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748da4d3e2757ad7b5e7fddcd3cfd2132e90a696
hdf5/java/src/jni/h5util.c
Allen Byrne 748da4d3e2 Java formatting of args
2019-05-30 15:56:02 -05:00

3519 lines
111 KiB
C
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/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* Copyright by The HDF Group. *
* Copyright by the Board of Trustees of the University of Illinois. *
* All rights reserved. *
* *
* This file is part of HDF5. The full HDF5 copyright notice, including *
* terms governing use, modification, and redistribution, is contained in *
* the COPYING file, which can be found at the root of the source code *
* distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. *
* If you do not have access to either file, you may request a copy from *
* help@hdfgroup.org. *
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
/*
* For details of the HDF libraries, see the HDF Documentation at:
* http://hdfgroup.org/HDF5/doc/
*
*/
#ifdef __cplusplus
extern "C" {
#endif /* __cplusplus */
#include <jni.h>
#include <stdio.h>
#include <string.h>
#include <stdlib.h>
#include "hdf5.h"
#include "h5util.h"
/* size of hyperslab buffer when a dataset is bigger than H5TOOLS_MALLOCSIZE */
hsize_t H5TOOLS_BUFSIZE = (32 * 1024 * 1024); /* 32 MB */
int H5TOOLS_TEXT_BLOCK = 16; /* Number of elements on a line in a text export file */
/*
* Pointer to the JNI's Virtual Machine; used for callback functions.
*/
JavaVM *jvm;
jobject copy_callback;
jobject close_callback;
jobject create_callback;
jobject compare_callback;
jobject get_callback;
jobject set_callback;
jobject delete_callback;
H5E_auto2_t efunc;
void *edata;
/********************/
/* Local Prototypes */
/********************/
static int h5str_dump_region_blocks(JNIEnv *env, h5str_t *str, hid_t region, hid_t region_obj);
static int h5str_dump_region_points(JNIEnv *env, h5str_t *str, hid_t region, hid_t region_obj);
static int h5str_is_zero(const void *_mem, size_t size);
static hid_t h5str_get_native_type(hid_t type);
static hid_t h5str_get_little_endian_type(hid_t type);
static hid_t h5str_get_big_endian_type(hid_t type);
static htri_t h5str_detect_vlen(hid_t tid);
static htri_t h5str_detect_vlen_str(hid_t tid);
static int h5tools_dump_simple_data(JNIEnv *env, FILE *stream, hid_t container, hid_t type, void *_mem, hsize_t nelmts);
static int h5str_render_bin_output(FILE *stream, hid_t container, hid_t tid, void *_mem, hsize_t block_nelmts);
static int render_bin_output_region_data_blocks(FILE *stream, hid_t region_id,
hid_t container, int ndims, hid_t type_id, hssize_t nblocks, hsize_t *ptdata);
static int render_bin_output_region_blocks(FILE *stream, hid_t region_space,
hid_t region_id, hid_t container);
static int render_bin_output_region_data_points(FILE *stream, hid_t region_space, hid_t region_id,
hid_t container, int ndims, hid_t type_id, hssize_t npoints, hsize_t *ptdata);
static int render_bin_output_region_points(FILE *stream, hid_t region_space,
hid_t region_id, hid_t container);
/** frees memory held by array of strings */
void
h5str_array_free
(char **strs, size_t len)
{
size_t i;
if (!strs || len <= 0)
return;
for (i = 0; i < len; i++) {
if (strs[i])
HDfree(strs[i]);
} /* for (i=0; i<n; i++)*/
HDfree(strs);
} /* end h5str_array_free */
/** allocate a new str with given length */
void
h5str_new
(h5str_t *str, size_t len)
{
if (str && len > 0) {
str->s = (char *)HDmalloc(len);
str->max = len;
str->s[0] = '\0';
} /* end if */
} /* end h5str_new */
/** free string memory */
void
h5str_free
(h5str_t *str)
{
if (str && str->max > 0) {
HDfree(str->s);
HDmemset(str, 0, sizeof(h5str_t));
} /* end if */
} /* end h5str_free */
/** reset the max size of the string */
/*
* TODO: no error return. malloc can fail.
*/
void
h5str_resize
(h5str_t *str, size_t new_len)
{
char *new_str;
if (!str || new_len <= 0 || str->max == new_len)
return;
if (NULL == (new_str = (char *) HDmalloc(new_len)))
return;
if (new_len > str->max) /* increase memory */
HDstrcpy(new_str, str->s);
else
HDstrncpy(new_str, str->s, new_len - 1);
HDfree(str->s);
str->s = new_str;
str->max = new_len;
} /* end h5str_resize */
/* appends a copy of the string pointed to by cstr to the h5str.
Return Value:
the char string point to str->s
*/
char*
h5str_append
(h5str_t *str, const char* cstr)
{
size_t len;
if (!str)
return NULL;
else if (!cstr)
return str->s;
len = HDstrlen(str->s) + HDstrlen(cstr);
while (len >= str->max) /* not enough to hold the new string, double the space */
{
h5str_resize(str, str->max * 2);
}
return HDstrcat(str->s, cstr);
} /* end h5str_append */
/*
* Converts the given data point string into a real data point.
*
* Returns:
* SUCCESS: Length of string token processed
* FAILURE: 0
*/
size_t
h5str_convert
(JNIEnv *env, char **in_str, hid_t container, hid_t tid, void *out_buf, size_t out_buf_offset)
{
unsigned char *ucptr = NULL;
static char fmt_llong[8], fmt_ullong[8];
H5T_class_t tclass = H5T_NO_CLASS;
const char delimiter[] = " ," H5_COMPOUND_BEGIN_INDICATOR H5_COMPOUND_END_INDICATOR \
H5_ARRAY_BEGIN_INDICATOR H5_ARRAY_END_INDICATOR \
H5_VLEN_BEGIN_INDICATOR H5_VLEN_END_INDICATOR;
size_t typeSize = 0;
hid_t mtid = H5I_INVALID_HID;
char *this_str = NULL;
char *token;
char *cptr = NULL;
int n;
size_t retVal = 0;
if (!in_str)
H5_NULL_ARGUMENT_ERROR(ENVONLY, "h5str_convert: in_str is NULL");
if (!out_buf)
H5_NULL_ARGUMENT_ERROR(ENVONLY, "h5str_convert: out_buf is NULL");
this_str = *in_str;
cptr = &(((char *) out_buf)[out_buf_offset]);
ucptr = &(((unsigned char *) out_buf)[out_buf_offset]);
if (H5T_NO_CLASS == (tclass = H5Tget_class(tid)))
H5_LIBRARY_ERROR(ENVONLY);
if (!(typeSize = H5Tget_size(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)
H5_JNI_FATAL_ERROR(ENVONLY, "h5str_convert: HDsprintf failure");
if (HDsprintf(fmt_ullong, "%%%su", H5_PRINTF_LL_WIDTH) < 0)
H5_JNI_FATAL_ERROR(ENVONLY, "h5str_convert: HDsprintf failure");
} /* end if */
switch (tclass) {
case H5T_FLOAT:
{
token = HDstrtok(this_str, delimiter);
switch (typeSize) {
case sizeof(float):
{
float tmp_float = 0.0;
sscanf(token, "%f", &tmp_float);
HDmemcpy(cptr, &tmp_float, sizeof(float));
break;
}
case sizeof(double):
{
double tmp_double = 0.0;
sscanf(token, "%lf", &tmp_double);
HDmemcpy(cptr, &tmp_double, sizeof(double));
break;
}
#if H5_SIZEOF_LONG_DOUBLE != 0 && H5_SIZEOF_LONG_DOUBLE != H5_SIZEOF_DOUBLE
case sizeof(long double):
{
long double tmp_ldouble = 0.0;
sscanf(token, "%Lf", &tmp_ldouble);
HDmemcpy(cptr, &tmp_ldouble, sizeof(long double));
break;
}
#endif
default:
H5_BAD_ARGUMENT_ERROR(ENVONLY, "h5str_convert: floating-point datatype size didn't match any of expected sizes");
break;
}
retVal = typeSize;
break;
}
case H5T_STRING:
{
size_t len = HDstrlen(this_str);
if (len > 0) {
HDstrncpy(cptr, this_str, typeSize);
cptr[typeSize - 1] = '\0';
retVal = typeSize;
}
else {
cptr = NULL;
}
break;
}
case H5T_INTEGER:
{
H5T_sign_t nsign = H5T_SGN_ERROR;
if (H5T_SGN_ERROR == (nsign = H5Tget_sign(tid)))
H5_LIBRARY_ERROR(ENVONLY);
token = HDstrtok(this_str, delimiter);
switch (typeSize) {
case sizeof(char):
{
unsigned char tmp_uchar = 0;
signed char tmp_char = 0;
if (H5T_SGN_NONE == nsign) {
sscanf(token, "%hhu", &tmp_uchar);
HDmemcpy(cptr, &tmp_uchar, sizeof(unsigned char));
}
else {
sscanf(token, "%hhd", &tmp_char);
HDmemcpy(cptr, &tmp_char, sizeof(char));
}
break;
}
case sizeof(short):
{
unsigned short tmp_ushort = 0;
short tmp_short = 0;
if (H5T_SGN_NONE == nsign) {
sscanf(token, "%hu", &tmp_ushort);
HDmemcpy(&tmp_ushort, cptr, sizeof(unsigned short));
}
else {
sscanf(token, "%hd", &tmp_short);
HDmemcpy(&tmp_short, cptr, sizeof(short));
}
break;
}
case sizeof(int):
{
unsigned int tmp_uint = 0;
int tmp_int = 0;
if (H5T_SGN_NONE == nsign) {
sscanf(token, "%u", &tmp_uint);
HDmemcpy(cptr, &tmp_uint, sizeof(unsigned int));
}
else {
sscanf(token, "%d", &tmp_int);
HDmemcpy(cptr, &tmp_int, sizeof(int));
}
break;
}
#if H5_SIZEOF_LONG != H5_SIZEOF_INT
case sizeof(long):
{
unsigned long tmp_ulong = 0;
long tmp_long = 0;
if (H5T_SGN_NONE == nsign) {
sscanf(token, "%lu", &tmp_ulong);
HDmemcpy(cptr, &tmp_ulong, sizeof(unsigned long));
}
else {
sscanf(token, "%ld", &tmp_long);
HDmemcpy(cptr, &tmp_long, sizeof(long));
}
break;
}
#endif
#if H5_SIZEOF_LONG_LONG != H5_SIZEOF_LONG
case sizeof(long long):
{
unsigned long long tmp_ullong = 0;
long long tmp_llong = 0;
if (H5T_SGN_NONE == nsign) {
sscanf(token, fmt_ullong, &tmp_ullong);
HDmemcpy(cptr, &tmp_ullong, sizeof(unsigned long long));
}
else {
sscanf(token, fmt_llong, &tmp_llong);
HDmemcpy(cptr, &tmp_llong, sizeof(long long));
}
break;
}
#endif
default:
H5_BAD_ARGUMENT_ERROR(ENVONLY, "h5str_convert: integer datatype size didn't match any of expected sizes");
break;
}
retVal = typeSize;
break;
}
case H5T_COMPOUND:
{
unsigned i;
size_t member_offset;
if ((n = H5Tget_nmembers(tid)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
/* Skip whitespace and compound indicators */
while (*this_str == ' ') this_str++;
if (*this_str == '{') this_str++;
while (*this_str == ' ') this_str++;
for (i = 0; i < (unsigned) n; i++) {
member_offset = H5Tget_member_offset(tid, i);
if ((mtid = H5Tget_member_type(tid, i)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if (!h5str_convert(ENVONLY, &this_str, container, mtid, out_buf, member_offset)) {
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
goto done;
}
/* Skip whitespace and commas */
while (*this_str == ' ') this_str++;
if (*this_str == ',') this_str++;
while (*this_str == ' ') this_str++;
if (H5Tclose(mtid) < 0)
H5_LIBRARY_ERROR(ENVONLY);
mtid = H5I_INVALID_HID;
}
/* Skip whitespace and compound indicators */
while (*this_str == ' ') this_str++;
if (*this_str == '}') this_str++;
while (*this_str == ' ') this_str++;
retVal = typeSize * (size_t) n;
break;
}
/* TODO handle reference writing */
case H5T_REFERENCE:
cptr = NULL;
break;
case H5T_ENUM:
{
void *value;
token = HDstrtok(this_str, delimiter);
switch (typeSize) {
case sizeof(char):
{
unsigned char tmp_uchar = 0;
value = &tmp_uchar;
break;
}
case sizeof(short):
{
unsigned short tmp_ushort = 0;
value = &tmp_ushort;
break;
}
#if H5_SIZEOF_LONG != H5_SIZEOF_INT
case sizeof(long):
{
unsigned long tmp_ulong = 0;
value = &tmp_ulong;
break;
}
#endif
#if H5_SIZEOF_LONG_LONG != H5_SIZEOF_LONG
case sizeof(long long):
{
unsigned long long tmp_ullong = 0;
value = &tmp_ullong;
break;
}
#endif
default:
{
unsigned int tmp_uint = 0;
value = &tmp_uint;
break;
}
}
if (H5Tenum_valueof(tid, token, value) < 0)
H5_LIBRARY_ERROR(ENVONLY);
