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EMAN::RotatePrecenterAligner Class Reference

rotational alignment assuming centers are correct More...

#include <aligner.h>

Inheritance diagram for EMAN::RotatePrecenterAligner:

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Collaboration diagram for EMAN::RotatePrecenterAligner:

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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_precenter"

Detailed Description

rotational alignment assuming centers are correct

Definition at line 371 of file aligner.h.


Member Function Documentation

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

Implements EMAN::Aligner.

Definition at line 377 of file aligner.h.

References align().

00378                 {
00379                         return align(this_img, to_img, "dot", Dict());
00380                 }

EMData * RotatePrecenterAligner::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 496 of file aligner.cpp.

References EMAN::Util::calc_best_fft_size(), EMAN::EMData::calc_ccfx(), data, EMAN::Util::find_max(), EMAN::EMData::get_data(), EMAN::EMData::get_ysize(), ny, EMAN::EMData::process(), EMAN::EMData::set_attr(), EMAN::Transform::set_rotation(), and EMAN::EMData::unwrap().

00498 {
00499         if (!to) {
00500                 return 0;
00501         }
00502 
00503         int ny = this_img->get_ysize();
00504         int size = Util::calc_best_fft_size((int) (M_PI * ny * 1.5));
00505         EMData *e1 = this_img->unwrap(4, ny * 7 / 16, size, 0, 0, 1);
00506         EMData *e2 = to->unwrap(4, ny * 7 / 16, size, 0, 0, 1);
00507         EMData *cf = e1->calc_ccfx(e2, 0, ny);
00508 
00509         float *data = cf->get_data();
00510 
00511         float peak = 0;
00512         int peak_index = 0;
00513         Util::find_max(data, size, &peak, &peak_index);
00514         float a = (float) ((1.0f - 1.0f * peak_index / size) * 180. * 2);
00515 
00516         Transform rot;
00517         rot.set_rotation(Dict("type","2d","alpha",(float)(a*180./M_PI)));
00518         EMData* rslt = this_img->process("xform",Dict("transform",&rot));
00519         rslt->set_attr("xform.align2d",&rot);
00520 //
00521 //      Transform* t = get_set_align_attr("xform.align2d",rslt,this_img);
00522 //      t->set_rotation(Dict("type","2d","alpha",-a));
00523 //
00524 //      EMData* result this_img->transform(Dict("type","2d","alpha",(float)(a*180./M_PI)));
00525 //
00526 //      cf->set_attr("xform.align2d",t);
00527 //      delete t;
00528 //      cf->update();
00529 
00530         if( e1 )
00531         {
00532                 delete e1;
00533                 e1 = 0;
00534         }
00535 
00536         if( e2 )
00537         {
00538                 delete e2;
00539                 e2 = 0;
00540         }
00541 
00542         if (cf) {
00543                 delete cf;
00544                 cf = 0;
00545         }
00546         return rslt;
00547 }

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

Implements EMAN::Aligner.

Definition at line 387 of file aligner.h.

00388                 {
00389                         return "Performs rotational alignment and works accurately if the image is precentered";
00390                 }

virtual string EMAN::RotatePrecenterAligner::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 382 of file aligner.h.

00383                 {
00384                         return NAME;
00385                 }

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

Implements EMAN::Aligner.

Definition at line 397 of file aligner.h.

00398                 {
00399                         TypeDict d;
00400                         return d;
00401                 }

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

Definition at line 392 of file aligner.h.

00393                 {
00394                         return new RotatePrecenterAligner();
00395                 }


Member Data Documentation

const string RotatePrecenterAligner::NAME = "rotate_precenter" [static]
 

Definition at line 62 of file aligner.cpp.


The documentation for this class was generated from the following files:
Generated on Tue Jun 11 13:47:42 2013 for EMAN2 by  doxygen 1.3.9.1