/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * 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://hdf.ncsa.uiuc.edu/HDF5/doc/Copyright.html. If you do not have * * access to either file, you may request a copy from hdfhelp@ncsa.uiuc.edu. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ #define H5D_PACKAGE /*suppress error about including H5Dpkg */ #ifdef H5_HAVE_FPHDF5 #define H5F_PACKAGE /*suppress error about including H5Fpkg */ #endif /* H5_HAVE_FPHDF5 */ /* Pablo information */ /* (Put before include files to avoid problems with inline functions) */ #define PABLO_MASK H5D_mask #include "H5private.h" /* Generic Functions */ #include "H5Dpkg.h" /* Datasets */ #include "H5Eprivate.h" /* Error handling */ #ifdef H5_HAVE_FPHDF5 #include "H5Fpkg.h" /* Files access */ #endif /* H5_HAVE_FPHDF5 */ #include "H5FDprivate.h" /* File drivers */ #include "H5FLprivate.h" /* Free Lists */ #include "H5FOprivate.h" /* File objects */ #include "H5HLprivate.h" /* Local heaps */ #include "H5Iprivate.h" /* IDs */ #include "H5MMprivate.h" /* Memory management */ #include "H5Sprivate.h" /* Dataspaces */ #include "H5Vprivate.h" /* Vectors and arrays */ #ifdef H5_HAVE_FPHDF5 #include "H5FPprivate.h" /* Flexible PHDF5 */ #endif /* H5_HAVE_FPHDF5 */ /*#define H5D_DEBUG*/ /* Interface initialization */ static int interface_initialize_g = 0; #define INTERFACE_INIT H5D_init_interface /* Local functions */ static herr_t H5D_init_interface(void); static herr_t H5D_init_storage(H5D_t *dataset, hbool_t full_overwrite, hid_t dxpl_id); static H5D_t * H5D_new(hid_t dcpl_id, hbool_t creating, hbool_t vl_type); static H5D_t * H5D_create(H5G_entry_t *loc, const char *name, hid_t type_id, const H5S_t *space, hid_t dcpl_id, hid_t dxpl_id); static H5D_t * H5D_open_oid(const H5G_entry_t *ent, hid_t dxpl_id); static herr_t H5D_get_space_status(const H5D_t *dset, H5D_space_status_t *allocation, hid_t dxpl_id); static hsize_t H5D_get_storage_size(const H5D_t *dset, hid_t dxpl_id); static haddr_t H5D_get_offset(const H5D_t *dset); static herr_t H5D_extend(H5D_t *dataset, const hsize_t *size, hid_t dxpl_id); static herr_t H5D_set_extent(H5D_t *dataset, const hsize_t *size, hid_t dxpl_id); static herr_t H5D_close(H5D_t *dataset); /* Internal data structure for computing variable-length dataset's total size */ typedef struct { hid_t dataset_id; /* ID of the dataset we are working on */ hid_t fspace_id; /* ID of the file dataset's dataspace we are working on */ hid_t mspace_id; /* ID of the memory dataset's dataspace we are working on */ void *fl_tbuf; /* Ptr to the temporary buffer we are using for fixed-length data */ void *vl_tbuf; /* Ptr to the temporary buffer we are using for VL data */ hid_t xfer_pid; /* ID of the dataset xfer property list */ hsize_t size; /* Accumulated number of bytes for the selection */ } H5D_vlen_bufsize_t; /* Declare a free list to manage the H5D_t struct */ H5FL_DEFINE_STATIC(H5D_t); /* Declare a free list to manage blocks of VL data */ H5FL_BLK_DEFINE_STATIC(vlen_vl_buf); /* Declare a free list to manage other blocks of VL data */ H5FL_BLK_DEFINE_STATIC(vlen_fl_buf); /* Define a static "default" dataset structure to use to initialize new datasets */ static H5D_t H5D_def_dset; /*------------------------------------------------------------------------- * Function: H5D_init * * Purpose: Initialize the interface from some other layer. * * Return: Success: non-negative * * Failure: negative * * Programmer: Quincey Koziol * Saturday, March 4, 2000 * * Modifications: * *------------------------------------------------------------------------- */ herr_t H5D_init(void) { herr_t ret_value=SUCCEED; /* Return value */ FUNC_ENTER_NOAPI(H5D_init, FAIL) /* FUNC_ENTER() does all the work */ done: FUNC_LEAVE_NOAPI(ret_value) } /*-------------------------------------------------------------------------- NAME H5D_init_interface -- Initialize interface-specific information USAGE herr_t H5D_init_interface() RETURNS Non-negative on success/Negative on failure DESCRIPTION Initializes any interface-specific data or routines. NOTES