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authorThomas White <taw@physics.org>2020-07-01 16:16:41 +0200
committerThomas White <taw@physics.org>2020-07-29 18:53:44 +0200
commit280eb2a5c9897ece5bb57b926e2a759a628e0c78 (patch)
tree2a2e6be497d38e33d4fd50d4f652aeaa29df3384
parent3a5729a9a99fbf9c640bb34da2d70f8a41af006c (diff)
Make sure all HDF5 resources are freed
-rw-r--r--libcrystfel/src/image-hdf5.c130
1 files changed, 81 insertions, 49 deletions
diff --git a/libcrystfel/src/image-hdf5.c b/libcrystfel/src/image-hdf5.c
index a9ced39a..7d6363ac 100644
--- a/libcrystfel/src/image-hdf5.c
+++ b/libcrystfel/src/image-hdf5.c
@@ -44,6 +44,34 @@
#include "datatemplate_priv.h"
+static void close_hdf5(hid_t fh)
+{
+ int n_ids, i;
+ hid_t ids[2048];
+
+ n_ids = H5Fget_obj_ids(fh, H5F_OBJ_ALL, 2048, ids);
+
+ for ( i=0; i<n_ids; i++ ) {
+
+ hid_t id;
+ H5I_type_t type;
+
+ id = ids[i];
+
+ type = H5Iget_type(id);
+
+ if ( type == H5I_GROUP ) H5Gclose(id);
+ if ( type == H5I_DATASET ) H5Dclose(id);
+ if ( type == H5I_DATATYPE ) H5Tclose(id);
+ if ( type == H5I_DATASPACE ) H5Sclose(id);
+ if ( type == H5I_ATTR ) H5Aclose(id);
+
+ }
+
+ H5Fclose(fh);
+}
+
+
/* Get the path parts of the event ID
* e.g. ev_orig = abc/def/ghi//5/2/7
* -> [abc, def, ghi], with *pn_plvals=3.
@@ -343,6 +371,7 @@ static int load_hdf5_hyperslab(struct panel_template *p,
if ( panel_full_path == NULL ) {
ERROR("Invalid path substitution: '%s' '%s'\n",
event, path_spec);
+ close_hdf5(fh);
return 1;
}
@@ -351,7 +380,7 @@ static int load_hdf5_hyperslab(struct panel_template *p,
ERROR("Cannot open data for panel %s (%s)\n",
p->name, panel_full_path);
free(panel_full_path);
- H5Fclose(fh);
+ close_hdf5(fh);
return 1;
}
@@ -364,7 +393,7 @@ static int load_hdf5_hyperslab(struct panel_template *p,
if ( ndims < 0 ) {
ERROR("Failed to get number of dimensions for panel %s\n",
p->name);
- H5Fclose(fh);
+ close_hdf5(fh);
return 1;
}
@@ -385,7 +414,7 @@ static int load_hdf5_hyperslab(struct panel_template *p,
"panel %s (%i, but expected %i or %i)\n",
p->name, ndims, total_dt_dims,
total_dt_dims - plh_dt_dims);
- H5Fclose(fh);
+ close_hdf5(fh);
return 1;
}
} else {
@@ -400,7 +429,7 @@ static int load_hdf5_hyperslab(struct panel_template *p,
f_count = malloc(ndims*sizeof(hsize_t));
if ( (f_offset == NULL) || (f_count == NULL ) ) {
ERROR("Failed to allocate offset or count.\n");
- H5Fclose(fh);
+ close_hdf5(fh);
return 1;
}
@@ -449,7 +478,7 @@ static int load_hdf5_hyperslab(struct panel_template *p,
p->name);
free(f_offset);
free(f_count);
- H5Fclose(fh);
+ close_hdf5(fh);
return 1;
}
@@ -462,7 +491,7 @@ static int load_hdf5_hyperslab(struct panel_template *p,
ERROR("Failed to allocate panel %s\n", p->name);
free(f_offset);
free(f_count);
- H5Fclose(fh);
+ close_hdf5(fh);
return 1;
}
@@ -474,15 +503,13 @@ static int load_hdf5_hyperslab(struct panel_template *p,
free(f_offset);
free(f_count);
free(data);
- H5Fclose(fh);
+ close_hdf5(fh);
return 1;
}
- H5Dclose(dh);
- H5Sclose(dataspace);
free(f_offset);
free(f_count);
- H5Fclose(fh);
+ close_hdf5(fh);
*pdata = data;
return 0;
@@ -605,14 +632,14 @@ double image_hdf5_get_value(const char *name, const char *filename,
