EMAN::TomoDotCmp Class Reference

Use dot product but normalize based on characteristics of the missing wedge. More...

#include <cmp.h>

Inheritance diagram for EMAN::TomoDotCmp:

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Collaboration diagram for EMAN::TomoDotCmp:

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List of all members.

Public Member Functions
virtual float	cmp (EMData *image, EMData *with) const
	To compare 'image' with another image passed in through its parameters.
virtual string	get_name () const
	Get the Cmp's name.
virtual string	get_desc () const
TypeDict	get_param_types () const
	Get Cmp parameter information in a dictionary.
Static Public Member Functions
static Cmp *	NEW ()
Static Public Attributes
static const string	NAME = "dot.tomo"

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Detailed Description

Use dot product but normalize based on characteristics of the missing wedge.

Author:

David Woolford (a port of Mike Schmid's code - Mike Schmid is the intellectual author)

Date:

2009-08-04

Parameters:

threshold

threshold value to count large fourier amplitudes in the ccf image

Definition at line 270 of file cmp.h.

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Member Function Documentation

float TomoDotCmp::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 455 of file cmp.cpp.

References EMAN::EMData::calc_ccf(), EMAN::EMData::do_fft(), EMAN::EMData::dot(), ENTERFUNC, EMAN::EMData::get_attr(), EMAN::EMData::get_size(), EMAN::EMData::get_value_at_wrap(), InvalidParameterException, norm(), EMAN::Cmp::params, EMAN::EMData::process_inplace(), EMAN::Dict::set_default(), and UnexpectedBehaviorException.

{
        ENTERFUNC;
        float threshold = params.set_default("threshold",0.f);
        if (threshold < 0.0f) throw InvalidParameterException("The threshold parameter must be greater than or equal to zero");

        if ( threshold > 0) {
                EMData* ccf = params.set_default("ccf",(EMData*) NULL);
                bool ccf_ownership = false;
                if (!ccf) {
                        ccf = image->calc_ccf(with);
                        ccf_ownership = true;
                }
                bool norm = params.set_default("norm",false);
                if (norm) ccf->process_inplace("normalize");
                int tx = params.set_default("tx",0); int ty = params.set_default("ty",0); int tz = params.set_default("tz",0);
                float best_score = ccf->get_value_at_wrap(tx,ty,tz)/static_cast<float>(image->get_size());
                EMData* ccf_fft = ccf->do_fft();// so cuda works, or else we could do an fft_inplace - though honestly doing an fft inplace is less efficient anyhow
                if (ccf_ownership) delete ccf; ccf = 0;
                ccf_fft->process_inplace("threshold.binary.fourier",Dict("value",threshold));
                float map_sum =  ccf_fft->get_attr("mean");
                if (map_sum == 0.0f) throw UnexpectedBehaviorException("The number of voxels in the Fourier image with an amplitude above your threshold is zero. Please adjust your parameters");
                best_score /= map_sum;
                delete ccf_fft; ccf_fft = 0;
                return -best_score;
        } else {
                return -image->dot(with);
        }


}

virtual string EMAN::TomoDotCmp::get_name

(

)

const [inline, virtual]

Get the Cmp's name.

Each Cmp is identified by a unique name.

Returns:

The Cmp's name.

Implements EMAN::Cmp.

Definition at line 275 of file cmp.h.

References NAME.

                {
                        return NAME;
                }

virtual string EMAN::TomoDotCmp::get_desc

(

)

const [inline, virtual]

Implements EMAN::Cmp.

Definition at line 280 of file cmp.h.

                {
                        return "straight dot product with consideration given for the missing wedge - normalization is applied by detecting significantly large Fourier amplitudes in the cross correlation image";
                }

static Cmp* EMAN::TomoDotCmp::NEW

(

)

[inline, static]

Definition at line 285 of file cmp.h.

                {
                        return new TomoDotCmp();
                }

TypeDict EMAN::TomoDotCmp::get_param_types

(

)

const [inline, virtual]

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 290 of file cmp.h.

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

                {
                        TypeDict d;
                        d.put("threshold", EMObject::FLOAT,"Threshold applied to the Fourier amplitudes of the ccf image - helps to correct for the missing wedge.");
                        d.put("norm", EMObject::BOOL,"Whether the cross correlation image should be normalized. Default is false.");
                        d.put("ccf", EMObject::EMDATA,"The ccf image, can be provided if it already exists to avoid recalculating it");
                        d.put("tx", EMObject::INT, "The x location of the maximum in the ccf image. May be negative. Useful thing to supply if you know the maximum is not at the phase origin");
                        d.put("ty", EMObject::INT, "The y location of the maximum in the ccf image. May be negative. Useful thing to supply if you know the maximum is not at the phase origin");
                        d.put("tz", EMObject::INT, "The z location of the maximum in the ccf image. May be negative. Useful thing to supply if you know the maximum is not at the phase origin");

                        return d;
                }

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Member Data Documentation

const string TomoDotCmp::NAME = "dot.tomo" [static]

Definition at line 303 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