aboutsummaryrefslogtreecommitdiff
path: root/src/geoptimiser.c
diff options
context:
space:
mode:
Diffstat (limited to 'src/geoptimiser.c')
-rw-r--r--src/geoptimiser.c129
1 files changed, 64 insertions, 65 deletions
diff --git a/src/geoptimiser.c b/src/geoptimiser.c
index f66ac709..e8aac2c4 100644
--- a/src/geoptimiser.c
+++ b/src/geoptimiser.c
@@ -3,13 +3,13 @@
*
* Refine detector geometry
*
- * Copyright © 2014-2016 Deutsches Elektronen-Synchrotron DESY,
+ * Copyright © 2014-2019 Deutsches Elektronen-Synchrotron DESY,
* a research centre of the Helmholtz Association.
*
* Authors:
* 2014-2015 Oleksandr Yefanov
* 2014-2015 Valerio Mariani
- * 2014-2016 Thomas White <taw@physics.org>
+ * 2014-2019 Thomas White <taw@physics.org>
*
* This file is part of CrystFEL.
*
@@ -77,13 +77,11 @@ static void show_help(const char *s)
"\n"
" --version Print CrystFEL version number and\n"
" exit.\n"
-" -i, --input=<filename> Specify stream file to be used for \n"
-" geometry optimization.\n"
-" -g. --geometry=<file> Get detector geometry from file.\n"
-" -o, --output=<filename> Output stream.\n"
+" -i, --input=<filename> Input stream\n"
+" -g. --geometry=<file> Input geometry file (if omitted: from stream).\n"
+" -o, --output=<filename> Output geometry file.\n"
" -q, --quadrants=<rg_coll> Rigid group collection for quadrants.\n"
-" -c, --connected=<rg_coll> Rigid group collection for connected\n"
-" ASICs.\n"
+" -c, --connected=<rg_coll> Rigid group collection for connected ASICs.\n"
" --no-error-maps Do not generate error map PNGs.\n"
" --stretch-map Generate stretch map PNG (panels distance).\n"
" -x, --min-num-peaks-per-pixel=<num> Minimum number of peaks per pixel.\n"
@@ -109,9 +107,7 @@ static void show_help(const char *s)
struct geoptimiser_params
{
- char *infile;
char *outfile;
- char *geometry_filename;
int min_num_peaks_per_pix;
int max_num_peaks_per_pix;
int min_num_pix_per_conn_group;
@@ -248,10 +244,9 @@ static double get_average_clen(struct image *image)
}
-static struct image *read_patterns_from_stream(const char *infile,
+static struct image *read_patterns_from_stream(Stream *st,
struct detector *det, int *n)
{
- Stream *st;
struct image *images;
int n_chunks = 0;
int max_images = 1024;
@@ -263,13 +258,6 @@ static struct image *read_patterns_from_stream(const char *infile,
return NULL;
}
- st = open_stream_for_read(infile);
- if ( st == NULL ) {
- ERROR("Failed to open input stream '%s'\n", infile);
- free(images);
- return NULL;
- }
-
do {
images[n_images].det = det;
@@ -313,11 +301,10 @@ static struct image *read_patterns_from_stream(const char *infile,
} while ( 1 );
- close_stream(st);
*n = n_images;
- STATUS("Found %i indexed patterns in file %s (from a total of %i).\n",
- n_images, infile, n_chunks);
+ STATUS("Found %i indexed patterns in stream (from a total of %i).\n",
+ n_images, n_chunks);
return images;
}
@@ -2288,7 +2275,7 @@ void recompute_avg_displ(struct rg_collection *connected,
}
-int optimize_geometry(struct geoptimiser_params *gparams,
+int optimize_geometry(struct geoptimiser_params *gparams, Stream *st,
struct detector *det,
struct rg_collection *quadrants,
struct rg_collection *connected)
@@ -2314,6 +2301,7 @@ int optimize_geometry(struct geoptimiser_params *gparams,
int n_images = 0;
UnitCell *avg_cell;
struct gpanel *gpanels;
+ const char *geometry_data = stream_geometry_file(st);
STATUS("Maximum distance between peaks: %0.1f pixels.\n",
gparams->max_peak_dist);
@@ -2346,10 +2334,9 @@ int optimize_geometry(struct geoptimiser_params *gparams,
"Please restart geometry optimization using the "
"optimized geometry from this run as input "
"geometry file.\n");
- geom_wr = write_detector_geometry_2(
- gparams->geometry_filename,
- gparams->outfile, det,
- gparams->command_line, 1);
+ geom_wr = write_detector_geometry_3(geometry_data,
+ gparams->outfile, det,
+ gparams->command_line, 1);
if ( geom_wr != 0 ) {
ERROR("Error in writing output geometry file.\n");
return 1;
@@ -2391,10 +2378,9 @@ int optimize_geometry(struct geoptimiser_params *gparams,
"Please restart geometry optimization using the "
