EMAN2
Public Types | Public Member Functions | Static Public Member Functions | Protected Member Functions | Protected Attributes | Private Member Functions
EMAN::Symmetry3D Class Reference

Symmetry3D - A base class for 3D Symmetry objects. More...

#include <symmetry.h>

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List of all members.

Public Types

typedef vector< vector< Vec3f >
>::const_iterator 
cit
typedef vector< vector< Vec3f >
>::iterator 
ncit

Public Member Functions

 Symmetry3D ()
virtual ~Symmetry3D ()
virtual Dict get_delimiters (const bool inc_mirror=false) const =0
 Every Symmetry3D object must return a dictionary containing the delimiters that define its asymmetric unit (this is not strictly true in the case of the PlatonicSym class)
virtual Transform get_sym (const int n) const =0
 Every Symmetry3D object must provide access to the full set of its symmetry operators via this function.
virtual int get_nsym () const =0
 The total number of unique symmetry operations that will be return by this object when a calling program access Symmetry3D::get_sym.
virtual float get_az_alignment_offset () const
 This functionality is only relevant to platonic symmetries.
virtual bool is_platonic_sym () const
 A function that is used to determine if this is a platonic symmetry object This function is only virtually overidden by the PlatonicSym symmetry, which returns true, not false.
virtual bool is_h_sym () const
 A function that is used to determine if this is a Helical symmetry object This function is only virtually overidden by the HSym symmetry, which returns true, not false.
virtual bool is_c_sym () const
 A function that is used to determine if this is a c symmetry object This function is only virtually overidden by the CSym object, which returns true.
virtual bool is_d_sym () const
 A function that is used to determine if this is a d symmetry object This function is only virtually overidden by the DSym object, which returns true.
virtual bool is_tet_sym () const
 A function that is used to determine if this is the tetrahedral symmetry object This function is only virtually overidden by the TetSym object, which returns true.
virtual int get_max_csym () const =0
 The Symmetry3D object must return the maximum degree of symmetry it exhibits about any one axis.
virtual vector< Vec3fget_asym_unit_points (bool inc_mirror) const =0
 The Symmetry3D object must be capable of returning an ordered list of points on the unit sphere that define its asymmetric unit (with mirror considerations).
vector< Transformgen_orientations (const string &generatorname="eman", const Dict &parms=Dict())
 Ask the Symmetry3D object to generate a set of orientations in its asymmetric unit using an OrientationGenerator constructed from the given parameters (using a Factory).
virtual bool is_in_asym_unit (const float &altitude, const float &azimuth, const bool inc_mirror) const =0
 A function to be used when generating orientations over portion of the unit sphere defined by parameters returned by get_delimiters.
virtual Transform reduce (const Transform &t3d, int n=0) const
 A function that will reduce an orientation, as characterized by Euler anges, into a specific asymmetric unit.
virtual int in_which_asym_unit (const Transform &t3d) const
 A function that will determine in which asymmetric unit a given orientation resides The asymmetric unit 'number' will depend entirely on the order in which different symmetry operations are return by the Symmetry3D::get_sym function.
virtual int point_in_which_asym_unit (const Vec3f &v) const
 A function that will determine in which asymmetric unit a given vector resides The asymmetric unit 'number' will depend entirely on the order in which different symmetry operations are return by the Symmetry3D::get_sym function The vector is a point.
virtual vector< vector< Vec3f > > get_asym_unit_triangles (bool inc_mirror) const =0
 Get triangles that precisely occlude the projection area of the default asymmetric unit.
virtual vector< Transformget_touching_au_transforms (bool inc_mirror=true) const
 Gets a vector of Transform objects that define the set of asymmetric units that touch the default asymmetric unit.
virtual vector< Transformget_syms () const

Static Public Member Functions

static vector< Transformget_symmetries (const string &symmetry)

Protected Member Functions

void cache_au_planes () const
 Establish the asymmetric unit planes cache.
void delete_au_planes ()
 Clear the asymmetric unit planes cache.

