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EMAN::Refine3DAlignerQuaternion Class Reference
[a function or class that is CUDA enabled]

Refine alignment. More...

#include <aligner.h>

Inheritance diagram for EMAN::Refine3DAlignerQuaternion:

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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 rotation along an arbitrary axis defined by a quaternion, whose rotation magnitude is defined by the vector length (hence the simplex varies the vecotr component of the quaternion). In addition the simplex varies translation. Using quaternions avoids gimbal lock. The simplex algorithm moves 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.

Parameters:
xform.align3d The Transform storing the starting guess. If unspecified the identity matrix is used
stepx The initial simplex step size in x
stepy The initial simplex step size in y
stepz The initial simplex step size in z
stepn0 The initial simplex step size in the first quaternion vecotr component
stepn1 The initial simplex step size in the second quaternion vecotr component
stepn2 The initial simplex step size in the third quaternion vecotr component
spin_coeff The multiplier appied to the spin (if it is too small or too large the simplex will not converge)
precision The precision which, if achieved, can stop the iterative refinement before reaching the maximum iterations
maxiter The maximum number of iterations that can be performed by the Simplex minimizer
maxshift Maximum translation in pixels in any direction.
Author:
John Flanagan (with code recyled from David Woolford)
Date:
Feb 3rd 2011

Definition at line 982 of file aligner.h.


Member Function Documentation

virtual EMData* EMAN::Refine3DAlignerQuaternion::align EMData this_img,
EMData to_img
const [inline, virtual]
 

Implements EMAN::Aligner.

Definition at line 988 of file aligner.h.

References align().

00989                         {
00990                                 return align(this_img, to_img, "sqeuclidean", Dict());
00991                         }

EMData * Refine3DAlignerQuaternion::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 1576 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(), refalin3d_perturbquat(), EMAN::EMData::set_attr(), EMAN::Dict::set_default(), status, t, x, and y.

01578 {
01579         
01580         if (!to || !this_img) throw NullPointerException("Input image is null"); // not sure if this is necessary, it was there before I started
01581 
01582         if (to->get_ndim() != 3 || this_img->get_ndim() != 3) throw ImageDimensionException("The Refine3D aligner only works for 3D images");
01583 
01584 #ifdef EMAN2_USING_CUDA 
01585         if(EMData::usecuda == 1) {
01586                 if(!this_img->cudarwdata) this_img->copy_to_cuda();
01587                 if(!to->cudarwdata) to->copy_to_cuda();
01588         }
01589 #endif
01590 
01591         float sdi = 0.0;
01592         float sdj = 0.0;
01593         float sdk = 0.0;
01594         float sdx = 0.0;
01595         float sdy = 0.0;
01596         float sdz = 0.0;
01597         bool mirror = false;
01598         
01599         Transform* t;
01600         if (params.has_key("xform.align3d") ) {
01601                 // Unlike the 2d refine aligner, this class doesn't require the starting transform's
01602                 // parameters to form the starting guess. Instead the Transform itself
01603                 // is perturbed carefully (using quaternion rotation) to overcome problems that arise
01604                 // when you use orthogonally-based Euler angles
01605                 t = params["xform.align3d"];
01606         }else {
01607                 t = new Transform(); // is the identity
01608         }
01609         
01610         float spincoeff =  params.set_default("spin_coeff",10.0f); // spin coefficient, controls speed of convergence (sort of)
01611         
01612         int np = 6; // the number of dimensions
01613         Dict gsl_params;
01614         gsl_params["this"] = this_img;
01615         gsl_params["with"] = to;
01616         gsl_params["snr"]  = params["snr"];
01617         gsl_params["mirror"] = mirror;
01618         gsl_params["transform"] = t;    
01619         gsl_params["spincoeff"] = spincoeff;
01620         Dict altered_cmp_params(cmp_params);
01621         
01622         const gsl_multimin_fminimizer_type *T = gsl_multimin_fminimizer_nmsimplex;
01623         gsl_vector *ss = gsl_vector_alloc(np);
01624         
01625         float stepi = params.set_default("stepi",1.0f); // doesn't really matter b/c the vecor part will be normalized anyway
01626         float stepj = params.set_default("stepj",1.0f); // doesn't really matter b/c the vecor part will be normalized anyway
01627         float stepk = params.set_default("stepk",1.0f); // doesn't really matter b/c the vecor part will be normalized anyway
01628         float stepx = params.set_default("stepx",1.0f);
01629         float stepy = params.set_default("stepy",1.0f);
01630         float stepz = params.set_default("stepz",1.0f);
01631         
01632         //gsl_vector_set(ss, 0, stepw);
01633         gsl_vector_set(ss, 0, stepi);
01634         gsl_vector_set(ss, 1, stepj);
01635         gsl_vector_set(ss, 2, stepk);
01636         gsl_vector_set(ss, 3, stepx);
01637         gsl_vector_set(ss, 4, stepy);
01638         gsl_vector_set(ss, 5, stepz);
01639         
01640         gsl_vector *x = gsl_vector_alloc(np);
01641         gsl_vector_set(x, 0, sdi);
01642         gsl_vector_set(x, 1, sdj);
01643         gsl_vector_set(x, 2, sdk);
01644         gsl_vector_set(x, 3, sdx);
01645         gsl_vector_set(x, 4, sdy);
01646         gsl_vector_set(x, 5, sdz);
01647         
01648         gsl_multimin_function minex_func;
01649         Cmp *c = Factory < Cmp >::get(cmp_name, altered_cmp_params);
01650                 
01651         gsl_params["cmp"] = (void *) c;
01652         minex_func.f = &refalifn3dquat;
01653 
01654         minex_func.n = np;
01655         minex_func.params = (void *) &gsl_params;
01656         
01657         gsl_multimin_fminimizer *s = gsl_multimin_fminimizer_alloc(T, np);
01658         gsl_multimin_fminimizer_set(s, &minex_func, x, ss);
01659         
01660         int rval = GSL_CONTINUE;
01661         int status = GSL_SUCCESS;
01662         int iter = 1;
01663         
01664         float precision = params.set_default("precision",0.01f);
01665         int maxiter = params.set_default("maxiter",100);
01666         while (rval == GSL_CONTINUE && iter < maxiter) {
01667                 iter++;
01668                 status = gsl_multimin_fminimizer_iterate(s);
01669                 if (status) {
01670                         break;
01671                 }
01672                 rval = gsl_multimin_test_size(gsl_multimin_fminimizer_size(s), precision);
01673         }
01674 
01675         int maxshift = params.set_default("maxshift",-1);
01676 
01677         if (maxshift <= 0) {
01678                 maxshift = this_img->get_xsize() / 4;
01679         }
01680         float fmaxshift = static_cast<float>(maxshift);
01681         
01682         EMData *result;
01683         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))
01684         {
01685                 float n0 = (float)gsl_vector_get(s->x, 0);
01686                 float n1 = (float)gsl_vector_get(s->x, 1);
01687                 float n2 = (float)gsl_vector_get(s->x, 2);
01688                 float x = (float)gsl_vector_get(s->x, 3);
01689                 float y = (float)gsl_vector_get(s->x, 4);
01690                 float z = (float)gsl_vector_get(s->x, 5);
01691                 
01692                 Transform tsoln = refalin3d_perturbquat(t,spincoeff,n0,n1,n2,x,y,z);
01693                         
01694                 result = this_img->process("xform",Dict("transform",&tsoln));
01695                 result->set_attr("xform.align3d",&tsoln);
01696                 result->set_attr("score", result->cmp(cmp_name,to,cmp_params));
01697                 
01698          //coda goes here
01699         } else { // The refine aligner failed - this shift went beyond the max shift
01700                 result = this_img->process("xform",Dict("transform",t));
01701                 result->set_attr("xform.align3d",t);
01702         }
01703         
01704         //EMData *result = this_img->process("xform",Dict("transform",t));
01705         delete t;
01706         t = 0;
01707         gsl_vector_free(x);
01708         gsl_vector_free(ss);
01709         gsl_multimin_fminimizer_free(s);
01710 
01711         if ( c != 0 ) delete c;
01712         return result;
01713 }

