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>

Inheritance diagram for EMAN::EvenOrientationGenerator:

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Collaboration diagram for EMAN::EvenOrientationGenerator:

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Public Member Functions
	EvenOrientationGenerator ()

virtual	~EvenOrientationGenerator ()

virtual string	get_name () const
	Return "even". More...

virtual string	get_desc () const
	Get a description. More...

virtual TypeDict	get_param_types () const
	Get a dictionary containing the permissable parameters of this class. More...

virtual vector< Transform >	gen_orientations (const Symmetry3D *const sym) const
	Generate even distributed orientations in the asymmetric unit of the symmetry. More...

Public Member Functions inherited from EMAN::OrientationGenerator
	OrientationGenerator ()

virtual	~OrientationGenerator ()

bool	add_orientation (vector< Transform > &v, const float &az, const float &alt) const
	This functions adds one or more Transform objects to the vector v, depending on the parameters stored in the dictionary (which the inheriting class may include by initializing the typedict in get_param_types by calling. More...

float	get_optimal_delta (const Symmetry3D *const sym, const int &n) const
	This function gets the optimal value of the delta (or angular spacing) of the orientations based on a desired total number of orientations (n). More...

Public Member Functions inherited from EMAN::FactoryBase
	FactoryBase ()

virtual	~FactoryBase ()

Dict	get_params () const
	get a copy of the parameters of this class More...

void	set_params (const Dict &new_params)
	Set new parameters. More...

void	set_param (const string key, const EMObject val)

void	insert_params (const Dict &new_params)
	Insert parameters. More...

Dict	copy_relevant_params (const FactoryBase *const that) const

Static Public Member Functions
static OrientationGenerator *	NEW ()
	Factory support function NEW. More...

Static Public Attributes
static const string	NAME = "even"
	The name of this class - used to access it from factories etc. Should be "icos". More...

Private Member Functions
	EvenOrientationGenerator (const EvenOrientationGenerator &)
	Disallow copy construction. More...

EvenOrientationGenerator &	operator= (const EvenOrientationGenerator &)
	Disallow assignment. More...

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. More...

Additional Inherited Members
Protected Member Functions inherited from EMAN::OrientationGenerator
void	get_az_max (const Symmetry3D *const sym, const float &altmax, const bool inc_mirror, const float &alt_iterator, const float &h, bool &d_odd_mirror_flag, float &azmax_adjusted) const

Protected Attributes inherited from EMAN::FactoryBase
Dict	params
	This is the dictionary the stores the parameters of the object. More...

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 1299 of file symmetry.h.

Constructor & Destructor Documentation

◆ EvenOrientationGenerator() [1/2]

EMAN::EvenOrientationGenerator::EvenOrientationGenerator ( )

inline

Definition at line 1302 of file symmetry.h.

1302{}

Referenced by NEW().

◆ ~EvenOrientationGenerator()

virtual EMAN::EvenOrientationGenerator::~EvenOrientationGenerator ( )

inlinevirtual

Definition at line 1303 of file symmetry.h.

1303{}

◆ EvenOrientationGenerator() [2/2]

EMAN::EvenOrientationGenerator::EvenOrientationGenerator ( const EvenOrientationGenerator & )

private

Disallow copy construction.

Member Function Documentation

◆ gen_orientations()

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

virtual

Generate even distributed 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 634 of file symmetry.cpp.

{
        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;
                else  detaz = delta/(float)sin(alt*EMConsts::deg2rad);
//              bool d_odd_mirror_flag = false;
//              get_az_max(sym,altmax, inc_mirror,alt, lt,d_odd_mirror_flag, detaz);
 
                float az = 0.0;
                while (az<azmax) {
                        if (sym->is_platonic_sym()) {
                                if ( sym->is_in_asym_unit(alt, az, inc_mirror)  ) add_orientation(ret,az+sym->get_az_alignment_offset(),alt);
                        } else  add_orientation(ret,az,alt);
                        if ( sym->is_h_sym() && inc_mirror && alt != altmin ) {
                                add_orientation(ret, az, 2.0f*altmin-alt);
                        }
                        az += detaz;
                }
        }
 
        return ret;
}

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().

◆ get_desc()

virtual string EMAN::EvenOrientationGenerator::get_desc ( ) const

inlinevirtual

Get a description.

Returns: a clear desciption of this class

Implements EMAN::FactoryBase.

Definition at line 1322 of file symmetry.h.

1322{ return "Generate quasi-evenly distributed orientations within an asymmetric unit using Penczek's (94) approach"; }

◆ get_name()

virtual string EMAN::EvenOrientationGenerator::get_name ( ) const

inlinevirtual

Return "even".

Returns: the unique name of this class

Implements EMAN::FactoryBase.

Definition at line 1317 of file symmetry.h.

1317{ return NAME; }

EMAN::EvenOrientationGenerator::NAME

static const string NAME

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

Definition: symmetry.h:1344

References NAME.

◆ get_orientations_tally()

int EvenOrientationGenerator::get_orientations_tally	(	const Symmetry3D *const	sym,
		const float &	delta
	)		const

privatevirtual

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 591 of file symmetry.cpp.

{
        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;
}

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().

◆ get_param_types()

virtual TypeDict EMAN::EvenOrientationGenerator::get_param_types ( ) const

inlinevirtual

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 1328 of file symmetry.h.

                {
                        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;
                }

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

◆ NEW()

static OrientationGenerator * EMAN::EvenOrientationGenerator::NEW ( )

inlinestatic

Factory support function NEW.

Returns: a newly instantiated class of this type

Definition at line 1308 of file symmetry.h.

                {
                        return new EvenOrientationGenerator();
                }

References EvenOrientationGenerator().

◆ operator=()

EvenOrientationGenerator & EMAN::EvenOrientationGenerator::operator= ( const EvenOrientationGenerator & )

private

Disallow assignment.

Member Data Documentation

◆ NAME

const string EvenOrientationGenerator::NAME = "even"

static

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

Definition at line 1344 of file symmetry.h.

Referenced by get_name().

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

Public Member Functions

Static Public Member Functions

Static Public Attributes

Private Member Functions

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ EvenOrientationGenerator() [1/2]

◆ ~EvenOrientationGenerator()

◆ EvenOrientationGenerator() [2/2]

Member Function Documentation

◆ gen_orientations()

◆ get_desc()

◆ get_name()

◆ get_orientations_tally()

◆ get_param_types()

◆ NEW()

◆ operator=()

Member Data Documentation

◆ NAME