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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 1306 of file symmetry.h.


Constructor & Destructor Documentation

EMAN::OptimumOrientationGenerator::OptimumOrientationGenerator  )  [inline]
 

Definition at line 1309 of file symmetry.h.

Referenced by NEW().

01309 {}

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

Definition at line 1310 of file symmetry.h.

01310 {}

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 731 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().

00732 {
00733         float delta = params.set_default("delta", 0.0f);
00734         int n = params.set_default("n", 0);
00735 
00736         bool inc_mirror = params.set_default("inc_mirror",false);
00737 
00738         if ( delta <= 0 && n <= 0 ) throw InvalidParameterException("Error, you must specify a positive non-zero delta or n");
00739         if ( delta > 0 && n > 0 ) throw InvalidParameterException("Error, the delta and the n arguments are mutually exclusive");
00740 
00741         string generatorname = params.set_default("use","saff");
00742 
00743         if ( n > 0 && generatorname != RandomOrientationGenerator::NAME ) {
00744                 params["delta"] = get_optimal_delta(sym,n);
00745                 params["n"] = (int)0;
00746         }
00747 
00748         // Force the orientation generator to include the mirror - this is because
00749         // We will enventually use it to generate orientations over the intire sphere
00750         // which is C1 symmetry, with the inc_mirror flag set to true
00751         params["inc_mirror"] = true;
00752         OrientationGenerator* g = Factory < OrientationGenerator >::get(generatorname);
00753         g->set_params(copy_relevant_params(g));
00754 
00755 
00756         // get the starting orientation distribution
00757         CSym* unit_sphere = new CSym();
00758         Dict nsym; nsym["nsym"] = 1; unit_sphere->set_params(nsym);
00759 
00760         vector<Transform> unitsphereorientations = g->gen_orientations(unit_sphere);
00761         delete g; g = 0;
00762         delete unit_sphere; unit_sphere = 0;
00763 
00764         vector<Vec3f> angles = optimize_distances(unitsphereorientations);
00765 
00766         vector<Transform> ret;
00767         for (vector<Vec3f>::const_iterator it = angles.begin(); it != angles.end(); ++it ) {
00768                 if ( sym->is_in_asym_unit((*it)[1],(*it)[0],inc_mirror) ) {
00769                         add_orientation(ret,(*it)[0],(*it)[1]);
00770                 }
00771         }
00772 
00773         // reset the params to what they were before they were acted upon by this class
00774         params["inc_mirror"] = inc_mirror;
00775         params["delta"] = delta;
00776         params["n"] = n;
00777 
00778         return ret;
00779 }

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 1328 of file symmetry.h.

01328 { 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 1323 of file symmetry.h.

References NAME.

01323 { 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 716 of file symmetry.cpp.

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

00717 {
00718         string deltaoptname = params.set_default("use","saff");
00719         Dict a;
00720         a["inc_mirror"] = (bool)params.set_default("inc_mirror",false);
00721         OrientationGenerator *g = Factory < OrientationGenerator >::get(deltaoptname,a);
00722         if (g) {
00723                 int tally = g->get_orientations_tally(sym,delta);
00724                 delete g;
00725                 g = 0;
00726                 return tally;
00727         }
00728         else throw;
00729 }

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 1334 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.

01335                 {
01336                         TypeDict d = OrientationGenerator::get_param_types();
01337                         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.");
01338                         d.put("inc_mirror", EMObject::BOOL, "Indicates whether or not to include the mirror portion of the asymmetric unit. Default is false.");
01339                         d.put("delta", EMObject::FLOAT, "The angular separation of orientations in degrees. This option is mutually exclusively of the n argument.");
01340                         d.put("use", EMObject::STRING, "The orientation generation technique used to generate the initial distribution on the unit sphere.");
01341                         return d;
01342                 }

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

Factory support function NEW.

Returns:
a newly instantiated class of this type

Definition at line 1315 of file symmetry.h.

References OptimumOrientationGenerator().

01316                 {
01317                         return new OptimumOrientationGenerator();
01318                 }

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 781 of file symmetry.cpp.

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

Referenced by gen_orientations().

00782 {
00783         vector<Vec3f> points;
00784 
00785         for (vector<Transform>::const_iterator it = v.begin(); it != v.end(); ++it ) {
00786                 points.push_back(Vec3f(0,0,1)*(*it));
00787         }
00788 
00789         if ( points.size() >= 2 ) {
00790                 int max_it = 100;
00791                 float percentage = 0.01f;
00792 
00793                 for ( int i = 0; i < max_it; ++i ){
00794                         unsigned int p1 = 0;
00795                         unsigned int p2 = 1;
00796 
00797                         float distsquared = (points[p1]-points[p2]).squared_length();
00798 
00799                         // Find the nearest points
00800                         for(unsigned int j = 0; j < points.size(); ++j) {
00801                                 for(unsigned int k = j+1; k < points.size(); ++k) {
00802                                         float d = (points[j]-points[k]).squared_length();
00803                                         if ( d < distsquared ) {
00804                                                 distsquared = d;
00805                                                 p1 = j;
00806                                                 p2 = k;
00807                                         }
00808                                 }
00809                         }
00810 
00811                         // Move them apart by a small fraction
00812                         Vec3f delta = percentage*(points[p2]-points[p1]);
00813 
00814                         points[p2] += delta;
00815                         points[p2].normalize();
00816                         points[p1] -= delta;
00817                         points[p1].normalize();
00818                 }
00819         }
00820 
00821         vector<Vec3f> ret;
00822         for (vector<Vec3f>::const_iterator it = points.begin(); it != points.end(); ++it ) {
00823                 float altitude = (float)(EMConsts::rad2deg*acos((*it)[2]));
00824                 float azimuth = (float)(EMConsts::rad2deg*atan2((*it)[1],(*it)[0]));
00825                 ret.push_back(Vec3f(90.0f+azimuth,altitude,0));
00826         }
00827 
00828         return ret;
00829 }


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 1351 of file symmetry.h.

Referenced by get_name().


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