CrystFEL Reference Manual
A
|
B
|
D
|
E
|
F
|
G
|
H
|
I
|
J
|
L
|
M
|
N
|
O
|
P
|
Q
|
R
|
S
|
T
|
U
|
V
|
W
|
X
API Index
A
add_copy_hdf5_field
, function in
hdf5-file
add_refl
, function in
RefList
add_refl_to_list
, function in
RefList
add_symop
, function in
Symmetry
assplode
, function in
Utilities
AssplodeFlag
, enum in
Utilities
asymmetric_indices
, function in
RefList utilities
B
beam_params
, struct in
beam-params
biggest
, macro in
Utilities
bravais_lattice
, function in
Unit cell utilities
build_indexer_list
, function in
indexing
D
deg2rad
, macro in
Utilities
describe_symmetry
, function in
Symmetry
dirax_cleanup
, function in
indexing
dirax_prepare
, function in
indexing
E
ELECTRON_CHARGE
, macro in
Utilities
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_pointgroup
, function in
UnitCell
cell_get_reciprocal
, function in
UnitCell
cell_get_unique_axis
, 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_cartesian_a
, function in
UnitCell
cell_set_cartesian_b
, function in
UnitCell
cell_set_cartesian_c
, function in
UnitCell
cell_set_centering
, function in
UnitCell
cell_set_lattice_type
, function in
UnitCell
cell_set_parameters
, function in
UnitCell
cell_set_pointgroup
, function in
UnitCell
cell_set_reciprocal
, function in
UnitCell
cell_set_unique_axis
, function in
UnitCell
cell_transform
, function in
UnitCell
cell_transform_inverse
, function in
UnitCell
ERROR
, macro in
Utilities
eV_to_J
, macro in
Utilities
F
fill_in_beam_parameters
, function in
beam-params
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_intersections
, function in
geometry
find_panel
, function in
Detector
find_panel_by_name
, function in
Detector
find_panel_number
, function in
Detector
find_refl
, function in
RefList
first_refl
, function in
RefList
flat_noise
, function in
Utilities
forbidden_reflection
, function in
Unit cell utilities
free_all_crystals
, function in
Image
free_beam_parameters
, function in
beam-params
free_copy_hdf5_field_list
, function in
hdf5-file
free_detector_geometry
, function in
Detector
free_symoplist
, function in
Symmetry
free_symopmask
, function in
Symmetry
G
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_beam_parameters
, function in
beam-params
get_detector_geometry
, function in
Detector
get_detector_pos
, function in
RefList
get_equiv
, function in
Symmetry
get_esd_intensity
, function in
RefList
get_excitation_error
, 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_partial
, function in
RefList
get_partiality
, function in
RefList
get_peak
, function in
RefList
get_peaks
, 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
get_value
, function in
hdf5-file
grainspotter_cleanup
, function in
indexing
grainspotter_index
, function in
indexing
grainspotter_prepare
, function in
indexing
H
hdf5_read
, 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_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_prefix
, function in
Utilities
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
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_remove_feature
, function in
Image
indexer_str
, function in
indexing
IndexingMethod
, enum in
indexing
IndexingPrivate
, typedef in
indexing
INDEXING_DEFAULTS_DIRAX
, macro in
indexing
INDEXING_DEFAULTS_GRAINSPOTTER
, macro in
indexing
INDEXING_DEFAULTS_MOSFLM
, macro in
indexing
INDEXING_DEFAULTS_REAX
, macro in
indexing
INDEXING_DEFAULTS_XDS
, macro in
indexing
INDEXING_METHOD_MASK
, macro in
indexing
index_pattern
, function in
indexing
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_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_odd
, macro in
Utilities
is_stream
, function in
stream
is_subgroup
, function in
Symmetry
J
J_to_eV
, macro in
Utilities
L
largest_q
, function in
Detector
LatticeType
, enum in
UnitCell
lattice_from_str
, function in
Unit cell utilities
cleanup_indexing
, function in
indexing
likely
, macro in
Utilities
load_cell_from_pdb
, function in
Unit cell utilities
lock_reflection
, function in
RefList
LORENTZ_SCALE
, macro in
geometry
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
copy_data
, function in
RefList
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
parse_symmetry_operations
, function in
Symmetry
PartialityModel
, enum in
geometry
PEAK_LIST_END_MARKER
, macro in
stream
PEAK_LIST_START_MARKER
, macro in
stream
peak_sanity_check
, function in
peaks
ph_en_to_lambda
, macro in
Utilities
ph_eV_to_lambda
, macro in
Utilities
ph_lambda_to_en
, macro in
Utilities
ph_lambda_to_eV
, macro in
Utilities
PLANCK
, macro in
Utilities
poisson_noise
, function in
Utilities
polarisation_correction
, function in
geometry
prepare_indexing
, function in
indexing
progress_bar
, function in
Utilities
Q
quaternion
, struct in
Quaternion
quaternion_modulus
, function in
Quaternion
quaternion_valid
, function in
Quaternion
quat_rot
, function in
Quaternion
R
rad2deg
, macro in
Utilities
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
reax_cleanup
, function in
indexing
reax_index
, function in
indexing
reax_prepare
, function in
indexing
record_image
, function in
Detector
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
render_scale
, function in
render
resolution
, function in
Unit cell utilities
resolution_limits
, function in
RefList utilities
res_cutoff
, function in
RefList utilities
reverse_2d_mapping
, function in
Detector
rewind_stream
, function in
stream
right_handed
, function in
Unit cell utilities
rotate_cell
, function in
Unit cell utilities
run_dirax
, function in
indexing
run_mosflm
, function in
indexing
run_threads
, function in
The thread pool
run_xds
, function in
indexing
Crystal
, typedef in
Crystal
crystal_copy
, function in
Crystal
CRYSTAL_END_MARKER
, macro in
stream
crystal_free
, function in
Crystal
crystal_get_cell
, function in
Crystal
crystal_get_image
, function in
Crystal
crystal_get_mosaicity
, 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_cell
, function in
Crystal
crystal_set_image
, function in
Crystal
crystal_set_mosaicity
, 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
S
safe_basename
, function in
Utilities
search_peaks
, function in
peaks
select_intersections
, function in
geometry
SERIAL
, macro in
RefList
set_detector_pos
, function in
RefList
set_esd_intensity
, function in
RefList
set_intensity
, function in
RefList
set_lorentz
, function in
RefList
set_mean_bg
, 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
smallest
, macro in
Utilities
smallest_q
, function in
Detector
special_position
, function in
Symmetry
SpectrumType
, enum in
Image
STATUS
, macro in
Utilities
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
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
twod_mapping
, function in
Detector
U
uncenter_cell
, function in
Unit cell utilities
UnitCell
, typedef in
UnitCell
UnitCellTransformation
, typedef in
UnitCell
unlikely
, macro in
Utilities
unlock_reflection
, function in
RefList
UNUSED
, macro in
Utilities
update_partialities
, function in
geometry
update_partialities_2
, function in
geometry
V
C_VACUO
, macro in
Utilities
validate_cell
, function in
Unit cell utilities
validate_peaks
, function in
peaks
W
write_chunk
, function in
stream
write_command
, function in
stream
write_detector_geometry
, 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