HDmemcpy(ucptr, value, typeSize);
retVal = typeSize;
break;
}
case H5T_ARRAY:
{
hsize_t i, dims[H5S_MAX_RANK], total_elmts;
size_t baseTypeSize;
int rank = 0;
/* Skip whitespace and array indicators */
while (*this_str == ' ') this_str++;
if (*this_str == '[') this_str++;
while (*this_str == ' ') this_str++;
if ((mtid = H5Tget_super(tid)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if (!(baseTypeSize = H5Tget_size(mtid)))
H5_LIBRARY_ERROR(ENVONLY);
if ((rank = H5Tget_array_ndims(tid)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if (H5Tget_array_dims2(tid, dims) < 0)
H5_LIBRARY_ERROR(ENVONLY);
for (i = 0, total_elmts = 1; i < (hsize_t) rank; i++)
total_elmts *= dims[i];
if (NULL == (cptr = (char *) HDcalloc((size_t)total_elmts, baseTypeSize)))
H5_JNI_FATAL_ERROR(ENVONLY, "h5str_convert: failed to allocate array buffer");
for (i = 0; i < total_elmts; i++) {
if (!(h5str_convert(ENVONLY, &this_str, container, mtid, out_buf, i * baseTypeSize))) {
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
goto done;
}
/* Skip whitespace and commas */
while (*this_str == ' ') this_str++;
if (*this_str == ',') this_str++;
while (*this_str == ' ') this_str++;
}
if (H5Tclose(mtid) < 0)
H5_LIBRARY_ERROR(ENVONLY);
mtid = H5I_INVALID_HID;
/* Skip whitespace and array indicators */
while (*this_str == ' ') this_str++;
if (*this_str == ']') this_str++;
while (*this_str == ' ') this_str++;
retVal = typeSize * total_elmts;
break;
}
case H5T_VLEN:
{
size_t i, baseTypeSize;
hvl_t *vl_buf = (hvl_t *) out_buf;
char cur_char;
if ((mtid = H5Tget_super(tid)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if (!(baseTypeSize = H5Tget_size(mtid)))
H5_LIBRARY_ERROR(ENVONLY);
if (NULL == (vl_buf->p = HDmalloc(baseTypeSize)))
H5_JNI_FATAL_ERROR(ENVONLY, "h5str_convert: failed to allocate vlen buffer");
vl_buf->len = 1;
/* Skip whitespace and vlen indicators */
while (*this_str == ' ') this_str++;
if (*this_str == '(') this_str++;
while (*this_str == ' ') this_str++;
cur_char = *this_str;
for (i = 0; cur_char != ')' && cur_char != '\0'; i++) {
if (i >= vl_buf->len) {
char *tmp_realloc;
if (NULL == (tmp_realloc = (char *) HDrealloc(vl_buf->p, vl_buf->len * 2 * baseTypeSize)))
H5_JNI_FATAL_ERROR(ENVONLY, "h5str_convert: failed to reallocate vlen buffer");
vl_buf->len *= 2;
vl_buf->p = tmp_realloc;
}
if (!(h5str_convert(ENVONLY, &this_str, container, mtid, vl_buf->p, i * baseTypeSize))) {
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
vl_buf->len = i;
goto done;
}
/* Skip whitespace and commas */
while (*this_str == ' ') this_str++;
if (*this_str == ',') this_str++;
while (*this_str == ' ') this_str++;
}
vl_buf->len = i;
if (H5Tclose(mtid) < 0)
H5_LIBRARY_ERROR(ENVONLY);
mtid = H5I_INVALID_HID;
/* Skip whitespace and vlen indicators */
while (*this_str == ' ') this_str++;
if (*this_str == ')') this_str++;
while (*this_str == ' ') this_str++;
retVal = typeSize;
break;
}
case H5T_NCLASSES:
case H5T_NO_CLASS:
{
H5_BAD_ARGUMENT_ERROR(ENVONLY, "h5str_convert: invalid datatype class");
break;
}
case H5T_TIME:
case H5T_BITFIELD:
case H5T_OPAQUE:
default:
{
/* All other types get copied raw */
HDmemcpy(ucptr, this_str, typeSize);
retVal = typeSize;
break;
}
} /* end switch */
done:
if (mtid >= 0)
H5Tclose(mtid);
return retVal;
} /* end h5str_convert */
/*
* Prints the value of a data point into a string.
*
* Returns:
* SUCCESS: Total number of characters printed
* FAILURE: 0
*/
size_t
h5str_sprintf
(JNIEnv *env, h5str_t *out_str, hid_t container, hid_t tid, void *in_buf, size_t in_buf_len, int expand_data)
{
unsigned char *ucptr = (unsigned char *) in_buf;
static char fmt_llong[8], fmt_ullong[8];
H5T_class_t tclass = H5T_NO_CLASS;
size_t typeSize = 0;
hid_t mtid = H5I_INVALID_HID;
char *cptr = (char *) in_buf;
char *this_str = NULL;
int n;
size_t retVal = 0;
if (!out_str)
H5_NULL_ARGUMENT_ERROR(ENVONLY, "h5str_sprintf: out_str is NULL");
if (!in_buf)
H5_NULL_ARGUMENT_ERROR(ENVONLY, "h5str_sprintf: in_buf is NULL");
if (H5T_NO_CLASS == (tclass = H5Tget_class(tid)))
H5_LIBRARY_ERROR(ENVONLY);
if (!(typeSize = H5Tget_size(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)
H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: sprintf failure");
if (HDsprintf(fmt_ullong, "%%%su", H5_PRINTF_LL_WIDTH) < 0)
H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: sprintf failure");
} /* end if */
switch (tclass) {
case H5T_FLOAT:
{
switch (typeSize) {
case sizeof(float):
{
float tmp_float = 0.0;
HDmemcpy(&tmp_float, cptr, sizeof(float));
if (NULL == (this_str = (char *) HDmalloc(25)))
H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: failed to allocate string buffer");
if (HDsprintf(this_str, "%g", tmp_float) < 0)
H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsprintf failure");
break;
}
case sizeof(double):
{
double tmp_double = 0.0;
HDmemcpy(&tmp_double, cptr, sizeof(double));
if (NULL == (this_str = (char *) HDmalloc(25)))
H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: failed to allocate string buffer");
if (HDsprintf(this_str, "%g", tmp_double) < 0)
H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsprintf failure");
break;
}
#if H5_SIZEOF_LONG_DOUBLE != 0 && H5_SIZEOF_LONG_DOUBLE != H5_SIZEOF_DOUBLE
case sizeof(long double):
{
long double tmp_ldouble = 0.0;
HDmemcpy(&tmp_ldouble, cptr, sizeof(long double));
if (NULL == (this_str = (char *) HDmalloc(27)))
H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: failed to allocate string buffer");
if (HDsprintf(this_str, "%Lf", tmp_ldouble) < 0)
H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsprintf failure");
break;
}
#endif
default:
H5_BAD_ARGUMENT_ERROR(ENVONLY, "h5str_sprintf: floating-point datatype size didn't match any of expected sizes");
break;
}
break;
}
case H5T_STRING:
{
htri_t is_variable;
char *tmp_str;
typeSize = 0;
if ((is_variable = H5Tis_variable_str(tid)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if (is_variable) {
if (NULL != (tmp_str = *(char **) in_buf))
typeSize = HDstrlen(tmp_str);
}
else {
tmp_str = cptr;
}
/* 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 {
if (typeSize > 0) {
if (NULL == (this_str = (char *) HDmalloc(typeSize + 1)))
H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: failed to allocate string buffer");
HDstrncpy(this_str, tmp_str, typeSize);
this_str[typeSize] = '\0';
}
}
break;
}
case H5T_INTEGER:
{
H5T_sign_t nsign = H5T_SGN_ERROR;
if (H5T_SGN_ERROR == (nsign = H5Tget_sign(tid)))
H5_LIBRARY_ERROR(ENVONLY);
switch (typeSize) {
case sizeof(char):
{
unsigned char tmp_uchar = 0;
char tmp_char = 0;
if (H5T_SGN_NONE == nsign) {
HDmemcpy(&tmp_uchar, cptr, sizeof(unsigned char));
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)
H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsprintf failure");
}
else {
HDmemcpy(&tmp_char, cptr, sizeof(char));
if (NULL == (this_str = (char *) HDmalloc(7)))
H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: failed to allocate string buffer");
if (HDsprintf(this_str, "%hhd", tmp_char) < 0)
H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsprintf failure");
}
break;
}
case sizeof(short):
{
unsigned short tmp_ushort = 0;
short tmp_short = 0;
if (H5T_SGN_NONE == nsign) {
HDmemcpy(&tmp_ushort, cptr, sizeof(unsigned short));
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)
H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsprintf failure");
}
else {
HDmemcpy(&tmp_short, cptr, sizeof(short));
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)
H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsprintf failure");
}
break;
}
case sizeof(int):
{
unsigned int tmp_uint = 0;
int tmp_int = 0;
if (H5T_SGN_NONE == nsign) {
HDmemcpy(&tmp_uint, cptr, sizeof(unsigned int));
if (NULL == (this_str = (char *) HDmalloc(14)))
H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: failed to allocate string buffer");
if (HDsprintf(this_str, "%u", tmp_uint) < 0)
H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsprintf failure");
}
else {
HDmemcpy(&tmp_int, cptr, sizeof(int));
if (NULL == (this_str = (char *) HDmalloc(14)))
H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: failed to allocate string buffer");
if (HDsprintf(this_str, "%d", tmp_int) < 0)
H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsprintf failure");
}
break;
}
#if H5_SIZEOF_LONG != H5_SIZEOF_INT
case sizeof(long):
{
unsigned long tmp_ulong = 0;
long tmp_long = 0;
if (H5T_SGN_NONE == nsign) {
HDmemcpy(&tmp_ulong, cptr, sizeof(unsigned long));
if (NULL == (this_str = (char *) HDmalloc(23)))
H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: failed to allocate string buffer");
if (HDsprintf(this_str, "%lu", tmp_ulong) < 0)
H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsprintf failure");
}
else {
HDmemcpy(&tmp_long, cptr, sizeof(long));
if (NULL == (this_str = (char *) HDmalloc(23)))
H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: failed to allocate string buffer");
if (HDsprintf(this_str, "%ld", tmp_long) < 0)
H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsprintf failure");
}
break;
}
#endif
#if H5_SIZEOF_LONG_LONG != H5_SIZEOF_LONG
case sizeof(long long):
{
unsigned long long tmp_ullong = 0;
long long tmp_llong = 0;
if (H5T_SGN_NONE == nsign) {
HDmemcpy(&tmp_ullong, cptr, sizeof(unsigned long long));
if (NULL == (this_str = (char *) HDmalloc(25)))
H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: failed to allocate string buffer");
if (HDsprintf(this_str, fmt_ullong, tmp_ullong) < 0)
H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsprintf failure");
}
else {
HDmemcpy(&tmp_llong, cptr, sizeof(long long));
if (NULL == (this_str = (char *) HDmalloc(25)))
H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: failed to allocate string buffer");
if (HDsprintf(this_str, fmt_llong, tmp_llong) < 0)
H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsprintf failure");
}
break;
}
#endif
default:
H5_BAD_ARGUMENT_ERROR(ENVONLY, "h5str_sprintf: integer datatype size didn't match any of expected sizes");
break;
}
break;
}
case H5T_COMPOUND:
{
unsigned i;
size_t offset;
if ((n = H5Tget_nmembers(tid)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if (!h5str_append(out_str, H5_COMPOUND_BEGIN_INDICATOR))
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
for (i = 0; i < (unsigned) n; i++) {
offset = H5Tget_member_offset(tid, i);
if ((mtid = H5Tget_member_type(tid, i)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if (!h5str_sprintf(ENVONLY, out_str, container, mtid, &cptr[offset], in_buf_len, expand_data))
