Update docs (and shake out buglets revealed along the way)

9 files changed, 148 insertions, 67 deletions

diff --git a/doc/reference/libcrystfel/CrystFEL-docs.sgml b/doc/reference/libcrystfel/CrystFEL-docs.sgml
index 4e6cc877..1c91e72f 100644
--- a/doc/reference/libcrystfel/CrystFEL-docs.sgml
+++ b/doc/reference/libcrystfel/CrystFEL-docs.sgml
@@ -43,6 +43,26 @@
   </chapter>
 
   <chapter>
+    <title>Geometry of diffraction</title>
+        <xi:include href="xml/geometry.xml"/>
+  </chapter>
+
+  <chapter>
+    <title>Beam parameters</title>
+        <xi:include href="xml/beam-params.xml"/>
+  </chapter>
+
+  <chapter>
+    <title>Peaks</title>
+        <xi:include href="xml/peaks.xml"/>
+  </chapter>
+
+  <chapter>
+    <title>Image filters</title>
+        <xi:include href="xml/filter.xml"/>
+  </chapter>
+
+  <chapter>
     <title>Statistics and R-factors</title>
         <xi:include href="xml/statistics.xml"><xi:fallback /></xi:include>
   </chapter>
diff --git a/doc/reference/libcrystfel/CrystFEL-sections.txt b/doc/reference/libcrystfel/CrystFEL-sections.txt
index 5df1f2d5..eb7ac054 100644
--- a/doc/reference/libcrystfel/CrystFEL-sections.txt
+++ b/doc/reference/libcrystfel/CrystFEL-sections.txt
@@ -63,6 +63,8 @@ res_cutoff
 check_list_symmetry
 copy_reflist
 find_equiv_in_list
+resolution_limits
+max_intensity
 </SECTION>
 
 <SECTION>
@@ -156,6 +158,10 @@ notrail
 smallest
 ph_en_to_lambda
 ph_lambda_to_en
+ph_eV_to_lambda
+ph_lambda_to_eV
+random_flat
+flat_noise
 </SECTION>
 
 <SECTION>
@@ -179,7 +185,9 @@ image_feature_count
 image_feature_list_free
 image_feature_list_new
 image_get_feature
+image_add_crystal
 image_remove_feature
+free_all_crystals
 </SECTION>
 
 <SECTION>
@@ -189,6 +197,8 @@ TPWorkFunc
 TPFinalFunc
 <SUBSECTION>
 run_threads
+stderr_lock
+get_status_label
 </SECTION>
 
 <SECTION>
@@ -210,14 +220,32 @@ stat_scale_intensity
 <FILE>indexing</FILE>
 IndexingMethod
 IndexingPrivate
-MAX_CELL_CANDIDATES
+INDEXING_DEFAULTS_DIRAX
+INDEXING_DEFAULTS_GRAINSPOTTER
+INDEXING_DEFAULTS_MOSFLM
+INDEXING_DEFAULTS_REAX
+INDEXING_DEFAULTS_XDS
+INDEXING_METHOD_MASK
 build_indexer_list
 cleanup_indexing
 prepare_indexing
 index_pattern
+indexer_str
+dirax_prepare
 run_dirax
+dirax_cleanup
+mosflm_prepare
 run_mosflm
-map_all_peaks
+mosflm_cleanup
+xds_prepare
+run_xds
+xds_cleanup
+reax_prepare
+reax_index
+reax_cleanup
+grainspotter_prepare
+grainspotter_index
+grainspotter_cleanup
 </SECTION>
 
 <SECTION>
@@ -228,6 +256,7 @@ SymOpMask
 free_symoplist
 num_equivs
 get_pointgroup
+add_symop
 get_equiv
 special_position
 get_asymm
@@ -284,6 +313,15 @@ get_tt
 smallest_q
 reverse_2d_mapping
 largest_q
+in_bad_region
+</SECTION>
+
+<SECTION>
+<FILE>beam-params</FILE>
+beam_params
+get_beam_parameters
+fill_in_beam_parameters
+free_beam_parameters
 </SECTION>
 
