#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 | |
static Aligner * | NEW () |
Static Public Attributes | |
static const string | NAME = "refine" |
Refines a preliminary 2D alignment using a simplex algorithm. Subpixel precision.
Definition at line 900 of file aligner.h.
virtual EMData* EMAN::RefineAligner::align | ( | EMData * | this_img, | |
EMData * | to_img | |||
) | const [inline, virtual] |
Implements EMAN::Aligner.
Definition at line 906 of file aligner.h.
References align().
00907 { 00908 return align(this_img, to_img, "sqeuclidean", Dict()); 00909 }
EMData * RefineAligner::align | ( | EMData * | this_img, | |
EMData * | to_img, | |||
const string & | cmp_name = "dot" , |
|||
const Dict & | cmp_params = Dict() | |||
) | 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 1458 of file aligner.cpp.
References EMAN::EMData::get_attr(), EMAN::EMData::get_xsize(), EMAN::Dict::has_key(), EMAN::Aligner::params, EMAN::EMData::process(), refalifn(), refalifnfast(), EMAN::EMData::set_attr(), EMAN::Dict::set_default(), EMAN::Transform::set_mirror(), EMAN::Transform::set_scale(), EMAN::Transform::set_trans(), status, t, and x.
Referenced by align().
01460 { 01461 01462 if (!to) { 01463 return 0; 01464 } 01465 01466 EMData *result; 01467 int mode = params.set_default("mode", 0); 01468 float saz = 0.0; 01469 float sdx = 0.0; 01470 float sdy = 0.0; 01471 float sscale = 1.0; 01472 bool mirror = false; 01473 Transform* t; 01474 if (params.has_key("xform.align2d") ) { 01475 t = params["xform.align2d"]; 01476 Dict params = t->get_params("2d"); 01477 saz = params["alpha"]; 01478 sdx = params["tx"]; 01479 sdy = params["ty"]; 01480 mirror = params["mirror"]; 01481 sscale = params["scale"]; 01482 } else { 01483 t = new Transform(); // is the identity 01484 } 01485 01486 // We do this to prevent the GSL routine from crashing on an invalid alignment 01487 if ((float)(this_img->get_attr("sigma"))==0.0 || (float)(to->get_attr("sigma"))==0.0) { 01488 result = this_img->process("xform",Dict("transform",t)); 01489 result->set_attr("xform.align2d",t); 01490 delete t; 01491 return result; 01492 } 01493 01494 float stepx = params.set_default("stepx",1.0f); 01495 float stepy = params.set_default("stepy",1.0f); 01496 // Default step is 5 degree - note in EMAN1 it was 0.1 radians 01497 float stepaz = params.set_default("stepaz",5.0f); 01498 float stepscale = params.set_default("stepscale",0.0f); 01499 01500 int np = 3; 01501 if (stepscale!=0.0) np++; 01502 Dict gsl_params; 01503 gsl_params["this"] = this_img; 01504 gsl_params["with"] = to; 01505 gsl_params["snr"] = params["snr"]; 01506 gsl_params["mirror"] = mirror; 01507 01508 const gsl_multimin_fminimizer_type *T = gsl_multimin_fminimizer_nmsimplex; 01509 gsl_vector *ss = gsl_vector_alloc(np); 01510 01511 01512 gsl_vector_set(ss, 0, stepx); 01513 gsl_vector_set(ss, 1, stepy); 01514 gsl_vector_set(ss, 2, stepaz); 01515 if (stepscale!=0.0) gsl_vector_set(ss,3,stepscale); 01516 01517 gsl_vector *x = gsl_vector_alloc(np); 01518 gsl_vector_set(x, 0, sdx); 01519 gsl_vector_set(x, 1, sdy); 01520 gsl_vector_set(x, 2, saz); 01521 if (stepscale!