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

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

#include <symmetry.h>

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List of all members.

Public Member Functions

 DSym ()
virtual ~DSym ()
virtual string get_name () const
 Return DSym::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 d 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 D symmetry, this is simply 2*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
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_d_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 = "d"
 The name of this class - used to access it from factories etc. Should be "d".

Private Member Functions

 DSym (const DSym &)
 Disallow copy construction.
DSymoperator= (const DSym &)
 Disallow assignment.

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

EMAN::DSym::DSym ( ) [inline]

Definition at line 343 of file symmetry.h.

Referenced by NEW().

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

Definition at line 344 of file symmetry.h.

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

Disallow copy construction.


Member Function Documentation

vector< Vec3f > DSym::get_asym_unit_points ( bool  inc_mirror = false) const [virtual]
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 to demarcate the asymmetric unit. The last should may be connected to the first.

Implements EMAN::Symmetry3D.

Definition at line 1489 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);

        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;

}
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_mirrorwhether to include the mirror portion of the asymmetric unit

Implements EMAN::Symmetry3D.

Definition at line 1434 of file symmetry.cpp.

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

                                                                         {
        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;
}
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_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 1382 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");

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

Get a description.

Returns:
a clear desciption of this class

Implements EMAN::FactoryBase.

Definition at line 362 of file symmetry.h.

{ return "D symmetry support"; }
virtual int EMAN::DSym::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:
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.

References EMAN::FactoryBase::params.

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

Return DSym::NAME.

Returns:
the unique name of this class

Implements EMAN::FactoryBase.

Definition at line 357 of file symmetry.h.

References NAME.

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

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.

References EMAN::FactoryBase::params.

{ return 2*(int)params["nsym"]; };
virtual TypeDict EMAN::DSym::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 367 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 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:
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 1414 of file symmetry.cpp.

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

{
        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);
}
virtual bool EMAN::DSym::is_d_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 428 of file symmetry.h.

{ return  true; }
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:
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 1397 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 && 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;
}
static Symmetry3D* EMAN::DSym::NEW ( ) [inline, static]

Factory support function NEW.

Returns:
a newly instantiated class of this type

Definition at line 349 of file symmetry.h.

References DSym().

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

Disallow assignment.


Member Data Documentation

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: