aboutsummaryrefslogtreecommitdiff
diff options
context:
space:
mode:
Diffstat
-rw-r--r--src/im-sandbox.c107
-rw-r--r--src/im-sandbox.h2
-rw-r--r--src/indexamajig.c14
-rw-r--r--src/process_image.c32
-rw-r--r--src/process_image.h2
5 files changed, 99 insertions, 58 deletions
diff --git a/src/im-sandbox.c b/src/im-sandbox.c
index a748b8e0..2c6e44ee 100644
--- a/src/im-sandbox.c
+++ b/src/im-sandbox.c
@@ -102,6 +102,8 @@ struct sandbox
int *stream_pipe_write;
char **last_filename;
+ char *tmpdir;
+
struct sb_reader *reader;
};
@@ -179,7 +181,7 @@ static char *get_pattern(FILE *fh, char **use_this_one_instead,
static void run_work(const struct index_args *iargs,
int filename_pipe, int results_pipe, Stream *st,
- int cookie)
+ int cookie, const char *tmpdir)
{
int allDone = 0;
FILE *fh;
@@ -226,7 +228,7 @@ static void run_work(const struct index_args *iargs,
pargs.filename = line;
pargs.n_crystals = 0;
- process_image(iargs, &pargs, st, cookie);
+ process_image(iargs, &pargs, st, cookie, tmpdir);
/* Request another image */
c = sprintf(buf, "%i\n", pargs.n_crystals);
@@ -448,44 +450,6 @@ static void *run_reader(void *rdv)
}
-static int create_temporary_folder(signed int n)
-{
- int r;
- char tmp[64];
- struct stat s;
-
- if ( n < 0 ) {
- snprintf(tmp, 63, "indexamajig.%i", getpid());
- } else {
- snprintf(tmp, 63, "worker.%i", n);
- }
-
- if ( stat(tmp, &s) == -1 ) {
- if ( errno != ENOENT ) {
- ERROR("Failed to stat temporary folder.\n");
- return 1;
- }
-
- r = mkdir(tmp, S_IRWXU | S_IRWXG | S_IROTH | S_IXOTH);
- if ( r ) {
- ERROR("Failed to create temporary folder: %s\n",
- strerror(errno));
- return 1;
- }
-
- }
-
- r = chdir(tmp);
- if ( r ) {
- ERROR("Failed to chdir to temporary folder: %s\n",
- strerror(errno));
- return 1;
- }
-
- return 0;
-}
-
-
static void start_worker_process(struct sandbox *sb, int slot,
int argc, char *argv[])
{
@@ -521,6 +485,9 @@ static void start_worker_process(struct sandbox *sb, int slot,
int j;
struct sigaction sa;
int r;
+ char *tmp;
+ struct stat s;
+ size_t ll;
/* First, disconnect the signal handler */
sa.sa_flags = 0;
@@ -532,7 +499,28 @@ static void start_worker_process(struct sandbox *sb, int slot,
return;
}
- create_temporary_folder(slot);
+ ll = 64 + strlen(sb->tmpdir);
+ tmp = malloc(ll);
+ if ( tmp == NULL ) {
+ ERROR("Failed to allocate temporary dir\n");
+ return;
+ }
+
+ snprintf(tmp, 63, "%s/worker.%i", sb->tmpdir, slot);
+
+ if ( stat(tmp, &s) == -1 ) {
+ if ( errno != ENOENT ) {
+ ERROR("Failed to stat temporary folder.\n");
+ return;
+ }
+
+ r = mkdir(tmp, S_IRWXU | S_IRWXG | S_IROTH | S_IXOTH);
+ if ( r ) {
+ ERROR("Failed to create temporary folder: %s\n",
+ strerror(errno));
+ return;
+ }
+ }
/* Free resources which will not be needed by worker */
for ( j=0; j<sb->n_proc; j++ ) {
@@ -562,7 +550,7 @@ static void start_worker_process(struct sandbox *sb, int slot,
write_command(st, argc, argv);
write_line(st, "FLUSH");
run_work(sb->iargs, filename_pipe[0], result_pipe[1],
- st, slot);
+ st, slot, tmp);
close_stream(st);
//close(filename_pipe[0]);
@@ -640,7 +628,7 @@ static void handle_zombie(struct sandbox *sb)
void create_sandbox(struct index_args *iargs, int n_proc, char *prefix,
int config_basename, FILE *fh, char *use_this_one_instead,
- int ofd, int argc, char *argv[])
+ int ofd, int argc, char *argv[], const char *tempdir)
{
int i;
int allDone;
@@ -648,6 +636,8 @@ void create_sandbox(struct index_args *iargs, int n_proc, char *prefix,
int r;
pthread_t reader_thread;
struct sandbox *sb;
+ size_t ll;
+ struct stat s;
sb = calloc(1, sizeof(struct sandbox));
if ( sb == NULL ) {
@@ -729,7 +719,35 @@ void create_sandbox(struct index_args *iargs, int n_proc, char *prefix,
return;
}
- if ( create_temporary_folder(-1) ) return;
+ if ( tempdir == NULL ) {
+ tempdir = strdup("");
+ }
+
+ ll = 64+strlen(tempdir);
+ sb->tmpdir = malloc(ll);
+ if ( sb->tmpdir == NULL ) {
+ ERROR("Failed to allocate temporary directory name\n");
+ return;
+ }
+ snprintf(sb->tmpdir, ll, "%s/indexamajig.%i", tempdir, getpid());
+
+ if ( stat(sb->tmpdir, &s) == -1 ) {
+
+ int r;
+
+ if ( errno != ENOENT ) {
+ ERROR("Failed to stat temporary folder.\n");
+ return;
+ }
+
+ r = mkdir(sb->tmpdir, S_IRWXU | S_IRWXG | S_IROTH | S_IXOTH);
+ if ( r ) {
+ ERROR("Failed to create temporary folder: %s\n",
+ strerror(errno));
+ return;
+ }
+
+ }
/* Fork the right number of times */
lock_sandbox(sb);
@@ -912,6 +930,7 @@ void create_sandbox(struct index_args *iargs, int n_proc, char *prefix,
free(sb->filename_pipes);
free(sb->result_fhs);
free(sb->pids);
+ free(sb->tmpdir);
pthread_mutex_destroy(&sb->lock);
diff --git a/src/im-sandbox.h b/src/im-sandbox.h
index 9248b226..c0c8eba4 100644
--- a/src/im-sandbox.h
+++ b/src/im-sandbox.h
@@ -39,4 +39,4 @@
extern void create_sandbox(struct index_args *iargs, int n_proc, char *prefix,
int config_basename, FILE *fh,
char *use_this_one_instead, int streamfd,
- int argc, char *argv[]);
+ int argc, char *argv[], const char *tempdir);
diff --git a/src/indexamajig.c b/src/indexamajig.c
index b36bbbc2..7d3747ba 100644
--- a/src/indexamajig.c
+++ b/src/indexamajig.c
@@ -132,6 +132,7 @@ static void show_help(const char *s)
"\n"
"\nOptions for greater performance:\n\n"
" -j <n> Run <n> analyses in parallel. Default 1.\n"
+" --temp-dir=<path> Put the temporary folder under <path>.\n"
"\n"
"\nOptions you probably won't need:\n\n"
" --no-check-prefix Don't attempt to correct the --prefix.\n"
@@ -171,6 +172,7 @@ int main(int argc, char *argv[])
struct index_args iargs;
char *intrad = NULL;
char *int_str = NULL;
+ char *tempdir = NULL;
/* Defaults */
iargs.cell = NULL;
@@ -253,6 +255,7 @@ int main(int argc, char *argv[])
{"int-radius", 1, NULL, 14},
{"median-filter", 1, NULL, 15},
{"integration", 1, NULL, 16},
+ {"temp-dir", 1, NULL, 17},
{0, 0, NULL, 0}
};
@@ -377,6 +380,10 @@ int main(int argc, char *argv[])
