#include <aligner.h>
Inheritance diagram for EMAN::RotateTranslateAlignerPawel:
Public Member Functions | |
virtual EMData * | align (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 EMData * | align (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 Aligner * | NEW () |
Static Public Attributes | |
static const string | NAME = "rotate_translate_resample" |
translation if found by varing to origin using for polar coordinate resampling in real space
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 |
Definition at line 444 of file aligner.h.
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.
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. |
Implements EMAN::Aligner.
Definition at line 482 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().
00484 { 00485 if (cmp_name != "dot" && cmp_name != "ccc") throw InvalidParameterException("Resample aligner only works for dot and ccc"); 00486 00487 int maxtx = params.set_default("tx", 0); 00488 int maxty = params.set_default("ty", 0); 00489 int r1 = params.set_default("r1",-1); 00490 int r2 = params.set_default("r2",-1); 00491 00492 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"); 00493 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"); 00494 00495 float best_peak = -numeric_limits<float>::infinity(); 00496 int best_peak_index = 0; 00497 int best_tx = 0; 00498 int best_ty = 0; 00499 int polarxsize = 0; 00500 00501 for(int x = -maxtx; x <= maxtx; x++){ 00502 for(int y = -maxty; y <= maxty; y++){ 00503 00504 EMData * to_polar = to->unwrap(r1,r2,-1,0,0,true); 00505 EMData * this_img_polar = this_img->unwrap(r1,r2,-1,x,y,true); 00506 EMData * cf = this_img_polar->calc_ccfx(to_polar, 0, this_img_polar->get_ysize()); 00507 00508 polarxsize = this_img_polar->get_xsize(); 00509 00510 //take out the garbage 00511 delete to_polar; to_polar = 0; 00512 delete this_img_polar; this_img_polar = 0; 00513 00514 float *data = cf->get_data(); 00515 float peak = 0; 00516 int peak_index = 0; 00517 Util::find_max(data, polarxsize, &peak, &peak_index); 00518 delete cf; cf = 0; 00519 00520 if(peak > best_peak) { 00521 best_peak = peak; 00522 best_peak_index = peak_index; 00523 best_tx = x; 00524 best_ty = y; 00525 } 00526 } 00527 } 00528 00529 float rot_angle = (float) (best_peak_index * 360.0f / polarxsize); 00530 00531 //return the result 00532 Transform tmp(Dict("type","2d","alpha",rot_angle,"tx",best_tx,"ty",best_ty)); 00533 EMData* rotimg=this_img->process("xform",Dict("transform",(Transform*)&tmp)); 00534 rotimg->set_attr("xform.align2d",&tmp); 00535 00536 return rotimg; 00537 00538 }
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] |
virtual TypeDict EMAN::RotateTranslateAlignerPawel::get_param_types | ( | ) | const [inline, virtual] |
Implements EMAN::Aligner.
Definition at line 470 of file aligner.h.
References EMAN::EMObject::INT, and 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 x 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 }
static Aligner* EMAN::RotateTranslateAlignerPawel::NEW | ( | ) | [inline, static] |
const string RotateTranslateAlignerPawel::NAME = "rotate_translate_resample" [static] |