Use gtk-doc for libcrystfel only (not the contents of src)

1 files changed, 329 insertions, 0 deletions

diff --git a/doc/reference/libcrystfel/CrystFEL-sections.txt b/doc/reference/libcrystfel/CrystFEL-sections.txt
new file mode 100644
index 00000000..5df1f2d5
--- /dev/null
+++ b/doc/reference/libcrystfel/CrystFEL-sections.txt
@@ -0,0 +1,329 @@
+<SECTION>
+<FILE>reflist</FILE>
+RefList
+Reflection
+RefListIterator
+<SUBSECTION>
+reflist_new
+reflist_free
+reflection_new
+reflection_free
+<SUBSECTION>
+add_refl
+add_refl_to_list
+<SUBSECTION>
+first_refl
+next_refl
+<SUBSECTION>
+find_refl
+next_found_refl
+<SUBSECTION>
+get_excitation_error
+get_detector_pos
+get_partiality
+get_indices
+get_symmetric_indices
+get_intensity
+get_partial
+get_scalable
+get_refinable
+get_redundancy
+get_esd_intensity
+get_phase
+get_temp1
+get_temp2
+<SUBSECTION>
+set_detector_pos
+set_partial
+set_intensity
+set_scalable
+set_refinable
+set_redundancy
+set_esd_intensity
+set_phase
+set_symmetric_indices
+set_temp1
+set_temp2
+<SUBSECTION>
+copy_data
+num_reflections
+tree_depth
+lock_reflection
+unlock_reflection
+</SECTION>
+
+<SECTION>
+<FILE>reflist-utils</FILE>
+write_reflist
+write_reflections_to_file
+read_reflections
+read_reflections_from_file
+asymmetric_indices
+res_cutoff
+check_list_symmetry
+copy_reflist
+find_equiv_in_list
+</SECTION>
+
+<SECTION>
+<FILE>unitcell</FILE>
+UnitCell
+LatticeType
+UnitCellTransformation
+<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_pointgroup
+cell_get_reciprocal
+cell_get_centering
+cell_get_lattice_type
+cell_get_unique_axis
+<SUBSECTION>
+cell_set_cartesian
+cell_set_cartesian_a
+cell_set_cartesian_b
+cell_set_cartesian_c
+cell_set_parameters
+cell_set_pointgroup
+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
+</SECTION>
+
+<SECTION>
+<FILE>utils</FILE>
+show_matrix_eqn
+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
+smallest
+ph_en_to_lambda
+ph_lambda_to_en
+</SECTION>
+
+<SECTION>
+<FILE>quaternion</FILE>
+quaternion
+<SUBSECTION>
+quaternion_modulus
+normalise_quaternion
+random_quaternion
+quaternion_valid
+quat_rot
+</SECTION>
+
+<SECTION>
+<FILE>image</FILE>
+image
+ImageFeatureList
+image_add_feature
+image_feature_closest
+image_feature_count
+image_feature_list_free
+image_feature_list_new
+image_get_feature
+image_remove_feature
+</SECTION>
+
+<SECTION>
+<FILE>thread-pool</FILE>
+TPGetTaskFunc
+TPWorkFunc
+TPFinalFunc
+<SUBSECTION>
+run_threads
+</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
+MAX_CELL_CANDIDATES
+build_indexer_list
+cleanup_indexing
+prepare_indexing
+index_pattern
+run_dirax
+run_mosflm
+map_all_peaks
+</SECTION>
+
+<SECTION>
+<FILE>symmetry</FILE>
+SymOpList
+SymOpMask
+<SUBSECTION>
+free_symoplist
+num_equivs
+get_pointgroup
+get_equiv
+special_position
+get_asymm
+get_ambiguities
+is_subgroup
+<SUBSECTION>
+new_symopmask
+free_symopmask
+<SUBSECTION>
+describe_symmetry
+symmetry_name
+is_centrosymmetric
+</SECTION>
+
+<SECTION>
+<FILE>integer_matrix</FILE>
+IntegerMatrix
+<SUBSECTION>
+intmat_new
+intmat_copy
+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>
+copy_geom
+fill_in_values
+free_detector_geometry
+get_detector_geometry
+write_detector_geometry
+find_panel
+find_panel_by_name
+find_panel_number
+simple_geometry
+record_image
+get_pixel_extents
+get_q
+get_q_for_panel
+get_tt
+smallest_q
+reverse_2d_mapping
+largest_q
+</SECTION>
+
+<SECTION>
+<FILE>crystal</FILE>
+Crystal
+crystal_new
+crystal_free
+</SECTION>
+
+<SECTION>
+<FILE>hdf5-file</FILE>
+hdf5_read
+hdf5_write
+hdfile
+hdfile_close
+hdfile_get_image_binned
+hdfile_get_string_value
+hdfile_open
+hdfile_read_group
+hdfile_set_first_image
+hdfile_set_image
+</SECTION>
+
+<SECTION>
+<FILE>stream</FILE>
+parse_stream_flags
+read_chunk
+write_chunk
+write_stream_header
+skip_some_files
+is_stream
+get_value
+count_patterns
+</SECTION>
+
+<SECTION>
+<FILE>render</FILE>
+render_get_colour_scale
+render_panels
+render_scale
+render_tiff_fp
+render_tiff_int16
+</SECTION>