EMAN::RTFSlowExhaustiveAligner Class Reference

rotational, translational and flip alignment using exhaustive search. More...

#include <aligner.h>

Inheritance diagram for EMAN::RTFSlowExhaustiveAligner:

Collaboration diagram for EMAN::RTFSlowExhaustiveAligner:

Public Member Functions
virtual EMData *	align (EMData *this_img, EMData *to_img, const string &cmp_name, const Dict &cmp_params) const
	To align 'this_img' with another image passed in through its parameters. More...
virtual EMData *	align (EMData *this_img, EMData *to_img) const
virtual string	get_name () const
	Get the Aligner's name. More...
virtual string	get_desc () const
virtual TypeDict	get_param_types () const
Public Member Functions inherited from EMAN::Aligner
virtual	~Aligner ()
virtual Dict	get_params () const
	Get the Aligner parameters in a key/value dictionary. More...
virtual void	set_params (const Dict &new_params)
	Set the Aligner parameters using a key/value dictionary. More...
virtual vector< Dict >	xform_align_nbest (EMData *this_img, EMData *to_img, const unsigned int nsoln, const string &cmp_name, const Dict &cmp_params) const
	This function first added in the context of the 3D aligners used by e2tomohunter: which wants the n best solutions, as opposed to just the best. More...

Static Public Member Functions
static Aligner *	NEW ()

Static Public Attributes
static const string	NAME = "rtf_slow_exhaustive"

Additional Inherited Members
Protected Attributes inherited from EMAN::Aligner
Dict	params

Detailed Description

rotational, translational and flip alignment using exhaustive search.

This is very slow but can ensure localization of the global maximum

Parameters

flip	Optional. This is the flipped version of the images that is being aligned. If specified it will be used for the handedness check, if not a flipped copy of the image will be made
maxshift	The maximum length of the detectable translational shift
transtep	The translation step to take when honing the alignment, which occurs after coarse alignment
angstep	The angular step (in degrees) to take in the exhaustive search for the solution angle. Typically very small i.e. 3 or smaller

Definition at line 1217 of file aligner.h.

Member Function Documentation

align() [1/2]

virtual EMData * EMAN::RTFSlowExhaustiveAligner::align ( EMData *  this_img, EMData *  to_img  ) const

inlinevirtual

Implements EMAN::Aligner.

Definition at line 1222 of file aligner.h.

                {
                        return align(this_img, to_img, "sqeuclidean", Dict());
                }

References align().

align() [2/2]

virtual EMData * EMAN::RTFSlowExhaustiveAligner::align ( EMData *  this_img, EMData *  to_img, const string &  cmp_name, const Dict &  cmp_params  ) const

virtual

To align 'this_img' with another image passed in through its parameters.

The alignment uses a user-given comparison method to compare the two images. If none is given, a default one is used.

Parameters

this_img	The image to be compared.
to_img	'this_img" is aligned with 'to_img'.
cmp_name	The comparison method to compare the two images.
cmp_params	The parameter dictionary for comparison method.

Returns

The aligned image.

Implements EMAN::Aligner.

Referenced by align().

get_desc()

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

inlinevirtual

Implements EMAN::Aligner.

Definition at line 1231 of file aligner.h.

                {
                        return "Experimental full 2D alignment with handedness check using more exhaustive search (not necessarily better than RTFBest)";
                }

get_name()

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

inlinevirtual

Get the Aligner's name.

Each Aligner is identified by a unique name.

Returns

The Aligner's name.

Implements EMAN::Aligner.

Definition at line 1226 of file aligner.h.

                {
                        return NAME;
                }

References NAME.

get_param_types()

virtual TypeDict EMAN::RTFSlowExhaustiveAligner::get_param_types ( ) const

inlinevirtual

Implements EMAN::Aligner.

Definition at line 1241 of file aligner.h.

                {
                        TypeDict d;
                        d.put("flip", EMObject::EMDATA,"Optional. This is the flipped version of the images that is being aligned. If specified it will be used for the handedness check, if not a flipped copy of the image will be made");
                        d.put("maxshift", EMObject::INT,"The maximum length of the detectable translational shift");
                        d.put("transtep", EMObject::FLOAT,"The translation step to take when honing the alignment, which occurs after coarse alignment");
                        d.put("angstep", EMObject::FLOAT,"The angular step (in degrees) to take in the exhaustive search for the solution angle. Typically very small i.e. 3 or smaller.");
                        return d;
                }

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

NEW()

static Aligner * EMAN::RTFSlowExhaustiveAligner::NEW ( )

inlinestatic

Definition at line 1236 of file aligner.h.

                {
                        return new RTFSlowExhaustiveAligner();
                }

Member Data Documentation

NAME

const string RTFSlowExhaustiveAligner::NAME = "rtf_slow_exhaustive"

static

Definition at line 1251 of file aligner.h.

Referenced by get_name().

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

• aligner.h
• aligner.cpp