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b32bd7bc3e5f8e74dc21f9f6df20a0c75495c34b
hdf5/java/src/jni/h5util.c
Allen Byrne ef2e93d239 Eliminate unreferenced local variable warning
2016-09-19 14:04:40 -05:00

2671 lines
95 KiB
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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 files COPYING and Copyright.html. COPYING can be found at the root *
* of the source code distribution tree; Copyright.html can be found at the *
* root level of an installed copy of the electronic HDF5 document set and *
* is linked from the top-level documents page. It can also be found at *
* http://hdfgroup.org/HDF5/doc/Copyright.html. 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://hdfdfgroup.org/HDF5/doc/
*
*/
#ifdef __cplusplus
extern "C" {
#endif /* __cplusplus */
#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 */
JavaVM *jvm;
jobject visit_callback;
jobject copy_callback;
jobject close_callback;
jobject create_callback;
jobject compare_callback;
jobject get_callback;
jobject set_callback;
jobject delete_callback;
/********************/
/* Local Prototypes */
/********************/
static int h5str_dump_region_blocks(h5str_t *str, hid_t region, hid_t region_obj);
static int h5str_dump_region_points(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(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 */
void
h5str_resize
(h5str_t *str, size_t new_len)
{
char *new_str;
if (!str || new_len <= 0 || str->max == new_len)
return;
new_str = (char *)HDmalloc(new_len);
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 */
/** 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_sprintf
(h5str_t *str, hid_t container, hid_t tid, void *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;
hvl_t *vlptr;
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);
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_FLOAT:
if (sizeof(float) == size) {
/* if (H5Tequal(tid, H5T_NATIVE_FLOAT)) */
HDmemcpy(&tmp_float, ptr, 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));
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));
this_str = (char*)HDmalloc(27);
sprintf(this_str, "%Lf", tmp_ldouble);
}
#endif
break;
case H5T_STRING:
{
char *tmp_str;
size = 0;
if (H5Tis_variable_str(tid)) {
tmp_str = *(char**) ptr;
if (tmp_str != NULL)
size = HDstrlen(tmp_str);
}
else {
tmp_str = cptr;
}
/* Check for NULL pointer for string */
if (tmp_str == NULL) {
this_str = (char *)HDmalloc(5);
HDstrncpy(this_str, "NULL", 4);
}
else {
if (size > 0) {
this_str = (char *)HDmalloc(size+1);
HDstrncpy(this_str, tmp_str, size);
}
}
}
break;
case H5T_INTEGER:
if (sizeof(char) == size) {
if(H5T_SGN_NONE == nsign) {
/* if (H5Tequal(tid, H5T_NATIVE_UCHAR)) */
HDmemcpy(&tmp_uchar, ptr, 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));
this_str = (char*)HDmalloc(7);
sprintf(this_str, "%hhd", tmp_char);
}
}
else if (sizeof(int) == size) {
if(H5T_SGN_NONE == nsign) {
/* if (H5Tequal(tid, H5T_NATIVE_UINT)) */
HDmemcpy(&tmp_uint, ptr, 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));
this_str = (char*)HDmalloc(14);
sprintf(this_str, "%d", tmp_int);
}
}
else if (sizeof(short) == size) {
if(H5T_SGN_NONE == nsign) {
/* if (H5Tequal(tid, H5T_NATIVE_USHORT)) */
HDmemcpy(&tmp_ushort, ptr, 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));
this_str = (char*)HDmalloc(9);
sprintf(this_str, "%d", tmp_short);
}
}
else if (sizeof(long) == size) {
if(H5T_SGN_NONE == nsign) {
/* if (H5Tequal(tid, H5T_NATIVE_ULONG)) */
HDmemcpy(&tmp_ulong, ptr, 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));
this_str = (char*)HDmalloc(23);
sprintf(this_str, "%ld", tmp_long);
}
}
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));
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));
this_str = (char*)HDmalloc(25);
sprintf(this_str, fmt_llong, tmp_llong);
}
}
break;
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, cptr + offset, expand_data);
if (i < n - 1)
h5str_append(str, ", ");
H5Tclose(mtid);
}
h5str_append(str, "} ");
}
break;
case H5T_ENUM:
{
char enum_name[1024];
if (H5Tenum_nameof(tid, ptr, enum_name, sizeof enum_name) >= 0) {
h5str_append(str, enum_name);
}
else {
size_t i;
nll = H5Tget_size(tid);
this_str = (char*)HDmalloc(4 * (nll + 1));
if (1 == nll) {
sprintf(this_str, "0x%02x", ucptr[0]);
}
else {
for (i = 0; i < (int)nll; i++)
sprintf(this_str, "%s%02x", i ? ":" : "", ucptr[i]);
}
}
}
break;
case H5T_REFERENCE:
if (h5str_is_zero(ptr, size)) {
h5str_append(str, "NULL");
}
else {
if (H5R_DSET_REG_REF_BUF_SIZE == size) {
/* if (H5Tequal(tid, H5T_STD_REF_DSETREG)) */
/*
* Dataset region reference --
* show the type and the referenced object
*/
char ref_name[1024];
hid_t region_obj;
hid_t region;
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);
if (region_obj >= 0) {
region = H5Rget_region(container, H5R_DATASET_REGION, ptr);
if (region >= 0) {
if(expand_data) {
region_type = H5Sget_select_type(region);
if(region_type==H5S_SEL_POINTS) {
h5str_dump_region_points_data(str, region, region_obj);
}
else {
h5str_dump_region_blocks_data(str, region, region_obj);
}
}
else {
if(H5Rget_name(region_obj, H5R_DATASET_REGION, ptr, (char*)ref_name, 1024) >= 0) {
h5str_append(str, ref_name);
}
region_type = H5Sget_select_type(region);
if(region_type==H5S_SEL_POINTS) {
h5str_append(str, " REGION_TYPE POINT");
h5str_dump_region_points(str, region, region_obj);
}
else {
h5str_append(str, " REGION_TYPE BLOCK");
h5str_dump_region_blocks(str, region, region_obj);
}
}
H5Sclose(region);
}
H5Dclose(region_obj);
}
}
else if (H5R_OBJ_REF_BUF_SIZE == size) {
/* if (H5Tequal(tid, H5T_STD_REF_OBJ)) */
/*
* Object references -- show the type and OID of the referenced
* object.