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
if ((i + 1) < (unsigned) n)
if (!h5str_append(out_str, ", "))
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
if (H5Tclose(mtid) < 0)
H5_LIBRARY_ERROR(ENVONLY);
mtid = H5I_INVALID_HID;
}
if (!h5str_append(out_str, H5_COMPOUND_END_INDICATOR))
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
break;
}
case H5T_ENUM:
{
char enum_name[1024];
if (H5Tenum_nameof(tid, cptr, enum_name, sizeof enum_name) >= 0) {
if (!h5str_append(out_str, enum_name))
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
}
else {
size_t i;
if (NULL == (this_str = (char *) HDmalloc(4 * (typeSize + 1))))
H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: failed to allocate string buffer");
if (1 == typeSize) {
if (HDsprintf(this_str, "%#02x", ucptr[0]) < 0)
H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsprintf failure");
}
else {
for (i = 0; i < typeSize; i++)
if (HDsprintf(this_str, "%s%02x", i ? ":" : "", ucptr[i]) < 0)
H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsprintf failure");
}
}
break;
}
case H5T_REFERENCE:
{
if (h5str_is_zero(cptr, typeSize)) {
if (!h5str_append(out_str, "NULL"))
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
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)
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"))
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
if (h5str_dump_region_points(ENVONLY, out_str, region, region_obj) < 0)
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
}
else {
if (!h5str_append(out_str, " REGION_TYPE BLOCK"))
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
if (h5str_dump_region_blocks(ENVONLY, out_str, region, region_obj) < 0)
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;
}
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;
}
break;
}
case H5T_ARRAY:
{
hsize_t dims[H5S_MAX_RANK], i, total_elmts;
size_t baseSize;
int rank = 0;
if (!h5str_append(out_str, H5_ARRAY_BEGIN_INDICATOR))
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
if ((mtid = H5Tget_super(tid)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if (!(baseSize = H5Tget_size(mtid)))
H5_LIBRARY_ERROR(ENVONLY);
if ((rank = H5Tget_array_ndims(tid)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if (H5Tget_array_dims2(tid, dims) < 0)
H5_LIBRARY_ERROR(ENVONLY);
for (i = 0, total_elmts = 1; i < (hsize_t) rank; i++)
total_elmts *= dims[i];
for (i = 0; i < total_elmts; i++) {
if (!h5str_sprintf(ENVONLY, out_str, container, mtid, &(cptr[i * baseSize]), in_buf_len, expand_data))
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
if ((i + 1) < total_elmts)
if (!h5str_append(out_str, ", "))
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
}
if (!h5str_append(out_str, H5_ARRAY_END_INDICATOR))
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
if (H5Tclose(mtid) < 0)
H5_LIBRARY_ERROR(ENVONLY);
mtid = H5I_INVALID_HID;
break;
}
case H5T_VLEN:
{
unsigned int i;
size_t baseSize;
hvl_t *vl_buf = (hvl_t *) in_buf;
if ((mtid = H5Tget_super(tid)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if (!(baseSize = H5Tget_size(mtid)))
H5_LIBRARY_ERROR(ENVONLY);
if (!h5str_append(out_str, H5_VLEN_BEGIN_INDICATOR))
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
for (i = 0; i < (unsigned) vl_buf->len; i++) {
if (!h5str_sprintf(ENVONLY, out_str, container, mtid, &(((char *) vl_buf->p)[i * baseSize]), vl_buf->len, expand_data))
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
if ((i + 1) < (unsigned) vl_buf->len)
if (!h5str_append(out_str, ", "))
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
}
if (!h5str_append(out_str, H5_VLEN_END_INDICATOR))
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
if (H5Tclose(mtid) < 0)
H5_LIBRARY_ERROR(ENVONLY);
mtid = H5I_INVALID_HID;
break;
}
case H5T_NO_CLASS:
case H5T_NCLASSES:
{
H5_BAD_ARGUMENT_ERROR(ENVONLY, "h5str_sprintf: invalid datatype class");
break;
}
case H5T_TIME:
case H5T_BITFIELD:
case H5T_OPAQUE:
default:
{
size_t i;
/* All other types get printed as hexadecimal */
if (NULL == (this_str = (char *) HDmalloc(4 * (typeSize + 1))))
H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: failed to allocate string buffer");
if (1 == typeSize) {
if (HDsprintf(this_str, "%#02x", ucptr[0]) < 0)
H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsprintf failure");
}
else {
for (i = 0; i < typeSize; i++)
if (HDsprintf(this_str, "%s%02x", i ? ":" : "", ucptr[i]) < 0)
H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsprintf failure");
}
break;
}
}
if (this_str) {
if (!h5str_append(out_str, this_str))
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
HDfree(this_str);
this_str = NULL;
} /* end if */
retVal = HDstrlen(out_str->s);
done:
if (mtid >= 0)
H5Tclose(mtid);
return retVal;
} /* end h5str_sprintf */
/*-------------------------------------------------------------------------
* Purpose: Print the data values from a dataset referenced by region blocks.
*
* Description:
* This is a special case subfunction to print the data in a region reference of type blocks.
*
* Return:
* The function returns FAIL if there was an error, otherwise SUCEED
*-------------------------------------------------------------------------
*/
static int
h5str_print_region_data_blocks
(JNIEnv *env, hid_t region_id, h5str_t *str, int ndims, hid_t type_id, hssize_t nblocks, hsize_t *ptdata)
{
unsigned indx;
hsize_t *dims1 = NULL;
hsize_t *start = NULL;
hsize_t *count = NULL;
hsize_t blkndx;
hsize_t total_size[H5S_MAX_RANK];
hsize_t numelem;
hsize_t numindex;
size_t jndx;
size_t type_size;
hid_t mem_space = H5I_INVALID_HID;
hid_t sid1 = H5I_INVALID_HID;
void *region_buf = NULL;
int ret_value = FAIL;
if (ndims < 0)
H5_BAD_ARGUMENT_ERROR(ENVONLY, "h5str_print_region_data_blocks: ndims < 0");
if (nblocks < 0)
H5_BAD_ARGUMENT_ERROR(ENVONLY, "h5str_print_region_data_blocks: nblocks < 0");
/* Get the dataspace of the dataset */
if ((sid1 = H5Dget_space(region_id)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
/* Allocate space for the dimension array */
if (NULL == (dims1 = (hsize_t *) HDmalloc(sizeof(hsize_t) * (size_t)ndims)))
H5_JNI_FATAL_ERROR(ENVONLY, "h5str_print_region_data_blocks: failed to allocate dimension array buffer");
/* Find the dimensions of each data space from the block coordinates */
for (jndx = 0, numelem = 1; jndx < (size_t) ndims; jndx++) {
dims1[jndx] = ptdata[jndx + (size_t)ndims] - ptdata[jndx] + 1;
numelem = dims1[jndx] * numelem;
} /* end for */
/* Create dataspace for reading buffer */
if ((mem_space = H5Screate_simple(ndims, dims1, NULL)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if (!(type_size = H5Tget_size(type_id)))
H5_LIBRARY_ERROR(ENVONLY);
if (NULL == (region_buf = HDmalloc(type_size * (size_t)numelem)))
H5_JNI_FATAL_ERROR(ENVONLY, "h5str_print_region_data_blocks: failed to allocate region buffer");
/* Select (x , x , ..., x ) x (y , y , ..., y ) hyperslab for reading memory dataset */
/* 1 2 n 1 2 n */
if (NULL == (start = (hsize_t *) HDmalloc(sizeof(hsize_t) * (size_t)ndims)))
H5_JNI_FATAL_ERROR(ENVONLY, "h5str_print_region_data_blocks: failed to allocate hyperslab start buffer");
if (NULL == (count = (hsize_t *) HDmalloc(sizeof(hsize_t) * (size_t)ndims)))
H5_JNI_FATAL_ERROR(ENVONLY, "h5str_print_region_data_blocks: failed to allocate hyperslab count buffer");
for (blkndx = 0; blkndx < (hsize_t) nblocks; blkndx++) {
for (indx = 0; indx < (unsigned) ndims; indx++) {
start[indx] = ptdata[indx + blkndx * (hsize_t)ndims * 2];
count[indx] = dims1[indx];
} /* end for */
if (H5Sselect_hyperslab(sid1, H5S_SELECT_SET, start, NULL, count, NULL) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if (H5Dread(region_id, type_id, mem_space, sid1, H5P_DEFAULT, region_buf) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if (H5Sget_simple_extent_dims(mem_space, total_size, NULL) < 0)
H5_LIBRARY_ERROR(ENVONLY);
for (numindex = 0; numindex < numelem; numindex++) {
if (!h5str_sprintf(ENVONLY, str, region_id, type_id, ((char *)region_buf + numindex * type_size), 0, 1))
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
if (numindex + 1 < numelem)
if (!h5str_append(str, ", "))
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
} /* end for (jndx = 0; jndx < numelem; jndx++, region_elmtno++, ctx.cur_elmt++) */
} /* end for (blkndx = 0; blkndx < nblocks; blkndx++) */
ret_value = SUCCEED;
done:
if (count)
HDfree(count);
if (start)
HDfree(start);
if (region_buf)
HDfree(region_buf);
if (mem_space >= 0)
H5Sclose(mem_space);
if (dims1)
HDfree(dims1);
if (sid1 >= 0)
H5Sclose(sid1);
return ret_value;
} /* end h5str_print_region_data_blocks */
int
h5str_dump_region_blocks_data
(JNIEnv *env, h5str_t *str, hid_t region, hid_t region_id)
{
hssize_t nblocks;
hsize_t alloc_size;
hsize_t *ptdata = NULL;
hid_t dtype = H5I_INVALID_HID;
hid_t type_id = H5I_INVALID_HID;
int ndims = -1;
int ret_value = FAIL;
/*
* This function fails if the region does not have blocks.
*/
H5E_BEGIN_TRY {
nblocks = H5Sget_select_hyper_nblocks(region);
} H5E_END_TRY;
if (nblocks < 0)
H5_LIBRARY_ERROR(ENVONLY);
if ((ndims = H5Sget_simple_extent_ndims(region)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
/* Print block information */
alloc_size = (hsize_t)nblocks * (hsize_t)ndims * 2 * (hsize_t)sizeof(ptdata[0]);
if (alloc_size == (hsize_t)((size_t) alloc_size)) {
if (NULL == (ptdata = (hsize_t *) HDmalloc((size_t) alloc_size)))
H5_JNI_FATAL_ERROR(ENVONLY, "h5str_dump_region_blocks_data: failed to allocate region block buffer");
if (H5Sget_select_hyper_blocklist(region, (hsize_t) 0, (hsize_t) nblocks, ptdata) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if ((dtype = H5Dget_type(region_id)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if ((type_id = H5Tget_native_type(dtype, H5T_DIR_DEFAULT)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if (h5str_print_region_data_blocks(ENVONLY, region_id, str, ndims, type_id, nblocks, ptdata) < 0)
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
} /* if (alloc_size == (hsize_t)((size_t)alloc_size)) */
ret_value = SUCCEED;
done:
if (type_id >= 0)
H5Tclose(type_id);
if (dtype >= 0)
H5Tclose(dtype);
if (ptdata)
HDfree(ptdata);
return ret_value;
} /* end h5str_dump_region_blocks_data */
static int
h5str_dump_region_blocks
(JNIEnv *env, h5str_t *str, hid_t region, hid_t region_id)
{
hssize_t nblocks;
hsize_t alloc_size;
hsize_t *ptdata = NULL;
char tmp_str[256];
int ndims = -1;
int ret_value = FAIL;
UNUSED(region_id);
/*
* This function fails if the region does not have blocks.
