diff options
Diffstat (limited to 'src/H5D.c')
| -rw-r--r-- | src/H5D.c | 480 |
1 files changed, 480 insertions, 0 deletions
@@ -53,6 +53,9 @@ hbool_t H5_PKG_INIT_VAR = FALSE; /* Library Private Variables */ /*****************************/ +/* Declare extern free list to manage the H5S_sel_iter_t struct */ +H5FL_EXTERN(H5S_sel_iter_t); + /* Declare extern the free list to manage blocks of type conversion data */ H5FL_BLK_EXTERN(type_conv); @@ -594,6 +597,483 @@ done: } /* end H5Dget_offset() */ /*------------------------------------------------------------------------- + * Function: H5Dread + * + * Purpose: Reads (part of) a DSET from the file into application + * memory BUF. The part of the dataset to read is defined with + * MEM_SPACE_ID and FILE_SPACE_ID. The data points are + * converted from their file type to the MEM_TYPE_ID specified. + * Additional miscellaneous data transfer properties can be + * passed to this function with the PLIST_ID argument. + * + * The FILE_SPACE_ID can be the constant H5S_ALL which indicates + * that the entire file dataspace is to be referenced. + * + * The MEM_SPACE_ID can be the constant H5S_ALL in which case + * the memory dataspace is the same as the file dataspace + * defined when the dataset was created. + * + * The number of elements in the memory dataspace must match + * the number of elements in the file dataspace. + * + * The PLIST_ID can be the constant H5P_DEFAULT in which + * case the default data transfer properties are used. + * + * Return: Non-negative on success/Negative on failure + * + * Programmer: Robb Matzke + * Thursday, December 4, 1997 + * + *------------------------------------------------------------------------- + */ +herr_t +H5Dread(hid_t dset_id, hid_t mem_type_id, hid_t mem_space_id, hid_t file_space_id, hid_t dxpl_id, + void *buf /*out*/) +{ + H5VL_object_t *vol_obj = NULL; + herr_t ret_value = SUCCEED; /* Return value */ + + FUNC_ENTER_API(FAIL) + H5TRACE6("e", "iiiiix", dset_id, mem_type_id, mem_space_id, file_space_id, dxpl_id, buf); + + /* Check arguments */ + if (mem_space_id < 0) + HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "invalid memory dataspace ID") + if (file_space_id < 0) + HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "invalid file dataspace ID") + + /* Get dataset pointer */ + if (NULL == (vol_obj = (H5VL_object_t *)H5I_object_verify(dset_id, H5I_DATASET))) + HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "dset_id is not a dataset ID") + + /* Get the default dataset transfer property list if the user didn't provide one */ + if (H5P_DEFAULT == dxpl_id) + dxpl_id = H5P_DATASET_XFER_DEFAULT; + else if (TRUE != H5P_isa_class(dxpl_id, H5P_DATASET_XFER)) + HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not xfer parms") + + /* Read the data */ + if ((ret_value = H5VL_dataset_read(vol_obj, mem_type_id, mem_space_id, file_space_id, dxpl_id, buf, + H5_REQUEST_NULL)) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "can't read data") + +done: + FUNC_LEAVE_API(ret_value) +} /* end H5Dread() */ + +/*------------------------------------------------------------------------- + * Function: H5Dread_chunk + * + * Purpose: Reads an entire chunk from the file directly. + * + * Return: Non-negative on success/Negative on failure + * + * Programmer: Matthew Strong (GE Healthcare) + * 14 February 2016 + * + *--------------------------------------------------------------------------- + */ +herr_t +H5Dread_chunk(hid_t dset_id, hid_t dxpl_id, const hsize_t *offset, uint32_t *filters, void *buf) +{ + H5VL_object_t *vol_obj = NULL; + herr_t ret_value = SUCCEED; /* Return value */ + + FUNC_ENTER_API(FAIL) + H5TRACE5("e", "ii*h*Iu*x", dset_id, dxpl_id, offset, filters, buf); + + /* Check arguments */ + if (NULL == (vol_obj = (H5VL_object_t *)H5I_object_verify(dset_id, H5I_DATASET))) + HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "dset_id is not a dataset ID") + if (!buf) + HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "buf cannot be NULL") + if (!offset) + HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "offset cannot be NULL") + if (!filters) + HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "filters cannot be NULL") + + /* Get the default dataset transfer property list if the user didn't provide one */ + if (H5P_DEFAULT == dxpl_id) + dxpl_id = H5P_DATASET_XFER_DEFAULT; + else if (TRUE != H5P_isa_class(dxpl_id, H5P_DATASET_XFER)) + HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "dxpl_id is not a dataset transfer property list ID") + + /* Read the raw chunk */ + if (H5VL_dataset_optional(vol_obj, H5VL_NATIVE_DATASET_CHUNK_READ, dxpl_id, H5_REQUEST_NULL, offset, + filters, buf) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "can't