rotational, translational, flip, scaling alignment More...

#include <aligner.h>

Inheritance diagram for EMAN::RotateTranslateFlipScaleAligner:

Collaboration diagram for EMAN::RotateTranslateFlipScaleAligner:

[legend]

Public Member Functions
	RotateTranslateFlipScaleAligner ()

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_trans_flip_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, flip, scaling alignment

Parameters

min	Minimum scaling (default: 0.95)
max	aximum scaling (default: 1.05)
step	Scaling step (default: 0.01)
flip	who knows what this means?
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 958 of file aligner.h.

Constructor & Destructor Documentation

◆ RotateTranslateFlipScaleAligner()

EMAN::RotateTranslateFlipScaleAligner::RotateTranslateFlipScaleAligner ( )

inline

Definition at line 962 of file aligner.h.

                                                  : ScaleAlignerABS("rotate_translate_flip")
                {
                }

Referenced by NEW().

Member Function Documentation

◆ align() [1/2]

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

inlinevirtual

Implements EMAN::Aligner.

Definition at line 969 of file aligner.h.

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

References align().

◆ align() [2/2]

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

inlinevirtual

Implements EMAN::Aligner.

Definition at line 979 of file aligner.h.

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

◆ get_name()

virtual string EMAN::RotateTranslateFlipScaleAligner::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 974 of file aligner.h.

                {
                        return NAME;
                }

References NAME.

◆ get_param_types()

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

inlinevirtual

Implements EMAN::Aligner.

Definition at line 989 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("flip", EMObject::EMDATA);
                        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::EMDATA, EMAN::EMObject::FLOAT, EMAN::EMObject::INT, and EMAN::TypeDict::put().

◆ NEW()

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

inlinestatic

Definition at line 984 of file aligner.h.

                {
                        return new RotateTranslateFlipScaleAligner();
                }

References RotateTranslateFlipScaleAligner().

Member Data Documentation

◆ NAME

const string RotateTranslateFlipScaleAligner::NAME = "rotate_trans_flip_scale"

static

Definition at line 1004 of file aligner.h.

Referenced by get_name().

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

Public Member Functions

Static Public Member Functions

Static Public Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ RotateTranslateFlipScaleAligner()

Member Function Documentation

◆ align() [1/2]

◆ align() [2/2]

◆ get_desc()

◆ get_name()

◆ get_param_types()

◆ NEW()

Member Data Documentation

◆ NAME