Care must be taken when using the H5P functions, since they can cause a deadlock in the library when the library is attempting to terminate -QAK --------------------------------------------------------------------------*/ static herr_t H5D_init_interface(void) { /* Dataset Transfer property class variables. In sequence, they are, * - Transfer Property list class to modify * - Default value for maximum temp buffer size * - Default value for type conversion buffer * - Default value for background buffer * - Default value for B-tree node split ratios * - Default value for hyperslab caching * - Default value for hyperslab cache limit * - Default value for vlen allocation function * - Default value for vlen allocation information * - Default value for vlen free function * - Default value for vlen free information * - Default value for file driver ID * - Default value for file driver info * - Default value for 'gather reads' property * - Default value for vector size * - Default value for I/O transfer mode * - Default value for EDC property * - Default value for filter callback */ H5P_genclass_t *xfer_pclass; size_t def_max_temp_buf = H5D_XFER_MAX_TEMP_BUF_DEF; void *def_tconv_buf = H5D_XFER_TCONV_BUF_DEF; void *def_bkgr_buf = H5D_XFER_BKGR_BUF_DEF; H5T_bkg_t def_bkgr_buf_type = H5D_XFER_BKGR_BUF_TYPE_DEF; double def_btree_split_ratio[3] = H5D_XFER_BTREE_SPLIT_RATIO_DEF; H5MM_allocate_t def_vlen_alloc = H5D_XFER_VLEN_ALLOC_DEF; void *def_vlen_alloc_info = H5D_XFER_VLEN_ALLOC_INFO_DEF; H5MM_free_t def_vlen_free = H5D_XFER_VLEN_FREE_DEF; void *def_vlen_free_info = H5D_XFER_VLEN_FREE_INFO_DEF; hid_t def_vfl_id = H5D_XFER_VFL_ID_DEF; void *def_vfl_info = H5D_XFER_VFL_INFO_DEF; size_t def_hyp_vec_size = H5D_XFER_HYPER_VECTOR_SIZE_DEF; H5FD_mpio_xfer_t def_io_xfer_mode = H5D_XFER_IO_XFER_MODE_DEF; H5Z_EDC_t enable_edc = H5D_XFER_EDC_DEF; H5Z_cb_t filter_cb = H5D_XFER_FILTER_CB_DEF; /* Dataset creation property class variables. In sequence, they are, * - Creation property list class to modify * - Default value for storage layout property * - Default value for chunk dimensionality property * - Default value for chunk size * - Default value for fill value * - Default value for external file list * - Default value for data filter pipeline */ H5P_genclass_t *crt_pclass; H5D_layout_t layout = H5D_CRT_LAYOUT_DEF; unsigned chunk_ndims = H5D_CRT_CHUNK_DIM_DEF; hsize_t chunk_size[H5O_LAYOUT_NDIMS] = H5D_CRT_CHUNK_SIZE_DEF; H5O_fill_t fill = H5D_CRT_FILL_VALUE_DEF; H5D_alloc_time_t alloc_time = H5D_CRT_ALLOC_TIME_DEF; H5D_fill_time_t fill_time = H5D_CRT_FILL_TIME_DEF; H5O_efl_t efl = H5D_CRT_EXT_FILE_LIST_DEF; H5O_pline_t pline = H5D_CRT_DATA_PIPELINE_DEF; H5P_genplist_t *def_dcpl; /* Default Dataset Creation Property list */ size_t nprops; /* Number of properties */ herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_NOINIT(H5D_init_interface) /* Initialize the atom group for the dataset IDs */ if (H5I_init_group(H5I_DATASET, H5I_DATASETID_HASHSIZE, H5D_RESERVED_ATOMS, (H5I_free_t)H5D_close)<0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize interface") /* =========Dataset Transfer Property Class Initialization========= */ /* Register the default dataset transfer properties */ assert(H5P_CLS_DATASET_XFER_g!=(-1)); /* Get the pointer to the dataset transfer class */ if (NULL == (xfer_pclass = H5I_object(H5P_CLS_DATASET_XFER_g))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a property list class") /* Get the number of properties in the class */ if(H5P_get_nprops_pclass(xfer_pclass,&nprops)<0) HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "can't query number of properties") /* Assume that if there are properties in the class, they are the default ones */ if(nprops==0) { /* Register the max. temp buffer size property */ if(H5P_register(xfer_pclass,H5D_XFER_MAX_TEMP_BUF_NAME,H5D_XFER_MAX_TEMP_BUF_SIZE,&def_max_temp_buf,NULL,NULL,NULL,NULL,NULL,NULL)<0) HGOTO_ERROR(H5E_PLIST, H5E_CANTINSERT, FAIL, "can't insert property into class") /* Register the type conversion buffer property */ if(H5P_register(xfer_pclass,H5D_XFER_TCONV_BUF_NAME,H5D_XFER_TCONV_BUF_SIZE,&def_tconv_buf,NULL,NULL,NULL,NULL,NULL,NULL)<0) HGOTO_ERROR(H5E_PLIST, H5E_CANTINSERT, FAIL, "can't insert property into class") /* Register the background buffer property */ if(H5P_register(xfer_pclass,H5D_XFER_BKGR_BUF_NAME,H5D_XFER_BKGR_BUF_SIZE,&def_bkgr_buf,NULL,NULL,NULL,NULL,NULL,NULL)<0) HGOTO_ERROR(H5E_PLIST, H5E_CANTINSERT, FAIL, "can't insert property into class") /* Register the background buffer type property */ if(H5P_register(xfer_pclass,H5D_XFER_BKGR_BUF_TYPE_NAME,H5D_XFER_BKGR_BUF_TYPE_SIZE,&def_bkgr_buf_type,NULL,NULL,NULL,NULL,NULL,NULL)<0) HGOTO_ERROR(H5E_PLIST, H5E_CANTINSERT, FAIL, "can't insert property into class") /* Register the B-Tree node splitting ratios property */ if(H5P_register(xfer_pclass,H5D_XFER_BTREE_SPLIT_RATIO_NAME,H5D_XFER_BTREE_SPLIT_RATIO_SIZE,def_btree_split_ratio,NULL,NULL,NULL,NULL,NULL,NULL)<0) HGOTO_ERROR(H5E_PLIST, H5E_CANTINSERT, FAIL, "can't insert property into class") /* Register the vlen allocation function property */ if(H5P_register(xfer_pclass,H5D_XFER_VLEN_ALLOC_NAME,H5D_XFER_VLEN_ALLOC_SIZE,&def_vlen_alloc,NULL,NULL,NULL,NULL,NULL,NULL)<0) HGOTO_ERROR(H5E_PLIST, H5E_CANTINSERT, FAIL, "can't insert property into class") /* Register the vlen allocation information property */ if(H5P_register(xfer_pclass,H5D_XFER_VLEN_ALLOC_INFO_NAME,H5D_XFER_VLEN_ALLOC_INFO_SIZE,&def_vlen_alloc_info,NULL,NULL,NULL,NULL,NULL,NULL)<0) HGOTO_ERROR(H5E_PLIST, H5E_CANTINSERT, FAIL, "can't insert property into class") /* Register the vlen free function property */ if(H5P_register(xfer_pclass,H5D_XFER_VLEN_FREE_NAME,H5D_XFER_VLEN_FREE_SIZE,&def_vlen_free,NULL,NULL,NULL,NULL,NULL,NULL)<0) HGOTO_ERROR(H5E_PLIST, H5E_CANTINSERT, FAIL, "can't insert property into class") /* Register the vlen free information property */ if(H5P_register(xfer_pclass,H5D_XFER_VLEN_FREE_INFO_NAME,H5D_XFER_VLEN_FREE_INFO_SIZE,&def_vlen_free_info,NULL,NULL,NULL,NULL,NULL,NULL)<0) HGOTO_ERROR(H5E_PLIST, H5E_CANTINSERT, FAIL, "can't insert property into class") /* Register the file driver ID property */ if(H5P_register(xfer_pclass,H5D_XFER_VFL_ID_NAME,H5D_XFER_VFL_ID_SIZE,&def_vfl_id,NULL,NULL,NULL,NULL,NULL,NULL)<0) HGOTO_ERROR(H5E_PLIST, H5E_CANTINSERT, FAIL, "can't insert property into class") /* Register the file driver info property */ if(H5P_register(xfer_pclass,H5D_XFER_VFL_INFO_NAME,H5D_XFER_VFL_INFO_SIZE,&def_vfl_info,NULL,NULL,NULL,NULL,NULL,NULL)<0) HGOTO_ERROR(H5E_PLIST, H5E_CANTINSERT, FAIL, "can't insert property into class") /* Register the vector size property */ if(H5P_register(xfer_pclass,H5D_XFER_HYPER_VECTOR_SIZE_NAME,H5D_XFER_HYPER_VECTOR_SIZE_SIZE,&def_hyp_vec_size,NULL,NULL,NULL,NULL,NULL,NULL)<0) HGOTO_ERROR(H5E_PLIST, H5E_CANTINSERT, FAIL, "can't insert property into class") /* Register the I/O transfer mode property */ if(H5P_register(xfer_pclass,H5D_XFER_IO_XFER_MODE_NAME,H5D_XFER_IO_XFER_MODE_SIZE,&def_io_xfer_mode,NULL,NULL,NULL,NULL,NULL,NULL)<0) HGOTO_ERROR(H5E_PLIST, H5E_CANTINSERT, FAIL, "can't insert property into class") /* Register the EDC property */ if(H5P_register(xfer_pclass,H5D_XFER_EDC_NAME,H5D_XFER_EDC_SIZE,&enable_edc,NULL,NULL,NULL,NULL,NULL,NULL)<0) HGOTO_ERROR(H5E_PLIST, H5E_CANTINSERT, FAIL, "can't insert property into class") /* Register the filter callback property */ if(H5P_register(xfer_pclass,H5D_XFER_FILTER_CB_NAME,H5D_XFER_FILTER_CB_SIZE,&filter_cb,NULL,NULL,NULL,NULL,NULL,NULL)<0) HGOTO_ERROR(H5E_PLIST, H5E_CANTINSERT, FAIL, "can't insert property into class") } /* end if */ /* Only register the default property list if it hasn't been created yet */ if(H5P_LST_DATASET_XFER_g==(-1)) { /* Register the default data transfer property list */ if ((H5P_LST_DATASET_XFER_g = H5P_create_id (xfer_pclass))<0) HGOTO_ERROR (H5E_PLIST, H5E_CANTREGISTER, FAIL, "can't register default property list") } /* end if */ /* =========Dataset Creation Property Class Initialization========== */ /* Register the default dataset creation properties */ assert(H5P_CLS_DATASET_CREATE_g != -1); /* Get the pointer to the dataset