#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 | |
| Aligner * | NEW () |
Static Public Attributes | |
| 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.
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Implements EMAN::Aligner. Definition at line 450 of file aligner.h. References align(). 00451 {
00452 return align(this_img, to_img, "sqeuclidean", Dict());
00453 }
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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.
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::EMData::process(), EMAN::EMData::set_attr(), EMAN::Dict::set_default(), EMAN::EMData::unwrap(), x, and y. 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 }
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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 }
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Get the Aligner's name. Each Aligner is identified by a unique name.
Implements EMAN::Aligner. Definition at line 455 of file aligner.h. 00456 {
00457 return NAME;
00458 }
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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 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 }
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Definition at line 465 of file aligner.h. 00466 {
00467 return new RotateTranslateAlignerPawel();
00468 }
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Definition at line 64 of file aligner.cpp. |
1.3.9.1