Protected Attributes

float ** cached_au_planes
 The asymmetric unit planes are cached to provide a great speed up the point_in_which_asym_unit function, which is called by reduce and by in_which_asym_unit.
int cache_size
 Have to remember the cache size.
int num_triangles
 This is stores the number of triangles returned by get_asym_unit_triangles(true)
vector< vector< Vec3f > > au_sym_triangles
 This cache is of size cache_size.

Private Member Functions

 Symmetry3D (const Symmetry3D &)
 Disallow copy construction.
Symmetry3Doperator= (const Symmetry3D &)
 Disallow assignment.

Detailed Description

Symmetry3D - A base class for 3D Symmetry objects.

Objects of this type must provide delimiters for the asymmetric unit (get_delimiters), and must also provide all of the rotational symmetric operations (get_sym(const int n)). They must also provide the total number of unique symmetric operations with get_nsym (except in helical symmetry). get_delimiter returns a dictionary with "alt_max" and "az_max" keys, which correspond to the encompassing azimuth and altitude angles of the asymmetric unit. These can be interpreted in a relatively straight forward fashion when dealing with C and D symmetries to demarcate the asymmetric unit, however when dealing with Platonic symmetries the asymmetric unit is not so trivial. see http://blake.bcm.edu/emanwiki/EMAN2/Symmetry for figures and description of what we're doing here, for all the symmetries, and look in the comments of the PlatonicSym classes themselves. It inherits from a factory base, making it amenable to incorporation in EMAN2 style factories

Author:
David Woolford with Philip Baldwin and Steven Ludtke
Date:
Feb 2008

Definition at line 56 of file symmetry.h.


Member Typedef Documentation

typedef vector<vector<Vec3f> >::const_iterator EMAN::Symmetry3D::cit

Definition at line 59 of file symmetry.h.

typedef vector<vector<Vec3f> >::iterator EMAN::Symmetry3D::ncit

Definition at line 60 of file symmetry.h.


Constructor & Destructor Documentation

Symmetry3D::Symmetry3D ( )

Definition at line 938 of file symmetry.cpp.

Symmetry3D::~Symmetry3D ( ) [virtual]

Definition at line 939 of file symmetry.cpp.

References cached_au_planes, and delete_au_planes().

                        {
        if (cached_au_planes != 0 ) {
                delete_au_planes();
        }
}
EMAN::Symmetry3D::Symmetry3D ( const Symmetry3D ) [private]

Disallow copy construction.


Member Function Documentation

void Symmetry3D::cache_au_planes ( ) const [protected]

Establish the asymmetric unit planes cache.

Definition at line 996 of file symmetry.cpp.

References au_sym_triangles, cache_size, cached_au_planes, EMAN::Util::equation_of_plane(), fit, get_asym_unit_triangles(), get_nsym(), get_sym(), num_triangles, t, and UnexpectedBehaviorException.

Referenced by point_in_which_asym_unit().

                                       {
        if (cached_au_planes == 0 ) {
                vector< vector<Vec3f> > au_triangles = get_asym_unit_triangles(true);
                num_triangles = au_triangles.size();
                cache_size = get_nsym()*au_triangles.size();

                cached_au_planes = new float*[cache_size];
                float** fit = cached_au_planes;
                for(int i =0; i < cache_size; ++i,++fit) {
                        float *t = new float[4];
                        *fit = t;
                }


                int k = 0;
                for(int i = 0; i < get_nsym(); ++i) {

                        for( ncit it = au_triangles.begin(); it != au_triangles.end(); ++it, ++k)
                        {
                                // For each given triangle
                                vector<Vec3f> points = *it;
                                if ( i != 0 ) {
                                        for (vector<Vec3f>::iterator iit = points.begin(); iit != points.end(); ++iit ) {
                                                // Rotate the points in the triangle so that the triangle occupies the
                                                // space of the current asymmetric unit
                                                *iit = (*iit)*get_sym(i);
                                        }
                                }

                                au_sym_triangles.push_back(points);

                                // Determine the equation of the plane for the points, store it in plane
                                Util::equation_of_plane(points[0],points[2],points[1],cached_au_planes[k]);
                        }
                }
        }
        else throw UnexpectedBehaviorException("Attempt to generate a cache when cache exists");
}
void Symmetry3D::delete_au_planes ( ) [protected]

Clear the asymmetric unit planes cache.

Definition at line 1035 of file symmetry.cpp.

References cache_size, cached_au_planes, fit, and UnexpectedBehaviorException.

Referenced by ~Symmetry3D().

                                  {
        if (cached_au_planes == 0 ) throw UnexpectedBehaviorException("Attempt to delete a cache that does not exist");
        float** fit = cached_au_planes;
        for(int i =0; i < cache_size; ++i,++fit) {
                if (*fit == 0) throw UnexpectedBehaviorException("Attempt to delete a cache that does not exist");
                delete [] *fit;
                *fit = 0;
        }

        delete [] cached_au_planes;
        cached_au_planes = 0;
}
vector< Transform > Symmetry3D::gen_orientations ( const string &  generatorname = "eman",
const Dict parms = Dict() 
)

Ask the Symmetry3D object to generate a set of orientations in its asymmetric unit using an OrientationGenerator constructed from the given parameters (using a Factory).

This is reminiscent of the strategy design pattern

Parameters:
generatornamethe string name of the OrientationGenerator, as accessed for the OrientationGenerator factory
parmsthe parameters handed to OrientationGenerator::set_params after initial construction
Returns:
a set of orientations in the unit sphere

Definition at line 165 of file symmetry.cpp.

References ENTERFUNC, EXITFUNC, EMAN::OrientationGenerator::gen_orientations(), and EMAN::Util::str_to_lower().

Referenced by EMAN::SymAlignProcessor::align(), and EMAN::RT3DSphereAligner::xform_align_nbest().

{
        ENTERFUNC;
        vector<Transform> ret;
        OrientationGenerator *g = Factory < OrientationGenerator >::get(Util::str_to_lower(generatorname), parms);
        if (g) {
                ret = g->gen_orientations(this);
                if( g )
                {
                        delete g;
                        g = 0;
                }
        }
        else throw;

        EXITFUNC;

        return ret;
}
virtual vector<Vec3f> EMAN::Symmetry3D::get_asym_unit_points ( bool  inc_mirror) const [pure virtual]

The Symmetry3D object must be capable of returning an ordered list of points on the unit sphere that define its asymmetric unit (with mirror considerations).

The list can be any length, and must be constructed carefully. If the list consists of points A B and C, then arcs on the unit sphere connecting A to B, then B to C, then C to A must define the asymmetric unit (with or without its mirror portion). i.e. it is a cyclic list, on any length

Parameters:
inc_mirrorwhether or not to include the mirror portion of the asymmetric unit
Returns:
a vector or points which define a cyclic set of great arcs on the unit sphere. Each point may be connected to the point that proceeds it, and the last point may be connected to the first point, and this demarcates the asymmetric unit.

Implemented in EMAN::CSym, EMAN::DSym, EMAN::HSym, EMAN::PlatonicSym, and EMAN::TetrahedralSym.

Referenced by get_touching_au_transforms().

virtual vector<vector<Vec3f> > EMAN::Symmetry3D::get_asym_unit_triangles ( bool  inc_mirror) const [pure virtual]

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

This will be used for collision detection in Symmetry3D::reduce

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

Implemented in EMAN::CSym, EMAN::DSym, EMAN::HSym, and EMAN::PlatonicSym.

Referenced by cache_au_planes().

virtual float EMAN::Symmetry3D::get_az_alignment_offset ( ) const [inline, virtual]

This functionality is only relevant to platonic symmetries.

But it could grow into functionality for the other symmetries.

Reimplemented in EMAN::TetrahedralSym, EMAN::IcosahedralSym, and EMAN::Icosahedral2Sym.

Definition at line 86 of file symmetry.h.

Referenced by EMAN::SaffOrientationGenerator::gen_orientations(), EMAN::EvenOrientationGenerator::gen_orientations(), EMAN::EmanOrientationGenerator::gen_orientations(), and EMAN::PlatonicSym::get_asym_unit_points().

