Random Orientation Generator - carefully generates uniformly random orientations in any asymmetric unit. More...

#include <symmetry.h>

Inheritance diagram for EMAN::RandomOrientationGenerator:

Collaboration diagram for EMAN::RandomOrientationGenerator:

[legend]

Public Member Functions
	RandomOrientationGenerator ()

virtual	~RandomOrientationGenerator ()

virtual string	get_name () const
	Return "random". 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 random orientations in the asymmetric unit of the symmetry. 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 should general do this by simulating the function gen_orientations. 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 = "rand"
	The name of this class - used to access it from factories etc. More...

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

RandomOrientationGenerator &	operator= (const RandomOrientationGenerator &)
	Disallow assignment. 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

Random Orientation Generator - carefully generates uniformly random orientations in any asymmetric unit.

For points distributed in the unit sphere, just use the CSym type with nysm = 1. (i.e. c1 symmetry)

Author: David Woolford

Date: March 2008

Definition at line 1234 of file symmetry.h.

Constructor & Destructor Documentation

◆ RandomOrientationGenerator() [1/2]

EMAN::RandomOrientationGenerator::RandomOrientationGenerator ( )

inline

Definition at line 1237 of file symmetry.h.

1237{}

Referenced by NEW().

◆ ~RandomOrientationGenerator()

virtual EMAN::RandomOrientationGenerator::~RandomOrientationGenerator ( )

inlinevirtual

Definition at line 1238 of file symmetry.h.

1238{}

◆ RandomOrientationGenerator() [2/2]

EMAN::RandomOrientationGenerator::RandomOrientationGenerator ( const RandomOrientationGenerator & )

private

Disallow copy construction.

Member Function Documentation

◆ gen_orientations()

vector< Transform > RandomOrientationGenerator::gen_orientations ( const Symmetry3D *const sym ) const

virtual

Generate random 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 546 of file symmetry.cpp.

{
        int n = params.set_default("n", 0);
 
        if ( n <= 0 ) throw InvalidParameterException("You must specify a positive, non zero n for the Random Orientation Generator");
 
        bool phitoo = params.set_default("phitoo", false);
        bool inc_mirror = params.set_default("inc_mirror", false);
 
        vector<Transform> ret;
 
        int i = 0;
        Dict d("type","eman");
        while ( i < n ){
                float u1 =  Util::get_frand(-1.0f,1.0f);
                float u2 =  Util::get_frand(-1.0f,1.0f);
                float s = u1*u1 + u2*u2;
                if ( s > 1.0f ) continue;
                float alpha = 2.0f*sqrtf(1.0f-s);
                float x = alpha * u1;
                float y = alpha * u2;
                float z = 2.0f*s-1.0f;
 
                float altitude = (float)EMConsts::rad2deg*acos(z);
                float azimuth = (float)EMConsts::rad2deg*atan2(y,x);
 
                float phi = 0.0f;
                if ( phitoo ) phi = Util::get_frand(0.0f,359.9999f);
 
                d["az"] = azimuth; d["phi"] = phi; d["alt"] = altitude;
                Transform t(d);
 
                if ( !(sym->is_c_sym() && sym->get_nsym() == 1)) t = sym->reduce(t); //reduce doesn't make sense for C1 symmetry
 
                if ( !sym->is_in_asym_unit(altitude,azimuth,inc_mirror) ){
                        // is_in_asym_unit has returned the wrong value!
                        // FIXME
//                      cout << "warning, there is an unresolved issue - email D Woolford" << endl;
                }
                ret.push_back(t);
                i++;
        }
        return ret;
}

References EMAN::Util::get_frand(), EMAN::Symmetry3D::get_nsym(), InvalidParameterException, EMAN::Symmetry3D::is_c_sym(), EMAN::Symmetry3D::is_in_asym_unit(), EMAN::FactoryBase::params, EMAN::EMConsts::rad2deg, EMAN::Symmetry3D::reduce(), EMAN::Dict::set_default(), x, and y.

◆ get_desc()

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

inlinevirtual

Get a description.

Returns: a clear desciption of this class

Implements EMAN::FactoryBase.

Definition at line 1256 of file symmetry.h.

1256{ return "Generate random orientations within an asymmetric unit"; }

◆ get_name()

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

inlinevirtual

Return "random".

Returns: the unique name of this class

Implements EMAN::FactoryBase.

Definition at line 1251 of file symmetry.h.

1251{ return NAME; }

EMAN::RandomOrientationGenerator::NAME

static const string NAME

The name of this class - used to access it from factories etc.

Definition: symmetry.h:1278

References NAME.

◆ get_orientations_tally()

virtual int EMAN::RandomOrientationGenerator::get_orientations_tally	(	const Symmetry3D *const	sym,
		const float &	delta
	)		const

inlinevirtual

This function returns how many orientations will be generated for a given delta (angular spacing) It should general do this by simulating the function 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 1280 of file symmetry.h.

1280{ (void)sym; (void)delta; return 0; }

◆ get_param_types()

virtual TypeDict EMAN::RandomOrientationGenerator::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 1262 of file symmetry.h.

                {
                        TypeDict d;
                        d.put("n", EMObject::INT, "The number of orientations to generate.");
                        d.put("inc_mirror", EMObject::BOOL, "Indicates whether or not to include the mirror portion of the asymmetric unit. Default is false.");
                        d.put("phitoo", EMObject::BOOL, "Makes phi random as well");
                        return d;
                }

References EMAN::EMObject::BOOL, EMAN::EMObject::INT, and EMAN::TypeDict::put().

◆ NEW()

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

inlinestatic

Factory support function NEW.

Returns: a newly instantiated class of this type

Definition at line 1243 of file symmetry.h.

                {
                        return new RandomOrientationGenerator();
                }

References RandomOrientationGenerator().

◆ operator=()

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

private

Disallow assignment.

Member Data Documentation

◆ NAME

const string RandomOrientationGenerator::NAME = "rand"

static

The name of this class - used to access it from factories etc.

Definition at line 1278 of file symmetry.h.

Referenced by EMAN::OptimumOrientationGenerator::gen_orientations(), and 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

◆ RandomOrientationGenerator() [1/2]

◆ ~RandomOrientationGenerator()

◆ RandomOrientationGenerator() [2/2]

Member Function Documentation

◆ gen_orientations()

◆ get_desc()

◆ get_name()

◆ get_orientations_tally()

◆ get_param_types()

◆ NEW()

◆ operator=()

Member Data Documentation

◆ NAME