creation class */ if(NULL == (crt_pclass = H5I_object(H5P_CLS_DATASET_CREATE_g))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a property list class") /* Get the number of properties in the class */ if(H5P_get_nprops_pclass(crt_pclass,&nprops)<0) HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "can't query number of properties") /* Assume that if there are properties in the class, they are the default ones */ if(nprops==0) { /* Register the storage layout property */ if(H5P_register(crt_pclass, H5D_CRT_LAYOUT_NAME, H5D_CRT_LAYOUT_SIZE, &layout, NULL, NULL, NULL, NULL, NULL, NULL) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTINSERT, FAIL, "can't insert property into class") /* Register the chunking dimensionality property */ if(H5P_register(crt_pclass, H5D_CRT_CHUNK_DIM_NAME, H5D_CRT_CHUNK_DIM_SIZE, &chunk_ndims, NULL, NULL, NULL, NULL, NULL, NULL) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTINSERT, FAIL, "can't insert property into class") /* Register the chunking size property */ if(H5P_register(crt_pclass, H5D_CRT_CHUNK_SIZE_NAME, H5D_CRT_CHUNK_SIZE_SIZE, chunk_size, NULL, NULL, NULL, NULL, NULL, NULL) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTINSERT, FAIL, "can't insert property into class") /* Register the fill value property */ if(H5P_register(crt_pclass, H5D_CRT_FILL_VALUE_NAME, H5D_CRT_FILL_VALUE_SIZE, &fill, NULL, NULL, NULL, NULL, NULL, NULL) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTINSERT, FAIL, "can't insert property into class") /* Register the space allocation time property */ if(H5P_register(crt_pclass, H5D_CRT_ALLOC_TIME_NAME, H5D_CRT_ALLOC_TIME_SIZE, &alloc_time, NULL, NULL, NULL, NULL, NULL, NULL) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTINSERT, FAIL, "can't insert property into class") /* Register the fill value writing time property */ if(H5P_register(crt_pclass, H5D_CRT_FILL_TIME_NAME, H5D_CRT_FILL_TIME_SIZE, &fill_time, NULL, NULL, NULL, NULL, NULL, NULL) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTINSERT, FAIL, "can't insert property into class") /* Register the external file list property */ if(H5P_register(crt_pclass, H5D_CRT_EXT_FILE_LIST_NAME, H5D_CRT_EXT_FILE_LIST_SIZE, &efl, NULL, NULL, NULL, NULL, NULL, NULL) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTINSERT, FAIL, "can't insert property into class") /* Register the data pipeline property */ if(H5P_register(crt_pclass, H5D_CRT_DATA_PIPELINE_NAME, H5D_CRT_DATA_PIPELINE_SIZE, &pline, NULL, NULL, NULL, NULL, NULL, NULL) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTINSERT, FAIL, "can't insert property into class") } /* end if */ /* Only register the default property list if it hasn't been created yet */ if(H5P_LST_DATASET_CREATE_g==(-1)) { /* Register the default data transfer property list */ if ((H5P_LST_DATASET_CREATE_g = H5P_create_id (crt_pclass))<0) HGOTO_ERROR (H5E_PLIST, H5E_CANTREGISTER, FAIL, "can't register default property list") } /* end if */ /* Reset the "default dataset" information */ HDmemset(&H5D_def_dset,0,sizeof(H5D_t)); /* Get the default dataset cretion property list values and initialize the * default dataset with them. */ if (NULL == (def_dcpl = H5I_object(H5P_LST_DATASET_CREATE_g))) HGOTO_ERROR(H5E_DATASET, H5E_BADTYPE, FAIL, "can't get default dataset creation property list") /* Set up the default allocation time information */ if(H5P_get(def_dcpl, H5D_CRT_ALLOC_TIME_NAME, &H5D_def_dset.alloc_time) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't retrieve space allocation time") if(H5D_def_dset.alloc_time==H5D_ALLOC_TIME_DEFAULT) H5D_def_dset.alloc_time=H5D_ALLOC_TIME_LATE; /* Get the default external file list information */ if(H5P_get(def_dcpl, H5D_CRT_EXT_FILE_LIST_NAME, &H5D_def_dset.efl) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't retrieve external file list") /* Get the default data storage method */ if(H5P_get(def_dcpl, H5D_CRT_LAYOUT_NAME, &H5D_def_dset.layout.type) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't retrieve layout") /* Get the default fill value time */ if (H5P_get(def_dcpl, H5D_CRT_FILL_TIME_NAME, &H5D_def_dset.fill_time) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't retrieve fill time") /* Get the default fill value */ if (H5P_get(def_dcpl, H5D_CRT_FILL_VALUE_NAME, &H5D_def_dset.fill) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't retrieve fill value") done: FUNC_LEAVE_NOAPI(ret_value) } /*------------------------------------------------------------------------- * Function: H5D_term_interface * * Purpose: Terminate this interface. * * Return: Success: Positive if anything was done that might * affect other interfaces; zero otherwise. * * Failure: Negative. * * Programmer: Robb Matzke * Friday, November 20, 1998 * * Modifications: * *------------------------------------------------------------------------- */ int H5D_term_interface(void) { int n=0; FUNC_ENTER_NOINIT(H5D_term_interface) if (interface_initialize_g) { if ((n=H5I_nmembers(H5I_DATASET))) { /* The dataset API uses the "force" flag set to true because it * is using the "file objects" (H5FO) API functions to track open * objects in the file. Using the H5FO code means that dataset * IDs can have reference counts >1, when an existing dataset is * opened more than once. However, the H5I code does not attempt * to close objects with reference counts>1 unless the "force" flag * is set to true. * * At some point (probably after the group and datatypes use the * the H5FO code), the H5FO code might need to be switched around * to storing pointers to the objects being tracked (H5D_t, H5G_t, * etc) and reference count those itself instead of relying on the * reference counting in the H5I layer. Then, the "force" flag can * be put back to false. * * Setting the "force" flag to true for all the interfaces won't * work because the "file driver" (H5FD) APIs use the H5I reference * counting to avoid closing a file driver out from underneath an * open file... * * QAK - 5/13/03 */ H5I_clear_group(H5I_DATASET, TRUE); } else { H5I_destroy_group(H5I_DATASET); interface_initialize_g = 0; n = 1; /*H5I*/ } } FUNC_LEAVE_NOAPI(n) } /*------------------------------------------------------------------------- * Function: H5D_crt_copy * * Purpose: Callback routine which is called whenever any dataset * creation property list is copied. This routine copies * the properties from the old list to the new list. * * Return: Success: Non-negative * * Failure: Negative * * Programmer: Raymond Lu * Tuesday, October 2, 2001 * * Modification: * *------------------------------------------------------------------------- */ herr_t H5D_crt_copy(hid_t new_plist_id, hid_t old_plist_id, void UNUSED *copy_data) { H5O_fill_t src_fill, dst_fill; H5O_efl_t src_efl, dst_efl; H5O_pline_t src_pline, dst_pline; H5P_genplist_t *old_plist; H5P_genplist_t *new_plist; herr_t ret_value=SUCCEED; FUNC_ENTER_NOAPI(H5D_crt_copy, FAIL) /* Verify property list ID */ if (NULL == (new_plist = H5I_object(new_plist_id))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset creation property list") if (NULL == (old_plist = H5I_object(old_plist_id))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset creation property list") /* Get the fill value, external file list, and data pipeline properties * from the old property list */ if(H5P_get(old_plist, H5D_CRT_FILL_VALUE_NAME, &src_fill) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't get fill value") if(H5P_get(old_plist, H5D_CRT_EXT_FILE_LIST_NAME, &src_efl) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't get external file list") if(H5P_get(old_plist, H5D_CRT_DATA_PIPELINE_NAME, &src_pline) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't get pipeline") /* Make copies of fill value, external file list, and data pipeline */ if(src_fill.buf) { if(NULL==H5O_copy(H5O_FILL_ID, &src_fill, &dst_fill)) HGOTO_ERROR(H5E_PLIST, H5E_CANTINIT, FAIL, "can't copy fill value") } /* end if */ else { dst_fill.type = dst_fill.buf = NULL; dst_fill.size = src_fill.size; } HDmemset(&dst_efl,0,sizeof(H5O_efl_t)); if(NULL==H5O_copy(H5O_EFL_ID, &src_efl, &dst_efl)) HGOTO_ERROR(H5E_PLIST, H5E_CANTINIT, FAIL, "can't copy