EMAN::CSym Class Reference

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

#include <symmetry.h>

Inheritance diagram for EMAN::CSym:

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Collaboration diagram for EMAN::CSym:

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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().

00236 {};

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

Definition at line 237 of file symmetry.h.

00237 {};

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_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

Implements EMAN::Symmetry3D.

Definition at line 1330 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().

01331 {
01332         Dict delim = get_delimiters(inc_mirror);
01333         int nsym = params.set_default("nsym",0);
01334         vector<Vec3f> ret;
01335 
01336         if ( nsym == 1 ) {
01337                 if (inc_mirror == false ) {
01338                         ret.push_back(Vec3f(0,-1,0));
01339                         ret.push_back(Vec3f(1,0,0));
01340                         ret.push_back(Vec3f(0,1,0));
01341                         ret.push_back(Vec3f(-1,0,0));
01342                 }
01343                 // else return ret; // an empty vector! this is fine
01344         }
01345         else if (nsym == 2 && !inc_mirror) {
01346                 ret.push_back(Vec3f(0,0,1));
01347                 ret.push_back(Vec3f(0,-1,0));
01348                 ret.push_back(Vec3f(1,0,0));
01349                 ret.push_back(Vec3f(0,1,0));
01350         }
01351         else {
01352                 ret.push_back(Vec3f(0,0,1));
01353                 ret.push_back(Vec3f(0,-1,0));
01354                 if (inc_mirror == true) {
01355                         ret.push_back(Vec3f(0,0,-1));
01356                 }
01357                 float angle = (float)(EMConsts::deg2rad*float(delim["az_max"]));
01358                 float y = -cos(angle);
01359                 float x = sin(angle);
01360                 ret.push_back(Vec3f(x,y,0));
01361         }
01362 
01363         return ret;
01364 
01365 }

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_mirror whether to include the mirror portion of the asymmetric unit

Implements EMAN::Symmetry3D.

Definition at line 1235 of file symmetry.cpp.

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

01235                                                                           {
01236         vector<Vec3f> v = get_asym_unit_points(inc_mirror);
01237         int nsym = params.set_default("nsym",0);
01238 
01239         vector<vector<Vec3f> > ret;
01240         if (v.size() == 0) return ret; // nsym == 1 and inc_mirror == true, this is the entire sphere!
01241         if (nsym == 1 && !inc_mirror) {
01242                 Vec3f z(0,0,1);
01243                 vector<Vec3f> tmp;
01244                 tmp.push_back(z);
01245                 tmp.push_back(v[1]);
01246                 tmp.push_back(v[0]);
01247                 ret.push_back(tmp);
01248 
01249                 vector<Vec3f> tmp2;
01250                 tmp2.push_back(z);
01251                 tmp2.push_back(v[2]);
01252                 tmp2.push_back(v[1]);
01253                 ret.push_back(tmp2);
01254 
01255                 vector<Vec3f> tmp3;
01256                 tmp3.push_back(z);
01257                 tmp3.push_back(v[3]);
01258                 tmp3.push_back(v[2]);
01259                 ret.push_back(tmp3);
01260 
01261                 vector<Vec3f> tmp4;
01262                 tmp4.push_back(z);
01263                 tmp4.push_back(v[0]);
01264                 tmp4.push_back(v[3]);
01265                 ret.push_back(tmp4);
01266         }
01267         else if (nsym == 2 && inc_mirror) {
01268                 Vec3f x(1,0,0);
01269                 vector<Vec3f> tmp;
01270                 tmp.push_back(v[1]);
01271                 tmp.push_back(v[0]);
01272                 tmp.push_back(x);
01273                 ret.push_back(tmp);
01274 
01275                 vector<Vec3f> tmp2;
01276                 tmp2.push_back(v[2]);
01277                 tmp2.push_back(v[1]);
01278                 tmp2.push_back(x);
01279                 ret.push_back(tmp2);
01280 
01281                 vector<Vec3f> tmp3;
01282                 tmp3.push_back(v[3]);
01283                 tmp3.push_back(v[2]);
01284                 tmp3.push_back(x);
01285                 ret.push_back(tmp3);
01286 
01287                 vector<Vec3f> tmp4;
01288                 tmp4.push_back(v[0]);
01289                 tmp4.push_back(v[3]);
01290                 tmp4.push_back(x);
01291                 ret.push_back(tmp4);
01292         }
01293         else if (nsym == 2 && !inc_mirror) {
01294                 vector<Vec3f> tmp;
01295                 tmp.push_back(v[0]);
01296                 tmp.push_back(v[2]);
01297                 tmp.push_back(v[1]);
01298                 ret.push_back(tmp);
01299 
01300                 vector<Vec3f> tmp2;
01301                 tmp2.push_back(v[2]);
01302                 tmp2.push_back(v[0]);
01303                 tmp2.push_back(v[3]);
01304                 ret.push_back(tmp2);
01305         }
01306         else if (v.size() == 3) {
01307                 vector<Vec3f> tmp;
01308                 tmp.push_back(v[0]);
01309                 tmp.push_back(v[2]);
01310                 tmp.push_back(v[1]);
01311                 ret.push_back(tmp);
01312         }
01313         else if (v.size() == 4) {
01314                 vector<Vec3f> tmp;
01315                 tmp.push_back(v[0]);
01316                 tmp.push_back(v[3]);
01317                 tmp.push_back(v[1]);
01318                 ret.push_back(tmp);
01319 
01320                 vector<Vec3f> tmp2;
01321                 tmp2.push_back(v[1]);
01322                 tmp2.push_back(v[3]);
01323                 tmp2.push_back(v[2]);
01324                 ret.push_back(tmp2);
01325         }
01326 
01327         return ret;
01328 }

