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-rw-r--r--src/gui_backend_local.c159
1 files changed, 89 insertions, 70 deletions
diff --git a/src/gui_backend_local.c b/src/gui_backend_local.c
index d78fc037..ba56bd7c 100644
--- a/src/gui_backend_local.c
+++ b/src/gui_backend_local.c
@@ -116,11 +116,7 @@ static int write_file_list(GFile *workdir,
if ( fh == NULL ) return 1;
for ( i=0; i<n_frames; i++ ) {
- if ( filenames[i][0] != '/' ) {
- fprintf(fh, "../%s", filenames[i]);
- } else {
- fprintf(fh, "%s", filenames[i]);
- }
+ fprintf(fh, "%s", filenames[i]);
if ( events[i] != NULL ) {
fprintf(fh, " %s\n", events[i]);
} else {
@@ -177,7 +173,7 @@ static struct local_job *start_local_job(char **args,
r = g_spawn_async_with_pipes(NULL, args, NULL,
G_SPAWN_SEARCH_PATH
| G_SPAWN_DO_NOT_REAP_CHILD,
- setup_subprocess, workdir_str,
+ setup_subprocess, NULL,
&job->pid,
NULL, NULL, &ch_stderr,
&error);
@@ -387,29 +383,37 @@ static void *run_ambi(const char *job_title,
struct local_job *job;
struct local_merging_opts *opts = opts_priv;
GFile *workdir;
- GFile *sc_gfile;
- gchar *sc_filename;
- GFile *stream_gfile;
- char *stream_str;
+ gchar *sc_rel_filename;
+ gchar *stream_rel_filename;
+ gchar *stderr_rel_filename;
+ gchar *stdout_rel_filename;
+ gchar *fg_rel_filename;
+ gchar *intermediate_rel_filename;
+ gchar *harvest_rel_filename;
workdir = make_job_folder(job_title, job_notes);
if ( workdir == NULL ) return NULL;
- stream_gfile = g_file_get_child(workdir, "ambi.stream");
- stream_str = g_file_get_path(stream_gfile);
- g_object_unref(stream_gfile);
+ stream_rel_filename = relative_to_cwd(workdir, "ambi.stream");
+ stdout_rel_filename = relative_to_cwd(workdir, "stdout.log");
+ stderr_rel_filename = relative_to_cwd(workdir, "stderr.log");
+ sc_rel_filename = relative_to_cwd(workdir, "run_ambigator.sh");
+ fg_rel_filename = relative_to_cwd(workdir, "fg.dat");
+ intermediate_rel_filename = relative_to_cwd(workdir, "ambigator-input.stream");
+ harvest_rel_filename = relative_to_cwd(workdir, "parameters.json");
snprintf(n_thread_str, 64, "%i", opts->n_threads);
- sc_gfile = g_file_get_child(workdir, "run_ambigator.sh");
- sc_filename = g_file_get_path(sc_gfile);
- g_object_unref(sc_gfile);
- if ( sc_filename == NULL ) return NULL;
- if ( !write_ambigator_script(sc_filename, input, n_thread_str,
- &proj->ambi_params, stream_str) )
+
+ if ( !write_ambigator_script(sc_rel_filename, input, n_thread_str,
+ &proj->ambi_params, stream_rel_filename,
+ stdout_rel_filename, stderr_rel_filename,
+ fg_rel_filename,
+ intermediate_rel_filename,
+ harvest_rel_filename) )
{
char *args[3];
args[0] = "sh";
- args[1] = sc_filename;
+ args[1] = sc_rel_filename;
args[2] = NULL;
job = start_local_job(args, job_title, workdir,
proj, GUI_JOB_AMBIGATOR);
@@ -419,10 +423,18 @@ static void *run_ambi(const char *job_title,
}
if ( job != NULL ) {
- add_indexing_result(proj, job_title, &stream_str, 1);
+ add_indexing_result(proj, job_title, &stream_rel_filename, 1);
}
g_object_unref(workdir);
+ free(sc_rel_filename);
+ free(stream_rel_filename);
+ free(stdout_rel_filename);
+ free(stderr_rel_filename);
+ free(fg_rel_filename);
+ free(intermediate_rel_filename);
+ free(harvest_rel_filename);
+
return job;
}
@@ -437,25 +449,32 @@ static void *run_merging(const char *job_title,
struct local_job *job;
struct local_merging_opts *opts = opts_priv;
GFile *workdir;
- GFile *sc_gfile;
- gchar *sc_filename;
+ gchar *sc_rel_filename;
+ gchar *output_rel_filename;
+ gchar *stderr_rel_filename;
+ gchar *stdout_rel_filename;
+ gchar *harvest_rel_filename;
workdir = make_job_folder(job_title, job_notes);
if ( workdir == NULL ) return NULL;
+ sc_rel_filename = relative_to_cwd(workdir, "run_merge.sh");
+ output_rel_filename = relative_to_cwd(workdir, "crystfel.hkl");
+ stdout_rel_filename = relative_to_cwd(workdir, "stdout.log");
+ stderr_rel_filename = relative_to_cwd(workdir, "stderr.log");
+ harvest_rel_filename = relative_to_cwd(workdir, "parameters.json");
+
snprintf(n_thread_str, 63, "%i", opts->n_threads);
- sc_gfile = g_file_get_child(workdir, "run_merge.sh");
- sc_filename = g_file_get_path(sc_gfile);
- g_object_unref(sc_gfile);
- if ( sc_filename == NULL ) return NULL;
- if ( !write_merge_script(sc_filename, input, n_thread_str,
