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-rw-r--r--java/src/jni/h5util.c716
1 files changed, 556 insertions, 160 deletions
diff --git a/java/src/jni/h5util.c b/java/src/jni/h5util.c
index fdabd76..33dca7f 100644
--- a/java/src/jni/h5util.c
+++ b/java/src/jni/h5util.c
@@ -21,6 +21,7 @@
extern "C" {
#endif /* __cplusplus */
+#include <jni.h>
#include <stdio.h>
#include <string.h>
#include <stdlib.h>
@@ -152,6 +153,513 @@ h5str_append
return HDstrcat(str->s, cstr);
} /* end h5str_append */
+/** print value of a vlen data point into string.
+ Return Value:
+ On success, the total number of characters printed is returned.
+ On error, a negative number is returned.
+ */
+size_t
+h5str_vlconvert
+ (char *str, hid_t container, hid_t tid, hvl_t *ptr, int expand_data)
+{
+ unsigned char tmp_uchar = 0;
+ char tmp_char = 0;
+ unsigned short tmp_ushort = 0;
+ short tmp_short = 0;
+ unsigned int tmp_uint = 0;
+ int tmp_int = 0;
+ unsigned long tmp_ulong = 0;
+ long tmp_long = 0;
+ unsigned long long tmp_ullong = 0;
+ long long tmp_llong = 0;
+ float tmp_float = 0.0;
+ double tmp_double = 0.0;
+ long double tmp_ldouble = 0.0;
+ static char fmt_llong[8], fmt_ullong[8];
+
+ hid_t mtid = -1;
+ size_t offset;
+ size_t nll;
+ char *this_str;
+ size_t this_strlen;
+ int n;
+ H5T_class_t tclass = H5Tget_class(tid);
+ size_t size = H5Tget_size(tid);
+ H5T_sign_t nsign = H5Tget_sign(tid);
+ int bdata_print = 0;
+
+ if (!str || !ptr)
+ return 0;
+
+ this_str = NULL;
+ this_strlen = 0;
+
+ switch (tclass) {
+ case H5T_COMPOUND:
+ {
+ unsigned i;
+ n = H5Tget_nmembers(tid);
+
+ /* remove compound indicators */
+ if (str[0] == ' ')
+ str++;
+ if (str[0] == '{')
+ str++;
+
+ ptr->p = HDcalloc((size_t)1, size);
+ ptr->len = size;
+ for (i = 0; i < n; i++) {
+ offset = H5Tget_member_offset(tid, i);
+ mtid = H5Tget_member_type(tid, i);
+ str += offset;
+ h5str_convert(&str, container, mtid, ptr, 0, expand_data);
+ /* remove compound indicators */
+ if (str[0] == ',')
+ str++;
+ if (str[0] == ' ')
+ str++;
+ H5Tclose(mtid);
+ }
+ /* remove compound indicators */
+ if (str[0] == '}')
+ str++;
+ if (str[0] == ' ')
+ str++;
+ }
+ break;
+ case H5T_ARRAY:
+ {
+ int rank = 0;
+ hsize_t i, dims[H5S_MAX_RANK], total_elmts;
+
+ /* remove array indicators */
+ if (str[0] == '[')
+ str++;
+ if (str[0] == ' ')
+ str++;
+
+ mtid = H5Tget_super(tid);
+ size = H5Tget_size(mtid);
+ rank = H5Tget_array_ndims(tid);
+
+ H5Tget_array_dims2(tid, dims);
+
+ total_elmts = 1;
+ for (i = 0; i < rank; i++)
+ total_elmts *= dims[i];
+
+ ptr->p = HDcalloc((size_t)total_elmts, size);
+ ptr->len = total_elmts;
+ h5str_convert(&str, container, mtid, ptr, 0, expand_data);
+ H5Tclose(mtid);
+ /* remove array indicators */
+ if (str[0] == ' ')
+ str++;
+ if (str[0] == ']')
+ str++;
+ if (str[0] == ' ')
+ str++;
+ }
+ break;
+ default:
+ ptr->len = size;
+ ptr->p = HDcalloc(1, size);
+ this_strlen = h5str_convert(&str, container, tid, ptr, 0, expand_data);
+ break;
+ } /* end switch */
+
+ return this_strlen;
+} /* end h5str_vlconvert */
+
+/** print value of a data point into string.
+ Return Value:
+ On success, the total number of characters printed is returned.
+ On error, a negative number is returned.
