#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 | |
OrientationGenerator * | NEW () |
Factory support function NEW. | |
Static Public Attributes | |
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. |
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 1165 of file symmetry.h.
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Definition at line 1168 of file symmetry.h. 01168 {}
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Definition at line 1169 of file symmetry.h. 01169 {}
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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 592 of file symmetry.cpp. References EMAN::OrientationGenerator::add_orientation(), 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(), and EMAN::Dict::set_default(). 00593 { 00594 float delta = params.set_default("delta", 0.0f); 00595 int n = params.set_default("n", 0); 00596 00597 if ( delta <= 0 && n <= 0 ) throw InvalidParameterException("Error, you must specify a positive non-zero delta or n"); 00598 if ( delta > 0 && n > 0 ) throw InvalidParameterException("Error, the delta and the n arguments are mutually exzclusive"); 00599 00600 if ( n > 0 ) { 00601 delta = get_optimal_delta(sym,n); 00602 } 00603 00604 bool inc_mirror = params.set_default("inc_mirror",false); 00605 Dict delimiters = sym->get_delimiters(inc_mirror); 00606 float altmax = delimiters["alt_max"]; 00607 float azmax = delimiters["az_max"]; 00608 00609 float altmin = 0.0f; 00610 // If it's a h symmetry then the alt iterator starts at very close 00611 // to the altmax... the object is a h symmetry then it knows its alt_min... 00612 if (sym->is_h_sym()) altmin = delimiters["alt_min"]; 00613 00614 vector<Transform> ret; 00615 00616 for (float alt = altmin; alt <= altmax; alt += delta) { 00617 float detaz; 00618 int lt; 00619 if ((0.0f == alt)||(180.0f == alt)) { 00620 detaz = 360.0f; 00621 lt = 1; 00622 } else { 00623 detaz = delta/(float)sin(alt*EMConsts::deg2rad); 00624 lt = int(azmax/detaz)-1; 00625 if (lt < 1) lt = 1; 00626 detaz = azmax/(float)lt; 00627 } 00628 // bool d_odd_mirror_flag = false; 00629 // get_az_max(sym,altmax, inc_mirror,alt, lt,d_odd_mirror_flag, detaz); 00630 00631 for (int i = 0; i < lt; i++) { 00632 float az = (float)i*detaz; 00633 if (sym->is_platonic_sym()) { 00634 if ( sym->is_in_asym_unit(alt, az,inc_mirror) == false ) continue; 00635 else { 00636 az += sym->get_az_alignment_offset(); // Align to the symmetry axes 00637 } 00638 } 00639 add_orientation(ret,az,alt); 00640 if ( sym->is_h_sym() && inc_mirror && alt != altmin ) { 00641 add_orientation(ret,az,2.0f*altmin-alt); 00642 } 00643 } 00644 } 00645 00646 return ret; 00647 }
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Get a description.
Implements EMAN::FactoryBase. Definition at line 1188 of file symmetry.h. 01188 { 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 1183 of file symmetry.h. 01183 { 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 549 of file symmetry.cpp. References EMAN::Symmetry3D::get_delimiters(), EMAN::Symmetry3D::is_h_sym(), EMAN::Symmetry3D::is_in_asym_unit(), EMAN::Symmetry3D::is_platonic_sym(), and EMAN::Dict::set_default(). 00550 { 00551 bool inc_mirror = params.set_default("inc_mirror",false); 00552 Dict delimiters = sym->get_delimiters(inc_mirror); 00553 float altmax = delimiters["alt_max"]; 00554 float azmax = delimiters["az_max"]; 00555 00556 float altmin = 0.0f; 00557 // #If it's a h symmetry then the alt iterator starts at very close 00558 // #to the altmax... the object is a h symmetry then it knows its alt_min... 00559 if (sym->is_h_sym()) altmin = delimiters["alt_min"]; 00560 00561 int tally = 0; 00562 00563 for (float alt = altmin; alt <= altmax; alt += delta) { 00564 float detaz; 00565 int lt; 00566 if ((0.0f == alt)||(180.0f == alt)) { 00567 detaz = 360.0f; 00568 lt = 1; 00569 } else { 00570 detaz = delta/(float)sin(alt*EMConsts::deg2rad); 00571 lt = int(azmax/detaz)-1; 00572 if (lt < 1) lt = 1; 00573 detaz = azmax/(float)lt; 00574 } 00575 // bool d_odd_mirror_flag = false; 00576 // get_az_max(sym,altmax, inc_mirror,alt, lt,d_odd_mirror_flag, detaz); 00577 for (int i = 0; i < lt; i++) { 00578 float az = (float)i*detaz; 00579 if (sym->is_platonic_sym()) { 00580 if ( sym->is_in_asym_unit(alt, az,inc_mirror) == false ) continue; 00581 } 00582 tally++; 00583 if ( sym->is_h_sym() && inc_mirror && alt != altmin ) { 00584 tally++; 00585 } 00586 } 00587 } 00588 00589 return tally; 00590 }
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Get a dictionary containing the permissable parameters of this class.
Reimplemented from EMAN::OrientationGenerator. Definition at line 1194 of file symmetry.h. References EMAN::TypeDict::put(). 01195 { 01196 TypeDict d = OrientationGenerator::get_param_types(); 01197 d.put("delta", EMObject::FLOAT, "The angular separation of orientations in degrees. This option is mutually exclusively of the n argument."); 01198 d.put("inc_mirror", EMObject::BOOL, "Indicates whether or not to include the mirror portion of the asymmetric unit. Default is false."); 01199 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."); 01200 return d; 01201 }
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Factory support function NEW.
Definition at line 1174 of file symmetry.h. 01175 { 01176 return new EvenOrientationGenerator(); 01177 }
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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 48 of file symmetry.cpp. |