/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* Copyright by The HDF Group. *
* 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://www.hdfgroup.org/licenses. *
* If you do not have access to either file, you may request a copy from *
* help@hdfgroup.org. *
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
#include "H5LDprivate.h"
/*-------------------------------------------------------------------------
*
* internal functions
*
*-------------------------------------------------------------------------
*/
static herr_t H5LD_construct_info(H5LD_memb_t *memb, hid_t par_tid);
static herr_t H5LD_get_dset_dims(hid_t did, hsize_t *cur_dims);
static size_t H5LD_get_dset_type_size(hid_t did, const char *fields);
static herr_t H5LD_get_dset_elmts(hid_t did, const hsize_t *prev_dims, const hsize_t *cur_dims,
const char *fields, void *buf);
/*-------------------------------------------------------------------------
* Function: H5LD_clean_vector
*
* Purpose: Process the vector of info:
* 1) free the array of pointers to member names in listv[n]
* 2) close the type id of the last member in listv[n]
* 3) free the H5LD_memb_t structure itself as pointed to by listv[n]
*
* Return: void
*
* Programmer: Vailin Choi; Aug 2010
*
*-------------------------------------------------------------------------
*/
void
H5LD_clean_vector(H5LD_memb_t *listv[])
{
unsigned n; /* Local index variable */
HDassert(listv);
/* Go through info for each field stored in listv[] */
for (n = 0; listv[n] != NULL; n++) {
if (listv[n]->names) {
HDfree(listv[n]->names);
listv[n]->names = NULL;
} /* end if */
/* Close the type id of the last member in the field */
if (!(listv[n]->last_tid < 0)) {
H5Tclose(listv[n]->last_tid);
listv[n]->last_tid = -1;
} /* end if */
/* Free the H5LD_memb_t structure for the field */
HDfree(listv[n]);
listv[n] = NULL;
} /* end for */
} /* H5LD_clean_vector() */
/*-------------------------------------------------------------------------
* Function: H5LD_construct_info()
*
* Purpose: Get the remaining info for a field:
* 1) Get the type id of the last member in the field
* 2) Get the total offset of all the members in the field
* 3) Get the type size of the last member in the field
*
* Return: Success: 0
* Failure: negative
*
* Programmer: Vailin Choi; Aug 2010
*
*-------------------------------------------------------------------------
*/
static herr_t
H5LD_construct_info(H5LD_memb_t *memb, hid_t par_tid)
{
hid_t tmp_tid = -1; /* Dataset type id */
unsigned i; /* Local index variable */
herr_t ret_value = FAIL; /* Return value */
/* Make a copy of the incoming datatype */
tmp_tid = H5Tcopy(par_tid);
/* Validate all the members in a field */
for (i = 0; memb->names[i] != NULL; i++) {
hid_t memb_tid; /* Type id for a member in a field */
int idx; /* Index # of a member in a compound datatype */
/* Get the member index and member type id */
if ((idx = H5Tget_member_index(tmp_tid, memb->names[i])) < 0)
goto done;
if ((memb_tid = H5Tget_member_type(tmp_tid, (unsigned)idx)) < 0)
goto done;
/* Sum up the offset of all the members in the field */
memb->tot_offset += H5Tget_member_offset(tmp_tid, (unsigned)idx);
if (H5Tclose(tmp_tid) < 0)
goto done;
tmp_tid = memb_tid;
} /* end for */
/* Get the type size of the last member in the field */
memb->last_tsize = H5Tget_size(tmp_tid);
/* Save the type id of the last member in the field */
memb->last_tid = H5Tcopy(tmp_tid);
/* Indicate success */
ret_value = SUCCEED;
