EMAN::RotateTranslateFlipAlignerPawel Class Reference

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

#include <aligner.h>

Inheritance diagram for EMAN::RotateTranslateFlipAlignerPawel:

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Collaboration diagram for EMAN::RotateTranslateFlipAlignerPawel:

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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_flip_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 9th 2011

Definition at line 1032 of file aligner.h.


Member Function Documentation

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

Implements EMAN::Aligner.

Definition at line 1038 of file aligner.h.

References align().

01039                 {
01040                         return align(this_img, to_img, "sqeuclidean", Dict());
01041                 }

EMData * RotateTranslateFlipAlignerPawel::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 915 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::process_inplace(), EMAN::EMData::set_attr(), EMAN::Dict::set_default(), EMAN::EMData::unwrap(), x, and y.

Referenced by align().

00917 {
00918         if (cmp_name != "dot" && cmp_name != "ccc") throw InvalidParameterException("Resample aligner only works for dot and ccc");
00919         
00920         int maxtx = params.set_default("tx", 0);
00921         int maxty = params.set_default("ty", 0);
00922         int r1 = params.set_default("r1",-1);
00923         int r2 = params.set_default("r2",-1);
00924         
00925         if(this_img->get_xsize()/2 - 1 - r2 - maxtx <= 0 || (r2 == -1 && maxtx > 0)){
00926                 cout << "\nRunTimeError: nx/2 - 1 - r2 - tx must be greater than or = 0\n" << endl; // For some reason the expection message is not being print, stupid C++
00927                 throw InvalidParameterException("nx/2 - 1 - r2 - tx must be greater than or = 0");
00928         }
00929         if(this_img->get_ysize()/2 - 1 - r2 - maxty <= 0 || (r2 == -1 && maxty > 0)){
00930                 cout << "\nRunTimeError:ny/2 - 1 - r2 - ty must be greater than or = 0\n" << endl; // For some reason the expection message is not being print, stupid C++
00931                 throw InvalidParameterException("ny/2 - 1 - r2 - ty must be greater than or = 0");
00932         }
00933         
00934 //      float best_peak = -numeric_limits<float>::infinity();
00935         float best_peak = -1.0e37;
00936         int best_peak_index = 0;
00937         int best_tx = 0;
00938         int best_ty = 0;
00939         int polarxsize = 0;
00940         bool flip = false;
00941         
00942         for(int x = -maxtx; x <= maxtx; x++){
00943                 for(int y = -maxty; y <= maxty; y++){
00944 
00945                         EMData * to_polar = to->unwrap(r1,r2,-1,0,0,true);
00946                         EMData * this_img_polar = this_img->unwrap(r1,r2,-1,x,y,true);
00947                         EMData * cfflip = this_img_polar->calc_ccfx(to_polar, 0, this_img_polar->get_ysize(), false, true);
00948                         EMData * cf = this_img_polar->calc_ccfx(to_polar, 0, this_img_polar->get_ysize());
00949                         
00950                         polarxsize = this_img_polar->get_xsize();
00951                         
00952                         //take out the garbage
00953                         delete to_polar; to_polar = 0;
00954                         delete this_img_polar; this_img_polar = 0;
00955         
00956                         float *data = cf->get_data();
00957                         float peak = 0;
00958                         int peak_index = 0;
00959                         Util::find_max(data, polarxsize, &peak, &peak_index);
00960                         delete cf; cf = 0;
00961 
00962                         if(peak > best_peak) {
00963                                 best_peak = peak;
00964                                 best_peak_index = peak_index;
00965                                 best_tx = x;
00966                                 best_ty = y;
00967                                 flip = false;
00968                         }
00969                         
00970                         data = cfflip->get_data();
00971                         Util::find_max(data, polarxsize, &peak, &peak_index);
00972                         delete cfflip; cfflip = 0;
00973 
00974                         if(peak > best_peak) {
00975                                 best_peak = peak;
00976                                 best_peak_index = peak_index;
00977                                 best_tx = x;
00978                                 best_ty = y;
00979                                 flip = true;
00980                         }
00981                 }
00982         }
00983         
00984         float rot_angle = (float) (best_peak_index * 360.0f / polarxsize);
00985                                 
00986         //return the result
00987         Transform tmptt(Dict("type","2d","alpha",0,"tx",-best_tx,"ty",-best_ty));
00988         Transform tmprot(Dict("type","2d","alpha",rot_angle,"tx",0,"ty",0));
00989         Transform total = tmprot*tmptt;
00990         EMData * rotimg=this_img->process("xform",Dict("transform",(Transform*)&total));
00991         rotimg->set_attr("xform.align2d",&total);
00992         if(flip == true) {
00993                 rotimg->process_inplace("xform.flip",Dict("axis", "x"));
00994         }
00995         
00996         return rotimg;
00997         
00998 }

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

Implements EMAN::Aligner.

Definition at line 1048 of file aligner.h.

01049                 {
01050                         return "Performs rotational alignment, translation align, and flip by resampling to polar coordinates in real space.";
01051                 }

virtual string EMAN::RotateTranslateFlipAlignerPawel::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 1043 of file aligner.h.

References NAME.

01044                 {
01045                         return NAME;
01046                 }

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

Implements EMAN::Aligner.

Definition at line 1058 of file aligner.h.

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

01059                 {
01060                         TypeDict d;
01061                         //d.put("usedot", EMObject::INT);
01062                         d.put("tx", EMObject::INT, "Maximum x translation in pixels, Default = 0");
01063                         d.put("ty", EMObject::INT, "Maximum y translation in pixels, Default = 0");
01064                         d.put("r1", EMObject::INT, "Inner ring, pixels");
01065                         d.put("r2", EMObject::INT, "Outer ring, pixels");
01066                         return d;
01067                 }

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

Definition at line 1053 of file aligner.h.

01054                 {
01055                         return new RotateTranslateFlipAlignerPawel();
01056                 }


Member Data Documentation

const string RotateTranslateFlipAlignerPawel::NAME = "rotate_translate_flip_resample" [static]

Definition at line 1069 of file aligner.h.

Referenced by get_name().


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