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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

AlignerNEW ()

Static Public Attributes

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 444 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 450 of file aligner.h.

References align().

00451                 {
00452                         return align(this_img, to_img, "sqeuclidean", Dict());
00453                 }

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 489 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::set_attr(), EMAN::Dict::set_default(), EMAN::EMData::unwrap(), x, and y.

00491 {
00492         if (cmp_name != "dot" && cmp_name != "ccc") throw InvalidParameterException("Resample aligner only works for dot and ccc");
00493         
00494         int maxtx = params.set_default("tx", 0);
00495         int maxty = params.set_default("ty", 0);
00496         int r1 = params.set_default("r1",-1);
00497         int r2 = params.set_default("r2",-1);
00498         
00499         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");
00500         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");
00501         
00502         float best_peak = -numeric_limits<float>::infinity();
00503         int best_peak_index = 0;
00504         int best_tx = 0;
00505         int best_ty = 0;
00506         int polarxsize = 0;
00507                 
00508         for(int x = -maxtx; x <= maxtx; x++){
00509                 for(int y = -maxty; y <= maxty; y++){
00510 
00511                         EMData * to_polar = to->unwrap(r1,r2,-1,0,0,true);
00512                         EMData * this_img_polar = this_img->unwrap(r1,r2,-1,x,y,true);
00513                         EMData * cf = this_img_polar->calc_ccfx(to_polar, 0, this_img_polar->get_ysize());
00514                         
00515                         polarxsize = this_img_polar->get_xsize();
00516                         
00517                         //take out the garbage
00518                         delete to_polar; to_polar = 0;
00519                         delete this_img_polar; this_img_polar = 0;
00520         
00521                         float *data = cf->get_data();
00522                         float peak = 0;
00523                         int peak_index = 0;
00524                         Util::find_max(data, polarxsize, &peak, &peak_index);
00525                         delete cf; cf = 0;
00526 
00527                         if(peak > best_peak) {
00528                                 best_peak = peak;
00529                                 best_peak_index = peak_index;
00530                                 best_tx = x;
00531                                 best_ty = y;
00532                         }
00533                 }
00534         }
00535         
00536         float rot_angle = (float) (best_peak_index * 360.0f / polarxsize);
00537                                 
00538         //return the result
00539         Transform tmptt(Dict("type","2d","alpha",0,"tx",-best_tx,"ty",-best_ty));
00540         Transform tmprot(Dict("type","2d","alpha",rot_angle,"tx",0,"ty",0));
00541         Transform total = tmprot*tmptt;
00542         EMData* rotimg=this_img->process("xform",Dict("transform",(Transform*)&total));
00543         rotimg->set_attr("xform.align2d",&total);
00544         
00545         return rotimg;
00546         
00547 }

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

Implements EMAN::Aligner.

Definition at line 460 of file aligner.h.

00461                 {
00462                         return "Performs rotational alignment and translation align by resampling to polar coordinates in real space.";
00463                 }

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 455 of file aligner.h.

00456                 {
00457                         return NAME;
00458                 }

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

Implements EMAN::Aligner.

Definition at line 470 of file aligner.h.

References EMAN::TypeDict::put().

00471                 {
00472                         TypeDict d;
00473                         //d.put("usedot", EMObject::INT);
00474                         d.put("tx", EMObject::INT, "Maximum x translation in pixels, Default = 0");
00475                         d.put("ty", EMObject::INT, "Maximum y translation in pixels, Default = 0");
00476                         d.put("r1", EMObject::INT, "Inner ring, pixels");
00477                         d.put("r2", EMObject::INT, "Outer ring, pixels");
00478                         return d;
00479                 }

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

Definition at line 465 of file aligner.h.

00466                 {
00467                         return new RotateTranslateAlignerPawel();
00468                 }


Member Data Documentation

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

Definition at line 65 of file aligner.cpp.


The documentation for this class was generated from the following files:
Generated on Thu Nov 17 12:45:13 2011 for EMAN2 by  doxygen 1.3.9.1