done:
H5E_BEGIN_TRY
H5Tclose(tmp_tid);
H5E_END_TRY
return (ret_value);
} /* H5LD_construct_info() */
/*-------------------------------------------------------------------------
* Function: H5LD_construct_vector
*
* Purpose: Process the comma-separated list of fields in "fields" as follows:
* Example:
* "fields": "a.b.c,d"
* listv[0]->tot_offset = total offset of "a" & "b" & "c"
* listv[0]->last_tid = type id of "c"
* listv[0]->last_tsize = type size of "c"
* listv[0]->names[0] = "a"
* listv[0]->names[1] = "b"
* listv[0]->names[2] = "c"
* listv[0]->names[3] = NULL
*
* listv[1]->tot_offset = offset of "d"
* listv[1]->last_tid = type id of "d"
* listv[1]->last_tsize = type size of "d"
* listv[1]->names[0] = "d"
* listv[1]->names[1] = NULL
*
* Return: Success: # of comma-separated fields in "fields"
* Failure: negative value
*
* Programmer: Vailin Choi; Aug 2010
*
*-------------------------------------------------------------------------
*/
int
H5LD_construct_vector(char *fields, H5LD_memb_t *listv[] /*OUT*/, hid_t par_tid)
{
int nfields; /* The # of comma-separated fields in "fields" */
hbool_t end_of_fields = FALSE; /* end of "fields" */
char *fields_ptr; /* Pointer to "fields" */
int ret_value = FAIL; /* Return value */
HDassert(listv);
HDassert(fields);
fields_ptr = fields;
nfields = 0;
/* Process till end of "fields" */
while (!end_of_fields) {
H5LD_memb_t *memb = NULL; /* Pointer to structure for storing a field's info */
char *cur; /* Pointer to a member in a field */
size_t len; /* Estimated # of members in a field */
hbool_t gotcomma = FALSE; /* A comma encountered */
hbool_t gotmember = FALSE; /* Getting member in a field */
hbool_t valid = TRUE; /* Whether a field being processed is valid or not */
int j = 0; /* The # of members in a field */
len = (HDstrlen(fields_ptr) / 2) + 2;
/* Allocate memory for an H5LD_memb_t for storing a field's info */
if (NULL == (memb = (H5LD_memb_t *)HDcalloc((size_t)1, sizeof(H5LD_memb_t))))
goto done;
/* Allocate memory for an array of pointers to member names */
if (NULL == (memb->names = (char **)HDcalloc(len, sizeof(char *))))
goto done;
memb->names[j] = fields_ptr;
memb->last_tid = -1;
cur = fields_ptr;
/* Continue processing till: not valid or comma encountered or "fields" ended */
while (valid && !gotcomma && !end_of_fields) {
switch (*fields_ptr) {
case '\0': /* end of list */
if (gotmember) { /* getting something and end of "fields" */
*cur++ = '\0';
;
memb->names[++j] = NULL;
} /* end if */
else /* getting nothing but end of list */
valid = FALSE;
end_of_fields = TRUE;
break;
case '\\': /* escape character */
++fields_ptr; /* skip it */
if (*fields_ptr == '\0')
valid = FALSE;
else {
*cur++ = *fields_ptr++;
gotmember = TRUE;
} /* end else */
break;
case '.': /* nested field separator */
*fields_ptr++ = *cur++ = '\0';
;
if (gotmember) {
memb->names[++j] = cur;
gotmember = FALSE;
} /* end if */
else
valid = FALSE;
break;
case ',': /* field separator */
*fields_ptr++ = *cur++ = '\0';
;
if (gotmember) {
memb->names[++j] = NULL;
gotmember = FALSE;
} /* end if */
else
valid = FALSE;
gotcomma = TRUE;
break;
default:
*cur++ = *fields_ptr++;
gotmember = TRUE;
break;
} /* end switch */
} /* while (valid && !gotcomma && !end_of_fields) */
/* If valid, put into listv and continue processing further info */
if (valid) {
listv[nfields++] = memb;
if (H5LD_construct_info(memb, par_tid) < 0)
goto done;
} /* end if */
else {
if (memb) {
HDfree(memb->names);
