Merge branch 'tom/speed'

7 files changed, 50 insertions, 15 deletions

diff --git a/libcrystfel/src/cell.c b/libcrystfel/src/cell.c
index 31d3b9b1..b6ea010b 100644
--- a/libcrystfel/src/cell.c
+++ b/libcrystfel/src/cell.c
@@ -694,7 +694,7 @@ static int same_vector(struct cvec a, struct cvec b)
 
 /* Attempt to make 'cell' fit into 'template' somehow */
 UnitCell *match_cell(UnitCell *cell, UnitCell *template, int verbose,
-                     float *tols, int reduce)
+                     const float *tols, int reduce)
 {
 	signed int n1l, n2l, n3l;
 	double asx, asy, asz;
diff --git a/libcrystfel/src/cell.h b/libcrystfel/src/cell.h
index cbe84772..bd2719dd 100644
--- a/libcrystfel/src/cell.h
+++ b/libcrystfel/src/cell.h
@@ -118,7 +118,7 @@ extern UnitCell *rotate_cell(UnitCell *in, double omega, double phi,
 extern void cell_print(UnitCell *cell);
 
 extern UnitCell *match_cell(UnitCell *cell, UnitCell *tempcell, int verbose,
-                            float *ltl, int reduce);
+                            const float *ltl, int reduce);
 
 extern UnitCell *match_cell_ab(UnitCell *cell, UnitCell *tempcell);
 
diff --git a/libcrystfel/src/index.c b/libcrystfel/src/index.c
index f4bc9d6c..102a5312 100644
--- a/libcrystfel/src/index.c
+++ b/libcrystfel/src/index.c
@@ -167,7 +167,7 @@ void map_all_peaks(struct image *image)
 
 void index_pattern(struct image *image, UnitCell *cell, IndexingMethod *indm,
                    int cellr, int verbose, IndexingPrivate **ipriv,
-                   int config_insane, float *ltl)
+                   int config_insane, const float *ltl)
 {
 	int i;
 	int n = 0;
diff --git a/libcrystfel/src/index.h b/libcrystfel/src/index.h
index c4e15f09..9d23f3fb 100644
--- a/libcrystfel/src/index.h
+++ b/libcrystfel/src/index.h
@@ -74,7 +74,8 @@ extern void map_all_peaks(struct image *image);
 
 extern void index_pattern(struct image *image, UnitCell *cell,
                           IndexingMethod *indm, int cellr, int verbose,
-                          IndexingPrivate **priv, int config_insane, float *ltl);
+                          IndexingPrivate **priv, int config_insane,
+                          const float *ltl);
 
 extern void cleanup_indexing(IndexingPrivate **priv);
 
diff --git a/libcrystfel/src/mosflm.c b/libcrystfel/src/mosflm.c
index 410b779a..ed118aa4 100644
--- a/libcrystfel/src/mosflm.c
+++ b/libcrystfel/src/mosflm.c
@@ -379,7 +379,6 @@ static int mosflm_readable(struct image *image, struct mosflm_data *mosflm)
 
 	rval = read(mosflm->pty, mosflm->rbuffer+mosflm->rbufpos,
 	            mosflm->rbuflen-mosflm->rbufpos);
-
 	if ( (rval == -1) || (rval == 0) ) return 1;
 
 	mosflm->rbufpos += rval;
@@ -436,7 +435,6 @@ static int mosflm_readable(struct image *image, struct mosflm_data *mosflm)
 				break;
 
 			case MOSFLM_INPUT_PROMPT :
-
 				mosflm_send_next(image, mosflm);
 				endbit_length = i+7;
 				break;
@@ -513,6 +511,7 @@ void run_mosflm(struct image *image, UnitCell *cell)
 	remove(mosflm->newmatfile);
 
 	mosflm->pid = forkpty(&mosflm->pty, NULL, NULL, NULL);
+
 	if ( mosflm->pid == -1 ) {
 		ERROR("Failed to fork for MOSFLM\n");
 		free(mosflm);
@@ -545,6 +544,7 @@ void run_mosflm(struct image *image, UnitCell *cell)
 	mosflm->step = 1;	/* This starts the "initialisation" procedure */
 	mosflm->finished_ok = 0;
 
+
 	do {
 
 		fd_set fds;
@@ -559,7 +559,7 @@ void run_mosflm(struct image *image, UnitCell *cell)
 
 		sval = select(mosflm->pty+1, &fds, NULL, NULL, &tv);
 
-		if ( sval == -1 ) {
+                if ( sval == -1 ) {
 			int err = errno;
 			ERROR("select() failed: %s\n", strerror(err));
 			rval = 1;
@@ -570,6 +570,7 @@ void run_mosflm(struct image *image, UnitCell *cell)
 			rval = 1;
 		}
 
