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

static AlignerNEW ()

Static Public Attributes

static 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 330 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 336 of file aligner.h.

References align().

00337                 {
00338                         return align(this_img, to_img, "dot", Dict());
00339                 }

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 532 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::Aligner::params, EMAN::EMData::process(), EMAN::EMData::set_attr(), EMAN::Dict::set_default(), and EMAN::EMData::unwrap().

Referenced by align().

00534 {
00535         int r1 = params.set_default("r1",-1);
00536         int r2 = params.set_default("r2",-1);
00537         //to start lest try the original size image. If needed, we can pad it....
00538         EMData * to_polar = to->unwrap(r1,r2,-1,0,0,true);
00539         EMData * this_img_polar = this_img->unwrap(r1,r2,-1,0,0,true);
00540         int this_img_polar_nx = this_img_polar->get_xsize();
00541         
00542         EMData * cf = this_img_polar->calc_ccfx(to_polar, 0, this_img->get_ysize());
00543         
00544         //take out the garbage
00545         delete to_polar; to_polar = 0;
00546         delete this_img_polar; this_img_polar = 0;
00547         
00548         float * data = cf->get_data();
00549         float peak = 0;
00550         int peak_index = 0;
00551         Util::find_max(data, this_img_polar_nx, &peak, &peak_index);
00552 
00553         delete cf; cf = 0;
00554         float rot_angle = (float) (peak_index * 360.0f / this_img_polar_nx);
00555         
00556         //return the result
00557         //cout << rot_angle << endl;
00558         Transform tmp(Dict("type","2d","alpha",rot_angle));
00559         EMData * rotimg=this_img->process("xform",Dict("transform",(Transform*)&tmp));
00560         rotimg->set_attr("xform.align2d",&tmp);
00561         
00562         return rotimg;
00563         
00564 }

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

Implements EMAN::Aligner.

Definition at line 346 of file aligner.h.

00347                 {
00348                         return "Performs rotational alignment using the SPIDER method";
00349                 }

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 341 of file aligner.h.

References NAME.

00342                 {
00343                         return NAME;
00344                 }

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

Implements EMAN::Aligner.

Definition at line 356 of file aligner.h.

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

00357                 {
00358                         TypeDict d;
00359                         d.put("r1", EMObject::INT, "Inner ring, pixels");
00360                         d.put("r2", EMObject::INT, "Outer ring, pixels");
00361                         return d;
00362                 }

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

Definition at line 351 of file aligner.h.

00352                 {
00353                         return new RotationalAlignerIterative();
00354                 }


Member Data Documentation

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

Definition at line 364 of file aligner.h.

Referenced by get_name().


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