int_str = strdup(optarg);
break;
+ case 17 :
+ tempdir = strdup(optarg);
+ break;
+
case 0 :
break;
@@ -391,6 +398,10 @@ int main(int argc, char *argv[])
}
+ if ( tempdir == NULL ) {
+ tempdir = strdup(".");
+ }
+
if ( filename == NULL ) {
filename = strdup("-");
}
@@ -559,9 +570,10 @@ int main(int argc, char *argv[])
iargs.ipriv = ipriv;
create_sandbox(&iargs, n_proc, prefix, config_basename, fh,
- use_this_one_instead, ofd, argc, argv);
+ use_this_one_instead, ofd, argc, argv, tempdir);
free(prefix);
+ free(tempdir);
free_detector_geometry(iargs.det);
return 0;
diff --git a/src/process_image.c b/src/process_image.c
index 6d214c33..0e8eedbc 100644
--- a/src/process_image.c
+++ b/src/process_image.c
@@ -33,6 +33,7 @@
#include <stdlib.h>
#include <hdf5.h>
#include <gsl/gsl_errno.h>
+#include <unistd.h>
#include "utils.h"
#include "hdf5-file.h"
@@ -50,7 +51,7 @@
void process_image(const struct index_args *iargs, struct pattern_args *pargs,
- Stream *st, int cookie)
+ Stream *st, int cookie, const char *tmpdir)
{
float *data_for_measurement;
size_t data_size;
@@ -58,27 +59,21 @@ void process_image(const struct index_args *iargs, struct pattern_args *pargs,
struct hdfile *hdfile;
struct image image;
int i;
- char filename[1024];
-
- /* Prefix to jump out of temporary folder */
- if ( pargs->filename[0] != '/' ) {
- snprintf(filename, 1023, "../../%s", pargs->filename);
- } else {
- snprintf(filename, 1023, "%s", pargs->filename);
- }
+ int r;
+ char *rn;
image.features = NULL;
image.data = NULL;
image.flags = NULL;
image.copyme = iargs->copyme;
image.id = cookie;
- image.filename = pargs->filename; /* Relative to top level */
+ image.filename = pargs->filename;
image.beam = iargs->beam;
image.det = iargs->det;
image.crystals = NULL;
image.n_crystals = 0;
- hdfile = hdfile_open(filename); /* Relative to temporary folder */
+ hdfile = hdfile_open(image.filename);
if ( hdfile == NULL ) return;
if ( iargs->element != NULL ) {
@@ -151,9 +146,24 @@ void process_image(const struct index_args *iargs, struct pattern_args *pargs,
free(image.data);
image.data = data_for_measurement;
+ rn = get_current_dir_name();
+
+ r = chdir(tmpdir);
+ if ( r ) {
+ ERROR("Failed to chdir to temporary folder: %s\n",
+ strerror(errno));
+ return;
+ }
+
/* Index the pattern */
index_pattern(&image, iargs->indm, iargs->ipriv);
+ r = chdir(rn);
+ if ( r ) {
+ ERROR("Failed to chdir: %s\n", strerror(errno));
+ return;
+ }
+
pargs->n_crystals = image.n_crystals;
/* Default beam parameters */
diff --git a/src/process_image.h b/src/process_image.h
index ac197927..b9339cd1 100644
--- a/src/process_image.h
+++ b/src/process_image.h
@@ -89,7 +89,7 @@ struct pattern_args
extern void process_image(const struct index_args *iargs,
struct pattern_args *pargs, Stream *st,
- int cookie);
+ int cookie, const char *tmpdir);
#endif /* PROCESS_IMAGEs_H */
generated by cgit v1.2.3 (git 2.25.1) at 2024-07-04 17:35:27 +0000