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_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 1209 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().

01209                                                      {
01210         Dict returnDict;
01211         // Get the parameters of interest
01212         int nsym = params.set_default("nsym",0);
01213         if ( nsym <= 0 ) throw InvalidValueException(nsym,"Error, you must specify a positive non zero nsym");
01214 
01215         if ( inc_mirror ) returnDict["alt_max"] = 180.0f;
01216         else  returnDict["alt_max"] = 90.0f;
01217 
01218         returnDict["az_max"] = 360.0f/(float)nsym;
01219 
01220         return returnDict;
01221 }

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.

00255 { 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.

00296 { 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.

00250 { 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.

00289 { 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().

00261                 {
00262                         TypeDict d;
00263                         d.put("nsym", EMObject::INT, "The symmetry number");
00264                         return d;
00265                 }

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:
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 1367 of file symmetry.cpp.

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

01367                                          {
01368         int nsym = params.set_default("nsym",0);
01369         if ( nsym <= 0 ) throw InvalidValueException(n,"Error, you must specify a positive non zero nsym");
01370 
01371         Dict d("type","eman");
01372         // courtesy of Phil Baldwin
01373         d["az"] = (n%nsym) * 360.0f / nsym;
01374         d["alt"] = 0.0f;
01375         d["phi"] = 0.0f;
01376         return Transform(d);
01377 }

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.

00320 { return  true; }

bool CSym::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 1223 of file symmetry.cpp.

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

01224 {
01225         Dict d = get_delimiters(inc_mirror);
01226         float alt_max = d["alt_max"];
01227         float az_max = d["az_max"];
01228 
01229         int nsym = params.set_default("nsym",0);
01230         if ( nsym != 1 && azimuth < 0) return false;
01231         if ( altitude <= alt_max && azimuth <= az_max ) return true;
01232         return false;
01233 }

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().

00243                 {
00244                         return new CSym();
00245                 }

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:
Generated on Tue Jun 11 12:45:25 2013 for EMAN2 by  doxygen 1.4.7