*/
H5O_info_t oi;
hid_t obj;
this_str = (char*)HDmalloc(64);
obj = H5Rdereference2(container, H5P_DEFAULT, H5R_OBJECT, ptr);
H5Oget_info(obj, &oi);
/* Print object data and close object */
sprintf(this_str, "%u-%lu", (unsigned) oi.type, oi.addr);
H5Oclose(obj);
}
}
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];
for (i = 0; i < total_elmts; i++) {
h5str_sprintf(str, container, mtid, cptr + i * size, expand_data);
if (i < total_elmts - 1)
h5str_append(str, ", ");
}
H5Tclose(mtid);
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, ", ");
}
H5Tclose(mtid);
}
break;
default:
{
/* All other types get printed as hexadecimal */
size_t i;
nll = H5Tget_size(tid);
this_str = (char*)HDmalloc(4 * (nll + 1));
if (1 == nll) {
sprintf(this_str, "0x%02x", ucptr[0]);
}
else {
for (i = 0; i < (int)nll; i++)
sprintf(this_str, "%s%02x", i ? ":" : "", ucptr[i]);
}
}
break;
} /* end switch */
if (this_str) {
h5str_append(str, this_str);
this_strlen = HDstrlen(str->s);
HDfree(this_str);
} /* end if */
return this_strlen;
} /* 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
(hid_t region_id, h5str_t *str, 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 blkndx;
hsize_t total_size[H5S_MAX_RANK];
hsize_t numelem;
hsize_t numindex;
size_t jndx;
unsigned indx;
size_t type_size;
int ret_value = SUCCEED;
hid_t mem_space = -1;
hid_t sid1 = -1;
void *region_buf = NULL;
/* Get the dataspace of the dataset */
if((sid1 = H5Dget_space(region_id)) >= 0) {
/* Allocate space for the dimension array */
if((dims1 = (hsize_t *)HDmalloc(sizeof(hsize_t) * (size_t)ndims)) != NULL) {
/* find the dimensions of each data space from the block coordinates */
numelem = 1;
for (jndx = 0; jndx < 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) {
if((type_size = H5Tget_size(type_id)) > 0) {
if((region_buf = HDmalloc(type_size * (size_t)numelem)) != NULL) {
/* Select (x , x , ..., x ) x (y , y , ..., y ) hyperslab for reading memory dataset */
/* 1 2 n 1 2 n */
if((start = (hsize_t *)HDmalloc(sizeof(hsize_t) * (size_t)ndims)) != NULL) {
if((count = (hsize_t *)HDmalloc(sizeof(hsize_t) * (size_t)ndims)) != NULL) {
for (blkndx = 0; blkndx < nblocks; blkndx++) {
for (indx = 0; indx < 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) {
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);
if (numindex + 1 < numelem)
h5str_append(str, ", ");
} /* end for (jndx = 0; jndx < numelem; jndx++, region_elmtno++, ctx.cur_elmt++) */
} /* end if(H5Sget_simple_extent_dims(mem_space, total_size, NULL) >= 0) */
} /* end if(H5Dread(region_id, type_id, mem_space, sid1, H5P_DEFAULT, region_buf) >= 0) */
} /* end if(H5Sselect_hyperslab(sid1, H5S_SELECT_SET, start, NULL, count, NULL) >= 0) */
} /* end for (blkndx = 0; blkndx < nblocks; blkndx++) */
HDfree(count);
} /* end if((count = (hsize_t *) HDmalloc(sizeof(hsize_t) * ndims)) != NULL) */
else
ret_value = -1;
HDfree(start);
} /* end if((start = (hsize_t *) HDmalloc(sizeof(hsize_t) * ndims)) != NULL) */
else
ret_value = -1;
HDfree(region_buf);
} /* end if((region_buf = HDmalloc(type_size * (size_t)numelem)) != NULL) */
else
ret_value = -1;
} /* end if((type_size = H5Tget_size(type_id)) > 0) */
else
ret_value = -1;
if(H5Sclose(mem_space) < 0)
ret_value = -1;
} /* end if((mem_space = H5Screate_simple(ndims, dims1, NULL)) >= 0) */
else
ret_value = -1;
HDfree(dims1);
} /* end if((dims1 = (hsize_t *) HDmalloc(sizeof(hsize_t) * ndims)) != NULL) */
else
ret_value = -1;
if(H5Sclose(sid1) < 0)
ret_value = -1;
} /* end if((sid1 = H5Dget_space(region_id)) >= 0) */
else
ret_value = -1;
return ret_value;
} /* end h5str_print_region_data_blocks */
int
h5str_dump_region_blocks_data
(h5str_t *str, hid_t region, hid_t region_id)
{
int ret_value = 0;
hssize_t nblocks;
hsize_t alloc_size;
hsize_t *ptdata;
hid_t dtype = -1;
hid_t type_id = -1;
int ndims = H5Sget_simple_extent_ndims(region);
/*
* This function fails if the region does not have blocks.
*/
H5E_BEGIN_TRY {
nblocks = H5Sget_select_hyper_nblocks(region);
} H5E_END_TRY;
/* Print block information */
if (nblocks > 0) {
alloc_size = (hsize_t)nblocks * (hsize_t)ndims * 2 * (hsize_t)sizeof(ptdata[0]);
if (alloc_size == (hsize_t)((size_t) alloc_size)) {
ptdata = (hsize_t *)HDmalloc((size_t) alloc_size);
H5Sget_select_hyper_blocklist(region, (hsize_t) 0,
(hsize_t) nblocks, ptdata);
if((dtype = H5Dget_type(region_id)) >= 0) {
if((type_id = H5Tget_native_type(dtype, H5T_DIR_DEFAULT)) >= 0) {
h5str_print_region_data_blocks(region_id, str, ndims, type_id, nblocks, ptdata);
if(H5Tclose(type_id) < 0)
ret_value = -1;
} /* end if((type_id = H5Tget_native_type(dtype, H5T_DIR_DEFAULT)) >= 0) */
else
ret_value = -1;
if(H5Tclose(dtype) < 0)
ret_value = -1;
} /* end if((dtype = H5Dget_type(region_id)) >= 0) */
else
ret_value = -1;
HDfree(ptdata);
} /* if (alloc_size == (hsize_t)((size_t)alloc_size)) */
} /* if (nblocks > 0) */
return ret_value;
} /* end h5str_dump_region_blocks_data */
static int
h5str_dump_region_blocks
(h5str_t *str, hid_t region, hid_t region_id)
{
int ret_value = 0;
hssize_t nblocks;
hsize_t alloc_size;
hsize_t *ptdata;
hid_t dtype = -1;
hid_t type_id = -1;
char tmp_str[256];
int ndims = H5Sget_simple_extent_ndims(region);
/*
* This function fails if the region does not have blocks.