+
 	} while ( !rval );
 
 	close(mosflm->pty);
diff --git a/libcrystfel/src/peaks.c b/libcrystfel/src/peaks.c
index ffe77290..0a6a439c 100644
--- a/libcrystfel/src/peaks.c
+++ b/libcrystfel/src/peaks.c
@@ -160,6 +160,8 @@ static int *make_BgMask(struct image *image, struct panel *p,
 	mask = calloc(w*h, sizeof(int));
 	if ( mask == NULL ) return NULL;
 
+	if ( image->reflections == NULL ) return mask;
+
 	/* Loop over all reflections */
 	for ( refl = first_refl(image->reflections, &iter);
 	      refl != NULL;
@@ -278,17 +280,26 @@ static int integrate_peak(struct image *image, int cfs, int css,
 
 			/* It must have all the "good" bits to be valid */
 			if ( !((flags & image->det->mask_good)
-			                   == image->det->mask_good) ) return 1;
+			                   == image->det->mask_good) ) {
+				free(bgPkMask);
+				return 1;
+			}
 
 			/* If it has any of the "bad" bits, reject */
-			if ( flags & image->det->mask_bad ) return 1;
+			if ( flags & image->det->mask_bad ) {
+				free(bgPkMask);
+				return 1;
+			}
 
 		}
 
 		val = image->data[idx];
 
 		/* Veto peak if it contains saturation in bg region */
-		if ( use_max_adu && (val > p->max_adu) ) return 1;
+		if ( use_max_adu && (val > p->max_adu) ) {
+			free(bgPkMask);
+			return 1;
+		}
 
 		bg_tot += val;
 		bg_tot_sq += pow(val, 2.0);
@@ -297,7 +308,10 @@ static int integrate_peak(struct image *image, int cfs, int css,
 	}
 	}
 
-	if ( bg_counts == 0 ) return 1;
+	if ( bg_counts == 0 ) {
+		free(bgPkMask);
+		return 1;
+	}
 	bg_mean = bg_tot / bg_counts;
 	bg_var = (bg_tot_sq/bg_counts) - pow(bg_mean, 2.0);
 
@@ -330,17 +344,26 @@ static int integrate_peak(struct image *image, int cfs, int css,
 
 			/* It must have all the "good" bits to be valid */
 			if ( !((flags & image->det->mask_good)
-			                   == image->det->mask_good) ) return 1;
+			                   == image->det->mask_good) ) {
+				free(bgPkMask);
+				return 1;
+			}
 
 			/* If it has any of the "bad" bits, reject */
-			if ( flags & image->det->mask_bad ) return 1;
+			if ( flags & image->det->mask_bad ) {
+				free(bgPkMask);
+				return 1;
+			}
 
 		}
 
 		val = image->data[idx] - bg_mean;
 
 		/* Veto peak if it contains saturation */
-		if ( use_max_adu && (image->data[idx] > p->max_adu) ) return 1;
+		if ( use_max_adu && (image->data[idx] > p->max_adu) ) {
+			free(bgPkMask);
+			return 1;
+		}
 
 		pk_counts++;
 		pk_total += val;
@@ -358,7 +381,10 @@ static int integrate_peak(struct image *image, int cfs, int css,
 
 	var = pk_counts * bg_var;
 	var += aduph * pk_total;
-	if ( var < 0.0 ) return 1;
+	if ( var < 0.0 ) {
+		free(bgPkMask);
+		return 1;
+	}
 
 	if ( intensity != NULL ) *intensity = pk_total;
 	if ( sigma != NULL ) *sigma = sqrt(var);
diff --git a/libcrystfel/src/reax.c b/libcrystfel/src/reax.c
index 58dce40a..3124a77c 100644
--- a/libcrystfel/src/reax.c
+++ b/libcrystfel/src/reax.c
@@ -348,6 +348,7 @@ static double iterate_refine_vector(double *x, double *y, double *z,
 
 	gsl_matrix_free(C);
 	gsl_vector_free(A);
+	gsl_vector_free(t);
 
 	return dtmax;
 }
@@ -1019,6 +1020,7 @@ void reax_index(IndexingPrivate *pp, struct image *image, UnitCell *cell)
 	fftw_complex *fft_out;
 	double pmax;
 	struct reax_search *s;
+	int i;
 
 	assert(pp->indm == INDEXING_REAX);
 	p = (struct reax_private *)pp;
@@ -1045,6 +1047,11 @@ void reax_index(IndexingPrivate *pp, struct image *image, UnitCell *cell)
 
 	assemble_cells_from_candidates(image, s, cell);
 
+	for ( i=0; i<s->n_search; i++ ) {
+		free(s->search[i].cand);
+	}
+	free(s->search);
+	free(s);
 	fftw_free(fft_in);
 	fftw_free(fft_out);
 }