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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

AlignerNEW ()

Static Public Attributes

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 726 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 732 of file aligner.h.

References align().

00733                 {
00734                         return align(this_img, to_img, "sqeuclidean", Dict());
00735                 }

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 724 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::EMData::process(), EMAN::EMData::process_inplace(), EMAN::EMData::set_attr(), EMAN::Dict::set_default(), EMAN::EMData::unwrap(), x, and y.

00726 {
00727         if (cmp_name != "dot" && cmp_name != "ccc") throw InvalidParameterException("Resample aligner only works for dot and ccc");
00728         
00729         int maxtx = params.set_default("tx", 0);
00730         int maxty = params.set_default("ty", 0);
00731         int r1 = params.set_default("r1",-1);
00732         int r2 = params.set_default("r2",-1);
00733         
00734         if(this_img->get_xsize()/2 - 1 - r2 - maxtx <= 0 || (r2 == -1 && maxtx > 0)){
00735                 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++
00736                 throw InvalidParameterException("nx/2 - 1 - r2 - tx must be greater than or = 0");
00737         }
00738         if(this_img->get_ysize()/2 - 1 - r2 - maxty <= 0 || (r2 == -1 && maxty > 0)){
00739                 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++
00740                 throw InvalidParameterException("ny/2 - 1 - r2 - ty must be greater than or = 0");
00741         }
00742         
00743         float best_peak = -numeric_limits<float>::infinity();
00744         int best_peak_index = 0;
00745         int best_tx = 0;
00746         int best_ty = 0;
00747         int polarxsize = 0;
00748         bool flip = false;
00749         
00750         for(int x = -maxtx; x <= maxtx; x++){
00751                 for(int y = -maxty; y <= maxty; y++){
00752 
00753                         EMData * to_polar = to->unwrap(r1,r2,-1,0,0,true);
00754                         EMData * this_img_polar = this_img->unwrap(r1,r2,-1,x,y,true);
00755                         EMData * cfflip = this_img_polar->calc_ccfx(to_polar, 0, this_img_polar->get_ysize(), false, true);
00756                         EMData * cf = this_img_polar->calc_ccfx(to_polar, 0, this_img_polar->get_ysize());
00757                         
00758                         polarxsize = this_img_polar->get_xsize();
00759                         
00760                         //take out the garbage
00761                         delete to_polar; to_polar = 0;
00762                         delete this_img_polar; this_img_polar = 0;
00763         
00764                         float *data = cf->get_data();
00765                         float peak = 0;
00766                         int peak_index = 0;
00767                         Util::find_max(data, polarxsize, &peak, &peak_index);
00768                         delete cf; cf = 0;
00769 
00770                         if(peak > best_peak) {
00771                                 best_peak = peak;
00772                                 best_peak_index = peak_index;
00773                                 best_tx = x;
00774                                 best_ty = y;
00775                                 flip = false;
00776                         }
00777                         
00778                         data = cfflip->get_data();
00779                         Util::find_max(data, polarxsize, &peak, &peak_index);
00780                         delete cfflip; cfflip = 0;
00781 
00782                         if(peak > best_peak) {
00783                                 best_peak = peak;
00784                                 best_peak_index = peak_index;
00785                                 best_tx = x;
00786                                 best_ty = y;
00787                                 flip = true;
00788                         }
00789                 }
00790         }
00791         
00792         float rot_angle = (float) (best_peak_index * 360.0f / polarxsize);
00793                                 
00794         //return the result
00795         Transform tmptt(Dict("type","2d","alpha",0,"tx",-best_tx,"ty",-best_ty));
00796         Transform tmprot(Dict("type","2d","alpha",rot_angle,"tx",0,"ty",0));
00797         Transform total = tmprot*tmptt;
00798         EMData* rotimg=this_img->process("xform",Dict("transform",(Transform*)&total));
00799         rotimg->set_attr("xform.align2d",&total);
00800         if(flip == true) {
00801                 rotimg->process_inplace("xform.flip",Dict("axis", "x"));
00802         }
00803         
00804         return rotimg;
00805         
00806 }

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

Implements EMAN::Aligner.

Definition at line 742 of file aligner.h.

00743                 {
00744                         return "Performs rotational alignment, translation align, and flip by resampling to polar coordinates in real space.";
00745                 }

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 737 of file aligner.h.

00738                 {
00739                         return NAME;
00740                 }

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

Implements EMAN::Aligner.

Definition at line 752 of file aligner.h.

References EMAN::TypeDict::put().

00753                 {
00754                         TypeDict d;
00755                         //d.put("usedot", EMObject::INT);
00756                         d.put("tx", EMObject::INT, "Maximum x translation in pixels, Default = 0");
00757                         d.put("ty", EMObject::INT, "Maximum y translation in pixels, Default = 0");
00758                         d.put("r1", EMObject::INT, "Inner ring, pixels");
00759                         d.put("r2", EMObject::INT, "Outer ring, pixels");
00760                         return d;
00761                 }

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

Definition at line 747 of file aligner.h.

00748                 {
00749                         return new RotateTranslateFlipAlignerPawel();
00750                 }


Member Data Documentation

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

Definition at line 70 of file aligner.cpp.


The documentation for this class was generated from the following files:
Generated on Tue Jul 12 13:51:06 2011 for EMAN2 by  doxygen 1.3.9.1