EMAN::RefineAligner Class Reference

refine alignment. More...

#include <aligner.h>

Inheritance diagram for EMAN::RefineAligner:

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Collaboration diagram for EMAN::RefineAligner:

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List of all members.

Public Member Functions

virtual EMDataalign (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 EMDataalign (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 AlignerNEW ()

Static Public Attributes

static const string NAME = "refine"

Detailed Description

refine alignment.

Refines a preliminary 2D alignment using a simplex algorithm. Subpixel precision.

Definition at line 853 of file aligner.h.


Member Function Documentation

virtual EMData* EMAN::RefineAligner::align ( EMData this_img,
EMData to_img 
) const [inline, virtual]

Implements EMAN::Aligner.

Definition at line 859 of file aligner.h.

References align().

00860                 {
00861                         return align(this_img, to_img, "sqeuclidean", Dict());
00862                 }

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.

Parameters:
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.
Returns:
The aligned image.

Implements EMAN::Aligner.

Definition at line 1389 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().

01391 {
01392 
01393         if (!to) {
01394                 return 0;
01395         }
01396 
01397         EMData *result;
01398         int mode = params.set_default("mode", 0);
01399         float saz = 0.0;
01400         float sdx = 0.0;
01401         float sdy = 0.0;
01402         float sscale = 1.0;
01403         bool mirror = false;
01404         Transform* t;
01405         if (params.has_key("xform.align2d") ) {
01406                 t = params["xform.align2d"];
01407                 Dict params = t->get_params("2d");
01408                 saz = params["alpha"];
01409                 sdx = params["tx"];
01410                 sdy = params["ty"];
01411                 mirror = params["mirror"];
01412                 sscale = params["scale"];
01413         } else {
01414                 t = new Transform(); // is the identity
01415         }
01416 
01417         // We do this to prevent the GSL routine from crashing on an invalid alignment
01418         if ((float)(this_img->get_attr("sigma"))==0.0 || (float)(to->get_attr("sigma"))==0.0) {
01419                 result = this_img->process("xform",Dict("transform",t));
01420                 result->set_attr("xform.align2d",t);
01421                 delete t;
01422                 return result;
01423         }
01424         
01425         float stepx = params.set_default("stepx",1.0f);
01426         float stepy = params.set_default("stepy",1.0f);
01427         // Default step is 5 degree - note in EMAN1 it was 0.1 radians
01428         float stepaz = params.set_default("stepaz",5.0f);
01429         float stepscale = params.set_default("stepscale",0.0f);
01430 
01431         int np = 3;
01432         if (stepscale!=0.0) np++;
01433         Dict gsl_params;
01434         gsl_params["this"] = this_img;
01435         gsl_params["with"] = to;
01436         gsl_params["snr"]  = params["snr"];
01437         gsl_params["mirror"] = mirror;
01438 
01439         const gsl_multimin_fminimizer_type *T = gsl_multimin_fminimizer_nmsimplex;
01440         gsl_vector *ss = gsl_vector_alloc(np);
01441 
01442 
01443         gsl_vector_set(ss, 0, stepx);
01444         gsl_vector_set(ss, 1, stepy);
01445         gsl_vector_set(ss, 2, stepaz);
01446         if (stepscale!=0.0) gsl_vector_set(ss,3,stepscale);
01447         
01448         gsl_vector *x = gsl_vector_alloc(np);
01449         gsl_vector_set(x, 0, sdx);
01450         gsl_vector_set(x, 1, sdy);
01451         gsl_vector_set(x, 2, saz);
01452         if (stepscale!=0.0) gsl_vector_set(x,3,1.0);
01453         
01454         Cmp *c = 0;
01455 
01456         gsl_multimin_function minex_func;
01457         if (mode == 2) {
01458                 minex_func.f = &refalifnfast;
01459         }
01460         else {
