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authorThomas White <taw@physics.org>2015-07-20 15:52:38 +0200
committerThomas White <taw@physics.org>2015-07-21 10:18:33 +0200
commit466402c6a1b2804c168aa0da40a54842243ca60a (patch)
tree65918872bd1b3a9e4db0560dae04bdaa7522bab5 /doc
parentd75b852f52b244796c0386c4f21cf36ca5bfcf70 (diff)
Update API docs
Diffstat (limited to 'doc')
-rw-r--r--doc/reference/libcrystfel/CrystFEL-docs.sgml5
-rw-r--r--doc/reference/libcrystfel/CrystFEL-sections.txt44
2 files changed, 36 insertions, 13 deletions
diff --git a/doc/reference/libcrystfel/CrystFEL-docs.sgml b/doc/reference/libcrystfel/CrystFEL-docs.sgml
index ae0a115a..6c7baa74 100644
--- a/doc/reference/libcrystfel/CrystFEL-docs.sgml
+++ b/doc/reference/libcrystfel/CrystFEL-docs.sgml
@@ -83,6 +83,11 @@
</chapter>
<chapter>
+ <title>Prediction refinement</title>
+ <xi:include href="xml/predict-refine.xml"><xi:fallback /></xi:include>
+ </chapter>
+
+ <chapter>
<title>Integration</title>
<xi:include href="xml/integration.xml"><xi:fallback /></xi:include>
</chapter>
diff --git a/doc/reference/libcrystfel/CrystFEL-sections.txt b/doc/reference/libcrystfel/CrystFEL-sections.txt
index 7b06c2cd..f423ee82 100644
--- a/doc/reference/libcrystfel/CrystFEL-sections.txt
+++ b/doc/reference/libcrystfel/CrystFEL-sections.txt
@@ -20,6 +20,7 @@ next_found_refl
<SUBSECTION>
get_excitation_error
get_detector_pos
+get_panel
get_partiality
get_lorentz
get_partial
@@ -33,8 +34,10 @@ get_mean_bg
get_peak
get_temp1
get_temp2
+get_flag
<SUBSECTION>
set_detector_pos
+set_panel
set_partiality
set_lorentz
set_partial
@@ -47,6 +50,7 @@ set_peak
set_symmetric_indices
set_temp1
set_temp2
+set_flag
<SUBSECTION>
copy_data
num_reflections
@@ -80,6 +84,7 @@ max_intensity
UnitCell
LatticeType
UnitCellTransformation
+rvec
<SUBSECTION>
cell_new
cell_new_from_cell
@@ -135,11 +140,13 @@ forbidden_reflection
load_cell_from_pdb
load_cell_from_file
lattice_from_str
+cell_get_volume
</SECTION>
<SECTION>
<FILE>utils</FILE>
show_matrix_eqn
+solve_svd
AssplodeFlag
C_VACUO
ELECTRON_CHARGE
@@ -253,10 +260,9 @@ stat_scale_intensity
IndexingMethod
IndexingPrivate
INDEXING_DEFAULTS_DIRAX
-INDEXING_DEFAULTS_GRAINSPOTTER
INDEXING_DEFAULTS_MOSFLM
-INDEXING_DEFAULTS_REAX
INDEXING_DEFAULTS_XDS
+INDEXING_DEFAULTS_ASDF
INDEXING_METHOD_MASK
build_indexer_list
cleanup_indexing
@@ -272,12 +278,9 @@ mosflm_cleanup
xds_prepare
run_xds
xds_cleanup
-reax_prepare
-reax_index
-reax_cleanup
-grainspotter_prepare
-grainspotter_index
-grainspotter_cleanup
+asdf_prepare
+run_asdf
+asdf_cleanup
</SECTION>
<SECTION>
@@ -365,12 +368,15 @@ panel_is_in_rigid_group
rigid_group_is_in_collection
single_panel_data_source
find_rigid_group_collection_by_name
+detector_has_clen_references
</SECTION>
<SECTION>
<FILE>events</FILE>
event
event_list
+dim_structure
+filename_plus_event
<SUBSECTION>
initialize_event
push_path_entry_to_event
@@ -417,8 +423,7 @@ hdfile_open
hdfile_read_group
hdfile_set_first_image
hdfile_set_image
-get_value
-get_ev_based_value
+hdfile_get_value
copy_hdf5_field
copy_hdf5_fields
add_copy_hdf5_field
@@ -443,34 +448,41 @@ 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_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
</SECTION>
<SECTION>
<FILE>geometry</FILE>
PartialityModel
+gparam
find_intersections
find_intersections_to_res
-select_intersections
update_partialities
-update_partialities_2
polarisation_correction
sphere_fraction
gaussian_fraction
+r_gradient
+x_gradient
+y_gradient
</SECTION>
<SECTION>
@@ -534,5 +546,11 @@ rewind_stream
is_stream
write_command
write_geometry_file
-extract_f_from_stuff
+stuff_from_stream
+</SECTION>
+
+<SECTION>
+<FILE>predict-refine</FILE>
+refine_prediction
+refine_radius
</SECTION>