| Bsoft 2.0.5 Bernard's software package

mg_tags.h
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1
9 // Do not change the constant names because they are referenced in code
10 // Changes in the tag strings will not affect program execution
11 // but old data files will be uninterpretable
12
13 // Data block tags or identifiers: Program block tags are in upper case
14 //#define IMAGE "image"
15 //#define STRUCFAC "structure_factors"
16 //#define MOLECULE "molecule"
17 //#define SEQUENCE "sequence"
18 //#define POLARFOURIER "PFT"
19 //#define THREEDIMRECON "3DR"
20
21 #define COMMENT "comment"
22 #define ID "id"
23
24 #define PROJECT "project"
25 #define FIELD "field"
26 #define FIELD_ID "field.id"
27 #define FIELD_SELECT "field.select"
28 #define FIELD_FOM "field.fom"
29
30 // Map tags
31 #define MAP "map.3D_reconstruction"
32 #define MAP_ID "map.3D_reconstruction.id"
33 #define MAP_REFERENCE "map.reference.file_name"
34 #define MAP_RECONSTRUCTION "map.3D_reconstruction.file_name"
35 #define MAP_TRANSFORM_FILE "map.3D_reconstruction_fourier_transform.file_name"
36 #define MAP_POWERSPEC_FILE "map.3D_reconstruction_powerspectrum.file_name"
37 #define MAP_SIZE_X "map.3D_reconstruction.size_x"
38 #define MAP_SIZE_Y "map.3D_reconstruction.size_y"
39 #define MAP_SIZE_Z "map.3D_reconstruction.size_z"
40 #define MAP_ORIGIN_X "map.3D_reconstruction.origin_x"
41 #define MAP_ORIGIN_Y "map.3D_reconstruction.origin_y"
42 #define MAP_ORIGIN_Z "map.3D_reconstruction.origin_z"
43 #define MAP_SCALE_X "map.3D_reconstruction.scale_x"
44 #define MAP_SCALE_Y "map.3D_reconstruction.scale_y"
45 #define MAP_SCALE_Z "map.3D_reconstruction.scale_z"
46 #define MAP_VOXEL_SIZE "map.3D_reconstruction.voxel_size"
47 #define MAP_SELECT "map.3D_reconstruction.select"
48 #define MAP_FOM "map.3D_reconstruction.fom"
49 #define MAP_MAGNIFICATION "map.magnification"
50 #define MAP_VIEW_X "map.view_x"
51 #define MAP_VIEW_Y "map.view_y"
52 #define MAP_VIEW_Z "map.view_z"
53 #define MAP_VIEW_ANGLE "map.view_angle"
54 #define MAP_BACK_RWEIGHT "map.back_projection.rweight"
55 #define MAP_MODEL "map.model"
56 #define MAP_SYMMETRY "map.symmetry"
57
58 // Parameters for micrographs
59 #define MICROGRAPH "micrograph"
60 #define MICROGRAPH_FILE "micrograph.file_name"
61 #define MICROGRAPH_FRAMES_FILE "micrograph_frames.file_name"
62 #define MICROGRAPH_FRAME "micrograph_frame.number"
63 #define MICROGRAPH_FRAME_SHIFT_X "micrograph_frame.shift_x"
64 #define MICROGRAPH_FRAME_SHIFT_Y "micrograph_frame.shift_y"
65 #define MICROGRAPH_FRAME_SELECT "micrograph_frame.select"
66 #define MICROGRAPH_FRAME_FOM "micrograph_frame.fom"
67 #define MICROGRAPH_PARTICLE_FILE "micrograph_particle.file_name" // deprecated
68 #define MICROGRAPH_FILAMENT_FILE "micrograph_filament.file_name" // deprecated
69 #define MICROGRAPH_TRANSFORM_FILE "micrograph_fourier_transform.file_name"
70 #define MICROGRAPH_POWERSPEC_FILE "micrograph_powerspectrum.file_name"
71 #define MICROGRAPH_ID "micrograph.id"
72 #define MICROGRAPH_FIELD_ID "micrograph.field_id"
73 #define MICROGRAPH_NUMBER "micrograph.number"
74 #define MICROGRAPH_SELECT "micrograph.select"
75 #define MICROGRAPH_FOM "micrograph.fom"
76 #define MICROGRAPH_MAGNIFICATION "micrograph.magnification"
77 #define MICROGRAPH_SAMPLING "micrograph.sampling"
78 #define MICROGRAPH_PIXEL "micrograph.pixel_size"
79 #define MICROGRAPH_UNITS "micrograph.units" // Supercede by general tag
80 #define MICROGRAPH_DOSE "micrograph.electron_dose"
81 #define MICROGRAPH_ORIGIN_X "micrograph.origin_x"
82 #define MICROGRAPH_ORIGIN_Y "micrograph.origin_y"
83 #define MICROGRAPH_ORIGIN_Z "micrograph.origin_z"
84 #define MICROGRAPH_SCALE_X "micrograph.scale_x"
85 #define MICROGRAPH_SCALE_Y "micrograph.scale_y"
86 #define MICROGRAPH_SCALE_Z "micrograph.scale_z"
87 #define MICROGRAPH_TILT_AXIS "micrograph.tilt_axis"
88 #define MICROGRAPH_TILT_ANGLE "micrograph.tilt_angle"
89 #define MICROGRAPH_LEVEL_ANGLE "micrograph.level_angle"
90 #define MICROGRAPH_ROT_ANGLE "micrograph.rotation_angle" // in-plane rotation
91 #define MICROGRAPH_VIEW_X "micrograph.view_x"
92 #define MICROGRAPH_VIEW_Y "micrograph.view_y"
93 #define MICROGRAPH_VIEW_Z "micrograph.view_z"
94 #define MICROGRAPH_VIEW_ANGLE "micrograph.view_angle"
95 #define MICROGRAPH_MATRIX_1_1 "micrograph.matrix_1_1"
96 #define MICROGRAPH_MATRIX_1_2 "micrograph.matrix_1_2"
97 #define MICROGRAPH_MATRIX_1_3 "micrograph.matrix_1_3"
98 #define MICROGRAPH_MATRIX_2_1 "micrograph.matrix_2_1"
99 #define MICROGRAPH_MATRIX_2_2 "micrograph.matrix_2_2"
100 #define MICROGRAPH_MATRIX_2_3 "micrograph.matrix_2_3"
101 #define MICROGRAPH_MATRIX_3_1 "micrograph.matrix_3_1"
102 #define MICROGRAPH_MATRIX_3_2 "micrograph.matrix_3_2"
103 #define MICROGRAPH_MATRIX_3_3 "micrograph.matrix_3_3"
104 #define MICROGRAPH_HVEC_X "micrograph.h_x"
105 #define MICROGRAPH_HVEC_Y "micrograph.h_y"
106 #define MICROGRAPH_HVEC_Z "micrograph.h_z"
107 #define MICROGRAPH_KVEC_X "micrograph.k_x"
108 #define MICROGRAPH_KVEC_Y "micrograph.k_y"
109 #define MICROGRAPH_KVEC_Z "micrograph.k_z"
110 #define MICROGRAPH_LVEC_X "micrograph.l_x"
111 #define MICROGRAPH_LVEC_Y "micrograph.l_y"
112 #define MICROGRAPH_LVEC_Z "micrograph.l_z"
113 #define MICROGRAPH_HELIX_AXIS "micrograph.helix_axis_angle"
114 #define MICROGRAPH_HELIX_RISE "micrograph.helix_subunit_rise"
115 #define MICROGRAPH_HELIX_ANGLE "micrograph.helix_subunit_angle"
116 #define MICROGRAPH_HELIX_RADIUS "micrograph.helix_radius"
117 #define MICROGRAPH_VOLTAGE "micrograph.voltage" // deprecated
118 #define MICROGRAPH_CTF_CS "micrograph.ctf.Cs" // deprecated
119 #define MICROGRAPH_CTF_CC "micrograph.ctf.Cc" // deprecated
120 #define MICROGRAPH_CTF_ALPHA "micrograph.ctf.alpha" // deprecated
121 #define MICROGRAPH_CTF_DE "micrograph.ctf.energy_spread" // deprecated
122 #define MICROGRAPH_CTF_AMP_CONT "micrograph.ctf.amp_contrast" // deprecated