*/
H5E_BEGIN_TRY {
nblocks = H5Sget_select_hyper_nblocks(region);
} H5E_END_TRY;
if (nblocks < 0)
H5_LIBRARY_ERROR(ENVONLY);
if ((ndims = H5Sget_simple_extent_ndims(region)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
/* Print block information */
alloc_size = (hsize_t)nblocks * (hsize_t)ndims * 2 * (hsize_t)sizeof(ptdata[0]);
if (alloc_size == (hsize_t)((size_t) alloc_size)) {
int i;
if (NULL == (ptdata = (hsize_t *) HDmalloc((size_t) alloc_size)))
H5_JNI_FATAL_ERROR(ENVONLY, "h5str_dump_region_blocks: failed to allocate region block buffer");
if (H5Sget_select_hyper_blocklist(region, (hsize_t) 0, (hsize_t) nblocks, ptdata) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if (!h5str_append(str, " {"))
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
for (i = 0; i < nblocks; i++) {
int j;
if (!h5str_append(str, " "))
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
/* Start coordinates and opposite corner */
for (j = 0; j < ndims; j++) {
tmp_str[0] = '\0';
if (HDsprintf(tmp_str, "%s%lu", j ? "," : "(",
(unsigned long) ptdata[i * 2 * ndims + j]) < 0)
H5_JNI_FATAL_ERROR(ENVONLY, "h5str_dump_region_blocks: HDsprintf failure");
if (!h5str_append(str, tmp_str))
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
}
for (j = 0; j < ndims; j++) {
tmp_str[0] = '\0';
if (HDsprintf(tmp_str, "%s%lu", j ? "," : ")-(",
(unsigned long) ptdata[i * 2 * ndims + j + ndims]) < 0)
H5_JNI_FATAL_ERROR(ENVONLY, "h5str_dump_region_blocks: HDsprintf failure");
if (!h5str_append(str, tmp_str))
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
}
if (!h5str_append(str, ") "))
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
tmp_str[0] = '\0';
}
if (!h5str_append(str, " }"))
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
} /* if (alloc_size == (hsize_t)((size_t)alloc_size)) */
ret_value = SUCCEED;
done:
if (ptdata)
HDfree(ptdata);
return ret_value;
} /* end h5str_dump_region_blocks */
/*-------------------------------------------------------------------------
* Purpose: Print the data values from a dataset referenced by region points.
*
* Description:
* This is a special case subfunction to print the data in a region reference of type points.
*
* Return:
* The function returns FAIL on error, otherwise SUCCEED
*-------------------------------------------------------------------------
*/
static int
h5str_print_region_data_points
(JNIEnv *env, hid_t region_space, hid_t region_id, h5str_t *str, int ndims, hid_t type_id, hssize_t npoints, hsize_t *ptdata)
{
hsize_t *dims1 = NULL;
hsize_t total_size[H5S_MAX_RANK];
size_t jndx;
size_t type_size;
hid_t mem_space = H5I_INVALID_HID;
void *region_buf = NULL;
int ret_value = FAIL;
UNUSED(ptdata);
if (npoints < 0)
H5_BAD_ARGUMENT_ERROR(ENVONLY, "h5str_print_region_data_points: npoints < 0");
/* Allocate space for the dimension array */
if (NULL == (dims1 = (hsize_t *) HDmalloc(sizeof(hsize_t) * (size_t)ndims)))
H5_JNI_FATAL_ERROR(ENVONLY, "h5str_print_region_data_points: failed to allocate dimension array buffer");
dims1[0] = (hsize_t)npoints;
/* Create dataspace for reading buffer */
if ((mem_space = H5Screate_simple(1, dims1, NULL)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if (!(type_size = H5Tget_size(type_id)))
H5_LIBRARY_ERROR(ENVONLY);
if (NULL == (region_buf = HDmalloc(type_size * (size_t)npoints)))
H5_JNI_FATAL_ERROR(ENVONLY, "h5str_print_region_data_points: failed to allocate region buffer");
if (H5Dread(region_id, type_id, mem_space, region_space, H5P_DEFAULT, region_buf) < 0)
H5_LIBRARY_ERROR(ENVONLY);
for (jndx = 0; jndx < (size_t) npoints; jndx++) {
if (H5Sget_simple_extent_dims(mem_space, total_size, NULL) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if (!h5str_sprintf(ENVONLY, str, region_id, type_id, ((char *)region_buf + jndx * type_size), 0, 1))
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
if (jndx + 1 < (size_t) npoints)
if (!h5str_append(str, ", "))
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
} /* end for (jndx = 0; jndx < npoints; jndx++, elmtno++) */
ret_value = SUCCEED;
done:
if (region_buf)
HDfree(region_buf);
if (mem_space >= 0)
H5Sclose(mem_space);
if (dims1)
HDfree(dims1);
return ret_value;
} /* end h5str_print_region_data_points */
int
h5str_dump_region_points_data
(JNIEnv *env, h5str_t *str, hid_t region, hid_t region_id)
{
hssize_t npoints;
hsize_t alloc_size;
hsize_t *ptdata = NULL;
hid_t dtype = H5I_INVALID_HID;
hid_t type_id = H5I_INVALID_HID;
int ndims = -1;
int ret_value = FAIL;
/*
* This function fails if the region does not have points.
*/
H5E_BEGIN_TRY {
npoints = H5Sget_select_elem_npoints(region);
} H5E_END_TRY;
if (npoints < 0)
H5_LIBRARY_ERROR(ENVONLY);
if ((ndims = H5Sget_simple_extent_ndims(region)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
/* Print point information */
if (npoints > 0) {
alloc_size = (hsize_t)npoints * (hsize_t)ndims * (hsize_t)sizeof(ptdata[0]);
if (alloc_size == (hsize_t)((size_t) alloc_size)) {
if (NULL == (ptdata = (hsize_t *) HDmalloc((size_t) alloc_size)))
H5_JNI_FATAL_ERROR(ENVONLY, "h5str_dump_region_points_data: failed to allocate region point data buffer");
if (H5Sget_select_elem_pointlist(region, (hsize_t) 0, (hsize_t) npoints, ptdata) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if ((dtype = H5Dget_type(region_id)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if ((type_id = H5Tget_native_type(dtype, H5T_DIR_DEFAULT)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if (h5str_print_region_data_points(ENVONLY, region, region_id,
str, ndims, type_id, npoints, ptdata) < 0)
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
}
}
ret_value = SUCCEED;
done:
if (type_id >= 0)
H5Tclose(type_id);
if (dtype >= 0)
H5Tclose(dtype);
if (ptdata)
HDfree(ptdata);
return ret_value;
} /* end h5str_dump_region_points_data */
static int
h5str_dump_region_points
(JNIEnv *env, h5str_t *str, hid_t region, hid_t region_id)
{
hssize_t npoints;
hsize_t alloc_size;
hsize_t *ptdata = NULL;
char tmp_str[256];
int ndims = -1;
int ret_value = FAIL;
UNUSED(region_id);
/*
* This function fails if the region does not have points.
*/
H5E_BEGIN_TRY {
npoints = H5Sget_select_elem_npoints(region);
} H5E_END_TRY;
if (npoints < 0)
H5_LIBRARY_ERROR(ENVONLY);
if ((ndims = H5Sget_simple_extent_ndims(region)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
/* Print point information */
if (npoints > 0) {
int i;
alloc_size = (hsize_t)npoints * (hsize_t)ndims * (hsize_t)sizeof(ptdata[0]);
if (alloc_size == (hsize_t)((size_t) alloc_size)) {
if (NULL == (ptdata = (hsize_t *) HDmalloc((size_t) alloc_size)))
H5_JNI_FATAL_ERROR(ENVONLY, "h5str_dump_region_points: failed to allocate region point buffer");
if (H5Sget_select_elem_pointlist(region, (hsize_t) 0, (hsize_t) npoints, ptdata) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if (!h5str_append(str, " {"))
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
for (i = 0; i < npoints; i++) {
int j;
if (!h5str_append(str, " "))
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
for (j = 0; j < ndims; j++) {
tmp_str[0] = '\0';
if (HDsprintf(tmp_str, "%s%lu", j ? "," : "(",
(unsigned long) (ptdata[i * ndims + j])) < 0)
H5_JNI_FATAL_ERROR(ENVONLY, "h5str_dump_region_points: HDsprintf failure");
if (!h5str_append(str, tmp_str))
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
} /* end for (j = 0; j < ndims; j++) */
if (!h5str_append(str, ") "))
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
} /* end for (i = 0; i < npoints; i++) */
if (!h5str_append(str, " }"))
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
} /* end if (alloc_size == (hsize_t)((size_t) alloc_size)) */
} /* end if (npoints > 0) */
ret_value = SUCCEED;
done:
if (ptdata)
HDfree(ptdata);
return ret_value;
} /* end h5str_dump_region_points */
static int
h5str_is_zero
(const void *_mem, size_t size)
{
const unsigned char *mem = (const unsigned char *) _mem;
while (size-- > 0)
if (mem[size])
return 0;
return 1;
} /* end h5str_is_zero */
/*-------------------------------------------------------------------------
* Function: h5str_detect_vlen
*
* Purpose: Recursive check for any variable length data in given type.
*
* Return:
* 1 : type contains any variable length data
* 0 : type doesn't contain any variable length data
* Negative value: error occurred
*-------------------------------------------------------------------------
*/
static htri_t
h5str_detect_vlen
(hid_t tid)
{
htri_t ret = FAIL;
/* Recursively detect any vlen data values in type (compound, array ...) */
ret = H5Tdetect_class(tid, H5T_VLEN);
if ((ret == 1) || (ret < 0))
goto done;
/* Recursively detect any vlen string in type (compound, array ...) */
ret = h5str_detect_vlen_str(tid);
if ((ret == 1) || (ret < 0))
goto done;
done:
return ret;
} /* end h5str_detect_vlen */
/*-------------------------------------------------------------------------
* Function: h5str_detect_vlen_str
*
* Purpose: Recursive check for variable length string of a datatype.
*
* Return:
* TRUE : type conatains any variable length string
* FALSE : type doesn't contain any variable length string
* Negative value: error occur
*
*-------------------------------------------------------------------------
*/
static htri_t
h5str_detect_vlen_str
(hid_t tid)
{
H5T_class_t tclass = H5T_NO_CLASS;
htri_t ret = 0;
ret = H5Tis_variable_str(tid);
if((ret == 1) || (ret < 0))
goto done;
tclass = H5Tget_class(tid);
if(tclass == H5T_ARRAY || tclass == H5T_VLEN) {
hid_t btid = H5Tget_super(tid);
if(btid < 0) {
ret = (htri_t)btid;
goto done;
} /* end if */
ret = h5str_detect_vlen_str(btid);
if((ret == 1) || (ret < 0)) {
H5Tclose(btid);
goto done;
} /* end if */
} /* end if */
else if(tclass == H5T_COMPOUND) {
unsigned i = 0;
int n = H5Tget_nmembers(tid);
if (n < 0)
goto done;
for(i = 0; i < (unsigned) n; i++) {
hid_t mtid = H5Tget_member_type(tid, i);
ret = h5str_detect_vlen_str(mtid);
if((ret == 1) || (ret < 0)) {
H5Tclose(mtid);
goto done;
}
H5Tclose(mtid);
} /* end for */
} /* end else */
done:
return ret;
} /* end h5str_detect_vlen_str */
/*-------------------------------------------------------------------------
* Function: h5str_get_native_type
*
* Purpose: Wrapper around H5Tget_native_type() to work around
* Problems with bitfields.
