path: root/doc/reference/libcrystfel/CrystFEL-sections.txt

<SECTION>
<FILE>reflist</FILE>
RefList
Reflection
RefListIterator
<SUBSECTION>
reflist_new
reflist_free
reflection_new
reflection_free
reflist_add_notes
reflist_get_notes
<SUBSECTION>
add_refl
add_refl_to_list
<SUBSECTION>
first_refl
next_refl
<SUBSECTION>
find_refl
next_found_refl
<SUBSECTION>
get_detector_pos
get_panel
get_partiality
get_lorentz
get_partial
get_indices
get_symmetric_indices
get_intensity
get_redundancy
get_esd_intensity
get_phase
get_mean_bg
get_peak
get_temp1
get_temp2
get_flag
<SUBSECTION>
set_detector_pos
set_panel
set_partiality
set_lorentz
set_partial
set_intensity
set_redundancy
set_esd_intensity
set_phase
set_mean_bg
set_peak
set_symmetric_indices
set_temp1
set_temp2
set_flag
<SUBSECTION>
copy_data
num_reflections
tree_depth
lock_reflection
unlock_reflection
GET_H
GET_K
GET_L
SERIAL
</SECTION>

<SECTION>
<FILE>reflist-utils</FILE>
write_reflist
write_reflist_2
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
reflist_add_command_and_version
</SECTION>

<SECTION>
<FILE>unitcell</FILE>
UnitCell
LatticeType
UnitCellTransformation
rvec
<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_reciprocal
cell_get_centering
cell_get_lattice_type
cell_get_unique_axis
cell_has_parameters
<SUBSECTION>
cell_set_cartesian
cell_set_parameters
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
load_cell_from_file
write_cell
lattice_from_str
cell_get_volume
</SECTION>

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

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

<SECTION>
<FILE>histogram</FILE>
Histogram
histogram_init
histogram_free
histogram_add_value
histogram_show
histogram_get_data
histogram_get_max
histogram_get_min
histogram_get_num_bins
histogram_set_max
histogram_set_min
histogram_set_num_bins
</SECTION>

<SECTION>
<FILE>image</FILE>
image
beam_params
imagefeature
ImageFeatureList
SpectrumType
sample
<SUBSECTION>
imagefile
imagefile_close
imagefile_copy_fields
imagefile_field_list
imagefile_get_hdfile
imagefile_get_type
imagefile_open
imagefile_read
imagefile_read_simple
<SUBSECTION>
new_imagefile_field_list
add_imagefile_field
free_imagefile_field_list
<SUBSECTION>
image_add_feature
image_feature_closest
image_reflection_closest
image_feature_count
image_feature_list_free
image_feature_list_new
image_get_feature
image_add_crystal
image_remove_feature
free_all_crystals
remove_flagged_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_MOSFLM
INDEXING_DEFAULTS_XDS
INDEXING_DEFAULTS_ASDF
INDEXING_DEFAULTS_FELIX
INDEXING_METHOD_MASK
INDEXING_CONTROL_FLAGS
setup_indexing
cleanup_indexing
get_indm_from_string
index_pattern
index_pattern_2
indexer_str
dirax_prepare
run_dirax
dirax_cleanup
mosflm_prepare
run_mosflm
mosflm_cleanup
xds_prepare
run_xds
xds_cleanup
asdf_prepare
run_asdf
asdf_cleanup
felix_prepare
felix_index
felix_cleanup
</SECTION>

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

<SECTION>
<FILE>integer_matrix</FILE>
IntegerMatrix
<SUBSECTION>
intmat_new
intmat_copy
intmat_identity
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>
detector
panel
badregion
rigid_group
rg_collection
<SUBSECTION>
copy_geom
fill_in_adu
free_detector_geometry
get_detector_geometry
get_detector_geometry_2
write_detector_geometry
write_detector_geometry_2
panel_number
find_panel_by_name
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
mark_resolution_range_as_bad
find_orig_panel
find_orig_panel_number
panel_is_in_rigid_group
rigid_group_is_in_collection
single_panel_data_source
find_rigid_group_collection_by_name
detector_has_clen_references
adjust_centering_for_rail
</SECTION>

<SECTION>
<FILE>events</FILE>
event
event_list
dim_structure
filename_plus_event
<SUBSECTION>
initialize_event
push_path_entry_to_event
pop_path_entry_from_event
push_dim_entry_to_event
pop_dim_entry_from_event
copy_event
free_event
find_event
get_event_string
get_event_from_event_string
event_path_placeholder_subst
partial_event_substitution
retrieve_full_path
initialize_filename_plus_event
free_filename_plus_event
initialize_event_list
append_event_to_event_list
add_non_existing_event_to_event_list
copy_event_list
free_event_list
initialize_dim_structure
default_dim_structure
set_dim_structure_entry
free_dim_structure_entry
free_dim_structure
</SECTION>

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

<SECTION>
<FILE>hdf5-file</FILE>
hdf5_read
hdf5_read2
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
hdfile_get_value
copy_hdf5_field
copy_hdf5_fields
add_copy_hdf5_field
new_copy_hdf5_field_list
free_copy_hdf5_field_list
get_peaks
get_peaks_2
get_peaks_cxi
get_peaks_cxi_2
hdfile_is_scalar
check_path_existence
fill_event_list
</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_Bfac
crystal_get_profile_radius
crystal_get_reflections
crystal_get_resolution_limit
crystal_get_user_flag
crystal_get_num_implausible_reflections
crystal_get_notes
crystal_get_det_shift
crystal_set_cell
crystal_set_image
crystal_set_mosaicity
crystal_set_num_saturated_reflections
crystal_set_osf
crystal_set_Bfac
crystal_set_profile_radius
crystal_set_reflections
crystal_set_resolution_limit
crystal_set_user_flag
crystal_set_num_implausible_reflections
crystal_set_notes
crystal_add_notes
crystal_set_det_shift
</SECTION>

<SECTION>
<FILE>geometry</FILE>
PartialityModel
gparam
find_intersections
find_intersections_to_res
update_partialities
polarisation_correction
sphere_fraction
gaussian_fraction
r_gradient
x_gradient
y_gradient
</SECTION>

<SECTION>
<FILE>peaks</FILE>
peak_sanity_check
search_peaks
search_peaks_peakfinder8
make_BgMask
peakfinder8
validate_peaks
sort_peaks
</SECTION>

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

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

<SECTION>
<FILE>integration</FILE>
INTEGRATION_DEFAULTS_PROF2D
INTEGRATION_DEFAULTS_RINGS
INTEGRATION_METHOD_MASK
IntegrationMethod
IntDiag
integrate_all
integrate_all_2
integrate_all_3
integrate_all_4
integration_method
</SECTION>

<SECTION>
<FILE>stream</FILE>
Stream
StreamReadFlags
CHUNK_START_MARKER
CHUNK_END_MARKER
CRYSTAL_START_MARKER
CRYSTAL_END_MARKER
PEAK_LIST_START_MARKER
PEAK_LIST_END_MARKER
REFLECTION_START_MARKER
REFLECTION_END_MARKER
GEOM_START_MARKER
GEOM_END_MARKER
CELL_START_MARKER
CELL_END_MARKER
open_stream_fd_for_write
open_stream_for_read
open_stream_for_write
open_stream_for_write_2
open_stream_for_write_3
get_stream_fd
close_stream
read_chunk
read_chunk_2
write_chunk
write_chunk_2
rewind_stream
is_stream
write_command
write_geometry_file
stuff_from_stream
</SECTION>

<SECTION>
<FILE>predict-refine</FILE>
refine_prediction
refine_radius
</SECTION>