#include <aligner.h>
Inheritance diagram for EMAN::RotateTranslateAligner:
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 () |
Static Public Attributes | |
const string | NAME = "rotate_translate" |
maxshift | Maximum translation in pixels | |
nozero | Zero translation not permitted (useful for CCD images) | |
rfp_mode | Either 0,1 or 2. A temporary flag for testing the rotational foot print |
Definition at line 298 of file aligner.h.
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Implements EMAN::Aligner. Definition at line 304 of file aligner.h. References align(). 00305 { 00306 return align(this_img, to_img, "sqeuclidean", Dict()); 00307 }
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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 353 of file aligner.cpp. References EMAN::EMData::align(), EMAN::RotationalAligner::align_180_ambiguous(), EMAN::EMData::cmp(), EMAN::EMData::copy(), EMAN::EMData::get_attr(), EMAN::Transform::get_rotation(), EMAN::EMData::process_inplace(), EMAN::EMData::set_attr(), EMAN::Dict::set_default(), EMAN::Transform::set_rotation(), and t. 00355 { 00356 // Get the 180 degree ambiguously rotationally aligned and its 180 degree rotation counterpart 00357 int rfp_mode = params.set_default("rfp_mode",0); 00358 EMData *rot_align = RotationalAligner::align_180_ambiguous(this_img,to,rfp_mode); 00359 Transform * tmp = rot_align->get_attr("xform.align2d"); 00360 Dict rot = tmp->get_rotation("2d"); 00361 float rotate_angle_solution = rot["alpha"]; 00362 delete tmp; 00363 00364 EMData *rot_align_180 = rot_align->copy(); 00365 rot_align_180->process_inplace("math.rotate.180"); 00366 00367 Dict trans_params; 00368 trans_params["intonly"] = 0; 00369 trans_params["maxshift"] = params.set_default("maxshift", -1); 00370 trans_params["useflcf"]=params.set_default("useflcf",0); 00371 00372 // Do the first case translational alignment 00373 trans_params["nozero"] = params.set_default("nozero",false); 00374 EMData* rot_trans = rot_align->align("translational", to, trans_params, cmp_name, cmp_params); 00375 if( rot_align ) { // Clean up 00376 delete rot_align; 00377 rot_align = 0; 00378 } 00379 00380 // Do the second case translational alignment 00381 EMData* rot_180_trans = rot_align_180->align("translational", to, trans_params, cmp_name, cmp_params); 00382 if( rot_align_180 ) { // Clean up 00383 delete rot_align_180; 00384 rot_align_180 = 0; 00385 } 00386 00387 // Finally decide on the result 00388 float cmp1 = rot_trans->cmp(cmp_name, to, cmp_params); 00389 float cmp2 = rot_180_trans->cmp(cmp_name, to, cmp_params); 00390 00391 EMData *result = 0; 00392 if (cmp1 < cmp2) { // Assumes smaller is better - thus all comparitors should support "smaller is better" 00393 if( rot_180_trans ) { 00394 delete rot_180_trans; 00395 rot_180_trans = 0; 00396 } 00397 result = rot_trans; 00398 } 00399 else { 00400 if( rot_trans ) { 00401 delete rot_trans; 00402 rot_trans = 0; 00403 } 00404 result = rot_180_trans; 00405 rotate_angle_solution -= 180.f; 00406 } 00407 00408 Transform* t = result->get_attr("xform.align2d"); 00409 t->set_rotation(Dict("type","2d","alpha",rotate_angle_solution)); 00410 result->set_attr("xform.align2d",t); 00411 delete t; 00412 00413 return result; 00414 }
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Implements EMAN::Aligner. Definition at line 314 of file aligner.h. 00315 { 00316 return "Performs rotational alignment and follows this with translational alignment."; 00317 }
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Get the Aligner's name. Each Aligner is identified by a unique name.
Implements EMAN::Aligner. Definition at line 309 of file aligner.h. 00310 {
00311 return NAME;
00312 }
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Implements EMAN::Aligner. Definition at line 324 of file aligner.h. References EMAN::TypeDict::put(). 00325 { 00326 TypeDict d; 00327 //d.put("usedot", EMObject::INT); 00328 d.put("maxshift", EMObject::INT, "Maximum translation in pixels"); 00329 d.put("nozero", EMObject::INT,"Zero translation not permitted (useful for CCD images)"); 00330 d.put("rfp_mode", EMObject::INT,"Either 0,1 or 2. A temporary flag for testing the rotational foot print"); 00331 d.put("useflcf", EMObject::INT,"Use Fast Local Correlation Function rather than CCF for translational alignment"); 00332 return d; 00333 }
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Definition at line 319 of file aligner.h. 00320 { 00321 return new RotateTranslateAligner(); 00322 }
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Definition at line 56 of file aligner.cpp. |