diff options
Diffstat (limited to 'src/indexamajig.c')
| -rw-r--r-- | src/indexamajig.c | 53 |
1 files changed, 30 insertions, 23 deletions
diff --git a/src/indexamajig.c b/src/indexamajig.c index 0af10f0e..36c52d7d 100644 --- a/src/indexamajig.c +++ b/src/indexamajig.c @@ -139,24 +139,31 @@ static void show_help(const char *s) " --taketwo-trace-tolerance\n" " Rotation matrix equivalence tolerance (in degrees)\n" "\n" -" --felix-tthrange-min Minimum 2theta to consider for indexing (degrees)\n" -" Default: 0\n" -" --felix-tthrange-max Maximum 2theta to consider for indexing (degrees)\n" -" Default: 30\n" -" --felix-min-measurements\n" -" How many Rodrigue lines cross in the first search\n" -" Default: 15\n" +" --felix-domega Degree range of omega (moscaicity) to consider.\n" +" Default: 2\n" +" --felix-fraction-max-visits\n" +" Cutoff for minimum fraction of the max visits.\n" +" Default: 0.75\n" +" --felix-max-internal-angle\n" +" Cutoff for maximum internal angle between observed\n" +" spots and predicted spots. Default: 0.25" +" --felix-max-uniqueness\n" +" Cutoff for maximum fraction of found spots which\n" +" can belong to other crystallites. Default: 0.5\n" " --felix-min-completeness\n" -" Fraction of projected spots found in the pattern\n" -" Default: 0.001\n" -" --felix-min-uniqueness\n" -" Fraction of found spots which can belong to other\n" -" crystallites. Default: 0.5\n" +" Cutoff for minimum fraction of projected spots\n" +" found in the pattern. Default: 0.001\n" +" --felix-min-visits\n" +" Cutoff for minimum number of voxel visits.\n" +" Default: 15\n" " --felix-num-voxels Number of voxels for Rodrigues space search\n" " Default: 100\n" -" --felix-test-fraction Fraction of space to test. Default: 0.75\n" " --felix-sigma The sigma of the 2theta, eta and omega angles.\n" " Default: 0.2\n" +" --felix-tthrange-max Maximum 2theta to consider for indexing (degrees)\n" +" Default: 30\n" +" --felix-tthrange-min Minimum 2theta to consider for indexing (degrees)\n" +" Default: 0\n" "\nIntegration options:\n\n" " --integration=<meth> Integration method (rings,prof2d)-(cen,nocen)\n" " Default: rings-nocen\n" @@ -292,11 +299,11 @@ int main(int argc, char *argv[]) iargs.taketwo_opts.trace_tol = -1.0; iargs.felix_opts.ttmin = -1.0; iargs.felix_opts.ttmax = -1.0; - iargs.felix_opts.min_measurements = 0; + iargs.felix_opts.min_visits = 0; iargs.felix_opts.min_completeness = -1.0; iargs.felix_opts.max_uniqueness = -1.0; iargs.felix_opts.n_voxels = 0; - iargs.felix_opts.test_fraction = -1.0; + iargs.felix_opts.fraction_max_visits = -1.0; iargs.felix_opts.sigma = -1.0; iargs.felix_opts.domega = -1.0; iargs.felix_opts.max_internal_angle = -1.0; @@ -384,15 +391,15 @@ int main(int argc, char *argv[]) {"taketwo-trace-tol", 1, NULL, 35}, /* compat */ {"felix-tthrange-min", 1, NULL, 36}, {"felix-tthrange-max", 1, NULL, 37}, - {"felix-min-measurements", 1, NULL, 38}, + {"felix-min-visits", 1, NULL, 38}, {"felix-min-completeness", 1, NULL, 39}, {"felix-max-uniqueness", 1, NULL, 40}, {"felix-num-voxels", 1, NULL, 41}, - {"felix-test-fraction", 1, NULL, 42}, + {"felix-fraction-max-visits", 1, NULL, 42}, {"felix-sigma", 1, NULL, 43}, {"serial-start", 1, NULL, 44}, {"felix-domega", 1, NULL, 45}, - {"felix-max-inter-angle", 1, NULL, 46}, + {"felix-max-internal-angle", 1, NULL, 46}, {0, 0, NULL, 0} }; @@ -648,9 +655,9 @@ int main(int argc, char *argv[]) break; case 38: - if ( sscanf(optarg, "%i", &iargs.felix_opts.min_measurements) != 1 ) + if ( sscanf(optarg, "%i", &iargs.felix_opts.min_visits) != 1 ) { - ERROR("Invalid value for --felix-min-measurements\n"); + ERROR("Invalid value for --felix-min-visits\n"); return 1; } break; @@ -680,9 +687,9 @@ int main(int argc, char *argv[]) break; case 42: - if ( sscanf(optarg, "%lf", &iargs.felix_opts.test_fraction) != 1 ) + if ( sscanf(optarg, "%lf", &iargs.felix_opts.fraction_max_visits) != 1 ) { - ERROR("Invalid value for --felix-test-fraction\n"); + ERROR("Invalid value for --felix-fraction-max-visits\n"); return 1; } break; @@ -714,7 +721,7 @@ int main(int argc, char *argv[]) case 46: if ( sscanf(optarg, "%lf", &iargs.felix_opts.max_internal_angle) != 1 ) { - ERROR("Invalid value for --felix-max-inter-angle\n"); + ERROR("Invalid value for --felix-max-internal-angle\n"); return 1; } break; |