*
* Return: Success: datatype ID
* Failure: FAIL
*-------------------------------------------------------------------------
*/
static hid_t
h5str_get_native_type
(hid_t type)
{
H5T_class_t type_class;
hid_t p_type = H5I_INVALID_HID;
if ((type_class = H5Tget_class(type)) < 0)
goto done;
if (type_class == H5T_BITFIELD)
p_type = H5Tcopy(type);
else
p_type = H5Tget_native_type(type, H5T_DIR_DEFAULT);
done:
return(p_type);
} /* end h5str_get_native_type */
/*-------------------------------------------------------------------------
* Function: h5str_get_little_endian_type
*
* Purpose: Get a little endian type from a file type
*
* Return: Success: datatype ID
* Failure: FAIL
*-------------------------------------------------------------------------
*/
static hid_t
h5str_get_little_endian_type
(hid_t tid)
{
H5T_class_t type_class;
H5T_sign_t sign;
size_t size;
hid_t p_type = H5I_INVALID_HID;
if ((type_class = H5Tget_class(tid)) < 0)
goto done;
if (!(size = H5Tget_size(tid)))
goto done;
if ((sign = H5Tget_sign(tid)) < 0)
goto done;
switch ( type_class ) {
case H5T_INTEGER:
{
if ( size == 1 && sign == H5T_SGN_2 )
p_type = H5Tcopy(H5T_STD_I8LE);
else if ( size == 2 && sign == H5T_SGN_2 )
p_type = H5Tcopy(H5T_STD_I16LE);
else if ( size == 4 && sign == H5T_SGN_2 )
p_type = H5Tcopy(H5T_STD_I32LE);
else if ( size == 8 && sign == H5T_SGN_2 )
p_type = H5Tcopy(H5T_STD_I64LE);
else if ( size == 1 && sign == H5T_SGN_NONE )
p_type = H5Tcopy(H5T_STD_U8LE);
else if ( size == 2 && sign == H5T_SGN_NONE )
p_type = H5Tcopy(H5T_STD_U16LE);
else if ( size == 4 && sign == H5T_SGN_NONE )
p_type = H5Tcopy(H5T_STD_U32LE);
else if ( size == 8 && sign == H5T_SGN_NONE )
p_type = H5Tcopy(H5T_STD_U64LE);
break;
}
case H5T_FLOAT:
{
if ( size == 4 )
p_type = H5Tcopy(H5T_IEEE_F32LE);
else if ( size == 8 )
p_type = H5Tcopy(H5T_IEEE_F64LE);
break;
}
case H5T_BITFIELD:
{
if ( size == 1 )
p_type = H5Tcopy(H5T_STD_B8LE);
else if ( size == 2 )
p_type = H5Tcopy(H5T_STD_B16LE);
else if ( size == 4 )
p_type = H5Tcopy(H5T_STD_B32LE);
else if ( size == 8 )
p_type = H5Tcopy(H5T_STD_B64LE);
break;
}
case H5T_NO_CLASS:
case H5T_NCLASSES:
{
goto done;
break;
}
case H5T_TIME:
case H5T_OPAQUE:
case H5T_STRING:
case H5T_COMPOUND:
case H5T_REFERENCE:
case H5T_ENUM:
case H5T_VLEN:
case H5T_ARRAY:
break;
default:
break;
}
done:
return(p_type);
} /* end h5str_get_little_endian_type */
/*-------------------------------------------------------------------------
* Function: h5str_get_big_endian_type
*
* Purpose: Get a big endian type from a file type
*
* Return: Success: datatype ID
* Failure: FAIL
*-------------------------------------------------------------------------
*/
static hid_t
h5str_get_big_endian_type
(hid_t tid)
{
H5T_class_t type_class;
H5T_sign_t sign;
size_t size;
hid_t p_type = H5I_INVALID_HID;
if ((type_class = H5Tget_class(tid)) < 0)
goto done;
if (!(size = H5Tget_size(tid)))
goto done;
if ((sign = H5Tget_sign(tid)) < 0)
goto done;
switch ( type_class ) {
case H5T_INTEGER:
{
if ( size == 1 && sign == H5T_SGN_2 )
p_type = H5Tcopy(H5T_STD_I8BE);
else if ( size == 2 && sign == H5T_SGN_2 )
p_type = H5Tcopy(H5T_STD_I16BE);
else if ( size == 4 && sign == H5T_SGN_2 )
p_type = H5Tcopy(H5T_STD_I32BE);
else if ( size == 8 && sign == H5T_SGN_2 )
p_type = H5Tcopy(H5T_STD_I64BE);
else if ( size == 1 && sign == H5T_SGN_NONE )
p_type = H5Tcopy(H5T_STD_U8BE);
else if ( size == 2 && sign == H5T_SGN_NONE )
p_type = H5Tcopy(H5T_STD_U16BE);
else if ( size == 4 && sign == H5T_SGN_NONE )
p_type = H5Tcopy(H5T_STD_U32BE);
else if ( size == 8 && sign == H5T_SGN_NONE )
p_type = H5Tcopy(H5T_STD_U64BE);
break;
}
case H5T_FLOAT:
{
if ( size == 4 )
p_type = H5Tcopy(H5T_IEEE_F32BE);
else if ( size == 8 )
p_type = H5Tcopy(H5T_IEEE_F64BE);
break;
}
case H5T_BITFIELD:
{
if ( size == 1 )
p_type = H5Tcopy(H5T_STD_B8BE);
else if ( size == 2 )
p_type = H5Tcopy(H5T_STD_B16BE);
else if ( size == 4 )
p_type = H5Tcopy(H5T_STD_B32BE);
else if ( size == 8 )
p_type = H5Tcopy(H5T_STD_B64BE);
break;
}
case H5T_NO_CLASS:
case H5T_NCLASSES:
{
goto done;
break;
}
case H5T_TIME:
case H5T_OPAQUE:
case H5T_STRING:
case H5T_COMPOUND:
case H5T_REFERENCE:
case H5T_ENUM:
case H5T_VLEN:
case H5T_ARRAY:
break;
default:
break;
}
done:
return(p_type);
} /* end h5str_get_big_endian_type */
/*-------------------------------------------------------------------------
* Function: render_bin_output
*
* Purpose: Write one element of memory buffer to a binary file stream
*
* Return: Success: SUCCEED
* Failure: FAIL
*-------------------------------------------------------------------------
*/
static int
h5str_render_bin_output
(FILE *stream, hid_t container, hid_t tid, void *_mem, hsize_t block_nelmts)
{
unsigned char *mem = (unsigned char*)_mem;
H5T_class_t type_class;
hsize_t block_index;
size_t size; /* datum size */
int ret_value = 0;
if (!(size = H5Tget_size(tid))) {
ret_value = FAIL;
goto done;
}
if ((type_class = H5Tget_class(tid)) < 0) {
ret_value = FAIL;
goto done;
}
switch (type_class) {
case H5T_INTEGER:
case H5T_FLOAT:
case H5T_ENUM:
{
block_index = block_nelmts * size;
while (block_index > 0) {
size_t bytes_in = 0; /* # of bytes to write */
size_t bytes_wrote = 0; /* # of bytes written */
if (block_index > sizeof(size_t))
bytes_in = sizeof(size_t);
else
bytes_in = (size_t)block_index;
bytes_wrote = fwrite(mem, 1, bytes_in, stream);
if (bytes_wrote != bytes_in || (0 == bytes_wrote && ferror(stream))) {
ret_value = FAIL;
break;
}
block_index -= (hsize_t)bytes_wrote;
mem = mem + bytes_wrote;
}
break;
}
case H5T_STRING:
{
unsigned char tempuchar;
unsigned int i;
H5T_str_t pad;
char *s;
if ((pad = H5Tget_strpad(tid)) < 0) {
ret_value = FAIL;
goto done;
}
for (block_index = 0; block_index < block_nelmts; block_index++) {
mem = ((unsigned char *)_mem) + block_index * size;
if (H5Tis_variable_str(tid)) {
s = *(char**) mem;
if (s != NULL)
size = HDstrlen(s);
}
else {
s = (char *) mem;
}
for (i = 0; i < size && (s[i] || pad != H5T_STR_NULLTERM); i++) {
HDmemcpy(&tempuchar, &s[i], sizeof(unsigned char));
if (1 != fwrite(&tempuchar, sizeof(unsigned char), 1, stream)) {
ret_value = FAIL;
break;
}
} /* i */
if (ret_value < 0)
break;
} /* for (block_index = 0; block_index < block_nelmts; block_index++) */
break;
}
case H5T_COMPOUND:
{
unsigned j;
size_t offset;
hid_t memb = H5I_INVALID_HID;
int nmembs;
if ((nmembs = H5Tget_nmembers(tid)) < 0) {
ret_value = FAIL;
goto done;
}
for (block_index = 0; block_index < block_nelmts; block_index++) {
mem = ((unsigned char*)_mem) + block_index * size;
for (j = 0; j < (unsigned) nmembs; j++) {
offset = H5Tget_member_offset(tid, j);
memb = H5Tget_member_type(tid, j);
if (h5str_render_bin_output(stream, container, memb, mem + offset, 1) < 0) {
H5Tclose(memb);
ret_value = FAIL;
break;
}
H5Tclose(memb);
}
if (ret_value < 0)
break;
}
break;
}
case H5T_ARRAY:
{
hsize_t dims[H5S_MAX_RANK], temp_nelmts, nelmts;
hid_t memb;
int k, ndims;
/* Get the array's base datatype for each element */
if ((memb = H5Tget_super(tid)) < 0) {
ret_value = FAIL;
goto done;
}
if ((ndims = H5Tget_array_ndims(tid)) < 0) {
ret_value = FAIL;
goto done;
}
if (H5Tget_array_dims2(tid, dims) < 0) {
ret_value = FAIL;
goto done;
}
/* Calculate the number of array elements */
for (k = 0, nelmts = 1; k < ndims; k++) {
temp_nelmts = nelmts;
temp_nelmts *= dims[k];
nelmts = (size_t) temp_nelmts;
}
for (block_index = 0; block_index < block_nelmts; block_index++) {
mem = ((unsigned char*)_mem) + block_index * size;
/* dump the array element */
if (h5str_render_bin_output(stream, container, memb, mem, nelmts) < 0) {
ret_value = FAIL;
break;
}
}
H5Tclose(memb);
break;
}
case H5T_VLEN:
{
hsize_t nelmts;
hid_t memb;
/* Get the VL sequences's base datatype for each element */
if ((memb = H5Tget_super(tid)) < 0) {
ret_value = FAIL;
goto done;
}
for (block_index = 0; block_index < block_nelmts; block_index++) {
mem = ((unsigned char*)_mem) + block_index * size;
/* Get the number of sequence elements */
nelmts = ((hvl_t *) mem)->len;
/* dump the array element */
if (h5str_render_bin_output(stream, container, memb, ((char *) (((hvl_t *) mem)->p)), nelmts) < 0) {
ret_value = FAIL;
break;
}
}
H5Tclose(memb);
break;
}
case H5T_REFERENCE:
{
if (H5Tequal(tid, H5T_STD_REF_DSETREG)) {
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)
continue;
if ((region_space = H5Rget_region(container, H5R_DATASET_REGION, mem)) < 0) {
H5Dclose(region_id);
continue;
}
if ((region_type = H5Sget_select_type(region_space)) < 0) {
H5Sclose(region_space);
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_OBJ)) {
;
}
break;
}
case H5T_NO_CLASS:
case H5T_NCLASSES:
{
ret_value = FAIL;
goto done;
break;
}
case H5T_TIME:
case H5T_BITFIELD:
case H5T_OPAQUE:
default:
for (block_index = 0; block_index < block_nelmts; block_index++) {
mem = ((unsigned char*)_mem) + block_index * size;
if (size != fwrite(mem, sizeof(char), size, stream)) {
ret_value = FAIL;
break;
}
}
break;
}
done:
return ret_value;
} /* end h5str_render_bin_output */
/*-------------------------------------------------------------------------
* Purpose: Print the data values from a dataset referenced by region blocks.
*
* Description:
* This is a special case subfunction to print the data in a region reference of type blocks.
*
* Return:
* The function returns FAIL if there was an error, otherwise SUCEED
*
*-------------------------------------------------------------------------
*/
static int
render_bin_output_region_data_blocks
(FILE *stream, hid_t region_id, hid_t container, int ndims, hid_t type_id, hssize_t nblocks, hsize_t *ptdata)
{
hsize_t *dims1 = NULL;
hsize_t *start = NULL;
hsize_t *count = NULL;
hsize_t numelem;
hsize_t total_size[H5S_MAX_RANK];
size_t type_size;
hid_t sid1 = H5I_INVALID_HID;
hid_t mem_space = H5I_INVALID_HID;
void *region_buf = NULL;
int blkndx;
int jndx;
int ret_value = SUCCEED;
/* Get the dataspace of the dataset */
if ((sid1 = H5Dget_space(region_id)) < 0) {
ret_value = FAIL;
goto done;
}
/* Allocate space for the dimension array */
if (NULL == (dims1 = (hsize_t *) HDmalloc(sizeof(hsize_t) * (size_t)ndims))) {
ret_value = FAIL;
goto done;
}
/* Find the dimensions of each data space from the block coordinates */
for (jndx = 0, numelem = 1; jndx < ndims; jndx++) {
dims1[jndx] = ptdata[jndx + ndims] - ptdata[jndx] + 1;
numelem = dims1[jndx] * numelem;
}
/* Create dataspace for reading buffer */
if ((mem_space = H5Screate_simple(ndims, dims1, NULL)) < 0) {
ret_value = FAIL;
goto done;
}
if (!(type_size = H5Tget_size(type_id))) {
ret_value = FAIL;
goto done;
}
if (NULL == (region_buf = HDmalloc(type_size * (size_t)numelem))) {
ret_value = FAIL;
goto done;
}
/* Select (x , x , ..., x ) x (y , y , ..., y ) hyperslab for reading memory dataset */
/* 1 2 n 1 2 n */
if (NULL == (start = (hsize_t *) HDmalloc(sizeof(hsize_t) * (size_t)ndims))) {
ret_value = FAIL;
goto done;
}
if (NULL == (count = (hsize_t *) HDmalloc(sizeof(hsize_t) * (size_t)ndims))) {
ret_value = FAIL;
goto done;
}
for (blkndx = 0; blkndx < nblocks; blkndx++) {
for (jndx = 0; jndx < ndims; jndx++) {
start[jndx] = ptdata[jndx + blkndx * ndims * 2];
count[jndx] = dims1[jndx];
}
if (H5Sselect_hyperslab(sid1, H5S_SELECT_SET, start, NULL, count, NULL) < 0) {
ret_value = FAIL;
goto done;
}
if (H5Dread(region_id, type_id, mem_space, sid1, H5P_DEFAULT, region_buf) < 0) {
ret_value = FAIL;
goto done;
}
if (H5Sget_simple_extent_dims(mem_space, total_size, NULL) < 0) {
ret_value = FAIL;
goto done;
}
if (h5str_render_bin_output(stream, container, type_id, (char *)region_buf, numelem) < 0) {
ret_value = FAIL;
goto done;
}
/* Render the region data element end */
} /* end for (blkndx = 0; blkndx < nblocks; blkndx++) */
done:
if (count)
HDfree(count);
if (start)
HDfree(start);
if (region_buf)
HDfree(region_buf);
if (mem_space >= 0)
H5Sclose(mem_space);
if (dims1)
HDfree(dims1);
if (sid1 >= 0)
H5Sclose(sid1);
return ret_value;
} /* end render_bin_output_region_data_blocks */
/*-------------------------------------------------------------------------
* Purpose: Print some values from a dataset referenced by region blocks.
