EMAN2
Public Member Functions | Static Public Member Functions | Static Public Attributes | List of all members
EMAN::RotateTranslateFlipAligner Class Reference

rotational, translational and flip alignment More...

#include <aligner.h>

Inheritance diagram for EMAN::RotateTranslateFlipAligner:
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Collaboration diagram for EMAN::RotateTranslateFlipAligner:
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Public Member Functions

virtual EMDataalign (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 EMDataalign (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< Dictxform_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 AlignerNEW ()
 
static TypeDict static_get_param_types ()
 

Static Public Attributes

static const string NAME = "rotate_translate_flip"
 

Additional Inherited Members

- Protected Attributes inherited from EMAN::Aligner
Dict params
 

Detailed Description

rotational, translational and flip alignment

Parameters
flip
usedot
maxshiftMaximum translation in pixels
rfp_modeEither 0,1 or 2. A temporary flag for testing the rotational foot print

Definition at line 900 of file aligner.h.

Member Function Documentation

◆ align() [1/2]

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

Implements EMAN::Aligner.

Definition at line 905 of file aligner.h.

906 {
907 return align(this_img, to_img, "sqeuclidean", Dict());
908 }
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.

References align().

◆ align() [2/2]

virtual EMData * EMAN::RotateTranslateFlipAligner::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_imgThe image to be compared.
to_img'this_img" is aligned with 'to_img'.
cmp_nameThe comparison method to compare the two images.
cmp_paramsThe parameter dictionary for comparison method.
Returns
The aligned image.

Implements EMAN::Aligner.

Referenced by align().

◆ get_desc()

virtual string EMAN::RotateTranslateFlipAligner::get_desc ( ) const
inlinevirtual

Implements EMAN::Aligner.

Definition at line 915 of file aligner.h.

916 {
917 return " Does two 'rotate_translate' alignments, one to accommodate for possible handedness change. Decided which alignment is better using a comparitor and returns the aligned image as the solution";
918 }

◆ get_name()

virtual string EMAN::RotateTranslateFlipAligner::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 910 of file aligner.h.

911 {
912 return NAME;
913 }
static const string NAME
Definition: aligner.h:944

References NAME.

◆ get_param_types()

virtual TypeDict EMAN::RotateTranslateFlipAligner::get_param_types ( ) const
inlinevirtual

Implements EMAN::Aligner.

Definition at line 925 of file aligner.h.

926 {
927 return static_get_param_types();
928 }
static TypeDict static_get_param_types()
Definition: aligner.h:930

References static_get_param_types().

◆ NEW()

static Aligner * EMAN::RotateTranslateFlipAligner::NEW ( )
inlinestatic

Definition at line 920 of file aligner.h.

921 {
922 return new RotateTranslateFlipAligner();
923 }

◆ static_get_param_types()

static TypeDict EMAN::RotateTranslateFlipAligner::static_get_param_types ( )
inlinestatic

Definition at line 930 of file aligner.h.

930 {
931 TypeDict d;
932
933 d.put("flip", EMObject::EMDATA);
934 d.put("usedot", EMObject::INT);
935 d.put("maxshift", EMObject::INT, "Maximum translation in pixels");
936 d.put("rfp_mode", EMObject::INT,"Either 0,1 or 2. A temporary flag for testing the rotational foot print");
937 d.put("usebispec", EMObject::INT,"Uses rotate_translate_bispec for subalignments and ignore rfp_mode.");
938 d.put("useharmonic", EMObject::INT,"Uses rotate_translate_bispec in harmonic mode for alignments and ignores rfp_mode.");
939 d.put("useflcf", EMObject::INT,"Use Fast Local Correlation Function rather than CCF for translational alignment");
940 d.put("zscore", EMObject::INT,"Either 0 or 1. This option is passed directly to the rotational aligner (default=false)");
941 return d;
942 }

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

Referenced by get_param_types().

Member Data Documentation

◆ NAME

const string RotateTranslateFlipAligner::NAME = "rotate_translate_flip"
static

Definition at line 944 of file aligner.h.

Referenced by get_name().


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