EMAN2
Public Member Functions | Static Public Member Functions | Static Public Attributes | Private Member Functions
EMAN::CSym Class Reference

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

#include <symmetry.h>

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List of all members.

Public Member Functions

 CSym ()
virtual ~CSym ()
virtual string get_name () const
 Return CSym::NAME.
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 Dict get_delimiters (const bool inc_mirror=false) const
 Get the altitude and phi angle of the c symmetry, which depends on nysm.
virtual Transform get_sym (const int n) const
 Provides access to the complete set of rotational symmetry operations associated with this symmetry.
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.
virtual int get_max_csym () const
 Gets the maximum symmetry of this object.
virtual vector< Vec3fget_asym_unit_points (bool inc_mirror=false) const
 to demarcate the asymmetric unit.
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.
virtual bool is_c_sym () const
 Returns true - this is indeed a c symmetry object.
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.

Static Public Member Functions

static Symmetry3DNEW ()
 Factory support function NEW.

Static Public Attributes

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

Private Member Functions

 CSym (const CSym &)
 Disallow copy construction.
CSymoperator= (const CSym &)
 Disallow assignment.

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

EMAN::CSym::CSym ( ) [inline]

Definition at line 236 of file symmetry.h.

Referenced by NEW().

{};
virtual EMAN::CSym::~CSym ( ) [inline, virtual]

Definition at line 237 of file symmetry.h.

{};
EMAN::CSym::CSym ( const CSym ) [private]

Disallow copy construction.


Member Function Documentation

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_mirrorwhether 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 1332 of file symmetry.cpp.

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

Referenced by get_asym_unit_triangles().

{
        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;

}
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_mirrorwhether to include the mirror portion of the asymmetric unit

Implements EMAN::Symmetry3D.

Definition at line 1237 of file symmetry.cpp.

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

                                                                          {
        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;
}
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_mirrorwhether 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:
InvalidValueExceptionif nsym is less than or equal to zero

Implements EMAN::Symmetry3D.

Definition at line 1211 of file symmetry.cpp.

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

Referenced by get_asym_unit_points(), and is_in_asym_unit().

                                                     {
        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;
}
virtual string EMAN::CSym::get_desc ( ) const [inline, virtual]

Get a description.

Returns:
a clear desciption of this class

Implements EMAN::FactoryBase.

Definition at line 255 of file symmetry.h.

{ return "C symmetry support"; }
virtual int EMAN::CSym::get_max_csym ( ) const [inline, virtual]

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.

References EMAN::FactoryBase::params.

{ return params["nsym"]; }
virtual string EMAN::CSym::get_name ( ) const [inline, virtual]

Return CSym::NAME.

Returns:
the unique name of this class

Implements EMAN::FactoryBase.

Definition at line 250 of file symmetry.h.

References NAME.

{ return NAME; }
virtual int EMAN::CSym::get_nsym ( ) const [inline, virtual]

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.

References EMAN::FactoryBase::params.

{ return params["nsym"]; };
virtual TypeDict EMAN::CSym::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

Implements EMAN::FactoryBase.

Definition at line 260 of file symmetry.h.

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

                {
                        TypeDict d;
                        d.put("nsym", EMObject::INT, "The symmetry number");
                        return d;
                }
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:
nthe 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:
InvalidValueExceptionif nsym is less than or equal to zero

Implements EMAN::Symmetry3D.

Definition at line 1369 of file symmetry.cpp.

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

                                         {
        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);
}
virtual bool EMAN::CSym::is_c_sym ( ) const [inline, virtual]

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.

{ return  true; }
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:
altitudethe EMAN style altitude of the 3D orientation in degrees
azimuththe EMAN style azimuth of the 3D orientation in degrees
inc_mirrorwhether 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 1225 of file symmetry.cpp.

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

{
        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;
}
static Symmetry3D* EMAN::CSym::NEW ( ) [inline, static]

Factory support function NEW.

Returns:
a newly instantiated class of this type

Definition at line 242 of file symmetry.h.

References CSym().

                {
                        return new CSym();
                }
CSym& EMAN::CSym::operator= ( const CSym ) [private]

Disallow assignment.


Member Data Documentation

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: