Iterative rotational, translational alignment with scaling. More...

#include <aligner.h>

Inheritance diagram for EMAN::RotateTranslateScaleAlignerIterative:

Collaboration diagram for EMAN::RotateTranslateScaleAlignerIterative:

[legend]

Public Member Functions
	RotateTranslateScaleAlignerIterative ()

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_scale_iter"

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

Iterative rotational, translational alignment with scaling.

Basically, we find the best translation, and move to that pointer then we find the best rotation and rotate to that point. Next we iterate X times. We do this for each scale of the image and return the optimal solution

Parameters

min	Minimum scaling (default: 0.95)
max	aximum scaling (default: 1.05)
step	Scaling step (default: 0.01)
maxshift	Maximum translation in pixels
r1	inner ring
r2	outer ring
maxiter	maximum number of alignment iterations
nozero	Zero translation not permitted (useful for CCD images)

Author: John Flanagan

Date: Oct 2010

Definition at line 665 of file aligner.h.

Constructor & Destructor Documentation

◆ RotateTranslateScaleAlignerIterative()

EMAN::RotateTranslateScaleAlignerIterative::RotateTranslateScaleAlignerIterative ( )

inline

Definition at line 669 of file aligner.h.

                                                       : ScaleAlignerABS("rotate_translate_iterative")
                {
                }

Referenced by NEW().

Member Function Documentation

◆ align() [1/2]

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

inlinevirtual

Implements EMAN::Aligner.

Definition at line 676 of file aligner.h.

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

References align().

◆ align() [2/2]

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

inlinevirtual

Implements EMAN::Aligner.

Definition at line 686 of file aligner.h.

                {
                        return "Performs rotational alignment and follows this with translational alignment using the iterative method. Does this for each scale and returns the best";
                }

◆ get_name()

virtual string EMAN::RotateTranslateScaleAlignerIterative::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 681 of file aligner.h.

                {
                        return NAME;
                }

References NAME.

◆ get_param_types()

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

inlinevirtual

Implements EMAN::Aligner.

Definition at line 696 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("r1", EMObject::INT, "Inner ring, pixels");
                        d.put("r2", EMObject::INT, "Outer ring, pixels");
                        d.put("maxiter", EMObject::INT, "Maximum number of iterations");
                        d.put("nozero", EMObject::INT,"Zero translation not permitted (useful for CCD images)");
                        d.put("useflcf", EMObject::INT,"Use Fast Local Correlation Function rather than CCF for translational alignment");
                        return d;
                }

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

◆ NEW()

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

inlinestatic

Definition at line 691 of file aligner.h.

                {
                        return new RotateTranslateScaleAlignerIterative();
                }

References RotateTranslateScaleAlignerIterative().

Member Data Documentation

◆ NAME

const string RotateTranslateScaleAlignerIterative::NAME = "rotate_trans_scale_iter"

static

Definition at line 711 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

◆ RotateTranslateScaleAlignerIterative()

Member Function Documentation

◆ align() [1/2]

◆ align() [2/2]

◆ get_desc()

◆ get_name()

◆ get_param_types()

◆ NEW()

Member Data Documentation

◆ NAME