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EMAN::OptimumOrientationGenerator Class Reference

Optimum orientation generator. More...

#include <symmetry.h>

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List of all members.

Public Member Functions

 OptimumOrientationGenerator ()
virtual ~OptimumOrientationGenerator ()
virtual string get_name () const
 Return "opt".
virtual string get_desc () const
 Get a description.
virtual TypeDict get_param_types () const
 Get a dictionary containing the permissable parameters of this class.
virtual vector< Transformgen_orientations (const Symmetry3D *const sym) const
 Generate Saff orientations in the asymmetric unit of the symmetry.

Static Public Member Functions

static OrientationGeneratorNEW ()
 Factory support function NEW.

Static Public Attributes

static const string NAME = "opt"
 The name of this class - used to access it from factories etc. Should be "icos".

Private Member Functions

 OptimumOrientationGenerator (const OptimumOrientationGenerator &)
 Disallow copy construction.
OptimumOrientationGeneratoroperator= (const OptimumOrientationGenerator &)
 Disallow assignment.
virtual int get_orientations_tally (const Symmetry3D *const sym, const float &delta) const
 This function returns how many orientations will be generated for a given delta (angular spacing) It does this by simulated gen_orientations.
vector< Vec3foptimize_distances (const vector< Transform > &v) const
 Optimize the distances in separating points on the unit sphere, as described by the the rotations in Transform objects.

Detailed Description

Optimum orientation generator.

Optimally distributes points on a unit sphere, then slices out a correctly sized asymmetric unit, depending on the symmetry type. The approach relies on an initial distribution of points on the unit sphere, which may be generated using any of the other orientation generators. By default, the Saff orientation generator is used.

Author:
David Woolford
Date:
March 2008

Definition at line 1303 of file symmetry.h.


Constructor & Destructor Documentation

EMAN::OptimumOrientationGenerator::OptimumOrientationGenerator  )  [inline]
 

Definition at line 1306 of file symmetry.h.

Referenced by NEW().

01306 {}

virtual EMAN::OptimumOrientationGenerator::~OptimumOrientationGenerator  )  [inline, virtual]
 

Definition at line 1307 of file symmetry.h.

01307 {}

EMAN::OptimumOrientationGenerator::OptimumOrientationGenerator const OptimumOrientationGenerator  )  [private]
 

Disallow copy construction.


Member Function Documentation

vector< Transform > OptimumOrientationGenerator::gen_orientations const Symmetry3D *const   sym  )  const [virtual]
 

Generate Saff orientations in the asymmetric unit of the symmetry.

Parameters:
sym the symmetry which defines the interesting asymmetric unit
Returns:
a vector of Transform objects containing the set of evenly distributed orientations

Implements EMAN::OrientationGenerator.

Definition at line 711 of file symmetry.cpp.

References EMAN::OrientationGenerator::add_orientation(), angles, EMAN::FactoryBase::copy_relevant_params(), EMAN::OrientationGenerator::gen_orientations(), EMAN::OrientationGenerator::get_optimal_delta(), InvalidParameterException, EMAN::Symmetry3D::is_in_asym_unit(), EMAN::RandomOrientationGenerator::NAME, optimize_distances(), EMAN::FactoryBase::params, EMAN::Dict::set_default(), and EMAN::FactoryBase::set_params().

00712 {
00713         float delta = params.set_default("delta", 0.0f);
00714         int n = params.set_default("n", 0);
00715 
00716         bool inc_mirror = params.set_default("inc_mirror",false);
00717 
00718         if ( delta <= 0 && n <= 0 ) throw InvalidParameterException("Error, you must specify a positive non-zero delta or n");
00719         if ( delta > 0 && n > 0 ) throw InvalidParameterException("Error, the delta and the n arguments are mutually exclusive");
00720 
00721         string generatorname = params.set_default("use","saff");
00722 
00723         if ( n > 0 && generatorname != RandomOrientationGenerator::NAME ) {
00724                 params["delta"] = get_optimal_delta(sym,n);
00725                 params["n"] = (int)0;
00726         }
00727 
00728         // Force the orientation generator to include the mirror - this is because
00729         // We will enventually use it to generate orientations over the intire sphere
00730         // which is C1 symmetry, with the inc_mirror flag set to true
00731         params["inc_mirror"] = true;
00732         OrientationGenerator* g = Factory < OrientationGenerator >::get(generatorname);
00733         g->set_params(copy_relevant_params(g));
00734 
00735 
00736         // get the starting orientation distribution
00737         CSym* unit_sphere = new CSym();
00738         Dict nsym; nsym["nsym"] = 1; unit_sphere->set_params(nsym);
00739 
00740         vector<Transform> unitsphereorientations = g->gen_orientations(unit_sphere);
00741         delete g; g = 0;
00742         delete unit_sphere; unit_sphere = 0;
00743 
00744         vector<Vec3f> angles = optimize_distances(unitsphereorientations);
00745 
00746         vector<Transform> ret;
00747         for (vector<Vec3f>::const_iterator it = angles.begin(); it != angles.end(); ++it ) {
00748                 if ( sym->is_in_asym_unit((*it)[1],(*it)[0],inc_mirror) ) {
00749                         add_orientation(ret,(*it)[0],(*it)[1]);
00750                 }
00751         }
00752 
00753         // reset the params to what they were before they were acted upon by this class
00754         params["inc_mirror"] = inc_mirror;
00755         params["delta"] = delta;
00756         params["n"] = n;
00757 
00758         return ret;
00759 }

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

Get a description.

Returns:
a clear desciption of this class

Implements EMAN::FactoryBase.

Definition at line 1325 of file symmetry.h.

