diff options
Diffstat (limited to 'libcrystfel/src/felix.c')
| -rw-r--r-- | libcrystfel/src/felix.c | 176 |
1 files changed, 176 insertions, 0 deletions
diff --git a/libcrystfel/src/felix.c b/libcrystfel/src/felix.c index ea27093a..cac12410 100644 --- a/libcrystfel/src/felix.c +++ b/libcrystfel/src/felix.c @@ -70,6 +70,21 @@ #define FELIX_VERBOSE 0 +struct felix_options +{ + double ttmin; /* radians */ + double ttmax; /* radians */ + int min_visits; + double min_completeness; + double max_uniqueness; + int n_voxels; + double fraction_max_visits; + double sigma; + double domega; + double max_internal_angle; +}; + + /* Global private data, prepared once */ struct felix_private { @@ -789,3 +804,164 @@ const char *felix_probe(UnitCell *cell) if ( ok ) return "felix"; return NULL; } + + +static void show_help() +{ + printf("Parameters for the Felix indexing algorithm:\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\n" +" --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" +" 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-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" +); +} + + +static error_t parse_arg(int key, char *arg, struct argp_state *state) +{ + struct felix_options **opts_ptr = state->input; + float tmp; + + switch ( key ) { + + case ARGP_KEY_INIT : + *opts_ptr = malloc(sizeof(struct felix_options)); + if ( *opts_ptr == NULL ) return ENOMEM; + (*opts_ptr)->ttmin = -1.0; + (*opts_ptr)->ttmax = -1.0; + (*opts_ptr)->min_visits = 0; + (*opts_ptr)->min_completeness = -1.0; + (*opts_ptr)->max_uniqueness = -1.0; + (*opts_ptr)->n_voxels = 0; + (*opts_ptr)->fraction_max_visits = -1.0; + (*opts_ptr)->sigma = -1.0; + (*opts_ptr)->domega = -1.0; + (*opts_ptr)->max_internal_angle = -1.0; + break; + + case 1 : + show_help(); + return EINVAL; + + case 2 : + if ( sscanf(arg, "%f", &tmp) != 1 ) { + ERROR("Invalid value for --felix-tthrange-min\n"); + return EINVAL; + } + (*opts_ptr)->ttmin = deg2rad(tmp); + break; + + case 3 : + if ( sscanf(arg, "%f", &tmp) != 1 ) { + ERROR("Invalid value for --felix-tthrange-max\n"); + return EINVAL; + } + (*opts_ptr)->ttmax = deg2rad(tmp); + break; + + case 4 : + if ( sscanf(arg, "%d", &(*opts_ptr)->min_visits) != 1 ) { + ERROR("Invalid value for --felix-min-visits\n"); + return EINVAL; + } + break; + + case 5 : + if ( sscanf(arg, "%lf", &(*opts_ptr)->min_completeness) != 1 ) { + ERROR("Invalid value for --felix-min-completeness\n"); + return EINVAL; + } + break; + + case 6 : + if ( sscanf(arg, "%lf", &(*opts_ptr)->max_uniqueness) != 1 ) { + ERROR("Invalid value for --felix-max-uniqueness\n"); + return EINVAL; + } + break; + + case 7 : + if ( sscanf(arg, "%d", &(*opts_ptr)->n_voxels) != 1 ) { + ERROR("Invalid value for --felix-num-voxels\n"); + return EINVAL; + } + break; + + case 8 : + if ( sscanf(arg, "%lf", &(*opts_ptr)->fraction_max_visits) != 1 ) { + ERROR("Invalid value for --felix-fraction-max-visits\n"); + return EINVAL; + } + break; + + case 9 : + if ( sscanf(arg, "%lf", &(*opts_ptr)->sigma) != 1 ) { + ERROR("Invalid value for --felix-sigma\n"); + return EINVAL; + } + break; + + case 10 : + if ( sscanf(arg, "%lf", &(*opts_ptr)->domega) != 1 ) { + ERROR("Invalid value for --felix-domega\n"); + return EINVAL; + } + break; + + case 11 : + if ( sscanf(arg, "%lf", &(*opts_ptr)->max_internal_angle) != 1 ) { + ERROR("Invalid value for --felix-max-internal-angle\n"); + return EINVAL; + } + break; + + default : + return ARGP_ERR_UNKNOWN; + + } + + return 0; +} + + +static struct argp_option options[] = { + + {"help-felix", 1, NULL, OPTION_NO_USAGE, + "Show options for Felix indexing algorithm", 99}, + {"felix-tthrange-min", 2, "2theta", OPTION_HIDDEN, NULL}, + {"felix-tthrange-max", 3, "2theta", OPTION_HIDDEN, NULL}, + {"felix-min-visits", 4, "n", OPTION_HIDDEN, NULL}, + {"felix-min-completeness", 5, "frac", OPTION_HIDDEN, NULL}, + {"felix-max-uniqueness", 6, "n", OPTION_HIDDEN, NULL}, + {"felix-num-voxels", 7, "n", OPTION_HIDDEN, NULL}, + {"felix-fraction-max-visits", 8, "n", OPTION_HIDDEN, NULL}, + {"felix-sigma", 9, "n", OPTION_HIDDEN, NULL}, + {"felix-domega", 10, "n", OPTION_HIDDEN, NULL}, + {"felix-max-internal-angle", 11, "ang", OPTION_HIDDEN, NULL}, + + {0} +}; + + +struct argp felix_argp = { options, parse_arg, NULL, NULL, NULL, NULL, NULL }; |