*
* Description:
* This is a special case subfunction to dump a region reference using blocks.
*
* Return:
* The function returns False if ERROR, otherwise True
*
*-------------------------------------------------------------------------
*/
static int
render_bin_output_region_blocks
(FILE *stream, hid_t region_space, hid_t region_id, hid_t container)
{
hssize_t nblocks;
hsize_t alloc_size;
hsize_t *ptdata = NULL;
hid_t dtype = H5I_INVALID_HID;
hid_t type_id = H5I_INVALID_HID;
int ndims;
int ret_value = SUCCEED;
if ((nblocks = H5Sget_select_hyper_nblocks(region_space)) < 0) {
ret_value = FAIL;
goto done;
}
if (nblocks > 0) {
/* Print block information */
if ((ndims = H5Sget_simple_extent_ndims(region_space)) < 0) {
ret_value = FAIL;
goto done;
}
alloc_size = (hsize_t)nblocks * (hsize_t)ndims * 2 * (hsize_t)sizeof(ptdata[0]);
if (NULL == (ptdata = (hsize_t *) HDmalloc((size_t)alloc_size))) {
ret_value = FAIL;
goto done;
}
if (H5Sget_select_hyper_blocklist(region_space, (hsize_t)0, (hsize_t)nblocks, ptdata) < 0) {
ret_value = FAIL;
goto done;
}
if ((dtype = H5Dget_type(region_id)) < 0) {
ret_value = FAIL;
goto done;
}
if ((type_id = H5Tget_native_type(dtype, H5T_DIR_DEFAULT)) < 0) {
ret_value = FAIL;
goto done;
}
if (render_bin_output_region_data_blocks(stream, region_id, container,
ndims, type_id, nblocks, ptdata) < 0) {
ret_value = FAIL;
goto done;
}
}
done:
if (type_id >= 0)
H5Tclose(type_id);
if (dtype >= 0)
H5Tclose(dtype);
if (ptdata)
HDfree(ptdata);
return ret_value;
} /* end render_bin_output_region_blocks */
/*-------------------------------------------------------------------------
* Purpose: Print the data values from a dataset referenced by region points.
*
* Description:
* This is a special case subfunction to print the data in a region reference of type points.
*
* Return:
* The function returns FAIL on error, otherwise SUCCEED
*
*-------------------------------------------------------------------------
*/
static int
render_bin_output_region_data_points
(FILE *stream, hid_t region_space, hid_t region_id,
hid_t container, int ndims, hid_t type_id, hssize_t npoints, hsize_t *ptdata)
{
hsize_t *dims1 = NULL;
size_t type_size;
hid_t mem_space = H5I_INVALID_HID;
void *region_buf = NULL;
int ret_value = SUCCEED;
UNUSED(ptdata);
if (!(type_size = H5Tget_size(type_id))) {
ret_value = FAIL;
goto done;
}
if (NULL == (region_buf = HDmalloc(type_size * (size_t)npoints))) {
ret_value = FAIL;
goto done;
}
/* Allocate space for the dimension array */
if (NULL == (dims1 = (hsize_t *) HDmalloc(sizeof(hsize_t) * (size_t)ndims))) {
ret_value = FAIL;
goto done;
}
dims1[0] = (hsize_t)npoints;
if ((mem_space = H5Screate_simple(1, dims1, NULL)) < 0) {
ret_value = FAIL;
goto done;
}
if (H5Dread(region_id, type_id, mem_space, region_space, H5P_DEFAULT, region_buf) < 0) {
ret_value = FAIL;
goto done;
}
if (H5Sget_simple_extent_dims(region_space, dims1, NULL) < 0) {
ret_value = FAIL;
goto done;
}
if (h5str_render_bin_output(stream, container, type_id, (char *)region_buf, (hsize_t)npoints) < 0) {
ret_value = FAIL;
goto done;
}
done:
if (dims1)
HDfree(dims1);
if (mem_space >= 0)
H5Sclose(mem_space);
if (region_buf)
HDfree(region_buf);
return ret_value;
} /* end render_bin_output_region_data_points */
/*-------------------------------------------------------------------------
* Purpose: Print some values from a dataset referenced by region points.
*
* Description:
* This is a special case subfunction to dump a region reference using points.
*
* Return:
* The function returns False if the last dimension has been reached, otherwise True
*
*-------------------------------------------------------------------------
*/
static int
render_bin_output_region_points
(FILE *stream, hid_t region_space, hid_t region_id, hid_t container)
{
hssize_t npoints;
hsize_t alloc_size;
hsize_t *ptdata = NULL;
hid_t dtype = H5I_INVALID_HID;
hid_t type_id = H5I_INVALID_HID;
int ndims;
int ret_value = SUCCEED;
if ((npoints = H5Sget_select_elem_npoints(region_space)) < 0) {
ret_value = FAIL;
goto done;
}
if (npoints > 0) {
/* Allocate space for the dimension array */
if ((ndims = H5Sget_simple_extent_ndims(region_space)) < 0) {
ret_value = FAIL;
goto done;
}
alloc_size = (hsize_t)npoints * (hsize_t)ndims * (hsize_t)sizeof(ptdata[0]);
if (NULL == (ptdata = (hsize_t *) HDmalloc((size_t)alloc_size))) {
ret_value = FAIL;
goto done;
}
if (H5Sget_select_elem_pointlist(region_space, (hsize_t)0, (hsize_t)npoints, ptdata) < 0) {
ret_value = FAIL;
goto done;
}
if ((dtype = H5Dget_type(region_id)) < 0) {
ret_value = FAIL;
goto done;
}
if ((type_id = H5Tget_native_type(dtype, H5T_DIR_DEFAULT)) < 0) {
ret_value = FAIL;
goto done;
}
if (render_bin_output_region_data_points(stream, region_space, region_id,
container, ndims, type_id, npoints, ptdata) < 0) {
ret_value = FAIL;
goto done;
}
}
done:
if (type_id >= 0)
H5Tclose(type_id);
if (dtype >= 0)
H5Tclose(dtype);
if (ptdata)
HDfree(ptdata);
return ret_value;
} /* end render_bin_output_region_points */
int
h5str_dump_simple_dset
(JNIEnv *env, FILE *stream, hid_t dset, int binary_order)
{
hsize_t elmtno; /* counter */
hsize_t zero[8]; /* vector of zeros */
hsize_t total_size[H5S_MAX_RANK]; /* total size of dataset*/
size_t i; /* counter */
hid_t f_space = H5I_INVALID_HID; /* file data space */
int ndims;
int carry; /* counter carry value */
/* Print info */
hsize_t p_nelmts; /* total selected elmts */
size_t p_type_nbytes; /* size of memory type */
/* Stripmine info */
unsigned char *sm_buf = NULL; /* buffer for raw data */
hsize_t sm_size[H5S_MAX_RANK]; /* stripmine size */
hsize_t sm_nbytes; /* bytes per stripmine */
hsize_t sm_nelmts; /* elements per stripmine */
hid_t sm_space = H5I_INVALID_HID; /* stripmine data space */
/* Hyperslab info */
hsize_t hs_offset[H5S_MAX_RANK]; /* starting offset */
hsize_t hs_size[H5S_MAX_RANK]; /* size this pass */
hsize_t hs_nelmts; /* elements in request */
/* VL data special information */
unsigned int vl_data = 0; /* contains VL datatypes */
hid_t p_type = H5I_INVALID_HID;
hid_t f_type = H5I_INVALID_HID;
int ret_value = FAIL;
if (dset < 0)
H5_BAD_ARGUMENT_ERROR(ENVONLY, "h5str_dump_simple_dset: dset ID < 0");
if ((f_type = H5Dget_type(dset)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
switch (binary_order) {
case 1:
{
if ((p_type = h5str_get_native_type(f_type)) < 0)
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
break;
}
case 2:
{
if ((p_type = h5str_get_little_endian_type(f_type)) < 0)
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
break;
}
case 3:
{
if ((p_type = h5str_get_big_endian_type(f_type)) < 0)
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
break;
}
default:
{
if ((p_type = H5Tcopy(f_type)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
break;
}
}
if ((f_space = H5Dget_space(dset)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if ((ndims = H5Sget_simple_extent_ndims(f_space)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if ((size_t)ndims <= (sizeof(sm_size) / sizeof(sm_size[0]))) {
if (H5Sget_simple_extent_dims(f_space, total_size, NULL) < 0)
H5_LIBRARY_ERROR(ENVONLY);
/* Calculate the number of elements we're going to print */
p_nelmts = 1;
if (ndims > 0) {
for (i = 0; i < (size_t) ndims; i++)
p_nelmts *= total_size[i];
} /* end if */
if (p_nelmts > 0) {
/* Check if we have VL data in the dataset's datatype */
if (h5str_detect_vlen(p_type) != 0)
vl_data = 1;
/*
* Determine the strip mine size and allocate a buffer. The strip mine is
* a hyperslab whose size is manageable.
