EMAN::RotateTranslateScaleAligner Class Reference

rotational, translational, scaling alignment More...

#include <aligner.h>

Inheritance diagram for EMAN::RotateTranslateScaleAligner:

Collaboration diagram for EMAN::RotateTranslateScaleAligner:

Public Member Functions
	RotateTranslateScaleAligner ()
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::ScaleAlignerABS
	ScaleAlignerABS (const string &ba)
	Constructor to initialize the basealigner string. More...
EMData *	align_using_base (EMData *this_img, EMData *to_img, const string &cmp_name="dot", const Dict &cmp_params=Dict()) const
	implmentation of the scale alignment using the base aligner set in set_base_aligner More...
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 = "rotate_translate_scale"

Additional Inherited Members
Protected Attributes inherited from EMAN::ScaleAlignerABS
const string	basealigner
Dict	basealigner_params
Protected Attributes inherited from EMAN::Aligner
Dict	params

Detailed Description

rotational, translational, scaling alignment

Parameters

min	Minimum scaling (default: 0.95)
max	aximum scaling (default: 1.05)
step	Scaling step (default: 0.01)
maxshift	Maximum translation in pixels
nozero	Zero translation not permitted (useful for CCD images)
rfp_mode	Either 0,1 or 2. A temporary flag for testing the rotational foot print

Author

John Flanagan

Date

March 2012

Definition at line 552 of file aligner.h.

Constructor & Destructor Documentation

RotateTranslateScaleAligner()

EMAN::RotateTranslateScaleAligner::RotateTranslateScaleAligner ( )

inline

Definition at line 557 of file aligner.h.

                                              : ScaleAlignerABS("rotate_translate")
                {
                }

Referenced by NEW().

Member Function Documentation

align() [1/2]

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

inlinevirtual

Implements EMAN::Aligner.

Definition at line 564 of file aligner.h.

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

References align().

align() [2/2]

virtual EMData * EMAN::RotateTranslateScaleAligner::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::RotateTranslateScaleAligner::get_desc ( ) const

inlinevirtual

Implements EMAN::Aligner.

Definition at line 574 of file aligner.h.

                {
                        return "Performs rotational alignment and follows this with translational and then scaling alignment.";
                }

get_name()

virtual string EMAN::RotateTranslateScaleAligner::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 569 of file aligner.h.

                {
                        return NAME;
                }

References NAME.

get_param_types()

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

inlinevirtual

Implements EMAN::Aligner.

Definition at line 584 of file aligner.h.

                {
                        TypeDict d;
                        d.put("min", EMObject::FLOAT, "Minimum scaling (default: 0.95)");
                        d.put("max", EMObject::FLOAT, "Maximum scaling (default: 1.05)");
                        d.put("step", EMObject::FLOAT, "Scaling step (default: 0.01)");
                        d.put("maxshift", EMObject::INT, "Maximum translation in pixels");
                        d.put("nozero", EMObject::INT,"Zero translation not permitted (useful for CCD images)");
                        d.put("rfp_mode", EMObject::INT,"Either 0,1 or 2. A temporary flag for testing the rotational foot print");
                        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::FLOAT, EMAN::EMObject::INT, and EMAN::TypeDict::put().

NEW()

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

inlinestatic

Definition at line 579 of file aligner.h.

                {
                        return new RotateTranslateScaleAligner();
                }

References RotateTranslateScaleAligner().

Member Data Documentation

NAME

const string RotateTranslateScaleAligner::NAME = "rotate_translate_scale"

static

Definition at line 598 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