subst_name = substitute_path(event, name);
if ( subst_name == NULL ) {
ERROR("Invalid event ID '%s'\n", event);
- H5Fclose(fh);
+ close_hdf5(fh);
return NAN;
}
dh = H5Dopen2(fh, subst_name, H5P_DEFAULT);
if ( dh < 0 ) {
ERROR("No such numeric field '%s'\n", subst_name);
- H5Fclose(fh);
+ close_hdf5(fh);
return NAN;
}
@@ -621,8 +648,7 @@ double image_hdf5_get_value(const char *name, const char *filename,
if ( (class != H5T_FLOAT) && (class != H5T_INTEGER) ) {
ERROR("Not a floating point or integer value.\n");
- H5Tclose(type);
- H5Dclose(dh);
+ close_hdf5(fh);
return NAN;
}
@@ -632,8 +658,7 @@ double image_hdf5_get_value(const char *name, const char *filename,
ndims = H5Sget_simple_extent_ndims(sh);
if ( ndims > 64 ) {
ERROR("Too many dimensions for numeric value\n");
- H5Tclose(type);
- H5Dclose(dh);
+ close_hdf5(fh);
return NAN;
}
H5Sget_simple_extent_dims(sh, size, NULL);
@@ -647,8 +672,7 @@ double image_hdf5_get_value(const char *name, const char *filename,
dim_vals = read_dim_parts(event, &n_dim_vals);
if ( dim_vals == NULL ) {
ERROR("Couldn't parse event '%s'\n");
- H5Tclose(type);
- H5Dclose(dh);
+ close_hdf5(fh);
return NAN;
}
@@ -656,8 +680,7 @@ double image_hdf5_get_value(const char *name, const char *filename,
f_count = malloc(ndims*sizeof(hsize_t));
if ( (f_offset == NULL) || (f_count == NULL) ) {
ERROR("Couldn't allocate dimension arrays\n");
- H5Tclose(type);
- H5Dclose(dh);
+ close_hdf5(fh);
return NAN;
}
@@ -674,6 +697,7 @@ double image_hdf5_get_value(const char *name, const char *filename,
" size %i)\n",
subst_name, i,
dim_vals[dim_val_pos], size[i]);
+ close_hdf5(fh);
return NAN;
}
@@ -696,6 +720,7 @@ double image_hdf5_get_value(const char *name, const char *filename,
ERROR("Error selecting dataspace for float value");
free(f_offset);
free(f_count);
+ close_hdf5(fh);
return NAN;
}
@@ -706,22 +731,21 @@ double image_hdf5_get_value(const char *name, const char *filename,
ERROR("Error selecting memory dataspace for float value");
free(f_offset);
free(f_count);
+ close_hdf5(fh);
return NAN;
}
r = H5Dread(dh, H5T_NATIVE_DOUBLE, ms, sh, H5P_DEFAULT, &val);
if ( r < 0 ) {
ERROR("Couldn't read value.\n");
- H5Tclose(type);
- H5Dclose(dh);
+ close_hdf5(fh);
return NAN;
}
free(f_offset);
free(f_count);
- H5Tclose(type);
free(subst_name);
- H5Fclose(fh);
+ close_hdf5(fh);
return val;
}
@@ -973,16 +997,28 @@ ImageFeatureList *image_hdf5_read_peaks_cxi(const DataTemplate *dtempl,
}
r = read_peak_count(fh, path_n, line, &num_peaks);
- if ( r != 0 ) return NULL;
+ if ( r != 0 ) {
+ close_hdf5(fh);
+ return NULL;
+ }
buf_x = read_peak_line(fh, path_x, line);
- if ( r != 0 ) return NULL;
+ if ( r != 0 ) {
+ close_hdf5(fh);
+ return NULL;
+ }
buf_y = read_peak_line(fh, path_y, line);
- if ( r != 0 ) return NULL;
+ if ( r != 0 ) {
+ close_hdf5(fh);
+ return NULL;
+ }
buf_i = read_peak_line(fh, path_i, line);
- if ( r != 0 ) return NULL;
+ if ( r != 0 ) {
+ close_hdf5(fh);
+ return NULL;
+ }
features = image_feature_list_new();
@@ -1008,6 +1044,8 @@ ImageFeatureList *image_hdf5_read_peaks_cxi(const DataTemplate *dtempl,
}
+ close_hdf5(fh);
+
return features;
}
