An encapsulation of cyclic 3D symmetry. More...

#include <symmetry.h>

Inheritance diagram for EMAN::CSym:

Collaboration diagram for EMAN::CSym:

[legend]

Public Member Functions
	CSym ()

virtual	~CSym ()

virtual string	get_name () const
	Return CSym::NAME. 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 Dict	get_delimiters (const bool inc_mirror=false) const
	Get the altitude and phi angle of the c symmetry, which depends on nysm. More...

virtual Transform	get_sym (const int n) const
	Provides access to the complete set of rotational symmetry operations associated with this symmetry. More...

virtual int	get_nsym () const
	Gets the total number of unique roational symmetry operations associated with this symmetry For C symmetry, this is simply nsym. More...

virtual int	get_max_csym () const
	Gets the maximum symmetry of this object. More...

virtual vector< Vec3f >	get_asym_unit_points (bool inc_mirror=false) const
	to demarcate the asymmetric unit. More...

virtual bool	is_in_asym_unit (const float &altitude, const float &azimuth, const bool inc_mirror) const
	A function to be used when generating orientations over portion of the unit sphere defined by parameters returned by get_delimiters. More...

virtual bool	is_c_sym () const
	Returns true - this is indeed a c symmetry object. More...

virtual vector< vector< Vec3f > >	get_asym_unit_triangles (bool inc_mirror) const
	Get triangles that precisely occlude the projection area of the default asymmetric unit. More...

Public Member Functions inherited from EMAN::Symmetry3D
	Symmetry3D ()

virtual	~Symmetry3D ()

virtual float	get_az_alignment_offset () const
	This functionality is only relevant to platonic symmetries. More...

virtual bool	is_platonic_sym () const
	A function that is used to determine if this is a platonic symmetry object This function is only virtually overidden by the PlatonicSym symmetry, which returns true, not false. More...

virtual bool	is_h_sym () const
	A function that is used to determine if this is a Helical symmetry object This function is only virtually overidden by the HSym symmetry, which returns true, not false. More...

virtual bool	is_d_sym () const
	A function that is used to determine if this is a d symmetry object This function is only virtually overidden by the DSym object, which returns true. More...

virtual bool	is_tet_sym () const
	A function that is used to determine if this is the tetrahedral symmetry object This function is only virtually overidden by the TetSym object, which returns true. More...

vector< Transform >	gen_orientations (const string &generatorname="eman", const Dict &parms=Dict())
	Ask the Symmetry3D object to generate a set of orientations in its asymmetric unit using an OrientationGenerator constructed from the given parameters (using a Factory). More...

virtual Transform	reduce (const Transform &t3d, int n=0) const
	A function that will reduce an orientation, as characterized by Euler anges, into a specific asymmetric unit. More...

virtual int	in_which_asym_unit (const Transform &t3d) const
	A function that will determine in which asymmetric unit a given orientation resides The asymmetric unit 'number' will depend entirely on the order in which different symmetry operations are return by the Symmetry3D::get_sym function. More...

virtual int	point_in_which_asym_unit (const Vec3f &v) const
	A function that will determine in which asymmetric unit a given vector resides The asymmetric unit 'number' will depend entirely on the order in which different symmetry operations are return by the Symmetry3D::get_sym function The vector is a point. More...

virtual vector< Transform >	get_touching_au_transforms (bool inc_mirror=true) const
	Gets a vector of Transform objects that define the set of asymmetric units that touch the default asymmetric unit. More...

virtual vector< Transform >	get_syms () const

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 Symmetry3D *	NEW ()
	Factory support function NEW. More...

Static Public Member Functions inherited from EMAN::Symmetry3D
static vector< Transform >	get_symmetries (const string &symmetry)

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

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

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

Additional Inherited Members
Public Types inherited from EMAN::Symmetry3D
typedef vector< vector< Vec3f > >::const_iterator	cit

typedef vector< vector< Vec3f > >::iterator	ncit

Protected Member Functions inherited from EMAN::Symmetry3D
void	cache_au_planes () const
	Establish the asymmetric unit planes cache. More...

void	delete_au_planes ()
	Clear the asymmetric unit planes cache. More...

