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 263 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 269 of file aligner.h.

References align().

00270                 {
00271                         return align(this_img, to_img, "dot", Dict());
00272                 }

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 410 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().

00412 {
00413         int r1 = params.set_default("r1",-1);
00414         int r2 = params.set_default("r2",-1);
00415         //to start lest try the original size image. If needed, we can pad it....
00416         EMData * to_polar = to->unwrap(r1,r2,-1,0,0,true);
00417         EMData * this_img_polar = this_img->unwrap(r1,r2,-1,0,0,true);
00418         int this_img_polar_nx = this_img_polar->get_xsize();
00419         
00420         EMData *cf = this_img_polar->calc_ccfx(to_polar, 0, this_img->get_ysize());
00421         
00422         //take out the garbage
00423         delete to_polar; to_polar = 0;
00424         delete this_img_polar; this_img_polar = 0;
00425         
00426         float *data = cf->get_data();
00427         float peak = 0;
00428         int peak_index = 0;
00429         Util::find_max(data, this_img_polar_nx, &peak, &peak_index);
00430 
00431         delete cf; cf = 0;
00432         float rot_angle = (float) (peak_index * 360.0f / this_img_polar_nx);
00433         
00434         //return the result
00435         //cout << rot_angle << endl;
00436         Transform tmp(Dict("type","2d","alpha",rot_angle));
00437         EMData * rotimg=this_img->process("xform",Dict("transform",(Transform*)&tmp));
00438         rotimg->set_attr("xform.align2d",&tmp);
00439         
00440         return rotimg;
00441         
00442 }

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

Implements EMAN::Aligner.

Definition at line 279 of file aligner.h.

00280                 {
00281                         return "Performs rotational alignment using the SPIDER method";
00282                 }

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 274 of file aligner.h.

References NAME.

00275                 {
00276                         return NAME;
00277                 }

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

Implements EMAN::Aligner.

Definition at line 289 of file aligner.h.

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

00290                 {
00291                         TypeDict d;
00292                         d.put("r1", EMObject::INT, "Inner ring, pixels");
00293                         d.put("r2", EMObject::INT, "Outer ring, pixels");
00294                         return d;
00295                 }

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

Definition at line 284 of file aligner.h.

00285                 {
00286                         return new RotationalAlignerIterative();
00287                 }


Member Data Documentation

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

Definition at line 297 of file aligner.h.

Referenced by get_name().


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