*/
if (!(sm_nbytes = p_type_nbytes = H5Tget_size(p_type)))
H5_LIBRARY_ERROR(ENVONLY);
if (ndims > 0) {
for (i = (size_t)ndims; i > 0; --i) {
hsize_t size = H5TOOLS_BUFSIZE / sm_nbytes;
if ( size == 0 ) /* datum size > H5TOOLS_BUFSIZE */
size = 1;
sm_size[i - 1] = (((total_size[i - 1]) < (size)) ? (total_size[i - 1]) : (size));
sm_nbytes *= sm_size[i - 1];
}
}
if (sm_nbytes > 0) {
if (NULL == (sm_buf = (unsigned char *) HDmalloc((size_t)sm_nbytes)))
H5_JNI_FATAL_ERROR(ENVONLY, "h5str_dump_simple_dset: failed to allocate sm_buf");
sm_nelmts = sm_nbytes / p_type_nbytes;
if ((sm_space = H5Screate_simple(1, &sm_nelmts, NULL)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
/* The stripmine loop */
HDmemset(hs_offset, 0, sizeof hs_offset);
HDmemset(zero, 0, sizeof zero);
for (elmtno = 0; elmtno < p_nelmts; elmtno += hs_nelmts) {
/* Calculate the hyperslab size */
if (ndims > 0) {
for (i = 0, hs_nelmts = 1; i < (size_t) ndims; i++) {
hs_size[i] = (((total_size[i] - hs_offset[i]) < (sm_size[i])) ? (total_size[i] - hs_offset[i]) : (sm_size[i]));
hs_nelmts *= hs_size[i];
}
if (H5Sselect_hyperslab(f_space, H5S_SELECT_SET, hs_offset, NULL, hs_size, NULL) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if (H5Sselect_hyperslab(sm_space, H5S_SELECT_SET, zero, NULL, &hs_nelmts, NULL) < 0)
H5_LIBRARY_ERROR(ENVONLY);
}
else {
if (H5Sselect_all(f_space) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if (H5Sselect_all(sm_space) < 0)
H5_LIBRARY_ERROR(ENVONLY);
hs_nelmts = 1;
}
/* Read the data */
if (H5Dread(dset, p_type, sm_space, f_space, H5P_DEFAULT, sm_buf) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if (binary_order == 99) {
if (h5tools_dump_simple_data(ENVONLY, stream, dset, p_type, sm_buf, hs_nelmts) < 0)
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
}
else {
if (h5str_render_bin_output(stream, dset, p_type, sm_buf, hs_nelmts) < 0)
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
}
/* Reclaim any VL memory, if necessary */
if (vl_data) {
if (H5Dvlen_reclaim(p_type, sm_space, H5P_DEFAULT, sm_buf) < 0)
H5_LIBRARY_ERROR(ENVONLY);
}
/* Calculate the next hyperslab offset */
for (i = (size_t)ndims, carry = 1; i > 0 && carry; --i) {
hs_offset[i - 1] += hs_size[i - 1];
if (hs_offset[i - 1] == total_size[i - 1])
hs_offset[i - 1] = 0;
else
carry = 0;
}
}
}
}
}
ret_value = SUCCEED;
done:
if (sm_space >= 0)
H5Sclose(sm_space);
if (sm_buf)
HDfree(sm_buf);
if (f_space >= 0)
H5Sclose(f_space);
if (p_type >= 0)
H5Tclose(p_type);
if (f_type >= 0)
H5Tclose(f_type);
return ret_value;
} /* end h5str_dump_simple_dset */
htri_t
H5Tdetect_variable_str(hid_t tid) {
htri_t ret_val = 0;
if (H5Tget_class(tid) == H5T_COMPOUND) {
unsigned i;
unsigned nm = (unsigned)H5Tget_nmembers(tid);
for(i = 0; i < nm; i++) {
htri_t status = 0;
hid_t mtid = 0;
if((mtid = H5Tget_member_type(tid, i)) < 0)
return FAIL; /* exit immediately on error */
if((status = H5Tdetect_variable_str(mtid)) < 0)
return status; /* exit immediately on error */
ret_val |= status;
H5Tclose (mtid);
} /* end for */
} /* end if */
else
ret_val = H5Tis_variable_str(tid);
return ret_val;
} /* end H5Tdetect_variable_str */
static int
h5tools_dump_simple_data
(JNIEnv *env, FILE *stream, hid_t container, hid_t type, void *_mem, hsize_t nelmts)
{
unsigned char *mem = (unsigned char *)_mem;
h5str_t buffer; /* string into which to render */
hsize_t i; /* element counter */
size_t size; /* datum size */
int line_count;
int ret_value = 0;
if (!(size = H5Tget_size(type)))
H5_LIBRARY_ERROR(ENVONLY);
for (i = 0, line_count = 0; i < nelmts; i++, line_count++) {
size_t bytes_in = 0; /* # of bytes to write */
void *memref = mem + i * size;
/* Render the data element*/
h5str_new(&buffer, 32 * size);
if (!buffer.s)
H5_JNI_FATAL_ERROR(ENVONLY, "h5tools_dump_simple_data: failed to allocate buffer");
if (!(bytes_in = h5str_sprintf(ENVONLY, &buffer, container, type, memref, 0, 1)))
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
if (i > 0) {
if (HDfprintf(stream, ", ") < 0)
H5_JNI_FATAL_ERROR(ENVONLY, "h5tools_dump_simple_data: HDfprintf failure");
if (line_count >= H5TOOLS_TEXT_BLOCK) {
line_count = 0;
if (HDfprintf(stream, "\n") < 0)
H5_JNI_FATAL_ERROR(ENVONLY, "h5tools_dump_simple_data: HDfprintf failure");
}
}
if (HDfprintf(stream, "%s", buffer.s) < 0)
H5_JNI_FATAL_ERROR(ENVONLY, "h5tools_dump_simple_data: HDfprintf failure");
h5str_free(&buffer);
} /* end for (i = 0; i < nelmts... */
if (HDfprintf(stream, "\n") < 0)
H5_JNI_FATAL_ERROR(ENVONLY, "h5tools_dump_simple_data: HDfprintf failure");
done:
if (buffer.s)
h5str_free(&buffer);
return ret_value;
} /* end h5tools_dump_simple_data */
/*
* Utility Java APIs
* Functions designed to workaround issues with the Java-C interface
*/
/*
* Class: hdf_hdf5lib_H5
* Method: H5AreadComplex
* Signature: (JJ[Ljava/lang/String;)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5AreadComplex
(JNIEnv *env, jclass clss, jlong attr_id, jlong mem_type_id, jobjectArray buf)
{
h5str_t h5str;
jstring jstr;
size_t size;
size_t i;
hid_t p_type = H5I_INVALID_HID;
jsize n;
char *readBuf = NULL;
herr_t status = FAIL;
UNUSED(clss);
HDmemset(&h5str, 0, sizeof(h5str_t));
if ((p_type = H5Tget_native_type(mem_type_id, H5T_DIR_DEFAULT)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
size = (((H5Tget_size(mem_type_id))>(H5Tget_size(p_type))) ? (H5Tget_size(mem_type_id)) : (H5Tget_size(p_type)));
if ((n = ENVPTR->GetArrayLength(ENVONLY, buf)) <= 0) {
CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE);
H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5AreadComplex: read buffer length <= 0");
}
if (NULL == (readBuf = (char *) HDmalloc((size_t)n * size)))
H5_JNI_FATAL_ERROR(ENVONLY, "H5AreadComplex: failed to allocate read buffer");
if ((status = H5Aread(attr_id, mem_type_id, readBuf)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
h5str_new(&h5str, 4 * size);
if (!h5str.s)
H5_JNI_FATAL_ERROR(ENVONLY, "H5AreadComplex: failed to allocate string buffer");
for (i = 0; i < (size_t) n; i++) {
h5str.s[0] = '\0';
if (!h5str_sprintf(ENVONLY, &h5str, attr_id, mem_type_id, readBuf + (i * size), 0, 0))
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
if (NULL == (jstr = ENVPTR->NewStringUTF(ENVONLY, h5str.s)))
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
ENVPTR->SetObjectArrayElement(ENVONLY, buf, (jsize) i, jstr);
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
ENVPTR->DeleteLocalRef(ENVONLY, jstr);
} /* end for */
done:
if (h5str.s)
h5str_free(&h5str);
if (readBuf)
HDfree(readBuf);
if (p_type >= 0)
H5Tclose(p_type);
return status;
}
/*
* Copies the content of one attribute to another attribute
* Class: hdf_hdf5lib_H5
* Method: H5Acopy
* Signature: (JJ)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Acopy
(JNIEnv *env, jclass clss, jlong src_id, jlong dst_id)
{
hssize_t npoints;
hsize_t total_size = 0;
size_t type_size;
jbyte *buf = NULL;
hid_t tid = H5I_INVALID_HID;
hid_t sid = H5I_INVALID_HID;
herr_t retVal = FAIL;
UNUSED(clss);
if ((sid = H5Aget_space((hid_t)src_id)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if ((tid = H5Aget_type((hid_t)src_id)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if ((npoints = H5Sget_simple_extent_npoints(sid)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if (!(type_size = H5Tget_size(tid)))
H5_LIBRARY_ERROR(ENVONLY);
total_size = (hsize_t)npoints * (hsize_t)type_size;
if (NULL == (buf = (jbyte *) HDmalloc((size_t)total_size * sizeof(jbyte))))
H5_JNI_FATAL_ERROR(ENVONLY, "H5Acopy: failed to allocate buffer");
if ((retVal = H5Aread((hid_t)src_id, tid, buf)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if (H5Tclose(tid) < 0)
H5_LIBRARY_ERROR(ENVONLY);
tid = H5I_INVALID_HID;
if ((tid = H5Aget_type((hid_t)dst_id)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if ((retVal = H5Awrite((hid_t)dst_id, tid, buf)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
done:
if (buf)
HDfree(buf);
if (tid >= 0)
H5Tclose(tid);
if (sid >= 0)
H5Sclose(sid);
return (jint)retVal;
} /* end Java_hdf_hdf5lib_H5_H5Acopy */
/*
* Copies the content of one dataset to another dataset
* Class: hdf_hdf5lib_H5
* Method: H5Dcopy
* Signature: (JJ)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Dcopy
(JNIEnv *env, jclass clss, jlong src_id, jlong dst_id)
{
hssize_t npoints;
hsize_t total_size = 0, total_allocated_size;
size_t type_size;
jbyte *buf = NULL;
hid_t tid = H5I_INVALID_HID;
hid_t sid = H5I_INVALID_HID;
herr_t retVal = FAIL;
UNUSED(clss);
if (!(total_allocated_size = H5Dget_storage_size((hid_t)src_id)))
return 0; // nothing to write
if ((sid = H5Dget_space((hid_t)src_id)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if ((tid = H5Dget_type((hid_t)src_id)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if ((npoints = H5Sget_simple_extent_npoints(sid)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if (!(type_size = H5Tget_size(tid)))
H5_LIBRARY_ERROR(ENVONLY);
total_size = (hsize_t)npoints * (hsize_t)type_size;
if (NULL == (buf = (jbyte *) HDmalloc((size_t)total_size * sizeof(jbyte))))
H5_JNI_FATAL_ERROR(ENVONLY, "H5Dcopy: failed to allocate buffer");
if ((retVal = H5Dread((hid_t)src_id, tid, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if (H5Tclose(tid) < 0)
H5_LIBRARY_ERROR(ENVONLY);
tid = H5I_INVALID_HID;
if ((tid = H5Dget_type((hid_t)dst_id)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if ((retVal = H5Dwrite((hid_t)dst_id, tid, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
done:
if (buf)
HDfree(buf);
if (tid >= 0)
H5Tclose(tid);
if (sid >= 0)
H5Sclose(sid);
return (jint)retVal;
} /* 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
//
/////////////////////////////////////////////////////////////////////////////////
*/
#ifdef __cplusplus
herr_t obj_info_all(hid_t g_id, const char *name, const H5L_info_t *linfo, void *op_data);
herr_t obj_info_max(hid_t g_id, const char *name, const H5L_info_t *linfo, void *op_data);
int H5Gget_obj_info_max(hid_t, char **, int *, int *, unsigned long *, long);
int H5Gget_obj_info_full( hid_t loc_id, char **objname, int *otype, int *ltype, unsigned long *fno, unsigned long *objno, int indexType, int indexOrder);
#else
static herr_t obj_info_all(hid_t g_id, const char *name, const H5L_info_t *linfo, void *op_data);
static herr_t obj_info_max(hid_t g_id, const char *name, const H5L_info_t *linfo, void *op_data);
static int H5Gget_obj_info_max(hid_t, char **, int *, int *, unsigned long *, long);
static int H5Gget_obj_info_full( hid_t loc_id, char **objname, int *otype, int *ltype, unsigned long *fno, unsigned long *objno, int indexType, int indexOrder);
#endif
typedef struct info_all
{
char **objname;
int *otype;
int *ltype;
unsigned long *objno;
unsigned long *fno;
unsigned long idxnum;
int count;
} info_all_t;
/*
* Class: hdf_hdf5lib_H5
* Method: H5Gget_obj_info_full
* Signature: (JLjava/lang/String;[Ljava/lang/String;[I[I[J[JIII)I
*/
/*
* NOTE: This is a dangerous call! The caller can supply any value they'd like
* for 'n' and if it exceeds the number of links in the group, we will most likely
* end up overwriting memory heap-tracking info.
