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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

Symmetry3DNEW ()
 Factory support function NEW.

Static Public Attributes

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.

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 1450 of file symmetry.cpp.

References get_delimiters(), EMAN::Dict::set_default(), EMAN::Vec3f, x, and y.

Referenced by get_asym_unit_triangles().

01451 {
01452         Dict delim = get_delimiters(inc_mirror);
01453 
01454         vector<Vec3f> ret;
01455         int nsym = params.set_default("nsym",0);
01456         if ( nsym == 1 ) {
01457                 if (inc_mirror == false ) {
01458                         ret.push_back(Vec3f(0,0,1));
01459                         ret.push_back(Vec3f(0,-1,0));
01460                         ret.push_back(Vec3f(1,0,0));
01461                         ret.push_back(Vec3f(0,1,0));
01462                 }
01463                 else {
01464                         ret.push_back(Vec3f(0,-1,0));
01465                         ret.push_back(Vec3f(1,0,0));
01466                         ret.push_back(Vec3f(0,1,0));
01467                         ret.push_back(Vec3f(-1,0,0));
01468                 }
01469         }
01470         else if ( nsym == 2 && inc_mirror ) {
01471                 ret.push_back(Vec3f(0,0,1));
01472                 ret.push_back(Vec3f(0,-1,0));
01473                 ret.push_back(Vec3f(1,0,0));
01474                 ret.push_back(Vec3f(0,1,0));
01475         }
01476         else {
01477                 float angle = (float)(EMConsts::deg2rad*float(delim["az_max"]));
01478                 ret.push_back(Vec3f(0,0,1));
01479                 ret.push_back(Vec3f(0,-1,0));
01480                 float y = -cos(angle);
01481                 float x = sin(angle);
01482                 ret.push_back(Vec3f(x,y,0));
01483         }
01484 
01485         return ret;
01486 
01487 }

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 1395 of file symmetry.cpp.

References get_asym_unit_points(), EMAN::Dict::set_default(), v, and EMAN::Vec3f.

01395                                                                          {
01396         vector<Vec3f> v = get_asym_unit_points(inc_mirror);
01397         int nsym = params.set_default("nsym",0);
01398         vector<vector<Vec3f> > ret;
01399         if ( (nsym == 1 && inc_mirror == false) || (nsym == 2 && inc_mirror)) {
01400                 vector<Vec3f> tmp;
01401                 tmp.push_back(v[0]);
01402                 tmp.push_back(v[2]);
01403                 tmp.push_back(v[1]);
01404                 ret.push_back(tmp);
01405 
01406                 vector<Vec3f> tmp2;
01407                 tmp2.push_back(v[2]);
01408                 tmp2.push_back(v[0]);
01409                 tmp2.push_back(v[3]);
01410                 ret.push_back(tmp2);
01411         }
01412         else if (nsym == 1) {
01413                 Vec3f z(0,0,1);
01414                 vector<Vec3f> tmp;
01415                 tmp.push_back(z);
01416                 tmp.push_back(v[1]);
01417                 tmp.push_back(v[0]);
01418                 ret.push_back(tmp);
01419 
01420                 vector<Vec3f> tmp2;
01421                 tmp2.push_back(z);
01422                 tmp2.push_back(v[2]);
01423                 tmp2.push_back(v[1]);
01424                 ret.push_back(tmp2);
01425 
01426                 vector<Vec3f> tmp3;
01427                 tmp3.push_back(z);
01428                 tmp3.push_back(v[3]);
01429                 tmp3.push_back(v[2]);
01430                 ret.push_back(tmp3);
01431 
01432                 vector<Vec3f> tmp4;
01433                 tmp4.push_back(z);
01434                 tmp4.push_back(v[0]);
01435                 tmp4.push_back(v[3]);
01436                 ret.push_back(tmp4);
01437         }
01438         else {
01439 //              if v.size() == 3
01440                 vector<Vec3f> tmp;
01441                 tmp.push_back(v[0]);
01442                 tmp.push_back(v[2]);
01443                 tmp.push_back(v[1]);
01444                 ret.push_back(tmp);
01445         }
01446 
01447         return ret;
01448 }

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 1343 of file symmetry.cpp.

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

Referenced by get_asym_unit_points(), and is_in_asym_unit().

01343                                                      {
01344         Dict returnDict;
01345 
01346         // Get the parameters of interest
01347         int nsym = params.set_default("nsym",0);
01348         if ( nsym <= 0 ) throw InvalidValueException(nsym,"Error, you must specify a positive non zero nsym");
01349 
01350         returnDict["alt_max"] = 90.0f;
01351 
01352         if ( inc_mirror )  returnDict["az_max"] = 360.0f/(float)nsym;
01353         else returnDict["az_max"] = 180.0f/(float)nsym;
01354 
01355         return returnDict;
01356 }

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.

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.

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.

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

Implements EMAN::Symmetry3D.

Definition at line 1375 of file symmetry.cpp.

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

01376 {
01377         int nsym = 2*params.set_default("nsym",0);
01378         if ( nsym <= 0 ) throw InvalidValueException(n,"Error, you must specify a positive non zero nsym");
01379 
01380         Dict d("type","eman");
01381         // courtesy of Phil Baldwin
01382         if (n >= nsym / 2) {
01383                 d["az"] = ( (n%nsym) - nsym/2) * 360.0f / (nsym / 2);
01384                 d["alt"] = 180.0f;
01385                 d["phi"] = 0.0f;
01386         }
01387         else {
01388                 d["az"] = (n%nsym) * 360.0f / (nsym / 2);
01389                 d["alt"] = 0.0f;
01390                 d["phi"] = 0.0f;
01391         }
01392         return Transform(d);
01393 }

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 1358 of file symmetry.cpp.

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

01359 {
01360         Dict d = get_delimiters(inc_mirror);
01361         float alt_max = d["alt_max"];
01362         float az_max = d["az_max"];
01363 
01364         int nsym = params.set_default("nsym",0);
01365 
01366         if ( nsym == 1 && inc_mirror ) {
01367                 if (altitude >= 0 && altitude <= alt_max && azimuth <= az_max ) return true;
01368         }
01369         else {
01370                 if ( altitude >= 0 && altitude <= alt_max && azimuth <= az_max && azimuth >= 0 ) return true;
01371         }
01372         return false;
01373 }

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.

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 41 of file symmetry.cpp.


The documentation for this class was generated from the following files:
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