+ */
+size_t
+h5str_convert
+ (char **str, hid_t container, hid_t tid, hvl_t *ptr, int ptroffset, int expand_data)
+{
+ unsigned char tmp_uchar = 0;
+ char tmp_char = 0;
+ unsigned short tmp_ushort = 0;
+ short tmp_short = 0;
+ unsigned int tmp_uint = 0;
+ int tmp_int = 0;
+ unsigned long tmp_ulong = 0;
+ long tmp_long = 0;
+ unsigned long long tmp_ullong = 0;
+ long long tmp_llong = 0;
+ float tmp_float = 0.0;
+ double tmp_double = 0.0;
+ long double tmp_ldouble = 0.0;
+ static char fmt_llong[8], fmt_ullong[8];
+ const char delimiter[] = " ,}]";
+
+ char *token;
+ hid_t mtid = -1;
+ size_t offset;
+ size_t nll;
+ char *this_str = *str;
+ size_t this_strlen;
+ int n;
+ char *cptr = ((char*) ((hvl_t *) ptr)->p) + ptroffset;
+ unsigned char *ucptr = ((unsigned char*) ((hvl_t *) ptr)->p) + ptroffset;
+ H5T_class_t tclass = H5Tget_class(tid);
+ size_t size = H5Tget_size(tid);
+ H5T_sign_t nsign = H5Tget_sign(tid);
+ int bdata_print = 0;
+
+ if (!str || !ptr)
+ return 0;
+
+ /* Build default formats for long long types */
+ if (!fmt_llong[0]) {
+ sprintf(fmt_llong, "%%%sd", H5_PRINTF_LL_WIDTH);
+ sprintf(fmt_ullong, "%%%su", H5_PRINTF_LL_WIDTH);
+ } /* end if */
+
+ this_strlen = HDstrlen(this_str);
+
+ switch (tclass) {
+ case H5T_FLOAT:
+ token = HDstrtok (this_str, delimiter);
+ if (sizeof(float) == size) {
+ /* if (H5Tequal(tid, H5T_NATIVE_FLOAT)) */
+ tmp_float = 0;
+ sscanf(token, "%f", &tmp_float);
+ HDmemcpy(cptr, &tmp_float, sizeof(float));
+ }
+ else if (sizeof(double) == size) {
+ /* if (H5Tequal(tid, H5T_NATIVE_DOUBLE)) */
+ tmp_double = 0;
+ sscanf(token, "%%lf", &tmp_double);
+ HDmemcpy(cptr, &tmp_double, sizeof(double));
+ }
+#if H5_SIZEOF_LONG_DOUBLE !=0
+ else if (sizeof(long double) == size) {
+ /* if (H5Tequal(tid, H5T_NATIVE_LDOUBLE)) */
+ tmp_ldouble = 0;
+ sscanf(token, "%Lf", &tmp_ldouble);
+ HDmemcpy(cptr, &tmp_ldouble, sizeof(long double));
+ }
+#endif
+ break;
+ case H5T_STRING:
+ {
+ if (this_strlen > 0) {
+ HDstrncpy(cptr, this_str, size);
+ }
+ else {
+ cptr = NULL;
+ }
+ }
+ break;
+ case H5T_INTEGER:
+ token = HDstrtok (this_str, delimiter);
+ if (sizeof(char) == size) {
+ if(H5T_SGN_NONE == nsign) {
+ /* if (H5Tequal(tid, H5T_NATIVE_UCHAR)) */
+ tmp_uchar = 0;
+ sscanf(token, "%hu", &tmp_uchar);
+ HDmemcpy(cptr, &tmp_uchar, sizeof(unsigned char));
+ }
+ else {
+ /* if (H5Tequal(tid, H5T_NATIVE_SCHAR)) */
+ tmp_char = 0;
+ sscanf(token, "%hd", &tmp_char);
+ HDmemcpy(cptr, &tmp_char, sizeof(char));
+ }
+ }
+ else if (sizeof(int) == size) {
+ if(H5T_SGN_NONE == nsign) {
+ /* if (H5Tequal(tid, H5T_NATIVE_UINT)) */
+ tmp_uint = 0;
+ sscanf(token, "%u", &tmp_uint);
+ HDmemcpy(cptr, &tmp_uint, sizeof(unsigned int));
+ }
+ else {
+ /* if (H5Tequal(tid, H5T_NATIVE_INT)) */
+ tmp_int = 0;
+ sscanf(token, "%d", &tmp_int);
+ HDmemcpy(cptr, &tmp_int, sizeof(int));
+ }
+ }
+ else if (sizeof(short) == size) {
+ if(H5T_SGN_NONE == nsign) {
+ /* if (H5Tequal(tid, H5T_NATIVE_USHORT)) */
+ tmp_ushort = 0;
+ sscanf(token, "%u", &tmp_ushort);
+ HDmemcpy(&tmp_ushort, cptr, sizeof(unsigned short));
+ }
+ else {
+ /* if (H5Tequal(tid, H5T_NATIVE_SHORT)) */
+ tmp_short = 0;
+ sscanf(token, "%d", &tmp_short);
+ HDmemcpy(&tmp_short, cptr, sizeof(short));
+ }
+ }
+ else if (sizeof(long) == size) {
+ if(H5T_SGN_NONE == nsign) {
+ /* if (H5Tequal(tid, H5T_NATIVE_ULONG)) */
+ tmp_ulong = 0;
+ sscanf(token, "%lu", &tmp_ulong);
+ HDmemcpy(cptr, &tmp_ulong, sizeof(unsigned long));
+ }
