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Diffstat (limited to 'java/src/jni/h5util.c')
-rw-r--r--java/src/jni/h5util.c344
1 files changed, 223 insertions, 121 deletions
diff --git a/java/src/jni/h5util.c b/java/src/jni/h5util.c
index 700f75f..5f1bccb 100644
--- a/java/src/jni/h5util.c
+++ b/java/src/jni/h5util.c
@@ -71,6 +71,12 @@ static int render_bin_output_region_data_points(FILE *stream, hid_t region_s
static int render_bin_output_region_points(FILE *stream, hid_t region_space,
hid_t region_id, hid_t container);
+/* Strings for output */
+#define H5_TOOLS_GROUP "GROUP"
+#define H5_TOOLS_DATASET "DATASET"
+#define H5_TOOLS_DATATYPE "DATATYPE"
+#define H5_TOOLS_ATTRIBUTE "ATTRIBUTE"
+
/** frees memory held by array of strings */
void
h5str_array_free
@@ -217,7 +223,7 @@ h5str_convert
switch (typeSize) {
case sizeof(float):
{
- float tmp_float = 0.0;
+ float tmp_float = 0.0f;
sscanf(token, "%f", &tmp_float);
HDmemcpy(cptr, &tmp_float, sizeof(float));
@@ -625,6 +631,69 @@ done:
return retVal;
} /* end h5str_convert */
+/*-------------------------------------------------------------------------
+ * Function: h5str_sprint_reference
+ *
+ * Purpose: Object reference -- show the name of the referenced object.
+ *
+ * Return: Nothing
+ *-------------------------------------------------------------------------
+ */
+void
+h5str_sprint_reference(JNIEnv *env, h5str_t *out_str, hid_t container, void *ref_p)
+{
+ ssize_t buf_size;
+ char *ref_name = NULL;
+ const H5R_ref_t *ref_vp = (H5R_ref_t *)ref_p;
+
+ UNUSED(container);
+
+ if (!h5str_append(out_str, " \""))
+ CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
+ buf_size = H5Rget_file_name(ref_vp, NULL, 0);
+ if (buf_size) {
+ ref_name = (char *)HDmalloc(sizeof(char) * (size_t)buf_size + 1);
+ if (H5Rget_file_name(ref_vp, ref_name, buf_size + 1) >= 0) {
+ ref_name[buf_size] = '\0';
+ if (!h5str_append(out_str, ref_name))
+ CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
+ }
+ HDfree(ref_name);
+ ref_name = NULL;
+ }
+
+ buf_size = H5Rget_obj_name(ref_vp, H5P_DEFAULT, NULL, 0);
+ if (buf_size) {
+ ref_name = (char *)HDmalloc(sizeof(char) * (size_t)buf_size + 1);
+ if (H5Rget_obj_name(ref_vp, H5P_DEFAULT, ref_name, buf_size + 1) >= 0) {
+ ref_name[buf_size] = '\0';
+ if (!h5str_append(out_str, ref_name))
+ CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
+ }
+ HDfree(ref_name);
+ ref_name = NULL;
+ }
+
+ if (H5Rget_type(ref_vp) == H5R_ATTR) {
+ buf_size = H5Rget_attr_name(ref_vp, NULL, 0);
+ if (buf_size) {
+ ref_name = (char *)HDmalloc(sizeof(char) * (size_t)buf_size + 1);
+ if (H5Rget_attr_name(ref_vp, ref_name, buf_size + 1) >= 0) {
+ ref_name[buf_size] = '\0';
+ if (!h5str_append(out_str, ref_name))
+ CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
+ }
+ HDfree(ref_name);
+ ref_name = NULL;
+ }
+ }
+ if (!h5str_append(out_str, "\""))
+ CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
+done:
+ if (ref_name)
+ HDfree(ref_name);
+}
+
/*
* Prints the value of a data point into a string.
