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-rw-r--r--src/indexamajig.c11
-rw-r--r--src/process_image.c88
-rw-r--r--src/process_image.h1
-rw-r--r--src/time-accounts.c7
-rw-r--r--src/time-accounts.h7
5 files changed, 95 insertions, 19 deletions
diff --git a/src/indexamajig.c b/src/indexamajig.c
index c0334d29..f9b2c94d 100644
--- a/src/indexamajig.c
+++ b/src/indexamajig.c
@@ -85,6 +85,7 @@ static void show_help(const char *s)
" --highres=<n> Absolute resolution cutoff in Angstroms\n"
" --profile Show timing data for performance monitoring\n"
" --temp-dir=<path> Put the temporary folder under <path>\n"
+" --wait-for-file=<n> Time to wait for each file before processing\n"
"\nPeak search options:\n\n"
" --peaks=<method> Peak search method (zaef,peakfinder8,peakfinder9,hdf5,cxi)\n"
" Default: zaef\n"
@@ -382,6 +383,7 @@ int main(int argc, char *argv[])
iargs.copyme = new_imagefile_field_list();
iargs.min_peaks = 0;
iargs.overpredict = 0;
+ iargs.wait_for_file = 0;
if ( iargs.copyme == NULL ) {
ERROR("Couldn't allocate HDF5 field list.\n");
return 1;
@@ -528,6 +530,7 @@ int main(int argc, char *argv[])
{"xgandalf-max-lattice-vector-length", 1, NULL, 356},
{"xgandalf-max-lvl", 1, NULL, 356},
{"spectrum-file", 1, NULL, 357},
+ {"wait-for-file", 1, NULL, 358},
{0, 0, NULL, 0}
};
@@ -922,6 +925,14 @@ int main(int argc, char *argv[])
spectrum_fn = strdup(optarg);
break;
+ case 358:
+ if (sscanf(optarg, "%d", &iargs.wait_for_file) != 1)
+ {
+ ERROR("Invalid value for --wait-for-file\n");
+ return 1;
+ }
+ break;
+
case 0 :
break;
diff --git a/src/process_image.c b/src/process_image.c
index 2fbf0e4a..31abcb21 100644
--- a/src/process_image.c
+++ b/src/process_image.c
@@ -37,6 +37,7 @@
#include <gsl/gsl_statistics_double.h>
#include <gsl/gsl_sort.h>
#include <unistd.h>
+#include <sys/stat.h>
#include "utils.h"
#include "hdf5-file.h"
@@ -102,7 +103,6 @@ void process_image(const struct index_args *iargs, struct pattern_args *pargs,
int serial, struct sb_shm *sb_shared, TimeAccounts *taccs,
char *last_task)
{
- int check;
struct imagefile *imfile;
struct image image;
int i;
@@ -111,6 +111,9 @@ void process_image(const struct index_args *iargs, struct pattern_args *pargs,
char *rn;
float **prefilter;
int any_crystals;
+ int wait_message_done = 0;
+ int read_retry_done = 0;
+ signed int file_wait_time = iargs->wait_for_file;
image.features = NULL;
image.copyme = iargs->copyme;
@@ -124,22 +127,81 @@ void process_image(const struct index_args *iargs, struct pattern_args *pargs,
image.serial = serial;
image.indexed_by = INDEXING_NONE;
+ time_accounts_set(taccs, TACC_WAITFILE);
+ set_last_task(last_task, "wait for file");
+
+ do {
+
+ struct stat statbuf;
+
+ sb_shared->pings[cookie]++;
+ r = stat(image.filename, &statbuf);
+ if ( r ) {
+
+ if ( (iargs->wait_for_file != 0)
+ && (file_wait_time != 0) )
+ {
+
+ if ( !wait_message_done ) {
+ STATUS("Waiting for '%s'\n",
+ image.filename);
+ wait_message_done = 1;
+ }
+
+ sleep(1);
+ if ( iargs->wait_for_file != -1 ) {
+ file_wait_time--;
+ }
+ continue;
+
+ }
+
+ ERROR("File %s not found\n", image.filename);
+ return;
+ }
+
+ } while ( r );
+
time_accounts_set(taccs, TACC_HDF5OPEN);
set_last_task(last_task, "open file");
sb_shared->pings[cookie]++;
- imfile = imagefile_open(image.filename);
- if ( imfile == NULL ) {
- ERROR("Couldn't open file: %s\n", image.filename);
- return;
- }
- time_accounts_set(taccs, TACC_HDF5READ);
- set_last_task(last_task, "read file");
- sb_shared->pings[cookie]++;
- check = imagefile_read(imfile, &image, image.event);
- if ( check ) {
- return;
- }
+ do {
+ imfile = imagefile_open(image.filename);
+ if ( imfile == NULL ) {
+ if ( iargs->wait_for_file && !read_retry_done ) {
+ read_retry_done = 1;
+ r = 1;
+ STATUS("File '%s' exists but could not be opened."
