EMAN2
Public Member Functions | Static Public Member Functions | Static Public Attributes
EMAN::RotateTranslateScaleAligner Class Reference

rotational, translational, scaling alignment More...

#include <aligner.h>

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List of all members.

Public Member Functions

 RotateTranslateScaleAligner ()
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.
virtual EMDataalign (EMData *this_img, EMData *to_img) const
virtual string get_name () const
 Get the Aligner's name.
virtual string get_desc () const
virtual TypeDict get_param_types () const

Static Public Member Functions

static AlignerNEW ()

Static Public Attributes

static const string NAME = "rotate_translate_scale"

Detailed Description

rotational, translational, scaling alignment

Parameters:
minMinimum scaling (default: 0.95)
maxaximum scaling (default: 1.05)
stepScaling step (default: 0.01)
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 463 of file aligner.h.


Constructor & Destructor Documentation

EMAN::RotateTranslateScaleAligner::RotateTranslateScaleAligner ( ) [inline]

Definition at line 468 of file aligner.h.

Referenced by NEW().

                                              : ScaleAlignerABS("rotate_translate")
                {
                }

Member Function Documentation

EMData * RotateTranslateScaleAligner::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.

Definition at line 778 of file aligner.cpp.

References EMAN::ScaleAlignerABS::align_using_base(), EMAN::ScaleAlignerABS::basealigner_params, EMAN::Aligner::params, and EMAN::Dict::set_default().

Referenced by align().

{
        
        //Basically copy params into rotate_translate
        basealigner_params["maxshift"] = params.set_default("maxshift", -1);
        basealigner_params["rfp_mode"] = params.set_default("rfp_mode",2);
        basealigner_params["useflcf"] = params.set_default("useflcf",0);
        basealigner_params["zscore"] = params.set_default("zscore",0);
        
        //return the correct results
        return align_using_base(this_img, to, cmp_name, cmp_params);
        
}
virtual EMData* EMAN::RotateTranslateScaleAligner::align ( EMData this_img,
EMData to_img 
) const [inline, virtual]

Implements EMAN::Aligner.

Definition at line 475 of file aligner.h.

References align().

                {
                        return align(this_img, to_img, "sqeuclidean", Dict());
                }
virtual string EMAN::RotateTranslateScaleAligner::get_desc ( ) const [inline, virtual]

Implements EMAN::Aligner.

Definition at line 485 of file aligner.h.

                {
                        return "Performs rotational alignment and follows this with translational and then scaling alignment.";
                }
virtual string EMAN::RotateTranslateScaleAligner::get_name ( ) const [inline, virtual]

Get the Aligner's name.

Each Aligner is identified by a unique name.

Returns:
The Aligner's name.

Implements EMAN::Aligner.

Definition at line 480 of file aligner.h.

References NAME.

                {
                        return NAME;
                }
virtual TypeDict EMAN::RotateTranslateScaleAligner::get_param_types ( ) const [inline, virtual]

Implements EMAN::Aligner.

Definition at line 495 of file aligner.h.

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

                {
                        TypeDict d;
                        d.put("min", EMObject::FLOAT, "Minimum scaling (default: 0.95)");
                        d.put("max", EMObject::FLOAT, "Maximum scaling (default: 1.05)");
                        d.put("step", EMObject::FLOAT, "Scaling step (default: 0.01)");
                        d.put("maxshift", EMObject::INT, "Maximum translation in pixels");
                        d.put("nozero", EMObject::INT,"Zero translation not permitted (useful for CCD images)");
                        d.put("rfp_mode", EMObject::INT,"Either 0,1 or 2. A temporary flag for testing the rotational foot print");
                        d.put("useflcf", EMObject::INT,"Use Fast Local Correlation Function rather than CCF for translational alignment");
                        d.put("zscore", EMObject::INT,"Either 0 or 1. This option is passed directly to the rotational aligner (default=false)");
                        return d;
                }
static Aligner* EMAN::RotateTranslateScaleAligner::NEW ( ) [inline, static]

Definition at line 490 of file aligner.h.

References RotateTranslateScaleAligner().

                {
                        return new RotateTranslateScaleAligner();
                }

Member Data Documentation

const string RotateTranslateScaleAligner::NAME = "rotate_translate_scale" [static]

Definition at line 509 of file aligner.h.

Referenced by get_name().


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