EMAN2
Public Member Functions | Static Public Member Functions | Static Public Attributes | Private Member Functions
EMAN::EvenOrientationGenerator Class Reference

Sparx even orientation generator - see util_sparx.cpp - Util::even_angles(...) This orientation generator is based on work presented in Penczek et al., 1994 P.A. More...

#include <symmetry.h>

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List of all members.

Public Member Functions

 EvenOrientationGenerator ()
virtual ~EvenOrientationGenerator ()
virtual string get_name () const
 Return "even".
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 even distributed 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 = "even"
 The name of this class - used to access it from factories etc. Should be "icos".

Private Member Functions

 EvenOrientationGenerator (const EvenOrientationGenerator &)
 Disallow copy construction.
EvenOrientationGeneratoroperator= (const EvenOrientationGenerator &)
 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

Sparx even orientation generator - see util_sparx.cpp - Util::even_angles(...) This orientation generator is based on work presented in Penczek et al., 1994 P.A.

Penczek, R.A. Grassucci and J. Frank, The ribosome at improved resolution: new techniques for merging and orientation refinement in 3D cryo-electron microscopy of biological particles, Ultramicroscopy 53 (1994).

This is a proportional approach very similar to the eman approach - the differences between these two approaches is mostly visible near altitude=0

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

Definition at line 1230 of file symmetry.h.


Constructor & Destructor Documentation

EMAN::EvenOrientationGenerator::EvenOrientationGenerator ( ) [inline]

Definition at line 1233 of file symmetry.h.

Referenced by NEW().

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

Definition at line 1234 of file symmetry.h.

{}
EMAN::EvenOrientationGenerator::EvenOrientationGenerator ( const EvenOrientationGenerator ) [private]

Disallow copy construction.


Member Function Documentation

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

Generate even distributed 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 600 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(), InvalidParameterException, EMAN::Symmetry3D::is_h_sym(), EMAN::Symmetry3D::is_in_asym_unit(), EMAN::Symmetry3D::is_platonic_sym(), EMAN::FactoryBase::params, and EMAN::Dict::set_default().

{
        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 exzclusive");

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

        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"];

        vector<Transform> ret;

        for (float alt = altmin; alt <= altmax; alt += delta) {
                float detaz;
                int lt;
                if ((0.0f == alt)||(180.0f == alt)) {
                        detaz = 360.0f;
                        lt = 1;
                } else {
                        detaz = delta/(float)sin(alt*EMConsts::deg2rad);
                        lt = int(azmax/detaz)-1;
                        if (lt < 1) lt = 1;
                        detaz = azmax/(float)lt;
                }
//              bool d_odd_mirror_flag = false;
//              get_az_max(sym,altmax, inc_mirror,alt, lt,d_odd_mirror_flag, detaz);

                for (int i = 0; i < lt; i++) {
                        float az = (float)i*detaz;
                        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);
                        if ( sym->is_h_sym() && inc_mirror && alt != altmin ) {
                                add_orientation(ret,az,2.0f*altmin-alt);
                        }
                }
        }

        return ret;
}
virtual string EMAN::EvenOrientationGenerator::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.

{ return "Generate quasi-evenly distributed orientations within an asymmetric unit using Penczek's (94) approach"; }
virtual string EMAN::EvenOrientationGenerator::get_name ( ) const [inline, virtual]

Return "even".

Returns:
the unique name of this class

Implements EMAN::FactoryBase.

Definition at line 1248 of file symmetry.h.

References NAME.

{ return NAME; }
int EvenOrientationGenerator::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 557 of file symmetry.cpp.

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

{
        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"];

        int tally = 0;

        for (float alt = altmin; alt <= altmax; alt += delta) {
                float detaz;
                int lt;
                if ((0.0f == alt)||(180.0f == alt)) {
                        detaz = 360.0f;
                        lt = 1;
                } else {
                        detaz = delta/(float)sin(alt*EMConsts::deg2rad);
                        lt = int(azmax/detaz)-1;
                        if (lt < 1) lt = 1;
                        detaz = azmax/(float)lt;
                }
//              bool d_odd_mirror_flag = false;
//              get_az_max(sym,altmax, inc_mirror,alt, lt,d_odd_mirror_flag, detaz);
                for (int i = 0; i < lt; i++) {
                        float az = (float)i*detaz;
                        if (sym->is_platonic_sym()) {
                                if ( sym->is_in_asym_unit(alt, az,inc_mirror) == false ) continue;
                        }
                        tally++;
                        if ( sym->is_h_sym() && inc_mirror && alt != altmin ) {
                                tally++;
                        }
                }
        }

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

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

Factory support function NEW.

Returns:
a newly instantiated class of this type

Definition at line 1239 of file symmetry.h.

References EvenOrientationGenerator().

                {
                        return new EvenOrientationGenerator();
                }
EvenOrientationGenerator& EMAN::EvenOrientationGenerator::operator= ( const EvenOrientationGenerator ) [private]

Disallow assignment.


Member Data Documentation

const string EvenOrientationGenerator::NAME = "even" [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: