API Index

A

add_copy_hdf5_field, function in hdf5-file
add_non_existing_event_to_event_list, function in events
add_refl, function in RefList
add_refl_to_list, function in RefList
add_symop, function in Symmetry
append_event_to_event_list, function in events
asdf_cleanup, function in indexing
asdf_prepare, function in indexing
assplode, function in Utilities
AssplodeFlag, enum in Utilities
asymmetric_indices, function in RefList utilities

B

badregion, struct in Detector
beam_params, struct in Image
bravais_lattice, function in Unit cell utilities
build_indexer_list, function in indexing

D

default_dim_structure, function in events
describe_symmetry, function in Symmetry
detector, struct in Detector
detector_has_clen_references, function in Detector
dim_structure, struct in events
dirax_cleanup, function in indexing
dirax_prepare, function in indexing

E

ELECTRON_CHARGE, macro in Utilities
CELL_END_MARKER, macro in stream
cell_free, function in UnitCell
cell_get_cartesian, function in UnitCell
cell_get_centering, function in UnitCell
cell_get_lattice_type, function in UnitCell
cell_get_parameters, function in UnitCell
cell_get_reciprocal, function in UnitCell
cell_get_unique_axis, function in UnitCell
cell_get_volume, function in Unit cell utilities
cell_has_parameters, function in UnitCell
cell_is_sensible, function in Unit cell utilities
cell_new, function in UnitCell
cell_new_from_cell, function in UnitCell
cell_new_from_direct_axes, function in UnitCell
cell_new_from_parameters, function in UnitCell
cell_new_from_reciprocal_axes, function in UnitCell
cell_print, function in Unit cell utilities
cell_rep, function in UnitCell
cell_rotate, function in Unit cell utilities
cell_set_cartesian, function in UnitCell
cell_set_centering, function in UnitCell
cell_set_lattice_type, function in UnitCell
cell_set_parameters, function in UnitCell
cell_set_reciprocal, function in UnitCell
cell_set_unique_axis, function in UnitCell
CELL_START_MARKER, macro in stream
cell_transform, function in UnitCell
cell_transform_inverse, function in UnitCell
event, struct in events
event_list, struct in events
event_path_placeholder_subst, function in events

F

felix_cleanup, function in indexing
felix_index, function in indexing
felix_prepare, function in indexing
filename_plus_event, struct in events
fill_event_list, function in hdf5-file
fill_in_values, function in Detector
filter_cm, function in filter
filter_median, function in filter
filter_noise, function in filter
find_equiv_in_list, function in RefList utilities
find_event, function in events
find_intersections, function in geometry
find_intersections_to_res, function in geometry
find_orig_panel, function in Detector
find_orig_panel_number, function in Detector
find_panel, function in Detector
find_panel_by_name, function in Detector
find_panel_number, function in Detector
find_refl, function in RefList
find_rigid_group_collection_by_name, function in Detector
first_refl, function in RefList
flat_noise, function in Utilities
forbidden_reflection, function in Unit cell utilities
free_all_crystals, function in Image
free_copy_hdf5_field_list, function in hdf5-file
free_detector_geometry, function in Detector
free_dim_structure, function in events
free_dim_structure_entry, function in events
free_event, function in events
free_event_list, function in events
free_filename_plus_event, function in events
free_symoplist, function in Symmetry
free_symopmask, function in Symmetry

G

gaussian_fraction, function in geometry
gaussian_noise, function in Utilities
GEOM_END_MARKER, macro in stream
GEOM_START_MARKER, macro in stream
get_ambiguities, function in Symmetry
get_asymm, function in Symmetry
get_detector_geometry, function in Detector
get_detector_pos, function in RefList
get_equiv, function in Symmetry
get_esd_intensity, function in RefList
get_event_from_event_string, function in events
get_event_string, function in events
get_flag, function in RefList
GET_H, macro in RefList
get_indices, function in RefList
get_intensity, function in RefList
GET_K, macro in RefList
GET_L, macro in RefList
get_lorentz, function in RefList
get_matrix_name, function in Symmetry
get_mean_bg, function in RefList
get_panel, function in RefList
get_partial, function in RefList
get_partiality, function in RefList
get_peak, function in RefList
get_peaks, function in hdf5-file
get_peaks_cxi, function in hdf5-file
get_phase, function in RefList
get_pixel_extents, function in Detector
get_pointgroup, function in Symmetry
get_q, function in Detector
get_q_for_panel, function in Detector
get_redundancy, function in RefList
get_status_label, function in The thread pool
get_stream_fd, function in stream
get_symmetric_indices, function in RefList
get_symop, function in Symmetry
get_temp1, function in RefList
get_temp2, function in RefList
get_tt, function in Detector
gparam, enum in geometry

