EMAN::RotateTranslateScaleAlignerIterative Class Reference

Iterative rotational, translational alignment with scaling. More...

#include <aligner.h>

Inheritance diagram for EMAN::RotateTranslateScaleAlignerIterative:

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Collaboration diagram for EMAN::RotateTranslateScaleAlignerIterative:

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List of all members.

Public Member Functions

 RotateTranslateScaleAlignerIterative ()
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_scale_iter"

Detailed Description

Iterative rotational, translational alignment with scaling.

Basically, we find the best translation, and move to that pointer then we find the best rotation and rotate to that point. Next we iterate X times. We do this for each scale of the image and return the optimal solution

Parameters:
min Minimum scaling (default: 0.95)
max aximum scaling (default: 1.05)
step Scaling step (default: 0.01)
maxshift Maximum translation in pixels
r1 inner ring
r2 outer ring
maxiter maximum number of alignment iterations
nozero Zero translation not permitted (useful for CCD images)
Author:
John Flanagan
Date:
Oct 2010

Definition at line 572 of file aligner.h.


Constructor & Destructor Documentation

EMAN::RotateTranslateScaleAlignerIterative::RotateTranslateScaleAlignerIterative (  )  [inline]

Definition at line 576 of file aligner.h.

Referenced by NEW().

00576                                                        : ScaleAlignerABS("rotate_translate_iterative")
00577                 {
00578                 }


Member Function Documentation

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

Implements EMAN::Aligner.

Definition at line 583 of file aligner.h.

References align().

00584                 {
00585                         return align(this_img, to_img, "sqeuclidean", Dict());
00586                 }

EMData * RotateTranslateScaleAlignerIterative::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 611 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().

00613 {
00614         
00615         //Basically copy params into rotate_translate
00616         basealigner_params["maxshift"] = params.set_default("maxshift", -1);
00617         basealigner_params["r1"] = params.set_default("r1",-1);
00618         basealigner_params["r2"] = params.set_default("r2",-1);
00619         basealigner_params["maxiter"] = params.set_default("maxiter",3);
00620         basealigner_params["nozero"] = params.set_default("nozero",false);
00621         basealigner_params["useflcf"] = params.set_default("useflcf",0);
00622         
00623         //return the correct results
00624         return align_using_base(this_img, to, cmp_name, cmp_params);
00625         
00626 }

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

Implements EMAN::Aligner.

Definition at line 593 of file aligner.h.

00594                 {
00595                         return "Performs rotational alignment and follows this with translational alignment using the iterative method. Does this for each scale and returns the best";
00596                 }

virtual string EMAN::RotateTranslateScaleAlignerIterative::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 588 of file aligner.h.

References NAME.

00589                 {
00590                         return NAME;
00591                 }

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

Implements EMAN::Aligner.

Definition at line 603 of file aligner.h.

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

00604                 {
00605                         TypeDict d;
00606                         d.put("min", EMObject::FLOAT, "Minimum scaling (default: 0.95)");
00607                         d.put("max", EMObject::FLOAT, "Maximum scaling (default: 1.05)");
00608                         d.put("step", EMObject::FLOAT, "Scaling step (default: 0.01)");
00609                         d.put("maxshift", EMObject::INT, "Maximum translation in pixels");
00610                         d.put("r1", EMObject::INT, "Inner ring, pixels");
00611                         d.put("r2", EMObject::INT, "Outer ring, pixels");
00612                         d.put("maxiter", EMObject::INT, "Maximum number of iterations");
00613                         d.put("nozero", EMObject::INT,"Zero translation not permitted (useful for CCD images)");
00614                         d.put("useflcf", EMObject::INT,"Use Fast Local Correlation Function rather than CCF for translational alignment");
00615                         return d;
00616                 }

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

Definition at line 598 of file aligner.h.

References RotateTranslateScaleAlignerIterative().

00599                 {
00600                         return new RotateTranslateScaleAlignerIterative();
00601                 }


Member Data Documentation

const string RotateTranslateScaleAlignerIterative::NAME = "rotate_trans_scale_iter" [static]

Definition at line 618 of file aligner.h.

Referenced by get_name().


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