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EMAN::CSym Class Reference

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

#include <symmetry.h>

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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 1290 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().

01291 {
01292         Dict delim = get_delimiters(inc_mirror);
01293         int nsym = params.set_default("nsym",0);
01294         vector<Vec3f> ret;
01295 
01296         if ( nsym == 1 ) {
01297                 if (inc_mirror == false ) {
01298                         ret.push_back(Vec3f(0,-1,0));
01299                         ret.push_back(Vec3f(1,0,0));
01300                         ret.push_back(Vec3f(0,1,0));
01301                         ret.push_back(Vec3f(-1,0,0));
01302                 }
01303                 // else return ret; // an empty vector! this is fine
01304         }
01305         else if (nsym == 2 && !inc_mirror) {
01306                 ret.push_back(Vec3f(0,0,1));
01307                 ret.push_back(Vec3f(0,-1,0));
01308                 ret.push_back(Vec3f(1,0,0));
01309                 ret.push_back(Vec3f(0,1,0));
01310         }
01311         else {
01312                 ret.push_back(Vec3f(0,0,1));
01313                 ret.push_back(Vec3f(0,-1,0));
01314                 if (inc_mirror == true) {
01315                         ret.push_back(Vec3f(0,0,-1));
01316                 }
01317                 float angle = (float)(EMConsts::deg2rad*float(delim["az_max"]));
01318                 float y = -cos(angle);
01319                 float x = sin(angle);
01320                 ret.push_back(Vec3f(x,y,0));
01321         }
01322 
01323         return ret;
01324 
01325 }

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 1195 of file symmetry.cpp.

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

01195                                                                           {
01196         vector<Vec3f> v = get_asym_unit_points(inc_mirror);
01197         int nsym = params.set_default("nsym",0);
01198 
01199         vector<vector<Vec3f> > ret;
01200         if (v.size() == 0) return ret; // nsym == 1 and inc_mirror == true, this is the entire sphere!
01201         if (nsym == 1 && !inc_mirror) {
01202                 Vec3f z(0,0,1);
01203                 vector<Vec3f> tmp;
01204                 tmp.push_back(z);
01205                 tmp.push_back(v[1]);
01206                 tmp.push_back(v[0]);
01207                 ret.push_back(tmp);
01208 
01209                 vector<Vec3f> tmp2;
01210                 tmp2.push_back(z);
01211                 tmp2.push_back(v[2]);
01212                 tmp2.push_back(v[1]);
01213                 ret.push_back(tmp2);
01214 
01215                 vector<Vec3f> tmp3;
01216                 tmp3.push_back(z);
01217                 tmp3.push_back(v[3]);
01218                 tmp3.push_back(v[2]);
01219                 ret.push_back(tmp3);
01220 
01221                 vector<Vec3f> tmp4;
01222                 tmp4.push_back(z);
01223                 tmp4.push_back(v[0]);
01224                 tmp4.push_back(v[3]);
01225                 ret.push_back(tmp4);
01226         }
01227         else if (nsym == 2 && inc_mirror) {
01228                 Vec3f x(1,0,0);
01229                 vector<Vec3f> tmp;
01230                 tmp.push_back(v[1]);
01231                 tmp.push_back(v[0]);
01232                 tmp.push_back(x);
01233                 ret.push_back(tmp);
01234 
01235                 vector<Vec3f> tmp2;
01236                 tmp2.push_back(v[2]);
01237                 tmp2.push_back(v[1]);
01238                 tmp2.push_back(x);
01239                 ret.push_back(tmp2);
01240 
01241                 vector<Vec3f> tmp3;
01242                 tmp3.push_back(v[3]);
01243                 tmp3.push_back(v[2]);
01244                 tmp3.push_back(x);
01245                 ret.push_back(tmp3);
01246 
01247                 vector<Vec3f> tmp4;
01248                 tmp4.push_back(v[0]);
01249                 tmp4.push_back(v[3]);
01250                 tmp4.push_back(x);
01251                 ret.push_back(tmp4);
01252         }
01253         else if (nsym == 2 && !inc_mirror) {
01254                 vector<Vec3f> tmp;
01255                 tmp.push_back(v[0]);
01256                 tmp.push_back(v[2]);
01257                 tmp.push_back(v[1]);
01258                 ret.push_back(tmp);
01259 
01260                 vector<Vec3f> tmp2;
01261                 tmp2.push_back(v[2]);
01262                 tmp2.push_back(v[0]);
01263                 tmp2.push_back(v[3]);
01264                 ret.push_back(tmp2);
01265         }
01266         else if (v.size() == 3) {
01267                 vector<Vec3f> tmp;
01268                 tmp.push_back(v[0]);
01269                 tmp.push_back(v[2]);
01270                 tmp.push_back(v[1]);
01271                 ret.push_back(tmp);
01272         }
01273         else if (v.size() == 4) {
01274                 vector<Vec3f> tmp;
01275                 tmp.push_back(v[0]);
01276                 tmp.push_back(v[3]);
01277                 tmp.push_back(v[1]);
01278                 ret.push_back(tmp);
01279 
01280                 vector<Vec3f> tmp2;
01281                 tmp2.push_back(v[1]);
01282                 tmp2.push_back(v[3]);
01283                 tmp2.push_back(v[2]);
01284                 ret.push_back(tmp2);
01285         }
01286 
01287         return ret;
01288 }

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 1169 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().

01169                                                      {
01170         Dict returnDict;
01171         // Get the parameters of interest
01172         int nsym = params.set_default("nsym",0);
01173         if ( nsym <= 0 ) throw InvalidValueException(nsym,"Error, you must specify a positive non zero nsym");
01174 
01175         if ( inc_mirror ) returnDict["alt_max"] = 180.0f;
01176         else  returnDict["alt_max"] = 90.0f;
01177 
01178         returnDict["az_max"] = 360.0f/(float)nsym;
01179 
01180         return returnDict;
01181 }

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

Implements EMAN::Symmetry3D.

Definition at line 1327 of file symmetry.cpp.

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

01327                                          {
01328         int nsym = params.set_default("nsym",0);
01329         if ( nsym <= 0 ) throw InvalidValueException(n,"Error, you must specify a positive non zero nsym");
01330 
01331         Dict d("type","eman");
01332         // courtesy of Phil Baldwin
01333         d["az"] = (n%nsym) * 360.0f / nsym;
01334         d["alt"] = 0.0f;
01335         d["phi"] = 0.0f;
01336         return Transform(d);
01337 }

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 1183 of file symmetry.cpp.

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

01184 {
01185         Dict d = get_delimiters(inc_mirror);
01186         float alt_max = d["alt_max"];
01187         float az_max = d["az_max"];
01188 
01189         int nsym = params.set_default("nsym",0);
01190         if ( nsym != 1 && azimuth < 0) return false;
01191         if ( altitude <= alt_max && azimuth <= az_max ) return true;
01192         return false;
01193 }

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 Mon Jul 19 13:07:58 2010 for EMAN2 by  doxygen 1.4.4