/**************************************************************************** * NCSA HDF * * Software Development Group * * National Center for Supercomputing Applications * * University of Illinois at Urbana-Champaign * * 605 E. Springfield, Champaign IL 61820 * * * * For conditions of distribution and use, see the accompanying * * hdf/COPYING file. * * * ****************************************************************************/ #ifdef RCSID static char RcsId[] = "@(#)$Revision$"; #endif /* $Id$ */ #include /* Generic Functions */ #include /* Atoms */ #include /* Cache */ #include /* Dataset functions */ #include /* Error handling */ #include /* Group headers */ #include /* Name heap */ #include /* Meta data */ #include /* File space allocation header */ #include /* Memory management */ #include /* Meta-Object API */ #include /* Object headers */ #include /* Property lists */ #define PABLO_MASK H5D_mask /* * A dataset is the following struct. */ struct H5D_t { H5G_entry_t ent; /*cached object header stuff */ H5T_t *type; /*datatype of this dataset */ H5S_t *space; /*dataspace of this dataset */ H5D_create_t *create_parms; /*creation parameters */ H5O_layout_t layout; /*data layout */ }; /* Default dataset creation property list */ const H5D_create_t H5D_create_dflt = { H5D_CONTIGUOUS, /* Layout */ 1, /* Chunk dimensions */ {1, 1, 1, 1, 1, 1, 1, 1, /* Chunk size. These default values....*/ 1, 1, 1, 1, 1, 1, 1, 1, /*...are quite useless. Larger chunks..*/ 1, 1, 1, 1, 1, 1, 1, 1, /*...produce fewer, but larger I/O......*/ 1, 1, 1, 1, 1, 1, 1, 1}, /*...requests. */ {H5F_ADDR_UNDEF, /* External file list heap address */ 0, /*...slots allocated */ 0, /*...slots used */ NULL} /*...slot array */ }; /* Default dataset transfer property list */ const H5D_xfer_t H5D_xfer_dflt = { 0, /* Place holder - remove this later */ }; /* Interface initialization? */ static hbool_t interface_initialize_g = FALSE; #define INTERFACE_INIT H5D_init_interface static herr_t H5D_init_interface(void); static void H5D_term_interface(void); /*-------------------------------------------------------------------------- NAME H5D_init_interface -- Initialize interface-specific information USAGE herr_t H5D_init_interface() RETURNS SUCCEED/FAIL DESCRIPTION Initializes any interface-specific data or routines. --------------------------------------------------------------------------*/ static herr_t H5D_init_interface(void) { herr_t ret_value = SUCCEED; FUNC_ENTER(H5D_init_interface, FAIL); /* Initialize the atom group for the dataset IDs */ if ((ret_value = H5A_init_group(H5_DATASET, H5A_DATASETID_HASHSIZE, H5D_RESERVED_ATOMS, (herr_t (*)(void *)) H5D_close)) != FAIL) { ret_value = H5_add_exit(H5D_term_interface); } FUNC_LEAVE(ret_value); } /*-------------------------------------------------------------------------- NAME H5D_term_interface PURPOSE Terminate various H5D objects USAGE void H5D_term_interface() RETURNS SUCCEED/FAIL DESCRIPTION Release the atom group and any other resources allocated. GLOBAL VARIABLES COMMENTS, BUGS, ASSUMPTIONS Can't report errors... EXAMPLES REVISION LOG --------------------------------------------------------------------------*/ static void H5D_term_interface(void) { H5A_destroy_group(H5_DATASET); } /*------------------------------------------------------------------------- * Function: H5Dcreate * * Purpose: Creates a new dataset named NAME in file FILE_ID, opens the * dataset for access, and associates with that dataset constant * and initial persistent properties including the type of each * datapoint as stored in the file (TYPE_ID), the size of the * dataset (SPACE_ID), and other initial miscellaneous * properties (CREATE_PARMS_ID). * * All arguments are copied into the dataset, so the caller is * allowed to derive new types, data spaces, and creation * parameters from the old ones and reuse them in calls to * create other datasets. * * Return: Success: The object ID of the new dataset. At this * point, the dataset is ready to receive its * raw data. Attempting to read raw data from * the dataset will probably return the fill * value. The dataset should be closed when * the caller is no longer interested in it. * * Failure: FAIL * * Errors: * ARGS BADTYPE Not a data space. * ARGS BADTYPE Not a dataset creation plist. * ARGS BADTYPE Not a file. * ARGS BADTYPE Not a type. * ARGS BADVALUE No name. * DATASET CANTINIT Can't create dataset. * DATASET CANTREGISTER Can't register dataset. * * Programmer: Robb Matzke * Wednesday, December 3, 1997 * * Modifications: * *------------------------------------------------------------------------- */ hid_t H5Dcreate(hid_t file_id, const char *name, hid_t type_id, hid_t space_id, hid_t create_parms_id) { H5F_t *f = NULL; H5T_t *type = NULL; H5S_t *space = NULL; H5D_t *new_dset = NULL; hid_t ret_value = FAIL; const H5D_create_t *create_parms = NULL; FUNC_ENTER(H5Dcreate, FAIL); /* Check arguments */ if (H5_FILE != H5A_group(file_id) || NULL == (f = H5A_object(file_id))) { HRETURN_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a file"); } if (!name || !*name) { HRETURN_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "no name"); } if (H5_DATATYPE != H5A_group(type_id) || NULL == (type = H5A_object(type_id))) { HRETURN_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a type"); } if (H5_DATASPACE != H5A_group(space_id) || NULL == (space = H5A_object(space_id))) { HRETURN_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a data space"); } if (create_parms_id >= 0) { if (H5P_DATASET_CREATE != H5Pget_class(create_parms_id) || NULL == (create_parms = H5A_object(create_parms_id))) { HRETURN_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset creation property list"); } } else { create_parms = &H5D_create_dflt; } /* build and open the new dataset */ if (NULL == (new_dset = H5D_create(f, name, type, space, create_parms))) { HRETURN_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to create dataset"); } /* Register the new datatype and get an ID for it */ if ((ret_value = H5A_register(H5_DATASET, new_dset)) < 0) { H5D_close(new_dset); HRETURN_ERROR(H5E_DATASET, H5E_CANTREGISTER, FAIL, "unable to register dataset"); } FUNC_LEAVE(ret_value); } /*------------------------------------------------------------------------- * Function: H5Dopen * * Purpose: Finds a dataset named NAME in file FILE_ID, opens it, and * returns its ID. The dataset should be close when the caller * is no longer interested in it. * * Return: Success: A new dataset ID * * Failure: FAIL * * Errors: * ARGS BADTYPE Not a file. * ARGS BADVALUE No name. * DATASET CANTREGISTER Can't register dataset. * DATASET NOTFOUND Dataset not found. * * Programmer: Robb Matzke * Thursday, December 4, 1997 * * Modifications: * *------------------------------------------------------------------------- */ hid_t H5Dopen(hid_t file_id, const char *name) { H5F_t *file = NULL; /*file holding the dataset */ H5D_t *dataset = NULL; /*the dataset */ hid_t ret_value = FAIL; FUNC_ENTER(H5Dopen, FAIL); /* Check args */ if (H5_FILE != H5A_group(file_id) || NULL == (file = H5A_object(file_id))) { HRETURN_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a file"); } if (!name || !*name) { HRETURN_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "no name"); } /* Find the dataset */ if (NULL == (dataset = H5D_open(file, name))) { HRETURN_ERROR(H5E_DATASET, H5E_NOTFOUND, FAIL, "dataset not found"); } /* Create an atom for the dataset */ if ((ret_value = H5A_register(H5_DATASET, dataset)) < 0) { H5D_close(dataset); HRETURN_ERROR(H5E_DATASET, H5E_CANTREGISTER, FAIL, "can't register dataset"); } FUNC_LEAVE(ret_value); } /*------------------------------------------------------------------------- * Function: H5Dclose * * Purpose: Closes access to a dataset (DATASET_ID) and releases * resources used by it. It is illegal to subsequently use that * same dataset ID in calls to other dataset functions. * * Return: Success: SUCCEED * * Failure: FAIL * * Errors: * ARGS BADTYPE Not a dataset. * DATASET CANTINIT Can't free. * * Programmer: Robb Matzke * Thursday, December 4, 1997 * * Modifications: * *------------------------------------------------------------------------- */ herr_t H5Dclose(hid_t dataset_id) { H5D_t *dataset = NULL; /* dataset object to release */ FUNC_ENTER(H5Dclose, FAIL); /* Check args */ if (H5_DATASET != H5A_group(dataset_id) || NULL == (dataset = H5A_object(dataset_id)) || NULL == dataset->ent.file) { HRETURN_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset"); } /* * Decrement the counter on the dataset. It will be freed if the count * reaches zero. */ if (H5A_dec_ref(dataset_id) < 0) { HRETURN_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "can't free"); } FUNC_LEAVE(SUCCEED); } /*------------------------------------------------------------------------- * Function: H5Dget_space * * Purpose: Returns a copy of the file data space for a dataset. * * Return: Success: ID for a copy of the data space. The data * space should be released by calling * H5Sclose(). * * Failure: FAIL * * Programmer: Robb Matzke * Wednesday, January 28, 1998 * * Modifications: * *------------------------------------------------------------------------- */ hid_t H5Dget_space (hid_t dataset_id) { H5D_t *dataset = NULL; H5S_t *copied_space = NULL; hid_t ret_value = FAIL; FUNC_ENTER (H5Dget_space, FAIL); /* Check args */ if (H5_DATASET!=H5A_group (dataset_id) || NULL==(dataset=H5A_object (dataset_id))) { HRETURN_ERROR (H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset"); } /* Copy the data space */ if (NULL==(copied_space=H5S_copy (dataset->space))) { HRETURN_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to copy the data space"); } /* Create an atom */ if ((ret_value=H5A_register (H5_DATASPACE, copied_space))<0) { HRETURN_ERROR (H5E_ATOM, H5E_CANTREGISTER, FAIL, "unable to register data space"); } FUNC_LEAVE (ret_value); } /*------------------------------------------------------------------------- * Function: H5Dget_type * * Purpose: Returns a copy of the file data type for a dataset. * * Return: Success: ID for a copy of the data type. The data * type should be released by calling * H5Tclose(). * * Failure: FAIL * * Programmer: Robb Matzke * Tuesday, February 3, 1998 * * Modifications: * *------------------------------------------------------------------------- */ hid_t H5Dget_type (hid_t dataset_id) { H5D_t *dataset = NULL; H5T_t *copied_type = NULL; hid_t ret_value = FAIL; FUNC_ENTER (H5Dget_type, FAIL); /* Check args */ if (H5_DATASET!