{ return 0.0; }
virtual Dict EMAN::Symmetry3D::get_delimiters ( const bool  inc_mirror = false) const [pure virtual]

Every Symmetry3D object must return a dictionary containing the delimiters that define its asymmetric unit (this is not strictly true in the case of the PlatonicSym class)

Parameters:
inc_mirrorwhether or not the mirror part of the asymmetric unit should be included in the consideration
Returns:
a dictionary containing atleast "alt_max" and "az_max"

Implemented in EMAN::CSym, EMAN::DSym, EMAN::HSym, and EMAN::PlatonicSym.

Referenced by EMAN::SaffOrientationGenerator::gen_orientations(), EMAN::EvenOrientationGenerator::gen_orientations(), EMAN::EmanOrientationGenerator::gen_orientations(), EMAN::SaffOrientationGenerator::get_orientations_tally(), EMAN::EvenOrientationGenerator::get_orientations_tally(), EMAN::EmanOrientationGenerator::get_orientations_tally(), and get_touching_au_transforms().

virtual int EMAN::Symmetry3D::get_max_csym ( ) const [pure virtual]

The Symmetry3D object must return the maximum degree of symmetry it exhibits about any one axis.

This function is only called in the AsymmUnitOrientationGenerator.

Implemented in EMAN::CSym, EMAN::DSym, EMAN::HSym, EMAN::TetrahedralSym, EMAN::OctahedralSym, EMAN::IcosahedralSym, and EMAN::Icosahedral2Sym.

Referenced by EMAN::EmanOrientationGenerator::gen_orientations(), EMAN::EmanOrientationGenerator::get_orientations_tally(), and EMAN::PlatonicSym::init().

virtual int EMAN::Symmetry3D::get_nsym ( ) const [pure virtual]
virtual Transform EMAN::Symmetry3D::get_sym ( const int  n) const [pure virtual]

Every Symmetry3D object must provide access to the full set of its symmetry operators via this function.

Parameters:
nthe symmetry operator number
Returns:
a Transform object describing the symmetry operation

Implemented in EMAN::CSym, EMAN::DSym, EMAN::HSym, EMAN::TetrahedralSym, EMAN::OctahedralSym, EMAN::IcosahedralSym, and EMAN::Icosahedral2Sym.

Referenced by cache_au_planes(), EMAN::EmanOrientationGenerator::gen_orientations(), EMAN::Transform::get_sym(), EMAN::Transform::get_sym_proj(), get_syms(), get_touching_au_transforms(), and reduce().

vector< Transform > Symmetry3D::get_symmetries ( const string &  symmetry) [static]
vector< Transform > Symmetry3D::get_syms ( ) const [virtual]

Definition at line 1186 of file symmetry.cpp.

References get_nsym(), and get_sym().

Referenced by EMAN::BackProjectionReconstructor::finish(), get_symmetries(), and EMAN::ApplySymProcessor::process().

{

        vector<Transform> ret;
//      if (t.is_identity()) {
                for(int i = 0; i < get_nsym(); ++i ) {
                        ret.push_back(get_sym(i));
                }
//      } else {
//              for(int i = 0; i < get_nsym(); ++i ) {
//                      ret.push_back(get_sym(i)*t);
//              }
//      }
        return ret;
}
vector< Transform > Symmetry3D::get_touching_au_transforms ( bool  inc_mirror = true) const [virtual]

Gets a vector of Transform objects that define the set of asymmetric units that touch the default asymmetric unit.

The 'default asymmetric unit' is defined by the results of Symmetry3d::get_asym_unit_points and is sensitive to whether or not you want to include the mirror part of the asymmetric unit. This function is useful when used in conjunction with Symmetry3D::reduce, and particularly when finding the angular deviation of particles through different stages of iterative Single Particle Reconstruction This function could be expanded to work for an asymmetric unit number supplied by the user.

Parameters:
inc_mirrorwhether or not to include the mirror portion of the asymmetric unit
Returns:
a vector of Transform objects that map the default asymmetric unit to the neighboring asymmetric unit

Definition at line 1117 of file symmetry.cpp.

