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authorThomas White <taw@physics.org>2014-02-13 11:58:25 +0100
committerThomas White <taw@physics.org>2014-02-13 11:58:25 +0100
commitda7099fb56730ab89ce9642c2caf090e7b902c72 (patch)
treed3eeb4d0a00add1ba74f988e675ded57a20824cd /src
parentcae96eaf563f6698b69e142cbf19da0f2888b2bb (diff)
pattern_sim: Add --template
Diffstat (limited to 'src')
-rw-r--r--src/pattern_sim.c87
1 files changed, 74 insertions, 13 deletions
diff --git a/src/pattern_sim.c b/src/pattern_sim.c
index f23be972..a747cd72 100644
--- a/src/pattern_sim.c
+++ b/src/pattern_sim.c
@@ -54,6 +54,7 @@
#include "reflist.h"
#include "reflist-utils.h"
#include "pattern_sim.h"
+#include "stream.h"
static void show_help(const char *s)
@@ -90,6 +91,7 @@ static void show_help(const char *s)
" -s, --sample-spectrum=<N> Use N samples from spectrum. Default 3.\n"
" -x, --spectrum=<type> Type of spectrum to simulate.\n"
" --background=<N> Add N photons of Poisson background (default 0).\n"
+" --template=<file> Take orientations from stream <file>.\n"
);
}
@@ -251,6 +253,8 @@ int main(int argc, char *argv[])
int nsamples = 3;
gsl_rng *rng;
int background = 0;
+ char *template_file = NULL;
+ Stream *st = NULL;
/* Long options */
const struct option longopts[] = {
@@ -276,6 +280,7 @@ int main(int argc, char *argv[])
{"min-size", 1, NULL, 3},
{"max-size", 1, NULL, 4},
{"background", 1, NULL, 5},
+ {"template", 1, NULL, 6},
{0, 0, NULL, 0}
};
@@ -375,6 +380,10 @@ int main(int argc, char *argv[])
}
break;
+ case 6 :
+ template_file = strdup(optarg);
+ break;
+
case 0 :
break;
@@ -406,6 +415,19 @@ int main(int argc, char *argv[])
}
}
+ if ( template_file != NULL ) {
+ if ( config_randomquat ) {
+ ERROR("You cannot use -r and --template together.\n");
+ return 1;
+ }
+ st = open_stream_for_read(template_file);
+ if ( st == NULL ) {
+ ERROR("Failed to open stream.\n");
+ return 1;
+ }
+ free(template_file);
+ }
+
if ( sym_str == NULL ) sym_str = strdup("1");
sym = get_pointgroup(sym_str);
/* sym_str is used below */
@@ -583,23 +605,62 @@ int main(int argc, char *argv[])
}
- /* Read quaternion from stdin */
- if ( config_randomquat ) {
- orientation = random_quaternion(rng);
+ if ( st == NULL ) {
+
+ if ( config_randomquat ) {
+ orientation = random_quaternion(rng);
+ } else {
+ orientation = read_quaternion();
+ }
+
+ STATUS("Orientation is %5.3f %5.3f %5.3f %5.3f\n",
+ orientation.w, orientation.x,
+ orientation.y, orientation.z);
+
+ if ( !quaternion_valid(orientation) ) {
+ ERROR("Orientation modulus is not zero!\n");
+ return 1;
+ }
+
+ cell = cell_rotate(input_cell, orientation);
+
} else {
- orientation = read_quaternion();
- }
- STATUS("Orientation is %5.3f %5.3f %5.3f %5.3f\n",
- orientation.w, orientation.x,
- orientation.y, orientation.z);
+ struct image image;
+ int i;
+ Crystal *cr;
- if ( !quaternion_valid(orientation) ) {
- ERROR("Orientation modulus is not zero!\n");
- return 1;
- }
+ image.det = NULL;
+
+ /* Get data from next chunk */
+ if ( read_chunk(st, &image) ) break;
- cell = cell_rotate(input_cell, orientation);
+ free(image.filename);
+ image_feature_list_free(image.features);
+
+ if ( image.n_crystals == 0 ) continue;
+
+ cr = image.crystals[0];
+ cell = crystal_get_cell(cr);
+
+ if ( image.n_crystals > 1 ) {
+ ERROR("Using the first crystal only.\n");
+ }
+
+ for ( i=1; i<image.n_crystals; i++ ) {
+
+ Crystal *cr = image.crystals[i];
+ cell = crystal_get_cell(cr);
+
+ reflist_free(crystal_get_reflections(cr));
+ cell_free(crystal_get_cell(cr));
+ crystal_free(cr);
+
+ }
+
+ free(image.crystals);
+
+ }
switch ( spectrum_type ) {