EMAN::SaffOrientationGenerator Class Reference

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

#include <symmetry.h>

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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 1296 of file symmetry.h.


Constructor & Destructor Documentation

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

Definition at line 1299 of file symmetry.h.

Referenced by NEW().

01299 {}

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

Definition at line 1300 of file symmetry.h.

01300 {}

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 696 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().

00697 {
00698         float delta = params.set_default("delta", 0.0f);
00699         int n = params.set_default("n", 0);
00700 
00701         if ( delta <= 0 && n <= 0 ) throw InvalidParameterException("Error, you must specify a positive non-zero delta or n");
00702         if ( delta > 0 && n > 0 ) throw InvalidParameterException("Error, the delta and the n arguments are mutually exclusive");
00703 
00704         if ( n > 0 ) {
00705                 delta = get_optimal_delta(sym,n);
00706         }
00707 
00708 //      if ( sym->is_platonic_sym() ) return gen_platonic_orientations(sym, delta);
00709 
00710         bool inc_mirror = params.set_default("inc_mirror",false);
00711         Dict delimiters = sym->get_delimiters(inc_mirror);
00712         float altmax = delimiters["alt_max"];
00713         float azmax = delimiters["az_max"];
00714 
00715         float altmin = 0.0f;
00716         // #If it's a h symmetry then the alt iterator starts at very close
00717         // #to the altmax... the object is a h symmetry then it knows its alt_min...
00718         if (sym->is_h_sym()){
00719                 altmin = delimiters["alt_min"];
00720                 if (inc_mirror) {
00721                         altmin -= (float) sym->get_params()["maxtilt"];
00722                 }
00723         }
00724 
00725         float Deltaz = (float)(cos(altmax*EMConsts::deg2rad)-cos(altmin*EMConsts::deg2rad));
00726         float s = delta*M_PI/180.0f;
00727         float NFactor = 3.6f/s;
00728         float wedgeFactor = fabs( Deltaz*(azmax)/720.0f) ;
00729         int NumPoints   =  static_cast<int> (NFactor*NFactor*wedgeFactor);
00730 
00731         vector<Transform> ret;
00732 
00733         if (!sym->is_h_sym()) add_orientation(ret,0,0);
00734         float az = 0.0f;
00735         float dz = (float)cos(altmin*EMConsts::deg2rad);
00736         for(int i = 1; i < NumPoints; ++i ){
00737                 float z = dz + Deltaz* (float)i/ float(NumPoints-1);
00738                 float r= sqrt(1.0f-z*z);
00739                 az = fmod(az + delta/r,azmax);
00740                 float alt = (float)(acos(z)*EMConsts::rad2deg);
00741                 if (sym->is_platonic_sym()) {
00742                         if ( sym->is_in_asym_unit(alt,az,inc_mirror) == false ) continue;
00743                         else {
00744                                 az += sym->get_az_alignment_offset(); // Align to the symmetry axes
00745                         }
00746                 }
00747                 add_orientation(ret,az,alt);
00748         }
00749 
00750         return ret;
00751 }

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 1318 of file symmetry.h.

01318 { 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 1313 of file symmetry.h.

References NAME.

01313 { 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 655 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().

00656 {
00657         bool inc_mirror = params.set_default("inc_mirror",false);
00658         Dict delimiters = sym->get_delimiters(inc_mirror);
00659         float altmax = delimiters["alt_max"];
00660         float azmax = delimiters["az_max"];
00661 
00662         float altmin = 0.0f;
00663         // #If it's a h symmetry then the alt iterator starts at very close
00664         // #to the altmax... the object is a h symmetry then it knows its alt_min...
00665         if (sym->is_h_sym()){
00666                 altmin = delimiters["alt_min"];
00667                 if (inc_mirror) {
00668                         altmin -= (float) sym->get_params()["maxtilt"];
00669                 }
00670         }
00671 
00672         float Deltaz = (float)(cos(altmax*EMConsts::deg2rad)-cos(altmin*EMConsts::deg2rad));
00673         float s = delta*M_PI/180.0f;
00674         float NFactor = 3.6f/s;
00675         float wedgeFactor = fabs( Deltaz*(azmax)/720.0f) ;
00676         int NumPoints   =  static_cast<int> (NFactor*NFactor*wedgeFactor);
00677 
00678         int tally = 0;
00679         if (!sym->is_h_sym()) ++tally;
00680         float az = 0.0f;
00681         float dz = (float)cos(altmin*EMConsts::deg2rad);
00682         for(int i = 1; i < NumPoints; ++i ){
00683                 float z = dz + Deltaz* (float)i/ float(NumPoints-1);
00684                 float r= sqrt(1.0f-z*z);
00685                 az = fmod(az + delta/r,azmax);
00686                 float alt = (float)(acos(z)*EMConsts::rad2deg);
00687                 if (sym->is_platonic_sym()) {
00688                         if ( sym->is_in_asym_unit(alt,az,inc_mirror) == false ) continue;
00689                 }
00690                 tally++;
00691         }
00692 
00693         return tally;
00694 }

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 1324 of file symmetry.h.

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

01325                 {
01326                         TypeDict d = OrientationGenerator::get_param_types();
01327                         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.");
01328                         d.put("inc_mirror", EMObject::BOOL, "Indicates whether or not to include the mirror portion of the asymmetric unit. Default is false.");
01329                         d.put("delta", EMObject::FLOAT, "The angular separation of orientations in degrees. This option is mutually exclusively of the n argument.");
01330                         return d;
01331                 }

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

Factory support function NEW.

Returns:
a newly instantiated class of this type

Definition at line 1305 of file symmetry.h.

References SaffOrientationGenerator().

01306                 {
01307                         return new SaffOrientationGenerator();
01308                 }

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 1340 of file symmetry.h.

Referenced by get_name().


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