References EMAN::EMConsts::deg2rad, get_asym_unit_points(), get_delimiters(), get_nsym(), get_sym(), is_d_sym(), is_platonic_sym(), EMAN::Vec3< Type >::squared_length(), t, x, and y.

{
        vector<Transform>  ret;
        vector<int> hit_cache;

        vector<Vec3f> points = get_asym_unit_points(inc_mirror);
        // Warning, this is a gross hack because it is assuming that the asym_unit_points
        // returned by DSym are in a particular orientation with respect to symmetric axes
        // if the internals of DSym change it could change what we should do here...
        // but for the time being it will do
        if (inc_mirror && is_d_sym() && (get_nsym()/2 % 2 == 0)) {
                Dict delim = get_delimiters(false);
                float angle = (float)(EMConsts::deg2rad*float(delim["az_max"]));
                float y = -cos(angle);
                float x = sin(angle);
                points.push_back(Vec3f(x,y,0));
        }
        else if ( is_d_sym() && (get_nsym()/2 % 2 == 1)) {
                Dict delim = get_delimiters(false);
                float angle = float(delim["az_max"])/2.0f;
//              cout << "Odd dsym using " << angle << endl;
                angle *= (float)EMConsts::deg2rad;
                float y = -cos(angle);
                float x = sin(angle);
                points.push_back(Vec3f(x,y,0));

                if ( inc_mirror ) {
                        angle = 3.0f*(float(delim["az_max"]))/2.0f;
                        angle *= (float)EMConsts::deg2rad;
                        float y = -cos(angle);
                        float x = sin(angle);
                        points.push_back(Vec3f(x,y,0));
                }
        }

        typedef vector<Vec3f>::const_iterator const_point_it;
        for(const_point_it point = points.begin(); point != points.end(); ++point ) {

                for(int i = 1; i < get_nsym(); ++i) {

                        if ( find(hit_cache.begin(),hit_cache.end(),i) != hit_cache.end() ) continue;
                        Transform t = get_sym(i);
                        Vec3f result = (*point)*t;

                        if (is_platonic_sym()) {
                                for(const_point_it tmp = points.begin(); tmp != points.end(); ++tmp ) {
                                        Vec3f tt = result-(*tmp);
                                        if (tt.squared_length() < 0.01f) {
                                                hit_cache.push_back(i);
                                                ret.push_back(t);
                                        }

                                }
                        }
                        else {
                                result -= *point;
                                if (result.squared_length() < 0.05f) {
                                        hit_cache.push_back(i);
                                        ret.push_back(t);
                                }
                        }
                }

        }

        return ret;
}
int Symmetry3D::in_which_asym_unit ( const Transform t3d) const [virtual]

A function that will determine in which asymmetric unit a given orientation resides The asymmetric unit 'number' will depend entirely on the order in which different symmetry operations are return by the Symmetry3D::get_sym function.

Parameters:
t3da Transform characterizing an orientation
Returns:
the asymmetric unit number the the orientation is in

Definition at line 977 of file symmetry.cpp.

References EMAN::Transform::invert(), and point_in_which_asym_unit().

Referenced by reduce().

{
        // Here it is assumed that final destination of the orientation (as encapsulated in the t3d object) is
        // in the z direction, so in essence we will start in the direction z and 'undo' the orientation to get the real
        // direction
        Vec3f p(0,0,1);

        Transform o(t3d);
        // Orientations are alway transposed when dealing with asymmetric units, projections,etc
        // We take the transpose to 'undo' the transform and get the true direction of the point.
        o.invert();
        // Figure out where the point would end up. No we could just as easily not transpose and do
        // left multiplation (as in what occurs in the FourierReconstructor during slice insertion)
        p = o*p;

        return point_in_which_asym_unit(p);
}
virtual bool EMAN::Symmetry3D::is_c_sym ( ) const [inline, virtual]

A function that is used to determine if this is a c symmetry object This function is only virtually overidden by the CSym object, which returns true.

Returns:
false - indicating that this is not a helical symmetry object

Reimplemented in EMAN::CSym.

