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 1293 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().

01294 {
01295         Dict delim = get_delimiters(inc_mirror);
01296         int nsym = params.set_default("nsym",0);
01297         vector<Vec3f> ret;
01298 
01299         if ( nsym == 1 ) {
01300                 if (inc_mirror == false ) {
01301                         ret.push_back(Vec3f(0,-1,0));
01302                         ret.push_back(Vec3f(1,0,0));
01303                         ret.push_back(Vec3f(0,1,0));
01304                         ret.push_back(Vec3f(-1,0,0));
01305                 }
01306                 // else return ret; // an empty vector! this is fine
01307         }
01308         else if (nsym == 2 && !inc_mirror) {
01309                 ret.push_back(Vec3f(0,0,1));
01310                 ret.push_back(Vec3f(0,-1,0));
01311                 ret.push_back(Vec3f(1,0,0));
01312                 ret.push_back(Vec3f(0,1,0));
01313         }
01314         else {
01315                 ret.push_back(Vec3f(0,0,1));
01316                 ret.push_back(Vec3f(0,-1,0));
01317                 if (inc_mirror == true) {
01318                         ret.push_back(Vec3f(0,0,-1));
01319                 }
01320                 float angle = (float)(EMConsts::deg2rad*float(delim["az_max"]));
01321                 float y = -cos(angle);
01322                 float x = sin(angle);
01323                 ret.push_back(Vec3f(x,y,0));
01324         }
01325 
01326         return ret;
01327 
01328 }

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 1198 of file symmetry.cpp.

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

01198                                                                           {
01199         vector<Vec3f> v = get_asym_unit_points(inc_mirror);
01200         int nsym = params.set_default("nsym",0);
01201 
01202         vector<vector<Vec3f> > ret;
01203         if (v.size() == 0) return ret; // nsym == 1 and inc_mirror == true, this is the entire sphere!
01204         if (nsym == 1 && !inc_mirror) {
01205                 Vec3f z(0,0,1);
01206                 vector<Vec3f> tmp;
01207                 tmp.push_back(z);
01208                 tmp.push_back(v[1]);
01209                 tmp.push_back(v[0]);
01210                 ret.push_back(tmp);
01211 
01212                 vector<Vec3f> tmp2;
01213                 tmp2.push_back(z);
01214                 tmp2.push_back(v[2]);
01215                 tmp2.push_back(v[1]);
01216                 ret.push_back(tmp2);
01217 
01218                 vector<Vec3f> tmp3;
01219                 tmp3.push_back(z);
01220                 tmp3.push_back(v[3]);
01221                 tmp3.push_back(v[2]);
01222                 ret.push_back(tmp3);
01223 
01224                 vector<Vec3f> tmp4;
01225                 tmp4.push_back(z);
01226                 tmp4.push_back(v[0]);
01227                 tmp4.push_back(v[3]);
01228                 ret.push_back(tmp4);
01229         }
01230         else if (nsym == 2 && inc_mirror) {
01231                 Vec3f x(1,0,0);
01232                 vector<Vec3f> tmp;
01233                 tmp.push_back(v[1]);
01234                 tmp.push_back(v[0]);
01235                 tmp.push_back(x);
01236                 ret.push_back(tmp);
01237 
01238                 vector<Vec3f> tmp2;
01239                 tmp2.push_back(v[2]);
01240                 tmp2.push_back(v[1]);
01241                 tmp2.push_back(x);
01242                 ret.push_back(tmp2);
01243 
01244                 vector<Vec3f> tmp3;
01245                 tmp3.push_back(v[3]);
01246                 tmp3.push_back(v[2]);
01247                 tmp3.push_back(x);
01248                 ret.push_back(tmp3);
01249 
01250                 vector<Vec3f> tmp4;
01251                 tmp4.push_back(v[0]);
01252                 tmp4.push_back(v[3]);
01253                 tmp4.push_back(x);
01254                 ret.push_back(tmp4);
01255         }
01256         else if (nsym == 2 && !inc_mirror) {
01257                 vector<Vec3f> tmp;
01258                 tmp.push_back(v[0]);
01259                 tmp.push_back(v[2]);
01260                 tmp.push_back(v[1]);
01261                 ret.push_back(tmp);
01262 
01263                 vector<Vec3f> tmp2;
01264                 tmp2.push_back(v[2]);
01265                 tmp2.push_back(v[0]);
01266                 tmp2.push_back(v[3]);
01267                 ret.push_back(tmp2);
01268         }
01269         else if (v.size() == 3) {
01270                 vector<Vec3f> tmp;
01271                 tmp.push_back(v[0]);
01272                 tmp.push_back(v[2]);
01273                 tmp.push_back(v[1]);
01274                 ret.push_back(tmp);
01275         }
01276         else if (v.size() == 4) {
01277                 vector<Vec3f> tmp;
01278                 tmp.push_back(v[0]);
01279                 tmp.push_back(v[3]);
01280                 tmp.push_back(v[1]);
01281                 ret.push_back(tmp);
01282 
01283                 vector<Vec3f> tmp2;
01284                 tmp2.push_back(v[1]);
01285                 tmp2.push_back(v[3]);
01286                 tmp2.push_back(v[2]);
01287                 ret.push_back(tmp2);
01288         }
01289 
01290         return ret;
01291 }

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 1172 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().

01172                                                      {
01173         Dict returnDict;
01174         // Get the parameters of interest
01175         int nsym = params.set_default("nsym",0);
01176         if ( nsym <= 0 ) throw InvalidValueException(nsym,"Error, you must specify a positive non zero nsym");
01177 
01178         if ( inc_mirror ) returnDict["alt_max"] = 180.0f;
01179         else  returnDict["alt_max"] = 90.0f;
01180 
01181         returnDict["az_max"] = 360.0f/(float)nsym;
01182 
01183         return returnDict;
01184 }

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 1330 of file symmetry.cpp.

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

01330                                          {
01331         int nsym = params.set_default("nsym",0);
01332         if ( nsym <= 0 ) throw InvalidValueException(n,"Error, you must specify a positive non zero nsym");
01333 
01334         Dict d("type","eman");
01335         // courtesy of Phil Baldwin
01336         d["az"] = (n%nsym) * 360.0f / nsym;
01337         d["alt"] = 0.0f;
01338         d["phi"] = 0.0f;
01339         return Transform(d);
01340 }

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 1186 of file symmetry.cpp.

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

01187 {
01188         Dict d = get_delimiters(inc_mirror);
01189         float alt_max = d["alt_max"];
01190         float az_max = d["az_max"];
01191 
01192         int nsym = params.set_default("nsym",0);
01193         if ( nsym != 1 && azimuth < 0) return false;
01194         if ( altitude <= alt_max && azimuth <= az_max ) return true;
01195         return false;
01196 }

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 Jul 12 13:50:19 2011 for EMAN2 by  doxygen 1.4.7