+ else {
+ /* if (H5Tequal(tid, H5T_NATIVE_LONG)) */
+ tmp_long = 0;
+ sscanf(token, "%ld", &tmp_long);
+ HDmemcpy(cptr, &tmp_long, sizeof(long));
+ }
+ }
+ else if (sizeof(long long) == size) {
+ if(H5T_SGN_NONE == nsign) {
+ /* if (H5Tequal(tid, H5T_NATIVE_ULLONG)) */
+ tmp_ullong = 0;
+ sscanf(token, fmt_ullong, &tmp_ullong);
+ HDmemcpy(cptr, &tmp_ullong, sizeof(unsigned long long));
+ }
+ else {
+ /* if (H5Tequal(tid, H5T_NATIVE_LLONG)) */
+ tmp_llong = 0;
+ sscanf(token, fmt_llong, &tmp_llong);
+ HDmemcpy(cptr, &tmp_llong, sizeof(long long));
+ }
+ }
+ break;
+ case H5T_COMPOUND:
+ {
+ unsigned i;
+ n = H5Tget_nmembers(tid);
+ /* remove compound indicators */
+ if ((*str)[0] == ' ')
+ (*str)++;
+ if ((*str)[0] == '{')
+ (*str)++;
+
+ for (i = 0; i < n; i++) {
+ offset = H5Tget_member_offset(tid, i);
+ mtid = H5Tget_member_type(tid, i);
+ h5str_convert(str, container, mtid, ptr, offset, expand_data);
+ /* remove compound indicators */
+ if ((*str)[0] == ',')
+ (*str)++;
+ if ((*str)[0] == ' ')
+ (*str)++;
+ H5Tclose(mtid);
+ }
+ /* remove compound indicators */
+ if ((*str)[0] == '}')
+ (*str)++;
+ if ((*str)[0] == ' ')
+ (*str)++;
+ }
+ break;
+ case H5T_ENUM:
+ {
+ char enum_name[1024];
+ void *value;
+ if (sizeof(char) == size) {
+ tmp_uchar = 0;
+ value = &tmp_uchar;
+ }
+ else if (sizeof(short) == size) {
+ tmp_ushort = 0;
+ value = &tmp_ushort;
+ }
+ else if (sizeof(long) == size) {
+ tmp_ulong = 0;
+ value = &tmp_ulong;
+ }
+ else if (sizeof(long long) == size) {
+ tmp_ullong = 0;
+ value = &tmp_ullong;
+ }
+ else {
+ tmp_uint = 0;
+ value = &tmp_uint;
+ }
+ token = HDstrtok (this_str, delimiter);
+ H5Tenum_valueof(tid, token, value);
+ HDmemcpy(ucptr, value, size);
+ }
+ break;
+ case H5T_REFERENCE:
+ /* TODO handle reference writing */
+ cptr = NULL;
+ break;
+ case H5T_ARRAY:
+ {
+ int rank = 0;
+ hsize_t i, dims[H5S_MAX_RANK], total_elmts;
+ /* remove array indicators */
+ if ((*str)[0] == '[')
+ (*str)++;
+ if ((*str)[0] == ' ')
+ (*str)++;
+
+ mtid = H5Tget_super(tid);
+ offset = H5Tget_size(mtid);
+ rank = H5Tget_array_ndims(tid);
+
+ H5Tget_array_dims2(tid, dims);
+
+ total_elmts = 1;
+ for (i = 0; i < rank; i++)
+ total_elmts *= dims[i];
+
+ cptr = HDcalloc((size_t)total_elmts, offset);
+ for (i = 0; i < total_elmts; i++) {
+ h5str_convert(str, container, mtid, cptr + (i*offset), offset, expand_data);
+ /* remove array indicators */
+ if ((*str)[0] == ',')
+ (*str)++;
+ if ((*str)[0] == ' ')
+ (*str)++;
+ }
+ H5Tclose(mtid);
+ /* remove array indicators */
+ if ((*str)[0] == ' ')
+ (*str)++;
+ if ((*str)[0] == ']')
+ (*str)++;
+ if ((*str)[0] == ' ')
+ (*str)++;
+ }
+ break;
+ case H5T_VLEN:
+ {
+ unsigned int i;
+ mtid = H5Tget_super(tid);
+ offset = H5Tget_size(mtid);
+
+ /* remove vlen indicators */
+ if ((*str)[0] == '{')
+ (*str)++;
+ cptr = HDcalloc(offset, sizeof(hvl_t));
+ for (i = 0; (i*offset) < (int)size; i++) {
+ h5str_convert(str, container, mtid, cptr + (i*offset), offset, expand_data);
+ /* remove vlen indicators */
+ if ((*str)[0] == ',')
+ (*str)++;
+ if ((*str)[0] == ' ')
+ (*str)++;
+ if ((*str)[0] == '}')
+ break;
+ }
+ H5Tclose(mtid);
+ /* remove vlen indicators */
+ if ((*str)[0] == '}')
+ (*str)++;
+ }
+ break;
+
+ default:
+ {
+ /* All other types get copied raw */
+ HDmemcpy(ucptr, this_str, size);
+ }
+ break;
+ } /* end switch */
+
+ return this_strlen;
+} /* end h5str_convert */
+
+/** print value of a vlen data point into string.
+ Return Value:
+ On success, the total number of characters printed is returned.
+ On error, a negative number is returned.
+ */
+size_t
+h5str_vlsprintf
+ (h5str_t *str, hid_t container, hid_t tid, hvl_t *ptr, int expand_data)
+{
+ unsigned char tmp_uchar = 0;
+ char tmp_char = 0;
+ unsigned short tmp_ushort = 0;
+ short tmp_short = 0;
+ unsigned int tmp_uint = 0;
+ int tmp_int = 0;
+ unsigned long tmp_ulong = 0;
+ long tmp_long = 0;
+ unsigned long long tmp_ullong = 0;
+ long long tmp_llong = 0;
+ float tmp_float = 0.0;
+ double tmp_double = 0.0;
+ long double tmp_ldouble = 0.0;
+ static char fmt_llong[8], fmt_ullong[8];
+
+ hid_t mtid = -1;
+ size_t offset;
+ size_t nll;
+ char *this_str;
+ size_t this_strlen;
+ int n;
+ H5T_class_t tclass = H5Tget_class(tid);
+ size_t size = H5Tget_size(tid);
+ H5T_sign_t nsign = H5Tget_sign(tid);
+ int bdata_print = 0;
+
+ if (!str || !ptr)
+ return 0;
+
+ /* Build default formats for long long types */
+ if (!fmt_llong[0]) {
+ sprintf(fmt_llong, "%%%sd", H5_PRINTF_LL_WIDTH);
+ sprintf(fmt_ullong, "%%%su", H5_PRINTF_LL_WIDTH);
+ } /* end if */
+
+ this_str = NULL;
+ this_strlen = 0;
+
+ switch (tclass) {
+ case H5T_COMPOUND:
+ {
+ unsigned i;
+ n = H5Tget_nmembers(tid);
+ h5str_append(str, " {");
+
+ for (i = 0; i < n; i++) {
+ offset = H5Tget_member_offset(tid, i);
+ mtid = H5Tget_member_type(tid, i);
+ h5str_sprintf(str, container, mtid, ((char *) (ptr->p)) + offset, ptr->len, expand_data);
+ if ((i + 1) < n)
+ h5str_append(str, ", ");
+ H5Tclose(mtid);
+ }
+ h5str_append(str, "} ");
+ }
+ break;
+ case H5T_ARRAY:
+ {
+ int rank = 0;
+ hsize_t i, dims[H5S_MAX_RANK], total_elmts;
+ h5str_append(str, "[ ");
+
+ mtid = H5Tget_super(tid);
+ size = H5Tget_size(mtid);
+ rank = H5Tget_array_ndims(tid);
+
+ H5Tget_array_dims2(tid, dims);
+
+ total_elmts = 1;
+ for (i = 0; i < rank; i++)
+ total_elmts *= dims[i];
+
+ h5str_sprintf(str, container, mtid, ((char *) (ptr->p)), ptr->len, expand_data);
+ H5Tclose(mtid);
+ h5str_append(str, " ] ");
+ }
+ break;
+ default:
+ this_strlen = h5str_sprintf(str, container, tid, ((char *) (ptr->p)), ptr->len, expand_data);
+ break;
+ } /* end switch */
+
+ return this_strlen;
+} /* end h5str_vlsprintf */
+
/** print value of a data point into string.
Return Value:
On success, the total number of characters printed is returned.
