diff options
Diffstat (limited to 'src/H5Dio.c')
| -rw-r--r-- | src/H5Dio.c | 252 |
1 files changed, 4 insertions, 248 deletions
diff --git a/src/H5Dio.c b/src/H5Dio.c index 5fbe72a..1bf5b04 100644 --- a/src/H5Dio.c +++ b/src/H5Dio.c @@ -53,8 +53,6 @@ /* Local Prototypes */ /********************/ -static herr_t H5D_fill(const void *fill, const H5T_t *fill_type, void *buf, - const H5T_t *buf_type, const H5S_t *space, hid_t dxpl_id); static herr_t H5D_read(H5D_t *dataset, hid_t mem_type_id, const H5S_t *mem_space, const H5S_t *file_space, hid_t dset_xfer_plist, void *buf/*out*/); @@ -77,11 +75,11 @@ static herr_t H5D_chunk_write(H5D_io_info_t *io_info, hsize_t nelmts, const H5T_t *mem_type, const H5S_t *mem_space, const H5S_t *file_space, H5T_path_t *tpath, hid_t src_id, hid_t dst_id, const void *buf); -static herr_t H5D_compound_opt_read(hsize_t nelmts, const H5S_t *mem_space, +static herr_t H5D_compound_opt_read(size_t nelmts, const H5S_t *mem_space, H5S_sel_iter_t *iter, const H5D_dxpl_cache_t *dxpl_cache, hid_t src_id, hid_t dst_id, H5T_subset_t subset, void *data_buf, void *user_buf/*out*/); -static herr_t H5D_compound_opt_write(hsize_t nelmts, hid_t src_id, hid_t dst_id, +static herr_t H5D_compound_opt_write(size_t nelmts, hid_t src_id, hid_t dst_id, void *data_buf); #ifdef H5_HAVE_PARALLEL @@ -113,9 +111,6 @@ static herr_t H5D_chunk_mem_cb(void *elem, hid_t type_id, unsigned ndims, /* Local Variables */ /*******************/ -/* Declare a free list to manage blocks of single datatype element data */ -H5FL_BLK_DEFINE(type_elem); - /* Declare a free list to manage blocks of type conversion data */ H5FL_BLK_DEFINE(type_conv); @@ -132,245 +127,6 @@ H5FL_SEQ_DEFINE_STATIC(hsize_t); /*-------------------------------------------------------------------------- NAME - H5Dfill - PURPOSE - Fill a selection in memory with a value - USAGE - herr_t H5Dfill(fill, fill_type, space, buf, buf_type) - const void *fill; IN: Pointer to fill value to use - hid_t fill_type_id; IN: Datatype of the fill value - void *buf; IN/OUT: Memory buffer to fill selection within - hid_t buf_type_id; IN: Datatype of the elements in buffer - hid_t space_id; IN: Dataspace describing memory buffer & - containing selection to use. - RETURNS - Non-negative on success/Negative on failure. - DESCRIPTION - Use the selection in the dataspace to fill elements in a memory buffer. - GLOBAL VARIABLES - COMMENTS, BUGS, ASSUMPTIONS - If "fill" parameter is NULL, use all zeros as fill value - EXAMPLES - REVISION LOG ---------------------------------------------------------------------------*/ -herr_t -H5Dfill(const void *fill, hid_t fill_type_id, void *buf, hid_t buf_type_id, hid_t space_id) -{ - H5S_t *space; /* Dataspace */ - H5T_t *fill_type; /* Fill-value datatype */ - H5T_t *buf_type; /* Buffer datatype */ - herr_t ret_value=SUCCEED; /* Return value */ - - FUNC_ENTER_API(H5Dfill, FAIL) - H5TRACE5("e", "*xi*xii", fill, fill_type_id, buf, buf_type_id, space_id); - - /* Check args */ - if (buf==NULL) - HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "invalid buffer") - if (NULL == (space=H5I_object_verify(space_id, H5I_DATASPACE))) - HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, 0, "not a dataspace") - if (NULL == (fill_type=H5I_object_verify(fill_type_id, H5I_DATATYPE))) - HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, 0, "not a datatype") - if (NULL == (buf_type=H5I_object_verify(buf_type_id, H5I_DATATYPE))) - HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, 0, "not a datatype") - - /* Fill the selection in the memory buffer */ - if(H5D_fill(fill,fill_type,buf,buf_type,space, H5AC_dxpl_id) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTENCODE, FAIL, "filling selection failed") - -done: - FUNC_LEAVE_API(ret_value) -} /* H5Dfill() */ - - -/*-------------------------------------------------------------------------- - NAME - H5D_fill - PURPOSE - Fill a selection in memory with a value (internal version) - USAGE - herr_t H5D_fill(fill, fill_type, buf, buf_type, space) - const void *fill; IN: Pointer to fill value to use - H5T_t *fill_type; IN: Datatype of the fill value - void *buf; IN/OUT: Memory buffer to fill selection within - H5T_t *buf_type; IN: Datatype of the elements in buffer - H5S_t *space; IN: Dataspace describing memory buffer & - containing selection to use. - RETURNS - Non-negative on success/Negative on failure. - DESCRIPTION - Use the selection in the dataspace to fill elements in a memory buffer. - GLOBAL VARIABLES - COMMENTS, BUGS, ASSUMPTIONS - If "fill" parameter is NULL, use all zeros as fill value. If "fill_type" - parameter is NULL, use "buf_type" for the fill value datatype. - EXAMPLES - REVISION LOG - Raymond Lu - 20 March 2007 - If there's VL type of data, the address of the data is copied multiple - times into the buffer, causing some trouble when the data is released. - Instead, make multiple copies of fill value first, then do conversion - on each element so that each of them has a copy of the VL data. ---------------------------------------------------------------------------*/ -static herr_t -H5D_fill(const void *fill, const H5T_t *fill_type, void *buf, const H5T_t *buf_type, const H5S_t *space, hid_t dxpl_id) -{ - uint8_t *tconv_buf = NULL; /* Data type conv buffer */ - uint8_t *bkg_buf = NULL; /* Background conversion buffer */ - uint8_t *tmp_buf = NULL; /* Temp conversion buffer */ - hid_t src_id = -1, dst_id = -1; /* Temporary type IDs */ - size_t src_type_size; /* Size of source type */ - size_t dst_type_size; /* Size of destination type*/ - size_t buf_size; /* Desired buffer size */ - herr_t ret_value=SUCCEED; /* Return value */ - - FUNC_ENTER_NOAPI_NOINIT(H5D_fill) - - /* Check args */ - HDassert(fill_type); - HDassert(buf); - HDassert(buf_type); - HDassert(space); - - /* Make sure the dataspace has an extent set (or is NULL) */ - if(!(H5S_has_extent(space))) - HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "dataspace extent has not been set") - - /* Get the memory and file datatype sizes */ - src_type_size = H5T_get_size(fill_type); - dst_type_size = H5T_get_size(buf_type); - - /* Get the maximum buffer size needed and allocate it */ - buf_size = MAX(src_type_size, dst_type_size); - - /* If there's no fill value, just use zeros */ - if(fill == NULL) { - /* Allocate space & initialize conversion buffer to zeros */ - if(NULL == (tconv_buf = H5FL_BLK_CALLOC(type_elem, buf_size))) - HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed") - - /* Fill the selection in the memory buffer */ - if(H5S_select_fill(tconv_buf, dst_type_size, space, buf) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTENCODE, FAIL, "filling selection failed") - } /* end if */ - else { - H5T_path_t *tpath; /* Conversion path information */ - - /* Set up type conversion function */ - if(NULL == (tpath = H5T_path_find(fill_type, buf_type, NULL, NULL, dxpl_id, FALSE))) - HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, FAIL, "unable to convert between src and dest datatype") - - /* Construct source & destination datatype IDs, if we will need them */ - if(!H5T_path_noop(tpath)) { - if((src_id = H5I_register(H5I_DATATYPE, H5T_copy(fill_type, H5T_COPY_ALL))) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTREGISTER, FAIL, "unable to register types for conversion") - - if((dst_id = H5I_register(H5I_DATATYPE, H5T_copy(buf_type, H5T_COPY_ALL))) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTREGISTER, FAIL, "unable to register types for conversion") - } /* end if */ - - /* If there's VL type of data, make multiple copies of fill value first, - * then do conversion on each element so that each of them has a copy - * of the VL data. - */ - if(TRUE == H5T_detect_class(fill_type, H5T_VLEN)) { - H5D_dxpl_cache_t _dxpl_cache; /* Data transfer property cache buffer */ - H5D_dxpl_cache_t *dxpl_cache = &_dxpl_cache; /* Data transfer property cache */ - H5S_sel_iter_t mem_iter; /* Memory selection iteration info */ - hssize_t nelmts; /* Number of data elements */ - - /* Get the number of elements in the selection */ - nelmts = H5S_GET_SELECT_NPOINTS(space); - HDassert(nelmts >= 0); - H5_CHECK_OVERFLOW(nelmts, hssize_t, size_t); - - /* Allocate a temporary buffer */ - if(NULL == (tmp_buf = H5FL_BLK_MALLOC(type_conv, (size_t)nelmts * buf_size))) - HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed") - - /* Allocate a background buffer, if necessary */ - if(H5T_path_bkg(tpath) && NULL == (bkg_buf = H5FL_BLK_CALLOC(type_conv, (size_t)nelmts * buf_size))) - HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed") - - /* Replicate the file's fill value into the temporary buffer */ - H5V_array_fill(tmp_buf, fill, src_type_size, (size_t)nelmts); - - /* Convert from file's fill value into memory form */ - if(H5T_convert(tpath, src_id, dst_id, (size_t)nelmts, (size_t)0, (size_t)0, tmp_buf, bkg_buf, dxpl_id) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTCONVERT, FAIL, "data type conversion failed") - - /* Fill the DXPL cache values for later use */ - if(H5D_get_dxpl_cache(dxpl_id, &dxpl_cache) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't fill dxpl cache") - - /* Create a selection iterator for scattering the elements to memory buffer */ - if(H5S_select_iter_init(&mem_iter, space, dst_type_size) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize memory selection information") - - /* Scatter the data into memory */ - if(H5D_select_mscat(tmp_buf, space, &mem_iter, (size_t)nelmts, dxpl_cache, buf/*out*/) < 0) { - H5S_SELECT_ITER_RELEASE(&mem_iter); - HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "scatter failed") - } /* end if */ - - /* Release the selection iterator */ - if(H5S_SELECT_ITER_RELEASE(&mem_iter) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "Can't release selection iterator") - } else { - const uint8_t *fill_buf; /* Buffer to use for writing fill values */ - - /* Convert disk buffer into memory buffer */ - if(!H5T_path_noop(tpath)) { - /* Allocate space for conversion buffer */ - if(NULL == (tconv_buf = H5FL_BLK_MALLOC(type_elem, buf_size))) - HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed") - - /* Copy the user's data into the buffer for conversion */ - HDmemcpy(tconv_buf, fill, src_type_size); - - /* If there's no VL type of data, do conversion first then fill the data into - * the memory buffer. */ - if(H5T_path_bkg(tpath) && NULL == (bkg_buf = H5FL_BLK_CALLOC(type_elem, buf_size))) - HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed") - - /* Perform datatype conversion */ - if(H5T_convert(tpath, src_id, dst_id, (size_t)1, (size_t)0, (size_t)0, tconv_buf, bkg_buf, dxpl_id) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTCONVERT, FAIL, "data type conversion failed") - - /* Point at temporary buffer */ - fill_buf = tconv_buf; - } /* end if */ - else - fill_buf = fill; - - /* Fill the selection in the memory buffer */ - if(H5S_select_fill(fill_buf, dst_type_size, space, buf) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTENCODE, FAIL, "filling selection failed") - } /* end else */ - } /* end else */ - -done: - if(src_id != (-1) && H5I_dec_ref(src_id) < 0) - HDONE_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "Can't decrement temporary datatype ID") - if(dst_id != (-1) && H5I_dec_ref(dst_id) < 0) - HDONE_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "Can't decrement temporary datatype ID") - if(tmp_buf) - H5FL_BLK_FREE(type_conv, tmp_buf); - if(tconv_buf) - H5FL_BLK_FREE(type_elem, tconv_buf); - if(bkg_buf) { - if(TRUE == H5T_detect_class(fill_type, H5T_VLEN)) - H5FL_BLK_FREE(type_conv, bkg_buf); - else - H5FL_BLK_FREE(type_elem, bkg_buf); - } /* end if */ - - FUNC_LEAVE_NOAPI(ret_value) -} /* H5D_fill() */ - - -/*-------------------------------------------------------------------------- - NAME H5D_get_dxpl_cache_real PURPOSE Get all the values for the DXPL cache. @@ -2238,7 +1994,7 @@ done: *------------------------------------------------------------------------- */ static herr_t -H5D_compound_opt_read(hsize_t nelmts, const H5S_t *space, +H5D_compound_opt_read(size_t nelmts, const H5S_t *space, H5S_sel_iter_t *iter, const H5D_dxpl_cache_t *dxpl_cache, hid_t src_id, hid_t dst_id, H5T_subset_t subset, void *data_buf, void *user_buf/*out*/) @@ -2377,7 +2133,7 @@ done: *------------------------------------------------------------------------- */ static herr_t -H5D_compound_opt_write(hsize_t nelmts, hid_t src_id, hid_t dst_id, void *data_buf) +H5D_compound_opt_write(size_t nelmts, hid_t src_id, hid_t dst_id, void *data_buf) { uint8_t *dbuf = (uint8_t *)data_buf; /*cast for pointer arithmetic */ uint8_t *xsbuf, *xdbuf; |