*
@@ -639,8 +708,11 @@ h5str_sprintf
unsigned char *ucptr = (unsigned char *) in_buf;
static char fmt_llong[8], fmt_ullong[8];
H5T_class_t tclass = H5T_NO_CLASS;
+ H5T_str_t pad;
size_t typeSize = 0;
+ H5T_sign_t nsign = H5T_SGN_ERROR;
hid_t mtid = H5I_INVALID_HID;
+ hid_t obj = H5I_INVALID_HID;
char *cptr = (char *) in_buf;
char *this_str = NULL;
int n;
@@ -655,12 +727,14 @@ h5str_sprintf
H5_LIBRARY_ERROR(ENVONLY);
if (!(typeSize = H5Tget_size(tid)))
H5_LIBRARY_ERROR(ENVONLY);
+ if (!(nsign = H5Tget_sign(tid)))
+ H5_LIBRARY_ERROR(ENVONLY);
/* Build default formats for long long types */
if (!fmt_llong[0]) {
- if (HDsprintf(fmt_llong, "%%%sd", H5_PRINTF_LL_WIDTH) < 0)
+ if (HDsnprintf(fmt_llong, sizeof(fmt_llong), "%%%sd", H5_PRINTF_LL_WIDTH) < 0)
H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: sprintf failure");
- if (HDsprintf(fmt_ullong, "%%%su", H5_PRINTF_LL_WIDTH) < 0)
+ if (HDsnprintf(fmt_ullong, sizeof(fmt_ullong), "%%%su", H5_PRINTF_LL_WIDTH) < 0)
H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: sprintf failure");
} /* end if */
@@ -670,7 +744,7 @@ h5str_sprintf
switch (typeSize) {
case sizeof(float):
{
- float tmp_float = 0.0;
+ float tmp_float = 0.0f;
HDmemcpy(&tmp_float, cptr, sizeof(float));
@@ -724,27 +798,28 @@ h5str_sprintf
case H5T_STRING:
{
- htri_t is_variable;
- char *tmp_str;
-
- typeSize = 0;
+ htri_t is_variable;
+ char *tmp_str;
if ((is_variable = H5Tis_variable_str(tid)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if (is_variable) {
- if (NULL != (tmp_str = *(char **) in_buf))
+ /* cp_vp is the pointer into the struct where a `char*' is stored. So we have
+ * to dereference the pointer to get the `char*' to pass to HDstrlen(). */
+ tmp_str = *(char **)in_buf;
+ if (NULL != tmp_str)
typeSize = HDstrlen(tmp_str);
}
else {
tmp_str = cptr;
}
+ pad = H5Tget_strpad(tid);
/* Check for NULL pointer for string */
if (!tmp_str) {
if (NULL == (this_str = (char *) HDmalloc(5)))
H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: failed to allocate string buffer");
-
HDstrncpy(this_str, "NULL", 5);
}
else {
@@ -762,7 +837,6 @@ h5str_sprintf
case H5T_INTEGER:
{
- H5T_sign_t nsign = H5T_SGN_ERROR;
if (H5T_SGN_ERROR == (nsign = H5Tget_sign(tid)))
H5_LIBRARY_ERROR(ENVONLY);
@@ -779,7 +853,7 @@ h5str_sprintf
if (NULL == (this_str = (char *) HDmalloc(7)))
H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: failed to allocate string buffer");
- if (HDsprintf(this_str, "%u", tmp_uchar) < 0)
+ if (HDsprintf(this_str, "%hhu", tmp_uchar) < 0)
H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsprintf failure");
}
else {
@@ -806,7 +880,7 @@ h5str_sprintf
if (NULL == (this_str = (char *) HDmalloc(9)))
H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: failed to allocate string buffer");
- if (HDsprintf(this_str, "%u", tmp_ushort) < 0)
+ if (HDsprintf(this_str, "%hu", tmp_ushort) < 0)
