Add missing cleanup on error paths

15 files changed, 124 insertions, 27 deletions

diff --git a/libcrystfel/src/cell-utils.c b/libcrystfel/src/cell-utils.c
index 30744bd4..2f3dfc6b 100644
--- a/libcrystfel/src/cell-utils.c
+++ b/libcrystfel/src/cell-utils.c
@@ -1588,7 +1588,10 @@ static Rational *find_candidates(double len, double *a, double *b, double *c,
 	if ( cands == NULL ) return NULL;
 
 	rat = rtnl_list(-5, 5, 1, csl ? 4 : 1, &nrat);
-	if ( rat == NULL ) return NULL;
+	if ( rat == NULL ) {
+		free(cands);
+		return NULL;
+	}
 
 	for ( ia=0; ia<nrat; ia++ ) {
 	for ( ib=0; ib<nrat; ib++ ) {
diff --git a/libcrystfel/src/fom.c b/libcrystfel/src/fom.c
index 33887bd8..2f74e945 100644
--- a/libcrystfel/src/fom.c
+++ b/libcrystfel/src/fom.c
@@ -88,10 +88,15 @@ static struct fom_context *init_fom(enum fom_type fom, int nmax, int nshells)
 		fctx->cts[i] = 0;
 	}
 
-	fctx->num = NULL;
-	fctx->den = NULL;
 	fctx->num2 = NULL;
 	fctx->den2 = NULL;
+	fctx->num = NULL;
+	fctx->den = NULL;
+	fctx->n_meas = NULL;
+	fctx->vec1 = NULL;
+	fctx->vec2 = NULL;
+	fctx->n = NULL;
+	fctx->n_within = NULL;
 	fctx->possible = NULL;
 
 	switch ( fctx->fom ) {
@@ -99,7 +104,7 @@ static struct fom_context *init_fom(enum fom_type fom, int nmax, int nshells)
 		case FOM_RANORSPLIT :
 		fctx->num2 = malloc(nshells*sizeof(double));
 		fctx->den2 = malloc(nshells*sizeof(double));
-		if ( (fctx->num2 == NULL) || (fctx->den2 == NULL) ) return NULL;
+		if ( (fctx->num2 == NULL) || (fctx->den2 == NULL) ) goto out;
 		for ( i=0; i<nshells; i++ ) {
 			fctx->num2[i] = 0.0;
 			fctx->den2[i] = 0.0;
@@ -116,7 +121,7 @@ static struct fom_context *init_fom(enum fom_type fom, int nmax, int nshells)
 		case FOM_REDUNDANCY :
 		fctx->num = malloc(nshells*sizeof(double));
 		fctx->den = malloc(nshells*sizeof(double));
-		if ( (fctx->num == NULL) || (fctx->den == NULL) ) return NULL;
+		if ( (fctx->num == NULL) || (fctx->den == NULL) ) goto out;
 		for ( i=0; i<nshells; i++ ) {
 			fctx->num[i] = 0.0;
 			fctx->den[i] = 0.0;
@@ -124,12 +129,12 @@ static struct fom_context *init_fom(enum fom_type fom, int nmax, int nshells)
 		break;
 
 		case FOM_COMPLETENESS :
-		/* Uses 'cts' and 'possible' only */
+		/* Uses 'cts' and 'possible' only - see calculate_possible() */
 		break;
 
 		case FOM_NUM_MEASUREMENTS :
 		fctx->n_meas = calloc(nshells, sizeof(long int));
-		if ( fctx->n_meas == NULL ) return NULL;
+		if ( fctx->n_meas == NULL ) goto out;
 		break;
 