Definition at line 106 of file symmetry.h.

Referenced by EMAN::RandomOrientationGenerator::gen_orientations(), and EMAN::OrientationGenerator::get_az_max().

{ return false; }
virtual bool EMAN::Symmetry3D::is_d_sym ( ) const [inline, virtual]

A function that is used to determine if this is a d symmetry object This function is only virtually overidden by the DSym object, which returns true.

Returns:
false - indicating that this is not a helical symmetry object

Reimplemented in EMAN::DSym.

Definition at line 112 of file symmetry.h.

Referenced by EMAN::OrientationGenerator::get_az_max(), and get_touching_au_transforms().

{ return false; }
virtual bool EMAN::Symmetry3D::is_h_sym ( ) const [inline, virtual]

A function that is used to determine if this is a Helical symmetry object This function is only virtually overidden by the HSym symmetry, which returns true, not false.

Returns:
false - indicating that this is not a helical symmetry object

Reimplemented in EMAN::HSym.

Definition at line 100 of file symmetry.h.

Referenced by EMAN::SaffOrientationGenerator::gen_orientations(), EMAN::EvenOrientationGenerator::gen_orientations(), EMAN::EmanOrientationGenerator::gen_orientations(), EMAN::SaffOrientationGenerator::get_orientations_tally(), EMAN::EvenOrientationGenerator::get_orientations_tally(), and EMAN::EmanOrientationGenerator::get_orientations_tally().

{ return false; }
virtual bool EMAN::Symmetry3D::is_in_asym_unit ( const float &  altitude,
const float &  azimuth,
const bool  inc_mirror 
) const [pure 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

Implemented in EMAN::CSym, EMAN::DSym, EMAN::HSym, EMAN::PlatonicSym, and EMAN::TetrahedralSym.

Referenced by EMAN::OptimumOrientationGenerator::gen_orientations(), EMAN::SaffOrientationGenerator::gen_orientations(), EMAN::EvenOrientationGenerator::gen_orientations(), EMAN::RandomOrientationGenerator::gen_orientations(), EMAN::EmanOrientationGenerator::gen_orientations(), EMAN::SaffOrientationGenerator::get_orientations_tally(), EMAN::EvenOrientationGenerator::get_orientations_tally(), and EMAN::EmanOrientationGenerator::get_orientations_tally().

virtual bool EMAN::Symmetry3D::is_platonic_sym ( ) const [inline, virtual]

A function that is used to determine if this is a platonic symmetry object This function is only virtually overidden by the PlatonicSym symmetry, which returns true, not false.

Returns:
false - indicating that this is not a platonic symmetry object

Reimplemented in EMAN::PlatonicSym.

Definition at line 94 of file symmetry.h.

Referenced by EMAN::SaffOrientationGenerator::gen_orientations(), EMAN::EvenOrientationGenerator::gen_orientations(), EMAN::EmanOrientationGenerator::gen_orientations(), EMAN::OrientationGenerator::get_az_max(), EMAN::SaffOrientationGenerator::get_orientations_tally(), EMAN::EvenOrientationGenerator::get_orientations_tally(), EMAN::EmanOrientationGenerator::get_orientations_tally(), and get_touching_au_transforms().

{ return false; }
virtual bool EMAN::Symmetry3D::is_tet_sym ( ) const [inline, virtual]

A function that is used to determine if this is the tetrahedral symmetry object This function is only virtually overidden by the TetSym object, which returns true.

Returns:
false - indicating that this is not a tetrahedral symmetry object

Reimplemented in EMAN::TetrahedralSym.

Definition at line 118 of file symmetry.h.

Referenced by EMAN::OrientationGenerator::get_az_max().

{ return false; }
Symmetry3D& EMAN::Symmetry3D::operator= ( const Symmetry3D ) [private]

Disallow assignment.

int Symmetry3D::point_in_which_asym_unit ( const Vec3f v) const [virtual]

A function that will determine in which asymmetric unit a given vector resides The asymmetric unit 'number' will depend entirely on the order in which different symmetry operations are return by the Symmetry3D::get_sym function The vector is a point.