01325 { return "Generate optimally distributed orientations within an asymmetric using a basic optimization technique"; }

virtual string EMAN::OptimumOrientationGenerator::get_name  )  const [inline, virtual]
 

Return "opt".

Returns:
the unique name of this class

Implements EMAN::FactoryBase.

Definition at line 1320 of file symmetry.h.

References NAME.

01320 { return NAME; }

int OptimumOrientationGenerator::get_orientations_tally const Symmetry3D *const   sym,
const float &  delta
const [private, virtual]
 

This function returns how many orientations will be generated for a given delta (angular spacing) It does this by simulated gen_orientations.

Parameters:
sym the symmetry which defines the interesting asymmetric unit
delta the desired angular spacing of the orientations
Returns:
the number of orientations that will be generated using these parameters

Implements EMAN::OrientationGenerator.

Definition at line 696 of file symmetry.cpp.

References EMAN::OrientationGenerator::get_orientations_tally(), EMAN::FactoryBase::params, and EMAN::Dict::set_default().

00697 {
00698         string deltaoptname = params.set_default("use","saff");
00699         Dict a;
00700         a["inc_mirror"] = (bool)params.set_default("inc_mirror",false);
00701         OrientationGenerator *g = Factory < OrientationGenerator >::get(deltaoptname,a);
00702         if (g) {
00703                 int tally = g->get_orientations_tally(sym,delta);
00704                 delete g;
00705                 g = 0;
00706                 return tally;
00707         }
00708         else throw;
00709 }

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

Get a dictionary containing the permissable parameters of this class.

Returns:
a dictionary containing the permissable parameters of this class parameters are explained in the dictionary itself

Reimplemented from EMAN::OrientationGenerator.

Definition at line 1331 of file symmetry.h.

References EMAN::EMObject::BOOL, EMAN::EMObject::FLOAT, EMAN::OrientationGenerator::get_param_types(), EMAN::EMObject::INT, EMAN::TypeDict::put(), and EMAN::EMObject::STRING.

01332                 {
01333                         TypeDict d = OrientationGenerator::get_param_types();
01334                         d.put("n", EMObject::INT, "The number of orientations to generate. This option is mutually exclusively of the delta argument.Will attempt to get as close to the number specified as possible.");
01335                         d.put("inc_mirror", EMObject::BOOL, "Indicates whether or not to include the mirror portion of the asymmetric unit. Default is false.");
01336                         d.put("delta", EMObject::FLOAT, "The angular separation of orientations in degrees. This option is mutually exclusively of the n argument.");
01337                         d.put("use", EMObject::STRING, "The orientation generation technique used to generate the initial distribution on the unit sphere.");
01338                         return d;
01339                 }

static OrientationGenerator* EMAN::OptimumOrientationGenerator::NEW  )  [inline, static]
 

Factory support function NEW.

Returns:
a newly instantiated class of this type

Definition at line 1312 of file symmetry.h.

References OptimumOrientationGenerator().

01313                 {
01314                         return new OptimumOrientationGenerator();
01315                 }

OptimumOrientationGenerator& EMAN::OptimumOrientationGenerator::operator= const OptimumOrientationGenerator  )  [private]
 

Disallow assignment.

vector< Vec3f > OptimumOrientationGenerator::optimize_distances const vector< Transform > &  v  )  const [private]
 

Optimize the distances in separating points on the unit sphere, as described by the the rotations in Transform objects.

Definition at line 761 of file symmetry.cpp.

References EMAN::Vec3< Type >::normalize(), and EMAN::EMConsts::rad2deg.

Referenced by gen_orientations().

00762 {
00763         vector<Vec3f> points;
00764 
00765         for (vector<Transform>::const_iterator it = v.begin(); it != v.end(); ++it ) {
00766                 points.push_back(Vec3f(0,0,1)*(*it));
00767         }
00768 
00769         if ( points.size() >= 2 ) {
00770                 int max_it = 100;
00771                 float percentage = 0.01f;
00772 
00773                 for ( int i = 0; i < max_it; ++i ){
00774                         unsigned int p1 = 0;
00775                         unsigned int p2 = 1;
00776 
00777                         float distsquared = (points[p1]-points[p2]).squared_length();
00778 
00779                         // Find the nearest points
00780                         for(unsigned int j = 0; j < points.size(); ++j) {
00781                                 for(unsigned int k = j+1; k < points.size(); ++k) {
00782                                         float d = (points[j]-points[k]).squared_length();
00783                                         if ( d < distsquared ) {
00784                                                 distsquared = d;
00785                                                 p1 = j;
00786                                                 p2 = k;
00787                                         }
00788                                 }
00789                         }
00790 
00791                         // Move them apart by a small fraction
00792                         Vec3f delta = percentage*(points[p2]-points[p1]);
00793 
00794                         points[p2] += delta;
00795                         points[p2].normalize();
00796                         points[p1] -= delta;
00797                         points[p1].normalize();
00798                 }
00799         }
00800 
00801         vector<Vec3f> ret;
00802         for (vector<Vec3f>::const_iterator it = points.begin(); it != points.end(); ++it ) {
00803                 float altitude = (float)(EMConsts::rad2deg*acos((*it)[2]));
00804                 float azimuth = (float)(EMConsts::rad2deg*atan2((*it)[1],(*it)[0]));
00805                 ret.push_back(Vec3f(90.0f+azimuth,altitude,0));
00806         }
00807 
00808         return ret;
00809 }


Member Data Documentation

const string OptimumOrientationGenerator::NAME = "opt" [static]
 

The name of this class - used to access it from factories etc. Should be "icos".

Definition at line 1348 of file symmetry.h.

Referenced by get_name().


The documentation for this class was generated from the following files:
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