#include <alignoptions.h>
Collaboration diagram for AlignOptions:
Definition at line 10 of file alignoptions.h.
AlignOptions::AlignOptions | ( | ) |
Definition at line 3 of file alignoptions.cpp.
References CTF, dtheta, first_ring, have_angles, last_ring, mask3D, maxit, ref_angle_type, ri, rstep, sirt_lam, sirt_maxit, sirt_tol, snr, step, symmetry, use_sirt, xrng, and yrng.
00004 { 00005 mask3D = NULL; 00006 first_ring = 1; 00007 last_ring = 0; 00008 rstep = 1; 00009 ri = 0; 00010 xrng = 1.0; 00011 yrng = 1.0; 00012 step = 1.0; 00013 dtheta = 15.0; 00014 snr = 1.0; 00015 symmetry = "c1"; 00016 CTF = false; 00017 have_angles = false; 00018 ref_angle_type = "P"; 00019 use_sirt = true; 00020 sirt_tol = 1.0e-1; 00021 sirt_lam = 1.0e-4; 00022 sirt_maxit = 100; 00023 maxit = 1; 00024 }
AlignOptions::AlignOptions | ( | Vec3i & | volsize | ) |
Definition at line 26 of file alignoptions.cpp.
References CTF, dtheta, first_ring, have_angles, last_ring, mask3D, maxit, ref_angle_type, ri, rstep, sirt_lam, sirt_maxit, sirt_tol, snr, step, symmetry, use_sirt, xrng, and yrng.
00027 { 00028 int min_dim = (volsize[0] < volsize[1] ? volsize[0] : volsize[1]); 00029 min_dim = (min_dim < volsize[2] ? min_dim : volsize[2]); 00030 // min_dim = min(nx,ny,nz) 00031 mask3D = NULL; 00032 first_ring = 1; 00033 last_ring = min_dim / 2 - 2; 00034 rstep = 1; 00035 ri = min_dim / 2 - 2; 00036 xrng = 1.0; 00037 yrng = 1.0; 00038 step = 1.0; 00039 dtheta = 15.0; 00040 snr = 1.0; 00041 symmetry = "c1"; 00042 CTF = false; 00043 have_angles = false; 00044 ref_angle_type = "P"; 00045 use_sirt = true; 00046 sirt_tol = 1.0e-1; 00047 sirt_lam = 1.0e-4; 00048 sirt_maxit = 100; 00049 maxit = 1; 00050 }
AlignOptions::AlignOptions | ( | const AlignOptions & | old_options | ) |
Definition at line 52 of file alignoptions.cpp.
References CTF, dtheta, first_ring, have_angles, last_ring, mask3D, maxit, ref_angle_type, ri, rstep, sirt_lam, sirt_maxit, sirt_tol, snr, step, symmetry, use_sirt, xrng, and yrng.
00053 { 00054 mask3D = old_options.mask3D; 00055 first_ring = old_options.first_ring; 00056 last_ring = old_options.last_ring; 00057 rstep = old_options.rstep; 00058 ri = old_options.ri; 00059 xrng = old_options.xrng; 00060 yrng = old_options.yrng; 00061 step = old_options.step; 00062 dtheta = old_options.dtheta; 00063 snr = old_options.snr; 00064 symmetry = old_options.symmetry; 00065 CTF = old_options.CTF; 00066 have_angles = old_options.have_angles; 00067 ref_angle_type = old_options.ref_angle_type; 00068 use_sirt = old_options.use_sirt; 00069 sirt_tol = old_options.sirt_tol; 00070 sirt_lam = old_options.sirt_lam; 00071 sirt_maxit = old_options.sirt_maxit; 00072 maxit = old_options.maxit; 00073 }
AlignOptions::~AlignOptions | ( | ) | [virtual] |
bool AlignOptions::get_CTF | ( | ) |
Definition at line 170 of file alignoptions.cpp.
References CTF.
Referenced by ali3d_d(), and ParseAlignOptions().
