5 files changed, 330 insertions, 54 deletions

diff --git a/src/gui_ambi.c b/src/gui_ambi.c
index 294196fc..8ab0acc3 100644
--- a/src/gui_ambi.c
+++ b/src/gui_ambi.c
@@ -452,3 +452,39 @@ gint ambi_sig(GtkWidget *widget, struct crystfelproject *proj)
 
 	return FALSE;
 }
+
+
+int write_ambigator_script(const char *filename,
+                           struct gui_indexing_result *input,
+                           const char *n_thread_str,
+                           struct ambi_params *params,
+                           const char *out_stream)
+{
+	FILE *fh;
+	char *exe_path;
+	int i;
+
+	fh = fopen(filename, "w");
+	if ( fh == NULL ) return 1;
+
+	fprintf(fh, "cat \\\n");
+	for ( i=0; i<input->n_streams; i++ ) {
+		fprintf(fh, "%s \\\n", input->streams[i]);
+	}
+
+	exe_path = get_crystfel_exe("ambigator");
+	if ( exe_path == NULL ) return 1;
+	fprintf(fh, "| %s - \\\n", exe_path);
+
+	fprintf(fh, " -j %s", n_thread_str);
+	fprintf(fh, " -o %s", out_stream);
+	fprintf(fh, " -y %s", params->sym);
+//	if ( params->source_sym != NULL ) {
+//		fprintf(fh, " -w %s", params->source_sym);
+//	}
+
+	fprintf(fh, " --iterations=%i", params->niter);
+
+	fclose(fh);
+	return 0;
+}
diff --git a/src/gui_ambi.h b/src/gui_ambi.h
index f63c29a0..f577e3c1 100644
--- a/src/gui_ambi.h
+++ b/src/gui_ambi.h
@@ -36,4 +36,10 @@
 extern gint ambi_sig(GtkWidget *widget,
                      struct crystfelproject *proj);
 
+extern int write_ambigator_script(const char *filename,
+                                  struct gui_indexing_result *input,
+                                  const char *n_thread_str,
+                                  struct ambi_params *params,
+                                  const char *out_stream);
+
 #endif
diff --git a/src/gui_backend_local.c b/src/gui_backend_local.c
index 3af63ea0..21d12aad 100644
--- a/src/gui_backend_local.c
+++ b/src/gui_backend_local.c
@@ -38,6 +38,7 @@
 #include "gui_project.h"
 #include "gui_index.h"
 #include "gui_merge.h"
+#include "gui_ambi.h"
 
 
 struct local_indexing_opts
@@ -123,14 +124,23 @@ static gboolean index_readable(GIOChannel *source, GIOCondition cond,
 }
 
 
-static int write_file_list(char **filenames,
+static int write_file_list(GFile *workdir,
+                           const char *listname,
+                           char **filenames,
                            char **events,
                            int n_frames)
 {
 	FILE *fh;
 	int i;
+	GFile *list_gfile;
+	char *list_str;
 
-	fh = fopen("files.lst", "w");
+	list_gfile = g_file_get_child(workdir, listname);
+	list_str = g_file_get_path(list_gfile);
+	if ( list_str == NULL ) return 1;
+
+	fh = fopen(list_str, "w");
+	free(list_str);
 	if ( fh == NULL ) return 1;
 
 	for ( i=0; i<n_frames; i++ ) {
@@ -157,21 +167,11 @@ void setup_subprocess(gpointer user_data)
 }
 
 
-static struct local_job *start_local_job(char **args,
-                                         const char *job_title,
-                                         const char *job_notes,
-                                         struct crystfelproject *proj,
-                                         GIOFunc readable_func)
+static GFile *make_job_folder(const char *job_title,
+                              const char *job_notes)
 {
-	GIOChannel *ioch;
-	int i;
-	int r;
-	int ch_stderr;
-	GError *error;
-	struct local_job *job;
 	struct stat s;
 	char *workdir;
-	const char *old_pwd;
 	GFile *workdir_file;
 	GFile *cwd_file;
 	GFile *notes_file;
@@ -197,6 +197,7 @@ static struct local_job *start_local_job(char **args,
 	workdir_file = g_file_get_child(cwd_file, workdir);
 	g_object_unref(cwd_file);
 