*/
H5E_BEGIN_TRY {
nblocks = H5Sget_select_hyper_nblocks(region);
} H5E_END_TRY;
/* Print block information */
if (nblocks > 0) {
int i;
alloc_size = (hsize_t)nblocks * (hsize_t)ndims * 2 * (hsize_t)sizeof(ptdata[0]);
if (alloc_size == (hsize_t)((size_t) alloc_size)) {
ptdata = (hsize_t *)HDmalloc((size_t) alloc_size);
H5Sget_select_hyper_blocklist(region, (hsize_t) 0,
(hsize_t) nblocks, ptdata);
h5str_append(str, " {");
for (i = 0; i < nblocks; i++) {
int j;
h5str_append(str, " ");
/* Start coordinates and opposite corner */
for (j = 0; j < ndims; j++) {
tmp_str[0] = '\0';
sprintf(tmp_str, "%s%lu", j ? "," : "(",
(unsigned long) ptdata[i * 2 * ndims + j]);
h5str_append(str, tmp_str);
}
for (j = 0; j < ndims; j++) {
tmp_str[0] = '\0';
sprintf(tmp_str, "%s%lu", j ? "," : ")-(",
(unsigned long) ptdata[i * 2 * ndims + j + ndims]);
h5str_append(str, tmp_str);
}
h5str_append(str, ") ");
tmp_str[0] = '\0';
}
h5str_append(str, " }");
HDfree(ptdata);
} /* if (alloc_size == (hsize_t)((size_t)alloc_size)) */
} /* if (nblocks > 0) */
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
(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;
int ret_value = SUCCEED;
hid_t mem_space = -1;
void *region_buf = NULL;
/* Allocate space for the dimension array */
if((dims1 = (hsize_t *)HDmalloc(sizeof(hsize_t) * (size_t)ndims)) != NULL) {
dims1[0] = (hsize_t)npoints;
/* Create dataspace for reading buffer */
if((mem_space = H5Screate_simple(1, dims1, NULL)) >= 0) {
if((type_size = H5Tget_size(type_id)) > 0) {
if((region_buf = HDmalloc(type_size * (size_t)npoints)) != NULL) {
if(H5Dread(region_id, type_id, mem_space, region_space, H5P_DEFAULT, region_buf) >= 0) {
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);
if (jndx + 1 < npoints)
h5str_append(str, ", ");
} /* end if(H5Sget_simple_extent_dims(mem_space, total_size, NULL) >= 0) */
} /* end for (jndx = 0; jndx < npoints; jndx++, elmtno++) */
} /* end if(H5Dread(region_id, type_id, mem_space, region_space, H5P_DEFAULT, region_buf) >= 0) */
else
ret_value = -1;
HDfree(region_buf);
} /* end if((region_buf = HDmalloc(type_size * (size_t)npoints)) != NULL) */
else
ret_value = -1;
} /* end if((type_size = H5Tget_size(type_id)) > 0) */
else
ret_value = -1;
if(H5Sclose(mem_space) < 0)
ret_value = -1;
} /* end if((mem_space = H5Screate_simple(1, dims1, NULL)) >= 0) */
else
ret_value = -1;
HDfree(dims1);
} /* end if((dims1 = (hsize_t *) HDmalloc(sizeof(hsize_t) * ndims)) != NULL) */
else
ret_value = -1;
return ret_value;
} /* end h5str_print_region_data_points */
int
h5str_dump_region_points_data
(h5str_t *str, hid_t region, hid_t region_id)
{
int ret_value = 0;
hssize_t npoints;
hsize_t alloc_size;
hsize_t *ptdata;
hid_t dtype = -1;
hid_t type_id = -1;
int ndims = H5Sget_simple_extent_ndims(region);
/*
* This function fails if the region does not have points.
*/
H5E_BEGIN_TRY {
npoints = H5Sget_select_elem_npoints(region);
} H5E_END_TRY;
/* 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)) {
ptdata = (hsize_t *)HDmalloc((size_t) alloc_size);
H5Sget_select_elem_pointlist(region, (hsize_t) 0,
(hsize_t) npoints, ptdata);
if((dtype = H5Dget_type(region_id)) >= 0) {
if((type_id = H5Tget_native_type(dtype, H5T_DIR_DEFAULT)) >= 0) {
h5str_print_region_data_points(region, region_id,
str, ndims, type_id, npoints, ptdata);
if(H5Tclose(type_id) < 0)
ret_value = -1;
} /* end if((type_id = H5Tget_native_type(dtype, H5T_DIR_DEFAULT)) >= 0) */
else
ret_value = -1;
if(H5Tclose(dtype) < 0)
ret_value = -1;
} /* end if((dtype = H5Dget_type(region_id)) >= 0) */
else
ret_value = -1;
HDfree(ptdata);
}
}
return ret_value;
} /* end h5str_dump_region_points_data */
static int
h5str_dump_region_points
(h5str_t *str, hid_t region, hid_t region_id)
{
int ret_value = 0;
hssize_t npoints;
hsize_t alloc_size;
hsize_t *ptdata;
char tmp_str[256];
hid_t dtype = -1;
hid_t type_id = -1;
int ndims = H5Sget_simple_extent_ndims(region);
/*
* This function fails if the region does not have points.
*/
H5E_BEGIN_TRY {
npoints = H5Sget_select_elem_npoints(region);
} H5E_END_TRY;
/* 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)) {
ptdata = (hsize_t *)HDmalloc((size_t) alloc_size);
H5Sget_select_elem_pointlist(region, (hsize_t) 0,
(hsize_t) npoints, ptdata);
h5str_append(str, " {");
for (i = 0; i < npoints; i++) {
int j;
h5str_append(str, " ");
for (j = 0; j < ndims; j++) {
tmp_str[0] = '\0';
sprintf(tmp_str, "%s%lu", j ? "," : "(",
(unsigned long) (ptdata[i * ndims + j]));
h5str_append(str, tmp_str);
} /* end for (j = 0; j < ndims; j++) */
h5str_append(str, ") ");
} /* end for (i = 0; i < npoints; i++) */
h5str_append(str, " }");
HDfree(ptdata);
} /* end if (alloc_size == (hsize_t)((size_t) alloc_size)) */
} /* end if (npoints > 0) */
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_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) {
n = ret;
goto done;
} /* end if */
for(i = 0; i < 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)
{
hid_t p_type;
H5T_class_t type_class;
type_class = H5Tget_class(type);
if(type_class==H5T_BITFIELD)
p_type=H5Tcopy(type);
else
p_type = H5Tget_native_type(type,H5T_DIR_DEFAULT);
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)
{
hid_t p_type=-1;
H5T_class_t type_class;
size_t size;
H5T_sign_t sign;
type_class = H5Tget_class(tid);
size = H5Tget_size(tid);
sign = H5Tget_sign(tid);
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_TIME:
case H5T_BITFIELD:
case H5T_OPAQUE:
case H5T_STRING:
case H5T_COMPOUND:
case H5T_REFERENCE:
case H5T_ENUM:
case H5T_VLEN:
case H5T_ARRAY:
break;
default:
break;
}
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)
{
hid_t p_type=-1;
H5T_class_t type_class;
size_t size;
H5T_sign_t sign;
type_class = H5Tget_class(tid);
size = H5Tget_size(tid);
sign = H5Tget_sign(tid);
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_TIME:
case H5T_BITFIELD:
case H5T_OPAQUE:
case H5T_STRING:
case H5T_COMPOUND:
case H5T_REFERENCE:
case H5T_ENUM:
case H5T_VLEN:
case H5T_ARRAY:
break;
default:
break;
}
return(p_type);
} /* end h5str_get_big_endian_type */
/*-------------------------------------------------------------------------
* Function: h5str_detect_vlen
*
* Purpose: Recursive check for any variable length data in given type.
