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

An encapsulation of helical 3D symmetry. More...

#include <symmetry.h>

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List of all members.

Public Member Functions

 HSym ()
virtual ~HSym ()
virtual string get_name () const
 Return HSym::NAME.
virtual string get_desc () const
 Get a description.
virtual TypeDict get_param_types () const
 Get a dictionary containing the permissable parameters of this class Of all the symmetries, helical has the most options.
virtual Dict get_delimiters (const bool inc_mirror=false) const
 Get the altitude and phi angle of the d symmetry, which depends on nysm.
virtual Transform get_sym (const int n) const
 Provides access to the complete set of rotational and translational symmetry operations associated with helical symmetry.
virtual int get_nsym () const
 For symmetries in general this function is supposed to return the number of unique symmetric operations that can be applied for the given Symmetry3D object.
virtual int get_max_csym () const
 Gets the maximum cylcic symmetry exhibited by this object.
virtual bool is_h_sym () const
 Determines whether or not this Symmetry3D is the helical type - returns true.
virtual bool is_in_asym_unit (const float &altitude, const float &azimuth, const bool inc_mirror) const
 A function to be used when generating orientations over portion of the unit sphere defined by parameters returned by get_delimiters.
virtual vector< Vec3fget_asym_unit_points (bool inc_mirror=false) const
virtual vector< vector< Vec3f > > get_asym_unit_triangles (bool inc_mirror) const
 Get triangles that precisely occlude the projection area of the default asymmetric unit.

Static Public Member Functions

static Symmetry3DNEW ()
 Factory support function NEW.

Static Public Attributes

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

Private Member Functions

 HSym (const HSym &)
 Disallow copy construction.
HSymoperator= (const HSym &)
 Disallow assignment.

Detailed Description

An encapsulation of helical 3D symmetry.

Author:
David Woolford (based on previous work by Phil Baldwin and Steve Ludtke)
Date:
Feb 2008

Definition at line 446 of file symmetry.h.


Constructor & Destructor Documentation

EMAN::HSym::HSym ( ) [inline]

Definition at line 449 of file symmetry.h.

Referenced by NEW().

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

Definition at line 450 of file symmetry.h.

{};
EMAN::HSym::HSym ( const HSym ) [private]

Disallow copy construction.


Member Function Documentation

vector< Vec3f > HSym::get_asym_unit_points ( bool  inc_mirror = false) const [virtual]
Parameters:
inc_mirrorwhether or not to include the mirror portion of the asymmetric unit
Returns:
a cyclic set of points which can be connected using great arcs on the unit sphere to demarcate the asymmetric unit. The last should may be connected to the first.

Implements EMAN::Symmetry3D.

Definition at line 1570 of file symmetry.cpp.

References b, get_delimiters(), EMAN::FactoryBase::params, and EMAN::Dict::set_default().

{
        vector<Vec3f> ret;

        Dict delim = get_delimiters(inc_mirror);
        int nsym = params.set_default("nsym",1);
        float az = -(float)delim["az_max"];


        bool tracing_arcs = false;


        if ( !tracing_arcs) {
                Vec3f a(0,-1,0);
                ret.push_back(a);

                if ( nsym > 2 ) {
                        Dict d("type","eman");
                        d["phi"] = 0.0f;
                        d["alt"] = 0.0f;
                        d["az"] = az;
                        Vec3f b = Transform(d)*a;
                        ret.push_back(b);
                }
                else
                {
                        ret.push_back(Vec3f(1,0,0));

                        ret.push_back(Vec3f(0,1,0));

                        if ( nsym == 1 ) {
                                ret.push_back(Vec3f(-1,0,0));
                                ret.push_back(a);
                        }
                }
        }
        return ret;

}
vector< vector< Vec3f > > HSym::get_asym_unit_triangles ( bool  inc_mirror) const [virtual]

Get triangles that precisely occlude the projection area of the default asymmetric unit.

This is used for collision detection in Symmetry3D::reduce

Parameters:
inc_mirrorwhether to include the mirror portion of the asymmetric unit

Implements EMAN::Symmetry3D.

Definition at line 1564 of file symmetry.cpp.

