#include <aligner.h>
Inheritance diagram for EMAN::RTFSlowExhaustiveAligner:
Public Member Functions | |
virtual EMData * | align (EMData *this_img, EMData *to_img, const string &cmp_name, const Dict &cmp_params) 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 Public Attributes | |
static const string | NAME = "rtf_slow_exhaustive" |
This is very slow but can ensure localization of the global maximum
flip | Optional. This is the flipped version of the images that is being aligned. If specified it will be used for the handedness check, if not a flipped copy of the image will be made | |
maxshift | The maximum length of the detectable translational shift | |
transtep | The translation step to take when honing the alignment, which occurs after coarse alignment | |
angstep | The angular step (in degrees) to take in the exhaustive search for the solution angle. Typically very small i.e. 3 or smaller |
Definition at line 1120 of file aligner.h.
virtual EMData* EMAN::RTFSlowExhaustiveAligner::align | ( | EMData * | this_img, | |
EMData * | to_img | |||
) | const [inline, virtual] |
Implements EMAN::Aligner.
Definition at line 1125 of file aligner.h.
References align().
01126 { 01127 return align(this_img, to_img, "sqeuclidean", Dict()); 01128 }
EMData * RTFSlowExhaustiveAligner::align | ( | EMData * | this_img, | |
EMData * | to_img, | |||
const string & | cmp_name, | |||
const Dict & | cmp_params | |||
) | const [virtual] |
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.
this_img | The image to be compared. | |
to_img | 'this_img" is aligned with 'to_img'. | |
cmp_name | The comparison method to compare the two images. | |
cmp_params | The parameter dictionary for comparison method. |
Implements EMAN::Aligner.
Definition at line 1351 of file aligner.cpp.
References EMAN::EMConsts::deg2rad, EMAN::EMData::get_xsize(), InvalidParameterException, nx, EMAN::Aligner::params, EMAN::EMData::process(), EMAN::EMConsts::rad2deg, EMAN::EMData::set_attr(), EMAN::Dict::set_default(), t, and v.
Referenced by align().
01353 { 01354 01355 EMData *flip = params.set_default("flip", (EMData *) 0); 01356 int maxshift = params.set_default("maxshift", -1); 01357 01358 EMData *flipped = 0; 01359 01360 bool delete_flipped = true; 01361 if (flip) { 01362 delete_flipped = false; 01363 flipped = flip; 01364 } 01365 else { 01366 flipped = to->process("xform.flip", Dict("axis", "x")); 01367 } 01368 01369 int nx = this_img->get_xsize(); 01370 01371 if (maxshift < 0) { 01372 maxshift = nx / 10; 01373 } 01374 01375 float angle_step = params.set_default("angstep", 0.0f); 01376 if ( angle_step == 0 ) angle_step = atan2(2.0f, (float)nx); 01377 else { 01378 angle_step *= (float)EMConsts::deg2rad; //convert to radians 01379 } 01380 float trans_step = params.set_default("transtep",1.0f); 01381 01382 if (trans_step <= 0) throw InvalidParameterException("transstep must be greater than 0"); 01383 if (angle_step <= 0) throw InvalidParameterException("angstep must be greater than 0"); 01384 01385 01386 Dict shrinkfactor("n",2); 01387 EMData *this_img_shrink = this_img->process("math.medianshrink",shrinkfactor); 01388 EMData *to_shrunk = to->process("math.medianshrink",shrinkfactor); 01389 EMData *flipped_shrunk = flipped->process("math.medianshrink",shrinkfactor); 01390 01391 int bestflip = 0; 01392 float bestdx = 0; 01393 float bestdy = 0; 01394 01395 float bestang = 0; 01396 float bestval = FLT_MAX; 01397 01398 int half_maxshift = maxshift / 2; 01399 01400 01401 for (int dy = -half_maxshift; dy <= half_maxshift; ++dy) { 01402 for (int dx = -half_maxshift; dx <= half_maxshift; ++dx) { 01403 if (hypot(dx, dy) <= maxshift) { 01404 for (float ang = -angle_step * 2.0f; ang <= (float)2 * M_PI; ang += angle_step * 4.0f) { 01405 EMData v(*this_img_shrink); 01406 Transform t(Dict("type","2d","alpha",static_cast<float>(ang*EMConsts::rad2deg))); 01407 t.set_trans((float)dx,(float)dy); 01408 v.transform(t); 