diff options
| -rw-r--r-- | doc/man/partial_sim.1 | 9 | ||||
| -rw-r--r-- | src/partial_sim.c | 25 |
2 files changed, 29 insertions, 5 deletions
diff --git a/doc/man/partial_sim.1 b/doc/man/partial_sim.1 index b3e5c9a2..2af472e9 100644 --- a/doc/man/partial_sim.1 +++ b/doc/man/partial_sim.1 @@ -105,7 +105,14 @@ Use \fIn\fR threads for simulation. Default: 1. .B .IP "\fB--images=\fR\fIprefix\fR" .PD -For each chunk in the output stream, write an image in HDF5 format to \fIprefix\fR\fB/sim-\fR\fINNN\fR\fB.h5\fR, where \fINNN\fR is the sequence number of the chunk in the output stream. This option is incompatible with \fB-j\fR. +For each chunk in the output stream, write a 'sketch' image in HDF5 format to \fIprefix\fR\fB/sim-\fR\fINNN\fR\fB.h5\fR, where \fINNN\fR is the sequence number of the chunk in the output stream. This option is incompatible with \fB-j\fR. The intensities in the peaks in the sketches will have th + +.PD 0 +.B +.IP "\fB--background=\fIval\fR" +.PD +Add a Poisson-distributed background with \fIval\fR photons to the sketches (see \fB--images\fR). The default is \fB--background=3000\fR.\fR. + .SH AUTHOR This page was written by Thomas White. diff --git a/src/partial_sim.c b/src/partial_sim.c index bbcc5a63..50f6ce57 100644 --- a/src/partial_sim.c +++ b/src/partial_sim.c @@ -170,11 +170,10 @@ static void calculate_partials(Crystal *cr, static void draw_and_write_image(struct image *image, RefList *reflections, - gsl_rng *rng) + gsl_rng *rng, double background) { Reflection *refl; RefListIterator *iter; - const int background = 3000; int i; image->data = calloc(image->width*image->height, sizeof(float)); @@ -234,7 +233,8 @@ static void show_help(const char *s) " --osf-stddev=<val> Standard deviation of the scaling factors.\n" " --full-stddev=<val> Standard deviation of the randomly\n" " generated full intensities, if not using -i.\n" -" --noise-stddev=<val> Set the standard deviation of the noise.\n" +" --noise-stddev=<val> Set the standard deviation of the noise.\n" +" --background=<val> Background level in photons. Default 3000.\n" "\n" ); } @@ -256,6 +256,7 @@ struct queue_args double osf_stddev; double full_stddev; double noise_stddev; + double background; struct image *template_image; double max_q; @@ -367,7 +368,7 @@ static void run_job(void *vwargs, int cookie) if ( qargs->image_prefix != NULL ) { draw_and_write_image(&wargs->image, reflections, - qargs->rngs[cookie]); + qargs->rngs[cookie], qargs->background); } /* Give a slightly incorrect cell in the stream */ @@ -431,6 +432,7 @@ int main(int argc, char *argv[]) double osf_stddev = 2.0; double full_stddev = 1000.0; double noise_stddev = 20.0; + double background = 3000.0; gsl_rng *rng_for_seeds; int config_random = 0; char *image_prefix = NULL; @@ -452,6 +454,7 @@ int main(int argc, char *argv[]) {"full-stddev", 1, NULL, 4}, {"noise-stddev", 1, NULL, 5}, {"images", 1, NULL, 6}, + {"background", 1, NULL, 7}, {"really-random", 0, &config_random, 1}, @@ -559,6 +562,19 @@ int main(int argc, char *argv[]) image_prefix = strdup(optarg); break; + case 7 : + background = strtod(optarg, &rval); + if ( *rval != '\0' ) { + ERROR("Invalid background level.\n"); + return 1; + } + if ( background < 0.0 ) { + ERROR("Invalid background level."); + ERROR(" (must be positive).\n"); + return 1; + } + break; + case 0 : break; @@ -701,6 +717,7 @@ int main(int argc, char *argv[]) qargs.osf_stddev = osf_stddev; qargs.full_stddev = full_stddev; qargs.noise_stddev = noise_stddev; + qargs.background = background; qargs.max_q = largest_q(&image); qargs.image_prefix = image_prefix; |