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 1447 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().

01448 {
01449         Dict delim = get_delimiters(inc_mirror);
01450 
01451         vector<Vec3f> ret;
01452         int nsym = params.set_default("nsym",0);
01453         if ( nsym == 1 ) {
01454                 if (inc_mirror == false ) {
01455                         ret.push_back(Vec3f(0,0,1));
01456                         ret.push_back(Vec3f(0,-1,0));
01457                         ret.push_back(Vec3f(1,0,0));
01458                         ret.push_back(Vec3f(0,1,0));
01459                 }
01460                 else {
01461                         ret.push_back(Vec3f(0,-1,0));
01462                         ret.push_back(Vec3f(1,0,0));
01463                         ret.push_back(Vec3f(0,1,0));
01464                         ret.push_back(Vec3f(-1,0,0));
01465                 }
01466         }
01467         else if ( nsym == 2 && inc_mirror ) {
01468                 ret.push_back(Vec3f(0,0,1));
01469                 ret.push_back(Vec3f(0,-1,0));
01470                 ret.push_back(Vec3f(1,0,0));
01471                 ret.push_back(Vec3f(0,1,0));
01472         }
01473         else {
01474                 float angle = (float)(EMConsts::deg2rad*float(delim["az_max"]));
01475                 ret.push_back(Vec3f(0,0,1));
01476                 ret.push_back(Vec3f(0,-1,0));
01477                 float y = -cos(angle);
01478                 float x = sin(angle);
01479                 ret.push_back(Vec3f(x,y,0));
01480         }
01481 
01482         return ret;
01483 
01484 }

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 1392 of file symmetry.cpp.

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

01392                                                                          {
01393         vector<Vec3f> v = get_asym_unit_points(inc_mirror);
01394         int nsym = params.set_default("nsym",0);
01395         vector<vector<Vec3f> > ret;
01396         if ( (nsym == 1 && inc_mirror == false) || (nsym == 2 && inc_mirror)) {
01397                 vector<Vec3f> tmp;
01398                 tmp.push_back(v[0]);
01399                 tmp.push_back(v[2]);
01400                 tmp.push_back(v[1]);
01401                 ret.push_back(tmp);
01402 
01403                 vector<Vec3f> tmp2;
01404                 tmp2.push_back(v[2]);
01405                 tmp2.push_back(v[0]);
01406                 tmp2.push_back(v[3]);
01407                 ret.push_back(tmp2);
01408         }
01409         else if (nsym == 1) {
01410                 Vec3f z(0,0,1);
01411                 vector<Vec3f> tmp;
01412                 tmp.push_back(z);
01413                 tmp.push_back(v[1]);
01414                 tmp.push_back(v[0]);
01415                 ret.push_back(tmp);
01416 
01417                 vector<Vec3f> tmp2;
01418                 tmp2.push_back(z);
01419                 tmp2.push_back(v[2]);
01420                 tmp2.push_back(v[1]);
01421                 ret.push_back(tmp2);
01422 
01423                 vector<Vec3f> tmp3;
01424                 tmp3.push_back(z);
01425                 tmp3.push_back(v[3]);
01426                 tmp3.push_back(v[2]);
01427                 ret.push_back(tmp3);
01428 
01429                 vector<Vec3f> tmp4;
01430                 tmp4.push_back(z);
01431                 tmp4.push_back(v[0]);
01432                 tmp4.push_back(v[3]);
01433                 ret.push_back(tmp4);
01434         }
01435         else {
01436 //              if v.size() == 3
01437                 vector<Vec3f> tmp;
01438                 tmp.push_back(v[0]);
01439                 tmp.push_back(v[2]);
01440                 tmp.push_back(v[1]);
01441                 ret.push_back(tmp);
01442         }
01443 
01444         return ret;
01445 }

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 1340 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().

01340                                                      {
01341         Dict returnDict;
01342 
01343         // Get the parameters of interest
01344         int nsym = params.set_default("nsym",0);
01345         if ( nsym <= 0 ) throw InvalidValueException(nsym,"Error, you must specify a positive non zero nsym");
01346 
01347         returnDict["alt_max"] = 90.0f;
01348 
01349         if ( inc_mirror )  returnDict["az_max"] = 360.0f/(float)nsym;
01350         else returnDict["az_max"] = 180.0f/(float)nsym;
01351 
01352         return returnDict;
01353 }

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 transform3d containing the correct rotational symmetric operation.
Exceptions:
InvalidValueException if nsym is less than or equal to zero

Implements EMAN::Symmetry3D.

Definition at line 1372 of file symmetry.cpp.

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

01373 {
01374         int nsym = 2*params.set_default("nsym",0);
01375         if ( nsym <= 0 ) throw InvalidValueException(n,"Error, you must specify a positive non zero nsym");
01376 
01377         Dict d("type","eman");
01378         // courtesy of Phil Baldwin
01379         if (n >= nsym / 2) {
01380                 d["az"] = ( (n%nsym) - nsym/2) * 360.0f / (nsym / 2);
01381                 d["alt"] = 180.0f;
01382                 d["phi"] = 0.0f;
01383         }
01384         else {
01385                 d["az"] = (n%nsym) * 360.0f / (nsym / 2);
01386                 d["alt"] = 0.0f;
01387                 d["phi"] = 0.0f;
01388         }
01389         return Transform(d);
01390 }

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 1355 of file symmetry.cpp.

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

01356 {
01357         Dict d = get_delimiters(inc_mirror);
01358         float alt_max = d["alt_max"];
01359         float az_max = d["az_max"];
01360 
01361         int nsym = params.set_default("nsym",0);
01362 
01363         if ( nsym == 1 && inc_mirror ) {
01364                 if (altitude >= 0 && altitude <= alt_max && azimuth <= az_max ) return true;
01365         }
01366         else {
01367                 if ( altitude >= 0 && altitude <= alt_max && azimuth <= az_max && azimuth >= 0 ) return true;
01368         }
01369         return false;
01370 }

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:
Generated on Mon Jul 19 12:44:49 2010 for EMAN2 by  doxygen 1.4.7