+	/* Write the notes into notes.txt */
 	notes_file = g_file_get_child(workdir_file, "notes.txt");
 	notes_path = g_file_get_path(notes_file);
 	fh = fopen(notes_path, "w");
@@ -205,18 +206,31 @@ static struct local_job *start_local_job(char **args,
 	g_free(notes_path);
 	g_object_unref(notes_file);
 
+	return workdir_file;
+}
+
+
+
+static struct local_job *start_local_job(char **args,
+                                         const char *job_title,
+                                         GFile *workdir_file,
+                                         struct crystfelproject *proj,
+                                         GIOFunc readable_func)
+{
+	GIOChannel *ioch;
+	int i;
+	int r;
+	int ch_stderr;
+	GError *error;
+	struct local_job *job;
+	char *workdir_str;
+
+	workdir_str = g_file_get_path(workdir_file);
+	if ( workdir_str == NULL ) return NULL;
+
 	job = malloc(sizeof(struct local_job));
 	if ( job == NULL ) return NULL;
 
-	old_pwd = getcwd(NULL, 0);
-	chdir(workdir);
-	if ( write_file_list(proj->filenames, proj->events, proj->n_frames) ) {
-		STATUS("Failed to write list\n");
-		free(job);
-		return NULL;
-	}
-	chdir(old_pwd);
-
 	job->frac_complete = 0.0;
 	job->workdir = workdir_file;
 
@@ -227,17 +241,16 @@ static struct local_job *start_local_job(char **args,
 	}
 	STATUS("\n");
 
+	error = NULL;
 	r = g_spawn_async_with_pipes(NULL, args, NULL,
 	                             G_SPAWN_SEARCH_PATH
 	                           | G_SPAWN_DO_NOT_REAP_CHILD,
-	                             setup_subprocess, workdir,
+	                             setup_subprocess, workdir_str,
 	                             &job->pid,
 	                             NULL, NULL, &ch_stderr,
 	                             &error);
 	if ( r == FALSE ) {
-		ERROR("Failed to start program: %s\n",
-		      error->message);
-		g_object_unref(workdir_file);
+		ERROR("Failed to start program: %s\n", error->message);
 		free(job);
 		return NULL;
 	}
@@ -442,13 +455,63 @@ static gboolean merge_readable(GIOChannel *source, GIOCondition cond,
 }
 
 
+static gboolean ambi_readable(GIOChannel *source, GIOCondition cond,
+                              void *vp)
+{
+	/* FIXME: Implementation */
+	return TRUE;
+}
+
+
 static void *run_ambi(const char *job_title,
                       const char *job_notes,
                       struct crystfelproject *proj,
                       struct gui_indexing_result *input,
                       void *opts_priv)
 {
-	return NULL;
+	char n_thread_str[64];
+	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;
+
+	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);
+
+	snprintf(n_thread_str, 64, "%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_ambigator_script(sc_filename, input, n_thread_str,
+	                             &proj->ambi_params, stream_str) )
+	{
+		char *args[2];
+		args[0] = "run_ambigator.sh";
+		args[1] = NULL;
+		job = start_local_job(args, job_title, workdir,
+		                      proj, ambi_readable);
+	} else {
+		job = NULL;
+	}
+
+	if ( job != NULL ) {
+		char **streams = malloc(sizeof(char *));
+		if ( streams != NULL ) {
+			streams[0] = stream_str;
+			add_indexing_result(proj, strdup(job_title), streams, 1);
+		}
+	}
+
+	g_object_unref(workdir);
+	return job;
 }
 