Protected Attributes inherited from EMAN::Symmetry3D
float **	cached_au_planes
	The asymmetric unit planes are cached to provide a great speed up the point_in_which_asym_unit function, which is called by reduce and by in_which_asym_unit. More...

int	cache_size
	Have to remember the cache size. More...

int	num_triangles
	This is stores the number of triangles returned by get_asym_unit_triangles(true) More...

vector< vector< Vec3f > >	au_sym_triangles
	This cache is of size cache_size. More...

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

Detailed Description

An encapsulation of cyclic 3D symmetry.

Author: David Woolford (based on previous work by Phil Baldwin and Steve Ludtke)

Date: Feb 2008

Definition at line 233 of file symmetry.h.

Constructor & Destructor Documentation

◆ CSym() [1/2]

EMAN::CSym::CSym ( )

inline

Definition at line 236 of file symmetry.h.

236{};

Referenced by NEW().

◆ ~CSym()

virtual EMAN::CSym::~CSym ( )

inlinevirtual

Definition at line 237 of file symmetry.h.

237{};

◆ CSym() [2/2]

EMAN::CSym::CSym ( const CSym & )

private

Disallow copy construction.

Member Function Documentation

◆ get_asym_unit_points()

vector< Vec3f > CSym::get_asym_unit_points ( bool inc_mirror = false ) const

virtual

to demarcate the asymmetric unit.

The last should may be connected to the first.

Parameters

inc_mirror whether or not to include the mirror portion of the asymmetric unit

Returns: a cyclic set of points which can be connected using great arcs on the unit sphere

Implements EMAN::Symmetry3D.

Definition at line 1370 of file symmetry.cpp.

{
        Dict delim = get_delimiters(inc_mirror);
        int nsym = params.set_default("nsym",0);
        vector<Vec3f> ret;
 
        if ( nsym == 1 ) {
                if (inc_mirror == false ) {
                        ret.push_back(Vec3f(0,-1,0));
                        ret.push_back(Vec3f(1,0,0));
                        ret.push_back(Vec3f(0,1,0));
                        ret.push_back(Vec3f(-1,0,0));
                }
                // else return ret; // an empty vector! this is fine
        }
        else if (nsym == 2 && !inc_mirror) {
                ret.push_back(Vec3f(0,0,1));
                ret.push_back(Vec3f(0,-1,0));
                ret.push_back(Vec3f(1,0,0));
                ret.push_back(Vec3f(0,1,0));
        }
        else {
                ret.push_back(Vec3f(0,0,1));
                ret.push_back(Vec3f(0,-1,0));
                if (inc_mirror == true) {
                        ret.push_back(Vec3f(0,0,-1));
                }
                float angle = (float)(EMConsts::deg2rad*float(delim["az_max"]));
                float y = -cos(angle);
                float x = sin(angle);
                ret.push_back(Vec3f(x,y,0));
        }
 
        return ret;
 
}

References EMAN::EMConsts::deg2rad, get_delimiters(), EMAN::FactoryBase::params, EMAN::Dict::set_default(), x, and y.

Referenced by get_asym_unit_triangles().

◆ get_asym_unit_triangles()

vector< vector< Vec3f > > CSym::get_asym_unit_triangles ( bool inc_mirror ) const

virtual

Get triangles that precisely occlude the projection area of the default asymmetric unit.

This is used for collision detection in Symmetry3D::reduce

Parameters

inc_mirror whether to include the mirror portion of the asymmetric unit

Implements EMAN::Symmetry3D.

Definition at line 1275 of file symmetry.cpp.

                                                                          {
        vector<Vec3f> v = get_asym_unit_points(inc_mirror);
        int nsym = params.set_default("nsym",0);
 
        vector<vector<Vec3f> > ret;
        if (v.size() == 0) return ret; // nsym == 1 and inc_mirror == true, this is the entire sphere!
        if (nsym == 1 && !inc_mirror) {
                Vec3f z(0,0,1);
                vector<Vec3f> tmp;
                tmp.push_back(z);
                tmp.push_back(v[1]);
                tmp.push_back(v[0]);
                ret.push_back(tmp);
 
                vector<Vec3f> tmp2;
                tmp2.push_back(z);
                tmp2.push_back(v[2]);
                tmp2.push_back(v[1]);
                ret.push_back(tmp2);
 
                vector<Vec3f> tmp3;
                tmp3.push_back(z);
                tmp3.push_back(v[3]);
                tmp3.push_back(v[2]);
                ret.push_back(tmp3);
 