HDfree(memb);
}
goto done;
} /* end else */
} /* while !end_of_fields */
/* Indicate success */
ret_value = nfields;
done:
listv[nfields] = NULL;
if (ret_value == FAIL)
H5LD_clean_vector(listv);
return (ret_value);
} /* H5LD_construct_vector() */
/*-------------------------------------------------------------------------
* Function: H5LD_get_dset_dims
*
* Purpose: To return the current size for each dimension of the
* dataset's dataspace
*
* Return: Success: 0
* Failure: negative value
*
* Programmer: Vailin Choi; March 2010
*
*-------------------------------------------------------------------------
*/
static herr_t
H5LD_get_dset_dims(hid_t did, hsize_t *cur_dims)
{
hid_t sid = -1; /* Dataspace ID */
herr_t ret_value = FAIL; /* Return Value */
/* Verify parameter */
if (cur_dims == NULL)
goto done;
/* Get the dataset's dataspace */
if ((sid = H5Dget_space(did)) < 0)
goto done;
/* Get the current dimension size */
if (H5Sget_simple_extent_dims(sid, cur_dims, NULL) < 0)
goto done;
/* Indicate success */
ret_value = SUCCEED;
done:
H5E_BEGIN_TRY
{
H5Sclose(sid);
}
H5E_END_TRY;
return (ret_value);
} /* H5LD_get_dset_dims() */
/*-------------------------------------------------------------------------
* Function: H5LD_get_dset_type_size
*
* Purpose: To return the size of the dataset's datatype in bytes
* null "fields": return the size of the dataset's datatype
* non-null "fields": return the size of the dataset's datatype
* with respect to the selection in "fields"
*
* Return: Success: size of the dataset's datatype
* Failure: 0 (valid datatypes are never zero size)
*
* Programmer: Vailin Choi; March 2010
*
*-------------------------------------------------------------------------
*/
static size_t
H5LD_get_dset_type_size(hid_t did, const char *fields)
{
hid_t dset_tid = -1; /* Dataset's type identifier */
hid_t tid = -1; /* Native Type identifier */
H5LD_memb_t **listv = NULL; /* Vector for storing information in "fields" */
char *dup_fields = NULL; /* A copy of "fields" */
size_t ret_value = 0; /* Return value */
/* Get the datatype of the dataset */
if ((dset_tid = H5Dget_type(did)) < 0)
goto done;
if ((tid = H5Tget_native_type(dset_tid, H5T_DIR_DEFAULT)) < 0)
goto done;
if (fields == NULL) /* If no "fields" is specified */
ret_value = H5Tget_size(tid);
else { /* "fields" are specified */
size_t len; /* Estimate the number of comma-separated fields in "fields" */
size_t tot = 0; /* Data type size of all the fields in "fields" */
int n = 0, num = 0; /* Local index variables */
HDassert(fields && *fields);
/* Should be a compound datatype if "fields" exists */
if (H5Tget_class(dset_tid) != H5T_COMPOUND)
goto done;
/* Get a copy of "fields" */
if (NULL == (dup_fields = HDstrdup(fields)))
goto done;
/* Allocate memory for a list of H5LD_memb_t pointers to store "fields" info */
len = (HDstrlen(fields) / 2) + 2;
if (NULL == (listv = (H5LD_memb_t **)HDcalloc(len, sizeof(H5LD_memb_t *))))
goto done;
/* Process and store info for "fields" */
if ((num = H5LD_construct_vector(dup_fields, listv /*OUT*/, tid)) < 0)
goto done;
/* Sum up the size of all the datatypes in "fields" */
for (n = 0; n < num; n++)
tot += listv[n]->last_tsize;
/* Clean up the vector of H5LD_memb_t structures */
H5LD_clean_vector(listv);
/* Return the total size */
ret_value = tot;
} /* end else */
done:
H5E_BEGIN_TRY
H5Tclose(tid);
H5Tclose(dset_tid);
H5E_END_TRY
/* Free the array of H5LD_memb_t pointers */
if (listv)
HDfree(listv);
