diff options
| -rw-r--r-- | AUTHORS | 10 | ||||
| -rw-r--r-- | doc/reference/libcrystfel/CrystFEL-sections.txt | 10 | ||||
| -rw-r--r-- | libcrystfel/src/symmetry.c | 49 | ||||
| -rw-r--r-- | libcrystfel/src/symmetry.h | 4 |
4 files changed, 22 insertions, 51 deletions
@@ -3,6 +3,7 @@ * Kenneth Beyerlein <kenneth.beyerlein@desy.de> Peak integration improvements + General bug finding and fixing * Richard Kirian <rkirian@asu.edu> MOSFLM auto-indexing, bug fixing. @@ -21,9 +22,7 @@ * Chun Hong Yoon <chun.hong.yoon@desy.de> Speed improvements to indexamajig pattern_sim overhaul and SASE spectrum simulation - -* Kenneth Beyerlein <kenneth.beyerlein@desy.de> - General bug finding and fixing + C++ compatibility * Nadia Zatsepin <nadia.zatsepin@asu.edu> General bug finding and fixing @@ -48,3 +47,8 @@ * Valerio Mariani <<alerio.mariani@desy.de> Packaging and general bug fixing + hdfsee calibration mode + --version options + +* Parker de Waal <Parker.deWaal@vai.org> + A small (but important) bug fix diff --git a/doc/reference/libcrystfel/CrystFEL-sections.txt b/doc/reference/libcrystfel/CrystFEL-sections.txt index 82e393d9..035ab935 100644 --- a/doc/reference/libcrystfel/CrystFEL-sections.txt +++ b/doc/reference/libcrystfel/CrystFEL-sections.txt @@ -26,8 +26,6 @@ get_partial get_indices get_symmetric_indices get_intensity -get_scalable -get_refinable get_redundancy get_esd_intensity get_phase @@ -41,8 +39,6 @@ set_partiality set_lorentz set_partial set_intensity -set_scalable -set_refinable set_redundancy set_esd_intensity set_phase @@ -291,6 +287,7 @@ get_pointgroup parse_symmetry_operations add_symop get_equiv +get_symop special_position get_asymm get_ambiguities @@ -455,12 +452,14 @@ IntegrationMethod IntDiag integrate_all integrate_all_2 +integrate_all_3 integration_method </SECTION> <SECTION> <FILE>stream</FILE> Stream +StreamReadFlags CHUNK_END_MARKER CHUNK_START_MARKER CRYSTAL_END_MARKER @@ -472,11 +471,12 @@ REFLECTION_START_MARKER open_stream_fd_for_write open_stream_for_read open_stream_for_write +get_stream_fd close_stream read_chunk +read_chunk_2 write_chunk rewind_stream is_stream write_command -write_line </SECTION> diff --git a/libcrystfel/src/symmetry.c b/libcrystfel/src/symmetry.c index 14b108b7..1a4fee1e 100644 --- a/libcrystfel/src/symmetry.c +++ b/libcrystfel/src/symmetry.c @@ -8,6 +8,7 @@ * * Authors: * 2010-2014 Thomas White <taw@physics.org> + * 2014 Kenneth Beyerlein <kenneth.beyerlein@desy.de> * * This file is part of CrystFEL. * @@ -215,7 +216,7 @@ static void add_symop_v(SymOpList *ops, * contained in the symmetry operator list, and identified by the specified * index. **/ -IntegerMatrix* get_symop(const SymOpList *ops, const SymOpMask *m, int idx) +IntegerMatrix *get_symop(const SymOpList *ops, const SymOpMask *m, int idx) { const int n = num_ops(ops); @@ -255,6 +256,7 @@ IntegerMatrix* get_symop(const SymOpList *ops, const SymOpMask *m, int idx) return ops->ops[idx]; } + static signed int *v(signed int h, signed int k, signed int i, signed int l) { signed int *vec = malloc(3*sizeof(signed int)); @@ -1130,47 +1132,10 @@ void get_equiv(const SymOpList *ops, const SymOpMask *m, int idx, signed int h, signed int k, signed int l, signed int *he, signed int *ke, signed int *le) { - const int n = num_ops(ops); - - if ( m != NULL ) { - - int i, c; - - c = 0; - for ( i=0; i<n; i++ ) { - - if ( (c == idx) && m->mask[i] ) { - do_op(ops->ops[i], h, k, l, he, ke, le); - return; - } - - if ( m->mask[i] ) { - c++; - } - - } - - ERROR("Index %i out of range for point group '%s' with" - " reflection %i %i %i\n", - idx, symmetry_name(ops), h, k, l); - - *he = 0; *ke = 0; *le = 0; - - return; - - } - - if ( idx >= n ) { - - ERROR("Index %i out of range for point group '%s'\n", idx, - symmetry_name(ops)); - - *he = 0; *ke = 0; *le = 0; - return; - - } - - do_op(ops->ops[idx], h, k, l, he, ke, le); + IntegerMatrix *op; + op = get_symop(ops, m, idx); + if ( op == NULL ) return; + do_op(op, h, k, l, he, ke, le); } diff --git a/libcrystfel/src/symmetry.h b/libcrystfel/src/symmetry.h index 42cbd9b3..d7373ba2 100644 --- a/libcrystfel/src/symmetry.h +++ b/libcrystfel/src/symmetry.h @@ -8,6 +8,7 @@ * * Authors: * 2010-2014 Thomas White <taw@physics.org> + * 2014 Kenneth Beyerlein <kenneth.beyerlein@desy.de> * * This file is part of CrystFEL. * @@ -61,7 +62,6 @@ extern "C" { extern void free_symoplist(SymOpList *ops); extern SymOpList *get_pointgroup(const char *sym); -extern IntegerMatrix* get_symop(const SymOpList *ops, const SymOpMask *m, int idx); extern SymOpMask *new_symopmask(const SymOpList *list); extern void free_symopmask(SymOpMask *m); @@ -75,6 +75,8 @@ extern int num_equivs(const SymOpList *ops, const SymOpMask *m); extern void get_equiv(const SymOpList *ops, const SymOpMask *m, int idx, signed int h, signed int k, signed int l, signed int *he, signed int *ke, signed int *le); +extern IntegerMatrix *get_symop(const SymOpList *ops, const SymOpMask *m, + int idx); extern SymOpList *get_ambiguities(const SymOpList *source, const SymOpList *target); |