external file list") if(NULL==H5O_copy(H5O_PLINE_ID, &src_pline, &dst_pline)) HGOTO_ERROR(H5E_PLIST, H5E_CANTINIT, FAIL, "can't copy data pipeline") /* Set the fill value, external file list, and data pipeline property * for the new property list */ if(H5P_set(new_plist, H5D_CRT_FILL_VALUE_NAME, &dst_fill) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTSET, FAIL, "can't set fill value") if(H5P_set(new_plist, H5D_CRT_EXT_FILE_LIST_NAME, &dst_efl) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTSET, FAIL, "can't set external file list") if(H5P_set(new_plist, H5D_CRT_DATA_PIPELINE_NAME, &dst_pline) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTSET, FAIL, "can't set pipeline") done: FUNC_LEAVE_NOAPI(ret_value) } /*lint !e715 !e818 Make lint ignore copy_data parameter */ /*------------------------------------------------------------------------- * Function: H5D_crt_close * * Purpose: Callback routine which is called whenever any dataset create * property list is closed. This routine performs any generic * cleanup needed on the properties the library put into the list. * * Return: Success: Non-negative * * Failure: Negative * * Programmer: Quincey Koziol * Wednesday, July 11, 2001 * * Modifications: * *------------------------------------------------------------------------- */ herr_t H5D_crt_close(hid_t dcpl_id, void UNUSED *close_data) { H5O_fill_t fill; H5O_efl_t efl; H5O_pline_t pline; H5P_genplist_t *plist; /* Property list */ herr_t ret_value=SUCCEED; /* Return value */ FUNC_ENTER_NOAPI(H5D_crt_close, FAIL) /* Check arguments */ if (NULL == (plist = H5I_object(dcpl_id))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset creation property list") /* Get the fill value, external file list, and data pipeline properties * from the old property list */ if(H5P_get(plist, H5D_CRT_FILL_VALUE_NAME, &fill) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't get fill value") if(H5P_get(plist, H5D_CRT_EXT_FILE_LIST_NAME, &efl) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't get external file list") if(H5P_get(plist, H5D_CRT_DATA_PIPELINE_NAME, &pline) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't get pipeline") /* Clean up any values set for the fill-value, external file-list and * data pipeline */ if(H5O_reset(H5O_FILL_ID, &fill)<0) HGOTO_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "can't release fill info") if(H5O_reset(H5O_EFL_ID, &efl)<0) HGOTO_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "can't release external file list info") if(H5O_reset(H5O_PLINE_ID, &pline)<0) HGOTO_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "can't release pipeline info") done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D_crt_close() */ /*lint !e715 !e818 Make lint ignore close_data parameter */ /*------------------------------------------------------------------------- * Function: H5D_xfer_create * * Purpose: Callback routine which is called whenever any dataset transfer * property list is created. This routine performs any generic * initialization needed on the properties the library put into * the list. * Right now, it's just allocating the driver-specific dataset * transfer information. * * Return: Success: Non-negative * * Failure: Negative * * Programmer: Quincey Koziol * Thursday, August 2, 2001 * * Notes: This same routine is currently used for the 'copy' callback. * Modifications: * *------------------------------------------------------------------------- */ herr_t H5D_xfer_create(hid_t dxpl_id, void UNUSED *create_data) { hid_t driver_id; /* VFL driver ID */ void *driver_info; /* VFL driver info */ H5P_genplist_t *plist; /* Property list */ herr_t ret_value=SUCCEED; /* Return value */ FUNC_ENTER_NOAPI(H5D_xfer_create, FAIL) /* Check arguments */ if (NULL == (plist = H5I_object(dxpl_id))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset transfer property list") /* Get the driver information */ if(H5P_get(plist, H5D_XFER_VFL_ID_NAME, &driver_id)<0) HGOTO_ERROR (H5E_PLIST, H5E_CANTGET, FAIL, "Can't retrieve VFL driver ID") if(H5P_get(plist, H5D_XFER_VFL_INFO_NAME, &driver_info)<0) HGOTO_ERROR (H5E_PLIST, H5E_CANTGET, FAIL, "Can't retrieve VFL driver info") /* Check if we have a valid driver ID */ if(driver_id>0) { /* Increment the reference count on the driver and copy the driver info */ if(H5I_inc_ref(driver_id)<0) HGOTO_ERROR (H5E_DATASET, H5E_CANTINC, FAIL, "Can't increment VFL driver ID") if(H5FD_dxpl_copy(driver_id, driver_info, &driver_info)<0) HGOTO_ERROR (H5E_DATASET, H5E_CANTCOPY, FAIL, "Can't copy VFL driver") /* Set the driver information for the new property list */ if(H5P_set(plist, H5D_XFER_VFL_ID_NAME, &driver_id)<0) HGOTO_ERROR (H5E_PLIST, H5E_CANTSET, FAIL, "Can't set VFL driver ID") if(H5P_set(plist, H5D_XFER_VFL_INFO_NAME, &driver_info)<0) HGOTO_ERROR (H5E_PLIST, H5E_CANTSET, FAIL, "Can't set VFL driver info") } /* end if */ done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D_xfer_create() */ /*lint !e715 !e818 Make lint ignore create_data parameter */ /*------------------------------------------------------------------------- * Function: H5D_xfer_copy * * Purpose: Callback routine which is called whenever any dataset * transfer property list is copied. This routine copies * the properties from the old list to the new list. * * Return: Success: Non-negative * * Failure: Negative * * Programmer: Raymond Lu * Tuesday, October 2, 2001 * * Modification: * *------------------------------------------------------------------------- */ herr_t H5D_xfer_copy(hid_t new_plist_id, hid_t UNUSED old_plist_id, void *copy_data) { herr_t ret_value=SUCCEED; /* Return value */ FUNC_ENTER_NOAPI(H5D_xfer_copy, FAIL) if(H5D_xfer_create(new_plist_id, copy_data) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTINIT, FAIL, "can't copy property list") done: FUNC_LEAVE_NOAPI(ret_value) } /*lint !e715 !e818 Make lint ignore old_plist_id parameter */ /*------------------------------------------------------------------------- * Function: H5D_xfer_close * * Purpose: Callback routine which is called whenever any dataset transfer * property list is closed. This routine performs any generic * cleanup needed on the properties the library put into the list. * Right now, it's just freeing the driver-specific dataset * transfer information. * * Return: Success: Non-negative * * Failure: Negative * * Programmer: Quincey Koziol * Wednesday, July 11, 2001 * * Modifications: * *------------------------------------------------------------------------- */ herr_t H5D_xfer_close(hid_t dxpl_id, void UNUSED *close_data) { hid_t driver_id; /* VFL driver ID */ void *driver_info; /* VFL driver info */ H5P_genplist_t *plist; /* Property list */ herr_t ret_value=SUCCEED; /* Return value */ FUNC_ENTER_NOAPI(H5D_xfer_close, FAIL) /* Check arguments */ if (NULL == (plist = H5I_object(dxpl_id))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset transfer property list") if(H5P_get(plist, H5D_XFER_VFL_ID_NAME, &driver_id)<0) HGOTO_ERROR (H5E_PLIST, H5E_CANTGET, FAIL, "Can't retrieve VFL driver ID") if(H5P_get(plist, H5D_XFER_VFL_INFO_NAME, &driver_info)<0) HGOTO_ERROR (H5E_PLIST, H5E_CANTGET, FAIL, "Can't retrieve VFL driver info") if(driver_id>0) { if(H5FD_dxpl_free(driver_id, driver_info)<0) HGOTO_ERROR (H5E_DATASET, H5E_CANTFREE, FAIL, "Can't free VFL driver") if(H5I_dec_ref(driver_id)<0) HGOTO_ERROR (H5E_DATASET, H5E_CANTFREE, FAIL, "Can't decrement VFL driver ID") } /* end if */ done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D_xfer_close() */ /*lint !e715 !e818 Make lint ignore close_data parameter */ /*------------------------------------------------------------------------- * Function: H5Dcreate * * Purpose: Creates a new dataset named NAME at LOC_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 (DCPL_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 loc_id, const char *name, hid_t type_id, hid_t space_id, hid_t dcpl_id) { H5G_entry_t *loc = NULL; /* Entry for group to insert dataset into */ H5D_t *new_dset = NULL; /* New dataset's info */ const H5S_t *space; /* Dataspace for dataset */ hid_t ret_value; /* Return value */ FUNC_ENTER_API(H5Dcreate, FAIL) H5TRACE5("i","isiii",loc_id,name,type_id,space_id,dcpl_id); /* Check arguments */ if (NULL == (loc = H5G_loc(loc_id))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a location ID") if (!name || !