/* Free memory */
if (dup_fields)
HDfree(dup_fields);
return (ret_value);
} /* H5LD_get_dset_type_size() */
/*-------------------------------------------------------------------------
* Function: H5LD_get_dset_elmts
*
* Purpose: To retrieve selected data from the dataset
*
* Return: Success: 0
* Failure: negative
*
* Programmer: Vailin Choi; August 2010
*
*-------------------------------------------------------------------------
*/
static herr_t
H5LD_get_dset_elmts(hid_t did, const hsize_t *prev_dims, const hsize_t *cur_dims, const char *fields,
void *buf)
{
hid_t dtid = -1, tid = -1; /* Dataset type id */
hid_t sid = -1, mid = -1; /* Dataspace and memory space id */
hssize_t snum_elmts; /* Number of dataset elements in the selection (signed) */
hsize_t num_elmts; /* Number of dataset elements in the selection */
hsize_t start[H5S_MAX_RANK]; /* Starting offset */
hsize_t count[H5S_MAX_RANK]; /* ??offset */
H5LD_memb_t **listv = NULL; /* Vector for storing information in "fields" */
char *dup_fields = NULL; /* A copy of "fields" */
char *sav_buf = NULL; /* Saved pointer temporary buffer */
unsigned ctr; /* Counter for # of curr_dims > prev_dims */
int ndims; /* Number of dimensions for the dataset */
int i; /* Local index variable */
herr_t ret_value = FAIL; /* Return value */
/* Verify parameters */
if (prev_dims == NULL || cur_dims == NULL || buf == NULL)
goto done;
/* Get dataset's dataspace */
if ((sid = H5Dget_space(did)) < 0)
goto done;
/* Get the number of dimensions */
if ((ndims = H5Sget_simple_extent_ndims(sid)) < 0)
goto done;
/* Verify that cur_dims must have one dimension whose size is greater than prev_dims */
HDmemset(start, 0, sizeof start);
HDmemset(count, 0, sizeof count);
ctr = 0;
for (i = 0; i < ndims; i++)
if (cur_dims[i] > prev_dims[i]) {
++ctr;
count[i] = cur_dims[i] - prev_dims[i];
start[i] = prev_dims[i];
} /* end if */
else { /* < or = */
start[i] = 0;
count[i] = MIN(prev_dims[i], cur_dims[i]);
} /* end else */
if (!ctr)
goto done;
if (ctr == 1) { /* changes for only one dimension */
/* Make the selection in the dataset based on "cur_dims" and "prev_dims" */
if (H5Sselect_hyperslab(sid, H5S_SELECT_SET, start, NULL, count, NULL) < 0)
goto done;
} /* end if */
else { /* changes for more than one dimensions */
HDmemset(start, 0, sizeof start);
/* Make the selection in the dataset based on "cur_dims" and "prev_dims" */
if (H5Sselect_hyperslab(sid, H5S_SELECT_SET, start, NULL, cur_dims, NULL) < 0)
goto done;
if (H5Sselect_hyperslab(sid, H5S_SELECT_NOTB, start, NULL, prev_dims, NULL) < 0)
goto done;
} /* end else */
/* Get the number of elements in the selection */
if (0 == (snum_elmts = H5Sget_select_npoints(sid)))
goto done;
num_elmts = (hsize_t)snum_elmts;
/* Create the memory space for the selection */
if ((mid = H5Screate_simple(1, &num_elmts, NULL)) < 0)
goto done;
/* Get the native datatype size */
if ((dtid = H5Dget_type(did)) < 0)
goto done;
if ((tid = H5Tget_native_type(dtid, H5T_DIR_DEFAULT)) < 0)
goto done;
if (fields == NULL) { /* nothing in "fields" */
/* Read and store all the elements in "buf" */
if (H5Dread(did, tid, mid, sid, H5P_DEFAULT, buf) < 0)
goto done;
} /* end if */
else { /* "fields" is specified */
unsigned char *buf_p = (unsigned char *)buf; /* Pointer to the destination buffer */
char *tmp_buf; /* Temporary buffer for data read */
size_t tot_tsize; /* Total datatype size */
size_t len; /* Estimate the number of comma-separated fields in "fields" */
