aboutsummaryrefslogtreecommitdiff
path: root/doc/reference/libcrystfel/CrystFEL-sections.txt
blob: 720cabff4f54355a19685ed770e1dfa71015623f (plain)
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
<SECTION>
<FILE>reflist</FILE>
RefList
Reflection
RefListIterator
<SUBSECTION>
reflist_new
reflist_free
reflection_new
reflection_free
<SUBSECTION>
add_refl
add_refl_to_list
<SUBSECTION>
first_refl
next_refl
<SUBSECTION>
find_refl
next_found_refl
<SUBSECTION>
get_excitation_error
get_detector_pos
get_partiality
get_indices
get_symmetric_indices
get_intensity
get_partial
get_scalable
get_refinable
get_redundancy
get_esd_intensity
get_phase
get_temp1
get_temp2
<SUBSECTION>
set_detector_pos
set_partial
set_intensity
set_scalable
set_refinable
set_redundancy
set_esd_intensity
set_phase
set_symmetric_indices
set_temp1
set_temp2
<SUBSECTION>
copy_data
num_reflections
tree_depth
lock_reflection
unlock_reflection
</SECTION>

<SECTION>
<FILE>reflist-utils</FILE>
write_reflist
write_reflections_to_file
read_reflections
read_reflections_from_file
asymmetric_indices
res_cutoff
check_list_symmetry
copy_reflist
find_equiv_in_list
resolution_limits
max_intensity
</SECTION>

<SECTION>
<FILE>unitcell</FILE>
UnitCell
LatticeType
UnitCellTransformation
<SUBSECTION>
cell_new
cell_new_from_cell
cell_new_from_direct_axes
cell_new_from_parameters
cell_new_from_reciprocal_axes
cell_free
<SUBSECTION>
cell_get_cartesian
cell_get_parameters
cell_get_pointgroup
cell_get_reciprocal
cell_get_centering
cell_get_lattice_type
cell_get_unique_axis
<SUBSECTION>
cell_set_cartesian
cell_set_cartesian_a
cell_set_cartesian_b
cell_set_cartesian_c
cell_set_parameters
cell_set_pointgroup
cell_set_reciprocal
cell_set_centering
cell_set_lattice_type
cell_set_unique_axis
<SUBSECTION>
cell_transform
cell_transform_inverse
tfn_combine
tfn_identity
tfn_from_intmat
tfn_inverse
tfn_print
tfn_vector
tfn_free
<SUBSECTION>

cell_rep
</SECTION>

<SECTION>
<FILE>cell-utils</FILE>
cell_rotate
rotate_cell
cell_print
resolution
match_cell
match_cell_ab
cell_is_sensible
validate_cell
uncenter_cell
bravais_lattice
right_handed
str_lattice
forbidden_reflection
load_cell_from_pdb
</SECTION>

<SECTION>
<FILE>utils</FILE>
show_matrix_eqn
AssplodeFlag
C_VACUO
ELECTRON_CHARGE
ERROR
J_to_eV
PLANCK
STATUS
THOMSON_LENGTH
assplode
biggest
check_prefix
chomp
deg2rad
eV_to_J
gaussian_noise
safe_basename
progress_bar
rad2deg
is_odd
poisson_noise
notrail
smallest
ph_en_to_lambda
ph_lambda_to_en
ph_eV_to_lambda
ph_lambda_to_eV
random_flat
flat_noise
</SECTION>

<SECTION>
<FILE>quaternion</FILE>
quaternion
<SUBSECTION>
quaternion_modulus
normalise_quaternion
random_quaternion
quaternion_valid
quat_rot
</SECTION>

<SECTION>
<FILE>image</FILE>
image
ImageFeatureList
image_add_feature
image_feature_closest
image_feature_count
image_feature_list_free
image_feature_list_new
image_get_feature
image_add_crystal
image_remove_feature
free_all_crystals
</SECTION>

<SECTION>
<FILE>thread-pool</FILE>
TPGetTaskFunc
TPWorkFunc
TPFinalFunc
<SUBSECTION>
run_threads
stderr_lock
get_status_label
</SECTION>

<SECTION>
<FILE>statistics</FILE>
stat_pearson_f_ignore
stat_pearson_f_zero
stat_pearson_i
stat_r1_i
stat_r1_ignore
stat_r1_zero
stat_r2
stat_rdiff_ignore
stat_rdiff_intensity
stat_rdiff_zero
stat_scale_intensity
</SECTION>