virtual string EMAN::Refine3DAlignerQuaternion::get_desc  )  const [inline, virtual]
 

Implements EMAN::Aligner.

Definition at line 998 of file aligner.h.

00999                         {
01000                                 return "Refines a preliminary 3D alignment using a simplex algorithm. Subpixel precision.";
01001                         }

virtual string EMAN::Refine3DAlignerQuaternion::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 993 of file aligner.h.

00994                         {
00995                                 return NAME;
00996                         }

virtual TypeDict EMAN::Refine3DAlignerQuaternion::get_param_types  )  const [inline, virtual]
 

Implements EMAN::Aligner.

Definition at line 1008 of file aligner.h.

References EMAN::TypeDict::put().

01009                         {
01010                                 TypeDict d;
01011                                 d.put("xform.align3d", EMObject::TRANSFORM,"The Transform storing the starting guess. If unspecified the identity matrix is used");
01012                                 d.put("stepx", EMObject::FLOAT, "The initial simplex step size in x. Default is 1");
01013                                 d.put("stepy", EMObject::FLOAT, "The initial simplex step size in y. Default is 1");
01014                                 d.put("stepz", EMObject::FLOAT, "The initial simplex step size in z. Default is 1." );
01015                                 d.put("stepn0", EMObject::FLOAT, "The initial simplex step size in the first quaternion vecotr component. Default is 1." );
01016                                 d.put("stepn1", EMObject::FLOAT, "The initial simplex step size in the second quaternion vecotr component. Default is 1." );
01017                                 d.put("stepn2", EMObject::FLOAT, "The initial simplex step size in the third quaternion vecotr component. Default is 1." );
01018                                 d.put("spin_coeff", EMObject::FLOAT,"The multiplier appied to the spin (if it is too small or too large the simplex will not converge).  Default is 10.");
01019                                 d.put("precision", EMObject::FLOAT, "The precision which, if achieved, can stop the iterative refinement before reaching the maximum iterations. Default is 0.01." );
01020                                 d.put("maxiter", EMObject::INT, "The maximum number of iterations that can be performed by the Simplex minimizer. Default is 100.");
01021                                 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.");
01022                                 return d;
01023                         }

Aligner* EMAN::Refine3DAlignerQuaternion::NEW  )  [inline, static]
 

Definition at line 1003 of file aligner.h.

01004                         {
01005                                 return new Refine3DAlignerQuaternion();
01006                         }


Member Data Documentation

const string Refine3DAlignerQuaternion::NAME = "refine_3d" [static]
 

Definition at line 75 of file aligner.cpp.


The documentation for this class was generated from the following files:
Generated on Thu Mar 10 22:59:09 2011 for EMAN2 by  doxygen 1.3.9.1