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EMAN::RotateTranslateAlignerIterative Class Reference

Iterative rotational, translational alignment. More...

#include <aligner.h>

Inheritance diagram for EMAN::RotateTranslateAlignerIterative:

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Collaboration diagram for EMAN::RotateTranslateAlignerIterative:

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List of all members.

Public Member Functions

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_translate_iterative"

Detailed Description

Iterative rotational, translational alignment.

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.

Parameters:
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 393 of file aligner.h.


Member Function Documentation

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

Implements EMAN::Aligner.

Definition at line 399 of file aligner.h.

References align().

00400                 {
00401                         return align(this_img, to_img, "sqeuclidean", Dict());
00402                 }

EMData * RotateTranslateAlignerIterative::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 439 of file aligner.cpp.

References EMAN::EMData::align(), EMAN::EMData::get_attr(), EMAN::EMData::process(), EMAN::EMData::set_attr(), EMAN::Dict::set_default(), and t.

00441 {
00442         int maxiter = params.set_default("maxiter", 3);
00443         
00444         Dict trans_params;
00445         trans_params["intonly"] = 0;
00446         trans_params["maxshift"] = params.set_default("maxshift", -1);
00447         trans_params["useflcf"] = params.set_default("useflcf",0);
00448         trans_params["nozero"] = params.set_default("nozero",false);
00449         
00450         Dict rot_params;
00451         rot_params["r1"] = params.set_default("r1", -1);
00452         rot_params["r2"] = params.set_default("r2", -1);
00453         
00454         Transform t;
00455         EMData * moving_img = this_img;
00456         for(int it = 0; it < maxiter; it++){
00457                 
00458                 // First do a translational alignment
00459                 EMData * trans_align = moving_img->align("translational", to, trans_params, cmp_name, cmp_params);
00460                 Transform * tt = trans_align->get_attr("xform.align2d");
00461                 t = *tt*t;
00462                 delete tt;
00463 
00464                 //now do rotation
00465                 EMData * rottrans_align = trans_align->align("rotational_iterative", to, rot_params, cmp_name, cmp_params);
00466                 Transform * rt = rottrans_align->get_attr("xform.align2d");
00467                 t = *rt*t;
00468                 delete trans_align; trans_align = 0;
00469                 delete rottrans_align; rottrans_align = 0;
00470                 delete rt;
00471                 
00472                 //this minimizes interpolation errors (all images that are futher processed will be interpolated at most twice)
00473                 if(it > 0){delete moving_img;}
00474                 
00475                 moving_img = this_img->process("xform",Dict("transform",&t));  //iterate
00476         }
00477         
00478         //write the total transformation; Avoids interpolation erros    
00479         moving_img->set_attr("xform.align2d", &t);
00480         
00481         return moving_img;
00482 }

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

Implements EMAN::Aligner.

Definition at line 409 of file aligner.h.

00410                 {
00411                         return "Performs rotational alignment and follows this with translational alignment using the iterative method.";
00412                 }

virtual string EMAN::RotateTranslateAlignerIterative::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 404 of file aligner.h.

00405                 {
00406                         return NAME;
00407                 }

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

Implements EMAN::Aligner.

Definition at line 419 of file aligner.h.

References EMAN::TypeDict::put().

00420                 {
00421                         TypeDict d;
00422                         //d.put("usedot", EMObject::INT);
00423                         d.put("maxshift", EMObject::INT, "Maximum translation in pixels");
00424                         d.put("r1", EMObject::INT, "Inner ring, pixels");
00425                         d.put("r2", EMObject::INT, "Outer ring, pixels");
00426                         d.put("maxiter", EMObject::INT, "Maximum number of iterations");
00427                         d.put("nozero", EMObject::INT,"Zero translation not permitted (useful for CCD images)");
00428                         d.put("useflcf", EMObject::INT,"Use Fast Local Correlation Function rather than CCF for translational alignment");
00429                         return d;
00430                 }

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

Definition at line 414 of file aligner.h.

00415                 {
00416                         return new RotateTranslateAlignerIterative();
00417                 }


Member Data Documentation

const string RotateTranslateAlignerIterative::NAME = "rotate_translate_iterative" [static]
 

Definition at line 63 of file aligner.cpp.


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