123 #define MICROGRAPH_CTF_ZERO "micrograph.ctf.first_zero" // deprecated
124 #define MICROGRAPH_CTF_DEF_AVG "micrograph.ctf.defocus_average" // deprecated
125 #define MICROGRAPH_CTF_DEF_DEV "micrograph.ctf.defocus_deviation" // deprecated
126 #define MICROGRAPH_CTF_DEF_MIN "micrograph.ctf.defocus_min" // deprecated
127 #define MICROGRAPH_CTF_DEF_MAX "micrograph.ctf.defocus_max" // deprecated
128 #define MICROGRAPH_CTF_AST_ANG "micrograph.ctf.astigmatism_angle" // deprecated
129 #define MICROGRAPH_CTF_BASELINE "micrograph.ctf.baseline" // deprecated
130 #define MICROGRAPH_CTF_ENVELOPE "micrograph.ctf.envelope" // deprecated
131 #define MICROGRAPH_BOX_RADIUS "micrograph.box_radius" // deprecated
132 #define MICROGRAPH_BOX_RADIUS_X "micrograph.box_radius_x" // deprecated
133 #define MICROGRAPH_BOX_RADIUS_Y "micrograph.box_radius_y" // deprecated
134 #define MICROGRAPH_BOX_RADIUS_Z "micrograph.box_radius_z" // deprecated
135 #define MICROGRAPH_BAD "micrograph.bad" // deprecated
136 #define MICROGRAPH_BAD_RADIUS "micrograph.bad_radius" // deprecated
137 #define MICROGRAPH_BAD_X "micrograph.bad_x" // deprecated
138 #define MICROGRAPH_BAD_Y "micrograph.bad_y" // deprecated
139 #define MICROGRAPH_BAD_Z "micrograph.bad_z" // deprecated
140 #define MICROGRAPH_MARKER_RADIUS "micrograph.marker_radius" // deprecated
141 #define MICROGRAPH_MARKER_ID "micrograph.marker_id" // deprecated
142 #define MICROGRAPH_MARKER_X "micrograph.marker_x" // deprecated
143 #define MICROGRAPH_MARKER_Y "micrograph.marker_y" // deprecated
144 #define MICROGRAPH_MARKER_Z "micrograph.marker_z" // deprecated
145 #define MICROGRAPH_MARKER_ERROR_X "micrograph.marker_error_x" // deprecated
146 #define MICROGRAPH_MARKER_ERROR_Y "micrograph.marker_error_y" // deprecated
147 #define MICROGRAPH_MARKER_ERROR_Z "micrograph.marker_error_z" // deprecated
148 #define MICROGRAPH_MARKER_FOM "micrograph.marker_fom" // deprecated
149 #define MICROGRAPH_FILAMENT_WIDTH "micrograph.filament_width" // deprecated
150 #define MICROGRAPH_FILNODE_RADIUS "micrograph.filament_node_radius" // deprecated
151
152 // Parameters for the CTF
153 #define CTF "ctf"
154 #define CTF_VOLTAGE "ctf.voltage"
155 #define CTF_CS "ctf.Cs"
156 #define CTF_CC "ctf.Cc"
157 #define CTF_ALPHA "ctf.alpha"
158 #define CTF_DE "ctf.energy_spread"
159 #define CTF_AMP "ctf.amp_contrast"
160 #define CTF_AMP_SHIFT "ctf.amplitude_phase_shift"
161 #define CTF_ZERO "ctf.first_zero"
162 #define CTF_DEF_AVG "ctf.defocus_average"
163 #define CTF_DEF_DEV "ctf.defocus_deviation"
164 #define CTF_DEF_MIN "ctf.defocus_min"
165 #define CTF_DEF_MAX "ctf.defocus_max"
166 #define CTF_AST_ANG "ctf.astigmatism_angle"
167 #define CTF_BASELINE "ctf.baseline"
168 #define CTF_ENVELOPE "ctf.envelope"
169
170 // Parameters for each individual particle image
171 #define PARTICLE "particle"
172 #define PARTICLE_FILE "particle.file_name"
