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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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List of all members.

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.
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

AlignerNEW ()

Static Public Attributes

const string NAME = "rotate_trans_flip_scale"

Detailed Description

rotational, translational, flip, scaling alignment

Parameters:
min Minimum scaling (default: 0.95)
max aximum scaling (default: 1.05)
step Scaling step (default: 0.01)
flip who knows what this means?
maxshift Maximum translation in pixels
nozero Zero translation not permitted (useful for CCD images)
rfp_mode Either 0,1 or 2. A temporary flag for testing the rotational foot print
Author:
John Flanagan
Date:
March 2012

Definition at line 867 of file aligner.h.


Constructor & Destructor Documentation

EMAN::RotateTranslateFlipScaleAligner::RotateTranslateFlipScaleAligner  )  [inline]
 

Definition at line 871 of file aligner.h.

00871                                                   : ScaleAlignerABS("rotate_translate_flip")
00872                 {
00873                 }


Member Function Documentation

virtual EMData* EMAN::RotateTranslateFlipScaleAligner::align EMData this_img,
EMData to_img
const [inline, virtual]
 

Implements EMAN::Aligner.

Definition at line 878 of file aligner.h.

References align().

00879                 {
00880                         return align(this_img, to_img, "sqeuclidean", Dict());
00881                 }

EMData * 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_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.

Definition at line 846 of file aligner.cpp.

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

00848 {
00849         
00850         //Basically copy params into rotate_translate
00851         basealigner_params["flip"] = params.set_default("flip", (EMData *) 0);
00852         basealigner_params["maxshift"] = params.set_default("maxshift", -1);
00853         basealigner_params["rfp_mode"] = params.set_default("rfp_mode",2);
00854         basealigner_params["useflcf"] = params.set_default("useflcf",0);
00855         basealigner_params["zscore"] = params.set_default("zscore",0);
00856         
00857         //return the correct results
00858         return align_using_base(this_img, to, cmp_name, cmp_params);
00859         
00860 }

virtual string EMAN::RotateTranslateFlipScaleAligner::get_desc  )  const [inline, virtual]
 

Implements EMAN::Aligner.

Definition at line 888 of file aligner.h.

00889                 {
00890                         return "Performs rotational alignment and follows this with translational and then scaling alignment.";
00891                 }

virtual string EMAN::RotateTranslateFlipScaleAligner::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 883 of file aligner.h.

00884                 {
00885                         return NAME;
00886                 }

virtual TypeDict EMAN::RotateTranslateFlipScaleAligner::get_param_types  )  const [inline, virtual]
 

Implements EMAN::Aligner.

Definition at line 898 of file aligner.h.

References EMAN::TypeDict::put().

00899                 {
00900                         TypeDict d;
00901                         d.put("min", EMObject::FLOAT, "Minimum scaling (default: 0.95)");
00902                         d.put("max", EMObject::FLOAT, "Maximum scaling (default: 1.05)");
00903                         d.put("step", EMObject::FLOAT, "Scaling step (default: 0.01)");
00904                         d.put("flip", EMObject::EMDATA);
00905                         d.put("maxshift", EMObject::INT, "Maximum translation in pixels");
00906                         d.put("nozero", EMObject::INT,"Zero translation not permitted (useful for CCD images)");
00907                         d.put("rfp_mode", EMObject::INT,"Either 0,1 or 2. A temporary flag for testing the rotational foot print");
00908                         d.put("useflcf", EMObject::INT,"Use Fast Local Correlation Function rather than CCF for translational alignment");
00909                         d.put("zscore", EMObject::INT,"Either 0 or 1. This option is passed directly to the rotational aligner (default=false)");
00910                         return d;
00911                 }

Aligner* EMAN::RotateTranslateFlipScaleAligner::NEW  )  [inline, static]
 

Definition at line 893 of file aligner.h.

00894                 {
00895                         return new RotateTranslateFlipScaleAligner();
00896                 }


Member Data Documentation

const string RotateTranslateFlipScaleAligner::NAME = "rotate_trans_flip_scale" [static]
 

Definition at line 72 of file aligner.cpp.


The documentation for this class was generated from the following files:
Generated on Tue Jun 11 13:41:49 2013 for EMAN2 by  doxygen 1.3.9.1