EMAN::SymAlignProcessor Class Reference

Aligns a particle with the specified symmetry into the standard orientation for that symmetry. More...

#include <aligner.h>

Inheritance diagram for EMAN::SymAlignProcessor:

Collaboration diagram for EMAN::SymAlignProcessor:

Public Member Functions
virtual EMData *	align (EMData *this_img, EMData *to_img, const string &cmp_name="ccc", 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 TypeDict	get_param_types () const
virtual string	get_desc () 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 = "symalign"

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

Detailed Description

Aligns a particle with the specified symmetry into the standard orientation for that symmetry.

Works by searching over a Grid and maximizing the recon variance after symmetrization. NOTE: This function is depricated. Use the SymAlignProcessorQuat procssor instead.

Author

Steve Ludtke and John Flanagan

Date

February 2011

Parameters

sym	A string specifying the symmetry under which to do the alignment

Definition at line 1261 of file aligner.h.

Member Function Documentation

align() [1/2]

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

inlinevirtual

Implements EMAN::Aligner.

Definition at line 1266 of file aligner.h.

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

References align().

align() [2/2]

virtual EMData * EMAN::SymAlignProcessor::align ( EMData *  this_img, EMData *  to_img, const string &  cmp_name = "ccc", 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::SymAlignProcessor::get_desc ( ) const

inlinevirtual

Implements EMAN::Aligner.

Definition at line 1292 of file aligner.h.

                        {
                                return "The image is centered and rotated to the standard orientation for the specified symmetry";
                        }

get_name()

virtual string EMAN::SymAlignProcessor::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 1270 of file aligner.h.

                        {
                                return NAME;
                        }

References NAME.

get_param_types()

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

inlinevirtual

Implements EMAN::Aligner.

Definition at line 1280 of file aligner.h.

                        {
                                TypeDict d;
                                d.put("sym", EMObject::STRING, "The symmetry under which to do the alignment, Default=c1" );
                                d.put("delta", EMObject::FLOAT,"Angle the separates points on the sphere. This is exclusive of the \'n\' paramater. Default is 10");
                                d.put("dphi", EMObject::FLOAT,"The angle increment in the phi direction. Default is 10");
                                d.put("lphi", EMObject::FLOAT,"Lower bound for phi. Default it 0");
                                d.put("uphi", EMObject::FLOAT,"Upper bound for phi. Default it 359.9");
                                d.put("avger", EMObject::STRING, "The sort of averager to use, Default=mean" );
                                return d;
                        }

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

NEW()

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

inlinestatic

Definition at line 1275 of file aligner.h.

                        {
                                return new SymAlignProcessor();
                        }

Member Data Documentation

NAME

const string SymAlignProcessor::NAME = "symalign"

static

Definition at line 1297 of file aligner.h.

Referenced by get_name().

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The documentation for this class was generated from the following files:

• aligner.h
• aligner.cpp