Main Page | Modules | Namespace List | Class Hierarchy | Alphabetical List | Class List | Directories | File List | Namespace Members | Class Members | File Members

EMAN::Symmetry3D Class Reference

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

#include <symmetry.h>

Inheritance diagram for EMAN::Symmetry3D:

Inheritance graph
[legend]
Collaboration diagram for EMAN::Symmetry3D:

Collaboration graph
[legend]
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

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.

Referenced by cache_au_planes().


Constructor & Destructor Documentation

Symmetry3D::Symmetry3D  ) 
 

Definition at line 899 of file symmetry.cpp.

Symmetry3D::~Symmetry3D  )  [virtual]
 

Definition at line 900 of file symmetry.cpp.

References cached_au_planes, and delete_au_planes().

00900                         {
00901         if (cached_au_planes != 0 ) {
00902                 delete_au_planes();
00903         }
00904 }

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 956 of file symmetry.cpp.

References au_sym_triangles, cache_size, cached_au_planes, EMAN::Vec3< Type >::end(), EMAN::Util::equation_of_plane(), fit, get_asym_unit_triangles(), get_nsym(), get_sym(), ncit, num_triangles, t, and UnexpectedBehaviorException.

Referenced by point_in_which_asym_unit().

00956                                        {
00957         if (cached_au_planes == 0 ) {
00958                 vector< vector<Vec3f> > au_triangles = get_asym_unit_triangles(true);
00959                 num_triangles = au_triangles.size();
00960                 cache_size = get_nsym()*au_triangles.size();
00961 
00962                 cached_au_planes = new float*[cache_size];
00963                 float** fit = cached_au_planes;
00964                 for(int i =0; i < cache_size; ++i,++fit) {
00965                         float *t = new float[4];
00966                         *fit = t;
00967                 }
00968 
00969 
00970                 int k = 0;
00971                 for(int i = 0; i < get_nsym(); ++i) {
00972 
00973                         for( ncit it = au_triangles.begin(); it != au_triangles.end(); ++it, ++k)
00974                         {
00975                                 // For each given triangle
00976                                 vector<Vec3f> points = *it;
00977                                 if ( i != 0 ) {
00978                                         for (vector<Vec3f>::iterator iit = points.begin(); iit != points.end(); ++iit ) {
00979                                                 // Rotate the points in the triangle so that the triangle occupies the
00980                                                 // space of the current asymmetric unit
00981                                                 *iit = (*iit)*get_sym(i);
00982                                         }
00983                                 }
00984 
00985                                 au_sym_triangles.push_back(points);
00986 
00987                                 // Determine the equation of the plane for the points, store it in plane
00988                                 Util::equation_of_plane(points[0],points[2],points[1],cached_au_planes[k]);
00989                         }
00990                 }
00991         }
00992         else throw UnexpectedBehaviorException("Attempt to generate a cache when cache exists");
00993 }

void Symmetry3D::delete_au_planes  )  [protected]
 

Clear the asymmetric unit planes cache.

Definition at line 995 of file symmetry.cpp.

References cached_au_planes, fit, and UnexpectedBehaviorException.

Referenced by ~Symmetry3D().

00995                                   {
00996         if (cached_au_planes == 0 ) throw UnexpectedBehaviorException("Attempt to delete a cache that does not exist");
00997         float** fit = cached_au_planes;
00998         for(int i =0; i < cache_size; ++i,++fit) {
00999                 if (*fit == 0) throw UnexpectedBehaviorException("Attempt to delete a cache that does not exist");
01000                 delete [] *fit;
01001                 *fit = 0;
01002         }
01003 
01004         delete [] cached_au_planes;
01005         cached_au_planes = 0;
01006 }

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

Definition at line 156 of file symmetry.cpp.

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

Referenced by EMAN::RT3DSphereAligner::xform_align_nbest().

00157 {
00158         ENTERFUNC;
00159         vector<Transform> ret;
00160         OrientationGenerator *g = Factory < OrientationGenerator >::get(Util::str_to_lower(generatorname), parms);
00161         if (g) {
00162                 ret = g->gen_orientations(this);
00163                 if( g )
00164                 {
00165                         delete g;
00166                         g = 0;
00167                 }
00168         }
00169         else throw;
00170 
00171         EXITFUNC;
00172 
00173         return ret;
00174 }

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_mirror whether 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_mirror whether 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, and EMAN::IcosahedralSym.

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().

00086 { 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_mirror whether 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, and EMAN::IcosahedralSym.

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

virtual int EMAN::Symmetry3D::get_nsym  )  const [pure virtual]
 

The total number of unique symmetry operations that will be return by this object when a calling program access Symmetry3D::get_sym.

