1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254
|
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* 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. *
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
/*
* Programmer: Raymond Lu <slu@ncsa.uiuc.edu>
* August 5, 2002
*
* Purpose: Compact dataset I/O functions. These routines are similar
* H5D_contig_* and H5D_istore_*.
*/
#define H5D_PACKAGE /*suppress error about including H5Dpkg */
#include "H5private.h" /* Generic Functions */
#include "H5Dpkg.h" /* Dataset functions */
#include "H5Eprivate.h" /* Error handling */
#include "H5Fprivate.h" /* Files */
#include "H5FDprivate.h" /* File drivers */
#include "H5FLprivate.h" /* Free Lists */
#include "H5Iprivate.h" /* IDs */
#include "H5Oprivate.h" /* Object headers */
#include "H5Vprivate.h" /* Vector and array functions */
/* Declare a free list to manage blocks of type conversion data */
H5FL_BLK_EXTERN(type_conv);
/*-------------------------------------------------------------------------
* Function: H5D_compact_fill
*
* Purpose: Write fill values to a compactly stored dataset.
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Quincey Koziol
* May 6, 2007
*
*-------------------------------------------------------------------------
*/
herr_t
H5D_compact_fill(H5D_t *dset, hid_t dxpl_id)
{
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_NOAPI(H5D_compact_fill, FAIL)
/* Check args */
HDassert(TRUE == H5P_isa_class(dxpl_id, H5P_DATASET_XFER));
HDassert(dset && H5D_COMPACT == dset->shared->layout.type);
HDassert(dset->shared->layout.u.compact.buf);
HDassert(dset->shared->type);
HDassert(dset->shared->space);
/* If the fill value is defined, initialize the data buffer with it */
if(dset->shared->fill.buf) {
hssize_t snpoints; /* Number of points in space (for error checking) */
size_t npoints; /* Number of points in space */
/* Get the number of elements in the dataset's dataspace */
snpoints = H5S_GET_EXTENT_NPOINTS(dset->shared->space);
HDassert(snpoints >= 0);
H5_ASSIGN_OVERFLOW(npoints, snpoints, hssize_t, size_t);
/* If necessary, convert fill value datatypes (which copies VL components, etc.) */
if(H5T_detect_class(dset->shared->type, H5T_VLEN) > 0) {
H5T_path_t *tpath; /* Datatype conversion path */
uint8_t *bkg_buf = NULL; /* Background conversion buffer */
H5T_t *mem_type; /* Pointer to memory datatype */
size_t mem_type_size, file_type_size; /* Size of datatype in memory and on disk */
hid_t mem_tid; /* Memory version of disk datatype */
/* Create temporary datatype for conversion operation */
if(NULL == (mem_type = H5T_copy(dset->shared->type, H5T_COPY_REOPEN)))
HGOTO_ERROR(H5E_DATATYPE, H5E_CANTCOPY, FAIL, "unable to copy file datatype")
if((mem_tid = H5I_register(H5I_DATATYPE, mem_type)) < 0) {
H5T_close(mem_type);
HGOTO_ERROR(H5E_DATATYPE, H5E_CANTREGISTER, FAIL, "unable to register memory datatype")
} /* end if */
/* Retrieve sizes of memory & file datatypes */
mem_type_size = H5T_get_size(mem_type);
HDassert(mem_type_size > 0);
file_type_size = H5T_get_size(dset->shared->type);
HDassert(file_type_size == dset->shared->fill.size);
/* Get the datatype conversion path for this operation */
if(NULL == (tpath = H5T_path_find(dset->shared->type, mem_type, NULL, NULL, dxpl_id))) {
H5I_dec_ref(mem_tid);
HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "unable to convert between src and dst datatypes")
} /* end if */
/* Allocate a background buffer, if necessary */
if(H5T_path_bkg(tpath) && NULL == (bkg_buf = H5FL_BLK_CALLOC(type_conv, (npoints * MAX(mem_type_size, file_type_size))))) {
H5I_dec_ref(mem_tid);
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed")
} /* end if */
/* Make a copy of the (disk-based) fill value into the compact buffer */
HDmemcpy(dset->shared->layout.u.compact.buf, dset->shared->fill.buf, file_type_size);
/* Type convert the compact dataset buffer, to copy any VL components */
if(H5T_convert(tpath, dset->shared->type_id, mem_tid, (size_t)1, (size_t)0, (size_t)0, dset->shared->layout.u.compact.buf, bkg_buf, dxpl_id) < 0) {
if(bkg_buf)
H5FL_BLK_FREE(type_conv, bkg_buf);
H5I_dec_ref(mem_tid);
HGOTO_ERROR(H5E_DATASET, H5E_CANTCONVERT, FAIL, "data type conversion failed")
} /* end if */
/* Replicate the fill value into the cached buffer */
H5V_array_fill(dset->shared->layout.u.compact.buf, dset->shared->layout.u.compact.buf, mem_type_size, npoints);
/* Get the inverse datatype conversion path for this operation */
