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-rw-r--r--doc/reference/libcrystfel/CrystFEL-sections.txt61
1 files changed, 42 insertions, 19 deletions
diff --git a/doc/reference/libcrystfel/CrystFEL-sections.txt b/doc/reference/libcrystfel/CrystFEL-sections.txt
index d58c5725..3968dd5d 100644
--- a/doc/reference/libcrystfel/CrystFEL-sections.txt
+++ b/doc/reference/libcrystfel/CrystFEL-sections.txt
@@ -8,6 +8,8 @@ reflist_new
reflist_free
reflection_new
reflection_free
+reflist_add_notes
+reflist_get_notes
<SUBSECTION>
add_refl
add_refl_to_list
@@ -18,7 +20,6 @@ next_refl
find_refl
next_found_refl
<SUBSECTION>
-get_excitation_error
get_detector_pos
get_panel
get_partiality
@@ -77,6 +78,7 @@ copy_reflist
find_equiv_in_list
resolution_limits
max_intensity
+reflist_add_command_and_version
</SECTION>
<SECTION>
@@ -151,32 +153,32 @@ solve_svd
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
+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
-random_flat
-flat_noise
-show_matrix
likely
unlikely
UNUSED
@@ -218,6 +220,20 @@ 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
@@ -268,10 +284,11 @@ INDEXING_DEFAULTS_ASDF
INDEXING_DEFAULTS_FELIX
INDEXING_METHOD_MASK
INDEXING_CONTROL_FLAGS
-build_indexer_list
+setup_indexing
cleanup_indexing
-prepare_indexing
+get_indm_from_string
index_pattern
+index_pattern_2
indexer_str
dirax_prepare
run_dirax
@@ -314,6 +331,7 @@ describe_symmetry
symmetry_name
set_symmetry_name
get_matrix_name
+pointgroup_warning
is_centrosymmetric
is_centric
</SECTION>
@@ -351,15 +369,14 @@ rigid_group
rg_collection
<SUBSECTION>
copy_geom
-fill_in_values
+fill_in_adu
free_detector_geometry
get_detector_geometry
get_detector_geometry_2
write_detector_geometry
write_detector_geometry_2
-find_panel
+panel_number
find_panel_by_name
-find_panel_number
simple_geometry
record_image
get_pixel_extents
@@ -378,6 +395,7 @@ 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>
@@ -466,6 +484,7 @@ 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
@@ -479,6 +498,7 @@ crystal_set_user_flag
crystal_set_num_implausible_reflections
crystal_set_notes
crystal_add_notes
+crystal_set_det_shift
</SECTION>
<SECTION>
@@ -500,7 +520,9 @@ y_gradient
<FILE>peaks</FILE>
peak_sanity_check
search_peaks
+search_peaks_peakfinder8
make_BgMask
+peakfinder8
validate_peaks
sort_peaks
</SECTION>
@@ -557,6 +579,7 @@ close_stream
read_chunk
read_chunk_2
write_chunk
+write_chunk_2
rewind_stream
is_stream
write_command