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authorThomas White <taw@physics.org>2015-02-16 16:40:50 +0100
committerThomas White <taw@physics.org>2015-02-16 16:41:47 +0100
commitceae2d277c9add4731cb24cf33570e988bb57c3e (patch)
treebe094470af9c309e329b38312d11e0c65243043f
parent838ab27246a6ce7c2b8bdd997136235f5e8b81b0 (diff)
Update API docs
-rw-r--r--doc/reference/libcrystfel/CrystFEL-docs.sgml5
-rw-r--r--doc/reference/libcrystfel/CrystFEL-sections.txt36
-rw-r--r--libcrystfel/src/cell-utils.c10
-rw-r--r--libcrystfel/src/detector.h1
4 files changed, 47 insertions, 5 deletions
diff --git a/doc/reference/libcrystfel/CrystFEL-docs.sgml b/doc/reference/libcrystfel/CrystFEL-docs.sgml
index 1aef3ddb..e9027306 100644
--- a/doc/reference/libcrystfel/CrystFEL-docs.sgml
+++ b/doc/reference/libcrystfel/CrystFEL-docs.sgml
@@ -43,6 +43,11 @@
</chapter>
<chapter>
+ <title>Events</title>
+ <xi:include href="xml/events.xml"/>
+ </chapter>
+
+ <chapter>
<title>Geometry of diffraction</title>
<xi:include href="xml/geometry.xml"/>
</chapter>
diff --git a/doc/reference/libcrystfel/CrystFEL-sections.txt b/doc/reference/libcrystfel/CrystFEL-sections.txt
index f3b5dc59..7b06c2cd 100644
--- a/doc/reference/libcrystfel/CrystFEL-sections.txt
+++ b/doc/reference/libcrystfel/CrystFEL-sections.txt
@@ -94,6 +94,7 @@ cell_get_reciprocal
cell_get_centering
cell_get_lattice_type
cell_get_unique_axis
+cell_has_parameters
<SUBSECTION>
cell_set_cartesian
cell_set_parameters
@@ -132,6 +133,7 @@ right_handed
str_lattice
forbidden_reflection
load_cell_from_pdb
+load_cell_from_file
lattice_from_str
</SECTION>
@@ -202,10 +204,15 @@ histogram_set_num_bins
<SECTION>
<FILE>image</FILE>
image
+beam_params
+imagefeature
ImageFeatureList
SpectrumType
+sample
+<SUBSECTION>
image_add_feature
image_feature_closest
+image_reflection_closest
image_feature_count
image_feature_list_free
image_feature_list_new
@@ -327,11 +334,18 @@ intmat_print
<SECTION>
<FILE>detector</FILE>
+detector
+panel
+badregion
+rigid_group
+rg_collection
+<SUBSECTION>
copy_geom
fill_in_values
free_detector_geometry
get_detector_geometry
write_detector_geometry
+write_detector_geometry_2
find_panel
find_panel_by_name
find_panel_number
@@ -342,15 +356,22 @@ get_q
get_q_for_panel
get_tt
smallest_q
-twod_mapping
reverse_2d_mapping
largest_q
in_bad_region
mark_resolution_range_as_bad
+find_orig_panel
+panel_is_in_rigid_group
+rigid_group_is_in_collection
+single_panel_data_source
+find_rigid_group_collection_by_name
</SECTION>
<SECTION>
<FILE>events</FILE>
+event
+event_list
+<SUBSECTION>
initialize_event
push_path_entry_to_event
pop_path_entry_from_event
@@ -358,6 +379,7 @@ 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
@@ -374,6 +396,7 @@ initialize_dim_structure
default_dim_structure
set_dim_structure_entry
free_dim_structure_entry
+free_dim_structure
</SECTION>
<SECTION>
@@ -383,6 +406,7 @@ free_dim_structure_entry
<SECTION>
<FILE>hdf5-file</FILE>
hdf5_read
+hdf5_read2
hdf5_write
hdf5_write_image
hdfile
@@ -394,13 +418,17 @@ hdfile_read_group
hdfile_set_first_image
hdfile_set_image
get_value
+get_ev_based_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_cxi
hdfile_is_scalar
+check_path_existence
+fill_event_list
</SECTION>
<SECTION>
@@ -419,6 +447,7 @@ crystal_get_profile_radius
crystal_get_reflections
crystal_get_resolution_limit
crystal_get_user_flag
+crystal_get_num_implausible_reflections
crystal_set_cell
crystal_set_image
crystal_set_mosaicity
@@ -428,16 +457,20 @@ crystal_set_profile_radius
crystal_set_reflections
crystal_set_resolution_limit
crystal_set_user_flag
+crystal_set_num_implausible_reflections
</SECTION>
<SECTION>
<FILE>geometry</FILE>
PartialityModel
find_intersections
+find_intersections_to_res
select_intersections
update_partialities
update_partialities_2
polarisation_correction
+sphere_fraction
+gaussian_fraction
</SECTION>
<SECTION>
@@ -501,4 +534,5 @@ rewind_stream
is_stream
write_command
write_geometry_file
+extract_f_from_stuff
</SECTION>
diff --git a/libcrystfel/src/cell-utils.c b/libcrystfel/src/cell-utils.c
index 95e7353e..7c7a58a6 100644
--- a/libcrystfel/src/cell-utils.c
+++ b/libcrystfel/src/cell-utils.c
@@ -3,13 +3,13 @@
*
* Unit Cell utility functions
*
- * Copyright © 2012-2014 Deutsches Elektronen-Synchrotron DESY,
+ * Copyright © 2012-2015 Deutsches Elektronen-Synchrotron DESY,
* a research centre of the Helmholtz Association.
* Copyright © 2012 Lorenzo Galli
*
* Authors:
- * 2009-2012,2014 Thomas White <taw@physics.org>
- * 2012 Lorenzo Galli
+ * 2009-2012,2014-2015 Thomas White <taw@physics.org>
+ * 2012 Lorenzo Galli
*
* This file is part of CrystFEL.
*
@@ -1090,8 +1090,9 @@ static void determine_lattice(UnitCell *cell,
/**
* load_cell_from_pdb:
+ * @filename: The filename from which to load the cell
*
- * Loads a unit cell from a PDB file.
+ * Loads a unit cell from the CRYST1 line of a PDB file.
*
* Returns: a newly allocated %UnitCell.
*
@@ -1225,6 +1226,7 @@ static int get_angle_rad(char **bits, int nbits, double *pl)
/**
* load_cell_from_file:
+ * @filename: The filename from which to load the cell
*
* Loads a unit cell from a file of any type (PDB or CrystFEL format)
*
diff --git a/libcrystfel/src/detector.h b/libcrystfel/src/detector.h
index 8f4d009c..a5a7b98a 100644
--- a/libcrystfel/src/detector.h
+++ b/libcrystfel/src/detector.h
@@ -38,6 +38,7 @@
#define DETECTOR_H
struct rigid_group;
+struct rg_collection;
struct detector;
struct panel;
struct badregion;