 
@@ -459,41 +522,58 @@ static void *run_merging(const char *job_title,
                          void *opts_priv)
 {
 	char n_thread_str[64];
-	char **args;
 	struct local_job *job;
 	struct local_merging_opts *opts = opts_priv;
-	GFile *hkl_gfile;
-	char *hkl;
-	char *hkl1;
-	char *hkl2;
+	GFile *workdir;
+	GFile *sc_gfile;
+	gchar *sc_filename;
+
+	workdir = make_job_folder(job_title, job_notes);
+	if ( workdir == NULL ) return NULL;
 
 	snprintf(n_thread_str, 63, "%i", opts->n_threads);
-	args = merging_command_line(n_thread_str,
-	                            input,
-	                            &proj->merging_params);
+	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") )
+	{
+		char *args[3];
+		args[0] = "sh";
+		args[1] = sc_filename;
+		args[2] = NULL;
+		job = start_local_job(args, job_title, workdir,
+		                      proj, merge_readable);
+	} else {
+		job = NULL;
+	}
+	g_free(sc_filename);
 
-	job = start_local_job(args, job_title, job_notes, proj,
-	                      merge_readable);
+	if ( job != NULL ) {
 
-	if ( job == NULL ) return NULL;
+		GFile *hkl_gfile;
+		char *hkl;
+		char *hkl1;
+		char *hkl2;
 
-	hkl_gfile = g_file_get_child(job->workdir,
-	                             "crystfel.hkl");
-	hkl = g_file_get_path(hkl_gfile);
-	g_object_unref(hkl_gfile);
+		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(job->workdir,
-	                             "crystfel.hkl1");
-	hkl1 = 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(job->workdir,
-	                             "crystfel.hkl2");
-	hkl2 = 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);
 
-	add_merge_result(proj, strdup(job_title), hkl, hkl1, hkl2);
+		add_merge_result(proj, strdup(job_title), hkl, hkl1, hkl2);
+	}
 
+	g_object_unref(workdir);
 	return job;
 }
 
@@ -509,6 +589,19 @@ static void *run_indexing(const char *job_title,
 	char **args;
 	char **streams;
 	int i;
+	GFile *workdir;
+
+	workdir = make_job_folder(job_title, job_notes);
+	if ( workdir == NULL ) return NULL;
+
+	if ( write_file_list(workdir, "files.lst",
+		             proj->filenames,
+		             proj->events,
+		             proj->n_frames) )
+	{
+		STATUS("Failed to write list\n");
+		return NULL;
+	}
 
 	snprintf(n_thread_str, 63, "%i", opts->n_processes);
 	args = indexamajig_command_line(proj->geom_filename,
@@ -524,8 +617,8 @@ static void *run_indexing(const char *job_title,
 	}
 	STATUS("\n");
 
-	job = start_local_job(args, job_title, job_notes, proj,
-	                      index_readable);
+	job = start_local_job(args, job_title, workdir,
+	                      proj, index_readable);
 	if ( job == NULL ) return NULL;
 
 	/* Indexing-specific job data */
diff --git a/src/gui_merge.c b/src/gui_merge.c
index ae94fd30..11d48117 100644
--- a/src/gui_merge.c
+++ b/src/gui_merge.c
@@ -522,3 +522,138 @@ char **merging_command_line(const char *n_thread_str,
 
