Main Page | Modules | Namespace List | Class Hierarchy | Alphabetical List | Class List | Directories | File List | Namespace Members | Class Members | File Members

EMAN::DSym Class Reference

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

#include <symmetry.h>

Inheritance diagram for EMAN::DSym:

Inheritance graph
[legend]
Collaboration diagram for EMAN::DSym:

Collaboration graph
[legend]
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 1487 of file symmetry.cpp.

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

Referenced by get_asym_unit_triangles().

01488 {
01489         Dict delim = get_delimiters(inc_mirror);
01490 
01491         vector<Vec3f> ret;
01492         int nsym = params.set_default("nsym",0);
01493         if ( nsym == 1 ) {
01494                 if (inc_mirror == false ) {
01495                         ret.push_back(Vec3f(0,0,1));
01496                         ret.push_back(Vec3f(0,-1,0));
01497                         ret.push_back(Vec3f(1,0,0));
01498                         ret.push_back(Vec3f(0,1,0));
01499                 }
01500                 else {
01501                         ret.push_back(Vec3f(0,-1,0));
01502                         ret.push_back(Vec3f(1,0,0));
01503                         ret.push_back(Vec3f(0,1,0));
01504                         ret.push_back(Vec3f(-1,0,0));
01505                 }
01506         }
01507         else if ( nsym == 2 && inc_mirror ) {
01508                 ret.push_back(Vec3f(0,0,1));
01509                 ret.push_back(Vec3f(0,-1,0));
01510                 ret.push_back(Vec3f(1,0,0));
01511                 ret.push_back(Vec3f(0,1,0));
01512         }
01513         else {
01514                 float angle = (float)(EMConsts::deg2rad*float(delim["az_max"]));
01515                 ret.push_back(Vec3f(0,0,1));
01516                 ret.push_back(Vec3f(0,-1,0));
01517                 float y = -cos(angle);
01518                 float x = sin(angle);
01519                 ret.push_back(Vec3f(x,y,0));
01520         }
01521 
01522         return ret;
01523 
01524 }

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 1432 of file symmetry.cpp.

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

01432                                                                          {
01433         vector<Vec3f> v = get_asym_unit_points(inc_mirror);
01434         int nsym = params.set_default("nsym",0);
01435         vector<vector<Vec3f> > ret;
01436         if ( (nsym == 1 && inc_mirror == false) || (nsym == 2 && inc_mirror)) {
01437                 vector<Vec3f> tmp;
01438                 tmp.push_back(v[0]);
01439                 tmp.push_back(v[2]);
01440                 tmp.push_back(v[1]);
01441                 ret.push_back(tmp);
01442 
01443                 vector<Vec3f> tmp2;
01444                 tmp2.push_back(v[2]);
01445                 tmp2.push_back(v[0]);
01446                 tmp2.push_back(v[3]);
01447                 ret.push_back(tmp2);
01448         }
01449         else if (nsym == 1) {
01450                 Vec3f z(0,0,1);
01451                 vector<Vec3f> tmp;
01452                 tmp.push_back(z);
01453                 tmp.push_back(v[1]);
01454                 tmp.push_back(v[0]);
01455                 ret.push_back(tmp);
01456 
01457                 vector<Vec3f> tmp2;
01458                 tmp2.push_back(z);
01459                 tmp2.push_back(v[2]);
01460                 tmp2.push_back(v[1]);
01461                 ret.push_back(tmp2);
01462 
01463                 vector<Vec3f> tmp3;
01464                 tmp3.push_back(z);
01465                 tmp3.push_back(v[3]);
01466                 tmp3.push_back(v[2]);
01467                 ret.push_back(tmp3);
01468 
01469                 vector<Vec3f> tmp4;
01470                 tmp4.push_back(z);
01471                 tmp4.push_back(v[0]);
01472                 tmp4.push_back(v[3]);
01473                 ret.push_back(tmp4);
01474         }
01475         else {
01476 //              if v.size() == 3
01477                 vector<Vec3f> tmp;
01478                 tmp.push_back(v[0]);
01479                 tmp.push_back(v[2]);
01480                 tmp.push_back(v[1]);
01481                 ret.push_back(tmp);
01482         }
01483 
01484         return ret;
01485 }

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 1380 of file symmetry.cpp.

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

Referenced by get_asym_unit_points(), and is_in_asym_unit().

01380                                                      {
01381         Dict returnDict;
01382 
01383         // Get the parameters of interest
01384         int nsym = params.set_default("nsym",0);
01385         if ( nsym <= 0 ) throw InvalidValueException(nsym,"Error, you must specify a positive non zero nsym");
01386 
01387         returnDict["alt_max"] = 90.0f;
01388 
01389         if ( inc_mirror )  returnDict["az_max"] = 360.0f/(float)nsym;
01390         else returnDict["az_max"] = 180.0f/(float)nsym;
01391 
01392         return returnDict;
01393 }

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 1412 of file symmetry.cpp.

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

01413 {
01414         int nsym = 2*params.set_default("nsym",0);
01415         if ( nsym <= 0 ) throw InvalidValueException(n,"Error, you must specify a positive non zero nsym");
01416 
01417         Dict d("type","eman");
01418         // courtesy of Phil Baldwin
01419         if (n >= nsym / 2) {
01420                 d["az"] = ( (n%nsym) - nsym/2) * 360.0f / (nsym / 2);
01421                 d["alt"] = 180.0f;
01422                 d["phi"] = 0.0f;
01423         }
01424         else {
01425                 d["az"] = (n%nsym) * 360.0f / (nsym / 2);
01426                 d["alt"] = 0.0f;
01427                 d["phi"] = 0.0f;
01428         }
01429         return Transform(d);
01430 }

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 1395 of file symmetry.cpp.

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

01396 {
01397         Dict d = get_delimiters(inc_mirror);
01398         float alt_max = d["alt_max"];
01399         float az_max = d["az_max"];
01400 
01401         int nsym = params.set_default("nsym",0);
01402 
01403         if ( nsym == 1 && inc_mirror ) {
01404                 if (altitude >= 0 && altitude <= alt_max && azimuth <= az_max ) return true;
01405         }
01406         else {
01407                 if ( altitude >= 0 && altitude <= alt_max && azimuth <= az_max && azimuth >= 0 ) return true;
01408         }
01409         return false;
01410 }

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:
Generated on Tue Jun 11 13:43:09 2013 for EMAN2 by  doxygen 1.3.9.1