hdf5-src 0.8.1

/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* 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.                                                        *
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */

#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);
	    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() */