00170 { 00171 return CTF; 00172 }
float AlignOptions::get_dtheta | ( | ) |
Definition at line 161 of file alignoptions.cpp.
References dtheta.
Referenced by ali3d_d(), and ParseAlignOptions().
00161 { 00162 return dtheta; 00163 }
int AlignOptions::get_first_ring | ( | ) |
Definition at line 140 of file alignoptions.cpp.
References first_ring.
Referenced by ali3d_d(), and ParseAlignOptions().
00140 { 00141 return first_ring; 00142 }
bool AlignOptions::get_have_angles | ( | ) |
Definition at line 173 of file alignoptions.cpp.
References have_angles.
Referenced by ali3d_d().
00173 { 00174 return have_angles; 00175 }
int AlignOptions::get_last_ring | ( | ) |
Definition at line 143 of file alignoptions.cpp.
References last_ring.
Referenced by ali3d_d(), and ParseAlignOptions().
00143 { 00144 return last_ring; 00145 }
EMData * AlignOptions::get_mask3D | ( | ) |
Definition at line 137 of file alignoptions.cpp.
References mask3D.
Referenced by ali3d_d().
00137 { 00138 return mask3D; 00139 }
int AlignOptions::get_maxit | ( | ) |
Definition at line 191 of file alignoptions.cpp.
References maxit.
Referenced by ali3d_d(), main(), and ParseAlignOptions().
00191 { 00192 return maxit; 00193 }
std::string AlignOptions::get_ref_angle_type | ( | ) |
Definition at line 176 of file alignoptions.cpp.
References ref_angle_type.
Referenced by ParseAlignOptions().
00176 { 00177 return ref_angle_type; 00178 }
int AlignOptions::get_ri | ( | ) |
Definition at line 149 of file alignoptions.cpp.
References ri.
Referenced by ali3d_d(), and ParseAlignOptions().
00149 { 00150 return ri; 00151 }
int AlignOptions::get_rstep | ( | ) |
Definition at line 146 of file alignoptions.cpp.
References rstep.
Referenced by ali3d_d(), and ParseAlignOptions().
00146 { 00147 return rstep; 00148 }
float AlignOptions::get_sirt_lam | ( | ) |
Definition at line 185 of file alignoptions.cpp.
References sirt_lam.
Referenced by ali3d_d(), and ParseAlignOptions().
00185 { 00186 return sirt_lam; 00187 }
int AlignOptions::get_sirt_maxit | ( | ) |
Definition at line 188 of file alignoptions.cpp.
References sirt_maxit.
Referenced by ali3d_d(), and ParseAlignOptions().
00188 { 00189 return sirt_maxit; 00190 }
float AlignOptions::get_sirt_tol | ( | ) |
Definition at line 182 of file alignoptions.cpp.
References sirt_tol.
Referenced by ali3d_d(), and ParseAlignOptions().
00182 { 00183 return sirt_tol; 00184 }
float AlignOptions::get_snr | ( | ) |
Definition at line 164 of file alignoptions.cpp.
References snr.
Referenced by ali3d_d(), and ParseAlignOptions().
00164 { 00165 return snr; 00166 }
float AlignOptions::get_step | ( | ) |
Definition at line 158 of file alignoptions.cpp.
References step.
Referenced by ali3d_d(), and ParseAlignOptions().
00158 { 00159 return step; 00160 }
std::string AlignOptions::get_symmetry | ( | ) |
Definition at line 167 of file alignoptions.cpp.
References symmetry.
Referenced by ali3d_d(), and ParseAlignOptions().
00167 { 00168 return symmetry; 00169 }
bool AlignOptions::get_use_sirt | ( | ) |
Definition at line 179 of file alignoptions.cpp.
References use_sirt.
Referenced by ali3d_d(), and ParseAlignOptions().
00179 { 00180 return use_sirt; 00181 }
float AlignOptions::get_xrng | ( | ) |
Definition at line 152 of file alignoptions.cpp.
References xrng.
Referenced by ali3d_d(), and ParseAlignOptions().