 	return arg_strings;
 }
+
+
+static int write_partialator_script(const char *filename,
+                                    struct gui_indexing_result *input,
+                                    const char *n_thread_str,
+                                    struct merging_params *params,
+                                    const char *out_hkl)
+{
+	FILE *fh;
+	char *exe_path;
+	int i;
+
+	fh = fopen(filename, "w");
+	if ( fh == NULL ) return 1;
+
+	exe_path = get_crystfel_exe("partialator");
+	if ( exe_path == NULL ) return 1;
+	fprintf(fh, "%s \\\n", exe_path);
+
+	for ( i=0; i<input->n_streams; i++ ) {
+		fprintf(fh, "%s \\\n", input->streams[i]);
+	}
+
+	fprintf(fh, " -j %s", n_thread_str);
+	fprintf(fh, " -o %s", out_hkl);
+	fprintf(fh, " -y %s", params->symmetry);
+
+	fprintf(fh, " --polarisation=%s", params->polarisation);
+	fprintf(fh, " --min-measurements=%i", params->min_measurements);
+	fprintf(fh, " --max-adu=%f", params->max_adu);
+	fprintf(fh, " --min-res=%f", params->min_res);
+	fprintf(fh, " --push-res=%f", params->push_res);
+
+	if ( params->twin_sym != NULL ) {
+		fprintf(fh, " -w %s", params->twin_sym);
+	}
+
+	if ( params->custom_split != NULL ) {
+		fprintf(fh, " --custom-split=%s", params->custom_split);
+	}
+
+	if ( !params->scale ) {
+		fprintf(fh, " --no-scale");
+	}
+
+	if ( !params->bscale ) {
+		fprintf(fh, " --no-bscale");
+	}
+
+	if ( !params->postref ) {
+		fprintf(fh, " --no-pr");
+	}
+
+	if ( !params->deltacchalf ) {
+		fprintf(fh, " --no-deltacchalf");
+	}
+
+	fprintf(fh, " --iterations=%i", params->niter);
+
+	fprintf(fh, "\n");
+
+	fclose(fh);
+	return 0;
+}
+
+
+static void add_process_hkl(FILE *fh,
+                            const char *exe_path,
+                            struct gui_indexing_result *input,
+                            struct merging_params *params,
+                            const char *out_hkl,
+                            const char *extra_arg,
+                            const char *out_suffix)
+{
+	int i;
+
+	fprintf(fh, "%s \\\n", exe_path);
+
+	for ( i=0; i<input->n_streams; i++ ) {
+		fprintf(fh, " %s \\\n", input->streams[i]);
+	}
+
+	fprintf(fh, " -o %s%s", out_hkl, out_suffix);
+	fprintf(fh, " -y %s", params->symmetry);
+
+	if ( params->scale ) {
+		fprintf(fh, " --scale");
+	}
+
+	fprintf(fh, " --polarisation=%s", params->polarisation);
+	fprintf(fh, " --min-measurements=%i", params->min_measurements);
+	fprintf(fh, " --max-adu=%f", params->max_adu);
+	fprintf(fh, " --min-res=%f", params->min_res);
+	fprintf(fh, " --push-res=%f", params->push_res);
+	fprintf(fh, " %s\n", extra_arg);
+}
+
+
+static int write_process_hkl_script(const char *filename,
+                                    struct gui_indexing_result *input,
+                                    struct merging_params *params,
+                                    const char *out_hkl)
+{
+	FILE *fh;
+	char *exe_path;
+
+	fh = fopen(filename, "w");
+	if ( fh == NULL ) return 1;
+
+	exe_path = get_crystfel_exe("process_hkl");
+	if ( exe_path == NULL ) return 1;
+
+	add_process_hkl(fh, exe_path, input, params, out_hkl, "", "");
+	add_process_hkl(fh, exe_path, input, params, out_hkl, "--even-only", "1");
+	add_process_hkl(fh, exe_path, input, params, out_hkl, "--odd-only", "2");
+
+	fclose(fh);
+	return 0;
+}
+
+
+int write_merge_script(const char *filename,
+                       struct gui_indexing_result *input,
+                       const char *n_thread_str,
+                       struct merging_params *params,
+                       const char *out_hkl)
+{
+	if ( strcmp(params->model, "process_hkl") == 0 ) {
+		return write_process_hkl_script(filename, input,
+		                                params, out_hkl);
+	} else {
+		return write_partialator_script(filename, input, n_thread_str,
+		                                params, out_hkl);
+	}
+}
diff --git a/src/gui_merge.h b/src/gui_merge.h
index 978a3dcd..46d6dcaf 100644
--- a/src/gui_merge.h
+++ b/src/gui_merge.h
@@ -40,4 +40,10 @@ extern char **merging_command_line(const char *n_thread_str,
                                    struct gui_indexing_result *input,
                                    struct merging_params *params);
 
+extern int write_merge_script(const char *filename,
+                              struct gui_indexing_result *input,
+                              const char *n_thread_str,
+                              struct merging_params *params,
+                              const char *out_hkl);
+
 #endif