H

hdf5_read, function in hdf5-file
hdf5_read2, function in hdf5-file
hdf5_write, function in hdf5-file
hdf5_write_image, function in hdf5-file
hdfile, struct in hdf5-file
hdfile_close, function in hdf5-file
hdfile_get_image_binned, function in hdf5-file
hdfile_get_string_value, function in hdf5-file
hdfile_get_value, function in hdf5-file
hdfile_is_scalar, function in hdf5-file
hdfile_open, function in hdf5-file
hdfile_read_group, function in hdf5-file
hdfile_set_first_image, function in hdf5-file
hdfile_set_image, function in hdf5-file
check_list_symmetry, function in RefList utilities
check_path_existence, function in hdf5-file
Histogram, typedef in histogram
histogram_add_value, function in histogram
histogram_free, function in histogram
histogram_get_data, function in histogram
histogram_get_max, function in histogram
histogram_get_min, function in histogram
histogram_get_num_bins, function in histogram
histogram_init, function in histogram
histogram_set_max, function in histogram
histogram_set_min, function in histogram
histogram_set_num_bins, function in histogram
histogram_show, function in histogram
chomp, function in Utilities
CHUNK_END_MARKER, macro in stream
CHUNK_START_MARKER, macro in stream

I

image, struct in Image
imagefeature, struct in Image
ImageFeatureList, typedef in Image
image_add_crystal, function in Image
image_add_feature, function in Image
image_feature_closest, function in Image
image_feature_count, function in Image
image_feature_list_free, function in Image
image_feature_list_new, function in Image
image_get_feature, function in Image
image_reflection_closest, function in Image
image_remove_feature, function in Image
indexer_str, function in indexing
IndexingMethod, enum in indexing
IndexingPrivate, typedef in indexing
INDEXING_CONTROL_FLAGS, macro in indexing
INDEXING_DEFAULTS_ASDF, macro in indexing
INDEXING_DEFAULTS_DIRAX, macro in indexing
INDEXING_DEFAULTS_FELIX, macro in indexing
INDEXING_DEFAULTS_MOSFLM, macro in indexing
INDEXING_DEFAULTS_XDS, macro in indexing
INDEXING_METHOD_MASK, macro in indexing
index_pattern, function in indexing
initialize_dim_structure, function in events
initialize_event, function in events
initialize_event_list, function in events
initialize_filename_plus_event, function in events
IntDiag, enum in integration
IntegerMatrix, typedef in Integer matrices
integrate_all, function in integration
integrate_all_2, function in integration
integrate_all_3, function in integration
integrate_all_4, function in integration
IntegrationMethod, enum in integration
INTEGRATION_DEFAULTS_PROF2D, macro in integration
INTEGRATION_DEFAULTS_RINGS, macro in integration
integration_method, function in integration
INTEGRATION_METHOD_MASK, macro in integration
intmat_copy, function in Integer matrices
intmat_det, function in Integer matrices
intmat_equals, function in Integer matrices
intmat_free, function in Integer matrices
intmat_get, function in Integer matrices
intmat_identity, function in Integer matrices
intmat_intmat_mult, function in Integer matrices
intmat_intvec_mult, function in Integer matrices
intmat_inverse, function in Integer matrices
intmat_is_identity, function in Integer matrices
intmat_is_inversion, function in Integer matrices
intmat_new, function in Integer matrices
intmat_print, function in Integer matrices
intmat_set, function in Integer matrices
in_bad_region, function in Detector
is_centric, function in Symmetry
is_centrosymmetric, function in Symmetry
is_stream, function in stream
is_subgroup, function in Symmetry