                                                               {

        vector<vector<Vec3f> > ret;
        return ret;
}
Dict HSym::get_delimiters ( const bool  inc_mirror = false) const [virtual]

Get the altitude and phi angle of the d symmetry, which depends on nysm.

The "alt_max" is always 90 The "alt_min" 90-maxtilt The "az_max" is always 360/nsym degrees Helical symmetry argument is the only symmetry not to act on the inc_mirror argument. The current policy is the orientation generator using this symmetry should make its own accomodation for the inclusion of mirror orientations if the symmetry is helical (hence the presence of the is_h_sym function in the Symmetry3D class).

Parameters:
inc_mirrorthis parameter is not specifically acted upon in this class
Returns:
a dictionary containing the keys "alt_max" and "az_max" and "alt_min"
Exceptions:
InvalidValueExceptionif nsym is less than or equal to zero

Implements EMAN::Symmetry3D.

Definition at line 1529 of file symmetry.cpp.

References InvalidValueException, EMAN::FactoryBase::params, and EMAN::Dict::set_default().

Referenced by get_asym_unit_points(), and is_in_asym_unit().

                                          {
        Dict returnDict;

        // Get the parameters of interest
        int nsym = params.set_default("nsym",0);
        if ( nsym <= 0 ) throw InvalidValueException(nsym,"Error, you must specify a positive non zero nsym");

        float maxtilt = params.set_default("maxtilt",5.0f);

        returnDict["alt_max"] = 90.0f;

        returnDict["alt_min"] = 90.0f - maxtilt;

        returnDict["az_max"] = 360.0f;

        return returnDict;
}
virtual string EMAN::HSym::get_desc ( ) const [inline, virtual]

Get a description.

Returns:
a clear desciption of this class

Implements EMAN::FactoryBase.

Definition at line 468 of file symmetry.h.

{ return "Helical symmetry, with support for N-start, pitch and limited tilt range. Specify as H<nsym>:<nstart>:<daz>:<tz in pix>[:<maxtilt>]"; }
virtual int EMAN::HSym::get_max_csym ( ) const [inline, virtual]

Gets the maximum cylcic symmetry exhibited by this object.

This is used by OrientationGenerators, and is probably not something a general user would utilize.

Returns:
nsym - this is the symmetry of the helix

Implements EMAN::Symmetry3D.

Definition at line 530 of file symmetry.h.

References EMAN::FactoryBase::params.

{ return (int)params["nstart"]; }       // may not be 
virtual string EMAN::HSym::get_name ( ) const [inline, virtual]

Return HSym::NAME.

Returns:
the unique name of this class

Implements EMAN::FactoryBase.

Definition at line 463 of file symmetry.h.

References NAME.

{ return NAME; }
virtual int EMAN::HSym::get_nsym ( ) const [inline, virtual]

For symmetries in general this function is supposed to return the number of unique symmetric operations that can be applied for the given Symmetry3D object.

For helical symmetries this is provided by the user as a parameter when setting up the helical symmetry. Generally a multiple of nstart.

Returns:
the number of symmetric rotations that can be applied without going beyond 360 degrees
Exceptions:
InvalidValueExceptionif d_az (as stored internally in parms) is less than or equal to zero

Implements EMAN::Symmetry3D.

Definition at line 519 of file symmetry.h.

References EMAN::FactoryBase::params.

{ return (int)params["nsym"]; }; 
virtual TypeDict EMAN::HSym::get_param_types ( ) const [inline, virtual]

Get a dictionary containing the permissable parameters of this class Of all the symmetries, helical has the most options.

This is because different approaches have to taken in regard to defining an asymmetric unit and to returning the set of rotational and translational symmetry operations

Returns:
a dictionary containing the permissable parameters of this class

Implements EMAN::FactoryBase.

Definition at line 476 of file symmetry.h.