*
* Return:
* 1 : type conatains any variable length data
* 0 : type doesn't contain any variable length data
* Negative value: error occur
*-------------------------------------------------------------------------
*/
static htri_t
h5str_detect_vlen
(hid_t tid)
{
htri_t ret;
/* recursive detect any vlen data values in type (compound, array ...) */
ret = H5Tdetect_class(tid, H5T_VLEN);
if((ret == 1) || (ret < 0))
goto done;
/* recursive 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: 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)
{
int ret_value = 0;
unsigned char *mem = (unsigned char*)_mem;
size_t size; /* datum size */
hsize_t block_index;
H5T_class_t type_class;
if((size = H5Tget_size(tid)) > 0) {
if((type_class = H5Tget_class(tid)) >= 0) {
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 */
size_t item_size = size; /* size of items in bytes */
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 = -1;
break;
}
block_index -= (hsize_t)bytes_wrote;
mem = mem + bytes_wrote;
}
break;
case H5T_STRING:
{
unsigned int i;
H5T_str_t pad;
char *s;
unsigned char tempuchar;
pad = H5Tget_strpad(tid);
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 = strlen(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 = -1;
break;
}
} /* i */
if(ret_value < 0)
break;
} /* for (block_index = 0; block_index < block_nelmts; block_index++) */
}
break;
case H5T_COMPOUND:
{
unsigned j;
hid_t memb;
unsigned nmembs;
size_t offset;
nmembs = (unsigned)H5Tget_nmembers(tid);
for (block_index = 0; block_index < block_nelmts; block_index++) {
mem = ((unsigned char*)_mem) + block_index * size;
for (j = 0; j < 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 = -1;
break;
}
H5Tclose(memb);
}
if(ret_value < 0)
break;
}
}
break;
case H5T_ARRAY:
{
int k, ndims;
hsize_t dims[H5S_MAX_RANK], temp_nelmts, nelmts;
hid_t memb;
/* get the array's base datatype for each element */
memb = H5Tget_super(tid);
ndims = H5Tget_array_ndims(tid);
H5Tget_array_dims2(tid, dims);
/* 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 = -1;
break;
}
}
H5Tclose(memb);
}
break;
case H5T_VLEN:
{
hsize_t nelmts;
hid_t memb;
/* get the VL sequences's base datatype for each element */
memb = H5Tget_super(tid);
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 = -1;
break;
}
}
H5Tclose(memb);
}
break;
case H5T_REFERENCE:
{
if (H5Tequal(tid, H5T_STD_REF_DSETREG)) {
/* region data */
hid_t region_id, region_space;
H5S_sel_type region_type;
for (block_index = 0; block_index < block_nelmts; block_index++) {
mem = ((unsigned char*)_mem) + block_index * size;
region_id = H5Rdereference2(container, H5P_DEFAULT, H5R_DATASET_REGION, mem);
if (region_id >= 0) {
region_space = H5Rget_region(container, H5R_DATASET_REGION, mem);
if (region_space >= 0) {
region_type = H5Sget_select_type(region_space);
if(region_type == H5S_SEL_POINTS)
ret_value = render_bin_output_region_points(stream, region_space, region_id, container);
else
ret_value = render_bin_output_region_blocks(stream, region_space, region_id, container);
H5Sclose(region_space);
} /* end if (region_space >= 0) */
H5Dclose(region_id);
} /* end if (region_id >= 0) */
if(ret_value < 0)
break;
}
}
else if (H5Tequal(tid, H5T_STD_REF_OBJ)) {
;
}
}
break;
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 = -1;
break;
}
}
break;
}
} /* end if((type_class = H5Tget_class(tid)) >= 0) */
else
ret_value = -1;
} /* end if((size = H5Tget_size(tid)) > 0) */
else
ret_value = -1;
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];
int jndx;
size_t type_size;
hid_t mem_space = -1;
void *region_buf = NULL;
int blkndx;
hid_t sid1 = -1;
int ret_value = SUCCEED;
/* Get the dataspace of the dataset */
if((sid1 = H5Dget_space(region_id)) >= 0) {
/* Allocate space for the dimension array */
if((dims1 = (hsize_t *)HDmalloc(sizeof(hsize_t) * (size_t)ndims)) != NULL) {
/* find the dimensions of each data space from the block coordinates */
numelem = 1;
for (jndx = 0; 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) {
if((type_size = H5Tget_size(type_id)) > 0) {
if((region_buf = HDmalloc(type_size * (size_t)numelem)) != NULL) {
/* Select (x , x , ..., x ) x (y , y , ..., y ) hyperslab for reading memory dataset */
/* 1 2 n 1 2 n */
if((start = (hsize_t *)HDmalloc(sizeof(hsize_t) * (size_t)ndims)) != NULL) {
if((count = (hsize_t *)HDmalloc(sizeof(hsize_t) * (size_t)ndims)) != NULL) {
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) {
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) {
ret_value = h5str_render_bin_output(stream, container, type_id, (char*)region_buf, numelem);
} /* end if(H5Sget_simple_extent_dims(mem_space, total_size, NULL) >= 0) */
else {
ret_value = -1;
break;
}
} /* end if(H5Dread(region_id, type_id, mem_space, sid1, H5P_DEFAULT, region_buf) >= 0) */
else {
ret_value = -1;
break;
}
} /* end if(H5Sselect_hyperslab(sid1, H5S_SELECT_SET, start, NULL, count, NULL) >= 0) */
else {
ret_value = -1;
break;
}
/* Render the region data element end */
} /* end for (blkndx = 0; blkndx < nblocks; blkndx++) */
HDfree(count);
} /* end if((count = (hsize_t *) HDmalloc(sizeof(hsize_t) * ndims)) != NULL) */
else
ret_value = -1;
HDfree(start);
} /* end if((start = (hsize_t *) HDmalloc(sizeof(hsize_t) * ndims)) != NULL) */
else
ret_value = -1;
HDfree(region_buf);
} /* end if((region_buf = HDmalloc(type_size * (size_t)numelem)) != NULL) */
else
ret_value = -1;
} /* end if((type_size = H5Tget_size(type_id)) > 0) */
else
ret_value = -1;
if(H5Sclose(mem_space) < 0)
ret_value = -1;
} /* end if((mem_space = H5Screate_simple(ndims, dims1, NULL)) >= 0) */
else
ret_value = -1;
HDfree(dims1);
} /* end if((dims1 = (hsize_t *) HDmalloc(sizeof(hsize_t) * ndims)) != NULL) */
else
ret_value = -1;
if(H5Sclose(sid1) < 0)
ret_value = -1;
} /* end if((sid1 = H5Dget_space(region_id)) >= 0) */
else
ret_value = -1;