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Gget_1obj_1info_1full
(JNIEnv *env, jclass clss, jlong loc_id, jstring group_name,
jobjectArray objName, jintArray oType, jintArray lType, jlongArray fNo,
jlongArray oRef, jint n, jint indx_type, jint indx_order)
{
unsigned long *refs = NULL;
unsigned long *fnos = NULL;
const char *gName = NULL;
char **oName = NULL;
jboolean isCopy;
jstring str;
jint *otarr = NULL;
jint *ltarr = NULL;
jlong *refP = NULL;
jlong *fnoP = NULL;
hid_t gid = (hid_t)loc_id;
int i;
int indexType = indx_type;
int indexOrder = indx_order;
herr_t ret_val = FAIL;
UNUSED(clss);
if (NULL == oType)
H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Gget_obj_info_full: oType is NULL");
if (NULL == lType)
H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Gget_obj_info_full: lType is NULL");
if (NULL == oRef)
H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Gget_obj_info_full: oRef is NULL");
if (NULL == fNo)
H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Gget_obj_info_full: fNo is NULL");
PIN_INT_ARRAY(ENVONLY, oType, otarr, &isCopy, "H5Gget_obj_info_full: oType not pinned");
PIN_INT_ARRAY(ENVONLY, lType, ltarr, &isCopy, "H5Gget_obj_info_full: lType not pinned");
PIN_LONG_ARRAY(ENVONLY, oRef, refP, &isCopy, "H5Gget_obj_info_full: oRef not pinned");
PIN_LONG_ARRAY(ENVONLY, fNo, fnoP, &isCopy, "H5Gget_obj_info_full: fNo not pinned");
if (NULL == (oName = (char **) HDcalloc((size_t)n, sizeof(*oName))))
H5_JNI_FATAL_ERROR(ENVONLY, "H5Gget_obj_info_full: failed to allocate buffer for object name");
if (NULL == (refs = (unsigned long *) HDcalloc((size_t)n, sizeof(unsigned long))))
H5_JNI_FATAL_ERROR(ENVONLY, "H5Gget_obj_info_full: failed to allocate buffer for ref. info");
if (NULL == (fnos = (unsigned long *) HDcalloc((size_t)n, sizeof(unsigned long))))
H5_JNI_FATAL_ERROR(ENVONLY, "H5Gget_obj_info_full: failed to allocate buffer for file number info");
if (group_name) {
PIN_JAVA_STRING(ENVONLY, group_name, gName, &isCopy, "H5Gget_obj_info_full: group_name not pinned");
if ((gid = H5Gopen2((hid_t)loc_id, gName, H5P_DEFAULT)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
}
if ((ret_val = H5Gget_obj_info_full(gid, oName, (int *)otarr, (int *)ltarr, fnos, refs, indexType, indexOrder)) < 0)
H5_JNI_FATAL_ERROR(ENVONLY, "H5Gget_obj_info_full: retrieval of object info failed");
for (i = 0; i < n; i++) {
refP[i] = (jlong)refs[i];
fnoP[i] = (jlong)fnos[i];
if (oName[i]) {
if (NULL == (str = ENVPTR->NewStringUTF(ENVONLY, oName[i])))
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
ENVPTR->SetObjectArrayElement(ENVONLY, objName, i, (jobject)str);
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
ENVPTR->DeleteLocalRef(ENVONLY, str);
} /* end if */
}
done:
if (gName) {
H5Gclose(gid);
UNPIN_JAVA_STRING(ENVONLY, group_name, gName);
}
if (fnos)
HDfree(fnos);
if (refs)
HDfree(refs);
if (oName)
h5str_array_free(oName, (size_t)n);
if (fnoP)
UNPIN_LONG_ARRAY(ENVONLY, fNo, fnoP, (ret_val < 0) ? JNI_ABORT : 0);
if (refP)
UNPIN_LONG_ARRAY(ENVONLY, oRef, refP, (ret_val < 0) ? JNI_ABORT : 0);
if (ltarr)
UNPIN_INT_ARRAY(ENVONLY, lType, ltarr, (ret_val < 0) ? JNI_ABORT : 0);
if (otarr)
UNPIN_INT_ARRAY(ENVONLY, oType, otarr, (ret_val < 0) ? JNI_ABORT : 0);
return ret_val;
} /* end Java_hdf_hdf5lib_H5_H5Gget_1obj_1info_1full */
/*
* Class: hdf_hdf5lib_H5
* Method: H5Gget_obj_info_max
* Signature: (J[Ljava/lang/String;[I[I[JJI)I
*/
/*
* NOTE: This is a dangerous call! The caller can supply any value they'd like
* for 'n' and if it exceeds the number of links reachable from the group, we
* will most likely end up overwriting memory heap-tracking info.
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Gget_1obj_1info_1max
(JNIEnv *env, jclass clss, jlong loc_id, jobjectArray objName,
jintArray oType, jintArray lType, jlongArray oRef, jlong maxnum, jint n)
{
unsigned long *refs = NULL;
jboolean isCopy;
jstring str;
jlong *refP = NULL;
char **oName = NULL;
jint *otarr = NULL;
jint *ltarr = NULL;
int i;
herr_t ret_val = FAIL;
UNUSED(clss);
if (NULL == oType)
H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Gget_obj_info_max: oType is NULL");
if (NULL == lType)
H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Gget_obj_info_max: lType is NULL");
if (NULL == oRef)
H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Gget_obj_info_max: oRef is NULL");
PIN_INT_ARRAY(ENVONLY, oType, otarr, &isCopy, "H5Gget_obj_info_max: oType not pinned");
PIN_INT_ARRAY(ENVONLY, lType, ltarr, &isCopy, "H5Gget_obj_info_max: lType not pinned");
PIN_LONG_ARRAY(ENVONLY, oRef, refP, &isCopy, "H5Gget_obj_info_max: oRef not pinned");
if (NULL == (oName = (char **) HDcalloc((size_t)n, sizeof(*oName))))
H5_JNI_FATAL_ERROR(ENVONLY, "H5Gget_obj_info_max: failed to allocate buffer for object name");
if (NULL == (refs = (unsigned long *) HDcalloc((size_t)n, sizeof(unsigned long))))
H5_JNI_FATAL_ERROR(ENVONLY, "H5Gget_obj_info_max: failed to allocate buffer for ref. info");
if ((ret_val = H5Gget_obj_info_max((hid_t)loc_id, oName, (int *)otarr, (int *)ltarr, refs, maxnum)) < 0)
H5_JNI_FATAL_ERROR(ENVONLY, "H5Gget_obj_info_max: retrieval of object info failed");
for (i = 0; i < n; i++) {
refP[i] = (jlong) refs[i];
if (oName[i]) {
if (NULL == (str = ENVPTR->NewStringUTF(ENVONLY, oName[i])))
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
ENVPTR->SetObjectArrayElement(ENVONLY, objName, i, (jobject)str);
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
ENVPTR->DeleteLocalRef(ENVONLY, str);
}
} /* end for */
done:
if (refs)
HDfree(refs);
if (oName)
h5str_array_free(oName, (size_t)n);
if (refP)
UNPIN_LONG_ARRAY(ENVONLY, oRef, refP, (ret_val < 0) ? JNI_ABORT : 0);
if (ltarr)
UNPIN_INT_ARRAY(ENVONLY, lType, ltarr, (ret_val < 0) ? JNI_ABORT : 0);
if (otarr)
UNPIN_INT_ARRAY(ENVONLY, oType, otarr, (ret_val < 0) ? JNI_ABORT : 0);
return ret_val;
} /* end Java_hdf_hdf5lib_H5_H5Gget_1obj_1info_1max */
int
H5Gget_obj_info_full
(hid_t loc_id, char **objname, int *otype, int *ltype, unsigned long *fno, unsigned long *objno, int indexType, int indexOrder)
{
info_all_t info;
info.objname = objname;
info.otype = otype;
info.ltype = ltype;
info.idxnum = 0;
info.fno = fno;
info.objno = objno;
info.count = 0;
if (H5Literate(loc_id, (H5_index_t)indexType, (H5_iter_order_t)indexOrder, NULL, obj_info_all, (void *)&info) < 0) {
/*
* Reset info stats; most importantly, reset the count.
*/
info.objname = objname;
info.otype = otype;
info.ltype = ltype;
info.idxnum = 0;
info.fno = fno;
info.objno = objno;
info.count = 0;
/* Iteration failed, try normal alphabetical order */
if (H5Literate(loc_id, H5_INDEX_NAME, H5_ITER_INC, NULL, obj_info_all, (void *)&info) < 0)
return -1;
}
return info.count;
} /* end H5Gget_obj_info_full */
int
H5Gget_obj_info_max
(hid_t loc_id, char **objname, int *otype, int *ltype, unsigned long *objno, long maxnum)
{
info_all_t info;
info.objname = objname;
info.otype = otype;
info.ltype = ltype;
info.idxnum = (unsigned long)maxnum;
info.objno = objno;
info.count = 0;
if (H5Lvisit(loc_id, H5_INDEX_NAME, H5_ITER_NATIVE, obj_info_max, (void *)&info) < 0)
return -1;
return info.count;
} /* end H5Gget_obj_info_max */
herr_t
obj_info_all
(hid_t loc_id, const char *name, const H5L_info_t *info, void *op_data)
{
info_all_t *datainfo = (info_all_t *)op_data;
H5O_info_t object_info;
htri_t object_exists;
size_t str_len;
datainfo->otype[datainfo->count] = -1;
datainfo->ltype[datainfo->count] = -1;
datainfo->objno[datainfo->count] = (unsigned long)-1;
str_len = HDstrlen(name);
if (NULL == (datainfo->objname[datainfo->count] = (char *) HDmalloc(str_len + 1)))
goto done;
HDstrncpy(datainfo->objname[datainfo->count], name, str_len);
(datainfo->objname[datainfo->count])[str_len] = '\0';
if ((object_exists = H5Oexists_by_name(loc_id, name, H5P_DEFAULT)) < 0)
goto done;
if (object_exists) {
if (H5Oget_info_by_name2(loc_id, name, &object_info, H5O_INFO_ALL, H5P_DEFAULT) < 0)
goto done;
datainfo->otype[datainfo->count] = object_info.type;
datainfo->ltype[datainfo->count] = info->type;
datainfo->fno[datainfo->count] = object_info.fileno;
datainfo->objno[datainfo->count] = (unsigned long)object_info.addr;
}
/*
if (info->type == H5L_TYPE_HARD)
datainfo->objno[datainfo->count] = (unsigned long)info->u.address;
else
datainfo->objno[datainfo->count] = info->u.val_size;
*/
done:
datainfo->count++;
return SUCCEED;
} /* end obj_info_all */
herr_t
obj_info_max
(hid_t loc_id, const char *name, const H5L_info_t *info, void *op_data)
{
info_all_t *datainfo = (info_all_t *)op_data;
H5O_info_t object_info;
size_t str_len;
datainfo->otype[datainfo->count] = -1;
datainfo->ltype[datainfo->count] = -1;
datainfo->objname[datainfo->count] = NULL;
datainfo->objno[datainfo->count] = (unsigned long)-1;
/* This will be freed by h5str_array_free(oName, n) */
str_len = HDstrlen(name);
if (NULL == (datainfo->objname[datainfo->count] = (char *) HDmalloc(str_len + 1)))
goto done;
HDstrncpy(datainfo->objname[datainfo->count], name, str_len);
(datainfo->objname[datainfo->count])[str_len] = '\0';
if (H5Oget_info2(loc_id, &object_info, H5O_INFO_ALL) < 0)
goto done;
datainfo->otype[datainfo->count] = object_info.type;
datainfo->ltype[datainfo->count] = info->type;
if (info->type == H5L_TYPE_HARD)
datainfo->objno[datainfo->count] = (unsigned long)info->u.address;
else
datainfo->objno[datainfo->count] = info->u.val_size;
done:
datainfo->count++;
if (datainfo->count >= (int)datainfo->idxnum)
return 1;
else
return SUCCEED;
} /* end obj_info_max */
/*
* Class: hdf_hdf5lib_H5
* Method: H5export_dataset
* Signature: (Ljava/lang/String;Ljava/lang/String;Ljava/lang/String;I)V
*/
JNIEXPORT void JNICALL
Java_hdf_hdf5lib_H5_H5export_1dataset
(JNIEnv *env, jclass clss, jstring file_export_name, jstring file_name, jstring object_path, jint binary_order)
{
const char *file_export = NULL;
const char *object_name = NULL;
const char *fileName = NULL;
jboolean isCopy;
herr_t ret_val = FAIL;
hid_t file_id = H5I_INVALID_HID;
hid_t dataset_id = H5I_INVALID_HID;
FILE *stream = NULL;
UNUSED(clss);
if (NULL == file_export_name)
H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5export_dataset: file_export_name is NULL");
if (NULL == file_name)
H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5export_dataset: file_name is NULL");
if (NULL == object_path)
H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5export_dataset: object_path is NULL");
PIN_JAVA_STRING(ENVONLY, file_name, fileName, NULL, "H5export_dataset: file name not pinned");
if ((file_id = H5Fopen(fileName, (unsigned)H5F_ACC_RDWR, (hid_t)H5P_DEFAULT)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
PIN_JAVA_STRING(ENVONLY, object_path, object_name, &isCopy, "H5export_dataset: object_path not pinned");
if ((dataset_id = H5Dopen2(file_id, object_name, H5P_DEFAULT)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
PIN_JAVA_STRING(ENVONLY, file_export_name, file_export, NULL, "H5export_dataset: file_export name not pinned");
if (NULL == (stream = HDfopen(file_export, "w+")))
H5_JNI_FATAL_ERROR(ENVONLY, "HDfopen failed");
if ((ret_val = h5str_dump_simple_dset(ENVONLY, stream, dataset_id, binary_order)) < 0)
H5_JNI_FATAL_ERROR(ENVONLY, "h5str_dump_simple_dset failed");
if (stream) {
HDfclose(stream);
stream = NULL;
}
done:
if (stream)
HDfclose(stream);
if (file_export)
UNPIN_JAVA_STRING(ENVONLY, file_export_name, file_export);
if (object_name)
UNPIN_JAVA_STRING(ENVONLY, object_path, object_name);
if (fileName)
UNPIN_JAVA_STRING(ENVONLY, file_name, fileName);
if (dataset_id >= 0)
H5Dclose(dataset_id);
if (file_id >= 0)
H5Fclose(file_id);
} /* end Java_hdf_hdf5lib_H5_H5export_1dataset */
#ifdef __cplusplus
}
#endif
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