Aligner class defines image alignment method. More...

#include <aligner.h>

Inheritance diagram for EMAN::Aligner:

[legend]

Collaboration diagram for EMAN::Aligner:

Public Member Functions
virtual	~Aligner ()

virtual EMData *	align (EMData this_img, EMData to_img) const =0

virtual EMData *	align (EMData this_img, EMData to_img, const string &cmp_name, const Dict &cmp_params) const =0
	To align 'this_img' with another image passed in through its parameters. More...

virtual string	get_name () const =0
	Get the Aligner's name. More...

virtual string	get_desc () const =0

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 TypeDict	get_param_types () const =0

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...

Protected Attributes
Dict	params

Detailed Description

Aligner class defines image alignment method.

It aligns 2 images based on a user-given comparison method. Aligner class is the base class for all aligners. Each specific Aligner class has a unique name. This name is used to create a new Aligner instance or call an Aligner.

All Aligner classes in EMAN are managed by a Factory
pattern. So each Aligner class must define:
  - a unique name to idenfity itself in the factory.
  - a static method to register itself in the factory.

Typical usage of Aligners:

How to get all the Aligner types
vector<string> all_aligners = Factory<Aligner>::get_list();

EMAN::Factory::get_list
static vector< string > get_list()
Definition: emobject.h:837
How to use an Aligner
EMData *image1 = ...;

EMData *image2 = ...;

image1->align("ALIGNER_NAME", image2);
How to define a new Aligner class
A new XYZAligner class should implement the following functions: (Please replace 'XYZ' with your own class name).
EMData *align(EMData * this_img, EMData * to_img, string cmp_name = "") const;

TypeDict get_param_types() const;

string get_name() const { return "XYZ"; }

static Aligner* NEW() { return new XYZAligner(); }

EMAN::Aligner::align
virtual EMData * align(EMData *this_img, EMData *to_img) const =0

EMAN::Aligner::get_param_types
virtual TypeDict get_param_types() const =0

EMAN::Aligner::get_name
virtual string get_name() const =0
Get the Aligner's name.

Definition at line 80 of file aligner.h.

Constructor & Destructor Documentation

◆ ~Aligner()

virtual EMAN::Aligner::~Aligner ( )

inlinevirtual

Definition at line 83 of file aligner.h.

84 {

85 }

Member Function Documentation

◆ align() [1/2]

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

pure virtual

◆ align() [2/2]

virtual EMData * EMAN::Aligner::align	(	EMData *	this_img,
		EMData *	to_img,
		const string &	cmp_name,
		const Dict &	cmp_params
	)		const

pure 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.

◆ get_desc()

virtual string EMAN::Aligner::get_desc ( ) const

pure virtual

◆ get_name()

virtual string EMAN::Aligner::get_name ( ) const

pure virtual

Get the Aligner's name.

Each Aligner is identified by a unique name.

Returns: The Aligner's name.

◆ get_param_types()

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

pure virtual

◆ get_params()

virtual Dict EMAN::Aligner::get_params ( ) const

inlinevirtual

Get the Aligner parameters in a key/value dictionary.

Returns: A key/value pair dictionary containing the parameters.

Definition at line 112 of file aligner.h.

                {
                        return params;
                }

References params.

Referenced by EMAN::RT2Dto3DTreeAligner::xform_align_nbest(), EMAN::RT3DTreeAligner::xform_align_nbest(), and EMAN::RT3DLocalTreeAligner::xform_align_nbest().

◆ set_params()

virtual void EMAN::Aligner::set_params ( const Dict & new_params )

inlinevirtual

Set the Aligner parameters using a key/value dictionary.

Parameters

new_params A dictionary containing the new parameters.

Definition at line 120 of file aligner.h.

                {
                        params = new_params;
                }

References params.

◆ xform_align_nbest()

vector< Dict > Aligner::xform_align_nbest	(	EMData *	this_img,
		EMData *	to_img,
		const unsigned int	nsoln,
		const string &	cmp_name,
		const Dict &	cmp_params
	)		const

virtual

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.

Return value is an ordered vector of Dicts of length nsoln. The data with idx 0 has the best solution in it. The Dicts in the vector have two keys, "score" (which is a floating point score, probably correlation score), and "xform.align3d", which is a Transform containing the alignment parameters

Parameters

this_img	the image that will be aligned (transformed) and compared to to_img as part of the process of finding the best alignment
to_img	the image that will stay still as this_img is transformed and compared to it
nsoln	the number of solutions you want to receive in the return vector.
cmp_name	the name of a comparator - may be unused
cmp_params	the params of the comparator - may be unused

Returns: an ordered vector of Dicts of length nsoln. The Dicts in the vector have keys "score" (i.e. correlation score) and "xform.align3d" (Transform containing the alignment)

Reimplemented in EMAN::RT3DGridAligner, EMAN::RT3DSphereAligner, EMAN::RT2DTreeAligner, EMAN::RT2Dto3DTreeAligner, EMAN::RT3DTreeAligner, EMAN::RT3DLocalTreeAligner, and EMAN::RT3DSymmetryAligner.

Definition at line 135 of file aligner.cpp.

{
        vector<Dict> solns;
        return solns;
}

Member Data Documentation

◆ params

Dict EMAN::Aligner::params

mutableprotected

Definition at line 147 of file aligner.h.

Referenced by EMAN::XYZAligner::align(), EMAN::ScaleAlignerABS::align_using_base(), get_params(), set_params(), EMAN::RT3DLocalTreeAligner::testort(), EMAN::RT2Dto3DTreeAligner::testort(), EMAN::RT3DTreeAligner::testort(), EMAN::RT3DGridAligner::xform_align_nbest(), EMAN::RT3DSphereAligner::xform_align_nbest(), EMAN::RT2DTreeAligner::xform_align_nbest(), EMAN::RT2Dto3DTreeAligner::xform_align_nbest(), EMAN::RT3DTreeAligner::xform_align_nbest(), EMAN::RT3DLocalTreeAligner::xform_align_nbest(), and EMAN::RT3DSymmetryAligner::xform_align_nbest().

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

Public Member Functions

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

◆ ~Aligner()

Member Function Documentation

◆ align() [1/2]

◆ align() [2/2]

◆ get_desc()

◆ get_name()

◆ get_param_types()

◆ get_params()

◆ set_params()

◆ xform_align_nbest()

Member Data Documentation

◆ params