EMAN2
Public Member Functions | Static Public Member Functions | Static Public Attributes | Private Member Functions
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().

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

Definition at line 1300 of file symmetry.h.

{}
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:
symthe 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 698 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().

{
        float delta = params.set_default("delta", 0.0f);
        int n = params.set_default("n", 0);

        if ( delta <= 0 && n <= 0 ) throw InvalidParameterException("Error, you must specify a positive non-zero delta or n");
        if ( delta > 0 && n > 0 ) throw InvalidParameterException("Error, the delta and the n arguments are mutually exclusive");

        if ( n > 0 ) {
                delta = get_optimal_delta(sym,n);
        }

//      if ( sym->is_platonic_sym() ) return gen_platonic_orientations(sym, delta);

        bool inc_mirror = params.set_default("inc_mirror",false);
        Dict delimiters = sym->get_delimiters(inc_mirror);
        float altmax = delimiters["alt_max"];
        float azmax = delimiters["az_max"];

        float altmin = 0.0f;
        // #If it's a h symmetry then the alt iterator starts at very close
        // #to the altmax... the object is a h symmetry then it knows its alt_min...
        if (sym->is_h_sym()){
                altmin = delimiters["alt_min"];
                if (inc_mirror) {
                        altmin -= (float) sym->get_params()["maxtilt"];
                }
        }

        float Deltaz = (float)(cos(altmax*EMConsts::deg2rad)-cos(altmin*EMConsts::deg2rad));
        float s = delta*M_PI/180.0f;
        float NFactor = 3.6f/s;
        float wedgeFactor = fabs( Deltaz*(azmax)/720.0f) ;
        int NumPoints   =  static_cast<int> (NFactor*NFactor*wedgeFactor);

        vector<Transform> ret;

        if (!sym->is_h_sym()) add_orientation(ret,0,0);
        float az = 0.0f;
        float dz = (float)cos(altmin*EMConsts::deg2rad);
        for(int i = 1; i < NumPoints; ++i ){
                float z = dz + Deltaz* (float)i/ float(NumPoints-1);
                float r= sqrt(1.0f-z*z);
                az = fmod(az + delta/r,azmax);
                float alt = (float)(acos(z)*EMConsts::rad2deg);
                if (sym->is_platonic_sym()) {
                        if ( sym->is_in_asym_unit(alt,az,inc_mirror) == false ) continue;
                        else {
                                az += sym->get_az_alignment_offset(); // Align to the symmetry axes
                        }
                }
                add_orientation(ret,az,alt);
        }

        return ret;
}
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.

{ 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.

{ 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:
symthe symmetry which defines the interesting asymmetric unit
deltathe desired angular spacing of the orientations
Returns:
the number of orientations that will be generated using these parameters

Implements EMAN::OrientationGenerator.

Definition at line 657 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().

{
        bool inc_mirror = params.set_default("inc_mirror",false);
        Dict delimiters = sym->get_delimiters(inc_mirror);
        float altmax = delimiters["alt_max"];
        float azmax = delimiters["az_max"];

        float altmin = 0.0f;
        // #If it's a h symmetry then the alt iterator starts at very close
        // #to the altmax... the object is a h symmetry then it knows its alt_min...
        if (sym->is_h_sym()){
                altmin = delimiters["alt_min"];
                if (inc_mirror) {
                        altmin -= (float) sym->get_params()["maxtilt"];
                }
        }

        float Deltaz = (float)(cos(altmax*EMConsts::deg2rad)-cos(altmin*EMConsts::deg2rad));
        float s = delta*M_PI/180.0f;
        float NFactor = 3.6f/s;
        float wedgeFactor = fabs( Deltaz*(azmax)/720.0f) ;
        int NumPoints   =  static_cast<int> (NFactor*NFactor*wedgeFactor);

        int tally = 0;
        if (!sym->is_h_sym()) ++tally;
        float az = 0.0f;
        float dz = (float)cos(altmin*EMConsts::deg2rad);
        for(int i = 1; i < NumPoints; ++i ){
                float z = dz + Deltaz* (float)i/ float(NumPoints-1);
                float r= sqrt(1.0f-z*z);
                az = fmod(az + delta/r,azmax);
                float alt = (float)(acos(z)*EMConsts::rad2deg);
                if (sym->is_platonic_sym()) {
                        if ( sym->is_in_asym_unit(alt,az,inc_mirror) == false ) continue;
                }
                tally++;
        }

        return tally;
}
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::EMObject::INT, and EMAN::TypeDict::put().

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

                {
                        return new SaffOrientationGenerator();
                }
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: