#include <alignoptions.h>
Collaboration diagram for AlignOptions:

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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 }
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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, EMAN::Vec3i, 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 }
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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 }
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Definition at line 75 of file alignoptions.cpp. 00076 {
00077 }
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Definition at line 170 of file alignoptions.cpp. Referenced by ali3d_d(), and ParseAlignOptions(). 00170 {
00171 return CTF;
00172 }
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Definition at line 161 of file alignoptions.cpp. Referenced by ali3d_d(), and ParseAlignOptions(). 00161 {
00162 return dtheta;
00163 }
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Definition at line 140 of file alignoptions.cpp. Referenced by ali3d_d(), and ParseAlignOptions(). 00140 {
00141 return first_ring;
00142 }
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Definition at line 173 of file alignoptions.cpp. Referenced by ali3d_d(). 00173 {
00174 return have_angles;
00175 }
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Definition at line 143 of file alignoptions.cpp. Referenced by ali3d_d(), and ParseAlignOptions(). 00143 {
00144 return last_ring;
00145 }
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Definition at line 137 of file alignoptions.cpp. Referenced by ali3d_d(). 00137 {
00138 return mask3D;
00139 }
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Definition at line 191 of file alignoptions.cpp. Referenced by ali3d_d(), main(), and ParseAlignOptions(). 00191 {
00192 return maxit;
00193 }
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Definition at line 176 of file alignoptions.cpp. Referenced by ParseAlignOptions(). 00176 {
00177 return ref_angle_type;
00178 }
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Definition at line 149 of file alignoptions.cpp. Referenced by ali3d_d(), and ParseAlignOptions(). 00149 {
00150 return ri;
00151 }
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Definition at line 146 of file alignoptions.cpp. Referenced by ali3d_d(), and ParseAlignOptions(). 00146 {
00147 return rstep;
00148 }
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Definition at line 185 of file alignoptions.cpp. Referenced by ali3d_d(), and ParseAlignOptions(). 00185 {
00186 return sirt_lam;
00187 }
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Definition at line 188 of file alignoptions.cpp. Referenced by ali3d_d(), and ParseAlignOptions(). 00188 {
00189 return sirt_maxit;
00190 }
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Definition at line 182 of file alignoptions.cpp. Referenced by ali3d_d(), and ParseAlignOptions(). 00182 {
00183 return sirt_tol;
00184 }
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Definition at line 164 of file alignoptions.cpp. Referenced by ali3d_d(), and ParseAlignOptions(). 00164 {
00165 return snr;
00166 }
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Definition at line 158 of file alignoptions.cpp. Referenced by ali3d_d(), and ParseAlignOptions(). 00158 {
00159 return step;
00160 }
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Definition at line 167 of file alignoptions.cpp. Referenced by ali3d_d(), and ParseAlignOptions(). 00167 {
00168 return symmetry;
00169 }
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Definition at line 179 of file alignoptions.cpp. Referenced by ali3d_d(), and ParseAlignOptions(). 00179 {
00180 return use_sirt;
00181 }
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Definition at line 152 of file alignoptions.cpp. Referenced by ali3d_d(), and ParseAlignOptions(). 00152 {
00153 return xrng;
00154 }
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Definition at line 155 of file alignoptions.cpp. Referenced by ali3d_d(), and ParseAlignOptions(). 00155 {
00156 return yrng;
00157 }
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Definition at line 112 of file alignoptions.cpp. References CTF. Referenced by ParseAlignOptions(). 00112 {
00113 CTF = in_CTF;
00114 }
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Definition at line 103 of file alignoptions.cpp. References dtheta. Referenced by ParseAlignOptions(). 00103 {
00104 dtheta = in_dtheta;
00105 }
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Definition at line 82 of file alignoptions.cpp. References first_ring. Referenced by ParseAlignOptions(). 00082 {
00083 first_ring = in_first_ring;
00084 }
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Definition at line 115 of file alignoptions.cpp. References have_angles. Referenced by main(). 00115 {
00116 have_angles = in_have_angles;
00117 }
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Definition at line 85 of file alignoptions.cpp. References last_ring. Referenced by ParseAlignOptions(). 00085 {
00086 last_ring = in_last_ring;
00087 }
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Definition at line 79 of file alignoptions.cpp. References mask3D. Referenced by ParseAlignOptions(). 00079 {
00080 mask3D = in_mask3D;
00081 }
