#include <symmetry.h>
Inheritance diagram for EMAN::EvenOrientationGenerator:
Public Member Functions | |
EvenOrientationGenerator () | |
virtual | ~EvenOrientationGenerator () |
virtual string | get_name () const |
Return "even". | |
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 even distributed orientations in the asymmetric unit of the symmetry. | |
Static Public Member Functions | |
static OrientationGenerator * | NEW () |
Factory support function NEW. | |
Static Public Attributes | |
static const string | NAME = "even" |
The name of this class - used to access it from factories etc. Should be "icos". | |
Private Member Functions | |
EvenOrientationGenerator (const EvenOrientationGenerator &) | |
Disallow copy construction. | |
EvenOrientationGenerator & | operator= (const EvenOrientationGenerator &) |
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. |
..) 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
Definition at line 1164 of file symmetry.h.
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Definition at line 1167 of file symmetry.h. Referenced by NEW().
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Definition at line 1168 of file symmetry.h.
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Disallow copy construction.
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Generate even distributed orientations in the asymmetric unit of the symmetry.
Implements EMAN::OrientationGenerator. Definition at line 541 of file symmetry.cpp. 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(). 00542 { 00543 float delta = params.set_default("delta", 0.0f); 00544 int n = params.set_default("n", 0); 00545 00546 if ( delta <= 0 && n <= 0 ) throw InvalidParameterException("Error, you must specify a positive non-zero delta or n"); 00547 if ( delta > 0 && n > 0 ) throw InvalidParameterException("Error, the delta and the n arguments are mutually exzclusive"); 00548 00549 if ( n > 0 ) { 00550 delta = get_optimal_delta(sym,n); 00551 } 00552 00553 bool inc_mirror = params.set_default("inc_mirror",false); 00554 Dict delimiters = sym->get_delimiters(inc_mirror); 00555 float altmax = delimiters["alt_max"]; 00556 float azmax = delimiters["az_max"]; 00557 00558 float altmin = 0.0f; 00559 // If it's a h symmetry then the alt iterator starts at very close 00560 // to the altmax... the object is a h symmetry then it knows its alt_min... 00561 if (sym->is_h_sym()) altmin = delimiters["alt_min"]; 00562 00563 vector<Transform> ret; 00564 00565 for (float alt = altmin; alt <= altmax; alt += delta) { 00566 float detaz; 00567 int lt; 00568 if ((0.0f == alt)||(180.0f == alt)) { 00569 detaz = 360.0f; 00570 lt = 1; 00571 } else { 00572 detaz = delta/(float)sin(alt*EMConsts::deg2rad); 00573 lt = int(azmax/detaz)-1; 00574 if (lt < 1) lt = 1; 00575 detaz = azmax/(float)lt; 00576 } 00577 // bool d_odd_mirror_flag = false; 00578 // get_az_max(sym,altmax, inc_mirror,alt, lt,d_odd_mirror_flag, detaz); 00579 00580 for (int i = 0; i < lt; i++) { 00581 float az = (float)i*detaz; 00582 if (sym->is_platonic_sym()) { 00583 if ( sym->is_in_asym_unit(alt, az,inc_mirror) == false ) continue; 00584 else { 00585 az += sym->get_az_alignment_offset(); // Align to the symmetry axes 00586 } 00587 } 00588 add_orientation(ret,az,alt); 00589 if ( sym->is_h_sym() && inc_mirror && alt != altmin ) { 00590 add_orientation(ret,az,2.0f*altmin-alt); 00591 } 00592 } 00593 } 00594 00595 return ret; 00596 }
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Get a description.
Implements EMAN::FactoryBase. Definition at line 1187 of file symmetry.h. 01187 { return "Generate quasi-evenly distributed orientations within an asymmetric unit using Penczek's (94) approach"; }
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Return "even".
Implements EMAN::FactoryBase. Definition at line 1182 of file symmetry.h. References NAME. 01182 { 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 498 of file symmetry.cpp. 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(). 00499 { 00500 bool inc_mirror = params.set_default("inc_mirror",false); 00501 Dict delimiters = sym->get_delimiters(inc_mirror); 00502 float altmax = delimiters["alt_max"]; 00503 float azmax = delimiters["az_max"]; 00504 00505 float altmin = 0.0f; 00506 // #If it's a h symmetry then the alt iterator starts at very close 00507 // #to the altmax... the object is a h symmetry then it knows its alt_min... 00508 if (sym->is_h_sym()) altmin = delimiters["alt_min"]; 00509 00510 int tally = 0; 00511 00512 for (float alt = altmin; alt <= altmax; alt += delta) { 00513 float detaz; 00514 int lt; 00515 if ((0.0f == alt)||(180.0f == alt)) { 00516 detaz = 360.0f; 00517 lt = 1; 00518 } else { 00519 detaz = delta/(float)sin(alt*EMConsts::deg2rad); 00520 lt = int(azmax/detaz)-1; 00521 if (lt < 1) lt = 1; 00522 detaz = azmax/(float)lt; 00523 } 00524 // bool d_odd_mirror_flag = false; 00525 // get_az_max(sym,altmax, inc_mirror,alt, lt,d_odd_mirror_flag, detaz); 00526 for (int i = 0; i < lt; i++) { 00527 float az = (float)i*detaz; 00528 if (sym->is_platonic_sym()) { 00529 if ( sym->is_in_asym_unit(alt, az,inc_mirror) == false ) continue; 00530 } 00531 tally++; 00532 if ( sym->is_h_sym() && inc_mirror && alt != altmin ) { 00533 tally++; 00534 } 00535 } 00536 } 00537 00538 return tally; 00539 }
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Get a dictionary containing the permissable parameters of this class.
Reimplemented from EMAN::OrientationGenerator. Definition at line 1193 of file symmetry.h. References EMAN::EMObject::BOOL, EMAN::EMObject::FLOAT, EMAN::OrientationGenerator::get_param_types(), EMAN::EMObject::INT, and EMAN::TypeDict::put(). 01194 { 01195 TypeDict d = OrientationGenerator::get_param_types(); 01196 d.put("delta", EMObject::FLOAT, "The angular separation of orientations in degrees. This option is mutually exclusively of the n argument."); 01197 d.put("inc_mirror", EMObject::BOOL, "Indicates whether or not to include the mirror portion of the asymmetric unit. Default is false."); 01198 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."); 01199 return d; 01200 }
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Factory support function NEW.
Definition at line 1173 of file symmetry.h. References EvenOrientationGenerator(). 01174 { 01175 return new EvenOrientationGenerator(); 01176 }
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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 1209 of file symmetry.h. Referenced by get_name(). |