#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 674 of file aligner.h.
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Implements EMAN::Aligner. Definition at line 679 of file aligner.h. References align(). 00680 { 00681 return align(this_img, to_img, "sqeuclidean", Dict()); 00682 }
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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 668 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. 00670 { 00671 // Get the non flipped rotational, tranlsationally aligned image 00672 Dict rt_params("maxshift", params["maxshift"],"r1",params.set_default("r1",-1),"r2",params.set_default("r2",-1)); 00673 EMData *rot_trans_align = this_img->align("rotate_translate.iterative",to,rt_params,cmp_name, cmp_params); 00674 00675 // Do the same alignment, but using the flipped version of the image 00676 EMData *flipped = params.set_default("flip", (EMData *) 0); 00677 bool delete_flag = false; 00678 if (flipped == 0) { 00679 flipped = to->process("xform.flip", Dict("axis", "x")); 00680 delete_flag = true; 00681 } 00682 00683 EMData * rot_trans_align_flip = this_img->align("rotate_translate.iterative", flipped, rt_params, cmp_name, cmp_params); 00684 Transform* t = rot_trans_align_flip->get_attr("xform.align2d"); 00685 t->set_mirror(true); 00686 rot_trans_align_flip->set_attr("xform.align2d",t); 00687 delete t; 00688 00689 // Now finally decide on what is the best answer 00690 float cmp1 = rot_trans_align->cmp(cmp_name, to, cmp_params); 00691 float cmp2 = rot_trans_align_flip->cmp(cmp_name, flipped, cmp_params); 00692 00693 if (delete_flag){ 00694 if(flipped) { 00695 delete flipped; 00696 flipped = 0; 00697 } 00698 } 00699 00700 EMData *result = 0; 00701 if (cmp1 < cmp2 ) { 00702 00703 if( rot_trans_align_flip ) { 00704 delete rot_trans_align_flip; 00705 rot_trans_align_flip = 0; 00706 } 00707 result = rot_trans_align; 00708 } 00709 else { 00710 if( rot_trans_align ) { 00711 delete rot_trans_align; 00712 rot_trans_align = 0; 00713 } 00714 result = rot_trans_align_flip; 00715 result->process_inplace("xform.flip",Dict("axis","x")); 00716 } 00717 00718 return result; 00719 }
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Implements EMAN::Aligner. Definition at line 689 of file aligner.h. 00690 { 00691 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"; 00692 }
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Get the Aligner's name. Each Aligner is identified by a unique name.
Implements EMAN::Aligner. Definition at line 684 of file aligner.h. 00685 {
00686 return NAME;
00687 }
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Implements EMAN::Aligner. Definition at line 699 of file aligner.h. 00700 { 00701 return static_get_param_types(); 00702 }
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Definition at line 694 of file aligner.h. 00695 { 00696 return new RotateTranslateFlipAlignerIterative(); 00697 }
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Definition at line 704 of file aligner.h. References EMAN::TypeDict::put(). 00704 { 00705 TypeDict d; 00706 d.put("flip", EMObject::EMDATA); 00707 d.put("r1", EMObject::INT, "Inner ring, pixels"); 00708 d.put("r2", EMObject::INT, "Outer ring, pixels"); 00709 d.put("maxiter", EMObject::INT, "Maximum number of iterations"); 00710 d.put("maxshift", EMObject::INT, "Maximum translation in pixels"); 00711 return d; 00712 }
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Definition at line 69 of file aligner.cpp. |