@@ -1044,6 +1082,7 @@ ImageFeatureList *image_hdf5_read_peaks_hdf5(const DataTemplate *dtempl,
if ( subst_name == NULL ) {
ERROR("Invalid peak path: '%s' '%s'\n",
event, dtempl->peak_list);
+ close_hdf5(fh);
return NULL;
}
@@ -1051,7 +1090,7 @@ ImageFeatureList *image_hdf5_read_peaks_hdf5(const DataTemplate *dtempl,
if ( dh < 0 ) {
ERROR("Peak list (%s) not found.\n", subst_name);
free(subst_name);
- H5Fclose(fh);
+ close_hdf5(fh);
return NULL;
}
free(subst_name);
@@ -1059,17 +1098,14 @@ ImageFeatureList *image_hdf5_read_peaks_hdf5(const DataTemplate *dtempl,
sh = H5Dget_space(dh);
if ( sh < 0 ) {
ERROR("Couldn't get dataspace for peak list.\n");
- H5Dclose(dh);
- H5Fclose(fh);
+ close_hdf5(fh);
return NULL;
}
if ( H5Sget_simple_extent_ndims(sh) != 2 ) {
ERROR("Peak list has the wrong dimensionality (%i).\n",
H5Sget_simple_extent_ndims(sh));
- H5Sclose(sh);
- H5Dclose(dh);
- H5Fclose(fh);
+ close_hdf5(fh);
return NULL;
}
@@ -1079,32 +1115,28 @@ ImageFeatureList *image_hdf5_read_peaks_hdf5(const DataTemplate *dtempl,
tw = size[1];
if ( (tw != 3) && (tw != 4) ) {
ERROR("Peak list has the wrong dimensions.\n");
- H5Dclose(dh);
- H5Fclose(fh);
+ close_hdf5(fh);
return NULL;
}
buf = malloc(sizeof(float)*size[0]*size[1]);
if ( buf == NULL ) {
ERROR("Couldn't reserve memory for the peak list.\n");
- H5Dclose(dh);
- H5Fclose(fh);
+ close_hdf5(fh);
return NULL;
}
r = H5Dread(dh, H5T_NATIVE_FLOAT, H5S_ALL, H5S_ALL,
H5P_DEFAULT, buf);
if ( r < 0 ) {
ERROR("Couldn't read peak list.\n");
- H5Dclose(dh);
- H5Fclose(fh);
+ close_hdf5(fh);
return NULL;
}
features = image_feature_list_new();
if ( features == NULL ) {
ERROR("Failed to allocate peak list\n");
- H5Dclose(dh);
- H5Fclose(fh);
+ close_hdf5(fh);
return NULL;
}
@@ -1131,8 +1163,7 @@ ImageFeatureList *image_hdf5_read_peaks_hdf5(const DataTemplate *dtempl,
}
free(buf);
- H5Dclose(dh);
- H5Fclose(fh);
+ close_hdf5(fh);
return features;
}
@@ -1470,7 +1501,7 @@ char **image_hdf5_expand_frames(const DataTemplate *dtempl,
&n_path_evs);
if ( path_evs == NULL ) {
ERROR("Failed to enumerate paths.\n");
- H5Fclose(fh);
+ close_hdf5(fh);
return NULL;
}
@@ -1510,7 +1541,7 @@ char **image_hdf5_expand_frames(const DataTemplate *dtempl,
ERROR("Error opening '%s'\n", path);
ERROR("Failed to enumerate events. "
"Check your geometry file.\n");
- H5Fclose(fh);
+ close_hdf5(fh);
return NULL;
}
@@ -1520,7 +1551,7 @@ char **image_hdf5_expand_frames(const DataTemplate *dtempl,
ERROR("Unexpected number of dimensions"
"(%s has %i, expected %i)\n",
path, dims, dims_expected);
- H5Fclose(fh);
+ close_hdf5(fh);
return NULL;
}
@@ -1528,13 +1559,13 @@ char **image_hdf5_expand_frames(const DataTemplate *dtempl,
placeholder_sizes = malloc(dims*sizeof(int));
if ( (size == NULL) || (placeholder_sizes == NULL) ) {
ERROR("Failed to allocate dimensions\n");
- H5Fclose(fh);
+ close_hdf5(fh);
return NULL;
}
if ( H5Sget_simple_extent_dims(sh, size, NULL) < 0 ) {
ERROR("Failed to get size\n");
- H5Fclose(fh);
+ close_hdf5(fh);
return NULL;
}
@@ -1579,6 +1610,7 @@ char **image_hdf5_expand_frames(const DataTemplate *dtempl,
}
+ close_hdf5(fh);
free(path_evs);
*pn_frames = full_evs.n_events;
return full_evs.events;