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

static AlignerNEW ()

Static Public Attributes

static 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 862 of file aligner.h.


Constructor & Destructor Documentation

EMAN::RotateTranslateFlipScaleAligner::RotateTranslateFlipScaleAligner (  )  [inline]

Definition at line 866 of file aligner.h.

Referenced by NEW().

00866                                                   : ScaleAlignerABS("rotate_translate_flip")
00867                 {
00868                 }


Member Function Documentation

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

Implements EMAN::Aligner.

Definition at line 873 of file aligner.h.

References align().

00874                 {
00875                         return align(this_img, to_img, "sqeuclidean", Dict());
00876                 }

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 827 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().

00829 {
00830         
00831         //Basically copy params into rotate_translate
00832         basealigner_params["flip"] = params.set_default("flip", (EMData *) 0);
00833         basealigner_params["maxshift"] = params.set_default("maxshift", -1);
00834         basealigner_params["rfp_mode"] = params.set_default("rfp_mode",0);
00835         basealigner_params["useflcf"] = params.set_default("useflcf",0);
00836         
00837         //return the correct results
00838         return align_using_base(this_img, to, cmp_name, cmp_params);
00839         
00840 }

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

Implements EMAN::Aligner.

Definition at line 883 of file aligner.h.

00884                 {
00885                         return "Performs rotational alignment and follows this with translational and then scaling alignment.";
00886                 }

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 878 of file aligner.h.

References NAME.

00879                 {
00880                         return NAME;
00881                 }

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

Implements EMAN::Aligner.

Definition at line 893 of file aligner.h.

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

00894                 {
00895                         TypeDict d;
00896                         d.put("min", EMObject::FLOAT, "Minimum scaling (default: 0.95)");
00897                         d.put("max", EMObject::FLOAT, "Maximum scaling (default: 1.05)");
00898                         d.put("step", EMObject::FLOAT, "Scaling step (default: 0.01)");
00899                         d.put("flip", EMObject::EMDATA);
00900                         d.put("maxshift", EMObject::INT, "Maximum translation in pixels");
00901                         d.put("nozero", EMObject::INT,"Zero translation not permitted (useful for CCD images)");
00902                         d.put("rfp_mode", EMObject::INT,"Either 0,1 or 2. A temporary flag for testing the rotational foot print");
00903                         d.put("useflcf", EMObject::INT,"Use Fast Local Correlation Function rather than CCF for translational alignment");
00904                         return d;
00905                 }

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

Definition at line 888 of file aligner.h.

References RotateTranslateFlipScaleAligner().

00889                 {
00890                         return new RotateTranslateFlipScaleAligner();
00891                 }


Member Data Documentation

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

Definition at line 907 of file aligner.h.

Referenced by get_name().


The documentation for this class was generated from the following files:
Generated on Thu May 3 10:08:45 2012 for EMAN2 by  doxygen 1.4.7