<SECTION>
<FILE>indexing</FILE>
IndexingMethod
IndexingPrivate
INDEXING_DEFAULTS_DIRAX
INDEXING_DEFAULTS_GRAINSPOTTER
INDEXING_DEFAULTS_MOSFLM
INDEXING_DEFAULTS_REAX
INDEXING_DEFAULTS_XDS
INDEXING_METHOD_MASK
build_indexer_list
cleanup_indexing
prepare_indexing
index_pattern
indexer_str
dirax_prepare
run_dirax
dirax_cleanup
mosflm_prepare
run_mosflm
mosflm_cleanup
xds_prepare
run_xds
xds_cleanup
reax_prepare
reax_index
reax_cleanup
grainspotter_prepare
grainspotter_index
grainspotter_cleanup
</SECTION>

<SECTION>
<FILE>symmetry</FILE>
SymOpList
SymOpMask
<SUBSECTION>
free_symoplist
num_equivs
get_pointgroup
add_symop
get_equiv
special_position
get_asymm
get_ambiguities
is_subgroup
<SUBSECTION>
new_symopmask
free_symopmask
<SUBSECTION>
describe_symmetry
symmetry_name
set_symmetry_name
is_centrosymmetric
</SECTION>

<SECTION>
<FILE>integer_matrix</FILE>
IntegerMatrix
<SUBSECTION>
intmat_new
intmat_copy
intmat_free
<SUBSECTION>
intmat_get
intmat_set
<SUBSECTION>
intmat_intmat_mult
intmat_intvec_mult
intmat_det
intmat_inverse
<SUBSECTION>
intmat_equals
intmat_is_identity
intmat_is_inversion
<SUBSECTION>
intmat_print
</SECTION>

<SECTION>
<FILE>detector</FILE>
copy_geom
fill_in_values
free_detector_geometry
get_detector_geometry
write_detector_geometry
find_panel
find_panel_by_name
find_panel_number
simple_geometry
record_image
get_pixel_extents
get_q
get_q_for_panel
get_tt
smallest_q
reverse_2d_mapping
largest_q
in_bad_region
</SECTION>

<SECTION>
<FILE>beam-params</FILE>
beam_params
get_beam_parameters
fill_in_beam_parameters
free_beam_parameters
</SECTION>

<SECTION>
<FILE>crystal</FILE>
</SECTION>

<SECTION>
<FILE>hdf5-file</FILE>
hdf5_read
hdf5_write
hdf5_write_image
hdfile
hdfile_close
hdfile_get_image_binned
hdfile_get_string_value
hdfile_open
hdfile_read_group
hdfile_set_first_image
hdfile_set_image
get_value
copy_hdf5_field
copy_hdf5_fields
add_copy_hdf5_field
new_copy_hdf5_field_list
free_copy_hdf5_field_list
get_peaks
</SECTION>

<SECTION>
<FILE>crystal</FILE>
Crystal
crystal_new
crystal_copy
crystal_free
<SUBSECTION>
crystal_get_cell
crystal_get_image
crystal_get_mosaicity
crystal_get_num_saturated_reflections
crystal_get_osf
crystal_get_profile_radius
crystal_get_reflections
crystal_get_resolution_limit
crystal_get_user_flag
crystal_set_cell
crystal_set_image
crystal_set_mosaicity
crystal_set_num_saturated_reflections
crystal_set_osf
crystal_set_profile_radius
crystal_set_reflections
crystal_set_resolution_limit
crystal_set_user_flag
</SECTION>

<SECTION>
<FILE>geometry</FILE>
find_intersections
select_intersections
update_partialities
</SECTION>

<SECTION>
<FILE>peaks</FILE>
peak_sanity_check
search_peaks
integrate_reflections
validate_peaks
</SECTION>

<SECTION>
<FILE>render</FILE>
render_scale
</SECTION>

<SECTION>
<FILE>filter</FILE>
filter_cm
filter_noise
</SECTION>

<SECTION>
<FILE>stream</FILE>
Stream
CHUNK_END_MARKER
CHUNK_START_MARKER
CRYSTAL_END_MARKER
CRYSTAL_START_MARKER
PEAK_LIST_END_MARKER
PEAK_LIST_START_MARKER
REFLECTION_END_MARKER
REFLECTION_START_MARKER
open_stream_fd_for_write
open_stream_for_read
open_stream_for_write
close_stream
read_chunk
write_chunk
rewind_stream
is_stream
write_command
write_line
</SECTION>