173 #define PARTICLE_NUMBER "particle.number" // Deprecated
174 #define PARTICLE_ID "particle.id"
175 #define PARTICLE_GROUP "particle.group_id"
176 #define PARTICLE_MG_ID "particle.micrograph_id"
177 #define PARTICLE_MG_X "particle.micrograph_x" // Deprecated
178 #define PARTICLE_MG_Y "particle.micrograph_y" // Deprecated
179 #define PARTICLE_MG_Z "particle.micrograph_z" // Deprecated
180 #define PARTICLE_X "particle.x"
181 #define PARTICLE_Y "particle.y"
182 #define PARTICLE_Z "particle.z"
183 #define PARTICLE_X_ORIGIN "particle.x_origin" // Deprecated
184 #define PARTICLE_Y_ORIGIN "particle.y_origin" // Deprecated
185 #define PARTICLE_Z_ORIGIN "particle.z_origin" // Deprecated
186 #define PARTICLE_ORIGIN_X "particle.origin_x"
187 #define PARTICLE_ORIGIN_Y "particle.origin_y"
188 #define PARTICLE_ORIGIN_Z "particle.origin_z"
189 #define PARTICLE_PSI "particle.psi"
190 #define PARTICLE_THETA "particle.theta"
191 #define PARTICLE_PHI "particle.phi"
192 #define PARTICLE_OMEGA "particle.omega"
193 #define PARTICLE_VIEW_X "particle.view_x"
194 #define PARTICLE_VIEW_Y "particle.view_y"
195 #define PARTICLE_VIEW_Z "particle.view_z"
196 #define PARTICLE_VIEW_ANGLE "particle.view_angle"
197 #define PARTICLE_MAGNIF "particle.magnification"
198 #define PARTICLE_PIXEL "particle.pixel_size"
199 #define PARTICLE_DEFOCUS "particle.defocus"
200 #define PARTICLE_DEF_DEV "particle.defocus_deviation"
201 #define PARTICLE_AST_ANG "particle.astigmatism_angle"
202 #define PARTICLE_SELECT "particle.select"
203 #define PARTICLE_FOM "particle.fom"
204 #define PARTICLE_FOM_CV "particle.fom_crossvalidation"
205 #define PARTICLE_FOM_SNR "particle.signal_to_noise"
206 #define PARTICLE_FOM_AVG "particle.fom_average"
207 #define PARTICLE_FOM_STD "particle.fom_stdev"
208 #define PARTICLE_FOM1 "particle.fom1"
209 #define PARTICLE_FOM2 "particle.fom2"
210 #define PARTICLE_FOM3 "particle.fom3"
211 #define PARTICLE_FOM4 "particle.fom4"
212 #define PARTICLE_FOM5 "particle.fom5"
213 #define PARTICLE_FOM6 "particle.fom6"
214 #define PARTICLE_FOM7 "particle.fom7"
215 #define PARTICLE_FOM8 "particle.fom8"
216 #define PARTICLE_FOM9 "particle.fom9"
217 #define PARTICLE_HANDA_FOM "particle.handa_fom"
218 #define PARTICLE_HANDB_FOM "particle.handb_fom"
219 #define PARTICLE_CC "particle.cc"
220 #define PARTICLE_CC_AVG "particle.cc_avg"
221 #define PARTICLE_PFT_CC "particle.pft_cc"
222 #define PARTICLE_PRJ_CC "particle.prj_cc"
223 #define PARTICLE_CMP_CC "particle.cmp_cc"
224 #define PARTICLE_RFACTORAB "particle.rfactorab"
225 #define PARTICLE_COVERAGE "particle.coverage"
226 #define PARTICLE_BOX_SIZE "particle.box_size"
227 #define PARTICLE_BOX_SIZE_X "particle.box_size_x"
228 #define PARTICLE_BOX_SIZE_Y "particle.box_size_y"
229 #define PARTICLE_BOX_SIZE_Z "particle.box_size_z"
230 #define PARTICLE_BOX_RADIUS "particle.box_radius" // Deprecated
231 #define PARTICLE_BOX_RADIUS_X "particle.box_radius_x" // Deprecated