 		case FOM_CC :
@@ -138,15 +143,19 @@ static struct fom_context *init_fom(enum fom_type fom, int nmax, int nshells)
 		case FOM_CRDANO :
 		fctx->vec1 = malloc(nshells*sizeof(double *));
 		fctx->vec2 = malloc(nshells*sizeof(double *));
-		if ( (fctx->vec1 == NULL) || (fctx->vec2 == NULL) ) return NULL;
+		if ( (fctx->vec1 == NULL) || (fctx->vec2 == NULL) ) goto out;
+		for ( i=0; i<nshells; i++ ) {
+			fctx->vec1[i] = NULL;
+			fctx->vec2[i] = NULL;
+		}
 		for ( i=0; i<nshells; i++ ) {
 			fctx->vec1[i] = malloc(nmax*sizeof(double));
-			if ( fctx->vec1[i] == NULL ) return NULL;
+			if ( fctx->vec1[i] == NULL ) goto out;
 			fctx->vec2[i] = malloc(nmax*sizeof(double));
-			if ( fctx->vec2[i] == NULL ) return NULL;
-			fctx->n = malloc(nshells*sizeof(int));
-			if ( fctx->n == NULL ) return NULL;
+			if ( fctx->vec2[i] == NULL ) goto out;
 		}
+		fctx->n = malloc(nshells*sizeof(int));
+		if ( fctx->n == NULL ) goto out;
 		for ( i=0; i<nshells; i++ ) {
 			fctx->n[i] = 0;
 		}
@@ -156,7 +165,7 @@ static struct fom_context *init_fom(enum fom_type fom, int nmax, int nshells)
 		case FOM_D1SIG :
 		case FOM_D2SIG :
 		fctx->n_within = malloc(nshells*sizeof(int));
-		if ( fctx->n_within == NULL ) return NULL;
+		if ( fctx->n_within == NULL ) goto out;
 		for ( i=0; i<nshells; i++ ) {
 			fctx->n_within[i] = 0;
 		}
@@ -165,6 +174,29 @@ static struct fom_context *init_fom(enum fom_type fom, int nmax, int nshells)
 	}
 
 	return fctx;
+
+out:
+	free(fctx->num2);
+	free(fctx->den2);
+	free(fctx->num);
+	free(fctx->den);
+	free(fctx->n_meas);
+	if ( fctx->vec1 != NULL ) {
+		for ( i=0; i<nshells; i++ ) {
+			free(fctx->vec1[i]);
+		}
+		free(fctx->vec1);
+	}
+	if ( fctx->vec2 != NULL ) {
+		for ( i=0; i<nshells; i++ ) {
+			free(fctx->vec2[i]);
+		}
+		free(fctx->vec2);
+	}
+	free(fctx->n);
+	free(fctx->n_within);
+	free(fctx);
+	return NULL;
 }
 
 
@@ -588,6 +620,8 @@ struct fom_shells *fom_make_resolution_shells(double rmin, double rmax,
 
 	if ( (s->rmins==NULL) || (s->rmaxs==NULL) ) {
 		ERROR("Couldn't allocate memory for resolution shells.\n");
+		free(s->rmins);
+		free(s->rmaxs);
 		free(s);
 		return NULL;
 	}
diff --git a/libcrystfel/src/image-cbf.c b/libcrystfel/src/image-cbf.c
index 859ef731..1e5659f4 100644
--- a/libcrystfel/src/image-cbf.c
+++ b/libcrystfel/src/image-cbf.c
@@ -314,7 +314,10 @@ static float *read_cbf_data(const char *filename, int gz, int *w, int *h)
 		} while ( len_read == bufinc );
 
 		fh = fmemopen(buf, len, "rb");
-		if ( fh == NULL ) return NULL;
+		if ( fh == NULL ) {
+			free(buf);
+			return NULL;
+		}
 
 		gzclose(gzfh);
 
@@ -507,7 +510,11 @@ signed int is_cbf_file(const char *filename)
 	fh = fopen(filename, "r");
 	if ( fh == NULL ) return -1;
 
