diff options
| -rw-r--r-- | libcrystfel/src/cell.c | 7 | ||||
| -rw-r--r-- | libcrystfel/src/cell.h | 2 | ||||
| -rw-r--r-- | libcrystfel/src/index.c | 6 | ||||
| -rw-r--r-- | libcrystfel/src/index.h | 2 | ||||
| -rw-r--r-- | src/indexamajig.c | 26 |
5 files changed, 33 insertions, 10 deletions
diff --git a/libcrystfel/src/cell.c b/libcrystfel/src/cell.c index c31697bc..a6df931b 100644 --- a/libcrystfel/src/cell.c +++ b/libcrystfel/src/cell.c @@ -669,7 +669,7 @@ static int same_vector(struct cvec a, struct cvec b) /* Attempt to make 'cell' fit into 'template' somehow */ UnitCell *match_cell(UnitCell *cell, UnitCell *template, int verbose, - int reduce) + float *tols, int reduce) { signed int n1l, n2l, n3l; double asx, asy, asz; @@ -683,8 +683,7 @@ UnitCell *match_cell(UnitCell *cell, UnitCell *template, int verbose, float best_fom = +999999999.9; /* Large number.. */ int ncand[3] = {0,0,0}; signed int ilow, ihigh; - float ltl = 5.0; /* percent */ - float angtol = deg2rad(1.5); + float angtol = deg2rad(tols[3]); if ( cell_get_reciprocal(template, &asx, &asy, &asz, &bsx, &bsy, &bsz, @@ -753,7 +752,7 @@ UnitCell *match_cell(UnitCell *cell, UnitCell *template, int verbose, /* Test modulus for agreement with moduli of template */ for ( i=0; i<3; i++ ) { - if ( !within_tolerance(lengths[i], tlen, ltl) ) + if ( !within_tolerance(lengths[i], tlen, tols[i]) ) continue; cand[i][ncand[i]].vec.u = tx; diff --git a/libcrystfel/src/cell.h b/libcrystfel/src/cell.h index 72c0b6df..e69ce721 100644 --- a/libcrystfel/src/cell.h +++ b/libcrystfel/src/cell.h @@ -96,7 +96,7 @@ extern UnitCell *rotate_cell(UnitCell *in, double omega, double phi, extern void cell_print(UnitCell *cell); extern UnitCell *match_cell(UnitCell *cell, UnitCell *tempcell, int verbose, - int reduce); + float *ltl, int reduce); extern UnitCell *match_cell_ab(UnitCell *cell, UnitCell *tempcell); diff --git a/libcrystfel/src/index.c b/libcrystfel/src/index.c index 34a5dda3..56b34baa 100644 --- a/libcrystfel/src/index.c +++ b/libcrystfel/src/index.c @@ -139,7 +139,7 @@ void map_all_peaks(struct image *image) void index_pattern(struct image *image, UnitCell *cell, IndexingMethod *indm, int cellr, int verbose, IndexingPrivate **ipriv, - int config_insane) + int config_insane, float *ltl) { int i; int n = 0; @@ -191,10 +191,10 @@ void index_pattern(struct image *image, UnitCell *cell, IndexingMethod *indm, new_cell = cell_new_from_cell(cand); break; case CELLR_REDUCE : - new_cell = match_cell(cand, cell, verbose, 1); + new_cell = match_cell(cand, cell, verbose, ltl, 1); break; case CELLR_COMPARE : - new_cell = match_cell(cand, cell, verbose, 0); + new_cell = match_cell(cand, cell, verbose, ltl, 0); break; case CELLR_COMPARE_AB : new_cell = match_cell_ab(cand, cell); diff --git a/libcrystfel/src/index.h b/libcrystfel/src/index.h index 9d4b69bd..1457e93f 100644 --- a/libcrystfel/src/index.h +++ b/libcrystfel/src/index.h @@ -54,7 +54,7 @@ extern void map_all_peaks(struct image *image); extern void index_pattern(struct image *image, UnitCell *cell, IndexingMethod *indm, int cellr, int verbose, - IndexingPrivate **priv, int config_insane); + IndexingPrivate **priv, int config_insane, float *ltl); extern void cleanup_indexing(IndexingPrivate **priv); diff --git a/src/indexamajig.c b/src/indexamajig.c index 7feb3968..6f3704bc 100644 --- a/src/indexamajig.c +++ b/src/indexamajig.c @@ -75,6 +75,7 @@ struct static_index_args IndexingPrivate **ipriv; int peaks; /* Peak detection method */ int cellr; + float tols[4]; struct beam_params *beam; const char *element; const char *hdf5_peak_path; @@ -171,6 +172,9 @@ static void show_help(const char *s) " compare : match by at most changing the order of\n" " the indices.\n" " compare_ab : compare 'a' and 'b' lengths only.\n" +" --tolerance=<a,b,c,angl> Set the tolerance for a,b,c axis (in %%)\n" +" and for the angles (in deg) when reducing\n" +" or comparing (default is 5%% and 1.5deg)\n" " --filter-cm Perform common-mode noise subtraction on images\n" " before proceeding. Intensities will be extracted\n" " from the image as it is after this processing.\n" @@ -354,7 +358,7 @@ static void process_image(void *pp, int cookie) image.profile_radius = 0.0001e9; index_pattern(&image, cell, indm, pargs->static_args.cellr, config_verbose, pargs->static_args.ipriv, - pargs->static_args.config_insane); + pargs->static_args.config_insane, pargs->static_args.tols); if ( image.indexed_cell != NULL ) { @@ -555,6 +559,8 @@ int main(int argc, char *argv[]) char *prefix = NULL; char *speaks = NULL; char *scellr = NULL; + char *toler = NULL; + float tols[4] = {5.0, 5.0, 5.0, 1.5}; /* for a,b,c in % and for the angles in deg */ int cellr; int peaks; int nthreads = 1; @@ -587,6 +593,7 @@ int main(int argc, char *argv[]) {"no-index", 0, &config_noindex, 1}, {"peaks", 1, NULL, 2}, {"cell-reduction", 1, NULL, 3}, + {"tolerance", 1, NULL, 13}, {"indexing", 1, NULL, 'z'}, {"geometry", 1, NULL, 'g'}, {"beam", 1, NULL, 'b'}, @@ -676,6 +683,10 @@ int main(int argc, char *argv[]) scellr = strdup(optarg); break; + case 13 : + toler = strdup(optarg); + break; + case 4 : min_gradient = strtof(optarg, NULL); break; @@ -868,6 +879,15 @@ int main(int argc, char *argv[]) /* No indexing -> no reduction */ if ( indm == NULL ) reduction_needs_cell = 0; + if ( toler != NULL ) { + int ttt; + ttt = sscanf(toler, "%f,%f,%f,%f", &tols[0], &tols[1], &tols[2], &tols[3] ); + if ( ttt != 4 ) { + ERROR("Invalid parameters for '--tolerance'\n"); + return 1; + } + } + if ( geometry == NULL ) { ERROR("You need to specify a geometry file with --geometry\n"); return 1; @@ -944,6 +964,10 @@ int main(int argc, char *argv[]) qargs.static_args.config_insane = config_insane; qargs.static_args.config_bgsub = config_bgsub; qargs.static_args.cellr = cellr; + qargs.static_args.tols[0] = tols[0]; + qargs.static_args.tols[1] = tols[1]; + qargs.static_args.tols[2] = tols[2]; + qargs.static_args.tols[3] = tols[3]; qargs.static_args.threshold = threshold; qargs.static_args.min_gradient = min_gradient; qargs.static_args.min_snr = min_snr; |