@@ -159,7 +667,7 @@ h5str_append
*/
size_t
h5str_sprintf
- (h5str_t *str, hid_t container, hid_t tid, void *ptr, int expand_data)
+ (h5str_t *str, hid_t container, hid_t tid, void *ptr, int ptr_len, int expand_data)
{
unsigned char tmp_uchar = 0;
char tmp_char = 0;
@@ -182,9 +690,8 @@ h5str_sprintf
char *this_str;
size_t this_strlen;
int n;
- hvl_t *vlptr;
- char *cptr = (char*) ptr;
- unsigned char *ucptr = (unsigned char*) ptr;
+ char *cptr = (char*) (ptr);
+ unsigned char *ucptr = (unsigned char*) (ptr);
H5T_class_t tclass = H5Tget_class(tid);
size_t size = H5Tget_size(tid);
H5T_sign_t nsign = H5Tget_sign(tid);
@@ -206,20 +713,20 @@ h5str_sprintf
case H5T_FLOAT:
if (sizeof(float) == size) {
/* if (H5Tequal(tid, H5T_NATIVE_FLOAT)) */
- HDmemcpy(&tmp_float, ptr, sizeof(float));
+ HDmemcpy(&tmp_float, cptr, sizeof(float));
this_str = (char*)HDmalloc(25);
sprintf(this_str, "%g", tmp_float);
}
else if (sizeof(double) == size) {
/* if (H5Tequal(tid, H5T_NATIVE_DOUBLE)) */
- HDmemcpy(&tmp_double, ptr, sizeof(double));
+ HDmemcpy(&tmp_double, cptr, sizeof(double));
this_str = (char*)HDmalloc(25);
sprintf(this_str, "%g", tmp_double);
}
#if H5_SIZEOF_LONG_DOUBLE !=0
else if (sizeof(long double) == size) {
/* if (H5Tequal(tid, H5T_NATIVE_LDOUBLE)) */
- HDmemcpy(&tmp_ldouble, ptr, sizeof(long double));
+ HDmemcpy(&tmp_ldouble, cptr, sizeof(long double));
this_str = (char*)HDmalloc(27);
sprintf(this_str, "%Lf", tmp_ldouble);
}
@@ -256,13 +763,13 @@ h5str_sprintf
if (sizeof(char) == size) {
if(H5T_SGN_NONE == nsign) {
/* if (H5Tequal(tid, H5T_NATIVE_UCHAR)) */
- HDmemcpy(&tmp_uchar, ptr, sizeof(unsigned char));
+ HDmemcpy(&tmp_uchar, cptr, sizeof(unsigned char));
this_str = (char*)HDmalloc(7);
sprintf(this_str, "%u", tmp_uchar);
}
else {
/* if (H5Tequal(tid, H5T_NATIVE_SCHAR)) */
- HDmemcpy(&tmp_char, ptr, sizeof(char));
+ HDmemcpy(&tmp_char, cptr, sizeof(char));
this_str = (char*)HDmalloc(7);
sprintf(this_str, "%hhd", tmp_char);
}
@@ -270,13 +777,13 @@ h5str_sprintf
else if (sizeof(int) == size) {
if(H5T_SGN_NONE == nsign) {
/* if (H5Tequal(tid, H5T_NATIVE_UINT)) */
- HDmemcpy(&tmp_uint, ptr, sizeof(unsigned int));
+ HDmemcpy(&tmp_uint, cptr, sizeof(unsigned int));
this_str = (char*)HDmalloc(14);
sprintf(this_str, "%u", tmp_uint);
}
else {
/* if (H5Tequal(tid, H5T_NATIVE_INT)) */
- HDmemcpy(&tmp_int, ptr, sizeof(int));
+ HDmemcpy(&tmp_int, cptr, sizeof(int));
this_str = (char*)HDmalloc(14);
sprintf(this_str, "%d", tmp_int);
}
@@ -284,13 +791,13 @@ h5str_sprintf
else if (sizeof(short) == size) {
if(H5T_SGN_NONE == nsign) {
/* if (H5Tequal(tid, H5T_NATIVE_USHORT)) */
- HDmemcpy(&tmp_ushort, ptr, sizeof(unsigned short));
+ HDmemcpy(&tmp_ushort, cptr, sizeof(unsigned short));
this_str = (char*)HDmalloc(9);
sprintf(this_str, "%u", tmp_ushort);
}
else {
/* if (H5Tequal(tid, H5T_NATIVE_SHORT)) */
- HDmemcpy(&tmp_short, ptr, sizeof(short));
+ HDmemcpy(&tmp_short, cptr, sizeof(short));
this_str = (char*)HDmalloc(9);
sprintf(this_str, "%d", tmp_short);
}
@@ -298,13 +805,13 @@ h5str_sprintf
else if (sizeof(long) == size) {
if(H5T_SGN_NONE == nsign) {
/* if (H5Tequal(tid, H5T_NATIVE_ULONG)) */