L

largest_q, function in Detector
LatticeType, enum in UnitCell
lattice_from_str, function in Unit cell utilities
cleanup_indexing, function in indexing
load_cell_from_file, function in Unit cell utilities
load_cell_from_pdb, function in Unit cell utilities
lock_reflection, function in RefList
close_stream, function in stream

M

make_BgMask, function in peaks
mark_resolution_range_as_bad, function in Detector
match_cell, function in Unit cell utilities
match_cell_ab, function in Unit cell utilities
max_intensity, function in RefList utilities
mosflm_cleanup, function in indexing
mosflm_prepare, function in indexing

N

new_copy_hdf5_field_list, function in hdf5-file
new_symopmask, function in Symmetry
next_found_refl, function in RefList
next_refl, function in RefList
normalise_quaternion, function in Quaternion
notrail, function in Utilities
num_equivs, function in Symmetry
num_reflections, function in RefList

O

open_stream_fd_for_write, function in stream
open_stream_for_read, function in stream
open_stream_for_write, function in stream
open_stream_for_write_2, function in stream
open_stream_for_write_3, function in stream
copy_data, function in RefList
copy_event, function in events
copy_event_list, function in events
copy_geom, function in Detector
copy_hdf5_field, struct in hdf5-file
copy_hdf5_fields, function in hdf5-file
copy_reflist, function in RefList utilities

P

panel, struct in Detector
panel_is_in_rigid_group, function in Detector
parse_symmetry_operations, function in Symmetry
PartialityModel, enum in geometry
partial_event_substitution, function in events
PEAK_LIST_END_MARKER, macro in stream
PEAK_LIST_START_MARKER, macro in stream
peak_sanity_check, function in peaks
PLANCK, macro in Utilities
poisson_noise, function in Utilities
polarisation_correction, function in geometry
pop_dim_entry_from_event, function in events
pop_path_entry_from_event, function in events
prepare_indexing, function in indexing
progress_bar, function in Utilities
push_dim_entry_to_event, function in events
push_path_entry_to_event, function in events

Q

quaternion, struct in Quaternion
quaternion_modulus, function in Quaternion
quaternion_valid, function in Quaternion
quat_rot, function in Quaternion

R

random_flat, function in Utilities
random_quaternion, function in Quaternion
read_chunk, function in stream
read_chunk_2, function in stream
read_reflections, function in RefList utilities
read_reflections_from_file, function in RefList utilities
record_image, function in Detector
refine_prediction, function in predict-refine
refine_radius, function in predict-refine
Reflection, typedef in RefList
REFLECTION_END_MARKER, macro in stream
reflection_free, function in RefList
reflection_new, function in RefList
REFLECTION_START_MARKER, macro in stream
RefList, typedef in RefList
RefListIterator, typedef in RefList
reflist_free, function in RefList
reflist_new, function in RefList
remove_flagged_crystals, function in Image
render_scale, function in render
resolution, function in Unit cell utilities
resolution_limits, function in RefList utilities
res_cutoff, function in RefList utilities
retrieve_full_path, function in events
reverse_2d_mapping, function in Detector
rewind_stream, function in stream
rg_collection, struct in Detector
right_handed, function in Unit cell utilities
rigid_group, struct in Detector
rigid_group_is_in_collection, function in Detector
rotate_cell, function in Unit cell utilities
run_asdf, function in indexing
run_dirax, function in indexing
run_mosflm, function in indexing
run_threads, function in The thread pool
run_xds, function in indexing
rvec, struct in UnitCell
Crystal, typedef in Crystal
crystal_add_notes, function in Crystal
crystal_copy, function in Crystal
CRYSTAL_END_MARKER, macro in stream
crystal_free, function in Crystal
crystal_get_Bfac, function in Crystal
crystal_get_cell, function in Crystal
crystal_get_image, function in Crystal
crystal_get_mosaicity, function in Crystal
crystal_get_notes, function in Crystal
crystal_get_num_implausible_reflections, function in Crystal
crystal_get_num_saturated_reflections, function in Crystal
crystal_get_osf, function in Crystal
crystal_get_profile_radius, function in Crystal
crystal_get_reflections, function in Crystal
crystal_get_resolution_limit, function in Crystal
crystal_get_user_flag, function in Crystal
crystal_new, function in Crystal
crystal_set_Bfac, function in Crystal
crystal_set_cell, function in Crystal
crystal_set_image, function in Crystal
crystal_set_mosaicity, function in Crystal
crystal_set_notes, function in Crystal
crystal_set_num_implausible_reflections, function in Crystal
crystal_set_num_saturated_reflections, function in Crystal
crystal_set_osf, function in Crystal
crystal_set_profile_radius, function in Crystal
crystal_set_reflections, function in Crystal
crystal_set_resolution_limit, function in Crystal
crystal_set_user_flag, function in Crystal
CRYSTAL_START_MARKER, macro in stream
r_gradient, function in geometry