=H5A_group (dataset_id) || NULL==(dataset=H5A_object (dataset_id))) { HRETURN_ERROR (H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset"); } /* Copy the data type */ if (NULL==(copied_type=H5T_copy (dataset->type))) { HRETURN_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to copy the data type"); } /* Create an atom */ if ((ret_value=H5A_register (H5_DATATYPE, copied_type))<0) { HRETURN_ERROR (H5E_ATOM, H5E_CANTREGISTER, FAIL, "unable to register data type"); } FUNC_LEAVE (ret_value); } /*------------------------------------------------------------------------- * Function: H5Dget_create_plist * * Purpose: Returns a copy of the dataset creation property list. * * Return: Success: ID for a copy of the dataset creation * property list. The template should be * released by calling H5Pclose(). * * Failure: FAIL * * Programmer: Robb Matzke * Tuesday, February 3, 1998 * * Modifications: * *------------------------------------------------------------------------- */ hid_t H5Dget_create_plist (hid_t dataset_id) { H5D_t *dataset = NULL; H5D_create_t *copied_parms = NULL; hid_t ret_value = FAIL; FUNC_ENTER (H5Dget_create_plist, FAIL); /* Check args */ if (H5_DATASET!=H5A_group (dataset_id) || NULL==(dataset=H5A_object (dataset_id))) { HRETURN_ERROR (H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset"); } /* Copy the creation property list */ if (NULL==(copied_parms=H5P_copy (H5P_DATASET_CREATE, dataset->create_parms))) { HRETURN_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to copy the creation property list"); } /* Create an atom */ if ((ret_value=H5A_register ((group_t)(H5_TEMPLATE_0+H5P_DATASET_CREATE), copied_parms))<0) { HRETURN_ERROR (H5E_ATOM, H5E_CANTREGISTER, FAIL, "unable to register creation property list"); } FUNC_LEAVE (ret_value); } /*------------------------------------------------------------------------- * Function: H5Dread * * Purpose: Reads (part of) a DATASET 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 XFER_PARMS_ID argument. * * The FILE_SPACE_ID can be the constant H5S_ALL which indicates * that the entire file data space is to be referenced. * * The MEM_SPACE_ID can be the constant H5S_ALL in which case * the memory data space is the same as the file data space * defined when the dataset was created. * * The number of elements in the memory data space must match * the number of elements in the file data space. * * The XFER_PARMS_ID can be the constant H5P_DEFAULT in which * case the default data transfer properties are used. * * Return: Success: SUCCEED * * Failure: FAIL * * Errors: * ARGS BADTYPE Not a data space. * ARGS BADTYPE Not a data type. * ARGS BADTYPE Not a dataset. * ARGS BADTYPE Not xfer parms. * ARGS BADVALUE No output buffer. * DATASET READERROR Can't read data. * * Programmer: Robb Matzke * Thursday, December 4, 1997 * * Modifications: * *------------------------------------------------------------------------- */ herr_t H5Dread(hid_t dataset_id, hid_t mem_type_id, hid_t mem_space_id, hid_t file_space_id, hid_t xfer_parms_id, void *buf/*out*/) { H5D_t *dataset = NULL; const H5T_t *mem_type = NULL; const H5S_t *mem_space = NULL; const H5S_t *file_space = NULL; const H5D_xfer_t *xfer_parms = NULL; FUNC_ENTER(H5Dread, FAIL); /* check arguments */ if (H5_DATASET != H5A_group(dataset_id) || NULL == (dataset = H5A_object(dataset_id)) || NULL == dataset->ent.file) { HRETURN_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset"); } if (H5_DATATYPE != H5A_group(mem_type_id) || NULL == (mem_type = H5A_object(mem_type_id))) { HRETURN_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a data type"); } if (H5S_ALL != mem_space_id) { if (H5_DATASPACE != H5A_group(mem_space_id) || NULL == (mem_space = H5A_object(mem_space_id))) { HRETURN_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a data space"); } } if (H5S_ALL != file_space_id) { if (H5_DATASPACE != H5A_group(file_space_id) || NULL == (file_space = H5A_object(file_space_id))) { HRETURN_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a data space"); } } if (H5P_DEFAULT == xfer_parms_id) { xfer_parms = &H5D_xfer_dflt; } else if (H5P_DATASET_XFER != H5Pget_class(xfer_parms_id) || NULL == (xfer_parms = H5A_object(xfer_parms_id))) { HRETURN_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not xfer parms"); } if (!buf) { HRETURN_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "no output buffer"); } /* read raw data */ if (H5D_read(dataset, mem_type, mem_space, file_space, xfer_parms, buf/*out*/) < 0) { HRETURN_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "can't read data"); } FUNC_LEAVE(SUCCEED); } /*------------------------------------------------------------------------- * Function: H5Dwrite * * Purpose: Writes (part of) a DATASET 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 data type. Additional miscellaneous data transfer * properties can be passed to this function with the * XFER_PARMS_ID argument. * * The FILE_SPACE_ID can be the constant H5S_ALL which indicates * that the entire file data space is to be referenced. * * The MEM_SPACE_ID can be the constant H5S_ALL in which case * the memory data space is the same as the file data space * defined when the dataset was created. * * The number of elements in the memory data space must match * the number of elements in the file data space. * * The XFER_PARMS_ID can be the constant H5P_DEFAULT in which * case the default data transfer properties are used. * * Return: Success: SUCCEED * * Failure: FAIL * * Errors: * * Programmer: Robb Matzke * Thursday, December 4, 1997 * * Modifications: * *------------------------------------------------------------------------- */ herr_t H5Dwrite(hid_t dataset_id, hid_t mem_type_id, hid_t mem_space_id, hid_t file_space_id, hid_t xfer_parms_id, const void *buf) { H5D_t *dataset = NULL; const H5T_t *mem_type = NULL; const H5S_t *mem_space = NULL; const H5S_t *file_space = NULL; const H5D_xfer_t *xfer_parms = NULL; FUNC_ENTER(H5Dwrite, FAIL); /* check arguments */ if (H5_DATASET != H5A_group(dataset_id) || NULL == (dataset = H5A_object(dataset_id)) || NULL == dataset->ent.file) { HRETURN_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset"); } if (H5_DATATYPE != H5A_group(mem_type_id) || NULL == (mem_type = H5A_object(mem_type_id))) { HRETURN_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a data type"); } if (H5S_ALL != mem_space_id) { if (H5_DATASPACE != H5A_group(mem_space_id) || NULL == (mem_space = H5A_object(mem_space_id))) { HRETURN_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a data space"); } } if (H5S_ALL != file_space_id) { if (H5_DATASPACE != H5A_group(file_space_id) || NULL == (file_space = H5A_object(file_space_id))) { HRETURN_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a data space"); } } if (H5P_DEFAULT == xfer_parms_id) { xfer_parms = &H5D_xfer_dflt; } else if (H5P_DATASET_XFER != H5Pget_class(xfer_parms_id) || NULL == (xfer_parms = H5A_object(xfer_parms_id))) { HRETURN_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not xfer parms"); } if (!buf) { HRETURN_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "no output buffer"); } /* write raw data */ if (H5D_write(dataset, mem_type, mem_space, file_space, xfer_parms, buf) < 0) { HRETURN_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "can't write data"); } FUNC_LEAVE(SUCCEED); } /*------------------------------------------------------------------------- * Function: H5Dextend * * Purpose: This function makes sure that the dataset is at least of size * SIZE. The dimensionality of SIZE is the same as the data * space of the dataset being changed. * * Return: Success: SUCCEED * * Failure: FAIL * * Programmer: Robb Matzke * Friday, January 30, 1998 * * Modifications: * *------------------------------------------------------------------------- */ herr_t H5Dextend (hid_t dataset_id, const size_t *size) { H5D_t *dataset = NULL; FUNC_ENTER (H5Dextend, FAIL); /* Check args */ if (H5_DATASET!=H5A_group (dataset_id) || NULL==(dataset=H5A_object (dataset_id))) { HRETURN_ERROR (H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset"); } if (!size) { HRETURN_ERROR (H5E_ARGS, H5E_BADVALUE, FAIL, "no size specified"); } /* Increase size */ if (H5D_extend (dataset, size)<0) { HRETURN_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to extend dataset"); } FUNC_LEAVE (SUCCEED); } /*------------------------------------------------------------------------- * Function: H5D_find_name * * Purpose: This is a callback for H5Mfind_name(). It does the same * thing as H5Dopen() except it takes an extra argument which * isn't used. * * Return: Success: SUCCEED * * Failure: FAIL * * Errors: * * Programmer: Robb Matzke * Thursday, December 4, 1997 * * Modifications: * *------------------------------------------------------------------------- */ hid_t H5D_find_name(hid_t file_id, group_t UNUSED, const char *name) { return H5Dopen(file_id, name); } /*------------------------------------------------------------------------- * Function: H5D_create * * Purpose: Creates a new dataset with name NAME in file F and associates * with it a datatype TYPE for each element as stored in the * file, dimensionality information or dataspace SPACE, and * other miscellaneous properties CREATE_PARMS. All arguments * are deep-copied before being associated with the new dataset, * so the caller is free to subsequently modify them without * affecting the