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authorThomas White <taw@bitwiz.org.uk>2010-09-25 22:49:02 +0200
committerThomas White <taw@physics.org>2012-02-22 15:26:59 +0100
commit73f10c77950e8f398e3a1e4540f1a46f398c108f (patch)
treeeacedafe03532601bbfa875baa4ef14a735deffc /src/reintegrate.c
parentc0a0414463442ff856399a4aad7f231a35fe84b6 (diff)
reintegrate: Add relevant options
Diffstat (limited to 'src/reintegrate.c')
-rw-r--r--src/reintegrate.c79
1 files changed, 65 insertions, 14 deletions
diff --git a/src/reintegrate.c b/src/reintegrate.c
index 3261ba72..53117163 100644
--- a/src/reintegrate.c
+++ b/src/reintegrate.c
@@ -47,6 +47,12 @@ struct process_args
UnitCell *cell;
struct detector *det;
pthread_mutex_t *output_mutex; /* Protects 'stdout' */
+ int config_cmfilter;
+ int config_polar;
+ int config_satcorr;
+ int config_sa;
+ int config_closer;
+ int config_sanity;
};
@@ -56,15 +62,28 @@ static void show_help(const char *s)
printf(
"Like 'indexamajig', but skip the indexing step.\n"
"\n"
-" -h, --help Display this help message.\n"
+" -h, --help Display this help message.\n"
"\n"
-" -i, --input=<filename> Specify the name of the input 'stream'.\n"
-" (must be a file, not e.g. stdin)\n"
-" -g. --geometry=<file> Get detector geometry from file.\n"
-" -x, --prefix=<p> Prefix filenames from input file with <p>.\n"
-" --basename Remove the directory parts of the filenames.\n"
-" --no-check-prefix Don't attempt to correct the --prefix.\n"
-" -j <n> Run <n> analyses in parallel.\n");
+" -i, --input=<filename> Specify the name of the input 'stream'.\n"
+" (must be a file, not e.g. stdin)\n"
+" -g. --geometry=<file> Get detector geometry from file.\n"
+" -x, --prefix=<p> Prefix filenames from input file with <p>.\n"
+" --basename Remove the directory parts of the filenames.\n"
+" --no-check-prefix Don't attempt to correct the --prefix.\n"
+" --check-sanity Check that indexed locations approximately correspond\n"
+" with detected peaks.\n"
+" --filter-cm Perform common-mode noise subtraction on images\n"
+" before proceeding. Intensities will be extracted\n"
+" from the image as it is after this processing.\n"
+" --unpolarized Don't correct for the polarisation of the X-rays.\n"
+" --sat-corr Correct values of saturated peaks using a table\n"
+" included in the HDF5 file.\n"
+" --no-sa Don't correct for the differing solid angles of\n"
+" the pixels.\n"
+" --no-closer-peak Don't integrate from the location of a nearby peak\n"
+" instead of the position closest to the reciprocal\n"
+" lattice point.\n"
+" -j <n> Run <n> analyses in parallel.\n");
}
@@ -100,12 +119,21 @@ static void process_image(struct process_args *pargs)
return;
}
- hdf5_read(hdfile, &image, 1);
+ hdf5_read(hdfile, &image, pargs->config_satcorr);
- output_intensities(&image, pargs->cell,
- pargs->output_mutex, 1,
- 1, 0,
+ /* Sanity check */
+ if ( pargs->config_sanity
+ && !peak_sanity_check(&image, image.indexed_cell, 0, 0.1) ) {
+
+ STATUS("Failed peak sanity check.\n");
+
+ } else {
+
+ output_intensities(&image, pargs->cell,
+ pargs->output_mutex, pargs->config_polar,
+ pargs->config_sa, pargs->config_closer,
0, 0.1);
+ }
free(image.data);
cell_free(pargs->cell);
@@ -149,7 +177,10 @@ static void *worker_thread(void *pargsv)
static void integrate_all(int nthreads, struct detector *det, FILE *fh,
- int config_basename, const char *prefix)
+ int config_basename, const char *prefix,
+ int config_cmfilter, int config_polar,
+ int config_satcorr, int config_sa, int config_closer,
+ int config_sanity)
{
pthread_t workers[MAX_THREADS];
struct process_args *worker_args[MAX_THREADS];
@@ -165,6 +196,12 @@ static void integrate_all(int nthreads, struct detector *det, FILE *fh,
worker_args[i]->filename = malloc(1024);
worker_active[i] = 0;
worker_args[i]->det = det;
+ worker_args[i]->config_cmfilter = config_cmfilter;
+ worker_args[i]->config_polar = config_polar;
+ worker_args[i]->config_sanity = config_sanity;
+ worker_args[i]->config_satcorr = config_satcorr;
+ worker_args[i]->config_sa = config_sa;
+ worker_args[i]->config_closer = config_closer;
pthread_mutex_init(&worker_args[i]->control_mutex, NULL);
worker_args[i]->output_mutex = &output_mutex;
@@ -293,6 +330,12 @@ int main(int argc, char *argv[])
int nthreads = 1;
int config_basename = 0;
int config_checkprefix = 1;
+ int config_closer = 1;
+ int config_polar = 1;
+ int config_sanity = 0;
+ int config_satcorr = 0;
+ int config_sa = 1;
+ int config_cmfilter = 0;
struct detector *det;
/* Long options */
@@ -303,6 +346,12 @@ int main(int argc, char *argv[])
{"prefix", 1, NULL, 'x'},
{"basename", 0, &config_basename, 1},
{"no-check-prefix", 0, &config_checkprefix, 0},
+ {"no-closer-peak", 0, &config_closer, 0},
+ {"unpolarized", 0, &config_polar, 0},
+ {"check-sanity", 0, &config_sanity, 1},
+ {"sat-corr", 0, &config_satcorr, 1},
+ {"no-sa", 0, &config_sa, 0},
+ {"filter-cm", 0, &config_cmfilter, 1},
{0, 0, NULL, 0}
};
@@ -371,7 +420,9 @@ int main(int argc, char *argv[])
free(geomfile);
rewind(fh);
- integrate_all(nthreads, det, fh, config_basename, prefix);
+ integrate_all(nthreads, det, fh, config_basename, prefix,
+ config_cmfilter, config_polar, config_satcorr, config_sa,
+ config_closer, config_sanity);
fclose(fh);
free(prefix);