- HDmemcpy(&tmp_ulong, ptr, sizeof(unsigned long));
+ HDmemcpy(&tmp_ulong, cptr, sizeof(unsigned long));
this_str = (char*)HDmalloc(23);
sprintf(this_str, "%lu", tmp_ulong);
}
else {
/* if (H5Tequal(tid, H5T_NATIVE_LONG)) */
- HDmemcpy(&tmp_long, ptr, sizeof(long));
+ HDmemcpy(&tmp_long, cptr, sizeof(long));
this_str = (char*)HDmalloc(23);
sprintf(this_str, "%ld", tmp_long);
}
@@ -312,13 +819,13 @@ h5str_sprintf
else if (sizeof(long long) == size) {
if(H5T_SGN_NONE == nsign) {
/* if (H5Tequal(tid, H5T_NATIVE_ULLONG)) */
- HDmemcpy(&tmp_ullong, ptr, sizeof(unsigned long long));
+ HDmemcpy(&tmp_ullong, cptr, sizeof(unsigned long long));
this_str = (char*)HDmalloc(25);
sprintf(this_str, fmt_ullong, tmp_ullong);
}
else {
/* if (H5Tequal(tid, H5T_NATIVE_LLONG)) */
- HDmemcpy(&tmp_llong, ptr, sizeof(long long));
+ HDmemcpy(&tmp_llong, cptr, sizeof(long long));
this_str = (char*)HDmalloc(25);
sprintf(this_str, fmt_llong, tmp_llong);
}
@@ -333,8 +840,8 @@ h5str_sprintf
for (i = 0; i < n; i++) {
offset = H5Tget_member_offset(tid, i);
mtid = H5Tget_member_type(tid, i);
- h5str_sprintf(str, container, mtid, cptr + offset, expand_data);
- if (i < n - 1)
+ h5str_sprintf(str, container, mtid, cptr + offset, ptr_len, expand_data);
+ if ((i + 1) < n)
h5str_append(str, ", ");
H5Tclose(mtid);
}
@@ -344,7 +851,7 @@ h5str_sprintf
case H5T_ENUM:
{
char enum_name[1024];
- if (H5Tenum_nameof(tid, ptr, enum_name, sizeof enum_name) >= 0) {
+ if (H5Tenum_nameof(tid, cptr, enum_name, sizeof enum_name) >= 0) {
h5str_append(str, enum_name);
}
else {
@@ -363,7 +870,7 @@ h5str_sprintf
}
break;
case H5T_REFERENCE:
- if (h5str_is_zero(ptr, size)) {
+ if (h5str_is_zero(cptr, size)) {
h5str_append(str, "NULL");
}
else {
@@ -379,9 +886,9 @@ h5str_sprintf
H5S_sel_type region_type;
/* get name of the dataset the region reference points to using H5Rget_name */
- region_obj = H5Rdereference2(container, H5P_DEFAULT, H5R_DATASET_REGION, ptr);
+ region_obj = H5Rdereference2(container, H5P_DEFAULT, H5R_DATASET_REGION, cptr);
if (region_obj >= 0) {
- region = H5Rget_region(container, H5R_DATASET_REGION, ptr);
+ region = H5Rget_region(container, H5R_DATASET_REGION, cptr);
if (region >= 0) {
if(expand_data) {
region_type = H5Sget_select_type(region);
@@ -393,7 +900,7 @@ h5str_sprintf
}
}
else {
- if(H5Rget_name(region_obj, H5R_DATASET_REGION, ptr, (char*)ref_name, 1024) >= 0) {
+ if(H5Rget_name(region_obj, H5R_DATASET_REGION, cptr, (char*)ref_name, 1024) >= 0) {
h5str_append(str, ref_name);
}
@@ -424,8 +931,8 @@ h5str_sprintf
hid_t obj;
this_str = (char*)HDmalloc(64);
- obj = H5Rdereference2(container, H5P_DEFAULT, H5R_OBJECT, ptr);
- H5Oget_info(obj, &oi);
+ obj = H5Rdereference2(container, H5P_DEFAULT, H5R_OBJECT, cptr);
+ H5Oget_info2(obj, &oi, H5O_INFO_ALL);
/* Print object data and close object */
sprintf(this_str, "%u-%lu", (unsigned) oi.type, oi.addr);
@@ -450,31 +957,30 @@ h5str_sprintf
total_elmts *= dims[i];
for (i = 0; i < total_elmts; i++) {
- h5str_sprintf(str, container, mtid, cptr + i * size, expand_data);
- if (i < total_elmts - 1)
+ h5str_sprintf(str, container, mtid, cptr + i * size, ptr_len, expand_data);