H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsprintf failure");
}
else {
@@ -815,7 +889,7 @@ h5str_sprintf
if (NULL == (this_str = (char *) HDmalloc(9)))
H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: failed to allocate string buffer");
- if (HDsprintf(this_str, "%d", tmp_short) < 0)
+ if (HDsprintf(this_str, "%hd", tmp_short) < 0)
H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsprintf failure");
}
@@ -984,96 +1058,122 @@ h5str_sprintf
break;
}
- if (H5R_DSET_REG_REF_BUF_SIZE == typeSize) {
- H5S_sel_type region_type = H5S_SEL_ERROR;
- hid_t region_obj = H5I_INVALID_HID;
- hid_t region = H5I_INVALID_HID;
- char ref_name[1024];
-
- /*
- * Dataset region reference --
- * show the type and the referenced object
- */
-
- /* Get name of the dataset the region reference points to using H5Rget_name */
- if ((region_obj = H5Rdereference2(container, H5P_DEFAULT, H5R_DATASET_REGION, cptr)) < 0)
- H5_LIBRARY_ERROR(ENVONLY);
-
- if ((region = H5Rget_region(container, H5R_DATASET_REGION, cptr)) < 0)
- H5_LIBRARY_ERROR(ENVONLY);
-
- if (expand_data) {
- if (H5S_SEL_ERROR == (region_type = H5Sget_select_type(region)))
- H5_LIBRARY_ERROR(ENVONLY);
-
- if (H5S_SEL_POINTS == region_type) {
- if (h5str_dump_region_points_data(ENVONLY, out_str, region, region_obj) < 0)
- CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
- }
- else {
- if (h5str_dump_region_blocks_data(ENVONLY, out_str, region, region_obj) < 0)
+ if (H5Tequal(tid, H5T_STD_REF)) {
+ H5O_type_t obj_type; /* Object type */
+ H5R_type_t ref_type; /* Reference type */
+ const H5R_ref_t *ref_vp = (H5R_ref_t *)cptr;
+
+ ref_type = H5Rget_type(ref_vp);
+ H5Rget_obj_type3(ref_vp, H5P_DEFAULT, &obj_type);
+ switch (ref_type) {
+ case H5R_OBJECT1:
+ {
+ /* Object references -- show the type and OID of the referenced object. */
+ H5O_info_t oi;
+
+ if((obj = H5Ropen_object(ref_vp, H5P_DEFAULT, H5P_DEFAULT)) >= 0) {
+ H5Oget_info2(obj, &oi, H5O_INFO_BASIC);
+ if(H5Oclose(obj) < 0)
+ CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
+ }
+ else
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
- }
- }
- else {
- if (H5Rget_name(region_obj, H5R_DATASET_REGION, cptr, (char *)ref_name, 1024) < 0)
- H5_LIBRARY_ERROR(ENVONLY);
- if (!h5str_append(out_str, ref_name))
- CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
-
- if (H5S_SEL_ERROR == (region_type = H5Sget_select_type(region)))
- H5_LIBRARY_ERROR(ENVONLY);
-
- if (H5S_SEL_POINTS == region_type) {
- if (!h5str_append(out_str, " REGION_TYPE POINT"))
+ if (NULL == (this_str = (char *) HDmalloc(14)))
+ H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: failed to allocate string buffer");
+ if (HDsprintf(this_str, "%u-", (unsigned) oi.type) < 0)
+ H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsprintf failure");
+ if (!h5str_append(out_str, this_str))
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
+ HDfree(this_str);
+ this_str = NULL;
+
