#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 518 of file aligner.h.
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Implements EMAN::Aligner. Definition at line 524 of file aligner.h. References align(). 00525 { 00526 return align(this_img, to_img, "sqeuclidean", Dict()); 00527 }
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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 566 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. 00568 { 00569 int maxiter = params.set_default("maxiter", 3); 00570 00571 Dict trans_params; 00572 trans_params["intonly"] = 0; 00573 trans_params["maxshift"] = params.set_default("maxshift", -1); 00574 trans_params["useflcf"] = params.set_default("useflcf",0); 00575 trans_params["nozero"] = params.set_default("nozero",false); 00576 00577 Dict rot_params; 00578 rot_params["r1"] = params.set_default("r1", -1); 00579 rot_params["r2"] = params.set_default("r2", -1); 00580 00581 Transform t; 00582 EMData * moving_img = this_img; 00583 for(int it = 0; it < maxiter; it++){ 00584 00585 // First do a translational alignment 00586 EMData * trans_align = moving_img->align("translational", to, trans_params, cmp_name, cmp_params); 00587 Transform * tt = trans_align->get_attr("xform.align2d"); 00588 t = *tt*t; 00589 delete tt; 00590 00591 //now do rotation 00592 EMData * rottrans_align = trans_align->align("rotational_iterative", to, rot_params, cmp_name, cmp_params); 00593 Transform * rt = rottrans_align->get_attr("xform.align2d"); 00594 t = *rt*t; 00595 delete trans_align; trans_align = 0; 00596 delete rottrans_align; rottrans_align = 0; 00597 delete rt; 00598 00599 //this minimizes interpolation errors (all images that are futher processed will be interpolated at most twice) 00600 if(it > 0){delete moving_img;} 00601 00602 moving_img = this_img->process("xform",Dict("transform",&t)); //iterate 00603 } 00604 00605 //write the total transformation; Avoids interpolation erros 00606 moving_img->set_attr("xform.align2d", &t); 00607 00608 return moving_img; 00609 }
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Implements EMAN::Aligner. Definition at line 534 of file aligner.h. 00535 { 00536 return "Performs rotational alignment and follows this with translational alignment using the iterative method."; 00537 }
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Get the Aligner's name. Each Aligner is identified by a unique name.
Implements EMAN::Aligner. Definition at line 529 of file aligner.h. 00530 {
00531 return NAME;
00532 }
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Implements EMAN::Aligner. Definition at line 544 of file aligner.h. References EMAN::TypeDict::put(). 00545 { 00546 TypeDict d; 00547 d.put("maxshift", EMObject::INT, "Maximum translation in pixels"); 00548 d.put("r1", EMObject::INT, "Inner ring, pixels"); 00549 d.put("r2", EMObject::INT, "Outer ring, pixels"); 00550 d.put("maxiter", EMObject::INT, "Maximum number of iterations"); 00551 d.put("nozero", EMObject::INT,"Zero translation not permitted (useful for CCD images)"); 00552 d.put("useflcf", EMObject::INT,"Use Fast Local Correlation Function rather than CCF for translational alignment"); 00553 return d; 00554 }
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Definition at line 539 of file aligner.h. 00540 { 00541 return new RotateTranslateAlignerIterative(); 00542 }
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Definition at line 65 of file aligner.cpp. |