From b6cdcc6cc47ee81ae63cdb33bc48ce320a90b36f Mon Sep 17 00:00:00 2001 From: "Kenneth R. Beyerlein" Date: Wed, 31 Jan 2018 23:29:01 +0100 Subject: Changed the naming of felix options and variables to make them more obvious. --- doc/man/indexamajig.1 | 12 ++++++----- libcrystfel/src/felix.c | 20 +++++++++---------- libcrystfel/src/felix.h | 4 ++-- src/indexamajig.c | 53 ++++++++++++++++++++++++++++--------------------- 4 files changed, 49 insertions(+), 40 deletions(-) diff --git a/doc/man/indexamajig.1 b/doc/man/indexamajig.1 index e4fa91bd..a434bf05 100644 --- a/doc/man/indexamajig.1 +++ b/doc/man/indexamajig.1 @@ -362,14 +362,16 @@ These set low-level parameters for the TakeTwo indexing algorithm. Respectively The defaults are: \fB--taketwo-member-threshold=20\fR, \fB--taketwo-len-tolernace=0.001\fR, \fB--taketwo-angle-tolerance=0.6\fR and \fB--taketwo-trace-tolerance=3\fR. .PD 0 -.IP \fB--felix-tthrange-min=\fIn\fR -.IP \fB--felix-tthrange-max=\fIn\fR -.IP \fB--felix-min-measurements=\fIn\fR +.IP \fB--felix-domega=\fIn\fR +.IP \fB--felix-fraction-max-visits=\fIn\fR +.IP \fB--felix-max-internal-angle=\fIn\fR +.IP \fB--felix-max-uniqueness=\fIn\fR .IP \fB--felix-min-completeness=\fIn\fR -.IP \fB--felix-min-uniqueness=\fIn\fR +.IP \fB--felix-min-visits=\fIn\fR .IP \fB--felix-num-voxels=\fIn\fR -.IP \fB--felix-test-fraction=\fIn\fR .IP \fB--felix-sigma=\fIn\fR +.IP \fB--felix-tthrange-max=\fIn\fR +.IP \fB--felix-tthrange-min=\fIn\fR .PD 0 These set low-level parameters for the Felix indexing algorithm. diff --git a/libcrystfel/src/felix.c b/libcrystfel/src/felix.c index e226b037..98b2c7b4 100644 --- a/libcrystfel/src/felix.c +++ b/libcrystfel/src/felix.c @@ -77,11 +77,11 @@ struct felix_private float domega; float omegarange_min; float omegarange_max; - int min_measurements; /* related to "cuts" */ + int min_visits; /* related to "cuts" */ float min_completeness; /* related to "cuts" */ float max_uniqueness; /* related to "cuts" */ int n_voxels; /* related to "frustsumsize" */ - float test_fraction; /* related to "frustsumsize" */ + float fraction_max_visits; /* related to "frustsumsize" */ float sigma_tth; /* related to "uncertainties" */ float sigma_eta; /* related to "uncertainties" */ float sigma_omega; /* related to "uncertainties" */ @@ -389,10 +389,10 @@ static char *write_ini(struct image *image, struct felix_private *gp) fprintf(fh, "domega %f\n", gp->domega); fprintf(fh, "omegarange %f %f\n", gp->omegarange_min, gp->omegarange_max); fprintf(fh, "filespecs %s %s\n", gveFilename, logFilename); - fprintf(fh, "cuts %i %f %f\n", gp->min_measurements, gp->min_completeness, + fprintf(fh, "cuts %i %f %f\n", gp->min_visits, gp->min_completeness, gp->max_uniqueness); fprintf(fh, "frustumsize %i %f\n", gp->n_voxels, - gp->test_fraction); + gp->fraction_max_visits); fprintf(fh, "uncertainties %f %f %f\n", gp->sigma_tth, gp->sigma_eta, gp->sigma_omega); fprintf(fh, "nsigmas %i\n", gp->n_sigmas); @@ -644,10 +644,10 @@ void *felix_prepare(IndexingMethod *indm, UnitCell *cell, gp->domega = 2; gp->omegarange_min = -1.0; gp->omegarange_max = 1.0; - gp->min_measurements = 15; + gp->min_visits = 15; gp->min_completeness = 0.001; gp->max_uniqueness = 0.5; - gp->test_fraction = 0.75; + gp->fraction_max_visits = 0.75; gp->sigma_tth = 0.2; gp->sigma_eta = 0.2; gp->sigma_omega = 0.2; @@ -667,8 +667,8 @@ void *felix_prepare(IndexingMethod *indm, UnitCell *cell, if ( opts->ttmax > 0.0 ) { gp->tthrange_max = opts->ttmax; } - if ( opts->min_measurements > 0 ) { - gp->min_measurements = opts->min_measurements; + if ( opts->min_visits > 0 ) { + gp->min_visits = opts->min_visits; } if ( opts->min_completeness > 0.0 ) { gp->min_completeness = opts->min_completeness; @@ -679,8 +679,8 @@ void *felix_prepare(IndexingMethod *indm, UnitCell *cell, if ( opts->n_voxels > 0 ) { gp->n_voxels = opts->n_voxels; } - if ( opts->test_fraction > 0.0 ) { - gp->test_fraction = opts->test_fraction; + if ( opts->fraction_max_visits > 0.0 ) { + gp->fraction_max_visits = opts->fraction_max_visits; } if ( opts->sigma > 0.0 ) { gp->sigma_tth = opts->sigma; diff --git a/libcrystfel/src/felix.h b/libcrystfel/src/felix.h index 6cd78fdb..b1776293 100644 --- a/libcrystfel/src/felix.h +++ b/libcrystfel/src/felix.h @@ -40,11 +40,11 @@ struct felix_options { double ttmin; /* radians */ double ttmax; /* radians */ - int min_measurements; + int min_visits; double min_completeness; double max_uniqueness; int n_voxels; - double test_fraction; + double fraction_max_visits; double sigma; double domega; double max_internal_angle; 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= 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; -- cgit v1.2.3