#include <aligner.h>
Inheritance diagram for EMAN::RotateTranslateFlipAligner:
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 | |
static Aligner * | NEW () |
static TypeDict | static_get_param_types () |
Static Public Attributes | |
static const string | NAME = "rotate_translate_flip" |
flip | ||
usedot | ||
maxshift | Maximum translation in pixels | |
rfp_mode | Either 0,1 or 2. A temporary flag for testing the rotational foot print |
Definition at line 431 of file aligner.h.
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Implements EMAN::Aligner. Definition at line 436 of file aligner.h. References align(). 00437 { 00438 return align(this_img, to_img, "sqeuclidean", Dict()); 00439 }
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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 419 of file aligner.cpp. References EMAN::EMData::align(), EMAN::EMData::cmp(), cmp1(), cmp2(), EMAN::EMData::get_attr(), EMAN::Aligner::params, EMAN::EMData::process(), EMAN::EMData::process_inplace(), EMAN::EMData::set_attr(), EMAN::Dict::set_default(), EMAN::Transform::set_mirror(), and t. Referenced by align(). 00421 { 00422 // Get the non flipped rotational, tranlsationally aligned image 00423 Dict rt_params("maxshift", params["maxshift"], "rfp_mode", params.set_default("rfp_mode",0),"useflcf",params.set_default("useflcf",0)); 00424 EMData *rot_trans_align = this_img->align("rotate_translate",to,rt_params,cmp_name, cmp_params); 00425 00426 // Do the same alignment, but using the flipped version of the image 00427 EMData *flipped = params.set_default("flip", (EMData *) 0); 00428 bool delete_flag = false; 00429 if (flipped == 0) { 00430 flipped = to->process("xform.flip", Dict("axis", "x")); 00431 delete_flag = true; 00432 } 00433 00434 EMData * rot_trans_align_flip = this_img->align("rotate_translate", flipped, rt_params, cmp_name, cmp_params); 00435 Transform* t = rot_trans_align_flip->get_attr("xform.align2d"); 00436 t->set_mirror(true); 00437 rot_trans_align_flip->set_attr("xform.align2d",t); 00438 delete t; 00439 00440 // Now finally decide on what is the best answer 00441 float cmp1 = rot_trans_align->cmp(cmp_name, to, cmp_params); 00442 float cmp2 = rot_trans_align_flip->cmp(cmp_name, flipped, cmp_params); 00443 00444 if (delete_flag){ 00445 if(flipped) { 00446 delete flipped; 00447 flipped = 0; 00448 } 00449 } 00450 00451 EMData *result = 0; 00452 if (cmp1 < cmp2 ) { 00453 00454 if( rot_trans_align_flip ) { 00455 delete rot_trans_align_flip; 00456 rot_trans_align_flip = 0; 00457 } 00458 result = rot_trans_align; 00459 } 00460 else { 00461 if( rot_trans_align ) { 00462 delete rot_trans_align; 00463 rot_trans_align = 0; 00464 } 00465 result = rot_trans_align_flip; 00466 result->process_inplace("xform.flip",Dict("axis","x")); 00467 } 00468 00469 return result; 00470 }
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Implements EMAN::Aligner. Definition at line 446 of file aligner.h. 00447 { 00448 return " Does two 'rotate_translate' alignments, one to accommodate for possible handedness change. Decided which alignment is better using a comparitor and returns the aligned image as the solution"; 00449 }
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Get the Aligner's name. Each Aligner is identified by a unique name.
Implements EMAN::Aligner. Definition at line 441 of file aligner.h. References NAME. 00442 { 00443 return NAME; 00444 }
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Implements EMAN::Aligner. Definition at line 456 of file aligner.h. References static_get_param_types(). 00457 { 00458 return static_get_param_types(); 00459 }
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Definition at line 451 of file aligner.h.
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Definition at line 461 of file aligner.h. References EMAN::EMObject::EMDATA, EMAN::EMObject::INT, and EMAN::TypeDict::put(). Referenced by get_param_types(). 00461 { 00462 TypeDict d; 00463 00464 d.put("flip", EMObject::EMDATA); 00465 d.put("usedot", EMObject::INT); 00466 d.put("maxshift", EMObject::INT, "Maximum translation in pixels"); 00467 d.put("rfp_mode", EMObject::INT,"Either 0,1 or 2. A temporary flag for testing the rotational foot print"); 00468 d.put("useflcf", EMObject::INT,"Use Fast Local Correlation Function rather than CCF for translational alignment"); 00469 return d; 00470 }
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Definition at line 472 of file aligner.h. Referenced by get_name(). |