partialator: Tidy up old log files, and add --no-logs

3 files changed, 42 insertions, 54 deletions

diff --git a/src/partialator.c b/src/partialator.c
index 760af036..d548e956 100644
--- a/src/partialator.c
+++ b/src/partialator.c
@@ -40,6 +40,7 @@
 #include <assert.h>
 #include <pthread.h>
 #include <gsl/gsl_errno.h>
+#include <sys/stat.h>
 
 #include <image.h>
 #include <utils.h>
@@ -325,7 +326,8 @@ static void show_help(const char *s)
 "  -j <n>                     Run <n> analyses in parallel.\n"
 "      --no-free              Disable cross-validation (testing only).\n"
 "      --custom-split         List of files for custom dataset splitting.\n"
-"      --max-rel-B            Maximum allowable relative |B| factor.\n");
+"      --max-rel-B            Maximum allowable relative |B| factor.\n"
+"      --no-logs              Do not write extensive log files.\n");
 }
 
 
@@ -738,35 +740,6 @@ static void show_all_residuals(Crystal **crystals, int n_crystals,
 }
 
 
-static void dump_parameters(const char *filename, Crystal **crystals,
-                            int n_crystals)
-{
-	FILE *fh;
-	fh = fopen(filename, "w");
-	if ( fh == NULL ) {
-		ERROR("Couldn't open partialator.params!\n");
-	} else {
-		fprintf(fh, "  cr        OSF       relB         div"
-		            " flag                      filename  event\n");
-		int i;
-		for ( i=0; i<n_crystals; i++ ) {
-			struct image *img;
-                        char *evt_str;
-			img = crystal_get_image(crystals[i]);
-                        evt_str = get_event_string(img->event);
-			fprintf(fh, "%4i %10.5f %10.2f %8.5e %-25s %s %s\n",
-			        i, crystal_get_osf(crystals[i]),
-			        crystal_get_Bfac(crystals[i])*1e20,
-			        crystal_get_image(crystals[i])->div,
-			        str_prflag(crystal_get_user_flag(crystals[i])),
-			        img->filename, evt_str);
-                        free(evt_str);
-		}
-		fclose(fh);
-	}
-}
-
-
 struct log_qargs
 {
 	int iter;
@@ -878,6 +851,7 @@ int main(int argc, char *argv[])
 	double max_B = 1e-18;
 	char *rfile = NULL;
 	RefList *reference = NULL;
+	int no_logs = 0;
 
 	/* Long options */
 	const struct option longopts[] = {
@@ -910,6 +884,7 @@ int main(int argc, char *argv[])
 		{"polarization",       0, &polarisation,       1}, /* compat */
 		{"no-free",            0, &no_free,            1},
 		{"output-every-cycle", 0, &output_everycycle,  1},
+		{"no-logs",            0, &no_logs,            1},
 
 		{0, 0, NULL, 0}
 	};
@@ -1084,7 +1059,22 @@ int main(int argc, char *argv[])
 
 	if ( (pmodel == PMODEL_UNITY) && !no_pr ) {
 		no_pr = 1;
-		STATUS("Setting --no-pr because we are not modelling partialities (--model=unity).\n");
+		STATUS("Setting --no-pr because we are not modelling "
+		       "partialities (--model=unity).\n");
+	}
+
+	if ( !no_logs ) {
+		int r = mkdir("pr-logs", S_IRWXU | S_IRWXG | S_IROTH | S_IXOTH);
+		if ( r ) {
+			if ( errno == EEXIST ) {
+				ERROR("A folder called 'pr-logs' exists in the "
+				      "working directory.\n");
+				ERROR("Please delete or move it first.\n");
+			} else {
+				ERROR("Failed to create pr-logs folder.\n");
+			}
+			return 1;
+		}
 	}
 
 	/* Read the custom split list (if applicable) */
@@ -1263,7 +1253,9 @@ int main(int argc, char *argv[])
 	check_rejection(crystals, n_crystals, full, max_B);
 	show_all_residuals(crystals, n_crystals, full);
 	write_pgraph(full, crystals, n_crystals, 0, "");
-	if ( !no_pr ) write_logs_parallel(crystals, n_crystals, full, 0, nthreads);
+	if ( !no_pr && !no_logs ) {
+		write_logs_parallel(crystals, n_crystals, full, 0, nthreads);
+	}
 
 	/* Iterate */
 	for ( i=0; i<n_iter; i++ ) {
@@ -1271,7 +1263,8 @@ int main(int argc, char *argv[])
 		STATUS("Scaling and refinement cycle %i of %i\n", i+1, n_iter);
 
 		if ( !no_pr ) {
-			refine_all(crystals, n_crystals, full, nthreads, pmodel, 0, i+1);
+			refine_all(crystals, n_crystals, full, nthreads, pmodel,
+			           0, i+1, no_logs);
 		} else if ( !no_scale ) {
 			scale_all_to_reference(crystals, n_crystals, full, nthreads);
 		}
@@ -1313,10 +1306,6 @@ int main(int argc, char *argv[])
 				}
 			}
 
-			/* Dump parameters */
-			snprintf(tmp, 1024, "iter%.2d_partialator.params", i+1);
-			dump_parameters(tmp, crystals, n_crystals);
-
 		}
 	}
 
