr("fft_overlap",(float)(2.0*norm/(image->get_xsize()*image->get_ysize()*image->get_zsize())));
//      printf("%f\t%f\t%f\t%f\t%f\n",s1,s2,sumsq1,sumsq2,norm);
        
        if (imageo!=image) delete image;
        if (witho!=with) delete with;
        
        if (negative) sum*=-1.0;
        return float(sum/(sqrt(sumsq1)*sqrt(sumsq2)));
}

References ENTERFUNC, InvalidCallException, is_complex(), EMAN::Util::is_nan(), EMAN::Cmp::params, EMAN::Dict::set_default(), sqrt(), EMAN::Util::square_sum(), x, and y.

get_desc()

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

inlinevirtual

Implements EMAN::Cmp.

Definition at line 362 of file cmp.h.

                {
                        return "Ccc of two FFTs with missing wedge taken into account explicitly. Also stores overlap as 'fft_overlap' in \
first input image. Individual voxels are include only if they exceed the threshold value in both images. fft_overlap expresses \
the fractional number of voxels included in the comparison. Actual returned correlations already account for this effect, but \
the overlap can be used to estimate the relative uncertainty in the resulting correlation coefficient.";
                }

get_name()

virtual string EMAN::TomoWedgeCccCmp::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 357 of file cmp.h.

                {
                        return NAME;
                }

References NAME.

get_param_types()

TypeDict EMAN::TomoWedgeCccCmp::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 375 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("sigmaimg", EMObject::FLOAT, "Sigma coefficient for thresholding values included in the dot product. default = 0.5");
                        d.put("sigmawith", EMObject::FLOAT, "Sigma coefficient for thresholding values included in the dot product in the 'with' image. Default = 0.5");
                        d.put("negative", EMObject::INT, "If set, returns -1 * ccc product. Set by default so smaller is better");
                        return d;
                }

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

NEW()

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

inlinestatic

Definition at line 370 of file cmp.h.

                {
                        return new TomoWedgeCccCmp();
                }

Member Data Documentation

NAME

const string TomoWedgeCccCmp::NAME = "ccc.tomo.thresh"

static

Definition at line 386 of file cmp.h.

Referenced by get_name().

---

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

• cmp.h
• cmp.cpp