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EMAN::RotationalAlignerIterative Class Reference

rotational alignment using the iterative method (in this case we only do one iteration b/c we are not doing a translation. More...

#include <aligner.h>

Inheritance diagram for EMAN::RotationalAlignerIterative:

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Collaboration diagram for EMAN::RotationalAlignerIterative:

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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 = "rotational_iterative"

Detailed Description

rotational alignment using the iterative method (in this case we only do one iteration b/c we are not doing a translation.

The advantage of this over the 'regular' rotational alinger is that this is done in real space and does not use invariants.

Parameters:
r1 inner ring
r2 outer ring
Author:
John Flanagan
Date:
Oct 2010

Definition at line 332 of file aligner.h.


Member Function Documentation

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

Implements EMAN::Aligner.

Definition at line 338 of file aligner.h.

References align().

00339                 {
00340                         return align(this_img, to_img, "dot", Dict());
00341                 }

EMData * RotationalAlignerIterative::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 549 of file aligner.cpp.

References EMAN::EMData::calc_ccfx(), data, EMAN::Util::find_max(), EMAN::EMData::get_data(), EMAN::EMData::get_xsize(), EMAN::EMData::get_ysize(), EMAN::EMData::process(), EMAN::EMData::set_attr(), EMAN::Dict::set_default(), and EMAN::EMData::unwrap().

00551 {
00552         int r1 = params.set_default("r1",-1);
00553         int r2 = params.set_default("r2",-1);
00554         //to start lest try the original size image. If needed, we can pad it....
00555         EMData * to_polar = to->unwrap(r1,r2,-1,0,0,true);
00556         EMData * this_img_polar = this_img->unwrap(r1,r2,-1,0,0,true);
00557         int this_img_polar_nx = this_img_polar->get_xsize();
00558         
00559         EMData * cf = this_img_polar->calc_ccfx(to_polar, 0, this_img->get_ysize());
00560         
00561         //take out the garbage
00562         delete to_polar; to_polar = 0;
00563         delete this_img_polar; this_img_polar = 0;
00564         
00565         float * data = cf->get_data();
00566         float peak = 0;
00567         int peak_index = 0;
00568         Util::find_max(data, this_img_polar_nx, &peak, &peak_index);
00569 
00570         delete cf; cf = 0;
00571         float rot_angle = (float) (peak_index * 360.0f / this_img_polar_nx);
00572         
00573         //return the result
00574         //cout << rot_angle << endl;
00575         Transform tmp(Dict("type","2d","alpha",rot_angle));
00576         EMData * rotimg=this_img->process("xform",Dict("transform",(Transform*)&tmp));
00577         rotimg->set_attr("xform.align2d",&tmp);
00578         
00579         return rotimg;
00580         
00581 }

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

Implements EMAN::Aligner.

Definition at line 348 of file aligner.h.

00349                 {
00350                         return "Performs rotational alignment using the SPIDER method";
00351                 }

virtual string EMAN::RotationalAlignerIterative::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 343 of file aligner.h.

00344                 {
00345                         return NAME;
00346                 }

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

Implements EMAN::Aligner.

Definition at line 358 of file aligner.h.

References EMAN::TypeDict::put().

00359                 {
00360                         TypeDict d;
00361                         d.put("r1", EMObject::INT, "Inner ring, pixels");
00362                         d.put("r2", EMObject::INT, "Outer ring, pixels");
00363                         return d;
00364                 }

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

Definition at line 353 of file aligner.h.

00354                 {
00355                         return new RotationalAlignerIterative();
00356                 }


Member Data Documentation

const string RotationalAlignerIterative::NAME = "rotational_iterative" [static]
 

Definition at line 61 of file aligner.cpp.


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