However in the case of HSym, this is really something else.

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

Referenced by cache_au_planes(), EMAN::BackProjectionReconstructor::finish(), EMAN::RandomOrientationGenerator::gen_orientations(), EMAN::OrientationGenerator::get_az_max(), EMAN::Transform::get_nsym(), get_syms(), get_touching_au_transforms(), and point_in_which_asym_unit().

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:
n the symmetry operator number
Returns:
a Transform object describing the symmetry operation

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

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

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

Definition at line 1160 of file symmetry.cpp.

References EMAN::Factory< T >::get(), and get_syms().

Referenced by EMAN::WienerFourierReconstructor::do_compare_slice_work(), EMAN::FourierReconstructor::do_compare_slice_work(), EMAN::WienerFourierReconstructor::do_insert_slice_work(), EMAN::FourierReconstructor::do_insert_slice_work(), and EMAN::SymSearchProcessor::process_inplace().

01161 {
01162         Symmetry3D* sym = Factory<Symmetry3D>::get(Util::str_to_lower(symmetry));
01163         vector<Transform> ret = sym->get_syms();
01164         delete sym;
01165         return ret;
01166 }

vector< Transform > Symmetry3D::get_syms  )  const [virtual]
 

Definition at line 1144 of file symmetry.cpp.

References get_nsym(), and get_sym().

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

01145 {
01146 
01147         vector<Transform> ret;
01148 //      if (t.is_identity()) {
01149                 for(int i = 0; i < get_nsym(); ++i ) {
01150                         ret.push_back(get_sym(i));
01151                 }
01152 //      } else {
01153 //              for(int i = 0; i < get_nsym(); ++i ) {
01154 //                      ret.push_back(get_sym(i)*t);
01155 //              }
01156 //      }
01157         return ret;
01158 }

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_mirror whether 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 1075 of file symmetry.cpp.

References EMAN::Dict::end(), get_asym_unit_points(), get_delimiters(), get_nsym(), get_sym(), is_d_sym(), is_platonic_sym(), EMAN::Vec3< Type >::squared_length(), t, EMAN::Vec3f, x, and y.

01076 {
01077         vector<Transform>  ret;
01078         vector<int> hit_cache;
01079 
01080         vector<Vec3f> points = get_asym_unit_points(inc_mirror);
01081         // Warning, this is a gross hack because it is assuming that the asym_unit_points
01082         // returned by DSym are in a particular orientation with respect to symmetric axes
01083         // if the internals of DSym change it could change what we should do here...
01084         // but for the time being it will do
01085         if (inc_mirror && is_d_sym() && (get_nsym()/2 % 2 == 0)) {
01086                 Dict delim = get_delimiters(false);
01087                 float angle = (float)(EMConsts::deg2rad*float(delim["az_max"]));
01088                 float y = -cos(angle);
01089                 float x = sin(angle);
01090                 points.push_back(Vec3f(x,y,0));
01091         }
01092         else if ( is_d_sym() && (get_nsym()/2 % 2 == 1)) {
01093                 Dict delim = get_delimiters(false);
01094                 float angle = float(delim["az_max"])/2.0f;
01095 //              cout << "Odd dsym using " << angle << endl;
01096                 angle *= (float)EMConsts::deg2rad;
01097                 float y = -cos(angle);
01098                 float x = sin(angle);
01099                 points.push_back(Vec3f(x,y,0));
01100 
01101                 if ( inc_mirror ) {
01102                         angle = 3.0f*(float(delim["az_max"]))/2.0f;
01103                         angle *= (float)EMConsts::deg2rad;
01104                         float y = -cos(angle);
01105                         float x = sin(angle);
01106                         points.push_back(Vec3f(x,y,0));
01107                 }
01108         }
01109 
01110         typedef vector<Vec3f>::const_iterator const_point_it;
01111         for(const_point_it point = points.begin(); point != points.end(); ++point ) {
01112 
01113                 for(int i = 1; i < get_nsym(); ++i) {
01114 
01115                         if ( find(hit_cache.begin(),hit_cache.end(),i) != hit_cache.end() ) continue;
01116                         Transform t = get_sym(i);
01117                         Vec3f result = (*point)*t;
01118 
01119                         if (is_platonic_sym()) {
01120                                 for(const_point_it tmp = points.begin(); tmp != points.end(); ++tmp ) {
01121                                         Vec3f tt = result-(*tmp);
01122                                         if (tt.squared_length() < 0.01f) {
01123                                                 hit_cache.push_back(i);
01124                                                 ret.push_back(t);
01125                                         }
01126 
01127                                 }
01128                         }
01129                         else {
01130                                 result -= *point;
01131                                 if (result.squared_length() < 0.05f) {
01132                                         hit_cache.push_back(i);
01133                                         ret.push_back(t);
01134                                 }
01135                         }
01136                 }
01137 
01138         }
01139 
01140         return ret;
01141 }

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:
t3d a Transform characterizing an orientation
Returns:
the asymmetric unit number the the orientation is in

Definition at line 937 of file symmetry.cpp.