-	if ( fgets(line, 1024, fh) == NULL ) return 0;
+	if ( fgets(line, 1024, fh) == NULL ) {
+		fclose(fh);
+		return 0;
+	}
+
 	fclose(fh);
 
 	if ( strstr(line, "CBF") == NULL ) {
diff --git a/libcrystfel/src/image-hdf5.c b/libcrystfel/src/image-hdf5.c
index 38ebf42b..9cad0a33 100644
--- a/libcrystfel/src/image-hdf5.c
+++ b/libcrystfel/src/image-hdf5.c
@@ -94,7 +94,10 @@ char **read_path_parts(const char *ev_orig, int *pn_plvals)
 	}
 
 	ev = strdup(ev_orig);
-	if ( ev == NULL ) return NULL;
+	if ( ev == NULL ) {
+		free(plvals);
+		return NULL;
+	}
 
 	start = ev;
 	do {
@@ -166,7 +169,10 @@ int *read_dim_parts(const char *ev_orig, int *pn_dvals)
 	}
 
 	ev = strdup(ev+2);
-	if ( ev == NULL ) return NULL;
+	if ( ev == NULL ) {
+		free(dvals);
+		return NULL;
+	}
 
 	start = ev;
 	done = 0;
diff --git a/libcrystfel/src/image.c b/libcrystfel/src/image.c
index 74e6d8d3..3c5af479 100644
--- a/libcrystfel/src/image.c
+++ b/libcrystfel/src/image.c
@@ -603,7 +603,10 @@ int create_detgeom(struct image *image, const DataTemplate *dtempl)
 	if ( detgeom == NULL ) return 1;
 
 	detgeom->panels = malloc(dtempl->n_panels*sizeof(struct detgeom_panel));
-	if ( detgeom->panels == NULL ) return 1;
+	if ( detgeom->panels == NULL ) {
+		free(detgeom);
+		return 1;
+	}
 
 	detgeom->n_panels = dtempl->n_panels;
 
@@ -1493,7 +1496,10 @@ char **image_expand_frames(const DataTemplate *dtempl,
 		list = malloc(sizeof(char *));
 		if ( list == NULL ) return NULL;
 		list[0] = strdup("//");
-		if ( list[0] == NULL ) return NULL;
+		if ( list[0] == NULL ) {
+			free(list);
+			return NULL;
+		}
 		*n_frames = 1;
 		return list;
 	}
diff --git a/libcrystfel/src/index.c b/libcrystfel/src/index.c
index ce341197..d8a135fc 100644
--- a/libcrystfel/src/index.c
+++ b/libcrystfel/src/index.c
@@ -410,11 +410,15 @@ IndexingPrivate *setup_indexing(const char *method_list,
 		                                          ttopts,
 		                                          fromfile_opts);
 
-		if ( ipriv->engine_private[i] == NULL ) return NULL;
+		if ( ipriv->engine_private[i] == NULL ) {
+			free(ipriv->engine_private);
+			return NULL;
+		}
 
 		for ( j=0; j<i; j++ ) {
 			if ( methods[i] == methods[j] ) {
 				ERROR("Duplicate indexing method.\n");
+				free(ipriv->engine_private);
 				return NULL;
 			}
 		}
diff --git a/libcrystfel/src/indexers/asdf.c b/libcrystfel/src/indexers/asdf.c
index a8943688..7030a3e7 100644
--- a/libcrystfel/src/indexers/asdf.c
+++ b/libcrystfel/src/indexers/asdf.c
@@ -180,11 +180,18 @@ static struct asdf_cell *asdf_cell_new(int n)
 	if (c->reflections == NULL) return NULL;
 
 	c->indices = malloc(sizeof(double *) * n);
-	if (c->indices == NULL) return NULL;
+	if (c->indices == NULL) {
+		free(c->reflections);
+		return NULL;
+	}
 
 	for ( i = 0; i < n; i++ ) {
 		c->indices[i] = malloc(sizeof(double) * 3);
-		if (c->indices[i] == NULL) return NULL;
+		if (c->indices[i] == NULL) {
+			free(c->reflections);
+			free(c->indices);
+			return NULL;
+		}
 	}
 
 	c->n = 0;
@@ -973,6 +980,7 @@ static int index_refls(gsl_vector **reflections, int N_reflections,
 	struct tvector *tvectors = malloc(N_triplets * sizeof(struct tvector));
 	if (tvectors == NULL) {
 		ERROR("Failed to allocate tvectors in index_refls!\n");
+		free(fits);
 		return 0;
 	}
 