01461                 c = Factory < Cmp >::get(cmp_name, cmp_params);
01462                 gsl_params["cmp"] = (void *) c;
01463                 minex_func.f = &refalifn;
01464         }
01465 
01466         minex_func.n = np;
01467         minex_func.params = (void *) &gsl_params;
01468 
01469         gsl_multimin_fminimizer *s = gsl_multimin_fminimizer_alloc(T, np);
01470         gsl_multimin_fminimizer_set(s, &minex_func, x, ss);
01471 
01472         int rval = GSL_CONTINUE;
01473         int status = GSL_SUCCESS;
01474         int iter = 1;
01475 
01476         float precision = params.set_default("precision",0.04f);
01477         int maxiter = params.set_default("maxiter",28);
01478 
01479 //      printf("Refine sx=%1.2f sy=%1.2f sa=%1.2f prec=%1.4f maxit=%d\n",stepx,stepy,stepaz,precision,maxiter);
01480 //      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));
01481 
01482         while (rval == GSL_CONTINUE && iter < maxiter) {
01483                 iter++;
01484                 status = gsl_multimin_fminimizer_iterate(s);
01485                 if (status) {
01486                         break;
01487                 }
01488                 rval = gsl_multimin_test_size(gsl_multimin_fminimizer_size(s), precision);
01489         }
01490 
01491         int maxshift = params.set_default("maxshift",-1);
01492 
01493         if (maxshift <= 0) {
01494                 maxshift = this_img->get_xsize() / 4;
01495         }
01496         float fmaxshift = static_cast<float>(maxshift);
01497         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))  )
01498         {
01499 //              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));
01500                 Transform  tsoln(Dict("type","2d","alpha",(float)gsl_vector_get(s->x, 2)));
01501                 tsoln.set_mirror(mirror);
01502                 tsoln.set_trans((float)gsl_vector_get(s->x, 0),(float)gsl_vector_get(s->x, 1));
01503                 if (stepscale!=0.0) tsoln.set_scale((float)gsl_vector_get(s->x, 3));
01504                 result = this_img->process("xform",Dict("transform",&tsoln));
01505                 result->set_attr("xform.align2d",&tsoln);
01506         } else { // The refine aligner failed - this shift went beyond the max shift
01507 //              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));
01508                 result = this_img->process("xform",Dict("transform",t));
01509                 result->set_attr("xform.align2d",t);
01510         }
01511 
01512         delete t;
01513         t = 0;
01514 
01515         gsl_vector_free(x);
01516         gsl_vector_free(ss);
01517         gsl_multimin_fminimizer_free(s);
01518 
01519         if ( c != 0 ) delete c;
01520         return result;
01521 }

virtual string EMAN::RefineAligner::get_desc (  )  const [inline, virtual]

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                 }

virtual string EMAN::RefineAligner::get_name (  )  const [inline, virtual]

Get the Aligner's name.

Each Aligner is identified by a unique name.

Returns:
The Aligner's name.

Implements EMAN::Aligner.

Definition at line 864 of file aligner.h.

References NAME.

00865                 {
00866                         return NAME;
00867                 }

virtual TypeDict EMAN::RefineAligner::get_param_types (  )  const [inline, virtual]

Implements EMAN::Aligner.

Definition at line 879 of file aligner.h.

References EMAN::EMObject::FLOAT, EMAN::EMObject::INT, EMAN::TypeDict::put(), and EMAN::EMObject::TRANSFORM.

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                 }

static Aligner* EMAN::RefineAligner::NEW (  )  [inline, static]

Definition at line 874 of file aligner.h.

00875                 {
00876                         return new RefineAligner();
00877                 }


Member Data Documentation

const string RefineAligner::NAME = "refine" [static]

Definition at line 895 of file aligner.h.

Referenced by get_name().


The documentation for this class was generated from the following files:
Generated on Mon Mar 7 18:08:41 2011 for EMAN2 by  doxygen 1.4.7