#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 444 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. 00446 { 00447 int maxiter = params.set_default("maxiter", 3); 00448 00449 Dict trans_params; 00450 trans_params["intonly"] = 0; 00451 trans_params["maxshift"] = params.set_default("maxshift", -1); 00452 trans_params["useflcf"] = params.set_default("useflcf",0); 00453 trans_params["nozero"] = params.set_default("nozero",false); 00454 00455 Dict rot_params; 00456 rot_params["r1"] = params.set_default("r1", -1); 00457 rot_params["r2"] = params.set_default("r2", -1); 00458 00459 Transform t; 00460 EMData * moving_img = this_img; 00461 for(int it = 0; it < maxiter; it++){ 00462 00463 // First do a translational alignment 00464 EMData * trans_align = moving_img->align("translational", to, trans_params, cmp_name, cmp_params); 00465 Transform * tt = trans_align->get_attr("xform.align2d"); 00466 t = *tt*t; 00467 delete tt; 00468 00469 //now do rotation 00470 EMData * rottrans_align = trans_align->align("rotational_iterative", to, rot_params, cmp_name, cmp_params); 00471 Transform * rt = rottrans_align->get_attr("xform.align2d"); 00472 t = *rt*t; 00473 delete trans_align; trans_align = 0; 00474 delete rottrans_align; rottrans_align = 0; 00475 delete rt; 00476 00477 //this minimizes interpolation errors (all images that are futher processed will be interpolated at most twice) 00478 if(it > 0){delete moving_img;} 00479 00480 moving_img = this_img->process("xform",Dict("transform",&t)); //iterate 00481 } 00482 00483 //write the total transformation; Avoids interpolation erros 00484 moving_img->set_attr("xform.align2d", &t); 00485 00486 return moving_img; 00487 }
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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 64 of file aligner.cpp. |