Parameters:
va Vec3f characterizing a point
Returns:
the asymmetric unit number the the orientation is in

Definition at line 1048 of file symmetry.cpp.

References au_sym_triangles, cache_au_planes(), cached_au_planes, EMAN::Vec3< Type >::dot(), EMAN::Transform::ERR_LIMIT, get_nsym(), num_triangles, t, and v.

Referenced by in_which_asym_unit(), and EMAN::AutoMaskAsymUnit::process_inplace().

{
        if (cached_au_planes == 0) {
                cache_au_planes();
        }
        
        float epsNow=0.01f;
        int k = 0;
        for(int i = 0; i < get_nsym(); ++i) {
                for( int j = 0; j < num_triangles; ++j,++k) {
                        vector<Vec3f> points = au_sym_triangles[k];

                        float* plane = cached_au_planes[k];
                        Vec3f tmp = p;

                        // Determine the intersection of p with the plane - do this by finding out how much p should be scaled by
                        float scale = plane[0]*tmp[0]+plane[1]*tmp[1]+plane[2]*tmp[2];
                        if ( scale != 0 )
                                scale = -plane[3]/scale;
                        else {
                                // parralel!
                                continue;
                        }

                        // If the scale factor is less than zero, then p is definitely not in this asymmetric unit
                        if (scale <= 0) continue;

                        // This is the intersection point
                        Vec3f pp = tmp*scale;

                        // Now we have to see if the point p is inside the region bounded by the points, or if it is outside
                        // If it is inside the region then p is in this asymmetric unit.

                        // This formula take from FIXME fill in once I get to work
                        Vec3f v = points[2]-points[0];
                        Vec3f u = points[1]-points[0];
                        Vec3f w = pp - points[0];

                        float udotu = u.dot(u);
                        float udotv = u.dot(v);
                        float udotw = u.dot(w);
                        float vdotv = v.dot(v);
                        float vdotw = v.dot(w);

                        float d = 1.0f/(udotv*udotv - udotu*vdotv);
                        float s = udotv*vdotw - vdotv*udotw;
                        s *= d;

                        float t = udotv*udotw - udotu*vdotw;
                        t *= d;

                        // We've done a few multiplications, so detect when there are tiny residuals that may throw off the final
                        // decision
                        if (fabs(s) < Transform::ERR_LIMIT ) s = 0;
                        if (fabs(t) < Transform::ERR_LIMIT ) t = 0;

                        if ( fabs((fabs(s)-1.0)) < Transform::ERR_LIMIT ) s = 1;
                        if ( fabs((fabs(t)-1.0)) < Transform::ERR_LIMIT ) t = 1;

                        // The final decision, if this is true then we've hit the jackpot
                        if ( s >= -epsNow && t >= -epsNow && (s+t) <= 1+epsNow ) {
//                              cout << " i " << i << " j " << j << " s " << s  << " t " << t << " s+t " << s+t << endl;
                                return i;
                        }
                }
        }

        return -1;
}

Member Data Documentation

vector< vector<Vec3f> > EMAN::Symmetry3D::au_sym_triangles [mutable, protected]

This cache is of size cache_size.

Definition at line 214 of file symmetry.h.

Referenced by cache_au_planes(), and point_in_which_asym_unit().

int EMAN::Symmetry3D::cache_size [mutable, protected]

Have to remember the cache size.

Definition at line 210 of file symmetry.h.

Referenced by cache_au_planes(), and delete_au_planes().

float** EMAN::Symmetry3D::cached_au_planes [mutable, protected]

The asymmetric unit planes are cached to provide a great speed up the point_in_which_asym_unit function, which is called by reduce and by in_which_asym_unit.

Definition at line 207 of file symmetry.h.

Referenced by cache_au_planes(), delete_au_planes(), point_in_which_asym_unit(), and ~Symmetry3D().

int EMAN::Symmetry3D::num_triangles [mutable, protected]

This is stores the number of triangles returned by get_asym_unit_triangles(true)

Definition at line 212 of file symmetry.h.

Referenced by cache_au_planes(), and point_in_which_asym_unit().


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