00152 { 00153 return xrng; 00154 }
float AlignOptions::get_yrng | ( | ) |
Definition at line 155 of file alignoptions.cpp.
References yrng.
Referenced by ali3d_d(), and ParseAlignOptions().
00155 { 00156 return yrng; 00157 }
void AlignOptions::set_CTF | ( | bool | CTF | ) |
Definition at line 112 of file alignoptions.cpp.
References CTF.
Referenced by ParseAlignOptions().
00112 { 00113 CTF = in_CTF; 00114 }
void AlignOptions::set_dtheta | ( | float | dtheta | ) |
Definition at line 103 of file alignoptions.cpp.
References dtheta.
Referenced by ParseAlignOptions().
00103 { 00104 dtheta = in_dtheta; 00105 }
void AlignOptions::set_first_ring | ( | int | first_ring | ) |
Definition at line 82 of file alignoptions.cpp.
References first_ring.
Referenced by ParseAlignOptions().
00082 { 00083 first_ring = in_first_ring; 00084 }
void AlignOptions::set_have_angles | ( | bool | have_angles | ) |
Definition at line 115 of file alignoptions.cpp.
References have_angles.
Referenced by main().
00115 { 00116 have_angles = in_have_angles; 00117 }
void AlignOptions::set_last_ring | ( | int | last_ring | ) |
Definition at line 85 of file alignoptions.cpp.
References last_ring.
Referenced by ParseAlignOptions().
00085 { 00086 last_ring = in_last_ring; 00087 }
void AlignOptions::set_mask3D | ( | EMData * | mask3D | ) |
Definition at line 79 of file alignoptions.cpp.
References mask3D.
Referenced by ParseAlignOptions().
00079 { 00080 mask3D = in_mask3D; 00081 }
void AlignOptions::set_maxit | ( | int | maxit | ) |
Definition at line 133 of file alignoptions.cpp.
References maxit.
Referenced by main(), and ParseAlignOptions().
00133 { 00134 maxit = in_maxit; 00135 }
void AlignOptions::set_ref_angle_type | ( | std::string | ref_angle_type | ) |
Definition at line 118 of file alignoptions.cpp.
References ref_angle_type.
Referenced by ParseAlignOptions().
00118 { 00119 ref_angle_type = in_ref_angle_type; 00120 }
void AlignOptions::set_ri | ( | int | ri | ) |
Definition at line 91 of file alignoptions.cpp.
References ri.
Referenced by ParseAlignOptions().
00091 { 00092 ri = in_ri; 00093 }
void AlignOptions::set_rstep | ( | int | rstep | ) |
Definition at line 88 of file alignoptions.cpp.
References rstep.
Referenced by ParseAlignOptions().
00088 { 00089 rstep = in_rstep; 00090 }
void AlignOptions::set_sirt_lam | ( | float | sirt_lam | ) |
Definition at line 127 of file alignoptions.cpp.
References sirt_lam.
Referenced by ParseAlignOptions().
00127 { 00128 sirt_lam = in_sirt_lam; 00129 }
void AlignOptions::set_sirt_maxit | ( | int | sirt_maxit | ) |
Definition at line 130 of file alignoptions.cpp.
References sirt_maxit.
Referenced by ParseAlignOptions().
00130 { 00131 sirt_maxit = in_sirt_maxit; 00132 }
void AlignOptions::set_sirt_tol | ( | float | sirt_tol | ) |
Definition at line 124 of file alignoptions.cpp.
References sirt_tol.
Referenced by ParseAlignOptions().
00124 { 00125 sirt_tol = in_sirt_tol; 00126 }
void AlignOptions::set_snr | ( | float | snr | ) |
Definition at line 106 of file alignoptions.cpp.
References snr.
Referenced by ParseAlignOptions().
00106 { 00107 snr = in_snr; 00108 }
void AlignOptions::set_step | ( | float | step | ) |
Definition at line 100 of file alignoptions.cpp.
References step.
Referenced by ParseAlignOptions().