 <SECTION>
@@ -297,6 +335,7 @@ crystal_free
 <FILE>hdf5-file</FILE>
 hdf5_read
 hdf5_write
+hdf5_write_image
 hdfile
 hdfile_close
 hdfile_get_image_binned
@@ -305,25 +344,85 @@ hdfile_open
 hdfile_read_group
 hdfile_set_first_image
 hdfile_set_image
+get_value
+copy_hdf5_field
+copy_hdf5_fields
+add_copy_hdf5_field
+new_copy_hdf5_field_list
+free_copy_hdf5_field_list
+get_peaks
 </SECTION>
 
 <SECTION>
-<FILE>stream</FILE>
-parse_stream_flags
-read_chunk
-write_chunk
-write_stream_header
-skip_some_files
-is_stream
-get_value
-count_patterns
+<FILE>crystal</FILE>
+Crystal
+crystal_new
+crystal_free
+crystal_get_cell
+crystal_get_image
+crystal_get_mosaicity
+crystal_get_num_saturated_reflections
+crystal_get_osf
+crystal_get_profile_radius
+crystal_get_reflections
+crystal_get_resolution_limit
+crystal_get_user_flag
+crystal_set_cell
+crystal_set_image
+crystal_set_mosaicity
+crystal_set_num_saturated_reflections
+crystal_set_osf
+crystal_set_profile_radius
+crystal_set_reflections
+crystal_set_resolution_limit
+crystal_set_user_flag
+</SECTION>
+
+<SECTION>
+<FILE>geometry</FILE>
+find_intersections
+select_intersections
+update_partialities
+</SECTION>
+
+<SECTION>
+<FILE>peaks</FILE>
+peak_sanity_check
+search_peaks
+integrate_reflections
+validate_peaks
 </SECTION>
 
 <SECTION>
 <FILE>render</FILE>
-render_get_colour_scale
-render_panels
 render_scale
-render_tiff_fp
-render_tiff_int16
+</SECTION>
+
+<SECTION>
+<FILE>filter</FILE>
+filter_cm
+filter_noise
+</SECTION>
+
+<SECTION>
+<FILE>stream</FILE>
+Stream
+CHUNK_END_MARKER
+CHUNK_START_MARKER
+CRYSTAL_END_MARKER
+CRYSTAL_START_MARKER
+PEAK_LIST_END_MARKER
+PEAK_LIST_START_MARKER
+REFLECTION_END_MARKER
+REFLECTION_START_MARKER
+open_stream_fd_for_write
+open_stream_for_read
+open_stream_for_write
+close_stream
+read_chunk
+write_chunk
+rewind_stream
+is_stream
+write_command
+write_line
 </SECTION>
diff --git a/libcrystfel/Makefile.am b/libcrystfel/Makefile.am
index 5f5ff7fa..ae717e55 100644
--- a/libcrystfel/Makefile.am
+++ b/libcrystfel/Makefile.am
@@ -24,7 +24,7 @@ libcrystfel_la_include_HEADERS = src/beam-parameters.h src/hdf5-file.h \
                                  src/geometry.h src/peaks.h src/stream.h \
                                  src/render.h src/index.h src/image.h \
                                  src/filters.h src/dirax.h src/mosflm.h \
-                                 src/index-priv.h src/reax.h src/cell-utils.h \
+                                 src/reax.h src/cell-utils.h \
                                  src/integer_matrix.h src/crystal.h \
                                  src/grainspotter.h src/xds.h
 