+ switch (obj_type) {
+ case H5O_TYPE_GROUP:
+ if (!h5str_append(out_str, H5_TOOLS_GROUP))
+ CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
+ break;
+
+ case H5O_TYPE_DATASET:
+ if (!h5str_append(out_str, H5_TOOLS_DATASET))
+ CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
+ break;
+
+ case H5O_TYPE_NAMED_DATATYPE:
+ if (!h5str_append(out_str, H5_TOOLS_DATATYPE))
+ CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
+ break;
+
+ case H5O_TYPE_MAP:
+ case H5O_TYPE_UNKNOWN:
+ case H5O_TYPE_NTYPES:
+ default:
+ break;
+ } /* end switch */
+ H5Oclose(obj);
+ h5str_sprint_reference(ENVONLY, out_str, container, ref_vp);
+
+ /* Print OID */
+ if (NULL == (this_str = (char *) HDmalloc(64)))
+ H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: failed to allocate string buffer");
+ if (HDsprintf(this_str, "%lu:"H5_PRINTF_HADDR_FMT" ", oi.fileno, oi.addr) < 0)
+ H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsprintf failure");
+ }
- if (h5str_dump_region_points(ENVONLY, out_str, region, region_obj) < 0)
+ break;
+ case H5R_DATASET_REGION1:
+ if (!h5str_append(out_str, H5_TOOLS_DATASET))
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
- }
- else {
- if (!h5str_append(out_str, " REGION_TYPE BLOCK"))
+ h5str_sprint_reference(ENVONLY, out_str, container, (void*)cptr);
+ break;
+ case H5R_OBJECT2:
+ switch (obj_type) {
+ case H5O_TYPE_GROUP:
+ if (!h5str_append(out_str, H5_TOOLS_GROUP))
+ CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
+ break;
+
+ case H5O_TYPE_DATASET:
+ if (!h5str_append(out_str, H5_TOOLS_DATASET))
+ CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
+ break;
+
+ case H5O_TYPE_NAMED_DATATYPE:
+ if (!h5str_append(out_str, H5_TOOLS_DATATYPE))
+ CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
+ break;
+
+ case H5O_TYPE_MAP:
+ case H5O_TYPE_UNKNOWN:
+ case H5O_TYPE_NTYPES:
+ default:
+ break;
+ } /* end switch */
+ h5str_sprint_reference(ENVONLY, out_str, container, (void*)cptr);
+ break;
+ case H5R_DATASET_REGION2:
+ if (!h5str_append(out_str, H5_TOOLS_DATASET))
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
-
- if (h5str_dump_region_blocks(ENVONLY, out_str, region, region_obj) < 0)
+ h5str_sprint_reference(ENVONLY, out_str, container, (void*)cptr);
+ break;
+ case H5R_ATTR:
+ if (!h5str_append(out_str, H5_TOOLS_ATTRIBUTE))
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
- }
- }
-
- if (H5Sclose(region) < 0)
- H5_LIBRARY_ERROR(ENVONLY);
- region = H5I_INVALID_HID;
-
- if (H5Dclose(region_obj) < 0)
- H5_LIBRARY_ERROR(ENVONLY);
- region_obj = H5I_INVALID_HID;
+ h5str_sprint_reference(ENVONLY, out_str, container, (void*)cptr);
+ break;
+ case H5R_BADTYPE:
+ case H5R_MAXTYPE:
+ default:
+ break;
+ } /* end switch */
}
- else if (H5R_OBJ_REF_BUF_SIZE == typeSize) {
- H5O_info_t oi;
- hid_t obj = H5I_INVALID_HID;
-
- /*
- * Object references -- show the type and OID of the referenced
- * object.