00100 { 00101 step = in_step; 00102 }
void AlignOptions::set_symmetry | ( | std::string | symmetry | ) |
Definition at line 109 of file alignoptions.cpp.
References symmetry.
Referenced by ParseAlignOptions().
00109 { 00110 symmetry = in_symmetry; 00111 }
void AlignOptions::set_use_sirt | ( | bool | use_sirt | ) |
Definition at line 121 of file alignoptions.cpp.
References use_sirt.
Referenced by ParseAlignOptions().
00121 { 00122 use_sirt = in_use_sirt; 00123 }
void AlignOptions::set_xrng | ( | float | xrng | ) |
Definition at line 94 of file alignoptions.cpp.
References xrng.
Referenced by ParseAlignOptions().
00094 { 00095 xrng = in_xrng; 00096 }
void AlignOptions::set_yrng | ( | float | yrng | ) |
Definition at line 97 of file alignoptions.cpp.
References yrng.
Referenced by ParseAlignOptions().
00097 { 00098 yrng = in_yrng; 00099 }
bool AlignOptions::CTF [private] |
Definition at line 69 of file alignoptions.h.
Referenced by AlignOptions(), get_CTF(), and set_CTF().
float AlignOptions::dtheta [private] |
Definition at line 66 of file alignoptions.h.
Referenced by AlignOptions(), get_dtheta(), and set_dtheta().
int AlignOptions::first_ring [private] |
Definition at line 59 of file alignoptions.h.
Referenced by AlignOptions(), get_first_ring(), and set_first_ring().
bool AlignOptions::have_angles [private] |
Definition at line 70 of file alignoptions.h.
Referenced by AlignOptions(), get_have_angles(), and set_have_angles().
int AlignOptions::last_ring [private] |
Definition at line 60 of file alignoptions.h.
Referenced by AlignOptions(), get_last_ring(), and set_last_ring().
EMData* AlignOptions::mask3D [private] |
Definition at line 58 of file alignoptions.h.
Referenced by AlignOptions(), get_mask3D(), and set_mask3D().
int AlignOptions::maxit [private] |
Definition at line 76 of file alignoptions.h.
Referenced by AlignOptions(), get_maxit(), and set_maxit().
std::string AlignOptions::ref_angle_type [private] |
Definition at line 71 of file alignoptions.h.
Referenced by AlignOptions(), get_ref_angle_type(), and set_ref_angle_type().
int AlignOptions::ri [private] |
int AlignOptions::rstep [private] |
Definition at line 61 of file alignoptions.h.
Referenced by AlignOptions(), get_rstep(), and set_rstep().
float AlignOptions::sirt_lam [private] |
Definition at line 74 of file alignoptions.h.
Referenced by AlignOptions(), get_sirt_lam(), and set_sirt_lam().
int AlignOptions::sirt_maxit [private] |
Definition at line 75 of file alignoptions.h.
Referenced by AlignOptions(), get_sirt_maxit(), and set_sirt_maxit().
float AlignOptions::sirt_tol [private] |
Definition at line 73 of file alignoptions.h.
Referenced by AlignOptions(), get_sirt_tol(), and set_sirt_tol().
float AlignOptions::snr [private] |
Definition at line 67 of file alignoptions.h.
Referenced by AlignOptions(), get_snr(), and set_snr().
float AlignOptions::step [private] |
Definition at line 65 of file alignoptions.h.
Referenced by AlignOptions(), get_step(), and set_step().
std::string AlignOptions::symmetry [private] |
Definition at line 68 of file alignoptions.h.
Referenced by AlignOptions(), get_symmetry(), and set_symmetry().
bool AlignOptions::use_sirt [private] |
Definition at line 72 of file alignoptions.h.
Referenced by AlignOptions(), get_use_sirt(), and set_use_sirt().
float AlignOptions::xrng [private] |
Definition at line 63 of file alignoptions.h.
Referenced by AlignOptions(), get_xrng(), and set_xrng().
float AlignOptions::yrng [private] |
Definition at line 64 of file alignoptions.h.
Referenced by AlignOptions(), get_yrng(), and set_yrng().