diff options
| -rw-r--r-- | doc/man/partial_sim.1 | 6 | ||||
| -rw-r--r-- | src/partial_sim.c | 34 |
2 files changed, 35 insertions, 5 deletions
diff --git a/doc/man/partial_sim.1 b/doc/man/partial_sim.1 index 5b417978..9f3436ea 100644 --- a/doc/man/partial_sim.1 +++ b/doc/man/partial_sim.1 @@ -77,6 +77,12 @@ Add random values with a flat distribution to the components of the reciprocal l .PD Save a table of values to \fIfilename\fR containing, in resolution shells, the following columns: resolution shell centre in nm^-1, number of reflections in shell, mean partiality, maximum partiality. +.PD 0 +.B +.IP "\fB--osf-stddev=\fR\fIval\fR +.PD +Set the standard deviation of the distribution of overall scaling factors to \fIval\fR. The distribution will be cut at zero, i.e. negative or zero scaling factors are not allowed. The distribution will be centered on 1. The default is \fB--osf-stddev=2.0\fR. + .SH AUTHOR This page was written by Thomas White. diff --git a/src/partial_sim.c b/src/partial_sim.c index 32e6666a..615c66a3 100644 --- a/src/partial_sim.c +++ b/src/partial_sim.c @@ -3,11 +3,11 @@ * * Generate partials for testing scaling * - * Copyright © 2012 Deutsches Elektronen-Synchrotron DESY, - * a research centre of the Helmholtz Association. + * Copyright © 2012-2013 Deutsches Elektronen-Synchrotron DESY, + * a research centre of the Helmholtz Association. * * Authors: - * 2011-2012 Thomas White <taw@physics.org> + * 2011-2013 Thomas White <taw@physics.org> * * This file is part of CrystFEL. * @@ -184,6 +184,7 @@ static void show_help(const char *s) " -c, --cnoise=<val> Add random noise, with a flat distribution, to the\n" " reciprocal lattice vector components given in the\n" " stream, with maximum error +/- <val> percent.\n" +" --osf-stddev=<val> Set the standard deviation of the scaling factors.\n" "\n" ); } @@ -202,6 +203,7 @@ struct queue_args int random_intensities; UnitCell *cell; double cnoise; + double osf_stddev; struct image *template_image; double max_q; @@ -255,6 +257,7 @@ static void run_job(void *vwargs, int cookie) int i; Crystal *cr; RefList *reflections; + double osf; cr = crystal_new(); if ( cr == NULL ) { @@ -264,7 +267,10 @@ static void run_job(void *vwargs, int cookie) wargs->crystal = cr; crystal_set_image(cr, &wargs->image); - crystal_set_osf(cr, gaussian_noise(1.0, 0.3)); + do { + osf = gaussian_noise(1.0, qargs->osf_stddev); + } while ( osf <= 0.0 ); + crystal_set_osf(cr, osf); crystal_set_profile_radius(cr, wargs->image.beam->profile_radius); /* Set up a random orientation */ @@ -344,6 +350,7 @@ int main(int argc, char *argv[]) int i; FILE *fh; char *phist_file = NULL; + double osf_stddev = 2.0; /* Long options */ const struct option longopts[] = { @@ -355,8 +362,11 @@ int main(int argc, char *argv[]) {"geometry", 1, NULL, 'g'}, {"symmetry", 1, NULL, 'y'}, {"save-random", 1, NULL, 'r'}, - {"pgraph", 1, NULL, 2}, {"cnoise", 1, NULL, 'c'}, + + {"pgraph", 1, NULL, 2}, + {"osf-stddev", 1, NULL, 3}, + {0, 0, NULL, 0} }; @@ -418,6 +428,19 @@ int main(int argc, char *argv[]) phist_file = strdup(optarg); break; + case 3 : + osf_stddev = strtod(optarg, &rval); + if ( *rval != '\0' ) { + ERROR("Invalid OSF standard deviation.\n"); + return 1; + } + if ( osf_stddev <= 0.0 ) { + ERROR("Invalid OSF standard deviation."); + ERROR(" (must be positive).\n"); + return 1; + } + break; + case 0 : break; @@ -549,6 +572,7 @@ int main(int argc, char *argv[]) qargs.template_image = ℑ qargs.stream = stream; qargs.cnoise = cnoise; + qargs.osf_stddev = osf_stddev; qargs.max_q = largest_q(&image); for ( i=0; i<NBINS; i++ ) { |