Conjugate gradient refine alignment. More...

#include <aligner.h>

Inheritance diagram for EMAN::RefineAlignerCG:

Collaboration diagram for EMAN::RefineAlignerCG:

[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 = "refinecg"

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

Detailed Description

Conjugate gradient refine alignment.

Refines a preliminary 2D alignment to subpixel precision. Faster than 'refine', but requires better local minimum

Parameters

xform.align2d	The Transform storing the starting guess. If unspecified the identity matrix is used
step	The initial increment used for stepping on the gradient. default=0.1
precision	The precision which, if achieved, can stop the iterative refinement before reaching the maximum iterations. Default is 0.02
maxiter	The maximum number of iterations. default=12
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 1369 of file aligner.h.

Member Function Documentation

◆ align() [1/2]

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

inlinevirtual

Implements EMAN::Aligner.

Definition at line 1375 of file aligner.h.

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

References align().

◆ align() [2/2]

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

inlinevirtual

Implements EMAN::Aligner.

Definition at line 1385 of file aligner.h.

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

◆ get_name()

virtual string EMAN::RefineAlignerCG::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 1380 of file aligner.h.

                {
                        return NAME;
                }

References NAME.

◆ get_param_types()

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

inlinevirtual

Implements EMAN::Aligner.

Definition at line 1395 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("step", EMObject::FLOAT, "The x increment used to create the starting simplex. Default is 0.1");
                        d.put("precision", EMObject::FLOAT, "The precision which, if achieved, can stop the iterative refinement before reaching the maximum iterations. Default is 0.02.");
                        d.put("maxiter", EMObject::INT,"The maximum number of iterations that can be performed by the Simplex minimizer. default=12");
                        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. 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::RefineAlignerCG::NEW ( )

inlinestatic

Definition at line 1390 of file aligner.h.

                {
                        return new RefineAlignerCG();
                }

Member Data Documentation

◆ NAME

const string RefineAlignerCG::NAME = "refinecg"

static

Definition at line 1411 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