if(NULL == (tpath = H5T_path_find(mem_type, dset->shared->type, NULL, NULL, dxpl_id))) {
if(bkg_buf)
H5FL_BLK_FREE(type_conv, bkg_buf);
H5I_dec_ref(mem_tid);
HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "unable to convert between src and dst datatypes")
} /* end if */
/* Allocate or reset the background buffer, if necessary */
if(H5T_path_bkg(tpath)) {
if(bkg_buf)
HDmemset(bkg_buf, 0, MAX(mem_type_size, file_type_size));
else {
if(NULL == (bkg_buf = H5FL_BLK_CALLOC(type_conv, (npoints * MAX(mem_type_size, file_type_size))))) {
H5I_dec_ref(mem_tid);
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed")
} /* end if */
} /* end else */
} /* end if */
/* Type convert the compact dataset buffer, to copy any VL components */
if(H5T_convert(tpath, mem_tid, dset->shared->type_id, npoints, (size_t)0, (size_t)0, dset->shared->layout.u.compact.buf, bkg_buf, dxpl_id) < 0) {
if(bkg_buf)
H5FL_BLK_FREE(type_conv, bkg_buf);
H5I_dec_ref(mem_tid);
HGOTO_ERROR(H5E_DATASET, H5E_CANTCONVERT, FAIL, "data type conversion failed")
} /* end if */
/* Release resources used */
if(bkg_buf)
H5FL_BLK_FREE(type_conv, bkg_buf);
H5I_dec_ref(mem_tid);
} /* end if */
else
/* Replicate the fill value into the cached buffer */
H5V_array_fill(dset->shared->layout.u.compact.buf, dset->shared->fill.buf, dset->shared->fill.size, npoints);
} /* end if */
else /* If the fill value is default, zero set data buf. */
HDmemset(dset->shared->layout.u.compact.buf, 0, dset->shared->layout.u.compact.size);
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D_compact_fill() */
/*-------------------------------------------------------------------------
* Function: H5D_compact_readvv
*
* Purpose: Reads some data vectors from a dataset into a buffer.
* The data is in compact dataset. The address is relative
* to the beginning address of the dataset. The offsets and
* sequence lengths are in bytes.
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Quincey Koziol
* May 7, 2003
*
* Notes:
* Offsets in the sequences must be monotonically increasing
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
ssize_t
H5D_compact_readvv(const H5D_io_info_t *io_info,
size_t dset_max_nseq, size_t *dset_curr_seq, size_t dset_size_arr[], hsize_t dset_offset_arr[],
size_t mem_max_nseq, size_t *mem_curr_seq, size_t mem_size_arr[], hsize_t mem_offset_arr[],
void *buf)
{
ssize_t ret_value; /* Return value */
FUNC_ENTER_NOAPI(H5D_compact_readvv, FAIL)
assert(io_info->dset);
/* Use the vectorized memory copy routine to do actual work */
if((ret_value=H5V_memcpyvv(buf,mem_max_nseq,mem_curr_seq,mem_size_arr,mem_offset_arr,io_info->dset->shared->layout.u.compact.buf,dset_max_nseq,dset_curr_seq,dset_size_arr,dset_offset_arr))<0)
HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "vectorized memcpy failed")
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D_compact_readvv() */
/*-------------------------------------------------------------------------
* Function: H5D_compact_writevv
*
* Purpose: Writes some data vectors from a dataset into a buffer.
* The data is in compact dataset. The address is relative
* to the beginning address for the file. The offsets and
* sequence lengths are in bytes. This function only copies
* data into the buffer in the LAYOUT struct and mark it
* as DIRTY. Later in H5D_close, the data is copied into
* header message in memory.
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Quincey Koziol
* May 2, 2003
*
* Notes:
* Offsets in the sequences must be monotonically increasing
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
ssize_t
H5D_compact_writevv(const H5D_io_info_t *io_info,
size_t dset_max_nseq, size_t *dset_curr_seq, size_t dset_size_arr[], hsize_t dset_offset_arr[],
size_t mem_max_nseq, size_t *mem_curr_seq, size_t mem_size_arr[], hsize_t mem_offset_arr[],
const void *buf)
{
ssize_t ret_value; /* Return value */
FUNC_ENTER_NOAPI(H5D_compact_writevv, FAIL)
assert(io_info->dset);
/* Use the vectorized memory copy routine to do actual work */
if((ret_value=H5V_memcpyvv(io_info->dset->shared->layout.u.compact.buf,dset_max_nseq,dset_curr_seq,dset_size_arr,dset_offset_arr,buf,mem_max_nseq,mem_curr_seq,mem_size_arr,mem_offset_arr))<0)
HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "vectorized memcpy failed")
io_info->dset->shared->layout.u.compact.dirty = TRUE;
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D_compact_writevv() */
|