#include <aligner.h>
Inheritance diagram for EMAN::RotateTranslateFlipAlignerIterative:
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 () |
TypeDict | static_get_param_types () |
Static Public Attributes | |
const string | NAME = "rotate_translate_flip.iterative" |
flip | ||
r1 | inner ring | |
r2 | outer ring | |
maxiter | maximum number of alignment iterations | |
maxshift | Maximum translation in pixels |
Definition at line 620 of file aligner.h.
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Implements EMAN::Aligner. Definition at line 625 of file aligner.h. References align(). 00626 { 00627 return align(this_img, to_img, "sqeuclidean", Dict()); 00628 }
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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 558 of file aligner.cpp. References EMAN::EMData::align(), EMAN::EMData::cmp(), EMAN::EMData::get_attr(), EMAN::EMData::process(), EMAN::EMData::process_inplace(), EMAN::EMData::set_attr(), EMAN::Dict::set_default(), EMAN::Transform::set_mirror(), and t. 00560 { 00561 // Get the non flipped rotational, tranlsationally aligned image 00562 Dict rt_params("maxshift", params["maxshift"],"r1",params.set_default("r1",-1),"r2",params.set_default("r2",-1)); 00563 EMData *rot_trans_align = this_img->align("rotate_translate.iterative",to,rt_params,cmp_name, cmp_params); 00564 00565 // Do the same alignment, but using the flipped version of the image 00566 EMData *flipped = params.set_default("flip", (EMData *) 0); 00567 bool delete_flag = false; 00568 if (flipped == 0) { 00569 flipped = to->process("xform.flip", Dict("axis", "x")); 00570 delete_flag = true; 00571 } 00572 00573 EMData * rot_trans_align_flip = this_img->align("rotate_translate.iterative", flipped, rt_params, cmp_name, cmp_params); 00574 Transform* t = rot_trans_align_flip->get_attr("xform.align2d"); 00575 t->set_mirror(true); 00576 rot_trans_align_flip->set_attr("xform.align2d",t); 00577 delete t; 00578 00579 // Now finally decide on what is the best answer 00580 float cmp1 = rot_trans_align->cmp(cmp_name, to, cmp_params); 00581 float cmp2 = rot_trans_align_flip->cmp(cmp_name, flipped, cmp_params); 00582 00583 if (delete_flag){ 00584 if(flipped) { 00585 delete flipped; 00586 flipped = 0; 00587 } 00588 } 00589 00590 EMData *result = 0; 00591 if (cmp1 < cmp2 ) { 00592 00593 if( rot_trans_align_flip ) { 00594 delete rot_trans_align_flip; 00595 rot_trans_align_flip = 0; 00596 } 00597 result = rot_trans_align; 00598 } 00599 else { 00600 if( rot_trans_align ) { 00601 delete rot_trans_align; 00602 rot_trans_align = 0; 00603 } 00604 result = rot_trans_align_flip; 00605 result->process_inplace("xform.flip",Dict("axis","x")); 00606 } 00607 00608 return result; 00609 }
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Implements EMAN::Aligner. Definition at line 635 of file aligner.h. 00636 { 00637 return " Does two 'rotate_translate.iterative' alignments, one to accommodate for possible handedness change. Decided which alignment is better using a comparitor and returns the aligned image as the solution"; 00638 }
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Get the Aligner's name. Each Aligner is identified by a unique name.
Implements EMAN::Aligner. Definition at line 630 of file aligner.h. 00631 {
00632 return NAME;
00633 }
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Implements EMAN::Aligner. Definition at line 645 of file aligner.h. 00646 { 00647 return static_get_param_types(); 00648 }
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Definition at line 640 of file aligner.h. 00641 { 00642 return new RotateTranslateFlipAlignerIterative(); 00643 }
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Definition at line 650 of file aligner.h. References EMAN::TypeDict::put(). 00650 { 00651 TypeDict d; 00652 d.put("flip", EMObject::EMDATA); 00653 d.put("r1", EMObject::INT, "Inner ring, pixels"); 00654 d.put("r2", EMObject::INT, "Outer ring, pixels"); 00655 d.put("maxiter", EMObject::INT, "Maximum number of iterations"); 00656 d.put("maxshift", EMObject::INT, "Maximum translation in pixels"); 00657 return d; 00658 }
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Definition at line 63 of file aligner.cpp. |