#include <aligner.h>
Inheritance diagram for EMAN::RefineAligner:


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 = "refine" |
Refines a preliminary 2D alignment using a simplex algorithm. Subpixel precision.
Definition at line 853 of file aligner.h.
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Implements EMAN::Aligner. Definition at line 859 of file aligner.h. References align(). 00860 {
00861 return align(this_img, to_img, "sqeuclidean", Dict());
00862 }
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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 1402 of file aligner.cpp. References EMAN::EMData::get_attr(), EMAN::Transform::get_params(), EMAN::EMData::get_xsize(), EMAN::Dict::has_key(), EMAN::Cmp::params, EMAN::EMData::process(), EMAN::EMData::set_attr(), EMAN::Dict::set_default(), status, t, and x. 01404 {
01405
01406 if (!to) {
01407 return 0;
01408 }
01409
01410 EMData *result;
01411 int mode = params.set_default("mode", 0);
01412 float saz = 0.0;
01413 float sdx = 0.0;
01414 float sdy = 0.0;
01415 float sscale = 1.0;
01416 bool mirror = false;
01417 Transform* t;
01418 if (params.has_key("xform.align2d") ) {
01419 t = params["xform.align2d"];
01420 Dict params = t->get_params("2d");
01421 saz = params["alpha"];
01422 sdx = params["tx"];
01423 sdy = params["ty"];
01424 mirror = params["mirror"];
01425 sscale = params["scale"];
01426 } else {
01427 t = new Transform(); // is the identity
01428 }
01429
01430 // We do this to prevent the GSL routine from crashing on an invalid alignment
01431 if ((float)(this_img->get_attr("sigma"))==0.0 || (float)(to->get_attr("sigma"))==0.0) {
01432 result = this_img->process("xform",Dict("transform",t));
01433 result->set_attr("xform.align2d",t);
01434 delete t;
01435 return result;
01436 }
01437
01438 float stepx = params.set_default("stepx",1.0f);
01439 float stepy = params.set_default("stepy",1.0f);
01440 // Default step is 5 degree - note in EMAN1 it was 0.1 radians
01441 float stepaz = params.set_default("stepaz",5.0f);
01442 float stepscale = params.set_default("stepscale",0.0f);
01443
01444 int np = 3;
01445 if (stepscale!=0.0) np++;
01446 Dict gsl_params;
01447 gsl_params["this"] = this_img;
01448 gsl_params["with"] = to;
01449 gsl_params["snr"] = params["snr"];
01450 gsl_params["mirror"] = mirror;
01451
01452 const gsl_multimin_fminimizer_type *T = gsl_multimin_fminimizer_nmsimplex;
01453 gsl_vector *ss = gsl_vector_alloc(np);
01454
01455
01456 gsl_vector_set(ss, 0, stepx);
01457 gsl_vector_set(ss, 1, stepy);
01458 gsl_vector_set(ss, 2, stepaz);
01459 if (stepscale!=0.0) gsl_vector_set(ss,3,stepscale);
01460
01461 gsl_vector *x = gsl_vector_alloc(np);
01462 gsl_vector_set(x, 0, sdx);
01463 gsl_vector_set(x, 1, sdy);
01464 gsl_vector_set(x, 2, saz);
01465 if (stepscale!=0.0) gsl_vector_set(x,3,1.0);
01466
01467 Cmp *c = 0;
01468
01469 gsl_multimin_function minex_func;
01470 if (mode == 2) {
01471 minex_func.f = &refalifnfast;
01472 }
01473 else {
01474 c = Factory < Cmp >::get(cmp_name, cmp_params);
01475 gsl_params["cmp"] = (void *) c;
01476 minex_func.f = &refalifn;
01477 }
01478
01479 minex_func.n = np;
01480 minex_func.params = (void *) &gsl_params;
01481
01482 gsl_multimin_fminimizer *s = gsl_multimin_fminimizer_alloc(T, np);
01483 gsl_multimin_fminimizer_set(s, &minex_func, x, ss);
01484
01485 int rval = GSL_CONTINUE;
01486 int status = GSL_SUCCESS;
01487 int iter = 1;
01488
01489 float precision = params.set_default("precision",0.04f);
01490 int maxiter = params.set_default("maxiter",28);
01491
01492 // printf("Refine sx=%1.2f sy=%1.2f sa=%1.2f prec=%1.4f maxit=%d\n",stepx,stepy,stepaz,precision,maxiter);
01493 // printf("%1.2f %1.2f %1.1f ->",(float)gsl_vector_get(s->x, 0),(float)gsl_vector_get(s->x, 1),(float)gsl_vector_get(s->x, 2));
01494
01495 while (rval == GSL_CONTINUE && iter < maxiter) {
01496 iter++;