@@ -1336,7 +1325,9 @@ int main(int argc, char *argv[])
 	/* Write final figures of merit (no rejection any more) */
 	show_all_residuals(crystals, n_crystals, full);
 	write_pgraph(full, crystals, n_crystals, -1, "");
-	if ( !no_pr ) write_logs_parallel(crystals, n_crystals, full, -1, nthreads);
+	if ( !no_pr && !no_logs ) {
+		write_logs_parallel(crystals, n_crystals, full, -1, nthreads);
+	}
 
 	/* Output results */
 	STATUS("Writing overall results to %s\n", outfile);
@@ -1356,9 +1347,6 @@ int main(int argc, char *argv[])
 		}
 	}
 
-	/* Dump parameters */
-	dump_parameters("partialator.params", crystals, n_crystals);
-
 	/* Clean up */
 	gsl_rng_free(rng);
 	for ( i=0; i<n_crystals; i++ ) {
diff --git a/src/post-refinement.c b/src/post-refinement.c
index f2355756..1c33e211 100644
--- a/src/post-refinement.c
+++ b/src/post-refinement.c
@@ -3,11 +3,11 @@
  *
  * Post refinement
  *
- * Copyright © 2012-2017 Deutsches Elektronen-Synchrotron DESY,
+ * Copyright © 2012-2018 Deutsches Elektronen-Synchrotron DESY,
  *                       a research centre of the Helmholtz Association.
  *
  * Authors:
- *   2010-2017 Thomas White <taw@physics.org>
+ *   2010-2018 Thomas White <taw@physics.org>
  *
  * This file is part of CrystFEL.
  *
@@ -545,8 +545,6 @@ void write_specgraph(Crystal *crystal, const RefList *full,
 		get_indices(refl, &h, &k, &l);
 		res = resolution(cell, h, k, l);
 
-		/* FIXME Free-flagged reflections only? */
-
 		match = find_refl(full, h, k, l);
 		if ( match == NULL ) continue;
 
@@ -688,7 +686,7 @@ void write_gridscan(Crystal *cr, const RefList *full,
 
 static void do_pr_refine(Crystal *cr, const RefList *full,
                          PartialityModel pmodel, int verbose, int serial,
-                         int cycle)
+                         int cycle, int write_logs)
 {
 	gsl_multimin_fminimizer *min;
 	struct rf_priv priv;
@@ -697,7 +695,6 @@ static void do_pr_refine(Crystal *cr, const RefList *full,
 	int r;
 	double G;
 	double residual_start, residual_free_start;
-	int write_logs = 1;
 	FILE *fh = NULL;
 
 	try_reindex(cr, full);
@@ -710,8 +707,6 @@ static void do_pr_refine(Crystal *cr, const RefList *full,
 		       residual_start, residual_free_start);
 	}
 
-	if ( serial % 20 ) write_logs = 0;
-
 	min = setup_minimiser(cr, full, verbose, serial, &priv);
 
 	if ( verbose ) {
@@ -865,13 +860,13 @@ static void do_pr_refine(Crystal *cr, const RefList *full,
 
 static struct prdata pr_refine(Crystal *cr, const RefList *full,
                                PartialityModel pmodel, int verbose, int serial,
-                               int cycle)
+                               int cycle, int write_logs)
 {
 	struct prdata prdata;
 
 	prdata.refined = 0;
 
-	do_pr_refine(cr, full, pmodel, verbose, serial, cycle);
+	do_pr_refine(cr, full, pmodel, verbose, serial, cycle, write_logs);
 
 	if ( crystal_get_user_flag(cr) == 0 ) {
 		prdata.refined = 1;
@@ -890,6 +885,7 @@ struct refine_args
 	struct prdata prdata;
 	int verbose;
 	int cycle;
+	int no_logs;
 };
 
 
@@ -907,9 +903,12 @@ static void refine_image(void *task, int id)
 {
 	struct refine_args *pargs = task;
 	Crystal *cr = pargs->crystal;
+	int write_logs = 0;
 
+	write_logs = !pargs->no_logs && (pargs->serial % 20 == 0);
 	pargs->prdata = pr_refine(cr, pargs->full, pargs->pmodel,
-	                          pargs->verbose, pargs->serial, pargs->cycle);
+	                          pargs->verbose, pargs->serial, pargs->cycle,
+	                          write_logs);
 }
 
 
@@ -943,7 +942,7 @@ static void done_image(void *vqargs, void *task)
 
 void refine_all(Crystal **crystals, int n_crystals,
                 RefList *full, int nthreads, PartialityModel pmodel,
-                int verbose, int cycle)
+                int verbose, int cycle, int no_logs)
 {
 	struct refine_args task_defaults;
 	struct queue_args qargs;
@@ -954,6 +953,7 @@ void refine_all(Crystal **crystals, int n_crystals,
 	task_defaults.prdata.refined = 0;
 	task_defaults.verbose = verbose;
 	task_defaults.cycle = cycle;
+	task_defaults.no_logs = no_logs;
 
 	qargs.task_defaults = task_defaults;
 	qargs.n_started = 0;
diff --git a/src/post-refinement.h b/src/post-refinement.h
index 13382623..3c4ac7ef 100644
--- a/src/post-refinement.h
+++ b/src/post-refinement.h
@@ -59,7 +59,7 @@ extern const char *str_prflag(enum prflag flag);
 
 extern void refine_all(Crystal **crystals, int n_crystals,
                        RefList *full, int nthreads, PartialityModel pmodel,
-                       int verbose, int cycle);
+                       int verbose, int cycle, int no_logs);
 
 extern void write_gridscan(Crystal *cr, const RefList *full,
                            int cycle, int serial);