Refine alignment. More...

#include <aligner.h>

Inheritance diagram for EMAN::Refine3DAlignerQuaternion:

Collaboration diagram for EMAN::Refine3DAlignerQuaternion:

[legend]

Public Member Functions
virtual EMData *	align (EMData this_img, EMData to_img, const string &cmp_name="sqeuclidean", 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_3d"

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

Detailed Description

Refine alignment.

Refines a preliminary 3D alignment using a simplex algorithm. Subpixel precision. Target function for the simplex algorithm is a rotation along an arbitrary axis defined by a quaternion, whose rotation magnitude is defined by the vector length (hence the simplex varies the vecotr component of the quaternion). In addition the simplex varies translation. Using quaternions avoids gimbal lock. The simplex algorithm moves the function downhill in a ameboa like fasion, hence it may get stuck in a local minima if the two 3D models are already roughly aligned.

Parameters

xform.align3d	The Transform storing the starting guess. If unspecified the identity matrix is used
stepx	The initial simplex step size in x
stepy	The initial simplex step size in y
stepz	The initial simplex step size in z
stepn0	The initial simplex step size in the first quaternion vecotr component
stepn1	The initial simplex step size in the second quaternion vecotr component
stepn2	The initial simplex step size in the third quaternion vecotr component
spin_coeff	The multiplier appied to the spin (if it is too small or too large the simplex will not converge)
precision	The precision which, if achieved, can stop the iterative refinement before reaching the maximum iterations
maxiter	The maximum number of iterations that can be performed by the Simplex minimizer
maxshift	Maximum translation in pixels in any direction.

Author: John Flanagan (with code recyled from David Woolford)

Date: Feb 3rd 2011

Definition at line 1546 of file aligner.h.

Member Function Documentation

◆ align() [1/2]

virtual EMData * EMAN::Refine3DAlignerQuaternion::align	(	EMData *	this_img,
		EMData *	to_img
	)		const

inlinevirtual

Implements EMAN::Aligner.

Definition at line 1552 of file aligner.h.

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

References align().

◆ align() [2/2]

virtual EMData * EMAN::Refine3DAlignerQuaternion::align	(	EMData *	this_img,
		EMData *	to_img,
		const string &	cmp_name = `"sqeuclidean"`,
		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::Refine3DAlignerQuaternion::get_desc ( ) const

inlinevirtual

Implements EMAN::Aligner.

Definition at line 1562 of file aligner.h.

                        {
                                return "Refines a preliminary 3D alignment using a simplex algorithm. Subpixel precision.";
                        }

◆ get_name()

virtual string EMAN::Refine3DAlignerQuaternion::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 1557 of file aligner.h.

                        {
                                return NAME;
                        }

References NAME.

◆ get_param_types()

virtual TypeDict EMAN::Refine3DAlignerQuaternion::get_param_types ( ) const

inlinevirtual

Implements EMAN::Aligner.

Definition at line 1572 of file aligner.h.

                        {
                                TypeDict d;
                                d.put("xform.align3d", EMObject::TRANSFORM,"The Transform storing the starting guess. If unspecified the identity matrix is used");
                                d.put("stepx", EMObject::FLOAT, "The initial simplex step size in x. Default is 1");
                                d.put("stepy", EMObject::FLOAT, "The initial simplex step size in y. Default is 1");
                                d.put("stepz", EMObject::FLOAT, "The initial simplex step size in z. Default is 1." );
                                d.put("stepn0", EMObject::FLOAT, "The initial simplex step size in the first quaternion vecotr component. Default is 1." );
                                d.put("stepn1", EMObject::FLOAT, "The initial simplex step size in the second quaternion vecotr component. Default is 1." );
                                d.put("stepn2", EMObject::FLOAT, "The initial simplex step size in the third quaternion vecotr component. Default is 1." );
                                d.put("spin_coeff", EMObject::FLOAT,"The multiplier appied to the spin (if it is too small or too large the simplex will not converge).  Default is 10.");
                                d.put("precision", EMObject::FLOAT, "The precision which, if achieved, can stop the iterative refinement before reaching the maximum iterations. Default is 0.01." );
                                d.put("maxiter", EMObject::INT, "The maximum number of iterations that can be performed by the Simplex minimizer. Default is 100.");
                                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.");
                                return d;
                        }

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

◆ NEW()

static Aligner * EMAN::Refine3DAlignerQuaternion::NEW ( )

inlinestatic

Definition at line 1567 of file aligner.h.

                        {
                                return new Refine3DAlignerQuaternion();
                        }

Member Data Documentation

◆ NAME

const string Refine3DAlignerQuaternion::NAME = "refine_3d"

static

Definition at line 1589 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