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

rotational, translational, flip, scaling alignment More...

#include <aligner.h>

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

 RotateTranslateFlipScaleAligner ()
 
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::ScaleAlignerABS
 ScaleAlignerABS (const string &ba)
 Constructor to initialize the basealigner string. More...
 
EMDataalign_using_base (EMData *this_img, EMData *to_img, const string &cmp_name="dot", const Dict &cmp_params=Dict()) const
 implmentation of the scale alignment using the base aligner set in set_base_aligner More...
 
- 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 Public Attributes

static const string NAME = "rotate_trans_flip_scale"
 

Additional Inherited Members

- Protected Attributes inherited from EMAN::ScaleAlignerABS
const string basealigner
 
Dict basealigner_params
 
- Protected Attributes inherited from EMAN::Aligner
Dict params
 

Detailed Description

rotational, translational, flip, scaling alignment

Parameters
minMinimum scaling (default: 0.95)
maxaximum scaling (default: 1.05)
stepScaling step (default: 0.01)
flipwho knows what this means?
maxshiftMaximum translation in pixels
nozeroZero translation not permitted (useful for CCD images)
rfp_modeEither 0,1 or 2. A temporary flag for testing the rotational foot print
Author
John Flanagan
Date
March 2012

Definition at line 958 of file aligner.h.

Constructor & Destructor Documentation

◆ RotateTranslateFlipScaleAligner()

EMAN::RotateTranslateFlipScaleAligner::RotateTranslateFlipScaleAligner ( )
inline

Definition at line 962 of file aligner.h.

962 : ScaleAlignerABS("rotate_translate_flip")
963 {
964 }
ScaleAlignerABS(const string &ba)
Constructor to initialize the basealigner string.
Definition: aligner.h:170

Referenced by NEW().

Member Function Documentation

◆ align() [1/2]

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

Implements EMAN::Aligner.

Definition at line 969 of file aligner.h.

970 {
971 return align(this_img, to_img, "sqeuclidean", Dict());
972 }
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::RotateTranslateFlipScaleAligner::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::RotateTranslateFlipScaleAligner::get_desc ( ) const
inlinevirtual

Implements EMAN::Aligner.

Definition at line 979 of file aligner.h.

980 {
981 return "Performs rotational alignment and follows this with translational and then scaling alignment.";
982 }

◆ get_name()

virtual string EMAN::RotateTranslateFlipScaleAligner::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 974 of file aligner.h.

975 {
976 return NAME;
977 }

References NAME.

◆ get_param_types()

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

Implements EMAN::Aligner.

Definition at line 989 of file aligner.h.

990 {
991 TypeDict d;
992 d.put("min", EMObject::FLOAT, "Minimum scaling (default: 0.95)");
993 d.put("max", EMObject::FLOAT, "Maximum scaling (default: 1.05)");
994 d.put("step", EMObject::FLOAT, "Scaling step (default: 0.01)");
995 d.put("flip", EMObject::EMDATA);
996 d.put("maxshift", EMObject::INT, "Maximum translation in pixels");
997 d.put("nozero", EMObject::INT,"Zero translation not permitted (useful for CCD images)");
998 d.put("rfp_mode", EMObject::INT,"Either 0,1 or 2. A temporary flag for testing the rotational foot print");
999 d.put("useflcf", EMObject::INT,"Use Fast Local Correlation Function rather than CCF for translational alignment");
1000 d.put("zscore", EMObject::INT,"Either 0 or 1. This option is passed directly to the rotational aligner (default=false)");
1001 return d;
1002 }

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

◆ NEW()

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

Definition at line 984 of file aligner.h.

985 {
987 }

References RotateTranslateFlipScaleAligner().

Member Data Documentation

◆ NAME

const string RotateTranslateFlipScaleAligner::NAME = "rotate_trans_flip_scale"
static

Definition at line 1004 of file aligner.h.

Referenced by get_name().


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