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)
{
int ret_value = SUCCEED;
hssize_t nblocks;
hsize_t alloc_size;
hsize_t *ptdata = NULL;
int ndims;
hid_t dtype;
hid_t type_id;
if((nblocks = H5Sget_select_hyper_nblocks(region_space)) > 0) {
/* Print block information */
if((ndims = H5Sget_simple_extent_ndims(region_space)) >= 0) {
alloc_size = (hsize_t)nblocks * (hsize_t)ndims * 2 * (hsize_t)sizeof(ptdata[0]);
if((ptdata = (hsize_t*)HDmalloc((size_t)alloc_size)) != NULL) {
if(H5Sget_select_hyper_blocklist(region_space, (hsize_t)0, (hsize_t)nblocks, ptdata) >= 0) {
if((dtype = H5Dget_type(region_id)) >= 0) {
if((type_id = H5Tget_native_type(dtype, H5T_DIR_DEFAULT)) >= 0) {
ret_value = render_bin_output_region_data_blocks(stream, region_id, container, ndims,
type_id, nblocks, ptdata);
if(H5Tclose(type_id) < 0)
ret_value = -1;
} /* end if((type_id = H5Tget_native_type(dtype, H5T_DIR_DEFAULT)) >= 0) */
else
ret_value = -1;
if(H5Tclose(dtype) < 0)
ret_value = -1;
} /* end if((dtype = H5Dget_type(region_id)) >= 0) */
else
ret_value = -1;
} /* end if(H5Sget_select_hyper_blocklist(region_space, (hsize_t) 0, (hsize_t) nblocks, ptdata) >= 0) */
else
ret_value = -1;
HDfree(ptdata);
} /* end if((ptdata = (hsize_t*) HDmalloc((size_t) alloc_size)) != NULL) */
else
ret_value = -1;
} /* end if((ndims = H5Sget_simple_extent_ndims(region_space)) >= 0) */
else
ret_value = -1;
} /* end if((nblocks = H5Sget_select_hyper_nblocks(region_space)) > 0) */
else
ret_value = -1;
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 = -1;
void *region_buf = NULL;
int ret_value = SUCCEED;
if((type_size = H5Tget_size(type_id)) > 0) {
if((region_buf = HDmalloc(type_size * (size_t)npoints)) != NULL) {
/* Allocate space for the dimension array */
if((dims1 = (hsize_t *)HDmalloc(sizeof(hsize_t) * (size_t)ndims)) != NULL) {
dims1[0] = (hsize_t)npoints;
if((mem_space = H5Screate_simple(1, dims1, NULL)) >= 0) {
if(H5Dread(region_id, type_id, mem_space, region_space, H5P_DEFAULT, region_buf) >= 0) {
if(H5Sget_simple_extent_dims(region_space, dims1, NULL) >= 0) {
ret_value = h5str_render_bin_output(stream, container, type_id, (char*)region_buf, (hsize_t)npoints);
} /* end if(H5Sget_simple_extent_dims(region_space, dims1, NULL) >= 0) */
else
ret_value = -1;
} /* end if(H5Dread(region_id, type_id, mem_space, region_space, H5P_DEFAULT, region_buf) >= 0) */
else
ret_value = -1;
} /* end if((mem_space = H5Screate_simple(1, dims1, NULL)) >= 0) */
else
ret_value = -1;
HDfree(dims1);
} /* end if((dims1 = (hsize_t *) malloc(sizeof(hsize_t) * ndims)) != NULL) */
else
ret_value = -1;
HDfree(region_buf);
} /* end if((region_buf = malloc(type_size * (size_t)npoints)) != NULL) */
else
ret_value = -1;
if(H5Sclose(mem_space) < 0)
ret_value = -1;
} /* end if((type_size = H5Tget_size(type_id)) > 0) */
else
ret_value = -1;
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)
{
int ret_value = SUCCEED;
hssize_t npoints;
hsize_t alloc_size;
hsize_t *ptdata;
int ndims;
hid_t dtype;
hid_t type_id;
if((npoints = H5Sget_select_elem_npoints(region_space)) > 0) {
/* Allocate space for the dimension array */
if((ndims = H5Sget_simple_extent_ndims(region_space)) >= 0) {
alloc_size = (hsize_t)npoints * (hsize_t)ndims * (hsize_t)sizeof(ptdata[0]);
if(NULL != (ptdata = (hsize_t *)HDmalloc((size_t)alloc_size))) {
if(H5Sget_select_elem_pointlist(region_space, (hsize_t)0, (hsize_t)npoints, ptdata) >= 0) {
if((dtype = H5Dget_type(region_id)) >= 0) {
if((type_id = H5Tget_native_type(dtype, H5T_DIR_DEFAULT)) >= 0) {
ret_value = render_bin_output_region_data_points(stream, region_space, region_id,
container, ndims, type_id, npoints, ptdata);
if(H5Tclose(type_id) < 0)
ret_value = -1;
} /* end if((type_id = H5Tget_native_type(dtype, H5T_DIR_DEFAULT)) >= 0) */
else
ret_value = -1;
if(H5Tclose(dtype) < 0)
ret_value = -1;
} /* end if((dtype = H5Dget_type(region_id)) >= 0) */
else
ret_value = -1;
} /* end if(H5Sget_select_elem_pointlist(region_space, (hsize_t) 0, (hsize_t) npoints, ptdata) >= 0) */
else
ret_value = -1;
HDfree(ptdata);
} /* end if(NULL != (ptdata = (hsize_t *)HDmalloc((size_t) alloc_size))) */
else
ret_value = -1;
} /* end if((ndims = H5Sget_simple_extent_ndims(region_space)) >= 0) */
else
ret_value = -1;
} /* end if((npoints = H5Sget_select_elem_npoints(region_space)) > 0) */
else
ret_value = -1;
return ret_value;
} /* end render_bin_output_region_points */
int
h5str_dump_simple_dset
(FILE *stream, hid_t dset, int binary_order)
{
int ret_value = SUCCEED;
hid_t f_space = -1; /* file data space */
hsize_t elmtno; /* counter */
size_t i; /* counter */
int ndims;
int carry; /* counter carry value */
hsize_t zero[8]; /* vector of zeros */
hsize_t total_size[H5S_MAX_RANK]; /* total size of dataset*/
/* Print info */
size_t p_type_nbytes; /* size of memory type */
hsize_t p_nelmts; /* total selected elmts */
/* Stripmine info */
hsize_t sm_size[H5S_MAX_RANK]; /* stripmine size */
hsize_t sm_nbytes; /* bytes per stripmine */
hsize_t sm_nelmts; /* elements per stripmine*/
unsigned char *sm_buf = NULL; /* buffer for raw data */
hid_t sm_space = -1; /* 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 = -1;
hid_t f_type = -1;
if(dset < 0) return -1;
f_type = H5Dget_type(dset);
if (binary_order == 1)
p_type = h5str_get_native_type(f_type);
else if (binary_order == 2)
p_type = h5str_get_little_endian_type(f_type);
else if (binary_order == 3)
p_type = h5str_get_big_endian_type(f_type);
else
p_type = H5Tcopy(f_type);
H5Tclose(f_type);
if (p_type >= 0) {
if((f_space = H5Dget_space(dset)) >= 0) {
ndims = H5Sget_simple_extent_ndims(f_space);
if ((size_t)ndims <= (sizeof(sm_size)/sizeof(sm_size[0]))) {
H5Sget_simple_extent_dims(f_space, total_size, NULL);
/* calculate the number of elements we're going to print */
p_nelmts = 1;
if (ndims > 0) {
for (i = 0; i < 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.
