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().

00343 {};

virtual EMAN::DSym::~DSym (  )  [inline, virtual]

Definition at line 344 of file symmetry.h.

00344 {};

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_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 1481 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().

01482 {
01483         Dict delim = get_delimiters(inc_mirror);
01484 
01485         vector<Vec3f> ret;
01486         int nsym = params.set_default("nsym",0);
01487         if ( nsym == 1 ) {
01488                 if (inc_mirror == false ) {
01489                         ret.push_back(Vec3f(0,0,1));
01490                         ret.push_back(Vec3f(0,-1,0));
01491                         ret.push_back(Vec3f(1,0,0));
01492                         ret.push_back(Vec3f(0,1,0));
01493                 }
01494                 else {
01495                         ret.push_back(Vec3f(0,-1,0));
01496                         ret.push_back(Vec3f(1,0,0));
01497                         ret.push_back(Vec3f(0,1,0));
01498                         ret.push_back(Vec3f(-1,0,0));
01499                 }
01500         }
01501         else if ( nsym == 2 && inc_mirror ) {
01502                 ret.push_back(Vec3f(0,0,1));
01503                 ret.push_back(Vec3f(0,-1,0));
01504                 ret.push_back(Vec3f(1,0,0));
01505                 ret.push_back(Vec3f(0,1,0));
01506         }
01507         else {
01508                 float angle = (float)(EMConsts::deg2rad*float(delim["az_max"]));
01509                 ret.push_back(Vec3f(0,0,1));
01510                 ret.push_back(Vec3f(0,-1,0));
01511                 float y = -cos(angle);
01512                 float x = sin(angle);
01513                 ret.push_back(Vec3f(x,y,0));
01514         }
01515 
01516         return ret;
01517 
01518 }

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 1426 of file symmetry.cpp.

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

01426                                                                          {
01427         vector<Vec3f> v = get_asym_unit_points(inc_mirror);
01428         int nsym = params.set_default("nsym",0);
01429         vector<vector<Vec3f> > ret;
01430         if ( (nsym == 1 && inc_mirror == false) || (nsym == 2 && inc_mirror)) {
01431                 vector<Vec3f> tmp;
01432                 tmp.push_back(v[0]);
01433                 tmp.push_back(v[2]);
01434                 tmp.push_back(v[1]);
01435                 ret.push_back(tmp);
01436 
01437                 vector<Vec3f> tmp2;
01438                 tmp2.push_back(v[2]);
01439                 tmp2.push_back(v[0]);
01440                 tmp2.push_back(v[3]);
01441                 ret.push_back(tmp2);
01442         }
01443         else if (nsym == 1) {
01444                 Vec3f z(0,0,1);
01445                 vector<Vec3f> tmp;
01446                 tmp.push_back(z);
01447                 tmp.push_back(v[1]);
01448                 tmp.push_back(v[0]);
01449                 ret.push_back(tmp);
01450 
01451                 vector<Vec3f> tmp2;
01452                 tmp2.push_back(z);
01453                 tmp2.push_back(v[2]);
01454                 tmp2.push_back(v[1]);
01455                 ret.push_back(tmp2);
01456 
01457                 vector<Vec3f> tmp3;
01458                 tmp3.push_back(z);
01459                 tmp3.push_back(v[3]);
01460                 tmp3.push_back(v[2]);
01461                 ret.push_back(tmp3);
01462 
01463                 vector<Vec3f> tmp4;
01464                 tmp4.push_back(z);
01465                 tmp4.push_back(v[0]);
01466                 tmp4.push_back(v[3]);
01467                 ret.push_back(tmp4);
01468         }
01469         else {
01470 //              if v.size() == 3
01471                 vector<Vec3f> tmp;
01472                 tmp.push_back(v[0]);
01473                 tmp.push_back(v[2]);
01474                 tmp.push_back(v[1]);
01475                 ret.push_back(tmp);
01476         }
01477 
01478         return ret;
01479 }

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 1374 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().

01374                                                      {
01375         Dict returnDict;
01376 
01377         // Get the parameters of interest
01378         int nsym = params.set_default("nsym",0);
01379         if ( nsym <= 0 ) throw InvalidValueException(nsym,"Error, you must specify a positive non zero nsym");
01380 
01381         returnDict["alt_max"] = 90.0f;
01382 
01383         if ( inc_mirror )  returnDict["az_max"] = 360.0f/(float)nsym;
01384         else returnDict["az_max"] = 180.0f/(float)nsym;
01385 
01386         return returnDict;
01387 }

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.

00362 { 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.

00404 { 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.

00357 { 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.

00397 { 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().

00368                 {
00369                         TypeDict d;
00370                         d.put("nsym", EMObject::INT, "The symmetry number");
00371                         return d;
00372                 }

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 1406 of file symmetry.cpp.

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

01407 {
01408         int nsym = 2*params.set_default("nsym",0);
01409         if ( nsym <= 0 ) throw InvalidValueException(n,"Error, you must specify a positive non zero nsym");
01410 
01411         Dict d("type","eman");
01412         // courtesy of Phil Baldwin
01413         if (n >= nsym / 2) {
01414                 d["az"] = ( (n%nsym) - nsym/2) * 360.0f / (nsym / 2);
01415                 d["alt"] = 180.0f;
01416                 d["phi"] = 0.0f;
01417         }
01418         else {
01419                 d["az"] = (n%nsym) * 360.0f / (nsym / 2);
01420                 d["alt"] = 0.0f;
01421                 d["phi"] = 0.0f;
01422         }
01423         return Transform(d);
01424 }

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.

00428 { return  true; }

bool DSym::is_in_asym_unit ( const float &  altitude,
const float &  azimuth,
const bool  inc_mirror 
) 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 1389 of file symmetry.cpp.

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

01390 {
01391         Dict d = get_delimiters(inc_mirror);
01392         float alt_max = d["alt_max"];
01393         float az_max = d["az_max"];
01394 
01395         int nsym = params.set_default("nsym",0);
01396 
01397         if ( nsym == 1 && inc_mirror ) {
01398                 if (altitude >= 0 && altitude <= alt_max && azimuth <= az_max ) return true;
01399         }
01400         else {
01401                 if ( altitude >= 0 && altitude <= alt_max && azimuth <= az_max && azimuth >= 0 ) return true;
01402         }
01403         return false;
01404 }

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().

00350                 {
00351                         return new DSym();
00352                 }

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:
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