EMAN::SaffOrientationGenerator Class Reference

Saff orientation generator - based on the work of Saff and Kuijlaars, 1997 E.B. More...

#include <symmetry.h>

Inheritance diagram for EMAN::SaffOrientationGenerator:

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List of all members.

Public Member Functions

 SaffOrientationGenerator ()
virtual ~SaffOrientationGenerator ()
virtual string get_name () const
 Return "saff".
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 vector< Transformgen_orientations (const Symmetry3D *const sym) const
 Generate Saff orientations in the asymmetric unit of the symmetry.

Static Public Member Functions

static OrientationGeneratorNEW ()
 Factory support function NEW.

Static Public Attributes

static const string NAME = "saff"
 The name of this class - used to access it from factories etc. Should be "icos".

Private Member Functions

 SaffOrientationGenerator (const SaffOrientationGenerator &)
 Disallow copy construction.
SaffOrientationGeneratoroperator= (const SaffOrientationGenerator &)
 Disallow assignment.
virtual int get_orientations_tally (const Symmetry3D *const sym, const float &delta) const
 This function returns how many orientations will be generated for a given delta (angular spacing) It does this by simulated gen_orientations.

Detailed Description

Saff orientation generator - based on the work of Saff and Kuijlaars, 1997 E.B.

Saff and A.B.J. Kuijlaars, Distributing many points on a sphere, Mathematical Intelligencer 19 (1997), pp. 5–11. This is a spiral based approach

Author:
David Woolford (ported directly from Sparx utilities.py, which is written by Pawel Penczek)
Date:
March 2008

Definition at line 1231 of file symmetry.h.


Constructor & Destructor Documentation

EMAN::SaffOrientationGenerator::SaffOrientationGenerator (  )  [inline]

Definition at line 1234 of file symmetry.h.

Referenced by NEW().

01234 {}

virtual EMAN::SaffOrientationGenerator::~SaffOrientationGenerator (  )  [inline, virtual]

Definition at line 1235 of file symmetry.h.

01235 {}

EMAN::SaffOrientationGenerator::SaffOrientationGenerator ( const SaffOrientationGenerator  )  [private]

Disallow copy construction.


Member Function Documentation

vector< Transform > SaffOrientationGenerator::gen_orientations ( const Symmetry3D *const   sym  )  const [virtual]

Generate Saff orientations in the asymmetric unit of the symmetry.

Parameters:
sym the symmetry which defines the interesting asymmetric unit
Returns:
a vector of Transform objects containing the set of evenly distributed orientations

Implements EMAN::OrientationGenerator.

Definition at line 690 of file symmetry.cpp.

References EMAN::OrientationGenerator::add_orientation(), EMAN::EMConsts::deg2rad, EMAN::Symmetry3D::get_az_alignment_offset(), EMAN::Symmetry3D::get_delimiters(), EMAN::OrientationGenerator::get_optimal_delta(), EMAN::FactoryBase::get_params(), InvalidParameterException, EMAN::Symmetry3D::is_h_sym(), EMAN::Symmetry3D::is_in_asym_unit(), EMAN::Symmetry3D::is_platonic_sym(), EMAN::FactoryBase::params, EMAN::EMConsts::rad2deg, EMAN::Dict::set_default(), and sqrt().

00691 {
00692         float delta = params.set_default("delta", 0.0f);
00693         int n = params.set_default("n", 0);
00694 
00695         if ( delta <= 0 && n <= 0 ) throw InvalidParameterException("Error, you must specify a positive non-zero delta or n");
00696         if ( delta > 0 && n > 0 ) throw InvalidParameterException("Error, the delta and the n arguments are mutually exclusive");
00697 
00698         if ( n > 0 ) {
00699                 delta = get_optimal_delta(sym,n);
00700         }
00701 
00702 //      if ( sym->is_platonic_sym() ) return gen_platonic_orientations(sym, delta);
00703 
00704         bool inc_mirror = params.set_default("inc_mirror",false);
00705         Dict delimiters = sym->get_delimiters(inc_mirror);
00706         float altmax = delimiters["alt_max"];
00707         float azmax = delimiters["az_max"];
00708 
00709         float altmin = 0.0f;
00710         // #If it's a h symmetry then the alt iterator starts at very close
00711         // #to the altmax... the object is a h symmetry then it knows its alt_min...
00712         if (sym->is_h_sym()){
00713                 altmin = delimiters["alt_min"];
00714                 if (inc_mirror) {
00715                         altmin -= (float) sym->get_params()["maxtilt"];
00716                 }
00717         }
00718 
00719         float Deltaz = (float)(cos(altmax*EMConsts::deg2rad)-cos(altmin*EMConsts::deg2rad));
00720         float s = delta*M_PI/180.0f;
00721         float NFactor = 3.6f/s;
00722         float wedgeFactor = fabs( Deltaz*(azmax)/720.0f) ;
00723         int NumPoints   =  static_cast<int> (NFactor*NFactor*wedgeFactor);
00724 
00725         vector<Transform> ret;
00726 
00727         if (!sym->is_h_sym()) add_orientation(ret,0,0);
00728         float az = 0.0f;
00729         float dz = (float)cos(altmin*EMConsts::deg2rad);
00730         for(int i = 1; i < NumPoints; ++i ){
00731                 float z = dz + Deltaz* (float)i/ float(NumPoints-1);
00732                 float r= sqrt(1.0f-z*z);
00733                 az = fmod(az + delta/r,azmax);
00734                 float alt = (float)(acos(z)*EMConsts::rad2deg);
00735                 if (sym->is_platonic_sym()) {
00736                         if ( sym->is_in_asym_unit(alt,az,inc_mirror) == false ) continue;
00737                         else {
00738                                 az += sym->get_az_alignment_offset(); // Align to the symmetry axes
00739                         }
00740                 }
00741                 add_orientation(ret,az,alt);
00742         }
00743 
00744         return ret;
00745 }

virtual string EMAN::SaffOrientationGenerator::get_desc (  )  const [inline, virtual]

Get a description.

