#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. |
1.3.9.1