EMAN::RotateTranslateAlignerPawel Class Reference

Rotational, translational alignment by resampling to polar coordinates. More...

#include <aligner.h>

Inheritance diagram for EMAN::RotateTranslateAlignerPawel:

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Collaboration diagram for EMAN::RotateTranslateAlignerPawel:

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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 = "rotate_translate_resample"

Detailed Description

Rotational, translational alignment by resampling to polar coordinates.

translation if found by varing to origin using for polar coordinate resampling in real space

Parameters:
tx maximum transltion in x direction, must by less than (n/2 - 1 - r2)
tu maximum transltion in y direction, must by less than (n/2 - 1 - r2)
r1 inner ring
r2 outer ring
Author:
John Flanagan
Date:
Feb 8th 2011

Definition at line 634 of file aligner.h.


Member Function Documentation

virtual EMData* EMAN::RotateTranslateAlignerPawel::align ( EMData this_img,
EMData to_img 
) const [inline, virtual]

Implements EMAN::Aligner.

Definition at line 640 of file aligner.h.

References align().

00641                 {
00642                         return align(this_img, to_img, "sqeuclidean", Dict());
00643                 }

EMData * RotateTranslateAlignerPawel::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 645 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(), InvalidParameterException, EMAN::Aligner::params, EMAN::EMData::process(), EMAN::EMData::set_attr(), EMAN::Dict::set_default(), EMAN::EMData::unwrap(), x, and y.

Referenced by align().

00647 {
00648         if (cmp_name != "dot" && cmp_name != "ccc") throw InvalidParameterException("Resample aligner only works for dot and ccc");
00649         
00650         int maxtx = params.set_default("tx", 0);
00651         int maxty = params.set_default("ty", 0);
00652         int r1 = params.set_default("r1",-1);
00653         int r2 = params.set_default("r2",-1);
00654         
00655         if(this_img->get_xsize()/2 - 1 - r2 - maxtx <= 0 || (r2 == -1 && maxtx > 0)) throw InvalidParameterException("nx/2 - 1 - r2 - tx must be greater than or = 0");
00656         if(this_img->get_ysize()/2 - 1 - r2 - maxty <= 0 || (r2 == -1 && maxty > 0)) throw InvalidParameterException("ny/2 - 1 - r2 - ty must be greater than or = 0");
00657         
00658 //      float best_peak = -numeric_limits<float>::infinity();
00659         float best_peak = -1.0e37;
00660         int best_peak_index = 0;
00661         int best_tx = 0;
00662         int best_ty = 0;
00663         int polarxsize = 0;
00664                 
00665         for(int x = -maxtx; x <= maxtx; x++){
00666                 for(int y = -maxty; y <= maxty; y++){
00667 
00668                         EMData * to_polar = to->unwrap(r1,r2,-1,0,0,true);
00669                         EMData * this_img_polar = this_img->unwrap(r1,r2,-1,x,y,true);
00670                         EMData * cf = this_img_polar->calc_ccfx(to_polar, 0, this_img_polar->get_ysize());
00671                         
00672                         polarxsize = this_img_polar->get_xsize();
00673                         
00674                         //take out the garbage
00675                         delete to_polar; to_polar = 0;
00676                         delete this_img_polar; this_img_polar = 0;
00677         
00678                         float *data = cf->get_data();
00679                         float peak = 0;
00680                         int peak_index = 0;
00681                         Util::find_max(data, polarxsize, &peak, &peak_index);
00682                         delete cf; cf = 0;
00683 
00684                         if(peak > best_peak) {
00685                                 best_peak = peak;
00686                                 best_peak_index = peak_index;
00687                                 best_tx = x;
00688                                 best_ty = y;
00689                         }
00690                 }
00691         }
00692         
00693         float rot_angle = (float) (best_peak_index * 360.0f / polarxsize);
00694                                 
00695         //return the result
00696         Transform tmptt(Dict("type","2d","alpha",0,"tx",-best_tx,"ty",-best_ty));
00697         Transform tmprot(Dict("type","2d","alpha",rot_angle,"tx",0,"ty",0));
00698         Transform total = tmprot*tmptt;
00699         EMData* rotimg=this_img->process("xform",Dict("transform",(Transform*)&total));
00700         rotimg->set_attr("xform.align2d",&total);
00701         
00702         return rotimg;
00703         
00704 }

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

Implements EMAN::Aligner.

Definition at line 650 of file aligner.h.

00651                 {
00652                         return "Performs rotational alignment and translation align by resampling to polar coordinates in real space.";
00653                 }

virtual string EMAN::RotateTranslateAlignerPawel::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 645 of file aligner.h.

References NAME.

00646                 {
00647                         return NAME;
00648                 }

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

Implements EMAN::Aligner.

Definition at line 660 of file aligner.h.

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

00661                 {
00662                         TypeDict d;
00663                         //d.put("usedot", EMObject::INT);
00664                         d.put("tx", EMObject::INT, "Maximum x translation in pixels, Default = 0");
00665                         d.put("ty", EMObject::INT, "Maximum y translation in pixels, Default = 0");
00666                         d.put("r1", EMObject::INT, "Inner ring, pixels");
00667                         d.put("r2", EMObject::INT, "Outer ring, pixels");
00668                         return d;
00669                 }

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

Definition at line 655 of file aligner.h.

00656                 {
00657                         return new RotateTranslateAlignerPawel();
00658                 }


Member Data Documentation

const string RotateTranslateAlignerPawel::NAME = "rotate_translate_resample" [static]

Definition at line 671 of file aligner.h.

Referenced by get_name().


The documentation for this class was generated from the following files:
Generated on Tue Jun 11 12:42:39 2013 for EMAN2 by  doxygen 1.4.7