Optimum orientation generator. More...

#include <symmetry.h>

Inheritance diagram for EMAN::OptimumOrientationGenerator:

Collaboration diagram for EMAN::OptimumOrientationGenerator:

[legend]

Public Member Functions
	OptimumOrientationGenerator ()

virtual	~OptimumOrientationGenerator ()

virtual string	get_name () const
	Return "opt". More...

virtual string	get_desc () const
	Get a description. More...

virtual TypeDict	get_param_types () const
	Get a dictionary containing the permissable parameters of this class. More...

virtual vector< Transform >	gen_orientations (const Symmetry3D *const sym) const
	Generate Saff orientations in the asymmetric unit of the symmetry. More...

Public Member Functions inherited from EMAN::OrientationGenerator
	OrientationGenerator ()

virtual	~OrientationGenerator ()

bool	add_orientation (vector< Transform > &v, const float &az, const float &alt) const
	This functions adds one or more Transform objects to the vector v, depending on the parameters stored in the dictionary (which the inheriting class may include by initializing the typedict in get_param_types by calling. More...

float	get_optimal_delta (const Symmetry3D *const sym, const int &n) const
	This function gets the optimal value of the delta (or angular spacing) of the orientations based on a desired total number of orientations (n). More...

Public Member Functions inherited from EMAN::FactoryBase
	FactoryBase ()

virtual	~FactoryBase ()

Dict	get_params () const
	get a copy of the parameters of this class More...

void	set_params (const Dict &new_params)
	Set new parameters. More...

void	set_param (const string key, const EMObject val)

void	insert_params (const Dict &new_params)
	Insert parameters. More...

Dict	copy_relevant_params (const FactoryBase *const that) const

Static Public Member Functions
static OrientationGenerator *	NEW ()
	Factory support function NEW. More...

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

Private Member Functions
	OptimumOrientationGenerator (const OptimumOrientationGenerator &)
	Disallow copy construction. More...

OptimumOrientationGenerator &	operator= (const OptimumOrientationGenerator &)
	Disallow assignment. More...

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. More...

vector< Vec3f >	optimize_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. More...

Additional Inherited Members
Protected Member Functions inherited from EMAN::OrientationGenerator
void	get_az_max (const Symmetry3D *const sym, const float &altmax, const bool inc_mirror, const float &alt_iterator, const float &h, bool &d_odd_mirror_flag, float &azmax_adjusted) const

Protected Attributes inherited from EMAN::FactoryBase
Dict	params
	This is the dictionary the stores the parameters of the object. More...

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 1438 of file symmetry.h.

Constructor & Destructor Documentation

◆ OptimumOrientationGenerator() [1/2]

EMAN::OptimumOrientationGenerator::OptimumOrientationGenerator ( )

inline

Definition at line 1441 of file symmetry.h.

1441{}

Referenced by NEW().

◆ ~OptimumOrientationGenerator()

virtual EMAN::OptimumOrientationGenerator::~OptimumOrientationGenerator ( )

inlinevirtual

Definition at line 1442 of file symmetry.h.

1442{}

◆ OptimumOrientationGenerator() [2/2]

EMAN::OptimumOrientationGenerator::OptimumOrientationGenerator ( const OptimumOrientationGenerator & )

private

Disallow copy construction.

Member Function Documentation

◆ gen_orientations()

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 794 of file symmetry.cpp.

{
        float delta = params.set_default("delta", 0.0f);
        int n = params.set_default("n", 0);
 
        bool inc_mirror = params.set_default("inc_mirror",false);
 
        if ( delta <= 0 && n <= 0 ) throw InvalidParameterException("Error, you must specify a positive non-zero delta or n");
        if ( delta > 0 && n > 0 ) throw InvalidParameterException("Error, the delta and the n arguments are mutually exclusive");
 
        string generatorname = params.set_default("use","saff");
 
        if ( n > 0 && generatorname != RandomOrientationGenerator::NAME ) {
                params["delta"] = get_optimal_delta(sym,n);
                params["n"] = (int)0;
        }
 
        // Force the orientation generator to include the mirror - this is because
        // We will enventually use it to generate orientations over the intire sphere
        // which is C1 symmetry, with the inc_mirror flag set to true
        params["inc_mirror"] = true;
        OrientationGenerator* g = Factory < OrientationGenerator >::get(generatorname);
        g->set_params(copy_relevant_params(g));
 
 
        // get the starting orientation distribution
        CSym* unit_sphere = new CSym();
        Dict nsym; nsym["nsym"] = 1; unit_sphere->set_params(nsym);
 
        vector<Transform> unitsphereorientations = g->gen_orientations(unit_sphere);
        delete g; g = 0;
        delete unit_sphere; unit_sphere = 0;
 
        vector<Vec3f> angles = optimize_distances(unitsphereorientations);
 
        vector<Transform> ret;
        for (vector<Vec3f>::const_iterator it = angles.begin(); it != angles.end(); ++it ) {
                if ( sym->is_in_asym_unit((*it)[1],(*it)[0],inc_mirror) ) {
                        add_orientation(ret,(*it)[0],(*it)[1]);
                }
        }
 
        // reset the params to what they were before they were acted upon by this class
        params["inc_mirror"] = inc_mirror;
        params["delta"] = delta;
        params["n"] = n;
 
        return ret;
}

References EMAN::OrientationGenerator::add_orientation(), 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().

