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

#include <symmetry.h>

Inheritance diagram for EMAN::DSym:

Collaboration diagram for EMAN::DSym:

[legend]

Public Member Functions
	DSym ()

virtual	~DSym ()

virtual string	get_name () const
	Return DSym::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 d 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 D symmetry, this is simply 2*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

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_d_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_c_sym () const
	A function that is used to determine if this is a c symmetry object This function is only virtually overidden by the CSym 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 = "d"
	The name of this class - used to access it from factories etc. Should be "d". More...

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

DSym &	operator= (const DSym &)
	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 dihedral 3D symmetry.

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

Date: Feb 2008

Definition at line 340 of file symmetry.h.

Constructor & Destructor Documentation

◆ DSym() [1/2]

EMAN::DSym::DSym ( )

inline

Definition at line 343 of file symmetry.h.

343{};

Referenced by NEW().

◆ ~DSym()

virtual EMAN::DSym::~DSym ( )

inlinevirtual

Definition at line 344 of file symmetry.h.

344{};

◆ DSym() [2/2]

EMAN::DSym::DSym ( const DSym & )

private

Disallow copy construction.

Member Function Documentation

◆ get_asym_unit_points()

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

virtual

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 to demarcate the asymmetric unit. The last should may be connected to the first.

Implements EMAN::Symmetry3D.

Definition at line 1527 of file symmetry.cpp.

{
        Dict delim = get_delimiters(inc_mirror);
 
        vector<Vec3f> ret;
        int nsym = params.set_default("nsym",0);
        if ( nsym == 1 ) {
                if (inc_mirror == false ) {
                        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,-1,0));
                        ret.push_back(Vec3f(1,0,0));
                        ret.push_back(Vec3f(0,1,0));
                        ret.push_back(Vec3f(-1,0,0));
                }
        }
        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 {
                float angle = (float)(EMConsts::deg2rad*float(delim["az_max"]));
                ret.push_back(Vec3f(0,0,1));
                ret.push_back(Vec3f(0,-1,0));
                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 > > DSym::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 1472 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 ( (nsym == 1 && inc_mirror == false) || (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 (nsym == 1) {
                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 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);
        }
 
        return ret;
}

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

◆ get_delimiters()

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

virtual

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

The "alt_max" is always 90 degrees The "az_max" is 360/nsym degrees of 180/nsym, depending the inc_mirror argument

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 1420 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");
 
        returnDict["alt_max"] = 90.0f;
 
        if ( inc_mirror )  returnDict["az_max"] = 360.0f/(float)nsym;
        else returnDict["az_max"] = 180.0f/(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::DSym::get_desc ( ) const

inlinevirtual

Get a description.

Returns: a clear desciption of this class

Implements EMAN::FactoryBase.

Definition at line 362 of file symmetry.h.

362{ return "D symmetry support"; }

◆ get_max_csym()

virtual int EMAN::DSym::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: nsym - this is the maximum symmetry about a given any axis for D symmetry

Implements EMAN::Symmetry3D.

Definition at line 404 of file symmetry.h.

404{ return params["nsym"]; }

References EMAN::FactoryBase::params.

◆ get_name()

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

inlinevirtual

Return DSym::NAME.

Returns: the unique name of this class

Implements EMAN::FactoryBase.

Definition at line 357 of file symmetry.h.

357{ return NAME; }

EMAN::DSym::NAME

static const string NAME

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

Definition: symmetry.h:423

References NAME.

◆ get_nsym()

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

inlinevirtual

Gets the total number of unique roational symmetry operations associated with this symmetry For D symmetry, this is simply 2*nsym.

Returns: two times nsym

Implements EMAN::Symmetry3D.

Definition at line 397 of file symmetry.h.

397{ return 2*(int)params["nsym"]; };

References EMAN::FactoryBase::params.

◆ get_param_types()

virtual TypeDict EMAN::DSym::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 367 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 DSym::get_sym ( const int n ) const

virtual

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

The first half symmetry operations returned by this function are all about the z axis (i.e. only azimuth is non zero. The second half of the symmetry operations are replicas of the first half, except that they have an additional 180 degree rotation about x (in EMAN terms, the altitude angle is 180).

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 1452 of file symmetry.cpp.

{
        int nsym = 2*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
        if (n >= nsym / 2) {
                d["az"] = ( (n%nsym) - nsym/2) * 360.0f / (nsym / 2);
                d["alt"] = 180.0f;
                d["phi"] = 0.0f;
        }
        else {
                d["az"] = (n%nsym) * 360.0f / (nsym / 2);
                d["alt"] = 0.0f;
                d["phi"] = 0.0f;
        }
        return Transform(d);
}

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

◆ is_d_sym()

virtual bool EMAN::DSym::is_d_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 428 of file symmetry.h.

428{ return true; }

◆ is_in_asym_unit()

bool DSym::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 1435 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 && inc_mirror ) {
                if (altitude >= 0 && altitude <= alt_max && azimuth < az_max ) return true;
        }
        else {
                if ( altitude >= 0 && altitude <= alt_max && azimuth < az_max && azimuth >= 0 ) return true;
        }
        return false;
}

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

◆ NEW()

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

inlinestatic

Factory support function NEW.

Returns: a newly instantiated class of this type

Definition at line 349 of file symmetry.h.

                {
                        return new DSym();
                }

References DSym().

◆ operator=()

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

private

Disallow assignment.

Member Data Documentation

◆ NAME

const string DSym::NAME = "d"

static

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

Definition at line 423 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

◆ DSym() [1/2]

◆ ~DSym()

◆ DSym() [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_d_sym()

◆ is_in_asym_unit()

◆ NEW()

◆ operator=()

Member Data Documentation

◆ NAME