+ if ((i + 1) < total_elmts)
h5str_append(str, ", ");
}
H5Tclose(mtid);
- h5str_append(str, "] ");
+ h5str_append(str, " ] ");
}
break;
case H5T_VLEN:
- {
- unsigned int i;
- mtid = H5Tget_super(tid);
- size = H5Tget_size(mtid);
-
- vlptr = (hvl_t *) cptr;
-
- nll = vlptr->len;
- for (i = 0; i < (int)nll; i++) {
- h5str_sprintf(str, container, mtid, ((char *) (vlptr->p)) + i * size, expand_data);
- if (i < (int)nll - 1)
- h5str_append(str, ", ");
+ {
+ unsigned int i;
+ mtid = H5Tget_super(tid);
+ size = H5Tget_size(mtid);
+
+ h5str_append(str, "{");
+ for (i = 0; i < (int)ptr_len; i++) {
+ h5str_sprintf(str, container, mtid, cptr + i * size, ptr_len, expand_data);
+ if ((i + 1) < (int)ptr_len)
+ h5str_append(str, ", ");
+ }
+ H5Tclose(mtid);
+ h5str_append(str, "}");
}
- H5Tclose(mtid);
- }
- break;
+ break;
default:
{
@@ -563,7 +1069,7 @@ h5str_print_region_data_blocks
if(H5Dread(region_id, type_id, mem_space, sid1, H5P_DEFAULT, region_buf) >= 0) {
if(H5Sget_simple_extent_dims(mem_space, total_size, NULL) >= 0) {
for (numindex = 0; numindex < numelem; numindex++) {
- h5str_sprintf(str, region_id, type_id, ((char*)region_buf + numindex * type_size), 1);
+ h5str_sprintf(str, region_id, type_id, ((char*)region_buf + numindex * type_size), 0, 1);
if (numindex + 1 < numelem)
h5str_append(str, ", ");
@@ -763,7 +1269,7 @@ h5str_print_region_data_points
for (jndx = 0; jndx < npoints; jndx++) {
if(H5Sget_simple_extent_dims(mem_space, total_size, NULL) >= 0) {
- h5str_sprintf(str, region_id, type_id, ((char*)region_buf + jndx * type_size), 1);
+ h5str_sprintf(str, region_id, type_id, ((char*)region_buf + jndx * type_size), 0, 1);
if (jndx + 1 < npoints)
h5str_append(str, ", ");
@@ -1883,7 +2389,7 @@ h5tools_dump_simple_data
/* Render the data element*/
h5str_new(&buffer, 32 * size);
- bytes_in = h5str_sprintf(&buffer, container, type, memref, 1);
+ bytes_in = h5str_sprintf(&buffer, container, type, memref, 0, 1);
if(i > 0) {
HDfprintf(stream, ", ");
if (line_count >= H5TOOLS_TEXT_BLOCK) {
@@ -1909,116 +2415,6 @@ h5tools_dump_simple_data
/*
* Class: hdf_hdf5lib_H5
- * Method: H5AwriteVL
- * Signature: (JJ[Ljava/lang/String;)I
- */
-JNIEXPORT jint JNICALL
-Java_hdf_hdf5lib_H5_H5AwriteVL
- (JNIEnv *env, jclass clss, jlong attr_id, jlong mem_type_id, jobjectArray buf)
-{
- herr_t status = -1;
- char **wdata;
- jsize size;
- jint i;
-
- size = ENVPTR->GetArrayLength(ENVPAR (jarray) buf);
-
- wdata = (char**)HDcalloc((size_t)size + 1, sizeof(char*));
- if (!wdata) {
- h5JNIFatalError(env, "H5AwriteVL: cannot allocate buffer");
- } /* end if */
- else {
- HDmemset(wdata, 0, (size_t)size * sizeof(char*));
- for (i = 0; i < size; ++i) {
- jstring obj = (jstring) ENVPTR->GetObjectArrayElement(ENVPAR (jobjectArray) buf, i);
- if (obj != 0) {
- jsize length = ENVPTR->GetStringUTFLength(ENVPAR obj);
- const char *utf8 = ENVPTR->GetStringUTFChars(ENVPAR obj, 0);
-
- if (utf8) {
- wdata[i] = (char*)HDmalloc((size_t)length + 1);
- if (wdata[i]) {
- HDmemset(wdata[i], 0, ((size_t)length + 1));
- HDstrncpy(wdata[i], utf8, (size_t)length);
- } /* end if */
- } /* end if */
