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-rw-r--r--src/facetron.c45
1 files changed, 33 insertions, 12 deletions
diff --git a/src/facetron.c b/src/facetron.c
index 8d66d549..806ce54f 100644
--- a/src/facetron.c
+++ b/src/facetron.c
@@ -31,6 +31,7 @@
#include "geometry.h"
#include "peaks.h"
#include "thread-pool.h"
+#include "beam-parameters.h"
static void show_help(const char *s)
@@ -45,6 +46,9 @@ static void show_help(const char *s)
" (must be a file, not e.g. stdin)\n"
" -o, --output=<filename> Output filename. Default: facetron.hkl.\n"
" -g. --geometry=<file> Get detector geometry from file.\n"
+" -b, --beam=<file> Get beam parameters from file (provides initial\n"
+" values for parameters, and nominal wavelengths\n"
+" if no per-shot value is found in an HDF5 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"
@@ -91,6 +95,7 @@ static void integrate_image(int mytask, void *tasks)
int j, n;
struct hdfile *hdfile;
struct image *image = pargs->image;
+ double nominal_photon_energy = pargs->image->beam->photon_energy;
hdfile = hdfile_open(image->filename);
if ( hdfile == NULL ) {
@@ -102,34 +107,31 @@ static void integrate_image(int mytask, void *tasks)
return;
}
- if ( hdf5_read(hdfile, pargs->image, 0) ) {
+ /* FIXME: Nominal photon energy */
+ if ( hdf5_read(hdfile, pargs->image, 0, nominal_photon_energy) ) {
ERROR("Couldn't read '%s'\n", image->filename);
hdfile_close(hdfile);
return;
}
/* Figure out which spots should appear in this pattern */
- spots = find_intersections(image, image->indexed_cell,
- image->div, image->bw, &n, 0);
+ spots = find_intersections(image, image->indexed_cell, &n, 1);
/* For each reflection, estimate the partiality */
for ( j=0; j<n; j++ ) {
signed int h, k, l;
float i_partial;
- double p;
float xc, yc;
+ float i_full_est;
h = spots[j].h;
k = spots[j].k;
l = spots[j].l;
- /* Calculated partiality of this spot in this pattern */
- p = partiality(image, h, k, l);
-
/* Don't attempt to use spots with very small
* partialities, since it won't be accurate. */
- if ( p < 0.1 ) continue;
+ if ( spots[j].p < 0.1 ) continue;
/* Actual measurement of this reflection from this
* pattern? */
@@ -139,8 +141,10 @@ static void integrate_image(int mytask, void *tasks)
continue;
}
+ i_full_est = i_partial * spots[j].p;
+
pthread_mutex_lock(pargs->list_lock);
- integrate_intensity(pargs->i_full, h, k, l, i_partial);
+ integrate_intensity(pargs->i_full, h, k, l, i_full_est);
integrate_count(pargs->cts, h, k, l, 1);
if ( !find_item(pargs->obs, h, k, l) ) {
add_item(pargs->obs, h, k, l);
@@ -249,6 +253,7 @@ int main(int argc, char *argv[])
int n_total_patterns;
struct image *images;
int n_iter = 10;
+ struct beam_params *beam = NULL;
/* Long options */
const struct option longopts[] = {
@@ -256,6 +261,7 @@ int main(int argc, char *argv[])
{"input", 1, NULL, 'i'},
{"output", 1, NULL, 'o'},
{"geometry", 1, NULL, 'g'},
+ {"beam", 1, NULL, 'b'},
{"prefix", 1, NULL, 'x'},
{"basename", 0, &config_basename, 1},
{"no-check-prefix", 0, &config_checkprefix, 0},
@@ -265,7 +271,7 @@ int main(int argc, char *argv[])
};
/* Short options */
- while ((c = getopt_long(argc, argv, "hi:g:x:j:y:o:",
+ while ((c = getopt_long(argc, argv, "hi:g:x:j:y:o:b:",
longopts, NULL)) != -1)
{
@@ -302,6 +308,15 @@ int main(int argc, char *argv[])
n_iter = atoi(optarg);
break;
+ case 'b' :
+ beam = get_beam_parameters(optarg);
+ if ( beam == NULL ) {
+ ERROR("Failed to load beam parameters"
+ " from '%s'\n", optarg);
+ return 1;
+ }
+ break;
+
case 0 :
break;
@@ -348,6 +363,11 @@ int main(int argc, char *argv[])
}
free(geomfile);
+ if ( beam == NULL ) {
+ ERROR("You must provide a beam parameters file.\n");
+ return 1;
+ }
+
/* Prepare for iteration */
i_full = new_list_intensity();
obs = new_items();
@@ -388,13 +408,14 @@ int main(int argc, char *argv[])
snprintf(fnamereal, 1023, "%s%s", prefix, filename);
images[i].filename = fnamereal;
- images[i].div = 0.5e-3;
- images[i].bw = 0.001;
+ images[i].div = beam->divergence;
+ images[i].bw = beam->bandwidth;
images[i].orientation.w = 1.0;
images[i].orientation.x = 0.0;
images[i].orientation.y = 0.0;
images[i].orientation.z = 0.0;
images[i].det = det;
+ images[i].beam = beam;
/* Muppet proofing */
images[i].data = NULL;