dataset. * * Return: Success: Pointer to a new dataset * * Failure: NULL * * Errors: * DATASET CANTINIT Can't update dataset header. * DATASET CANTINIT Problem with the dataset name. * * Programmer: Robb Matzke * Thursday, December 4, 1997 * * Modifications: * *------------------------------------------------------------------------- */ H5D_t * H5D_create(H5F_t *f, const char *name, const H5T_t *type, const H5S_t *space, const H5D_create_t *create_parms) { H5D_t *new_dset = NULL; H5D_t *ret_value = NULL; intn i, ndims; size_t max_dim[H5O_LAYOUT_NDIMS]; H5O_efl_t *efl = NULL; FUNC_ENTER(H5D_create, NULL); /* check args */ assert(f); assert(name && *name); assert(type); assert(space); assert(create_parms); /* Initialize the dataset object */ new_dset = H5MM_xcalloc(1, sizeof(H5D_t)); H5F_addr_undef(&(new_dset->ent.header)); new_dset->type = H5T_copy(type); new_dset->space = H5S_copy(space); new_dset->create_parms = H5P_copy (H5P_DATASET_CREATE, create_parms); efl = &(new_dset->create_parms->efl); /* Total raw data size */ new_dset->layout.type = new_dset->create_parms->layout; new_dset->layout.ndims = H5S_get_ndims(space) + 1; assert(new_dset->layout.ndims <= NELMTS(new_dset->layout.dim)); new_dset->layout.dim[new_dset->layout.ndims - 1] = H5T_get_size(type); switch (new_dset->create_parms->layout) { case H5D_CONTIGUOUS: /* * The maximum size of the dataset cannot exceed the storage size. * Also, only the slowest varying dimension of a simple data space * can be extendible. */ if ((ndims=H5S_get_dims(space, new_dset->layout.dim, max_dim)) < 0) { HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "unable to initialize contiguous storage"); } for (i=1; inew_dset->layout.dim[i]) { HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, NULL, "only the first dimension can be extendible"); } } if (efl->nused>0) { size_t max_points = H5S_get_npoints_max (space); size_t max_storage = H5O_efl_total_size (efl); if (H5S_UNLIMITED==max_points) { if (H5O_EFL_UNLIMITED!=max_storage) { HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, NULL, "unlimited data space but finite storage"); } } else if (max_points * H5T_get_size (type) < max_points) { HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, NULL, "data space * type size overflowed"); } else if (max_points * H5T_get_size (type) > max_storage) { HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, NULL, "data space size exceeds external storage size"); } } else if (max_dim[0]>new_dset->layout.dim[0]) { HGOTO_ERROR (H5E_DATASET, H5E_UNSUPPORTED, NULL, "extendible contiguous non-external dataset"); } break; case H5D_CHUNKED: /* * Chunked storage allows any type of data space extension, so we * don't even bother checking. */ if (new_dset->create_parms->chunk_ndims != H5S_get_ndims(space)) { HGOTO_ERROR(H5E_DATASET, H5E_BADVALUE, NULL, "dimensionality of chunks doesn't match the data space"); } if (efl->nused>0) { HGOTO_ERROR (H5E_DATASET, H5E_BADVALUE, NULL, "external storage not supported with chunked layout"); } for (i = 0; i < new_dset->layout.ndims - 1; i++) { new_dset->layout.dim[i] = new_dset->create_parms->chunk_size[i]; } break; default: HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, NULL, "not implemented yet"); } /* Create (open for write access) an object header */ if (H5O_create(f, 0, &(new_dset->ent)) < 0) { HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "unable to create dataset object header"); } /* Update the type and space header messages */ if (H5O_modify(&(new_dset->ent), H5O_DTYPE, 0, H5O_FLAG_CONSTANT, new_dset->type) < 0 || H5S_modify(&(new_dset->ent), new_dset->space) < 0) { HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "can't update type or space header messages"); } /* * Initialize storage. We assume that external storage is already * initialized by the caller, or at least will be before I/O is * performed. */ if (0==efl->nused) { if (H5F_arr_create(f, &(new_dset->layout)) < 0) { HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "unable to initialize storage"); } } else { H5F_addr_undef (&(new_dset->layout.addr)); } /* Update layout message */ if (H5O_modify (&(new_dset->ent), H5O_LAYOUT, 0, H5O_FLAG_CONSTANT, &(new_dset->layout)) < 0) { HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, NULL, "unable to update layout message"); } /* Update external storage message */ if (efl->nused>0) { size_t heap_size = H5H_ALIGN (1); for (i=0; inused; i++) { heap_size += H5H_ALIGN (strlen (efl->slot[i].name)+1); } if (H5H_create (f, H5H_LOCAL, heap_size, &(efl->heap_addr))<0 || (size_t)(-1)==H5H_insert (f, &(efl->heap_addr), 1, "")) { HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, NULL, "unable to create external file list name heap"); } if (H5O_modify (&(new_dset->ent), H5O_EFL, 0, H5O_FLAG_CONSTANT, efl)<0) { HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, NULL, "unable to update external file list message"); } } /* Give the dataset a name */ if (H5G_insert(name, &(new_dset->ent)) < 0) { HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "unable to name dataset"); } /* Success */ ret_value = new_dset; done: if (!ret_value && new_dset) { if (new_dset->type) H5T_close(new_dset->type); if (new_dset->space) H5S_close(new_dset->space); if (new_dset->create_parms) { H5P_close (H5P_DATASET_CREATE, new_dset->create_parms); new_dset->create_parms = NULL; } if (H5F_addr_defined(&(new_dset->ent.header))) { H5O_close(&(new_dset->ent)); } new_dset->ent.file = NULL; H5MM_xfree(new_dset); } FUNC_LEAVE(ret_value); } /*------------------------------------------------------------------------- * Function: H5D_open * * Purpose: Finds a dataset named NAME in file F and builds a descriptor * for it, opening it for access. * * Return: Success: Pointer to a new dataset descriptor. * * Failure: NULL * * Errors: * * Programmer: Robb Matzke * Thursday, December 4, 1997 * * Modifications: * *------------------------------------------------------------------------- */ H5D_t * H5D_open(H5F_t *f, const char *name) { H5D_t *dataset = NULL; /*the dataset which was found */ H5D_t *ret_value = NULL; /*return value */ intn i; FUNC_ENTER(H5D_open, NULL); /* check args */ assert(f); assert(name && *name); dataset = H5MM_xcalloc(1, sizeof(H5D_t)); dataset->create_parms = H5P_copy (H5P_DATASET_CREATE, &H5D_create_dflt); H5F_addr_undef(&(dataset->ent.header)); /* Open the dataset object */ if (H5G_find(f, name, NULL, &(dataset->ent)) < 0) { HGOTO_ERROR(H5E_DATASET, H5E_NOTFOUND, NULL, "not found"); } if (H5O_open(f, &(dataset->ent)) < 0) { HGOTO_ERROR(H5E_DATASET, H5E_CANTOPENOBJ, NULL, "unable to open"); } /* Get the type and space */ if (NULL==(dataset->type=H5O_read(&(dataset->ent), H5O_DTYPE, 0, NULL)) || NULL==(dataset->space=H5S_read(f, &(dataset->ent)))) { HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "unable to load type or space info from dataset header"); } /* * Get the raw data layout info. It's actually stored in two locations: * the storage message of the dataset (dataset->storage) and certain * values are copied to the dataset create plist so the user can query * them. */ if (NULL==H5O_read(&(dataset->ent), H5O_LAYOUT, 0, &(dataset->layout))) { HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "unable to read data layout message"); } switch (dataset->layout.type) { case H5D_CONTIGUOUS: dataset->create_parms->layout = H5D_CONTIGUOUS; break; case H5D_CHUNKED: /* * Chunked storage. The creation plist's dimension is one less than * the chunk dimension because the chunk includes a dimension for the * individual bytes of the data type. */ dataset->create_parms->layout = H5D_CHUNKED; dataset->create_parms->chunk_ndims = dataset->layout.ndims - 1; for (i = 0; i < dataset->layout.ndims - 1; i++) { dataset->create_parms->chunk_size[i] = dataset->layout.dim[i]; } break; default: assert("not implemented yet" && 0); HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, NULL, "not implemented yet"); } /* Get the external file list message, which might not exist */ if (NULL==H5O_read (&(dataset->ent), H5O_EFL, 0, &(dataset->create_parms->efl)) && !H5F_addr_defined (&(dataset->layout.addr))) { HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, NULL, "storage address is undefined an no external file list"); } /* Success */ ret_value = dataset; done: if (!ret_value && dataset) { if (H5F_addr_defined(&(dataset->ent.header))) { H5O_close(&(dataset->ent)); } if (dataset->type) { H5T_close(dataset->type); } if (dataset->space) { H5S_close(dataset->space); } if (dataset->create_parms) { H5P_close (H5P_DATASET_CREATE, dataset->create_parms); } dataset->ent.file = NULL; H5MM_xfree(dataset); } FUNC_LEAVE(ret_value); } /*------------------------------------------------------------------------- * Function: H5D_close * * Purpose: Insures that all data has been saved to the file, closes the * dataset object header, and frees all resources used by the * descriptor. * * Return: Success: SUCCEED * * Failure: FAIL * * Errors: * DATASET CANTINIT Couldn't free the type or space, * but the dataset was freed anyway. * * Programmer: Robb Matzke * Thursday, December 4, 1997 * * Modifications: * *------------------------------------------------------------------------- */ herr_t H5D_close(H5D_t *dataset) { uintn free_failed; FUNC_ENTER(H5D_close, FAIL); /* check args */ assert(dataset && dataset->ent.file); /* * Release dataset type and space - there isn't much we can do if one of * these fails, so we just continue. */ free_failed = (H5T_close(dataset->type) < 0 || H5S_close(dataset->space) < 0 || H5P_close (H5P_DATASET_CREATE, dataset->create_parms)); /* Close the dataset object */ H5O_close(&(dataset->ent)); /* * Free memory. Before freeing the memory set the file pointer to NULL. * We always check for a null file pointer in other H5D functions to be * sure we're not accessing an already freed dataset (see the assert() * above). */ dataset->ent.file = NULL; H5MM_xfree(dataset); if (free_failed) { HRETURN_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "couldn't free the type or space, but the dataset was " "freed anyway."); } FUNC_LEAVE(SUCCEED); } /*------------------------------------------------------------------------- * Function: H5D_read * * Purpose: Reads (part of) a DATASET into application memory BUF. See * H5Dread() for complete details. * * Return: Success: SUCCEED * * Failure: FAIL * * Programmer: Robb Matzke * Thursday, December 4, 1997 * * Modifications: * *------------------------------------------------------------------------- */ herr_t H5D_read(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space, const H5S_t *file_space, const H5D_xfer_t *xfer_parms, void *buf/*out*/) { size_t nelmts ; /*number of elements */ uint8 *tconv_buf = NULL; /*data type conv buffer */ uint8 *bkg_buf = NULL; /*background buffer */ H5T_conv_t tconv_func = NULL; /*conversion function */ hid_t src_id = -1, dst_id = -1;/*temporary type atoms */ const H5S_conv_t *sconv_func = NULL; /*space conversion funcs*/ H5S_number_t numbering; /*element numbering info*/ H5T_cdata_t *cdata = NULL; /*type conversion data */ herr_t ret_value = FAIL; FUNC_ENTER(H5D_read, FAIL); /* check args */ assert(dataset && dataset->ent.file); assert(mem_type); assert(xfer_parms); assert(buf); if (!file_space) file_space = dataset->space; if (!mem_space) mem_space = file_space; /* * Convert data types to atoms because the conversion functions are * application-level functions. */ if ((src_id = H5A_register(H5_DATATYPE, H5T_copy(dataset->type))) < 0 || (dst_id = H5A_register(H5_DATATYPE, H5T_copy(mem_type))) < 0) { HGOTO_ERROR(H5E_DATASET, H5E_CANTREGISTER, FAIL, "unable to register types for conversion"); } /* * Locate the type conversion function and data space conversion * functions, and set up the element numbering information. */ if (NULL == (tconv_func = H5T_find(dataset->type, mem_type, &cdata))) { HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, FAIL, "unable to convert between src and dest data types"); } if (NULL==(sconv_func=H5S_find (mem_space, file_space))) { HGOTO_ERROR (H5E_DATASET, H5E_UNSUPPORTED, FAIL, "unable to convert from file to memory data space"); } if (sconv_func->init && (sconv_func->init)(&(dataset->layout), mem_space, file_space, &numbering/*out*/)<=0) { HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize element numbering information"); } else { HDmemset (&numbering, 0, sizeof numbering); } if (H5S_get_npoints (mem_space)!=H5S_get_npoints (file_space)) { HGOTO_ERROR (H5E_ARGS, H5E_BADVALUE, FAIL, "src and dest data spaces have different sizes"); } /* * Compute the size of the request and allocate scratch buffers. */ nelmts = H5S_get_npoints(mem_space); #ifndef LATER /* * Note: this prototype version allocates a buffer large enough to * satisfy the entire request; strip mining is not implemented. */ { size_t src_size = nelmts * H5T_get_size(dataset->type); size_t dst_size = nelmts * H5T_get_size(mem_type); tconv_buf = H5MM_xmalloc(MAX(src_size, dst_size)); if (cdata->need_bkg) bkg_buf = H5MM_xmalloc (dst_size); } #endif /* * Gather the data from disk into the data type conversion buffer. Also * gather data from application to background buffer (this step is not * needed for most conversions, but we leave that as an exercise for * later ;-) */ if ((sconv_func->fgath)(dataset->ent.file, &(dataset->layout), &(dataset->create_parms->efl), H5T_get_size (dataset->type), file_space, &numbering, 0, nelmts, tconv_buf/*out*/)!=nelmts) { HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "file gather failed"); } if (H5T_BKG_YES==cdata->need_bkg) { if ((sconv_func->mgath)(buf, H5T_get_size (mem_type), mem_space, &numbering, 0, nelmts, bkg_buf/*out*/)!=nelmts) { HGOTO_ERROR (H5E_IO, H5E_READERROR, FAIL, "mem gather failed"); } } /* * Perform data type conversion. */ cdata->command = H5T_CONV_CONV; cdata->ncalls++; if ((tconv_func) (src_id, dst_id, cdata, nelmts, tconv_buf, bkg_buf)<0) { HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "data type conversion failed"); } cdata->nelmts += nelmts; /* * Scatter the data into memory. */ if ((sconv_func->mscat)(tconv_buf, H5T_get_size (mem_type), mem_space, &numbering, 0, nelmts, buf/*out*/)<0) { HGOTO_ERROR (H5E_IO, H5E_READERROR, FAIL, "scatter failed"); } ret_value = SUCCEED; done: if (src_id >= 0) H5A_dec_ref(src_id); if (dst_id >= 0) H5A_dec_ref(dst_id); tconv_buf = H5MM_xfree(tconv_buf); bkg_buf = H5MM_xfree (bkg_buf); FUNC_LEAVE(ret_value); } /*------------------------------------------------------------------------- * Function: H5D_write * * Purpose: Writes (part of) a DATASET to a file from application memory * BUF. See H5Dwrite() for complete details. * * Return: Success: SUCCEED * * Failure: FAIL * * Programmer: Robb Matzke * Thursday, December 4, 1997 * * Modifications: * *------------------------------------------------------------------------- */ herr_t H5D_write(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space, const H5S_t *file_space, const H5D_xfer_t *xfer_parms, const void *buf) { size_t nelmts; uint8 *tconv_buf = NULL; /*data type conv buffer */ uint8 *bkg_buf = NULL; /*background buffer */ H5T_conv_t tconv_func = NULL; /*conversion function */ hid_t src_id = -1, dst_id = -1;/*temporary type atoms */ const H5S_conv_t *sconv_func = NULL; /*space conversion funcs*/ H5S_number_t numbering; /*element numbering info*/ H5T_cdata_t *cdata = NULL; /*type conversion data */ herr_t ret_value = FAIL; FUNC_ENTER(H5D_write, FAIL); /* check args */ assert(dataset && dataset->ent.file); assert(mem_type); assert(xfer_parms); assert(buf); if (!file_space) file_space = dataset->space; if (!mem_space) mem_space = file_space; /* * Convert data types to atoms because the conversion functions are * application-level functions. */ if ((src_id = H5A_register(H5_DATATYPE, H5T_copy(mem_type)))<0 || (dst_id = H5A_register(H5_DATATYPE, H5T_copy(dataset->type)))<0) { HGOTO_ERROR(H5E_DATASET, H5E_CANTREGISTER, FAIL, "unable to register types for conversion"); } /* * Locate the type conversion function and data space conversion * functions, and set up the element numbering information. */ if (NULL == (tconv_func = H5T_find(mem_type, dataset->type, &cdata))) { HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, FAIL, "unable to convert between src and dest data types"); } if (NULL==(sconv_func=H5S_find (mem_space, file_space))) { HGOTO_ERROR (H5E_DATASET, H5E_UNSUPPORTED, FAIL, "unable to convert from memory to file data space"); } if (sconv_func->init && (sconv_func->init)(&(dataset->layout), mem_space, file_space, &numbering/*out*/)<=0) { HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize element numbering information"); } else { HDmemset (&numbering, 0, sizeof numbering); } if (H5S_get_npoints (mem_space)!=H5S_get_npoints (file_space)) { HGOTO_ERROR (H5E_ARGS, H5E_BADVALUE, FAIL, "src and dest data spaces have different sizes"); } /* * Compute the size of the request and allocate scratch buffers. */ nelmts = H5S_get_npoints(mem_space); #ifndef LATER /* * Note: This prototype version allocates a buffer large enough to * satisfy the entire request; strip mining is not implemented. */ { size_t src_size = nelmts * H5T_get_size(mem_type); size_t dst_size = nelmts * H5T_get_size(dataset->type); tconv_buf = H5MM_xmalloc(MAX(src_size, dst_size)); if (cdata->need_bkg) bkg_buf = H5MM_xmalloc (dst_size); } #endif /* * Gather data from application buffer into the data type conversion * buffer. Also gather data from the file into the background buffer * (this step is not needed for most conversions, but we leave that as an * exercise for later ;-) */ if ((sconv_func->mgath)(buf, H5T_get_size (mem_type), mem_space, &numbering, 0, nelmts, tconv_buf/*out*/)!=nelmts) { HGOTO_ERROR (H5E_IO, H5E_WRITEERROR, FAIL, "mem gather failed"); } if (H5T_BKG_YES==cdata->need_bkg) { if ((sconv_func->fgath)(dataset->ent.file, &(dataset->layout), &(dataset->create_parms->efl), H5T_get_size (dataset->type), file_space, &numbering, 0, nelmts, bkg_buf/*out*/)!=nelmts) { HGOTO_ERROR (H5E_IO, H5E_WRITEERROR, FAIL, "file gather failed"); } } /* * Perform data type conversion. */ cdata->command = H5T_CONV_CONV; cdata->ncalls++; if ((tconv_func) (src_id, dst_id, cdata, nelmts, tconv_buf, bkg_buf)<0) { HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "data type conversion failed"); } cdata->nelmts += nelmts; /* * Scatter the data out to the file. */ if ((sconv_func->fscat)(dataset->ent.file, &(dataset->layout), &(dataset->create_parms->efl), H5T_get_size (dataset->type), file_space, &numbering, 0, nelmts, tconv_buf)<0) { HGOTO_ERROR (H5E_DATASET, H5E_WRITEERROR, FAIL, "scatter failed"); } ret_value = SUCCEED; done: if (src_id >= 0) H5A_dec_ref(src_id); if (dst_id >= 0) H5A_dec_ref(dst_id); tconv_buf = H5MM_xfree(tconv_buf); bkg_buf = H5MM_xfree (bkg_buf); FUNC_LEAVE(ret_value); } /*------------------------------------------------------------------------- * Function: H5D_extend * * Purpose: Increases the size of a dataset. * * Return: Success: SUCCEED * * Failure: FAIL * * Programmer: Robb Matzke * Friday, January 30, 1998 * * Modifications: * *------------------------------------------------------------------------- */ herr_t H5D_extend (H5D_t *dataset, const size_t *size) { herr_t changed; FUNC_ENTER (H5D_extend, FAIL); /* Check args */ assert (dataset); assert (size); /* * Restrictions on extensions were checked when the dataset was created. * All extensions are allowed here since none should be able to muck * things up. */ /*void*/ /* Increase the size of the data space */ if ((changed=H5S_extend (dataset->space, size))<0) { HRETURN_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to increase size of data space"); } /* Save the new dataspace in the file if necessary */ if (changed>0 && H5S_modify (&(dataset->ent), dataset->space)<0) { HRETURN_ERROR (H5E_DATASET, H5E_WRITEERROR, FAIL, "unable to update file with new dataspace"); } FUNC_LEAVE (SUCCEED); }