diff --git a/libcrystfel/src/indexers/felix.c b/libcrystfel/src/indexers/felix.c
index db9cccf8..b7d2a8a3 100644
--- a/libcrystfel/src/indexers/felix.c
+++ b/libcrystfel/src/indexers/felix.c
@@ -143,6 +143,7 @@ static int read_felix(struct felix_private *gp, struct image *image,
 	/* Read and discard first line */
 	if ( fgets( line, 1024, fh ) == NULL ) {
 		ERROR("Failed to read *.felix file.\n");
+		fclose(fh);
 		return 0;
 	}
 
@@ -639,6 +640,7 @@ void *felix_prepare(IndexingMethod *indm, UnitCell *cell,
 	if ( gp->spacegroup == 0 ) {
 		ERROR("Couldn't determine representative space group for your cell.\n");
 		ERROR("Try again with a more conventional cell.\n");
+		free(gp);
 		return NULL;
 	}
 
diff --git a/libcrystfel/src/indexers/fromfile.c b/libcrystfel/src/indexers/fromfile.c
index f0372489..d7dfbd09 100644
--- a/libcrystfel/src/indexers/fromfile.c
+++ b/libcrystfel/src/indexers/fromfile.c
@@ -211,7 +211,10 @@ void *fromfile_prepare(IndexingMethod *indm, struct fromfile_options *opts)
 	}
 
 	dp = malloc(sizeof(struct fromfile_private));
-	if ( dp == NULL ) return NULL;
+	if ( dp == NULL ) {
+		fclose(fh);
+		return NULL;
+	}
 
 	dp->sol_hash = NULL;
 
diff --git a/libcrystfel/src/indexers/mosflm.c b/libcrystfel/src/indexers/mosflm.c
index c56f3ae6..129e6859 100644
--- a/libcrystfel/src/indexers/mosflm.c
+++ b/libcrystfel/src/indexers/mosflm.c
@@ -244,6 +244,7 @@ static int read_newmat(struct mosflm_data *mosflm, const char *filename,
 	n += fscanf(fh, "%f %f %f\n", &asz, &bsz, &csz);
 	if ( n != 9 ) {
 		STATUS("Fewer than 9 parameters found in NEWMAT file.\n");
+		fclose(fh);
 		return 1;
 	}
 
@@ -371,6 +372,7 @@ static void write_img(struct image *image, const char *filename)
 	fh = fopen(filename, "w");
 	if ( !fh ) {
 		ERROR("Couldn't open temporary file '%s'\n", filename);
+		free(intimage);
 		return;
 	}
 
diff --git a/libcrystfel/src/indexers/taketwo.c b/libcrystfel/src/indexers/taketwo.c
index 60bb6fed..cd4d87a6 100644
--- a/libcrystfel/src/indexers/taketwo.c
+++ b/libcrystfel/src/indexers/taketwo.c
@@ -1769,6 +1769,10 @@ static int match_obs_to_cell_vecs(struct TheoryVec *cell_vecs, int cell_vec_coun
 		match_array = &(obs_vecs[i].matches);
 		match_count = &(obs_vecs[i].match_num);
 
+		if ( for_sort == NULL ) {
+			return 0;
+		}
+
 		/* Sort in order to get most agreeable matches first */
 		qsort(for_sort, count, sizeof(struct sortme), sort_theory_distances);
 		*match_array = malloc(count*sizeof(struct TheoryVec));
@@ -1831,6 +1835,7 @@ static int gen_observed_vecs(struct rvec *rlps, int rlp_count,
 				spot_vec.match_num = 0;
 				spot_vec.her_rlp = &rlps[i];
 				spot_vec.his_rlp = &rlps[j];
+				spot_vec.in_network = 0;
 
 				cell->obs_vecs[count - 1] = spot_vec;
 			}
diff --git a/libcrystfel/src/integration.c b/libcrystfel/src/integration.c
index b2b6ccfa..326e3183 100644
--- a/libcrystfel/src/integration.c
+++ b/libcrystfel/src/integration.c
@@ -509,6 +509,7 @@ struct intcontext *intcontext_new(struct image *image,
 	ic->bm = malloc(ic->w * ic->w * sizeof(enum boxmask_val));
 	if ( ic->bm == NULL ) {
 		ERROR("Failed to allocate box mask.\n");
+		free(ic);
 		return NULL;
 	}
 