- &proj->merging_params, "crystfel.hkl") )
+ if ( !write_merge_script(sc_rel_filename, input, n_thread_str,
+ &proj->merging_params, output_rel_filename,
+ stdout_rel_filename, stderr_rel_filename,
+ harvest_rel_filename) )
{
char *args[3];
enum gui_job_type type;
args[0] = "sh";
- args[1] = sc_filename;
+ args[1] = sc_rel_filename;
args[2] = NULL;
if ( strcmp(proj->merging_params.model, "process_hkl") == 0 ) {
if ( proj->merging_params.scale ) {
@@ -470,34 +489,27 @@ static void *run_merging(const char *job_title,
} else {
job = NULL;
}
- g_free(sc_filename);
if ( job != NULL ) {
- GFile *hkl_gfile;
- char *hkl;
char *hkl1;
char *hkl2;
- hkl_gfile = g_file_get_child(workdir, "crystfel.hkl");
- hkl = g_file_get_path(hkl_gfile);
- g_object_unref(hkl_gfile);
-
- hkl_gfile = g_file_get_child(workdir, "crystfel.hkl1");
- hkl1 = g_file_get_path(hkl_gfile);
- g_object_unref(hkl_gfile);
-
- hkl_gfile = g_file_get_child(workdir, "crystfel.hkl2");
- hkl2 = g_file_get_path(hkl_gfile);
- g_object_unref(hkl_gfile);
+ hkl1 = relative_to_cwd(workdir, "crystfel.hkl1");
+ hkl2 = relative_to_cwd(workdir, "crystfel.hkl2");
- add_merge_result(proj, job_title, hkl, hkl1, hkl2);
- g_free(hkl);
+ add_merge_result(proj, job_title, output_rel_filename,
+ hkl1, hkl2);
g_free(hkl1);
g_free(hkl2);
}
g_object_unref(workdir);
+ g_free(sc_rel_filename);
+ free(output_rel_filename);
+ free(stdout_rel_filename);
+ free(stderr_rel_filename);
+ free(harvest_rel_filename);
return job;
}
@@ -513,9 +525,12 @@ static void *run_indexing(const char *job_title,
struct local_job *job;
char n_thread_str[64];
GFile *workdir;
- GFile *sc_gfile;
- gchar *sc_filename;
- GFile *stderr_gfile;
+ gchar *sc_rel_filename;
+ gchar *stdout_rel_filename;
+ gchar *stderr_rel_filename;
+ gchar *files_rel_filename;
+ gchar *stream_rel_filename;
+ gchar *harvest_rel_filename;
workdir = make_job_folder(job_title, job_notes);
if ( workdir == NULL ) return NULL;
@@ -530,16 +545,23 @@ static void *run_indexing(const char *job_title,
}
snprintf(n_thread_str, 63, "%i", opts->n_processes);
- sc_gfile = g_file_get_child(workdir, "run_indexamajig.sh");
- sc_filename = g_file_get_path(sc_gfile);
- g_object_unref(sc_gfile);
- if ( sc_filename == NULL ) return NULL;
- if ( !write_indexamajig_script(sc_filename,
+
+ sc_rel_filename = relative_to_cwd(workdir, "run_indexamajig.sh");
+ stdout_rel_filename = relative_to_cwd(workdir, "stdout.log");
+ stderr_rel_filename = relative_to_cwd(workdir, "stderr.log");
+ files_rel_filename = relative_to_cwd(workdir, "files.lst");
+ stream_rel_filename = relative_to_cwd(workdir, "crystfel.stream");
+ harvest_rel_filename = relative_to_cwd(workdir, "parameters.json");
+
+ if ( !write_indexamajig_script(sc_rel_filename,
proj->geom_filename,
n_thread_str,
- "files.lst",
- "crystfel.stream",
- NULL, 1,
+ files_rel_filename,
+ stream_rel_filename,
+ stdout_rel_filename,
+ stderr_rel_filename,
+ harvest_rel_filename,
+ NULL,
&proj->peak_search_params,
&proj->indexing_params,
wavelength_estimate,
@@ -547,7 +569,7 @@ static void *run_indexing(const char *job_title,
{
char *args[3];
args[0] = "sh";
- args[1] = sc_filename;
+ args[1] = sc_rel_filename;
args[2] = NULL;
job = start_local_job(args, job_title, workdir,
proj, GUI_JOB_INDEXING);
@@ -557,23 +579,20 @@ static void *run_indexing(const char *job_title,
if ( job != NULL ) {
- char *stream_fn;
-
/* Indexing-specific job data */
job->n_frames = proj->n_frames;
+ job->stderr_filename = strdup(stderr_rel_filename);
+ add_indexing_result(proj, job_title, &stream_rel_filename, 1);
- stderr_gfile = g_file_get_child(workdir, "stderr.log");
- job->stderr_filename = g_file_get_path(stderr_gfile);
- g_object_unref(stderr_gfile);
-
- GFile *stream_gfile = g_file_get_child(job->workdir,
- "crystfel.stream");
- stream_fn = g_file_get_path(stream_gfile);
- g_object_unref(stream_gfile);
- add_indexing_result(proj, job_title, &stream_fn, 1);
- g_free(stream_fn);
+ } else {
}
g_object_unref(workdir);
+ free(sc_rel_filename);
+ free(files_rel_filename);
+ free(stream_rel_filename);
+ free(stdout_rel_filename);
+ free(stderr_rel_filename);
+ free(harvest_rel_filename);
return job;
}
generated by cgit v1.2.3 (git 2.25.1) at 2024-09-29 14:12:37 +0000