"optimized geometry from this run as input "
"geometry file.\n");
- geom_wr = write_detector_geometry_2(
- gparams->geometry_filename,
- gparams->outfile, det,
- gparams->command_line, 1);
+ geom_wr = write_detector_geometry_3(geometry_data,
+ gparams->outfile, det,
+ gparams->command_line, 1);
if ( geom_wr != 0 ) {
ERROR("Error in writing output geometry file.\n");
return 1;
@@ -2413,7 +2399,7 @@ int optimize_geometry(struct geoptimiser_params *gparams,
}
}
- images = read_patterns_from_stream(gparams->infile, det, &n_images);
+ images = read_patterns_from_stream(st, det, &n_images);
if ( (n_images < 1) || (images == NULL) ) {
ERROR("Error reading stream file\n");
return 1;
@@ -2603,7 +2589,7 @@ int optimize_geometry(struct geoptimiser_params *gparams,
STATUS("Detector-wide error after correction: RMSD = %0.4f pixels.\n",
total_error);
- write_ret = write_detector_geometry_2(gparams->geometry_filename,
+ write_ret = write_detector_geometry_3(geometry_data,
gparams->outfile, det,
gparams->command_line, 1);
if ( write_ret != 0 ) {
@@ -2632,21 +2618,20 @@ int main(int argc, char *argv[])
int ret_val;
char buffer[256];
char command_line[1024];
-
+ char *infile = NULL;
char *quadrant_coll_name = NULL;
char *connected_coll_name = NULL;
-
+ Stream *st;
struct geoptimiser_params *gparams;
struct detector *det = NULL;
struct rg_collection *quadrants;
struct rg_collection *connected;
struct beam_params beam;
+ char *geometry_filename = NULL;
gparams = malloc(sizeof(struct geoptimiser_params));
gparams->outfile = NULL;
- gparams->infile = NULL;
- gparams->geometry_filename = NULL;
gparams->min_num_peaks_per_pix = 3;
gparams->max_num_peaks_per_pix = 0;
gparams->min_num_pix_per_conn_group = 100;
@@ -2714,18 +2699,11 @@ int main(int argc, char *argv[])
break;
case 'i' :
- gparams->infile = strdup(optarg);
+ infile = strdup(optarg);
break;
case 'g' :
- gparams->geometry_filename = strdup(optarg);
- det = get_detector_geometry(gparams->geometry_filename,
- &beam);
- if ( det == NULL ) {
- ERROR("Failed to read detector geometry from "
- "'%s'\n", optarg);
- return 1;
- }
+ geometry_filename = strdup(optarg);
break;
case 'q' :
@@ -2772,12 +2750,7 @@ int main(int argc, char *argv[])
}
}
- if ( gparams->geometry_filename == NULL ) {
- ERROR("You must provide a geometry to optimize.\n");
- return 1;
- }
-
- if ( gparams->infile == NULL ) {
+ if ( infile == NULL ) {
ERROR("You must provide an input stream file.\n");
return 1;
}
@@ -2799,7 +2772,43 @@ int main(int argc, char *argv[])
return 1;
}
- strcpy(command_line, "\0");
+ command_line[0] = '\0';
+ for ( i=0; i<argc; i++ ) {
+ if ( i > 0 ) strcat(command_line, " ");
+ strcpy(buffer, argv[i]);
+ strcat(command_line, buffer);
+ }
+
+#ifdef CAN_SAVE_TO_PNG
+#if !GLIB_CHECK_VERSION(2,36,0)
+ g_type_init();
+#endif
+#endif
+
+ st = open_stream_for_read(infile);
+ if ( st == NULL ) {
+ ERROR("Failed to open input stream '%s'\n", infile);
+ return 1;
+ }
+
+ if ( geometry_filename == NULL ) {
+ const char *stgeom = stream_geometry_file(st);
+ if ( stgeom != NULL ) {
+ det = get_detector_geometry_from_string(stgeom, &beam, NULL);
+ } else {
+ ERROR("No input geometry file given, and no geometry "
+ "found in stream.\n");
+ return 1;
+ }
+ } else {
+ det = get_detector_geometry(geometry_filename, &beam);
+ free(geometry_filename);
+ }
+
+ if ( det == NULL ) {
+ ERROR("Failed to read initial detector geometry.\n");
+ return 1;
+ }
quadrants = find_rigid_group_collection_by_name(det, quadrant_coll_name);
if ( quadrants == NULL ) {
@@ -2816,19 +2825,9 @@ int main(int argc, char *argv[])
return 1;
}
- for ( i=0; i<argc; i++ ) {
- if ( i > 0 ) strcat(command_line, " ");
- strcpy(buffer, argv[i]);
- strcat(command_line, buffer);
- }
+ ret_val = optimize_geometry(gparams, st, det, quadrants, connected);
-#ifdef CAN_SAVE_TO_PNG
-#if !GLIB_CHECK_VERSION(2,36,0)
- g_type_init();
-#endif
-#endif
-
- ret_val = optimize_geometry(gparams, det, quadrants, connected);
+ close_stream(st);
return ret_val;
}
generated by cgit v1.2.3 (git 2.25.1) at 2024-11-16 05:57:44 +0000