-
- ENVPTR->ReleaseStringUTFChars(ENVPAR obj, utf8);
- ENVPTR->DeleteLocalRef(ENVPAR obj);
- } /* end if */
- } /* end for (i = 0; i < size; ++i) */
-
- status = H5Awrite((hid_t)attr_id, (hid_t)mem_type_id, wdata);
-
- for (i = 0; i < size; i++) {
- if(wdata[i]) {
- HDfree(wdata[i]);
- } /* end if */
- } /* end for */
- HDfree(wdata);
-
- if (status < 0)
- h5libraryError(env);
- } /* end else */
-
- return (jint)status;
-} /* end Java_hdf_hdf5lib_H5_H5AwriteVL */
-
-/*
- * Class: hdf_hdf5lib_H5
- * Method: H5AreadVL
- * Signature: (JJ[Ljava/lang/String;)I
- */
-JNIEXPORT jint JNICALL
-Java_hdf_hdf5lib_H5_H5AreadVL
- (JNIEnv *env, jclass clss, jlong attr_id, jlong mem_type_id, jobjectArray buf)
-{
- herr_t status = -1;
- jstring jstr;
- char **strs;
- int i, n;
- hid_t sid;
- hsize_t dims[H5S_MAX_RANK];
-
- n = ENVPTR->GetArrayLength(ENVPAR buf);
-
- strs =(char **)HDmalloc((size_t)n * sizeof(char *));
- if (strs == NULL) {
- h5JNIFatalError( env, "H5AreadVL: failed to allocate buff for read variable length strings");
- } /* end if */
- else {
- status = H5Aread(attr_id, mem_type_id, strs);
- if (status < 0) {
- dims[0] = (hsize_t)n;
- sid = H5Screate_simple(1, dims, NULL);
- H5Dvlen_reclaim(mem_type_id, sid, H5P_DEFAULT, strs);
- H5Sclose(sid);
- HDfree(strs);
- h5JNIFatalError(env, "H5AreadVL: failed to read variable length strings");
- } /* end if */
- else {
- for (i=0; i<n; i++) {
- jstr = ENVPTR->NewStringUTF(ENVPAR strs[i]);
- ENVPTR->SetObjectArrayElement(ENVPAR buf, i, jstr);
- HDfree (strs[i]);
- } /* end for */
-
- /*
- for repeatedly reading an attribute with a large number of strs (e.g., 1,000,000 strings,
- H5Dvlen_reclaim() may crash on Windows because the Java GC will not be able to collect
- free space in time. Instead, use "free(strs[i])" to free individual strings
- after it is done.
- H5Dvlen_reclaim(tid, sid, H5P_DEFAULT, strs);
- */
-
- HDfree(strs);
- } /* end else */
- } /* end else */
- return status;
-} /* end Java_hdf_hdf5lib_H5_H5AreadVL */
-
-/*
- * Class: hdf_hdf5lib_H5
* Method: H5AreadComplex
* Signature: (JJ[Ljava/lang/String;)I
*/
@@ -2059,7 +2455,7 @@ Java_hdf_hdf5lib_H5_H5AreadComplex
else {
for (i = 0; i < n; i++) {
h5str.s[0] = '\0';
- h5str_sprintf(&h5str, attr_id, mem_type_id, rdata + ((size_t)i * size), 0);
+ h5str_sprintf(&h5str, attr_id, mem_type_id, rdata + ((size_t)i * size), 0, 0);
jstr = ENVPTR->NewStringUTF(ENVPAR h5str.s);
ENVPTR->SetObjectArrayElement(ENVPAR buf, i, jstr);
} /* end for */
@@ -2552,7 +2948,7 @@ obj_info_all
info_all_t *datainfo = (info_all_t*)op_data;
H5O_info_t object_info;
- retVal = H5Oget_info_by_name(loc_id, name, &object_info, H5P_DEFAULT);
+ retVal = H5Oget_info_by_name2(loc_id, name, &object_info, H5O_INFO_ALL, H5P_DEFAULT);
if (retVal < 0) {
*(datainfo->otype+datainfo->count) = -1;
@@ -2591,7 +2987,7 @@ obj_info_max
info_all_t *datainfo = (info_all_t*)op_data;
H5O_info_t object_info;
- retVal = H5Oget_info(loc_id, &object_info);
+ retVal = H5Oget_info2(loc_id, &object_info, H5O_INFO_ALL);
if (retVal < 0) {
*(datainfo->otype+datainfo->count) = -1;
*(datainfo->ltype+datainfo->count) = -1;