diff options
Diffstat (limited to 'libcrystfel/src/index.c')
| -rw-r--r-- | libcrystfel/src/index.c | 127 |
1 files changed, 112 insertions, 15 deletions
diff --git a/libcrystfel/src/index.c b/libcrystfel/src/index.c index 28f33388..f65265ae 100644 --- a/libcrystfel/src/index.c +++ b/libcrystfel/src/index.c @@ -65,20 +65,26 @@ IndexingPrivate **prepare_indexing(IndexingMethod *indm, UnitCell *cell, for ( n=0; n<nm; n++ ) { + int i; + IndexingMethod in; + + in = indm[n]; + switch ( indm[n] & INDEXING_METHOD_MASK ) { case INDEXING_DIRAX : - iprivs[n] = dirax_prepare(indm[n], cell, filename, det, + iprivs[n] = dirax_prepare(&indm[n], cell, filename, det, beam, ltl); break; case INDEXING_MOSFLM : - iprivs[n] = mosflm_prepare(indm[n], cell, filename, det, + iprivs[n] = mosflm_prepare(&indm[n], cell, filename, det, beam, ltl); break; case INDEXING_REAX : - iprivs[n] = reax_prepare(cell, filename, det, beam); + iprivs[n] = reax_prepare(&indm[n], cell, filename, det, + beam, ltl); break; default : @@ -90,6 +96,25 @@ IndexingPrivate **prepare_indexing(IndexingMethod *indm, UnitCell *cell, if ( iprivs[n] == NULL ) return NULL; + STATUS("Prepared indexing method %i: %s\n", + n, indexer_str(indm[n])); + + if ( in != indm[n] ) { + ERROR("Note: flags were altered to take into account " + "the limitations of the indexing method.\n"); + } + + for ( i=0; i<n; i++ ) { + if ( indm[i] == indm[n] ) { + ERROR("Duplicate indexing method.\n"); + ERROR("Have you specified some flags which " + "aren't accepted by one of your " + "chosen indexing methods?\n"); + return NULL; + } + } + + } iprivs[n] = NULL; @@ -160,7 +185,7 @@ void map_all_peaks(struct image *image) /* Return non-zero for "success" */ static int try_indexer(struct image *image, IndexingMethod indm, - IndexingPrivate *ipriv) + IndexingPrivate *ipriv) { switch ( indm & INDEXING_METHOD_MASK ) { @@ -206,14 +231,8 @@ void index_pattern(struct image *image, n++; } -} - -/* Set the default indexer flags. May need tweaking depending on the method */ -static IndexingMethod defaults(IndexingMethod a) -{ - return a | INDEXING_CHECK_CELL_COMBINATIONS | INDEXING_CHECK_PEAKS - | INDEXING_USE_LATTICE_TYPE; + image->indexed_by = indms[n]; } @@ -242,6 +261,14 @@ static IndexingMethod set_axes(IndexingMethod a) } +/* Set the indexer flags for "combination mode" ("--cell-reduction=reduce") */ +static IndexingMethod set_comb(IndexingMethod a) +{ + return (a & ~INDEXING_CHECK_CELL_AXES) + | INDEXING_CHECK_CELL_COMBINATIONS; +} + + /* Set the indexer flags for "use no lattice type information" */ static IndexingMethod set_nolattice(IndexingMethod a) { @@ -249,6 +276,71 @@ static IndexingMethod set_nolattice(IndexingMethod a) } +/* Set the indexer flags for "use lattice type information" */ +static IndexingMethod set_lattice(IndexingMethod a) +{ + return a | INDEXING_USE_LATTICE_TYPE; +} + + +char *indexer_str(IndexingMethod indm) +{ + char *str; + + str = malloc(32); + if ( str == NULL ) { + ERROR("Failed to allocate string.\n"); + return NULL; + } + str[0] = '\0'; + + switch ( indm & INDEXING_METHOD_MASK ) { + + case INDEXING_NONE : + strcpy(str, "none"); + return str; + + case INDEXING_DIRAX : + strcpy(str, "dirax"); + break; + + case INDEXING_MOSFLM : + strcpy(str, "mosflm"); + break; + + case INDEXING_REAX : + strcpy(str, "reax"); + break; + + default : + ERROR("Unrecognised indexing method %i\n", indm); + strcpy(str, "(unknown)"); + break; + + } + + if ( indm & INDEXING_CHECK_CELL_COMBINATIONS ) { + strcat(str, "-comb"); + } else if ( indm & INDEXING_CHECK_CELL_AXES ) { + strcat(str, "-axes"); + } else { + strcat(str, "-raw"); + } + + if ( !(indm & INDEXING_CHECK_PEAKS) ) { + strcat(str, "-bad"); + } + + if ( indm & INDEXING_USE_LATTICE_TYPE ) { + strcat(str, "-latt"); + } else { + strcat(str, "-nolatt"); + } + + return str; +} + + IndexingMethod *build_indexer_list(const char *str) { int n, i; @@ -263,14 +355,13 @@ IndexingMethod *build_indexer_list(const char *str) for ( i=0; i<n; i++ ) { if ( strcmp(methods[i], "dirax") == 0) { - list[++nmeth] = defaults(INDEXING_DIRAX); + list[++nmeth] = INDEXING_DEFAULTS_DIRAX; } else if ( strcmp(methods[i], "mosflm") == 0) { - list[++nmeth] = defaults(INDEXING_MOSFLM); + list[++nmeth] = INDEXING_DEFAULTS_MOSFLM; } else if ( strcmp(methods[i], "reax") == 0) { - /* ReAx doesn't need any cell check */ - list[++nmeth] = set_raw(defaults(INDEXING_REAX)); + list[++nmeth] = INDEXING_DEFAULTS_REAX; } else if ( strcmp(methods[i], "none") == 0) { list[++nmeth] = INDEXING_NONE; @@ -282,9 +373,15 @@ IndexingMethod *build_indexer_list(const char *str) } else if ( strcmp(methods[i], "bad") == 0) { list[nmeth] = set_bad(list[nmeth]); + } else if ( strcmp(methods[i], "comb") == 0) { + list[nmeth] = set_comb(list[nmeth]); /* Default */ + } else if ( strcmp(methods[i], "axes") == 0) { list[nmeth] = set_axes(list[nmeth]); + } else if ( strcmp(methods[i], "latt") == 0) { + list[nmeth] = set_lattice(list[nmeth]); + } else if ( strcmp(methods[i], "nolatt") == 0) { list[nmeth] = set_nolattice(list[nmeth]); |