01409 // v.rotate_translate(ang*EMConsts::rad2deg, 0.0f, 0.0f, (float)dx, (float)dy, 0.0f); 01410 01411 float lc = v.cmp(cmp_name, to_shrunk, cmp_params); 01412 01413 if (lc < bestval) { 01414 bestval = lc; 01415 bestang = ang; 01416 bestdx = (float)dx; 01417 bestdy = (float)dy; 01418 bestflip = 0; 01419 } 01420 01421 lc = v.cmp(cmp_name,flipped_shrunk , cmp_params); 01422 if (lc < bestval) { 01423 bestval = lc; 01424 bestang = ang; 01425 bestdx = (float)dx; 01426 bestdy = (float)dy; 01427 bestflip = 1; 01428 } 01429 } 01430 } 01431 } 01432 } 01433 01434 if( to_shrunk ) 01435 { 01436 delete to_shrunk; 01437 to_shrunk = 0; 01438 } 01439 if( flipped_shrunk ) 01440 { 01441 delete flipped_shrunk; 01442 flipped_shrunk = 0; 01443 } 01444 if( this_img_shrink ) 01445 { 01446 delete this_img_shrink; 01447 this_img_shrink = 0; 01448 } 01449 01450 bestdx *= 2; 01451 bestdy *= 2; 01452 bestval = FLT_MAX; 01453 01454 float bestdx2 = bestdx; 01455 float bestdy2 = bestdy; 01456 float bestang2 = bestang; 01457 01458 for (float dy = bestdy2 - 3; dy <= bestdy2 + 3; dy += trans_step) { 01459 for (float dx = bestdx2 - 3; dx <= bestdx2 + 3; dx += trans_step) { 01460 if (hypot(dx, dy) <= maxshift) { 01461 for (float ang = bestang2 - angle_step * 6.0f; ang <= bestang2 + angle_step * 6.0f; ang += angle_step) { 01462 EMData v(*this_img); 01463 Transform t(Dict("type","2d","alpha",static_cast<float>(ang*EMConsts::rad2deg))); 01464 t.set_trans(dx,dy); 01465 v.transform(t); 01466 // v.rotate_translate(ang*EMConsts::rad2deg, 0.0f, 0.0f, (float)dx, (float)dy, 0.0f); 01467 01468 float lc = v.cmp(cmp_name, to, cmp_params); 01469 01470 if (lc < bestval) { 01471 bestval = lc; 01472 bestang = ang; 01473 bestdx = dx; 01474 bestdy = dy; 01475 bestflip = 0; 01476 } 01477 01478 lc = v.cmp(cmp_name, flipped, cmp_params); 01479 01480 if (lc < bestval) { 01481 bestval = lc; 01482 bestang = ang; 01483 bestdx = dx; 01484 bestdy = dy; 01485 bestflip = 1; 01486 } 01487 } 01488 } 01489 } 01490 } 01491 01492 if (delete_flipped) { delete flipped; flipped = 0; } 01493 01494 bestang *= (float)EMConsts::rad2deg; 01495 Transform t(Dict("type","2d","alpha",(float)bestang)); 01496 t.set_trans(bestdx,bestdy); 01497 01498 if (bestflip) { 01499 t.set_mirror(true); 01500 } 01501 01502 EMData* rslt = this_img->process("xform",Dict("transform",&t)); 01503 rslt->set_attr("xform.align2d",&t); 01504 01505 return rslt; 01506 }
virtual string EMAN::RTFSlowExhaustiveAligner::get_desc | ( | ) | const [inline, virtual] |
Implements EMAN::Aligner.
Definition at line 1134 of file aligner.h.
01135 { 01136 return "Experimental full 2D alignment with handedness check using more exhaustive search (not necessarily better than RTFBest)"; 01137 }
virtual string EMAN::RTFSlowExhaustiveAligner::get_name | ( | ) | const [inline, virtual] |
virtual TypeDict EMAN::RTFSlowExhaustiveAligner::get_param_types | ( | ) | const [inline, virtual] |
Implements EMAN::Aligner.
Definition at line 1144 of file aligner.h.
References EMAN::EMObject::EMDATA, EMAN::EMObject::FLOAT, EMAN::EMObject::INT, and EMAN::TypeDict::put().
01145 { 01146 TypeDict d; 01147 d.put("flip", EMObject::EMDATA,"Optional. This is the flipped version of the images that is being aligned. If specified it will be used for the handedness check, if not a flipped copy of the image will be made"); 01148 d.put("maxshift", EMObject::INT,"The maximum length of the detectable translational shift"); 01149 d.put("transtep", EMObject::FLOAT,"The translation step to take when honing the alignment, which occurs after coarse alignment"); 01150 d.put("angstep", EMObject::FLOAT,"The angular step (in degrees) to take in the exhaustive search for the solution angle. Typically very small i.e. 3 or smaller."); 01151 return d; 01152 }
static Aligner* EMAN::RTFSlowExhaustiveAligner::NEW | ( | ) | [inline, static] |
const string RTFSlowExhaustiveAligner::NAME = "rtf_slow_exhaustive" [static] |