#include <symmetry.h>
Inheritance diagram for EMAN::SaffOrientationGenerator:
Public Member Functions | |
SaffOrientationGenerator () | |
virtual | ~SaffOrientationGenerator () |
virtual string | get_name () const |
Return "saff". | |
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< Transform > | gen_orientations (const Symmetry3D *const sym) const |
Generate Saff orientations in the asymmetric unit of the symmetry. | |
Static Public Member Functions | |
OrientationGenerator * | NEW () |
Factory support function NEW. | |
Static Public Attributes | |
const string | NAME = "saff" |
The name of this class - used to access it from factories etc. Should be "icos". | |
Private Member Functions | |
SaffOrientationGenerator (const SaffOrientationGenerator &) | |
Disallow copy construction. | |
SaffOrientationGenerator & | operator= (const SaffOrientationGenerator &) |
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. |
Saff and A.B.J. Kuijlaars, Distributing many points on a sphere, Mathematical Intelligencer 19 (1997), pp. 5–11. This is a spiral based approach
Definition at line 1231 of file symmetry.h.
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Definition at line 1234 of file symmetry.h. 01234 {}
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Definition at line 1235 of file symmetry.h. 01235 {}
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Disallow copy construction.
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Generate Saff orientations in the asymmetric unit of the symmetry.
Implements EMAN::OrientationGenerator. Definition at line 690 of file symmetry.cpp. References EMAN::OrientationGenerator::add_orientation(), EMAN::Symmetry3D::get_az_alignment_offset(), EMAN::Symmetry3D::get_delimiters(), EMAN::OrientationGenerator::get_optimal_delta(), EMAN::FactoryBase::get_params(), InvalidParameterException, EMAN::Symmetry3D::is_h_sym(), EMAN::Symmetry3D::is_in_asym_unit(), EMAN::Symmetry3D::is_platonic_sym(), EMAN::Dict::set_default(), and sqrt(). 00691 { 00692 float delta = params.set_default("delta", 0.0f); 00693 int n = params.set_default("n", 0); 00694 00695 if ( delta <= 0 && n <= 0 ) throw InvalidParameterException("Error, you must specify a positive non-zero delta or n"); 00696 if ( delta > 0 && n > 0 ) throw InvalidParameterException("Error, the delta and the n arguments are mutually exclusive"); 00697 00698 if ( n > 0 ) { 00699 delta = get_optimal_delta(sym,n); 00700 } 00701 00702 // if ( sym->is_platonic_sym() ) return gen_platonic_orientations(sym, delta); 00703 00704 bool inc_mirror = params.set_default("inc_mirror",false); 00705 Dict delimiters = sym->get_delimiters(inc_mirror); 00706 float altmax = delimiters["alt_max"]; 00707 float azmax = delimiters["az_max"]; 00708 00709 float altmin = 0.0f; 00710 // #If it's a h symmetry then the alt iterator starts at very close 00711 // #to the altmax... the object is a h symmetry then it knows its alt_min... 00712 if (sym->is_h_sym()){ 00713 altmin = delimiters["alt_min"]; 00714 if (inc_mirror) { 00715 altmin -= (float) sym->get_params()["maxtilt"]; 00716 } 00717 } 00718 00719 float Deltaz = (float)(cos(altmax*EMConsts::deg2rad)-cos(altmin*EMConsts::deg2rad)); 00720 float s = delta*M_PI/180.0f; 00721 float NFactor = 3.6f/s; 00722 float wedgeFactor = fabs( Deltaz*(azmax)/720.0f) ; 00723 int NumPoints = static_cast<int> (NFactor*NFactor*wedgeFactor); 00724 00725 vector<Transform> ret; 00726 00727 if (!sym->is_h_sym()) add_orientation(ret,0,0); 00728 float az = 0.0f; 00729 float dz = (float)cos(altmin*EMConsts::deg2rad); 00730 for(int i = 1; i < NumPoints; ++i ){ 00731 float z = dz + Deltaz* (float)i/ float(NumPoints-1); 00732 float r= sqrt(1.0f-z*z); 00733 az = fmod(az + delta/r,azmax); 00734 float alt = (float)(acos(z)*EMConsts::rad2deg); 00735 if (sym->is_platonic_sym()) { 00736 if ( sym->is_in_asym_unit(alt,az,inc_mirror) == false ) continue; 00737 else { 00738 az += sym->get_az_alignment_offset(); // Align to the symmetry axes 00739 } 00740 } 00741 add_orientation(ret,az,alt); 00742 } 00743 00744 return ret; 00745 }
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Get a description.