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Definition at line 133 of file alignoptions.cpp. References maxit. Referenced by main(), and ParseAlignOptions(). 00133 {
00134 maxit = in_maxit;
00135 }
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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 }
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Definition at line 91 of file alignoptions.cpp. References ri. Referenced by ParseAlignOptions(). 00091 {
00092 ri = in_ri;
00093 }
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Definition at line 88 of file alignoptions.cpp. References rstep. Referenced by ParseAlignOptions(). 00088 {
00089 rstep = in_rstep;
00090 }
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Definition at line 127 of file alignoptions.cpp. References sirt_lam. Referenced by ParseAlignOptions(). 00127 {
00128 sirt_lam = in_sirt_lam;
00129 }
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Definition at line 130 of file alignoptions.cpp. References sirt_maxit. Referenced by ParseAlignOptions(). 00130 {
00131 sirt_maxit = in_sirt_maxit;
00132 }
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Definition at line 124 of file alignoptions.cpp. References sirt_tol. Referenced by ParseAlignOptions(). 00124 {
00125 sirt_tol = in_sirt_tol;
00126 }
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Definition at line 106 of file alignoptions.cpp. References snr. Referenced by ParseAlignOptions(). 00106 {
00107 snr = in_snr;
00108 }
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Definition at line 100 of file alignoptions.cpp. References step. Referenced by ParseAlignOptions(). 00100 {
00101 step = in_step;
00102 }
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Definition at line 109 of file alignoptions.cpp. References symmetry. Referenced by ParseAlignOptions(). 00109 {
00110 symmetry = in_symmetry;
00111 }
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Definition at line 121 of file alignoptions.cpp. References use_sirt. Referenced by ParseAlignOptions(). 00121 {
00122 use_sirt = in_use_sirt;
00123 }
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Definition at line 94 of file alignoptions.cpp. References xrng. Referenced by ParseAlignOptions(). 00094 {
00095 xrng = in_xrng;
00096 }
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Definition at line 97 of file alignoptions.cpp. References yrng. Referenced by ParseAlignOptions(). 00097 {
00098 yrng = in_yrng;
00099 }
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Definition at line 69 of file alignoptions.h. Referenced by AlignOptions(), and set_CTF(). |
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Definition at line 66 of file alignoptions.h. Referenced by AlignOptions(), and set_dtheta(). |
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Definition at line 59 of file alignoptions.h. Referenced by AlignOptions(), and set_first_ring(). |
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Definition at line 70 of file alignoptions.h. Referenced by AlignOptions(), and set_have_angles(). |
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Definition at line 60 of file alignoptions.h. Referenced by AlignOptions(), and set_last_ring(). |
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Definition at line 58 of file alignoptions.h. Referenced by AlignOptions(), and set_mask3D(). |
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Definition at line 76 of file alignoptions.h. Referenced by AlignOptions(), and set_maxit(). |
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Definition at line 71 of file alignoptions.h. Referenced by AlignOptions(), and set_ref_angle_type(). |
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Definition at line 62 of file alignoptions.h. Referenced by AlignOptions(), and set_ri(). |
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Definition at line 61 of file alignoptions.h. Referenced by AlignOptions(), and set_rstep(). |
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Definition at line 74 of file alignoptions.h. Referenced by AlignOptions(), and set_sirt_lam(). |
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Definition at line 75 of file alignoptions.h. Referenced by AlignOptions(), and set_sirt_maxit(). |
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Definition at line 73 of file alignoptions.h. Referenced by AlignOptions(), and set_sirt_tol(). |
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Definition at line 67 of file alignoptions.h. Referenced by AlignOptions(), and set_snr(). |
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Definition at line 65 of file alignoptions.h. Referenced by AlignOptions(), and set_step(). |
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Definition at line 68 of file alignoptions.h. Referenced by AlignOptions(), and set_symmetry(). |
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Definition at line 72 of file alignoptions.h. Referenced by AlignOptions(), and set_use_sirt(). |
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Definition at line 63 of file alignoptions.h. Referenced by AlignOptions(), and set_xrng(). |
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Definition at line 64 of file alignoptions.h. Referenced by AlignOptions(), and set_yrng(). |
1.3.9.1