                vector<Vec3f> tmp4;
                tmp4.push_back(z);
                tmp4.push_back(v[0]);
                tmp4.push_back(v[3]);
                ret.push_back(tmp4);
        }
        else if (nsym == 2 && inc_mirror) {
                Vec3f x(1,0,0);
                vector<Vec3f> tmp;
                tmp.push_back(v[1]);
                tmp.push_back(v[0]);
                tmp.push_back(x);
                ret.push_back(tmp);
 
                vector<Vec3f> tmp2;
                tmp2.push_back(v[2]);
                tmp2.push_back(v[1]);
                tmp2.push_back(x);
                ret.push_back(tmp2);
 
                vector<Vec3f> tmp3;
                tmp3.push_back(v[3]);
                tmp3.push_back(v[2]);
                tmp3.push_back(x);
                ret.push_back(tmp3);
 
                vector<Vec3f> tmp4;
                tmp4.push_back(v[0]);
                tmp4.push_back(v[3]);
                tmp4.push_back(x);
                ret.push_back(tmp4);
        }
        else if (nsym == 2 && !inc_mirror) {
                vector<Vec3f> tmp;
                tmp.push_back(v[0]);
                tmp.push_back(v[2]);
                tmp.push_back(v[1]);
                ret.push_back(tmp);
 
                vector<Vec3f> tmp2;
                tmp2.push_back(v[2]);
                tmp2.push_back(v[0]);
                tmp2.push_back(v[3]);
                ret.push_back(tmp2);
        }
        else if (v.size() == 3) {
                vector<Vec3f> tmp;
                tmp.push_back(v[0]);
                tmp.push_back(v[2]);
                tmp.push_back(v[1]);
                ret.push_back(tmp);
        }
        else if (v.size() == 4) {
                vector<Vec3f> tmp;
                tmp.push_back(v[0]);
                tmp.push_back(v[3]);
                tmp.push_back(v[1]);
                ret.push_back(tmp);
 
                vector<Vec3f> tmp2;
                tmp2.push_back(v[1]);
                tmp2.push_back(v[3]);
                tmp2.push_back(v[2]);
                ret.push_back(tmp2);
        }
 
        return ret;
}

References get_asym_unit_points(), EMAN::FactoryBase::params, EMAN::Dict::set_default(), and x.

◆ get_delimiters()

Dict CSym::get_delimiters ( const bool inc_mirror = false ) const

virtual

Get the altitude and phi angle of the c symmetry, which depends on nysm.

The "alt_max" value in the return dicts is 180 or 90 degrees, depending inc_mirror The "az_max" is 360/nsym degrees.

Parameters

inc_mirror whether or not to include the part of the asymmetric unit which contains the mirror projections of the other half

Returns: a dictionary containing the keys "alt_max" and "az_max"

Exceptions

InvalidValueException if nsym is less than or equal to zero

Implements EMAN::Symmetry3D.

Definition at line 1249 of file symmetry.cpp.

                                                     {
        Dict returnDict;
        // Get the parameters of interest
        int nsym = params.set_default("nsym",0);
        if ( nsym <= 0 ) throw InvalidValueException(nsym,"Error, you must specify a positive non zero nsym");
 
        if ( inc_mirror ) returnDict["alt_max"] = 180.0f;
        else  returnDict["alt_max"] = 90.0f;
 
        returnDict["az_max"] = 360.0f/(float)nsym;
 
        return returnDict;
}

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

Referenced by get_asym_unit_points(), and is_in_asym_unit().

◆ get_desc()

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

inlinevirtual

Get a description.

Returns: a clear desciption of this class

Implements EMAN::FactoryBase.

Definition at line 255 of file symmetry.h.

255{ return "C symmetry support"; }

◆ get_max_csym()

virtual int EMAN::CSym::get_max_csym ( ) const

inlinevirtual

Gets the maximum symmetry of this object.

This is used by OrientationGenerators, and is probably not something a general user would utilize.

Returns: the degree of of cyclic symmetry (nsym) - this is the maximum symmetry

Implements EMAN::Symmetry3D.

Definition at line 296 of file symmetry.h.

296{ return params["nsym"]; }

References EMAN::FactoryBase::params.

◆ get_name()

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

inlinevirtual

Return CSym::NAME.

Returns: the unique name of this class

Implements EMAN::FactoryBase.

Definition at line 250 of file symmetry.h.