- */
-
- if (NULL == (this_str = (char *) HDmalloc(64)))
- H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: failed to allocate string buffer");
-
- if ((obj = H5Rdereference2(container, H5P_DEFAULT, H5R_OBJECT, cptr)) < 0)
- H5_LIBRARY_ERROR(ENVONLY);
-
- if (H5Oget_info2(obj, &oi, H5O_INFO_ALL) < 0)
- H5_LIBRARY_ERROR(ENVONLY);
-
- /* Print object data and close object */
- if (HDsprintf(this_str, "%u-%lu", (unsigned) oi.type, oi.addr) < 0)
- H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsprintf failure");
-
- if (H5Oclose(obj) < 0)
- H5_LIBRARY_ERROR(ENVONLY);
- obj = H5I_INVALID_HID;
+ else if (H5Tequal(tid, H5T_STD_REF_DSETREG)) {
+ /* (H5R_DSET_REG_REF_BUF_SIZE == typeSize) */
+ H5_LIBRARY_ERROR(ENVONLY);
+ }
+ else if (H5Tequal(tid, H5T_STD_REF_OBJ)) {
+ /* (H5R_OBJ_REF_BUF_SIZE == typeSize) */
+ H5_LIBRARY_ERROR(ENVONLY);
}
break;
@@ -2204,20 +2304,28 @@ h5str_render_bin_output
case H5T_REFERENCE:
{
- if (H5Tequal(tid, H5T_STD_REF_DSETREG)) {
+ if (H5Tequal(tid, H5T_STD_REF)) {
+ hid_t region_id = H5I_INVALID_HID;
+ hid_t region_space = H5I_INVALID_HID;
H5S_sel_type region_type;
- hid_t region_id, region_space;
/* Region data */
for (block_index = 0; block_index < block_nelmts; block_index++) {
mem = ((unsigned char*)_mem) + block_index * size;
-
- if ((region_id = H5Rdereference2(container, H5P_DEFAULT, H5R_DATASET_REGION, mem)) < 0)
+ if((region_id = H5Ropen_object((const H5R_ref_t *)mem, H5P_DEFAULT, H5P_DEFAULT)) < 0)
continue;
-
- if ((region_space = H5Rget_region(container, H5R_DATASET_REGION, mem)) < 0) {
+ else {
+ if((region_space = H5Ropen_region((const H5R_ref_t *)mem, H5P_DEFAULT, H5P_DEFAULT)) >= 0) {
+ if (!h5str_is_zero(mem, H5Tget_size(H5T_STD_REF))) {
+ region_type = H5Sget_select_type(region_space);
+ if (region_type == H5S_SEL_POINTS)
+ ret_value = render_bin_output_region_points(stream, region_space, region_id, container);
+ else
+ ret_value = render_bin_output_region_blocks(stream, region_space, region_id, container);
+ }
+ H5Sclose(region_space);
+ } /* end if (region_space >= 0) */
H5Dclose(region_id);
- continue;
}
if ((region_type = H5Sget_select_type(region_space)) < 0) {
@@ -2225,19 +2333,13 @@ h5str_render_bin_output
H5Dclose(region_id);
continue;
}
-
- if (region_type == H5S_SEL_POINTS)
- ret_value = render_bin_output_region_points(stream, region_space, region_id, container);
- else
- ret_value = render_bin_output_region_blocks(stream, region_space, region_id, container);
-
- H5Sclose(region_space);
- H5Dclose(region_id);
-
if (ret_value < 0)
break;
}
}
+ else if (H5Tequal(tid, H5T_STD_REF_DSETREG)) {
+ ;
+ }
else if (H5Tequal(tid, H5T_STD_REF_OBJ)) {
;
}
@@ -3091,15 +3193,15 @@ done:
} /* end Java_hdf_hdf5lib_H5_H5Dcopy */
/*
-/////////////////////////////////////////////////////////////////////////////////
-//
-//
-// Add these methods so that we don't need to call H5Gget_objtype_by_idx
-// in a loop to get information for all the objects in a group, which takes
-// a lot of time to finish if the number of objects is more than 10,000
-//
-/////////////////////////////////////////////////////////////////////////////////
-*/
+ * /////////////////////////////////////////////////////////////////////////////////
+ * //
+ * //
+ * // Add these methods so that we don't need to call H5Gget_objtype_by_idx
+ * // in a loop to get information for all the objects in a group, which takes
+ * // a lot of time to finish if the number of objects is more than 10,000
+ * //
+ * /////////////////////////////////////////////////////////////////////////////////
+ */
#ifdef __cplusplus
herr_t obj_info_all(hid_t g_id, const char *name, const H5L_info_t *linfo, void *op_data);
generated by cgit v0.12 at 2024-11-03 11:16:04 (GMT)