Implements EMAN::FactoryBase. Definition at line 1253 of file symmetry.h. 01253 { return "Generate quasi-evenly distributed orientations within an asymmetric unit using a spiraling method attributed to Saff"; }
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Return "saff".
Implements EMAN::FactoryBase. Definition at line 1248 of file symmetry.h. 01248 { return NAME; }
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This function returns how many orientations will be generated for a given delta (angular spacing) It does this by simulated gen_orientations.
Implements EMAN::OrientationGenerator. Definition at line 649 of file symmetry.cpp. References EMAN::Symmetry3D::get_delimiters(), EMAN::FactoryBase::get_params(), EMAN::Symmetry3D::is_h_sym(), EMAN::Symmetry3D::is_in_asym_unit(), EMAN::Symmetry3D::is_platonic_sym(), EMAN::Dict::set_default(), and sqrt(). 00650 { 00651 bool inc_mirror = params.set_default("inc_mirror",false); 00652 Dict delimiters = sym->get_delimiters(inc_mirror); 00653 float altmax = delimiters["alt_max"]; 00654 float azmax = delimiters["az_max"]; 00655 00656 float altmin = 0.0f; 00657 // #If it's a h symmetry then the alt iterator starts at very close 00658 // #to the altmax... the object is a h symmetry then it knows its alt_min... 00659 if (sym->is_h_sym()){ 00660 altmin = delimiters["alt_min"]; 00661 if (inc_mirror) { 00662 altmin -= (float) sym->get_params()["maxtilt"]; 00663 } 00664 } 00665 00666 float Deltaz = (float)(cos(altmax*EMConsts::deg2rad)-cos(altmin*EMConsts::deg2rad)); 00667 float s = delta*M_PI/180.0f; 00668 float NFactor = 3.6f/s; 00669 float wedgeFactor = fabs( Deltaz*(azmax)/720.0f) ; 00670 int NumPoints = static_cast<int> (NFactor*NFactor*wedgeFactor); 00671 00672 int tally = 0; 00673 if (!sym->is_h_sym()) ++tally; 00674 float az = 0.0f; 00675 float dz = (float)cos(altmin*EMConsts::deg2rad); 00676 for(int i = 1; i < NumPoints; ++i ){ 00677 float z = dz + Deltaz* (float)i/ float(NumPoints-1); 00678 float r= sqrt(1.0f-z*z); 00679 az = fmod(az + delta/r,azmax); 00680 float alt = (float)(acos(z)*EMConsts::rad2deg); 00681 if (sym->is_platonic_sym()) { 00682 if ( sym->is_in_asym_unit(alt,az,inc_mirror) == false ) continue; 00683 } 00684 tally++; 00685 } 00686 00687 return tally; 00688 }
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Get a dictionary containing the permissable parameters of this class.
Reimplemented from EMAN::OrientationGenerator. Definition at line 1259 of file symmetry.h. References EMAN::TypeDict::put(). 01260 { 01261 TypeDict d = OrientationGenerator::get_param_types(); 01262 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."); 01263 d.put("inc_mirror", EMObject::BOOL, "Indicates whether or not to include the mirror portion of the asymmetric unit. Default is false."); 01264 d.put("delta", EMObject::FLOAT, "The angular separation of orientations in degrees. This option is mutually exclusively of the n argument."); 01265 return d; 01266 }
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Factory support function NEW.
Definition at line 1240 of file symmetry.h. 01241 { 01242 return new SaffOrientationGenerator(); 01243 }
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Disallow assignment.
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The name of this class - used to access it from factories etc. Should be "icos".
Definition at line 47 of file symmetry.cpp. |