@@ -516,12 +517,21 @@ struct intcontext *intcontext_new(struct image *image,
 	ic->n_reference_profiles = 1;
 	ic->reference_profiles = calloc(ic->n_reference_profiles,
 	                                sizeof(double *));
-	if ( ic->reference_profiles == NULL ) return NULL;
+	if ( ic->reference_profiles == NULL ) {
+		free(ic);
+		return NULL;
+	}
 	ic->reference_den = calloc(ic->n_reference_profiles, sizeof(double *));
-	if ( ic->reference_den == NULL ) return NULL;
+	if ( ic->reference_den == NULL ) {
+		free(ic);
+		return NULL;
+	}
 	ic->n_profiles_in_reference = calloc(ic->n_reference_profiles,
 	                                     sizeof(int));
-	if ( ic->n_profiles_in_reference == NULL ) return NULL;
+	if ( ic->n_profiles_in_reference == NULL ) {
+		free(ic);
+		return NULL;
+	}
 	for ( i=0; i<ic->n_reference_profiles; i++ ) {
 		ic->reference_profiles[i] = malloc(ic->w*ic->w*sizeof(double));
 		if ( ic->reference_profiles[i] == NULL ) return NULL;
@@ -534,6 +544,7 @@ struct intcontext *intcontext_new(struct image *image,
 	ic->n_boxes = 0;
 	ic->max_boxes = 0;
 	if ( alloc_boxes(ic, 32) ) {
+		free(ic);
 		return NULL;
 	}
 
diff --git a/libcrystfel/src/spectrum.c b/libcrystfel/src/spectrum.c
index 78ad2e6e..bf38a73a 100644
--- a/libcrystfel/src/spectrum.c
+++ b/libcrystfel/src/spectrum.c
@@ -435,6 +435,7 @@ Spectrum *spectrum_load(const char *filename)
 	if ( fgets(line, 1024, fh) != line ) {
 		ERROR("Failed to read '%s'\n", filename);
 		spectrum_free(s);
+		fclose(fh);
 		return NULL;
 	}
 
@@ -444,6 +445,7 @@ Spectrum *spectrum_load(const char *filename)
 			ERROR("Failed to read ESRF spectrum from %s\n",
 			      filename);
 			spectrum_free(s);
+			fclose(fh);
 			return NULL;
 		}
 	} else {
diff --git a/libcrystfel/src/stream.c b/libcrystfel/src/stream.c
index cd64a485..8ffaed1a 100644
--- a/libcrystfel/src/stream.c
+++ b/libcrystfel/src/stream.c
@@ -1568,7 +1568,10 @@ static void add_index_record(StreamIndex *index,
 
 		new_ptrs = realloc(index->ptrs,
 		                   new_max_keys*sizeof(long int));
-		if ( new_ptrs == NULL ) return;
+		if ( new_ptrs == NULL ) {
+			free(new_keys);
+			return;
+		}
 
 		index->keys = new_keys;
 		index->ptrs = new_ptrs;
diff --git a/libcrystfel/src/utils.c b/libcrystfel/src/utils.c
index 864b1a30..4aecfc37 100644
--- a/libcrystfel/src/utils.c
+++ b/libcrystfel/src/utils.c
@@ -820,6 +820,7 @@ char *load_entire_file(const char *filename)
 
 	if ( fread(contents, 1, statbuf.st_size, fh) != statbuf.st_size ) {
 		ERROR("Failed to read file '%s'\n", filename);
+		fclose(fh);
 		free(contents);
 		return NULL;
 	}