*/
sm_nbytes = p_type_nbytes = H5Tget_size(p_type);
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) {
sm_buf = (unsigned char *)HDmalloc((size_t)sm_nbytes);
sm_nelmts = sm_nbytes / p_type_nbytes;
sm_space = H5Screate_simple(1, &sm_nelmts, NULL);
/* 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 < 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];
}
H5Sselect_hyperslab(f_space, H5S_SELECT_SET, hs_offset, NULL, hs_size, NULL);
H5Sselect_hyperslab(sm_space, H5S_SELECT_SET, zero, NULL, &hs_nelmts, NULL);
}
else {
H5Sselect_all(f_space);
H5Sselect_all(sm_space);
hs_nelmts = 1;
}
/* Read the data */
if (H5Dread(dset, p_type, sm_space, f_space, H5P_DEFAULT, sm_buf) >= 0) {
if (binary_order == 99)
ret_value = h5tools_dump_simple_data(stream, dset, p_type, sm_buf, hs_nelmts);
else
ret_value = h5str_render_bin_output(stream, dset, p_type, sm_buf, hs_nelmts);
/* Reclaim any VL memory, if necessary */
if (vl_data)
H5Dvlen_reclaim(p_type, sm_space, H5P_DEFAULT, sm_buf);
}
else {
ret_value = -1;
break;
}
if(ret_value < 0) break;
/* 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;
}
}
if(sm_buf)
HDfree(sm_buf);
}
if(sm_space >= 0 && H5Sclose(sm_space) < 0)
ret_value = -1;
}
}
if(f_space >= 0 && H5Sclose(f_space) < 0)
ret_value = -1;
} /* end if((f_space = H5Dget_space(dset)) >= 0) */
else
ret_value = -1;
if (p_type >= 0)
H5Tclose(p_type);
}
return ret_value;
} /* end h5str_dump_simple_dset */
static int
h5tools_dump_simple_data
(FILE *stream, hid_t container, hid_t type, void *_mem, hsize_t nelmts)
{
int ret_value = 0;
int line_count;
unsigned char *mem = (unsigned char*)_mem;
size_t size; /* datum size */
hsize_t i; /*element counter */
h5str_t buffer; /*string into which to render */
if((size = H5Tget_size(type)) > 0) {
for (i = 0, line_count = 0; i < nelmts; i++, line_count++) {
size_t bytes_in = 0; /* # of bytes to write */
size_t bytes_wrote = 0; /* # of bytes written */
void* memref = mem + i * size;
/* Render the data element*/
h5str_new(&buffer, 32 * size);
bytes_in = h5str_sprintf(&buffer, container, type, memref, 1);
if(i > 0) {
HDfprintf(stream, ", ");
if (line_count >= H5TOOLS_TEXT_BLOCK) {
line_count = 0;
HDfprintf(stream, "\n");
}
}
HDfprintf(stream, "%s", buffer.s);
h5str_free(&buffer);
} /* end for (i = 0; i < nelmts... */
HDfprintf(stream, "\n");
} /* end if((size = H5Tget_size(tid)) > 0) */
else
ret_value = -1;
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: 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
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5AreadComplex
(JNIEnv *env, jclass clss, jlong attr_id, jlong mem_type_id, jobjectArray buf)
{
herr_t status = -1;
int i;
int n;
char *rdata;
size_t max_len = 0;
size_t size;
h5str_t h5str;
hid_t p_type = -1;
jstring jstr;
p_type = H5Tget_native_type(mem_type_id, H5T_DIR_DEFAULT);
size = (((H5Tget_size(mem_type_id))>(H5Tget_size(p_type))) ? (H5Tget_size(mem_type_id)) : (H5Tget_size(p_type)));
H5Tclose(p_type);
n = ENVPTR->GetArrayLength(ENVPAR buf);
rdata = (char *)malloc((size_t)n * size);
if (rdata == NULL) {
h5JNIFatalError(env, "H5AreadComplex: failed to allocate buff for read");
} /* end if */
else {
status = H5Aread(attr_id, mem_type_id, rdata);
if (status < 0) {
h5JNIFatalError(env, "H5AreadComplex: failed to read data");
} /* end if */
else {
HDmemset(&h5str, 0, sizeof(h5str_t));
h5str_new(&h5str, 4 * size);
if (h5str.s == NULL) {
h5JNIFatalError(env, "H5AreadComplex: failed to allocate string buf");
} /* end if */
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);
jstr = ENVPTR->NewStringUTF(ENVPAR h5str.s);
ENVPTR->SetObjectArrayElement(ENVPAR buf, i, jstr);
} /* end for */
} /* end else */
h5str_free(&h5str);
} /* end else */
HDfree(rdata);
} /* end else */
return status;
}
/*
* Copies the content of one dataset to another dataset
* 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)
{
jbyte *buf;
herr_t retVal = -1;
hid_t src_did = (hid_t)src_id;
hid_t dst_did = (hid_t)dst_id;
hid_t tid = -1;
hid_t sid = -1;
hsize_t total_size = 0;
sid = H5Aget_space(src_did);
if (sid < 0) {
h5libraryError(env);
} /* end if */
else {
tid = H5Aget_type(src_did);
if (tid < 0) {
H5Sclose(sid);
h5libraryError(env);
} /* end if */
else {
total_size = (hsize_t)H5Sget_simple_extent_npoints(sid) * (hsize_t)H5Tget_size(tid);
H5Sclose(sid);
buf = (jbyte *)HDmalloc( (size_t)total_size * sizeof(jbyte));
if (buf == NULL) {
H5Tclose(tid);
h5outOfMemory( env, "H5Acopy: malloc failed");
} /* end if */
else {
retVal = H5Aread(src_did, tid, buf);
H5Tclose(tid);
if (retVal < 0) {
HDfree(buf);
h5libraryError(env);
} /* end if */
else {
tid = H5Aget_type(dst_did);
if (tid < 0) {
HDfree(buf);
h5libraryError(env);
} /* end if */
else {
retVal = H5Awrite(dst_did, tid, buf);
H5Tclose(tid);
HDfree(buf);
if (retVal < 0)
h5libraryError(env);
} /* end else */
} /* end else */
} /* end else */
} /* end else */
} /* end else */
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)
{
jbyte *buf;
herr_t retVal = -1;
hid_t src_did = (hid_t)src_id;
hid_t dst_did = (hid_t)dst_id;
hid_t tid = -1;
hid_t sid = -1;
hsize_t total_size = 0, total_allocated_size;
total_allocated_size = H5Dget_storage_size(src_did);
if (total_allocated_size <=0)
return 0; // nothing to write;
sid = H5Dget_space(src_did);
if (sid < 0) {
h5libraryError(env);
return -1;
} /* end if */
tid = H5Dget_type(src_did);
if (tid < 0) {
H5Sclose(sid);
h5libraryError(env);
return -1;
} /* end if */
total_size = (hsize_t)H5Sget_simple_extent_npoints(sid) * (hsize_t)H5Tget_size(tid);
H5Sclose(sid);
buf = (jbyte*)HDmalloc((size_t)total_size * sizeof(jbyte));
if (buf == NULL) {
H5Tclose(tid);
h5outOfMemory(env, "H5Dcopy: malloc failed");
return -1;
} /* end if */
retVal = H5Dread(src_did, tid, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf);
H5Tclose(tid);
if (retVal < 0) {
HDfree(buf);
