Main Page | Modules | Namespace List | Class Hierarchy | Alphabetical List | Class List | Directories | File List | Namespace Members | Class Members | File Members

EMAN::Refine3DAligner Class Reference

Refine alignment. More...

#include <aligner.h>

Inheritance diagram for EMAN::Refine3DAligner:

Inheritance graph
[legend]
Collaboration diagram for EMAN::Refine3DAligner:

Collaboration graph
[legend]
List of all members.

Public Member Functions

virtual EMDataalign (EMData *this_img, EMData *to_img, const string &cmp_name="sqeuclidean", 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

AlignerNEW ()

Static Public Attributes

const string NAME = "refine.3d"

Detailed Description

Refine alignment.

Refines a preliminary 3D alignment using a simplex algorithm. Subpixel precision. Target function for the simplex algorithm is a transformation of the 3D model by az, alt, phi, tx, ty, tz The simplex algorithm downs the function downhill in a ameboa like fasion, hence it may get stuck in a local minima if the two 3D models are already roughly aligned.

Author:
David Woolford and John Flanagan
Date:
June 23 2009 and Oct 8th 2010

Definition at line 809 of file aligner.h.


Member Function Documentation

virtual EMData* EMAN::Refine3DAligner::align EMData this_img,
EMData to_img
const [inline, virtual]
 

Implements EMAN::Aligner.

Definition at line 815 of file aligner.h.

References align().

00816                         {
00817                                 return align(this_img, to_img, "sqeuclidean", Dict());
00818                         }

EMData * Refine3DAligner::align EMData this_img,
EMData to_img,
const string &  cmp_name = "sqeuclidean",
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 1447 of file aligner.cpp.

References EMAN::EMData::cmp(), EMAN::EMData::get_ndim(), EMAN::EMData::get_xsize(), EMAN::Dict::has_key(), ImageDimensionException, NullPointerException, EMAN::Cmp::params, EMAN::EMData::process(), EMAN::EMData::set_attr(), EMAN::Dict::set_default(), status, t, and x.

01449 {
01450         
01451         if (!to || !this_img) throw NullPointerException("Input image is null"); // not sure if this is necessary, it was there before I started
01452 
01453         if (to->get_ndim() != 3 || this_img->get_ndim() != 3) throw ImageDimensionException("The Refine3D aligner only works for 3D images");
01454 
01455         float saz = 0.0;
01456         float sphi = 0.0;
01457         float salt = 0.0;
01458         float sdx = 0.0;
01459         float sdy = 0.0;
01460         float sdz = 0.0;
01461         bool mirror = false;
01462         Transform* t;
01463         if (params.has_key("xform.align3d") ) {
01464                 // Unlike the 2d refine aligner, this class doesn't require the starting transform's
01465                 // parameters to form the starting guess. Instead the Transform itself
01466                 // is perturbed carefully (using quaternion rotation) to overcome problems that arise
01467                 // when you use orthogonally-based Euler angles
01468                 t = params["xform.align3d"];
01469         }else {
01470                 t = new Transform(); // is the identity
01471         }
01472 
01473         int np = 6; // the number of dimensions
01474         Dict gsl_params;
01475         gsl_params["this"] = this_img;
01476         gsl_params["with"] = to;
01477         gsl_params["snr"]  = params["snr"];
01478         gsl_params["mirror"] = mirror;
01479         gsl_params["transform"] = t;    
01480         Dict altered_cmp_params(cmp_params);
01481         if(cmp_name == "ccc.tomo"){
01482             altered_cmp_params["zeroori"] = true;
01483         }
01484         
01485         const gsl_multimin_fminimizer_type *T = gsl_multimin_fminimizer_nmsimplex;
01486         gsl_vector *ss = gsl_vector_alloc(np);
01487 
01488         float stepx = params.set_default("stepx",1.0f);
01489         float stepy = params.set_default("stepy",1.0f);
01490         float stepz = params.set_default("stepz",1.0f);
01491         // Default step is 5 degree - note in EMAN1 it was 0.1 radians
01492         //float half_circle_step = 180.0f; // This shouldn't be altered
01493         //float stepphi = params.set_default("stephi",5.0f);
01494         //float stepdelta = params.set_default("stepdelta",5.0f);
01495         float stepaz = params.set_default("stepaz",5.0f);
01496         float stepalt = params.set_default("stepalt",5.0f);
01497         float stepphi = params.set_default("stepphi",5.0f);
01498 
01499         gsl_vector_set(ss, 0, stepx);
01500         gsl_vector_set(ss, 1, stepy);
01501         gsl_vector_set(ss, 2, stepz);
01502         //gsl_vector_set(ss, 3, half_circle_step);
01503         //gsl_vector_set(ss, 4, stepdelta);
01504         //gsl_vector_set(ss, 5, stepphi);
01505         gsl_vector_set(ss, 3, stepaz);
01506         gsl_vector_set(ss, 4, stepalt);
01507         gsl_vector_set(ss, 5, stepphi);
01508 
01509         gsl_vector *x = gsl_vector_alloc(np);
01510         gsl_vector_set(x, 0, sdx);
01511         gsl_vector_set(x, 1, sdy);
01512         gsl_vector_set(x, 2, sdz);
01513         gsl_vector_set(x, 3, saz);
01514         gsl_vector_set(x, 4, salt);
01515         gsl_vector_set(x, 5, sphi);
01516 
01517         gsl_multimin_function minex_func;
01518         Cmp *c = Factory < Cmp >::get(cmp_name, altered_cmp_params);
01519         gsl_params["cmp"] = (void *) c;
01520         minex_func.f = &refalifn3d;
01521 
01522         minex_func.n = np;
01523         minex_func.params = (void *) &gsl_params;
01524 
01525         gsl_multimin_fminimizer *s = gsl_multimin_fminimizer_alloc(T, np);
01526         gsl_multimin_fminimizer_set(s, &minex_func, x, ss);
01527 
01528         int rval = GSL_CONTINUE;
01529         int status = GSL_SUCCESS;
01530         int iter = 1;
01531 
01532         float precision = params.set_default("precision",0.04f);
01533         int maxiter = params.set_default("maxiter",60);
01534         while (rval == GSL_CONTINUE && iter < maxiter) {
01535                 iter++;
01536                 status = gsl_multimin_fminimizer_iterate(s);
01537                 if (status) {
01538                         break;
01539                 }
01540                 rval = gsl_multimin_test_size(gsl_multimin_fminimizer_size(s), precision);
01541         }
01542 
01543         int maxshift = params.set_default("maxshift",-1);
01544 
01545         if (maxshift <= 0) {
01546                 maxshift = this_img->get_xsize() / 4;
01547         }
01548         float fmaxshift = static_cast<float>(maxshift);
01549         EMData *result;
01550         if ( fmaxshift >= (float)gsl_vector_get(s->x, 0) && fmaxshift >= (float)gsl_vector_get(s->x, 1)  && fmaxshift >= (float)gsl_vector_get(s->x, 2))
01551         {
01552 
01553                 //float x = (float)gsl_vector_get(s->x, 0);
01554                 //float y = (float)gsl_vector_get(s->x, 1);
01555                 //float z = (float)gsl_vector_get(s->x, 2);
01556                 //float arc = (float)gsl_vector_get(s->x, 3);
01557                 //float delta = (float)gsl_vector_get(s->x, 4);
01558                 //float phi = (float)gsl_vector_get(s->x, 5);
01559 
01560                 //Transform tsoln = refalin3d_perturb(t,delta,arc,phi,x,y,z);
01561 
01562                 //result = this_img->process("xform",Dict("transform",&tsoln));
01563                 //result->set_attr("xform.align3d",&tsoln);
01564                 Dict parms;
01565                 parms["type"] = "eman";
01566                 parms["tx"] = (float)gsl_vector_get(s->x, 0);
01567                 parms["ty"] = (float)gsl_vector_get(s->x, 1);
01568                 parms["tz"] = (float)gsl_vector_get(s->x, 2);
01569                 parms["az"] = (float)gsl_vector_get(s->x, 3);
01570                 parms["alt"] = (float)gsl_vector_get(s->x, 4);
01571                 parms["phi"] = (float)gsl_vector_get(s->x, 5);
01572                 
01573                 Transform tsoln(parms);
01574                 result = this_img->process("xform",Dict("transform",&tsoln));
01575                 result->set_attr("xform.align3d",&tsoln);
01576                 result->set_attr("score", result->cmp(cmp_name,to,cmp_params));
01577 
01578         } else { // The refine aligner failed - this shift went beyond the max shift
01579                 result = this_img->process("xform",Dict("transform",t));
01580                 result->set_attr("xform.align3d",t);
01581         }
01582 
01583         delete t;
01584         t = 0;
01585 
01586         gsl_vector_free(x);
01587         gsl_vector_free(ss);
01588         gsl_multimin_fminimizer_free(s);
01589 
01590         if ( c != 0 ) delete c;
01591         return result;
01592 }

