diff options
| -rw-r--r-- | libcrystfel/src/dirax.c | 2 | ||||
| -rw-r--r-- | libcrystfel/src/image.h | 14 | ||||
| -rw-r--r-- | libcrystfel/src/mosflm.c | 1 | ||||
| -rw-r--r-- | libcrystfel/src/reax.c | 8 | ||||
| -rw-r--r-- | src/im-sandbox.c | 9 | ||||
| -rw-r--r-- | src/indexamajig.c | 3 |
6 files changed, 17 insertions, 20 deletions
diff --git a/libcrystfel/src/dirax.c b/libcrystfel/src/dirax.c index 2cbb0ec1..414e6406 100644 --- a/libcrystfel/src/dirax.c +++ b/libcrystfel/src/dirax.c @@ -91,7 +91,7 @@ struct dirax_data { int read_cell; int best_acl; int best_acl_nh; - int acls_tried[MAX_CELL_CANDIDATES]; + int acls_tried[MAX_DIRAX_CELL_CANDIDATES]; int n_acls_tried; UnitCell *cur_cell; int done; diff --git a/libcrystfel/src/image.h b/libcrystfel/src/image.h index 67fc9c49..8f9e296f 100644 --- a/libcrystfel/src/image.h +++ b/libcrystfel/src/image.h @@ -44,9 +44,6 @@ #include "crystal.h" -#define MAX_CELL_CANDIDATES (32) - - /* Structure describing a feature in an image */ struct imagefeature { @@ -112,14 +109,9 @@ typedef struct _imagefeaturelist ImageFeatureList; * by-product of the scattering vector calculation and can be used later for * calculating intensities from differential scattering cross sections. * - * <structfield>candidate_cells</structfield> is an array of unit cells directly - * returned by the low-level indexing system. <structfield>ncells</structfield> - * is the number of candidate unit cells which were found. The maximum number - * of cells which may be returned is <function>MAX_CELL_CANDIDATES</function>. - * <structfield>indexed_cell</structfield> contains the "correct" unit cell - * after cell reduction or matching has been performed. The job of the cell - * reduction is to convert the list of candidate cells into a single indexed - * cell, or <function>NULL</function> on failure. + * <structfield>crystals</structfield> is an array of %Crystal directly + * returned by the low-level indexing system. <structfield>n_crystals</structfield> + * is the number of crystals which were found in the image. * * <structfield>copyme</structfield> represents a list of HDF5 fields to copy * to the output stream. diff --git a/libcrystfel/src/mosflm.c b/libcrystfel/src/mosflm.c index d1d3c134..4f7b0c3c 100644 --- a/libcrystfel/src/mosflm.c +++ b/libcrystfel/src/mosflm.c @@ -643,6 +643,7 @@ int run_mosflm(struct image *image, IndexingPrivate *ipriv) mosflm->done = 0; mosflm->success = 0; + rval = 0; do { fd_set fds; diff --git a/libcrystfel/src/reax.c b/libcrystfel/src/reax.c index b144e266..4717dcb4 100644 --- a/libcrystfel/src/reax.c +++ b/libcrystfel/src/reax.c @@ -65,6 +65,9 @@ #define MAX_CANDIDATES (1024) +/* Choose the best solution from this many candidate cells */ +#define MAX_REAX_CELL_CANDIDATES (32) + struct dvec { double x; @@ -907,7 +910,7 @@ static void add_cell_candidate(struct cell_candidate_list *cl, UnitCell *cnew, } - if ( cl->n_cand >= MAX_CELL_CANDIDATES ) { + if ( cl->n_cand >= MAX_REAX_CELL_CANDIDATES ) { /* "cshift" just fell off the end of the list */ } else { cl->cand[cl->n_cand++] = cshift; @@ -953,7 +956,8 @@ static void assemble_cells_from_candidates(struct image *image, signed int ti, tj, tk; struct cell_candidate_list cl; - cl.cand = calloc(MAX_CELL_CANDIDATES, sizeof(struct cell_candidate)); + cl.cand = calloc(MAX_REAX_CELL_CANDIDATES, + sizeof(struct cell_candidate)); if ( cl.cand == NULL ) { ERROR("Failed to allocate cell candidate list.\n"); return; diff --git a/src/im-sandbox.c b/src/im-sandbox.c index f14d5a11..17dc3dc6 100644 --- a/src/im-sandbox.c +++ b/src/im-sandbox.c @@ -955,11 +955,10 @@ void create_sandbox(struct index_args *iargs, int n_proc, char *prefix, tNow = get_monotonic_seconds(); if ( tNow >= sb->t_last_stats+STATS_EVERY_N_SECONDS ) { - STATUS("%i images processed so far, " - "%i had at least one indexable crystal." - "%i crystals found so far." - "%i images processed since the last message\n", - sb->n_processed, sb->n_hadcrystals, + STATUS("%4i indexable out of %4i processed, " + "%4i crystals so far. " + "%4i images processed since the last message.\n", + sb->n_hadcrystals, sb->n_processed, sb->n_crystals, sb->n_processed - sb->n_processed_last_stats); diff --git a/src/indexamajig.c b/src/indexamajig.c index d36b2811..97fb1743 100644 --- a/src/indexamajig.c +++ b/src/indexamajig.c @@ -98,7 +98,7 @@ static void show_help(const char *s) " Default: /processing/hitfinder/peakinfo\n" "\n\n" "For more control over the process, you might need:\n\n" -" --tolerance=<tol> Set the tolerances for cell reduction.\n" +" --tolerance=<tol> Set the tolerances for cell comparison.\n" " Default: 5,5,5,1.5.\n" " --filter-cm Perform common-mode noise subtraction on images\n" " before proceeding. Intensities will be extracted\n" @@ -515,6 +515,7 @@ int main(int argc, char *argv[]) return 1; } free(pdb); + STATUS("This is what I understood your unit cell to be:\n"); cell_print(cell); } else { STATUS("No unit cell given.\n"); |