Refine alignment. More...

#include <aligner.h>

Inheritance diagram for EMAN::Refine3DAlignerGrid:

Collaboration diagram for EMAN::Refine3DAlignerGrid:

[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_grid"

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

Detailed Description

Refine alignment.

Refines a preliminary 3D alignment using a sampling grid. This is a port from tomohunter, but the az sampling scheme is altered cuch that the points on the sphere are equidistant (Improves speed several hundered times). The distance between the points on the sphere is 'delta' and the range(distance from the pole, 0,0,0 position) is given as 'range'. IN general this refinement scheme is a bit slower than the Quaternion Simplex aligner, but perfroms better in the presence of noise(according to current dogma).

Parameters

xform.align3d	The Transform from the previous course alignment. If unspecified the identity matrix is used
delta	The angluar distance bewteen points on the spehere used in the grid
range	The size of the grid. Measured in angluar distance from the north pole
dotrans	Do a translational search
search	The maximum length of the detectable translational shift - if you supply this parameter you can not supply the maxshiftx, maxshifty or maxshiftz parameters. Each approach is mutually exclusive
searchx	The maximum length of the detectable translational shift in the x direction- if you supply this parameter you can not supply the maxshift parameters
searchy	The maximum length of the detectable translational shift in the y direction- if you supply this parameter you can not supply the maxshift parameters
searchz	The maximum length of the detectable translational shift in the z direction- if you supply this parameter you can not supply the maxshift parameters
verbose	Turn this on to have useful information printed to standard out

Author: John Flanagan

Date: Mar 2011

Definition at line 1481 of file aligner.h.

Member Function Documentation

◆ align() [1/2]

virtual EMData * EMAN::Refine3DAlignerGrid::align	(	EMData *	this_img,
		EMData *	to_img
	)		const

inlinevirtual

Implements EMAN::Aligner.

Definition at line 1487 of file aligner.h.

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

References align().

◆ align() [2/2]

virtual EMData * EMAN::Refine3DAlignerGrid::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::Refine3DAlignerGrid::get_desc ( ) const

inlinevirtual

Implements EMAN::Aligner.

Definition at line 1497 of file aligner.h.

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

◆ get_name()

virtual string EMAN::Refine3DAlignerGrid::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 1492 of file aligner.h.

                        {
                                return NAME;
                        }

References NAME.

◆ get_param_types()

virtual TypeDict EMAN::Refine3DAlignerGrid::get_param_types ( ) const

inlinevirtual

Implements EMAN::Aligner.

Definition at line 1507 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("delta", EMObject::FLOAT, "The angular step size. Default is 1." );
                                d.put("range", EMObject::FLOAT, "The angular range size. Default is 10." );
                                d.put("dotrans", EMObject::BOOL,"Do a translational search. Default is True(1)");
                                d.put("search", EMObject::INT,"The maximum length of the detectable translational shift - if you supply this parameter you can not supply the maxshiftx, maxshifty or maxshiftz parameters. Each approach is mutually exclusive.");
                                d.put("searchx", EMObject::INT,"The maximum length of the detectable translational shift in the x direction- if you supply this parameter you can not supply the maxshift parameters. Default is 3.");
                                d.put("searchy", EMObject::INT,"The maximum length of the detectable translational shift in the y direction- if you supply this parameter you can not supply the maxshift parameters. Default is 3.");
                                d.put("searchz", EMObject::INT,"The maximum length of the detectable translational shift in the z direction- if you supply this parameter you can not supply the maxshift parameters. Default is 3");
                                d.put("verbose", EMObject::BOOL,"Turn this on to have useful information printed to standard out.");
                                return d;
                        }

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

◆ NEW()

static Aligner * EMAN::Refine3DAlignerGrid::NEW ( )

inlinestatic

Definition at line 1502 of file aligner.h.

                        {
                                return new Refine3DAlignerGrid();
                        }

Member Data Documentation

◆ NAME

const string Refine3DAlignerGrid::NAME = "refine_3d_grid"

static

Definition at line 1522 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