◆ get_desc()

virtual string EMAN::OptimumOrientationGenerator::get_desc ( ) const

inlinevirtual

Get a description.

Returns: a clear desciption of this class

Implements EMAN::FactoryBase.

Definition at line 1460 of file symmetry.h.

1460{ return "Generate optimally distributed orientations within an asymmetric using a basic optimization technique"; }

◆ get_name()

virtual string EMAN::OptimumOrientationGenerator::get_name ( ) const

inlinevirtual

Return "opt".

Returns: the unique name of this class

Implements EMAN::FactoryBase.

Definition at line 1455 of file symmetry.h.

1455{ return NAME; }

EMAN::OptimumOrientationGenerator::NAME

static const string NAME

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

Definition: symmetry.h:1483

References NAME.

◆ get_orientations_tally()

int OptimumOrientationGenerator::get_orientations_tally	(	const Symmetry3D *const	sym,
		const float &	delta
	)		const

privatevirtual

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 779 of file symmetry.cpp.

{
        string deltaoptname = params.set_default("use","saff");
        Dict a;
        a["inc_mirror"] = (bool)params.set_default("inc_mirror",false);
        OrientationGenerator *g = Factory < OrientationGenerator >::get(deltaoptname,a);
        if (g) {
                int tally = g->get_orientations_tally(sym,delta);
                delete g;
                g = 0;
                return tally;
        }
        else throw;
}

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

◆ get_param_types()

virtual TypeDict EMAN::OptimumOrientationGenerator::get_param_types ( ) const

inlinevirtual

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 1466 of file symmetry.h.

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

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

◆ NEW()

static OrientationGenerator * EMAN::OptimumOrientationGenerator::NEW ( )

inlinestatic

Factory support function NEW.

Returns: a newly instantiated class of this type

Definition at line 1447 of file symmetry.h.

                {
                        return new OptimumOrientationGenerator();
                }

References OptimumOrientationGenerator().

◆ operator=()

OptimumOrientationGenerator & EMAN::OptimumOrientationGenerator::operator= ( const OptimumOrientationGenerator & )

private

Disallow assignment.

◆ optimize_distances()

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 844 of file symmetry.cpp.

{
        vector<Vec3f> points;
 
        for (vector<Transform>::const_iterator it = v.begin(); it != v.end(); ++it ) {
                points.push_back(Vec3f(0,0,1)*(*it));
        }
 
        if ( points.size() >= 2 ) {
                int max_it = 100;
                float percentage = 0.01f;
 
                for ( int i = 0; i < max_it; ++i ){
                        unsigned int p1 = 0;
                        unsigned int p2 = 1;
 
                        float distsquared = (points[p1]-points[p2]).squared_length();
 
                        // Find the nearest points
                        for(unsigned int j = 0; j < points.size(); ++j) {
                                for(unsigned int k = j+1; k < points.size(); ++k) {
                                        float d = (points[j]-points[k]).squared_length();
                                        if ( d < distsquared ) {
                                                distsquared = d;
                                                p1 = j;
                                                p2 = k;
                                        }
                                }
                        }
 
                        // Move them apart by a small fraction
                        Vec3f delta = percentage*(points[p2]-points[p1]);
 
                        points[p2] += delta;
                        points[p2].normalize();
                        points[p1] -= delta;
                        points[p1].normalize();
                }
        }
 
        vector<Vec3f> ret;
        for (vector<Vec3f>::const_iterator it = points.begin(); it != points.end(); ++it ) {
                float altitude = (float)(EMConsts::rad2deg*acos((*it)[2]));
                float azimuth = (float)(EMConsts::rad2deg*atan2((*it)[1],(*it)[0]));
                ret.push_back(Vec3f(90.0f+azimuth,altitude,0));
        }
 
        return ret;
}

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

Referenced by gen_orientations().

Member Data Documentation

◆ NAME

const string OptimumOrientationGenerator::NAME = "opt"

static

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

Definition at line 1483 of file symmetry.h.

Referenced by get_name().

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

Public Member Functions

Static Public Member Functions

Static Public Attributes

Private Member Functions

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ OptimumOrientationGenerator() [1/2]

◆ ~OptimumOrientationGenerator()

◆ OptimumOrientationGenerator() [2/2]

Member Function Documentation

◆ gen_orientations()

◆ get_desc()

◆ get_name()

◆ get_orientations_tally()

◆ get_param_types()

◆ NEW()

◆ operator=()

◆ optimize_distances()

Member Data Documentation

◆ NAME