h5libraryError(env);
return (jint)retVal;
} /* end if */
tid = H5Dget_type(dst_did);
if (tid < 0) {
HDfree(buf);
h5libraryError(env);
return -1;
} /* end if */
retVal = H5Dwrite(dst_did, tid, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf);
H5Tclose(tid);
HDfree(buf);
if (retVal < 0) {
h5libraryError(env);
} /* end if */
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 object 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
*/
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)
{
herr_t ret_val = -1;
const char *gName = NULL;
char **oName = NULL;
jboolean isCopy;
jstring str;
jint *otarr;
jint *ltarr;
jlong *refP;
jlong *fnoP;
unsigned long *refs=NULL;
unsigned long *fnos=NULL;
hid_t gid = (hid_t)loc_id;
int i;
int indexType = indx_type;
int indexOrder = indx_order;
if (oType == NULL) {
h5nullArgument(env, "H5Gget_obj_info_full: oType is NULL");
}
else if (lType == NULL) {
h5nullArgument(env, "H5Gget_obj_info_full: lType is NULL");
}
else if (oRef == NULL) {
h5nullArgument(env, "H5Gget_obj_info_full: oRef is NULL");
}
else if (fNo == NULL) {
h5nullArgument(env, "H5Gget_obj_info_full: fNo is NULL");
}
else {
otarr = ENVPTR->GetIntArrayElements(ENVPAR oType, &isCopy);
if (otarr == NULL) {
h5JNIFatalError(env, "H5Gget_obj_info_full: otype not pinned");
return -1;
} /* end if */
ltarr = ENVPTR->GetIntArrayElements(ENVPAR lType, &isCopy);
if (ltarr == NULL) {
ENVPTR->ReleaseIntArrayElements(ENVPAR oType, otarr, JNI_ABORT);
h5JNIFatalError(env, "H5Gget_obj_info_full: ltype not pinned");
return -1;
} /* end if */
refP = ENVPTR->GetLongArrayElements(ENVPAR oRef, &isCopy);
if (refP == NULL) {
ENVPTR->ReleaseIntArrayElements(ENVPAR lType, ltarr, JNI_ABORT);
ENVPTR->ReleaseIntArrayElements(ENVPAR oType, otarr, JNI_ABORT);
h5JNIFatalError(env, "H5Gget_obj_info_full: oRef not pinned");
return -1;
} /* end if */
fnoP = ENVPTR->GetLongArrayElements(ENVPAR fNo, &isCopy);
if (fnoP == NULL) {
ENVPTR->ReleaseIntArrayElements(ENVPAR lType, ltarr, JNI_ABORT);
ENVPTR->ReleaseIntArrayElements(ENVPAR oType, otarr, JNI_ABORT);
ENVPTR->ReleaseLongArrayElements(ENVPAR oRef, refP, JNI_ABORT);
h5JNIFatalError(env, "H5Gget_obj_info_full: fNo not pinned");
return -1;
} /* end if */
oName = (char **)HDcalloc((size_t)n, sizeof(*oName));
if (!oName) {
ENVPTR->ReleaseIntArrayElements(ENVPAR lType, ltarr, JNI_ABORT);
ENVPTR->ReleaseIntArrayElements(ENVPAR oType, otarr, JNI_ABORT);
ENVPTR->ReleaseLongArrayElements(ENVPAR oRef, refP, JNI_ABORT);
ENVPTR->ReleaseLongArrayElements(ENVPAR fNo, fnoP, JNI_ABORT);
h5JNIFatalError(env, "H5Gget_obj_info_full: oName not allocated");
return -1;
} /* end if */
refs = (unsigned long *)HDcalloc((size_t)n, sizeof(unsigned long));
fnos = (unsigned long *)HDcalloc((size_t)n, sizeof(unsigned long));
if (!refs || !fnos) {
ENVPTR->ReleaseIntArrayElements(ENVPAR lType, ltarr, JNI_ABORT);
ENVPTR->ReleaseIntArrayElements(ENVPAR oType, otarr, JNI_ABORT);
ENVPTR->ReleaseLongArrayElements(ENVPAR oRef, refP, JNI_ABORT);
ENVPTR->ReleaseLongArrayElements(ENVPAR fNo, fnoP, JNI_ABORT);
h5str_array_free(oName, (size_t)n);
if (refs)
HDfree(refs);
if (fnos)
HDfree(fnos);
h5JNIFatalError(env, "H5Gget_obj_info_full: result arrays not allocated");
return -1;
} /* end if */
if (group_name != NULL) {
gid = -1;
gName = ENVPTR->GetStringUTFChars(ENVPAR group_name, &isCopy);
if (gName != NULL) {
gid = H5Gopen2((hid_t)loc_id, gName, H5P_DEFAULT);
ENVPTR->ReleaseStringUTFChars(ENVPAR group_name, gName);
} /* end if */
if(gid < 0) {
ENVPTR->ReleaseIntArrayElements(ENVPAR lType, ltarr, JNI_ABORT);
ENVPTR->ReleaseIntArrayElements(ENVPAR oType, otarr, JNI_ABORT);
ENVPTR->ReleaseLongArrayElements(ENVPAR oRef, refP, JNI_ABORT);
ENVPTR->ReleaseLongArrayElements(ENVPAR fNo, fnoP, JNI_ABORT);
h5str_array_free(oName, (size_t)n);
HDfree(refs);
HDfree(fnos);
h5JNIFatalError(env, "H5Gget_obj_info_full: could not get group identifier");
return -1;
} /* end if */
} /* end if */
ret_val = H5Gget_obj_info_full(gid, oName, (int *)otarr, (int *)ltarr, fnos, refs, indexType, indexOrder);
ENVPTR->ReleaseIntArrayElements(ENVPAR lType, ltarr, 0);
ENVPTR->ReleaseIntArrayElements(ENVPAR oType, otarr, 0);
if (group_name != NULL)
H5Gclose(gid);
if (ret_val < 0) {
ENVPTR->ReleaseLongArrayElements(ENVPAR oRef, refP, JNI_ABORT);
ENVPTR->ReleaseLongArrayElements(ENVPAR fNo, fnoP, JNI_ABORT);
h5str_array_free(oName, (size_t)n);
HDfree(refs);
HDfree(fnos);
h5libraryError(env);
} /* end if */
else {
for (i=0; i<n; i++) {
refP[i] = (jlong)refs[i];
} /* end for */
HDfree(refs);
ENVPTR->ReleaseLongArrayElements(ENVPAR oRef, refP, 0);
for (i=0; i<n; i++) {
fnoP[i] = (jlong)fnos[i];
} /* end for */
HDfree(fnos);
ENVPTR->ReleaseLongArrayElements(ENVPAR fNo, fnoP, 0);
for (i=0; i<n; i++) {
if (*(oName+i)) {
str = ENVPTR->NewStringUTF(ENVPAR *(oName+i));
ENVPTR->SetObjectArrayElement(ENVPAR objName, i, (jobject)str);
} /* end if */
} /* for (i=0; i<n; i++)*/
h5str_array_free(oName, (size_t)n);
} /* end else */
} /* end else */
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
*/
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)
{
herr_t ret_val = -1;
char **oName=NULL;
jboolean isCopy;
jstring str;
jint *otarr;
jint *ltarr;
jlong *refP;
unsigned long *refs;
int i;
if (oType == NULL) {
h5nullArgument(env, "H5Gget_obj_info_max: oType is NULL");
} /* end if */
else if (lType == NULL) {
h5nullArgument(env, "H5Gget_obj_info_max: lType is NULL");
} /* end else if */
else if (oRef == NULL) {
h5nullArgument(env, "H5Gget_obj_info_max: oRef is NULL");
} /* end else if */
else {
otarr = ENVPTR->GetIntArrayElements(ENVPAR oType, &isCopy);
if (otarr == NULL) {
h5JNIFatalError(env, "H5Gget_obj_info_max: otype not pinned");
return -1;
} /* end if */
ltarr = ENVPTR->GetIntArrayElements(ENVPAR lType, &isCopy);
if (ltarr == NULL) {
