refine alignment. More...

#include <aligner.h>

Inheritance diagram for EMAN::RefineAligner:

Collaboration diagram for EMAN::RefineAligner:

[legend]

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 Public Attributes
static const string	NAME = "refine"

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

Detailed Description

refine alignment.

Refines a preliminary 2D alignment using a simplex algorithm. Subpixel precision.

Parameters

xform.align2d	The Transform storing the starting guess. If unspecified the identity matrix is used
stepx	The x increment used to create the starting simplex. Default is 1
stepy	The y increment used to create the starting simplex. Default is 1
stepaz	The rotational increment used to create the starting simplex. Default is 5
precision	The precision which, if achieved, can stop the iterative refinement before reaching the maximum iterations. Default is 0.04
maxiter	The maximum number of iterations. default=28
maxshift	Maximum translation in pixels in any direction. If the solution yields a shift beyond this value in any direction, then the refinement is judged a failure and the original alignment is used as the solution
stepscale	If set to any non-zero value, scale will be included in the alignment, and this will be the initial step. Images should be edgenormalized. If the scale goes beyond +-30% alignment will fail
verbose	This will cause debugging information to be printed on the screen for the iterative refinement. Larger numbers -> more info. default=0

Definition at line 1312 of file aligner.h.

Member Function Documentation

◆ align() [1/2]

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

inlinevirtual

Implements EMAN::Aligner.

Definition at line 1318 of file aligner.h.

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

References align().

◆ align() [2/2]

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

inlinevirtual

Implements EMAN::Aligner.

Definition at line 1328 of file aligner.h.

                {
                        return "Refines a preliminary 2D alignment using a simplex algorithm. Subpixel precision.";
                }

◆ get_name()

virtual string EMAN::RefineAligner::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 1323 of file aligner.h.

                {
                        return NAME;
                }

References NAME.

◆ get_param_types()

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

inlinevirtual

Implements EMAN::Aligner.

Definition at line 1338 of file aligner.h.

                {
                        TypeDict d;
 
                        d.put("mode", EMObject::INT, "Currently unused");
                        d.put("xform.align2d", EMObject::TRANSFORM, "The Transform storing the starting guess. If unspecified the identity matrix is used");
                        d.put("stepx", EMObject::FLOAT, "The x increment used to create the starting simplex. Default is 1");
                        d.put("stepy", EMObject::FLOAT, "The y increment used to create the starting simplex. Default is 1");
                        d.put("stepaz", EMObject::FLOAT, "The rotational increment used to create the starting simplex. Default is 5");
                        d.put("precision", EMObject::FLOAT, "The precision which, if achieved, can stop the iterative refinement before reaching the maximum iterations. Default is 0.04.");
                        d.put("maxiter", EMObject::INT,"The maximum number of iterations that can be performed by the Simplex minimizer. default=28");
                        d.put("maxshift", EMObject::INT,"Maximum translation in pixels in any direction. If the solution yields a shift beyond this value in any direction, then the refinement is judged a failure and the original alignment is used as the solution.");
                        d.put("stepscale", EMObject::FLOAT, "If set to any non-zero value, scale will be included in the alignment, and this will be the initial step. Images should be edgenormalized. If the scale goes beyond +-30% alignment will fail.");
                        d.put("mask", EMObject::EMDATA, "A mask to be applied to the image being aligned prior to each similarity comparison.");
                        d.put("verbose", EMObject::INT, "This will cause debugging information to be printed on the screen for the iterative refinement. Larger numbers -> more info. default=0");
                        return d;
                }

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

◆ NEW()

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

inlinestatic

Definition at line 1333 of file aligner.h.

                {
                        return new RefineAligner();
                }

Member Data Documentation

◆ NAME

const string RefineAligner::NAME = "refine"

static

Definition at line 1356 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

Member Function Documentation

◆ align() [1/2]

◆ align() [2/2]

◆ get_desc()

◆ get_name()

◆ get_param_types()

◆ NEW()

Member Data Documentation

◆ NAME