+ " Trying again after 10 seconds.\n",
+ image.filename);
+ sleep(10);
+ continue;
+ }
+ ERROR("Couldn't open file: %s\n", image.filename);
+ return;
+ }
+
+ time_accounts_set(taccs, TACC_HDF5READ);
+ set_last_task(last_task, "read file");
+ sb_shared->pings[cookie]++;
+
+ r = imagefile_read(imfile, &image, image.event);
+ if ( r ) {
+ if ( iargs->wait_for_file && !read_retry_done ) {
+ read_retry_done = 1;
+ imagefile_close(imfile);
+ STATUS("File '%s' exists but could not be read."
+ " Trying again after 10 seconds.\n",
+ image.filename);
+ sleep(10);
+ continue;
+ }
+ ERROR("Couldn't open file: %s\n", image.filename);
+ return;
+ }
+
+ } while ( r );
/* Take snapshot of image before applying horrible noise filters */
time_accounts_set(taccs, TACC_FILTER);
diff --git a/src/process_image.h b/src/process_image.h
index d4b1ce59..90925592 100644
--- a/src/process_image.h
+++ b/src/process_image.h
@@ -113,6 +113,7 @@ struct index_args
struct xgandalf_options xgandalf_opts;
struct felix_options felix_opts;
struct spectrum *spectrum;
+ signed int wait_for_file; /* -1 means wait forever */
};
diff --git a/src/time-accounts.c b/src/time-accounts.c
index 15a984cd..2c1b5c7c 100644
--- a/src/time-accounts.c
+++ b/src/time-accounts.c
@@ -3,11 +3,11 @@
*
* Simple profiling according to wall clock time
*
- * Copyright © 2016 Deutsches Elektronen-Synchrotron DESY,
- * a research centre of the Helmholtz Association.
+ * Copyright © 2016-2018 Deutsches Elektronen-Synchrotron DESY,
+ * a research centre of the Helmholtz Association.
*
* Authors:
- * 2016 Thomas White <taw@physics.org>
+ * 2016-2018 Thomas White <taw@physics.org>
*
* This file is part of CrystFEL.
*
@@ -173,6 +173,7 @@ static const char *taccname(enum timeaccount acc)
case TACC_ENDCHECK : return "Checking end";
case TACC_WAKEUP : return "Waking up workers";
case TACC_WAITPID : return "Waiting on workers";
+ case TACC_WAITFILE : return "Waiting for image file";
case TACC_HDF5OPEN : return "Opening image file";
case TACC_HDF5READ : return "Reading image file";
case TACC_FILTER : return "Image filters";
diff --git a/src/time-accounts.h b/src/time-accounts.h
index 92b459e1..43cc56ea 100644
--- a/src/time-accounts.h
+++ b/src/time-accounts.h
@@ -3,11 +3,11 @@
*
* Simple profiling according to wall clock time
*
- * Copyright © 2016 Deutsches Elektronen-Synchrotron DESY,
- * a research centre of the Helmholtz Association.
+ * Copyright © 2016-2018 Deutsches Elektronen-Synchrotron DESY,
+ * a research centre of the Helmholtz Association.
*
* Authors:
- * 2016 Thomas White <taw@physics.org>
+ * 2016-2018 Thomas White <taw@physics.org>
*
* This file is part of CrystFEL.
*
@@ -44,6 +44,7 @@ enum timeaccount
TACC_ENDCHECK,
TACC_WAKEUP,
TACC_WAITPID,
+ TACC_WAITFILE,
TACC_HDF5OPEN,
TACC_HDF5READ,
TACC_FILTER,
generated by cgit v1.2.3 (git 2.25.1) at 2024-11-05 21:51:50 +0000