#include <aligner.h>
Inheritance diagram for EMAN::RotateTranslateAlignerIterative:


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_iterative" |
Basically, we find the best translation, and move to that pointer then we find the best rotation and rotate to that point. Next we iterate X times.
| maxshift | Maximum translation in pixels | |
| r1 | inner ring | |
| r2 | outer ring | |
| maxiter | maximum number of alignment iterations | |
| nozero | Zero translation not permitted (useful for CCD images) |
Definition at line 393 of file aligner.h.
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Implements EMAN::Aligner. Definition at line 399 of file aligner.h. References align(). 00400 {
00401 return align(this_img, to_img, "sqeuclidean", Dict());
00402 }
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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 437 of file aligner.cpp. References EMAN::EMData::align(), EMAN::EMData::get_attr(), EMAN::EMData::process(), EMAN::EMData::set_attr(), EMAN::Dict::set_default(), and t. 00439 {
00440 int maxiter = params.set_default("maxiter", 3);
00441
00442 Dict trans_params;
00443 trans_params["intonly"] = 0;
00444 trans_params["maxshift"] = params.set_default("maxshift", -1);
00445 trans_params["useflcf"] = params.set_default("useflcf",0);
00446 trans_params["nozero"] = params.set_default("nozero",false);
00447
00448 Dict rot_params;
00449 rot_params["r1"] = params.set_default("r1", -1);
00450 rot_params["r2"] = params.set_default("r2", -1);
00451
00452 Transform t;
00453 EMData * moving_img = this_img;
00454 for(int it = 0; it < maxiter; it++){
00455
00456 // First do a translational alignment
00457 EMData * trans_align = moving_img->align("translational", to, trans_params, cmp_name, cmp_params);
00458 Transform * tt = trans_align->get_attr("xform.align2d");
00459 t = *tt*t;
00460 delete tt;
00461
00462 //now do rotation
00463 EMData * rottrans_align = trans_align->align("rotational.iterative", to, rot_params, cmp_name, cmp_params);
00464 Transform * rt = rottrans_align->get_attr("xform.align2d");
00465 t = *rt*t;
00466 delete trans_align; trans_align = 0;
00467 delete rottrans_align; rottrans_align = 0;
00468 delete rt;
00469
00470 //this minimizes interpolation errors (all images that are futher processed will be interpolated at most twice)
00471 if(it > 0){delete moving_img;}
00472
00473 moving_img = this_img->process("xform",Dict("transform",&t)); //iterate
00474 }
00475
00476 //write the total transformation;
00477 moving_img->set_attr("xform.align2d", &t);
00478
00479 return moving_img;
00480 }
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Implements EMAN::Aligner. Definition at line 409 of file aligner.h. 00410 {
00411 return "Performs rotational alignment and follows this with translational alignment using the iterative method.";
00412 }
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Get the Aligner's name. Each Aligner is identified by a unique name.
Implements EMAN::Aligner. Definition at line 404 of file aligner.h. 00405 {
00406 return NAME;
00407 }
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Implements EMAN::Aligner. Definition at line 419 of file aligner.h. References EMAN::TypeDict::put(). 00420 {
00421 TypeDict d;
00422 //d.put("usedot", EMObject::INT);
00423 d.put("maxshift", EMObject::INT, "Maximum translation in pixels");
00424 d.put("r1", EMObject::INT, "Inner ring, pixels");
00425 d.put("r2", EMObject::INT, "Outer ring, pixels");
00426 d.put("maxiter", EMObject::INT, "Maximum number of iterations");
00427 d.put("nozero", EMObject::INT,"Zero translation not permitted (useful for CCD images)");
00428 d.put("useflcf", EMObject::INT,"Use Fast Local Correlation Function rather than CCF for translational alignment");
00429 return d;
00430 }
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Definition at line 414 of file aligner.h. 00415 {
00416 return new RotateTranslateAlignerIterative();
00417 }
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Definition at line 63 of file aligner.cpp. |
1.3.9.1