From 5fa1c22d6bbeff12c2509e1222090a43a994f7a9 Mon Sep 17 00:00:00 2001 From: Thomas White Date: Fri, 1 Mar 2013 14:50:30 +0100 Subject: Update docs (and shake out buglets revealed along the way) --- doc/reference/libcrystfel/CrystFEL-docs.sgml | 20 ++++ doc/reference/libcrystfel/CrystFEL-sections.txt | 129 +++++++++++++++++++++--- libcrystfel/Makefile.am | 2 +- libcrystfel/src/index-priv.h | 45 --------- libcrystfel/src/index.c | 1 - libcrystfel/src/index.h | 12 +++ libcrystfel/src/peaks.h | 3 - libcrystfel/src/reax.c | 1 - libcrystfel/src/symmetry.h | 2 +- 9 files changed, 148 insertions(+), 67 deletions(-) delete mode 100644 libcrystfel/src/index-priv.h 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 @@ -42,6 +42,26 @@ + + Geometry of diffraction + + + + + Beam parameters + + + + + Peaks + + + + + Image filters + + + Statistics and R-factors 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
@@ -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
@@ -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
@@ -189,6 +197,8 @@ TPWorkFunc TPFinalFunc run_threads +stderr_lock +get_status_label
@@ -210,14 +220,32 @@ stat_scale_intensity indexing 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
@@ -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 +
+ +
+beam-params +beam_params +get_beam_parameters +fill_in_beam_parameters +free_beam_parameters
@@ -297,6 +335,7 @@ crystal_free hdf5-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
-stream -parse_stream_flags -read_chunk -write_chunk -write_stream_header -skip_some_files -is_stream -get_value -count_patterns +crystal +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 +
+ +
+geometry +find_intersections +select_intersections +update_partialities +
+ +
+peaks +peak_sanity_check +search_peaks +integrate_reflections +validate_peaks
render -render_get_colour_scale -render_panels render_scale -render_tiff_fp -render_tiff_int16 +
+ +
+filter +filter_cm +filter_noise +
+ +
+stream +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
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 - * - * 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 . - * - */ - -#ifndef INDEXPRIV_H -#define INDEXPRIV_H - -#ifdef HAVE_CONFIG_H -#include -#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 */ -- cgit v1.2.3