ENVPTR->ReleaseIntArrayElements(ENVPAR oType, otarr, JNI_ABORT);
h5JNIFatalError(env, "H5Gget_obj_info_max: ltype not pinned");
return -1;
} /* end if */
refP = ENVPTR->GetLongArrayElements(ENVPAR oRef, &isCopy);
if (refP == NULL) {
ENVPTR->ReleaseIntArrayElements(ENVPAR oType, otarr, JNI_ABORT);
ENVPTR->ReleaseIntArrayElements(ENVPAR lType, ltarr, JNI_ABORT);
h5JNIFatalError(env, "H5Gget_obj_info_max: oRef not pinned");
return -1;
} /* end if */
oName = (char **)HDcalloc((size_t)n, sizeof(*oName));
if (!oName) {
ENVPTR->ReleaseIntArrayElements(ENVPAR lType, ltarr, JNI_ABORT);
ENVPTR->ReleaseIntArrayElements(ENVPAR oType, otarr, JNI_ABORT);
ENVPTR->ReleaseLongArrayElements(ENVPAR oRef, refP, JNI_ABORT);
h5JNIFatalError(env, "H5Gget_obj_info_max: oName not allocated");
return -1;
} /* end if */
refs = (unsigned long *)HDcalloc((size_t)n, sizeof(unsigned long));
if (!refs) {
ENVPTR->ReleaseIntArrayElements(ENVPAR lType, ltarr, JNI_ABORT);
ENVPTR->ReleaseIntArrayElements(ENVPAR oType, otarr, JNI_ABORT);
ENVPTR->ReleaseLongArrayElements(ENVPAR oRef, refP, JNI_ABORT);
h5str_array_free(oName, (size_t)n);
h5JNIFatalError(env, "H5Gget_obj_info_max: result array not allocated");
return -1;
} /* end if */
ret_val = H5Gget_obj_info_max((hid_t)loc_id, oName, (int*)otarr, (int*)ltarr, refs, maxnum );
ENVPTR->ReleaseIntArrayElements(ENVPAR lType, ltarr, 0);
ENVPTR->ReleaseIntArrayElements(ENVPAR oType, otarr, 0);
if (ret_val < 0) {
ENVPTR->ReleaseLongArrayElements(ENVPAR oRef, refP, JNI_ABORT);
h5str_array_free(oName, (size_t)n);
HDfree(refs);
h5libraryError(env);
} /* end if */
else {
for (i=0; i<n; i++) {
refP[i] = (jlong) refs[i];
} /* end for */
HDfree(refs);
ENVPTR->ReleaseLongArrayElements(ENVPAR oRef, refP, 0);
for (i=0; i<n; i++) {
if (*(oName+i)) {
str = ENVPTR->NewStringUTF(ENVPAR *(oName+i));
ENVPTR->SetObjectArrayElement(ENVPAR objName, i, (jobject)str);
}
} /* for (i=0; i<n; i++)*/
h5str_array_free(oName, (size_t)n);
} /* end else */
} /* end else */
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) {
/* iterate failed, try normal alphabetical order */
if(H5Literate(loc_id, H5_INDEX_NAME, H5_ITER_INC, NULL, obj_info_all, (void *)&info) < 0)
return -1;
} /* end if */
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)
{
int type = -1;
hid_t oid = -1;
herr_t retVal = -1;
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);
if (retVal < 0) {
*(datainfo->otype+datainfo->count) = -1;
*(datainfo->ltype+datainfo->count) = -1;
*(datainfo->objname+datainfo->count) = (char *)HDmalloc(strlen(name)+1);
HDstrcpy(*(datainfo->objname+datainfo->count), name);
*(datainfo->objno+datainfo->count) = (unsigned long)-1;
} /* end if */
else {
*(datainfo->otype+datainfo->count) = object_info.type;
*(datainfo->ltype+datainfo->count) = info->type;
*(datainfo->objname+datainfo->count) = (char *)HDmalloc(HDstrlen(name)+1);
HDstrcpy(*(datainfo->objname+datainfo->count), name);
*(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;
*/
} /* end else */
datainfo->count++;
return 0;
} /* end obj_info_all */
herr_t
obj_info_max
(hid_t loc_id, const char *name, const H5L_info_t *info, void *op_data)
{
int type = -1;
herr_t retVal = 0;
info_all_t *datainfo = (info_all_t*)op_data;
H5O_info_t object_info;
retVal = H5Oget_info(loc_id, &object_info);
if (retVal < 0) {
*(datainfo->otype+datainfo->count) = -1;
*(datainfo->ltype+datainfo->count) = -1;
*(datainfo->objname+datainfo->count) = NULL;
*(datainfo->objno+datainfo->count) = (unsigned long)-1;
return 1;
} /* end if */
else {
*(datainfo->otype+datainfo->count) = object_info.type;
*(datainfo->ltype+datainfo->count) = info->type;
/* this will be freed by h5str_array_free(oName, n)*/
*(datainfo->objname+datainfo->count) = (char *)HDmalloc(HDstrlen(name)+1);
strcpy(*(datainfo->objname+datainfo->count), name);
if(info->type==H5L_TYPE_HARD)
*(datainfo->objno+datainfo->count) = (unsigned long)info->u.address;
else
*(datainfo->objno+datainfo->count) = info->u.val_size;
} /* end else */
datainfo->count++;
if(datainfo->count < (int)datainfo->idxnum)
return 0;
else
return 1;
} /* 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 cls, jstring file_export_name, jstring file_name, jstring object_path, jint binary_order)
{
herr_t status = -1;
herr_t ret_val = -1;
hid_t file_id = -1;
hid_t dataset_id = -1;
FILE *stream;
const char *file_export;
const char *object_name;
const char *fileName;
jboolean isCopy2;
if (file_export_name == NULL) {
h5nullArgument(env, "HDF5Library_export_data: file_export_name is NULL");
} /* end if */
else if (object_path == NULL) {
h5nullArgument(env, "HDF5Library_export_data: object_path is NULL");
} /* end else if */
else {
PIN_JAVA_STRING(file_name, fileName);
if (fileName != NULL) {
file_id = H5Fopen(fileName, (unsigned)H5F_ACC_RDWR, (hid_t)H5P_DEFAULT);
UNPIN_JAVA_STRING(file_name, fileName);
if (file_id < 0) {
/* throw exception */
h5libraryError(env);
} /* end if */
else {
object_name = ENVPTR->GetStringUTFChars(ENVPAR object_path, &isCopy2);
if (object_name == NULL) {
h5JNIFatalError( env, "H5Dopen: object name not pinned");
} /* end if */
else {
dataset_id = H5Dopen2(file_id, object_name, H5P_DEFAULT);
ENVPTR->ReleaseStringUTFChars(ENVPAR object_path, object_name);
if (dataset_id < 0) {
H5Fclose(file_id);
h5libraryError(env);
} /* end if */
else {
file_export = ENVPTR->GetStringUTFChars(ENVPAR file_export_name, 0);
stream = HDfopen(file_export, "w+");
ENVPTR->ReleaseStringUTFChars(ENVPAR file_export_name, file_export);
ret_val = h5str_dump_simple_dset(stream, dataset_id, binary_order);
if (stream)
HDfclose(stream);
H5Dclose(dataset_id);
H5Fclose(file_id);
if (ret_val < 0)
h5libraryError(env);
} /* end else */
} /* end else */
} /* end else */
}
} /* end else */
} /* end Java_hdf_hdf5lib_H5_H5export_1dataset */
#ifdef __cplusplus
}
#endif
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