250{ return NAME; }

EMAN::CSym::NAME

static const string NAME

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

Definition: symmetry.h:299

References NAME.

◆ get_nsym()

virtual int EMAN::CSym::get_nsym ( ) const

inlinevirtual

Gets the total number of unique roational symmetry operations associated with this symmetry For C symmetry, this is simply nsym.

Returns: the degree of of cyclic symmetry (nsym)

Implements EMAN::Symmetry3D.

Definition at line 289 of file symmetry.h.

289{ return params["nsym"]; };

References EMAN::FactoryBase::params.

◆ get_param_types()

virtual TypeDict EMAN::CSym::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

Implements EMAN::FactoryBase.

Definition at line 260 of file symmetry.h.

                {
                        TypeDict d;
                        d.put("nsym", EMObject::INT, "The symmetry number");
                        return d;
                }

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

◆ get_sym()

Transform CSym::get_sym ( const int n ) const

virtual

Provides access to the complete set of rotational symmetry operations associated with this symmetry.

Rotational symmetry operations for C symmetry are always about the z-axis (in the EMAN convention), and therefore the only non zero return angle is azimuth. Specifically, it is n*360/nsym degrees.

Parameters

n	the rotational symmetry operation number. If n is greater than nsym we take n modulo nsym

Returns: a transform containing the correct rotational symmetric operation.

Exceptions

InvalidValueException if nsym is less than or equal to zero

Implements EMAN::Symmetry3D.

Definition at line 1407 of file symmetry.cpp.

                                         {
        int nsym = params.set_default("nsym",0);
        if ( nsym <= 0 ) throw InvalidValueException(n,"Error, you must specify a positive non zero nsym");
 
        Dict d("type","eman");
        // courtesy of Phil Baldwin
        d["az"] = (n%nsym) * 360.0f / nsym;
        d["alt"] = 0.0f;
        d["phi"] = 0.0f;
        return Transform(d);
}

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

◆ is_c_sym()

virtual bool EMAN::CSym::is_c_sym ( ) const

inlinevirtual

Returns true - this is indeed a c symmetry object.

Returns: true - indicating that this is a c symmetry object

Reimplemented from EMAN::Symmetry3D.

Definition at line 320 of file symmetry.h.

320{ return true; }

◆ is_in_asym_unit()

bool CSym::is_in_asym_unit	(	const float &	altitude,
		const float &	azimuth,
		const bool	inc_mirror = `false`
	)		const

virtual

A function to be used when generating orientations over portion of the unit sphere defined by parameters returned by get_delimiters.

In platonic symmetry altitude and azimuth alone are not enough to correctly demarcate the asymmetric unit. See the get_delimiters comments.

Parameters

altitude	the EMAN style altitude of the 3D orientation in degrees
azimuth	the EMAN style azimuth of the 3D orientation in degrees
inc_mirror	whether or not to include orientations if they are in the mirror portion of the asymmetric unit

Returns: true or false, depending on whether or not the orientation is within the asymmetric unit

Implements EMAN::Symmetry3D.

Definition at line 1263 of file symmetry.cpp.

{
        Dict d = get_delimiters(inc_mirror);
        float alt_max = d["alt_max"];
        float az_max = d["az_max"];
 
        int nsym = params.set_default("nsym",0);
        if ( nsym != 1 && azimuth < 0) return false;
        if ( altitude <= alt_max && azimuth < az_max ) return true;
        return false;
}

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

◆ NEW()

static Symmetry3D * EMAN::CSym::NEW ( )

inlinestatic

Factory support function NEW.

Returns: a newly instantiated class of this type

Definition at line 242 of file symmetry.h.

                {
                        return new CSym();
                }

References CSym().

◆ operator=()

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

private

Disallow assignment.

Member Data Documentation

◆ NAME

const string CSym::NAME = "c"

static

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

Definition at line 299 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

◆ CSym() [1/2]

◆ ~CSym()

◆ CSym() [2/2]

Member Function Documentation

◆ get_asym_unit_points()

◆ get_asym_unit_triangles()

◆ get_delimiters()

◆ get_desc()

◆ get_max_csym()

◆ get_name()

◆ get_nsym()

◆ get_param_types()

◆ get_sym()

◆ is_c_sym()

◆ is_in_asym_unit()

◆ NEW()

◆ operator=()

Member Data Documentation

◆ NAME