read unprocessed chunk data") + +done: + FUNC_LEAVE_API(ret_value) +} /* end H5Dread_chunk() */ + +/*------------------------------------------------------------------------- + * Function: H5Dwrite + * + * Purpose: Writes (part of) a DSET from application memory BUF to the + * file. The part of the dataset to write is defined with the + * MEM_SPACE_ID and FILE_SPACE_ID arguments. The data points + * are converted from their current type (MEM_TYPE_ID) to their + * file datatype. Additional miscellaneous data transfer + * properties can be passed to this function with the + * PLIST_ID argument. + * + * The FILE_SPACE_ID can be the constant H5S_ALL which indicates + * that the entire file dataspace is to be referenced. + * + * The MEM_SPACE_ID can be the constant H5S_ALL in which case + * the memory dataspace is the same as the file dataspace + * defined when the dataset was created. + * + * The number of elements in the memory dataspace must match + * the number of elements in the file dataspace. + * + * The PLIST_ID can be the constant H5P_DEFAULT in which + * case the default data transfer properties are used. + * + * Return: Non-negative on success/Negative on failure + * + * Programmer: Robb Matzke + * Thursday, December 4, 1997 + * + *------------------------------------------------------------------------- + */ +herr_t +H5Dwrite(hid_t dset_id, hid_t mem_type_id, hid_t mem_space_id, hid_t file_space_id, hid_t dxpl_id, + const void *buf) +{ + H5VL_object_t *vol_obj = NULL; + herr_t ret_value = SUCCEED; /* Return value */ + + FUNC_ENTER_API(FAIL) + H5TRACE6("e", "iiiii*x", dset_id, mem_type_id, mem_space_id, file_space_id, dxpl_id, buf); + + /* Check arguments */ + if (mem_space_id < 0) + HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "invalid memory dataspace ID") + if (file_space_id < 0) + HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "invalid file dataspace ID") + + /* Get dataset pointer */ + if (NULL == (vol_obj = (H5VL_object_t *)H5I_object_verify(dset_id, H5I_DATASET))) + HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "dset_id is not a dataset ID") + + /* Get the default dataset transfer property list if the user didn't provide one */ + if (H5P_DEFAULT == dxpl_id) + dxpl_id = H5P_DATASET_XFER_DEFAULT; + else if (TRUE != H5P_isa_class(dxpl_id, H5P_DATASET_XFER)) + HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not xfer parms") + + /* Write the data */ + if ((ret_value = H5VL_dataset_write(vol_obj, mem_type_id, mem_space_id, file_space_id, dxpl_id, buf, + H5_REQUEST_NULL)) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "can't write data") + +done: + FUNC_LEAVE_API(ret_value) +} /* end H5Dwrite() */ + +/*------------------------------------------------------------------------- + * Function: H5Dwrite_chunk + * + * Purpose: Writes an entire chunk to the file directly. + * + * Return: Non-negative on success/Negative on failure + * + * Programmer: Raymond Lu + * 30 July 2012 + * + *------------------------------------------------------------------------- + */ +herr_t +H5Dwrite_chunk(hid_t dset_id, hid_t dxpl_id, uint32_t filters, const hsize_t *offset, size_t data_size, + const void *buf) +{ + H5VL_object_t *vol_obj = NULL; + uint32_t data_size_32; /* Chunk data size (limited to 32-bits currently) */ + herr_t ret_value = SUCCEED; /* Return value */ + + FUNC_ENTER_API(FAIL) + H5TRACE6("e", "iiIu*hz*x", dset_id, dxpl_id, filters, offset, data_size, buf); + + /* Check arguments */ + if (NULL == (vol_obj = (H5VL_object_t *)H5I_object_verify(dset_id, H5I_DATASET))) + HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "invalid dataset ID") + if (!buf) + HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "buf cannot be NULL") + if (!offset) + HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "offset cannot be NULL") + if (0 == data_size) + HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "data_size cannot be zero") + + /* Make sure data size is less than 4 GiB */ + data_size_32 = (uint32_t)data_size; + if (data_size != (size_t)data_size_32) + HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "invalid data_size - chunks cannot be > 4 GiB") + + /* Get the default dataset transfer property list if the user didn't provide one */ + if (H5P_DEFAULT == dxpl_id) + dxpl_id = H5P_DATASET_XFER_DEFAULT; + else if (TRUE != H5P_isa_class(dxpl_id, H5P_DATASET_XFER)) + HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "dxpl_id is not a dataset transfer property list ID") + + /* Write chunk */ + if (H5VL_dataset_optional(vol_obj, H5VL_NATIVE_DATASET_CHUNK_WRITE, dxpl_id, H5_REQUEST_NULL, filters, + offset, data_size_32, buf) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "can't