diff options
Diffstat (limited to 'src')
| -rw-r--r-- | src/indexamajig.c | 133 | ||||
| -rw-r--r-- | src/process_image.h | 3 |
2 files changed, 113 insertions, 23 deletions
diff --git a/src/indexamajig.c b/src/indexamajig.c index 691d6e11..88b61563 100644 --- a/src/indexamajig.c +++ b/src/indexamajig.c @@ -129,6 +129,7 @@ static void show_help(const char *s) " --no-refine Skip the prediction refinement step\n" " --check-peaks Check that most of the peaks can be accounted for\n" " by the indexing solution\n" +"\n" " --taketwo-member-threshold\n" " Minimum number of members in network\n" " --taketwo-len-tolerance\n" @@ -137,8 +138,25 @@ static void show_help(const char *s) " Reciprocal space angle tolerance (in degrees)\n" " --taketwo-trace-tolerance\n" " Rotation matrix equivalence tolerance (in degrees)\n" -" --felix-options Change the default arguments passed to the indexer\n" -" Comma-separated list of options, key=val\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-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" +" --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" "\nIntegration options:\n\n" " --integration=<meth> Integration method (rings,prof2d)-(cen,nocen)\n" " Default: rings-nocen\n" @@ -208,7 +226,6 @@ int main(int argc, char *argv[]) char *geom_filename = NULL; struct beam_params beam; int have_push_res = 0; - int len; char *command_line_peak_path = NULL; int if_refine = 1; int if_nocomb = 0; @@ -266,12 +283,19 @@ int main(int argc, char *argv[]) iargs.fix_profile_r = -1.0; iargs.fix_bandwidth = -1.0; iargs.fix_divergence = -1.0; - iargs.felix_options = NULL; iargs.profile = 0; iargs.taketwo_opts.member_thresh = -1; iargs.taketwo_opts.len_tol = -1.0; iargs.taketwo_opts.angle_tol = -1.0; 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_completeness = -1.0; + iargs.felix_opts.min_uniqueness = -1.0; + iargs.felix_opts.n_voxels = 0; + iargs.felix_opts.test_fraction = -1.0; + iargs.felix_opts.sigma = -1.0; /* Long options */ const struct option longopts[] = { @@ -347,13 +371,21 @@ int main(int argc, char *argv[]) {"max-res", 1, NULL, 30}, {"min-peaks", 1, NULL, 31}, {"taketwo-member-threshold", 1, NULL, 32}, - {"taketwo-member-thresh", 1, NULL, 32}, + {"taketwo-member-thresh", 1, NULL, 32}, /* compat */ {"taketwo-len-tolerance", 1, NULL, 33}, - {"taketwo-len-tol", 1, NULL, 33}, + {"taketwo-len-tol", 1, NULL, 33}, /* compat */ {"taketwo-angle-tolerance", 1, NULL, 34}, - {"taketwo-angle-tol", 1, NULL, 34}, + {"taketwo-angle-tol", 1, NULL, 34}, /* compat */ {"taketwo-trace-tolerance", 1, NULL, 35}, - {"taketwo-trace-tol", 1, NULL, 35}, + {"taketwo-trace-tol", 1, NULL, 35}, /* compat */ + {"felix-ttrange-min", 1, NULL, 36}, + {"felix-ttrange-max", 1, NULL, 37}, + {"felix-min-measurements", 1, NULL, 38}, + {"felix-min-completeness", 1, NULL, 39}, + {"felix-min-uniqueness", 1, NULL, 40}, + {"felix-num-voxels", 1, NULL, 41}, + {"felix-test-fraction", 1, NULL, 42}, + {"felix-sigma", 1, NULL, 43}, {0, 0, NULL, 0} }; @@ -524,18 +556,9 @@ int main(int argc, char *argv[]) break; case 25 : - /* Remove leading and trailing quotes */ - len = strlen(optarg); - if ( optarg[len-1] == '\'' || optarg[len-1] == '\"' ){ - optarg[len-1] = 0; - } - if ( optarg[0] == '\'' || optarg[0] == '\"' ){ - iargs.felix_options = strdup( optarg+1 ); - } - else { - iargs.felix_options = strdup( optarg ); - } - break; + ERROR("--felix-options is no longer used.\n"); + ERROR("See --help for the new Felix options.\n"); + return 1; case 26: iargs.min_pix_count = atoi(optarg); @@ -599,6 +622,72 @@ int main(int argc, char *argv[]) iargs.taketwo_opts.trace_tol = deg2rad(iargs.taketwo_opts.trace_tol); break; + case 36: + if ( sscanf(optarg, "%lf", &iargs.felix_opts.ttmin) != 1 ) + { + ERROR("Invalid value for --felix-tthrange-min\n"); + return 1; + } + iargs.felix_opts.ttmin = deg2rad(iargs.felix_opts.ttmin); + break; + + case 37: + if ( sscanf(optarg, "%lf", &iargs.felix_opts.ttmax) != 1 ) + { + ERROR("Invalid value for --felix-tthrange-max\n"); + return 1; + } + iargs.felix_opts.ttmax = deg2rad(iargs.felix_opts.ttmax); + break; + + case 38: + if ( sscanf(optarg, "%i", &iargs.felix_opts.min_measurements) != 1 ) + { + ERROR("Invalid value for --felix-min-measurements\n"); + return 1; + } + break; + + case 39: + if ( sscanf(optarg, "%lf", &iargs.felix_opts.min_completeness) != 1 ) + { + ERROR("Invalid value for --felix-min-completeness\n"); + return 1; + } + break; + + case 40: + if ( sscanf(optarg, "%lf", &iargs.felix_opts.min_uniqueness) != 1 ) + { + ERROR("Invalid value for --felix-min-uniqueness\n"); + return 1; + } + break; + + case 41: + if ( sscanf(optarg, "%i", &iargs.felix_opts.n_voxels) != 1 ) + { + ERROR("Invalid value for --felix-num-voxels\n"); + return 1; + } + break; + + case 42: + if ( sscanf(optarg, "%lf", &iargs.felix_opts.test_fraction) != 1 ) + { + ERROR("Invalid value for --felix-test-fraction\n"); + return 1; + } + break; + + case 43: + if ( sscanf(optarg, "%lf", &iargs.felix_opts.sigma) != 1 ) + { + ERROR("Invalid value for --felix-sigma\n"); + return 1; + } + break; + case 0 : break; @@ -892,8 +981,8 @@ int main(int argc, char *argv[]) iargs.ipriv = setup_indexing(indm_str, iargs.cell, iargs.det, iargs.tols, flags, - iargs.felix_options, - &iargs.taketwo_opts); + &iargs.taketwo_opts, + &iargs.felix_opts); if ( iargs.ipriv == NULL ) { ERROR("Failed to set up indexing system\n"); return 1; diff --git a/src/process_image.h b/src/process_image.h index 3e87b922..861ee203 100644 --- a/src/process_image.h +++ b/src/process_image.h @@ -40,6 +40,7 @@ struct index_args; #include "im-sandbox.h" #include "time-accounts.h" #include "taketwo.h" +#include "felix.h" enum { @@ -99,9 +100,9 @@ struct index_args float fix_profile_r; float fix_bandwidth; float fix_divergence; - char *felix_options; int profile; /* Whether or not to do wall clock profiling */ struct taketwo_options taketwo_opts; + struct felix_options felix_opts; }; |