Returns:
a clear desciption of this class

Implements EMAN::FactoryBase.

Definition at line 1253 of file symmetry.h.

01253 { return "Generate quasi-evenly distributed orientations within an asymmetric unit using a spiraling method attributed to Saff"; }

virtual string EMAN::SaffOrientationGenerator::get_name (  )  const [inline, virtual]

Return "saff".

Returns:
the unique name of this class

Implements EMAN::FactoryBase.

Definition at line 1248 of file symmetry.h.

References NAME.

01248 { return NAME; }

int SaffOrientationGenerator::get_orientations_tally ( const Symmetry3D *const   sym,
const float &  delta 
) const [private, virtual]

This function returns how many orientations will be generated for a given delta (angular spacing) It does this by simulated gen_orientations.

Parameters:
sym the symmetry which defines the interesting asymmetric unit
delta the desired angular spacing of the orientations
Returns:
the number of orientations that will be generated using these parameters

Implements EMAN::OrientationGenerator.

Definition at line 649 of file symmetry.cpp.

References EMAN::EMConsts::deg2rad, EMAN::Symmetry3D::get_delimiters(), EMAN::FactoryBase::get_params(), EMAN::Symmetry3D::is_h_sym(), EMAN::Symmetry3D::is_in_asym_unit(), EMAN::Symmetry3D::is_platonic_sym(), EMAN::FactoryBase::params, EMAN::EMConsts::rad2deg, EMAN::Dict::set_default(), and sqrt().

00650 {
00651         bool inc_mirror = params.set_default("inc_mirror",false);
00652         Dict delimiters = sym->get_delimiters(inc_mirror);
00653         float altmax = delimiters["alt_max"];
00654         float azmax = delimiters["az_max"];
00655 
00656         float altmin = 0.0f;
00657         // #If it's a h symmetry then the alt iterator starts at very close
00658         // #to the altmax... the object is a h symmetry then it knows its alt_min...
00659         if (sym->is_h_sym()){
00660                 altmin = delimiters["alt_min"];
00661                 if (inc_mirror) {
00662                         altmin -= (float) sym->get_params()["maxtilt"];
00663                 }
00664         }
00665 
00666         float Deltaz = (float)(cos(altmax*EMConsts::deg2rad)-cos(altmin*EMConsts::deg2rad));
00667         float s = delta*M_PI/180.0f;
00668         float NFactor = 3.6f/s;
00669         float wedgeFactor = fabs( Deltaz*(azmax)/720.0f) ;
00670         int NumPoints   =  static_cast<int> (NFactor*NFactor*wedgeFactor);
00671 
00672         int tally = 0;
00673         if (!sym->is_h_sym()) ++tally;
00674         float az = 0.0f;
00675         float dz = (float)cos(altmin*EMConsts::deg2rad);
00676         for(int i = 1; i < NumPoints; ++i ){
00677                 float z = dz + Deltaz* (float)i/ float(NumPoints-1);
00678                 float r= sqrt(1.0f-z*z);
00679                 az = fmod(az + delta/r,azmax);
00680                 float alt = (float)(acos(z)*EMConsts::rad2deg);
00681                 if (sym->is_platonic_sym()) {
00682                         if ( sym->is_in_asym_unit(alt,az,inc_mirror) == false ) continue;
00683                 }
00684                 tally++;
00685         }
00686 
00687         return tally;
00688 }

virtual TypeDict EMAN::SaffOrientationGenerator::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 parameters are explained in the dictionary itself

Reimplemented from EMAN::OrientationGenerator.

Definition at line 1259 of file symmetry.h.

References EMAN::EMObject::BOOL, EMAN::EMObject::FLOAT, EMAN::OrientationGenerator::get_param_types(), EMAN::EMObject::INT, and EMAN::TypeDict::put().

01260                 {
01261                         TypeDict d = OrientationGenerator::get_param_types();
01262                         d.put("n", EMObject::INT, "The number of orientations to generate. This option is mutually exclusively of the delta argument.Will attempt to get as close to the number specified as possible.");
01263                         d.put("inc_mirror", EMObject::BOOL, "Indicates whether or not to include the mirror portion of the asymmetric unit. Default is false.");
01264                         d.put("delta", EMObject::FLOAT, "The angular separation of orientations in degrees. This option is mutually exclusively of the n argument.");
01265                         return d;
01266                 }

static OrientationGenerator* EMAN::SaffOrientationGenerator::NEW (  )  [inline, static]

Factory support function NEW.

Returns:
a newly instantiated class of this type

Definition at line 1240 of file symmetry.h.

References SaffOrientationGenerator().

01241                 {
01242                         return new SaffOrientationGenerator();
01243                 }

SaffOrientationGenerator& EMAN::SaffOrientationGenerator::operator= ( const SaffOrientationGenerator  )  [private]

Disallow assignment.


Member Data Documentation

const string SaffOrientationGenerator::NAME = "saff" [static]

The name of this class - used to access it from factories etc. Should be "icos".

Definition at line 1275 of file symmetry.h.

Referenced by get_name().


The documentation for this class was generated from the following files:
Generated on Thu May 3 10:11:46 2012 for EMAN2 by  doxygen 1.4.7