write unprocessed chunk data") + +done: + FUNC_LEAVE_API(ret_value) +} /* end H5Dwrite_chunk() */ + +/*------------------------------------------------------------------------- + * Function: H5Dscatter + * + * Purpose: Scatters data provided by the callback op to the + * destination buffer dst_buf, where the dimensions of + * dst_buf and the selection to be scattered to are specified + * by the dataspace dst_space_id. The type of the data to be + * scattered is specified by type_id. + * + * Return: Non-negative on success/Negative on failure + * + * Programmer: Neil Fortner + * 14 Jan 2013 + * + *------------------------------------------------------------------------- + */ +herr_t +H5Dscatter(H5D_scatter_func_t op, void *op_data, hid_t type_id, hid_t dst_space_id, void *dst_buf /*out*/) +{ + H5T_t * type; /* Datatype */ + H5S_t * dst_space; /* Dataspace */ + H5S_sel_iter_t *iter = NULL; /* Selection iteration info*/ + hbool_t iter_init = FALSE; /* Selection iteration info has been initialized */ + const void * src_buf = NULL; /* Source (contiguous) data buffer */ + size_t src_buf_nbytes = 0; /* Size of src_buf */ + size_t type_size; /* Datatype element size */ + hssize_t nelmts; /* Number of remaining elements in selection */ + size_t nelmts_scatter = 0; /* Number of elements to scatter to dst_buf */ + herr_t ret_value = SUCCEED; /* Return value */ + + FUNC_ENTER_API(FAIL) + H5TRACE5("e", "DS*xiix", op, op_data, type_id, dst_space_id, dst_buf); + + /* Check args */ + if (op == NULL) + HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "invalid callback function pointer") + if (NULL == (type = (H5T_t *)H5I_object_verify(type_id, H5I_DATATYPE))) + HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a datatype") + if (NULL == (dst_space = (H5S_t *)H5I_object_verify(dst_space_id, H5I_DATASPACE))) + HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataspace") + if (dst_buf == NULL) + HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "no destination buffer provided") + + /* Get datatype element size */ + if (0 == (type_size = H5T_GET_SIZE(type))) + HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get datatype size") + + /* Get number of elements in dataspace */ + if ((nelmts = (hssize_t)H5S_GET_SELECT_NPOINTS(dst_space)) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTCOUNT, FAIL, "unable to get number of elements in selection") + + /* Allocate the selection iterator */ + if (NULL == (iter = H5FL_MALLOC(H5S_sel_iter_t))) + HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "can't allocate selection iterator") + + /* Initialize selection iterator */ + if (H5S_select_iter_init(iter, dst_space, type_size, 0) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize selection iterator information") + iter_init = TRUE; + + /* Loop until all data has been scattered */ + while (nelmts > 0) { + /* Make callback to retrieve data */ + if (op(&src_buf, &src_buf_nbytes, op_data) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CALLBACK, FAIL, "callback operator returned failure") + + /* Calculate number of elements */ + nelmts_scatter = src_buf_nbytes / type_size; + + /* Check callback results */ + if (!src_buf) + HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "callback did not return a buffer") + if (src_buf_nbytes == 0) + HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "callback returned a buffer size of 0") + if (src_buf_nbytes % type_size) + HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "buffer size is not a multiple of datatype size") + if (nelmts_scatter > (size_t)nelmts) + HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "callback returned more elements than in selection") + + /* Scatter data */ + if (H5D__scatter_mem(src_buf, iter, nelmts_scatter, dst_buf) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTCOPY, FAIL, "scatter failed") + + nelmts -= (hssize_t)nelmts_scatter; + } /* end while */ + +done: + /* Release selection iterator */ + if (iter_init && H5S_SELECT_ITER_RELEASE(iter) < 0) + HDONE_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "Can't release selection iterator") + if (iter) + iter = H5FL_FREE(H5S_sel_iter_t, iter); + + FUNC_LEAVE_API(ret_value) +} /* H5Dscatter() */ + +/*------------------------------------------------------------------------- + * Function: H5Dgather + * + * Purpose: Gathers data provided from the source buffer src_buf to + * contiguous buffer dst_buf, then calls the callback op. + * The dimensions of src_buf and the selection to be gathered + * are specified by the dataspace src_space_id. The type of + * the data to be gathered is specified by type_id. + * + * Return: Non-negative on success/Negative on failure + * + * Programmer: Neil Fortner + * 16 Jan 2013 + * + *------------------------------------------------------------------------- + */ +herr_t +H5Dgather(hid_t src_space_id, const void *src_buf, hid_t type_id, size_t dst_buf_size, void *dst_buf /*out*/, + H5D_gather_func_t op, void *op_data) +{ + H5T_t * type; /* Datatype */ + H5S_t * src_space; /* Dataspace */ + H5S_sel_iter_t *iter = NULL; /* Selection iteration info*/ + hbool_t iter_init = FALSE; /* Selection iteration info has been initialized */ + size_t type_size; /* Datatype element size */ + hssize_t nelmts; /* Number of remaining elements in selection */ + size_t dst_buf_nelmts; /* Number of elements that can fit in dst_buf */ + size_t nelmts_gathered; /* Number of elements gathered from src_buf */ + herr_t ret_value = SUCCEED; /* Return value */ + + FUNC_ENTER_API(FAIL) + H5TRACE7("e", "i*xizxDg*x", src_space_id, src_buf, type_id, dst_buf_size, dst_buf, op, op_data); + + /* Check args */ + if (NULL == (src_space = (H5S_t *)H5I_object_verify(src_space_id, H5I_DATASPACE))) + HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataspace") + if (src_buf == NULL) + HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "no source buffer provided") + if (NULL == (type = (H5T_t *)H5I_object_verify(type_id, H5I_DATATYPE))) + HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a datatype") + if (dst_buf_size == 0) + HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "destination buffer size is 0") + if (dst_buf == NULL) + HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "no destination buffer provided") + + /* Get datatype element size */ + if (0 == (type_size = H5T_GET_SIZE(type))) + HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get datatype size") + + /* Get number of elements in dst_buf_size */ + dst_buf_nelmts = dst_buf_size / type_size; + if (dst_buf_nelmts == 0) + HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, + "destination buffer is not large enough to hold one element") + + /* Get number of elements in dataspace */ + if ((nelmts = (hssize_t)H5S_GET_SELECT_NPOINTS(src_space)) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTCOUNT, FAIL, "unable to get number of elements in selection") + + /* If dst_buf is not large enough to hold all the elements, make sure there + * is a callback */ + if (((size_t)nelmts > dst_buf_nelmts) && (op == NULL)) + HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "no callback supplied and destination buffer too small") + + /* Allocate the selection iterator */ + if (NULL == (iter = H5FL_MALLOC(H5S_sel_iter_t))) + HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "can't allocate selection iterator") + + /* Initialize selection iterator */ + if (H5S_select_iter_init(iter, src_space, type_size, 0) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize selection iterator information") + iter_init = TRUE; + + /* Loop until all data has been scattered */ + while (nelmts > 0) { + /* Gather data */ + if (0 == + (nelmts_gathered = H5D__gather_mem(src_buf, iter, MIN(dst_buf_nelmts, (size_t)nelmts), dst_buf))) + HGOTO_ERROR(H5E_IO, H5E_CANTCOPY, FAIL, "gather failed") + HDassert(nelmts_gathered == MIN(dst_buf_nelmts, (size_t)nelmts)); + + /* Make callback to process dst_buf */ + if (op && op(dst_buf, nelmts_gathered * type_size, op_data) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CALLBACK, FAIL, "callback operator returned failure") + + nelmts -= (hssize_t)nelmts_gathered; + HDassert(op || (nelmts == 0)); + } /* end while */ + +done: + /* Release selection iterator */ + if (iter_init && H5S_SELECT_ITER_RELEASE(iter) < 0) + HDONE_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "Can't release selection iterator") + if (iter) + iter = H5FL_FREE(H5S_sel_iter_t, iter); + + FUNC_LEAVE_API(ret_value) +} /* H5Dgather() */ + +/*-------------------------------------------------------------------------- + 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(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 = (H5S_t *)H5I_object_verify(space_id, H5I_DATASPACE))) + HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, 0, "not a dataspace") + if (NULL == (fill_type = (H5T_t *)H5I_object_verify(fill_type_id, H5I_DATATYPE))) + HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, 0, "not a datatype") + if (NULL == (buf_type = (H5T_t *)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) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTENCODE, FAIL, "filling selection failed") + +done: + FUNC_LEAVE_API(ret_value) +} /* H5Dfill() */ + +/*------------------------------------------------------------------------- * Function: H5Diterate * * Purpose: This routine iterates over all the elements selected in a memory |