diff --git a/libcrystfel/src/index-priv.h b/libcrystfel/src/index-priv.h
deleted file mode 100644
index 6fccee9f..00000000
--- a/libcrystfel/src/index-priv.h
+++ /dev/null
@@ -1,45 +0,0 @@
-/*
- * index-priv.h
- *
- * Indexing private data
- *
- * Copyright © 2012 Deutsches Elektronen-Synchrotron DESY,
- *                  a research centre of the Helmholtz Association.
- *
- * Authors:
- *   2010,2012 Thomas White <taw@physics.org>
- *
- * This file is part of CrystFEL.
- *
- * CrystFEL is free software: you can redistribute it and/or modify
- * it under the terms of the GNU General Public License as published by
- * the Free Software Foundation, either version 3 of the License, or
- * (at your option) any later version.
- *
- * CrystFEL is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with CrystFEL.  If not, see <http://www.gnu.org/licenses/>.
- *
- */
-
-#ifndef INDEXPRIV_H
-#define INDEXPRIV_H
-
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
-
-#include "index.h"
-
-struct _indexingprivate
-{
-	IndexingMethod indm;
-};
-
-
-#endif	/* INDEXPRIV_H */
diff --git a/libcrystfel/src/index.c b/libcrystfel/src/index.c
index 311dc2ce..bd187cf5 100644
--- a/libcrystfel/src/index.c
+++ b/libcrystfel/src/index.c
@@ -48,7 +48,6 @@
 #include "xds.h"
 #include "detector.h"
 #include "index.h"
-#include "index-priv.h"
 #include "reax.h"
 #include "grainspotter.h"
 #include "geometry.h"
diff --git a/libcrystfel/src/index.h b/libcrystfel/src/index.h
index f8f6e55b..31ee4339 100644
--- a/libcrystfel/src/index.h
+++ b/libcrystfel/src/index.h
@@ -64,6 +64,18 @@
  * @INDEXING_DIRAX: Invoke DirAx
  * @INDEXING_MOSFLM: Invoke MOSFLM
  * @INDEXING_REAX: DPS algorithm using known cell parameters
+ * @INDEXING_GRAINSPOTTER: Invoke GrainSpotter
+ * @INDEXING_XDS: Invokve XDS
+ * @INDEXING_CHECK_CELL_COMBINATIONS: Check linear combinations of unit cell
+ *   axes for agreement with given cell.
+ * @INDEXING_CHECK_CELL_AXES: Check unit cell axes for agreement with given
+ *   cell, and permute them if necessary.
+ * @INDEXING_CHECK_PEAKS: Check that the peaks can be explained by the indexing
+ *   result.
+ * @INDEXING_USE_LATTICE_TYPE: Use lattice type and centering information to
+ *   guide the indexing process.
+ * @INDEXING_USE_CELL_PARAMETERS: Use the unit cell parameters to guide the
+ *   indexingprocess.
  *
  * An enumeration of all the available indexing methods.
  **/
diff --git a/libcrystfel/src/peaks.h b/libcrystfel/src/peaks.h
index 6be728fe..f788bae5 100644
--- a/libcrystfel/src/peaks.h
+++ b/libcrystfel/src/peaks.h
@@ -50,9 +50,6 @@ extern void integrate_reflections(struct image *image,
 extern int peak_sanity_check(struct image *image, Crystal **crystals,
                              int n_cryst);
 
-extern void estimate_resolution(RefList *list, UnitCell *cell,
-                                double *min, double *max);
-
 extern void validate_peaks(struct image *image, double min_snr,
                            int ir_inn, int ir_mid, int ir_out,
                            int use_saturated);
diff --git a/libcrystfel/src/reax.c b/libcrystfel/src/reax.c
index 3460a4f2..4ecb870b 100644
--- a/libcrystfel/src/reax.c
+++ b/libcrystfel/src/reax.c
@@ -48,7 +48,6 @@
 #include "cell.h"
 #include "cell-utils.h"
 #include "index.h"
-#include "index-priv.h"
 
 
 /* Minimum number of standard deviations above the mean a peak must be in the
diff --git a/libcrystfel/src/symmetry.h b/libcrystfel/src/symmetry.h
index 4a8f98d3..7c80522a 100644
--- a/libcrystfel/src/symmetry.h
+++ b/libcrystfel/src/symmetry.h
@@ -79,6 +79,6 @@ extern int is_centrosymmetric(const SymOpList *s);
 extern const char *symmetry_name(const SymOpList *ops);
 extern void describe_symmetry(const SymOpList *s);
 
-extern void add_symop(SymOpList *s, IntegerMatrix *m);
+extern void add_symop(SymOpList *ops, IntegerMatrix *m);
 
 #endif	/* SYMMETRY_H */