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authorThomas White <taw@bitwiz.org.uk>2010-06-11 15:35:44 -0700
committerThomas White <taw@bitwiz.org.uk>2010-06-11 15:35:44 -0700
commit29e67fab67793ce42b889405cf6e7ef1a32d0bdc (patch)
treee9b66ffb56fae17a109d27e15222eba664515831 /src/indexamajig.c
parent1915044fdd7b7de700330450445be9fe5d5b2001 (diff)
Get detector geometry from file
Diffstat (limited to 'src/indexamajig.c')
-rw-r--r--src/indexamajig.c38
1 files changed, 31 insertions, 7 deletions
diff --git a/src/indexamajig.c b/src/indexamajig.c
index 0fb97bfe..39ceea2b 100644
--- a/src/indexamajig.c
+++ b/src/indexamajig.c
@@ -59,6 +59,7 @@ struct process_args
int config_nomatch;
int config_unpolar;
int config_sanity;
+ struct detector *det;
IndexingMethod indm;
const double *intensities;
const unsigned int *counts;
@@ -86,6 +87,7 @@ static void show_help(const char *s)
" --indexing=<method> Use 'method' for indexing. Choose from:\n"
" none : no indexing\n"
" dirax : invoke DirAx\n"
+" -g. --geometry=<file> Get detector geometry from file.\n"
"\n\nWith just the above options, this program does not do much of practical "
"use.\nYou should also enable some of the following:\n\n"
" --near-bragg Output a list of reflection intensities to stdout.\n"
@@ -159,7 +161,7 @@ static struct image *get_simage(struct image *template, int alternate)
* - not necessarily the same as the original. */
image->width = 1024;
image->height = 1024;
- image->det.n_panels = 2;
+ image->det->n_panels = 2;
if ( alternate ) {
@@ -183,12 +185,12 @@ static struct image *get_simage(struct image *template, int alternate)
panels[1].clen = 56.7e-2; /* 56.7 cm */
panels[1].res = 13333.3; /* 75 microns/pixel */
- image->det.panels = panels;
+ image->det->panels = panels;
} else {
/* Copy pointer to old geometry */
- image->det.panels = template->det.panels;
+ image->det->panels = template->det->panels;
}
@@ -263,6 +265,7 @@ static void *process_image(void *pargsv)
image.filename = filename;
image.hits = NULL;
image.n_hits = 0;
+ image.det = pargs->det;
/* View head-on (unit cell is tilted) */
image.orientation.w = 1.0;
@@ -285,8 +288,6 @@ static void *process_image(void *pargsv)
return result;
}
- #include "geometry-lcls.tmp"
-
hdf5_read(hdfile, &image);
if ( config_cmfilter ) {
@@ -372,7 +373,6 @@ static void *process_image(void *pargsv)
done:
free(image.data);
free(image.flags);
- free(image.det.panels);
image_feature_list_free(image.features);
free(image.hits);
hdfile_close(hdfile);
@@ -409,6 +409,8 @@ int main(int argc, char *argv[])
int config_alternate = 0;
int config_unpolar = 0;
int config_sanity = 0;
+ struct detector *det;
+ char *geometry = NULL;
IndexingMethod indm;
char *indm_str = NULL;
UnitCell *cell;
@@ -435,6 +437,7 @@ int main(int argc, char *argv[])
{"near-bragg", 0, &config_nearbragg, 1},
{"write-drx", 0, &config_writedrx, 1},
{"indexing", 1, NULL, 'z'},
+ {"geometry", 1, NULL, 'g'},
{"simulate", 0, &config_simulate, 1},
{"filter-cm", 0, &config_cmfilter, 1},
{"filter-noise", 0, &config_noisefilter, 1},
@@ -450,7 +453,8 @@ int main(int argc, char *argv[])
};
/* Short options */
- while ((c = getopt_long(argc, argv, "hi:wp:j:x:", longopts, NULL)) != -1) {
+ while ((c = getopt_long(argc, argv, "hi:wp:j:x:g:",
+ longopts, NULL)) != -1) {
switch (c) {
case 'h' : {
@@ -488,6 +492,11 @@ int main(int argc, char *argv[])
break;
}
+ case 'g' : {
+ geometry = strdup(optarg);
+ break;
+ }
+
case 0 : {
break;
}
@@ -550,6 +559,18 @@ int main(int argc, char *argv[])
}
free(indm_str);
+ if ( geometry == NULL ) {
+ ERROR("You need to specify a geometry file with --geometry\n");
+ return 1;
+ }
+
+ det = get_detector_geometry(geometry);
+ if ( det == NULL ) {
+ ERROR("Failed to read detector geometry from '%s'\n", geometry);
+ return 1;
+ }
+ free(geometry);
+
cell = load_cell_from_pdb(pdb);
if ( cell == NULL ) {
if ( pdb == NULL ) {
@@ -603,6 +624,7 @@ int main(int argc, char *argv[])
pargs->config_unpolar = config_unpolar;
pargs->config_sanity = config_sanity;
pargs->cell = cell;
+ pargs->det = det;
pargs->indm = indm;
pargs->intensities = intensities;
pargs->counts = counts;
@@ -695,6 +717,8 @@ int main(int argc, char *argv[])
}
free(prefix);
+ free(det->panels);
+ free(det);
free(cell);
fclose(fh);