diff options
| -rw-r--r-- | src/gui_ambi.c | 36 | ||||
| -rw-r--r-- | src/gui_ambi.h | 6 | ||||
| -rw-r--r-- | src/gui_backend_local.c | 201 | ||||
| -rw-r--r-- | src/gui_merge.c | 135 | ||||
| -rw-r--r-- | src/gui_merge.h | 6 |
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 |