virtual string EMAN::Refine3DAligner::get_desc  )  const [inline, virtual]
 

Implements EMAN::Aligner.

Definition at line 825 of file aligner.h.

00826                         {
00827                                 return "Refines a preliminary 3D alignment using a simplex algorithm. Subpixel precision.";
00828                         }

virtual string EMAN::Refine3DAligner::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 820 of file aligner.h.

00821                         {
00822                                 return NAME;
00823                         }

virtual TypeDict EMAN::Refine3DAligner::get_param_types  )  const [inline, virtual]
 

Implements EMAN::Aligner.

Definition at line 835 of file aligner.h.

References EMAN::TypeDict::put().

00836                         {
00837                                 TypeDict d;
00838                                 d.put("xform.align3d", EMObject::TRANSFORM,"The Transform storing the starting guess. If unspecified the identity matrix is used");
00839                                 d.put("stepx", EMObject::FLOAT, "The x increment used to create the starting simplex. Default is 1");
00840                                 d.put("stepy", EMObject::FLOAT, "The y increment used to create the starting simplex. Default is 1");
00841                                 d.put("stepz", EMObject::FLOAT, "The z increment used to create the starting simplex. Default is 1." );
00842                                 d.put("stepaz", EMObject::FLOAT, "The az increment used to create the starting simplex. Default is 5." );
00843                                 d.put("stepalt", EMObject::FLOAT, "The alt increment used to create the starting simplex. Default is 5." );
00844                                 d.put("stepphi", EMObject::FLOAT, "The phi incremenent used to create the starting simplex. Default is 5." );
00845                                 d.put("precision", EMObject::FLOAT, "The precision which, if achieved, can stop the iterative refinement before reaching the maximum iterations. Default is 0.04." );
00846                                 d.put("maxiter", EMObject::INT, "The maximum number of iterations that can be performed by the Simplex minimizer. Default is 60.");
00847                                 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.");
00848                                 return d;
00849                         }

Aligner* EMAN::Refine3DAligner::NEW  )  [inline, static]
 

Definition at line 830 of file aligner.h.

00831                         {
00832                                 return new Refine3DAligner();
00833                         }


Member Data Documentation

const string Refine3DAligner::NAME = "refine.3d" [static]
 

Definition at line 67 of file aligner.cpp.


The documentation for this class was generated from the following files:
Generated on Thu Dec 9 13:47:11 2010 for EMAN2 by  doxygen 1.3.9.1