EMAN::RotateTranslateFlipAligner Class Reference

rotational, translational and flip alignment More...

#include <aligner.h>

Inheritance diagram for EMAN::RotateTranslateFlipAligner:

Collaboration diagram for EMAN::RotateTranslateFlipAligner:

Public Member Functions
virtual EMData *	align (EMData *this_img, EMData *to_img, const string &cmp_name="dot", const Dict &cmp_params=Dict()) 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 TypeDict	static_get_param_types ()

Static Public Attributes
static const string	NAME = "rotate_translate_flip"

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

Detailed Description

rotational, translational and flip alignment

Parameters

flip
usedot
maxshift	Maximum translation in pixels
rfp_mode	Either 0,1 or 2. A temporary flag for testing the rotational foot print

Definition at line 900 of file aligner.h.

Member Function Documentation

align() [1/2]

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

inlinevirtual

Implements EMAN::Aligner.

Definition at line 905 of file aligner.h.

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

References align().

align() [2/2]

virtual EMData * EMAN::RotateTranslateFlipAligner::align ( EMData *  this_img, EMData *  to_img, const string &  cmp_name = "dot", const Dict &  cmp_params = Dict()  ) 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::RotateTranslateFlipAligner::get_desc ( ) const

inlinevirtual

Implements EMAN::Aligner.

Definition at line 915 of file aligner.h.

                {
                        return " Does two 'rotate_translate' alignments, one to accommodate for possible handedness change. Decided which alignment is better using a comparitor and returns the aligned image as the solution";
                }

get_name()

virtual string EMAN::RotateTranslateFlipAligner::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 910 of file aligner.h.

                {
                        return NAME;
                }

References NAME.

get_param_types()

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

inlinevirtual

Implements EMAN::Aligner.

Definition at line 925 of file aligner.h.

                {
                        return static_get_param_types();
                }

References static_get_param_types().

NEW()

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

inlinestatic

Definition at line 920 of file aligner.h.

                {
                        return new RotateTranslateFlipAligner();
                }

static_get_param_types()

static TypeDict EMAN::RotateTranslateFlipAligner::static_get_param_types ( )

inlinestatic

Definition at line 930 of file aligner.h.

                                                         {
                        TypeDict d;
 
                        d.put("flip", EMObject::EMDATA);
                        d.put("usedot", EMObject::INT);
                        d.put("maxshift", EMObject::INT, "Maximum translation in pixels");
                        d.put("rfp_mode", EMObject::INT,"Either 0,1 or 2. A temporary flag for testing the rotational foot print");
                        d.put("usebispec", EMObject::INT,"Uses rotate_translate_bispec for subalignments and ignore rfp_mode.");
                        d.put("useharmonic", EMObject::INT,"Uses rotate_translate_bispec in harmonic mode for alignments and ignores rfp_mode.");
                        d.put("useflcf", EMObject::INT,"Use Fast Local Correlation Function rather than CCF for translational alignment");
                        d.put("zscore", EMObject::INT,"Either 0 or 1. This option is passed directly to the rotational aligner (default=false)");
                        return d;
                }

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

Referenced by get_param_types().

Member Data Documentation

NAME

const string RotateTranslateFlipAligner::NAME = "rotate_translate_flip"

static

Definition at line 944 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