#include <symmetry.h>
Inheritance diagram for EMAN::CSym:
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< Vec3f > | get_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 Symmetry3D * | NEW () |
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. | |
CSym & | operator= (const CSym &) |
Disallow assignment. |
Definition at line 233 of file symmetry.h.
EMAN::CSym::CSym | ( | ) | [inline] |
virtual EMAN::CSym::~CSym | ( | ) | [inline, virtual] |
EMAN::CSym::CSym | ( | const CSym & | ) | [private] |
Disallow copy construction.
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.
inc_mirror | whether or not to include the mirror portion of the asymmetric unit |
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
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.
inc_mirror | whether or not to include the part of the asymmetric unit which contains the mirror projections of the other half |
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.
Implements EMAN::FactoryBase.
Definition at line 255 of file symmetry.h.
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.
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.
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.
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.
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.
n | the rotational symmetry operation number. If n is greater than nsym we take n modulo nsym |
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.
Reimplemented from EMAN::Symmetry3D.
Definition at line 320 of file symmetry.h.
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.
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 |
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.
Definition at line 242 of file symmetry.h.
References CSym().
00243 { 00244 return new CSym(); 00245 }
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().