S

sample, struct in Image
search_peaks, function in peaks
SERIAL, macro in RefList
set_detector_pos, function in RefList
set_dim_structure_entry, function in events
set_esd_intensity, function in RefList
set_flag, function in RefList
set_intensity, function in RefList
set_lorentz, function in RefList
set_mean_bg, function in RefList
set_panel, function in RefList
set_partial, function in RefList
set_partiality, function in RefList
set_peak, function in RefList
set_phase, function in RefList
set_redundancy, function in RefList
set_symmetric_indices, function in RefList
set_symmetry_name, function in Symmetry
set_temp1, function in RefList
set_temp2, function in RefList
show_matrix, function in Utilities
show_matrix_eqn, function in Utilities
simple_geometry, function in Detector
single_panel_data_source, function in Detector
smallest_q, function in Detector
solve_svd, function in Utilities
sort_peaks, function in peaks
special_position, function in Symmetry
SpectrumType, enum in Image
sphere_fraction, function in geometry
stat_pearson_f_ignore, function in Statistics
stat_pearson_f_zero, function in Statistics
stat_pearson_i, function in Statistics
stat_r1_i, function in Statistics
stat_r1_ignore, function in Statistics
stat_r1_zero, function in Statistics
stat_r2, function in Statistics
stat_rdiff_ignore, function in Statistics
stat_rdiff_intensity, function in Statistics
stat_rdiff_zero, function in Statistics
stat_scale_intensity, function in Statistics
stderr_lock, variable in The thread pool
Stream, typedef in stream
StreamReadFlags, enum in stream
str_lattice, function in Unit cell utilities
stuff_from_stream, struct in stream
symmetry_name, function in Symmetry
SymOpList, typedef in Symmetry
SymOpMask, typedef in Symmetry

T

tfn_combine, function in UnitCell
tfn_free, function in UnitCell
tfn_from_intmat, function in UnitCell
tfn_identity, function in UnitCell
tfn_inverse, function in UnitCell
tfn_print, function in UnitCell
tfn_vector, function in UnitCell
THOMSON_LENGTH, macro in Utilities
TPFinalFunc, user_function in The thread pool
TPGetTaskFunc, user_function in The thread pool
TPWorkFunc, user_function in The thread pool
tree_depth, function in RefList

U

uncenter_cell, function in Unit cell utilities
UnitCell, typedef in UnitCell
UnitCellTransformation, typedef in UnitCell
unlock_reflection, function in RefList
update_partialities, function in geometry

V

C_VACUO, macro in Utilities
validate_cell, function in Unit cell utilities
validate_peaks, function in peaks

W

write_cell, function in Unit cell utilities
write_chunk, function in stream
write_command, function in stream
write_detector_geometry, function in Detector
write_detector_geometry_2, function in Detector
write_geometry_file, function in stream
write_reflections_to_file, function in RefList utilities
write_reflist, function in RefList utilities
write_reflist_2, function in RefList utilities

X

xds_cleanup, function in indexing
xds_prepare, function in indexing
x_gradient, function in geometry

Y

y_gradient, function in geometry