=0.0) gsl_vector_set(x,3,1.0); 01522 01523 Cmp *c = 0; 01524 01525 gsl_multimin_function minex_func; 01526 if (mode == 2) { 01527 minex_func.f = &refalifnfast; 01528 } 01529 else { 01530 c = Factory < Cmp >::get(cmp_name, cmp_params); 01531 gsl_params["cmp"] = (void *) c; 01532 minex_func.f = &refalifn; 01533 } 01534 01535 minex_func.n = np; 01536 minex_func.params = (void *) &gsl_params; 01537 01538 gsl_multimin_fminimizer *s = gsl_multimin_fminimizer_alloc(T, np); 01539 gsl_multimin_fminimizer_set(s, &minex_func, x, ss); 01540 01541 int rval = GSL_CONTINUE; 01542 int status = GSL_SUCCESS; 01543 int iter = 1; 01544 01545 float precision = params.set_default("precision",0.04f); 01546 int maxiter = params.set_default("maxiter",28); 01547 01548 // printf("Refine sx=%1.2f sy=%1.2f sa=%1.2f prec=%1.4f maxit=%d\n",stepx,stepy,stepaz,precision,maxiter); 01549 // 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)); 01550 01551 while (rval == GSL_CONTINUE && iter < maxiter) { 01552 iter++; 01553 status = gsl_multimin_fminimizer_iterate(s); 01554 if (status) { 01555 break; 01556 } 01557 rval = gsl_multimin_test_size(gsl_multimin_fminimizer_size(s), precision); 01558 } 01559 01560 int maxshift = params.set_default("maxshift",-1); 01561 01562 if (maxshift <= 0) { 01563 maxshift = this_img->get_xsize() / 4; 01564 } 01565 float fmaxshift = static_cast<float>(maxshift); 01566 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)) ) 01567 { 01568 // 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)); 01569 Transform tsoln(Dict("type","2d","alpha",(float)gsl_vector_get(s->x, 2))); 01570 tsoln.set_mirror(mirror); 01571 tsoln.set_trans((float)gsl_vector_get(s->x, 0),(float)gsl_vector_get(s->x, 1)); 01572 if (stepscale!=0.0) tsoln.set_scale((float)gsl_vector_get(s->x, 3)); 01573 result = this_img->process("xform",Dict("transform",&tsoln)); 01574 result->set_attr("xform.align2d",&tsoln); 01575 } else { // The refine aligner failed - this shift went beyond the max shift 01576 // 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)); 01577 result = this_img->process("xform",Dict("transform",t)); 01578 result->set_attr("xform.align2d",t); 01579 } 01580 01581 delete t; 01582 t = 0; 01583 01584 gsl_vector_free(x); 01585 gsl_vector_free(ss); 01586 gsl_multimin_fminimizer_free(s); 01587 01588 if ( c != 0 ) delete c; 01589 return result; 01590 }
virtual string EMAN::RefineAligner::get_desc | ( | ) | const [inline, virtual] |
Implements EMAN::Aligner.
Definition at line 916 of file aligner.h.
00917 { 00918 return "Refines a preliminary 2D alignment using a simplex algorithm. Subpixel precision."; 00919 }
virtual string EMAN::RefineAligner::get_name | ( | ) | const [inline, virtual] |
virtual TypeDict EMAN::RefineAligner::get_param_types | ( | ) | const [inline, virtual] |
Implements EMAN::Aligner.
Definition at line 926 of file aligner.h.
References EMAN::EMObject::FLOAT, EMAN::EMObject::INT, EMAN::TypeDict::put(), and EMAN::EMObject::TRANSFORM.
00927 { 00928 TypeDict d; 00929 00930 d.put("mode", EMObject::INT, "Currently unused"); 00931 d.put("xform.align2d", EMObject::TRANSFORM, "The Transform storing the starting guess. If unspecified the identity matrix is used"); 00932 d.put("stepx", EMObject::FLOAT, "The x increment used to create the starting simplex. Default is 1"); 00933 d.put("stepy", EMObject::FLOAT, "The y increment used to create the starting simplex. Default is 1"); 00934 d.put("stepaz", EMObject::FLOAT, "The rotational increment used to create the starting simplex. Default is 5"); 00935 d.put("precision", EMObject::FLOAT, "The precision which, if achieved, can stop the iterative refinement before reaching the maximum iterations. Default is 0.04."); 00936 d.put("maxiter", EMObject::INT,"The maximum number of iterations that can be performed by the Simplex minimizer"); 00937 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."); 00938 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."); 00939 return d; 00940 }
static Aligner* EMAN::RefineAligner::NEW | ( | ) | [inline, static] |
const string RefineAligner::NAME = "refine" [static] |