References EMAN::Transform::invert(), point_in_which_asym_unit(), and EMAN::Vec3f.

Referenced by reduce().

00938 {
00939         // Here it is assumed that final destination of the orientation (as encapsulated in the t3d object) is
00940         // in the z direction, so in essence we will start in the direction z and 'undo' the orientation to get the real
00941         // direction
00942         Vec3f p(0,0,1);
00943 
00944         Transform o(t3d);
00945         // Orientations are alway transposed when dealing with asymmetric units, projections,etc
00946         // We take the transpose to 'undo' the transform and get the true direction of the point.
00947         o.invert();
00948         // Figure out where the point would end up. No we could just as easily not transpose and do
00949         // left multiplation (as in what occurs in the FourierReconstructor during slice insertion)
00950         p = o*p;
00951 
00952         return point_in_which_asym_unit(p);
00953 }

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().

00106 { 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().

00112 { 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().

00100 { 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:
altitude the EMAN style altitude of the 3D orientation in degrees
azimuth the EMAN style azimuth of the 3D orientation in degrees
inc_mirror whether 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().

00094 { 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().

00118 { 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:
v a Vec3f characterizing a point
Returns:
the asymmetric unit number the the orientation is in

Definition at line 1008 of file symmetry.cpp.

References au_sym_triangles, cache_au_planes(), cached_au_planes, EMAN::Vec3< Type >::dot(), get_nsym(), t, v, and EMAN::Vec3f.

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

01009 {
01010         if (cached_au_planes == 0) {
01011                 cache_au_planes();
01012         }
01013 
01014         int k = 0;
01015         for(int i = 0; i < get_nsym(); ++i) {
01016                 for( int j = 0; j < num_triangles; ++j,++k) {
01017                         vector<Vec3f> points = au_sym_triangles[k];
01018 
01019                         float* plane = cached_au_planes[k];
01020                         Vec3f tmp = p;
01021 
01022                         // Determine the intersection of p with the plane - do this by finding out how much p should be scaled by
01023                         float scale = plane[0]*tmp[0]+plane[1]*tmp[1]+plane[2]*tmp[2];
01024                         if ( scale != 0 )
01025                                 scale = -plane[3]/scale;
01026                         else {
01027                                 // parralel!
01028                                 continue;
01029                         }
01030 
01031                         // If the scale factor is less than zero, then p is definitely not in this asymmetric unit
01032                         if (scale <= 0) continue;
01033 
01034                         // This is the intersection point
01035                         Vec3f pp = tmp*scale;
01036 
01037                         // Now we have to see if the point p is inside the region bounded by the points, or if it is outside
01038                         // If it is inside the region then p is in this asymmetric unit.
01039 
01040                         // This formula take from FIXME fill in once I get to work
01041                         Vec3f v = points[2]-points[0];
01042                         Vec3f u = points[1]-points[0];
01043                         Vec3f w = pp - points[0];
01044 
01045                         float udotu = u.dot(u);
01046                         float udotv = u.dot(v);
01047                         float udotw = u.dot(w);
01048                         float vdotv = v.dot(v);
01049                         float vdotw = v.dot(w);
01050 
01051                         float d = 1.0f/(udotv*udotv - udotu*vdotv);
01052                         float s = udotv*vdotw - vdotv*udotw;
01053                         s *= d;
01054 
01055                         float t = udotv*udotw - udotu*vdotw;
01056                         t *= d;
01057 
01058                         // We've done a few multiplications, so detect when there are tiny residuals that may throw off the final
01059                         // decision
01060                         if (fabs(s) < Transform::ERR_LIMIT ) s = 0;
01061                         if (fabs(t) < Transform::ERR_LIMIT ) t = 0;
01062 
01063                         if ( fabs((fabs(s)-1.0)) < Transform::ERR_LIMIT ) s = 1;
01064                         if ( fabs((fabs(t)-1.0)) < Transform::ERR_LIMIT ) t = 1;
01065 
01066                         // The final decision, if this is true then we've hit the jackpot
01067                         if ( s >= 0 && t >= 0 && (s+t) <= 1 ) {
01068                                 return i;
01069                         }
01070                 }
01071         }
01072 
01073         return -1;
01074 }


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().

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().


The documentation for this class was generated from the following files:
Generated on Thu Dec 9 13:48:50 2010 for EMAN2 by  doxygen 1.3.9.1