#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 | |
Aligner * | NEW () |
TypeDict | static_get_param_types () |
Static Public Attributes | |
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 621 of file aligner.h.
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Implements EMAN::Aligner. Definition at line 626 of file aligner.h. References align(). 00627 { 00628 return align(this_img, to_img, "sqeuclidean", Dict()); 00629 }
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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 618 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. 00620 { 00621 // Get the non flipped rotational, tranlsationally aligned image 00622 Dict rt_params("maxshift", params["maxshift"], "rfp_mode", params.set_default("rfp_mode",0),"useflcf",params.set_default("useflcf",0)); 00623 EMData *rot_trans_align = this_img->align("rotate_translate",to,rt_params,cmp_name, cmp_params); 00624 00625 // Do the same alignment, but using the flipped version of the image 00626 EMData *flipped = params.set_default("flip", (EMData *) 0); 00627 bool delete_flag = false; 00628 if (flipped == 0) { 00629 flipped = to->process("xform.flip", Dict("axis", "x")); 00630 delete_flag = true; 00631 } 00632 00633 EMData * rot_trans_align_flip = this_img->align("rotate_translate", flipped, rt_params, cmp_name, cmp_params); 00634 Transform* t = rot_trans_align_flip->get_attr("xform.align2d"); 00635 t->set_mirror(true); 00636 rot_trans_align_flip->set_attr("xform.align2d",t); 00637 delete t; 00638 00639 // Now finally decide on what is the best answer 00640 float cmp1 = rot_trans_align->cmp(cmp_name, to, cmp_params); 00641 float cmp2 = rot_trans_align_flip->cmp(cmp_name, flipped, cmp_params); 00642 00643 if (delete_flag){ 00644 if(flipped) { 00645 delete flipped; 00646 flipped = 0; 00647 } 00648 } 00649 00650 EMData *result = 0; 00651 if (cmp1 < cmp2 ) { 00652 00653 if( rot_trans_align_flip ) { 00654 delete rot_trans_align_flip; 00655 rot_trans_align_flip = 0; 00656 } 00657 result = rot_trans_align; 00658 } 00659 else { 00660 if( rot_trans_align ) { 00661 delete rot_trans_align; 00662 rot_trans_align = 0; 00663 } 00664 result = rot_trans_align_flip; 00665 result->process_inplace("xform.flip",Dict("axis","x")); 00666 } 00667 00668 return result; 00669 }
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Implements EMAN::Aligner. Definition at line 636 of file aligner.h. 00637 { 00638 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"; 00639 }
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Get the Aligner's name. Each Aligner is identified by a unique name.
Implements EMAN::Aligner. Definition at line 631 of file aligner.h. 00632 {
00633 return NAME;
00634 }
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Implements EMAN::Aligner. Definition at line 646 of file aligner.h. 00647 { 00648 return static_get_param_types(); 00649 }
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Definition at line 641 of file aligner.h. 00642 { 00643 return new RotateTranslateFlipAligner(); 00644 }
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Definition at line 651 of file aligner.h. References EMAN::TypeDict::put(). 00651 { 00652 TypeDict d; 00653 00654 d.put("flip", EMObject::EMDATA); 00655 d.put("usedot", EMObject::INT); 00656 d.put("maxshift", EMObject::INT, "Maximum translation in pixels"); 00657 d.put("rfp_mode", EMObject::INT,"Either 0,1 or 2. A temporary flag for testing the rotational foot print"); 00658 d.put("useflcf", EMObject::INT,"Use Fast Local Correlation Function rather than CCF for translational alignment"); 00659 return d; 00660 }
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Definition at line 68 of file aligner.cpp. |