01497 status = gsl_multimin_fminimizer_iterate(s);
01498 if (status) {
01499 break;
01500 }
01501 rval = gsl_multimin_test_size(gsl_multimin_fminimizer_size(s), precision);
01502 }
01503
01504 int maxshift = params.set_default("maxshift",-1);
01505
01506 if (maxshift <= 0) {
01507 maxshift = this_img->get_xsize() / 4;
01508 }
01509 float fmaxshift = static_cast<float>(maxshift);
01510 if ( fmaxshift >= fabs((float)gsl_vector_get(s->x, 0)) && fmaxshift >= fabs((float)gsl_vector_get(s->x, 1)) && (stepscale==0 || (((float)gsl_vector_get(s->x, 3))<1.3 && ((float)gsl_vector_get(s->x, 3))<0.7)) )
01511 {
01512 // printf(" Refine good %1.2f %1.2f %1.1f\n",(float)gsl_vector_get(s->x, 0),(float)gsl_vector_get(s->x, 1),(float)gsl_vector_get(s->x, 2));
01513 Transform tsoln(Dict("type","2d","alpha",(float)gsl_vector_get(s->x, 2)));
01514 tsoln.set_mirror(mirror);
01515 tsoln.set_trans((float)gsl_vector_get(s->x, 0),(float)gsl_vector_get(s->x, 1));
01516 if (stepscale!=0.0) tsoln.set_scale((float)gsl_vector_get(s->x, 3));
01517 result = this_img->process("xform",Dict("transform",&tsoln));
01518 result->set_attr("xform.align2d",&tsoln);
01519 } else { // The refine aligner failed - this shift went beyond the max shift
01520 // printf(" Refine Failed %1.2f %1.2f %1.1f\n",(float)gsl_vector_get(s->x, 0),(float)gsl_vector_get(s->x, 1),(float)gsl_vector_get(s->x, 2));
01521 result = this_img->process("xform",Dict("transform",t));
01522 result->set_attr("xform.align2d",t);
01523 }
01524
01525 delete t;
01526 t = 0;
01527
01528 gsl_vector_free(x);
01529 gsl_vector_free(ss);
01530 gsl_multimin_fminimizer_free(s);
01531
01532 if ( c != 0 ) delete c;
01533 return result;
01534 }
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Implements EMAN::Aligner. Definition at line 869 of file aligner.h. 00870 {
00871 return "Refines a preliminary 2D alignment using a simplex algorithm. Subpixel precision.";
00872 }
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Get the Aligner's name. Each Aligner is identified by a unique name.
Implements EMAN::Aligner. Definition at line 864 of file aligner.h. 00865 {
00866 return NAME;
00867 }
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Implements EMAN::Aligner. Definition at line 879 of file aligner.h. References EMAN::TypeDict::put(). 00880 {
00881 TypeDict d;
00882
00883 d.put("mode", EMObject::INT, "Currently unused");
00884 d.put("xform.align2d", EMObject::TRANSFORM, "The Transform storing the starting guess. If unspecified the identity matrix is used");
00885 d.put("stepx", EMObject::FLOAT, "The x increment used to create the starting simplex. Default is 1");
00886 d.put("stepy", EMObject::FLOAT, "The y increment used to create the starting simplex. Default is 1");
00887 d.put("stepaz", EMObject::FLOAT, "The rotational increment used to create the starting simplex. Default is 5");
00888 d.put("precision", EMObject::FLOAT, "The precision which, if achieved, can stop the iterative refinement before reaching the maximum iterations. Default is 0.04.");
00889 d.put("maxiter", EMObject::INT,"The maximum number of iterations that can be performed by the Simplex minimizer");
00890 d.put("maxshift", EMObject::INT,"Maximum translation in pixels in any direction. If the solution yields a shift beyond this value in any direction, then the refinement is judged a failure and the original alignment is used as the solution.");
00891 d.put("stepscale", EMObject::FLOAT, "If set to any non-zero value, scale will be included in the alignment, and this will be the initial step. Images should be edgenormalized. If the scale goes beyond +-30% alignment will fail.");
00892 return d;
00893 }
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Definition at line 874 of file aligner.h. 00875 {
00876 return new RefineAligner();
00877 }
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Definition at line 73 of file aligner.cpp. |
1.3.9.1