/* should be a compound datatype if "fields" exists */
if (H5Tget_class(tid) != H5T_COMPOUND)
goto done;
/* Get the total size of the dataset's datatypes */
if (0 == (tot_tsize = H5LD_get_dset_type_size(did, NULL)))
goto done;
/* Allocate memory for reading in the elements in the dataset selection */
if (NULL == (sav_buf = tmp_buf = (char *)HDcalloc((size_t)num_elmts, tot_tsize)))
goto done;
/* Read the dataset elements in the selection */
if (H5Dread(did, tid, mid, sid, H5P_DEFAULT, tmp_buf) < 0)
goto done;
/* Make a copy of "fields" */
if (NULL == (dup_fields = HDstrdup(fields)))
goto done;
/* Allocate memory for the vector of H5LD_memb_t pointers */
len = (HDstrlen(fields) / 2) + 2;
if (NULL == (listv = (H5LD_memb_t **)HDcalloc(len, sizeof(H5LD_memb_t *))))
goto done;
/* Process and store information for "fields" */
if (H5LD_construct_vector(dup_fields, listv, tid) < 0)
goto done;
/* Copy data for each dataset element in the selection */
for (i = 0; i < (int)num_elmts; i++) {
int j; /* Local index variable */
/* Copy data for "fields" to the input buffer */
for (j = 0; listv[j] != NULL; j++) {
HDmemcpy(buf_p, tmp_buf + listv[j]->tot_offset, listv[j]->last_tsize);
buf_p += listv[j]->last_tsize;
} /* end for */
tmp_buf += tot_tsize;
} /* end for */
/* Clean up the vector of H5LD_memb_t structures */
H5LD_clean_vector(listv);
} /* end else */
/* Indicate success */
ret_value = SUCCEED;
done:
H5E_BEGIN_TRY
H5Tclose(dtid);
H5Tclose(tid);
H5Sclose(sid);
H5Sclose(mid);
H5E_END_TRY
/* Free the array of H5LD_memb_t pointers */
if (listv)
HDfree(listv);
/* Free memory */
if (dup_fields)
HDfree(dup_fields);
if (sav_buf)
HDfree(sav_buf);
return (ret_value);
} /* H5LD_get_dset_elmts() */
/*-------------------------------------------------------------------------
*
* Public functions
*
*-------------------------------------------------------------------------
*/
/*-------------------------------------------------------------------------
* Function: H5LDget_dset_dims
*
* Purpose: To retrieve the current dimension sizes for a dataset
*
* Return: Success: 0
* Failure: negative value
*
* Programmer: Vailin Choi; March 2010
*
*-------------------------------------------------------------------------
*/
herr_t
H5LDget_dset_dims(hid_t did, hsize_t *cur_dims)
{
return (H5LD_get_dset_dims(did, cur_dims));
} /* H5LDget_dset_dims() */
/*-------------------------------------------------------------------------
* Function: H5LDget_dset_type_size
*
* Purpose: To return the size in bytes of the datatype for the dataset
*
* Return: Success: size in bytes of the dataset's datatype
* Failure: 0 (valid datatypes are never zero size)
*
* Programmer: Vailin Choi; March 2010
*
*-------------------------------------------------------------------------
*/
size_t
H5LDget_dset_type_size(hid_t did, const char *fields)
{
return (H5LD_get_dset_type_size(did, fields));
} /* H5LDget_dset_type_size() */
/*-------------------------------------------------------------------------
* Function: H5LDget_dset_elmts
*
* Purpose: To retrieve selected data from the dataset
*
* Return: Success: 0
* Failure: negative value
*
* Programmer: Vailin Choi; March 2010
*
*-------------------------------------------------------------------------
*/
herr_t
H5LDget_dset_elmts(hid_t did, const hsize_t *prev_dims, const hsize_t *cur_dims, const char *fields,
void *buf)
{
return (H5LD_get_dset_elmts(did, prev_dims, cur_dims, fields, buf));
} /* H5LDget_dset_elmts() */