232 #define PARTICLE_BOX_RADIUS_Y "particle.box_radius_y" // Deprecated
233 #define PARTICLE_BOX_RADIUS_Z "particle.box_radius_z" // Deprecated
234 #define PARTICLE_BAD "particle.bad"
235 #define PARTICLE_BAD_RADIUS "particle.bad_radius"
236 #define PARTICLE_BAD_X "particle.bad_x"
237 #define PARTICLE_BAD_Y "particle.bad_y"
238 #define PARTICLE_BAD_Z "particle.bad_z"
239
240 // Tag for class average section
241 #define CLASS_AVERAGE "class_average"
242
243 // Parameters for filaments
244 #define FILAMENT "filament"
245 #define FILAMENT_FILE "filament.file_name"
246 #define FILAMENT_ID "filament.id"
247 #define FILAMENT_NODE "filament.node"
248 #define FILAMENT_NODE_ID "filament.node_id"
249 #define FILAMENT_NODE_X "filament.x"
250 #define FILAMENT_NODE_Y "filament.y"
251 #define FILAMENT_NODE_Z "filament.z"
252 #define FILAMENT_WIDTH "filament.width"
253 #define FILNODE_RADIUS "filament.node_radius"
254
255 // Orientation parameter sets
256 #define ORIENT_ID "orient.id"
257 #define ORIENT_ORIGIN_X "orient.origin_x"
258 #define ORIENT_ORIGIN_Y "orient.origin_y"
259 #define ORIENT_ORIGIN_Z "orient.origin_z"
260 #define ORIENT_VIEW_X "orient.view_x"
261 #define ORIENT_VIEW_Y "orient.view_y"
262 #define ORIENT_VIEW_Z "orient.view_z"
263 #define ORIENT_VIEW_ANGLE "orient.view_angle"
264 #define ORIENT_FOM "orient.fom"
265 #define ORIENT_SELECT "orient.select"
266
267 // Marker parameters
268 #define MARKER "marker"
269 #define MARKER_RADIUS "marker.radius"
270 #define MARKER_ID "marker.id"
271 #define MARKER_X "marker.x"
272 #define MARKER_Y "marker.y"
273 #define MARKER_Z "marker.z"
274 #define MARKER_ERROR_X "marker.error_x"
275 #define MARKER_ERROR_Y "marker.error_y"
276 #define MARKER_ERROR_Z "marker.error_z"
277 #define MARKER_IMAGE "marker.image_number"
278 #define MARKER_RESIDUAL "marker.residual"
279 #define MARKER_FOM "marker.fom"
280 #define MARKER_SELECT "marker.select"
281
282 // Structure factors
283 #define REFLEX "refln"
284 #define REFLEX_RADIUS "refln.radius"
285 #define REFLEX_X "refln.location_x"
286 #define REFLEX_Y "refln.location_y"
287 #define REFLEX_Z "refln.location_z"
288 #define REFLEX_H "refln.index_h"
289 #define REFLEX_K "refln.index_k"
290 #define REFLEX_L "refln.index_l"
291 #define REFLEX_AMP "refln.F_meas_au"
292 //#define REFLEX_SIGAMP "refln.F_sigma"
293 #define REFLEX_SIGAMP "refln.F_meas_sigma_au"
294 #define REFLEX_PHI "refln.phase_meas"
295 #define REFLEX_SIGPHI "refln.phase_sigma"
296 #define REFLEX_FOM "refln.weight"
297 #define REFLEX_STATUS "refln.status"
298
299 // Layer lines
300 #define LAYERLINE "layer_line"
301 #define LAYERLINE_NUMBER "layer_line.number"
302 #define LAYERLINE_ORDER "layer_line.bessel_order"
303 #define LAYERLINE_DISTANCE "layer_line.distance"
304 #define LAYERLINE_FREQ "layer_line.frequency"
305 #define LAYERLINE_AMP "layer_line.amplitude"
306 #define LAYERLINE_FOM "layer_line.fom"
307 #define LAYERLINE_SELECT "layer_line.select"