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

                {
                        TypeDict d;
                        d.put("nsym", EMObject::INT, "The number of asymmetric units to generate. This could be infinite for helical symmetry. Normally a multiple of nstart.");
                        d.put("nstart", EMObject::INT, "The Cn symmetry of a single Z-slice of the helix.");
                        d.put("tz", EMObject::FLOAT, "The translational distance (along z) between successive identical subunits in angstroms (default A/pix is 1)");
                        d.put("daz", EMObject::FLOAT, "The rotational angle (about z) between successive identical subunits in degrees");
                        d.put("apix", EMObject::FLOAT, "Angstroms per pixel, default is 1.0, used only for tz");
                        d.put("maxtilt", EMObject::FLOAT, "When generating projections, normally only 'side views' are created (3-D Z along Y in 2-D). This is the maximum out of plane tilt in degrees.");
                        return d;
                }
Transform HSym::get_sym ( const int  n) const [virtual]

Provides access to the complete set of rotational and translational symmetry operations associated with helical symmetry.

This symmetry operations are generated in a straightforward way from the parameters of this class, specifically the return Transform object has an azimuth of n times the "d_az" (as specified in the parameters of this class), and has a post translation of "tz" in the z direction.

Parameters:
nthe helical symmetry operation number.
Returns:
a transform containing the correct rotational and translational symmetry operation.

Implements EMAN::Symmetry3D.

Definition at line 1610 of file symmetry.cpp.

References EMAN::FactoryBase::params, EMAN::Dict::set_default(), and EMAN::Transform::set_trans().

{
        int nstart=params["nstart"];
        //int nsym=params["nsym"];
        float apix = params.set_default("apix",1.0f);
        float daz= params["daz"];
        float tz=params["tz"];
        float dz=tz/apix;
        Dict d("type","eman");

        // courtesy of Phil Baldwin
        //d["az"] = (n%nsym) * 360.0f / nsym;
        //d["az"]=(((int) n/hsym)%nstart)*360.f/nstart+(n%hsym)*daz;
        //d["az"] = n * daz;
        d["az"]=(n%nstart)*(360.0/nstart)+floor(float(n)/nstart)*daz;   // corrected by steve, 7/21/11. No dependency on nsym
        d["alt"] = 0.0f;
        d["phi"] = 0.0f;
        Transform ret(d);
        ret.set_trans(0,0,(n/nstart)*dz);
        return ret;
}
virtual bool EMAN::HSym::is_h_sym ( ) const [inline, virtual]

Determines whether or not this Symmetry3D is the helical type - returns true.

Returns:
true - indicating that this is a helical symmetry object

Reimplemented from EMAN::Symmetry3D.

Definition at line 538 of file symmetry.h.

{ return true; }
bool HSym::is_in_asym_unit ( const float &  altitude,
const float &  azimuth,
const bool  inc_mirror = false 
) const [virtual]

A function to be used when generating orientations over portion of the unit sphere defined by parameters returned by get_delimiters.

In platonic symmetry altitude and azimuth alone are not enough to correctly demarcate the asymmetric unit. See the get_delimiters comments.

Parameters:
altitudethe EMAN style altitude of the 3D orientation in degrees
azimuththe EMAN style azimuth of the 3D orientation in degrees
inc_mirrorwhether or not to include orientations if they are in the mirror portion of the asymmetric unit
Returns:
true or false, depending on whether or not the orientation is within the asymmetric unit

Implements EMAN::Symmetry3D.

Definition at line 1547 of file symmetry.cpp.

References get_delimiters(), EMAN::FactoryBase::params, and EMAN::Dict::set_default().

{
        Dict d = get_delimiters(inc_mirror);
        float alt_max = d["alt_max"];
        float alt_min = d["alt_min"];

        if (inc_mirror) {
                float e = params.set_default("maxtilt",5.0f);
                alt_min -= e;
        }

        float az_max = d["az_max"];

        if ( altitude >=alt_min && altitude <= alt_max && azimuth <= az_max && azimuth >= 0 ) return true;
        return false;
}
static Symmetry3D* EMAN::HSym::NEW ( ) [inline, static]

Factory support function NEW.

Returns:
a newly instantiated class of this type

Definition at line 455 of file symmetry.h.

References HSym().

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

Disallow assignment.


Member Data Documentation

const string HSym::NAME = "h" [static]

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

Definition at line 533 of file symmetry.h.

Referenced by get_name().


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