*name) HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "no name") if (H5I_DATATYPE != H5I_get_type(type_id)) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a datatype ID") if (NULL == (space = H5I_object_verify(space_id,H5I_DATASPACE))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataspace ID") if(H5P_DEFAULT == dcpl_id) dcpl_id = H5P_DATASET_CREATE_DEFAULT; else if(TRUE != H5P_isa_class(dcpl_id, H5P_DATASET_CREATE)) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not dataset create property list ID") /* build and open the new dataset */ if (NULL == (new_dset = H5D_create(loc, name, type_id, space, dcpl_id, H5AC_dxpl_id))) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to create dataset") /* Register the new dataset to get an ID for it */ if ((ret_value = H5I_register(H5I_DATASET, new_dset)) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTREGISTER, FAIL, "unable to register dataset") /* Add the dataset to the list of opened objects in the file */ if(H5FO_insert(new_dset->ent.file,new_dset->ent.header,ret_value)<0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINSERT, FAIL, "can't insert dataset into list of open objects") done: if(ret_value<0) { if(new_dset!=NULL) { if(H5D_close(new_dset)<0) HDONE_ERROR(H5E_DATASET, H5E_CLOSEERROR, FAIL, "unable to release dataset"); } /* end if */ } /* end if */ FUNC_LEAVE_API(ret_value) } /*------------------------------------------------------------------------- * Function: H5Dopen * * Purpose: Finds a dataset named NAME at LOC_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: * * Programmer: Robb Matzke * Thursday, December 4, 1997 * * Modifications: * *------------------------------------------------------------------------- */ hid_t H5Dopen(hid_t loc_id, const char *name) { H5G_entry_t *loc = NULL; /*location holding the dataset */ H5G_entry_t ent; /*dataset symbol table entry */ hid_t ret_value; FUNC_ENTER_API(H5Dopen, FAIL) H5TRACE2("i","is",loc_id,name); /* Check args */ if (NULL == (loc = H5G_loc(loc_id))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a location") if (!name || !*name) HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "no name") /* Find the dataset object */ if (H5G_find(loc, name, NULL, &ent, H5AC_dxpl_id) < 0) HGOTO_ERROR(H5E_DATASET, H5E_NOTFOUND, FAIL, "not found") /* Open the dataset */ if ((ret_value = H5D_open(&ent, H5AC_dxpl_id)) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTREGISTER, FAIL, "can't register dataset") done: FUNC_LEAVE_API(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: Non-negative on success/Negative on failure * * Errors: * ARGS BADTYPE Not a dataset. * DATASET CANTINIT Can't free. * * Programmer: Robb Matzke * Thursday, December 4, 1997 * * Modifications: * *------------------------------------------------------------------------- */ herr_t H5Dclose(hid_t dset_id) { H5D_t *dset = NULL; /* Dataset object to release */ herr_t ret_value=SUCCEED; /* Return value */ FUNC_ENTER_API(H5Dclose, FAIL) H5TRACE1("e","i",dset_id); /* Check args */ if (NULL == (dset = H5I_object_verify(dset_id, H5I_DATASET))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset") if (NULL == dset->ent.file) HGOTO_ERROR(H5E_DATASET, H5E_BADTYPE, FAIL, "not a dataset") /* * Decrement the counter on the dataset. It will be freed if the count * reaches zero. */ if (H5I_dec_ref(dset_id) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "can't free") done: FUNC_LEAVE_API(ret_value) } /*------------------------------------------------------------------------- * 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: * Robb Matzke, 9 Jun 1998 * The data space is not constant and is no longer cached by the dataset * struct. *------------------------------------------------------------------------- */ hid_t H5Dget_space(hid_t dset_id) { H5D_t *dset = NULL; H5S_t *space = NULL; hid_t ret_value; FUNC_ENTER_API(H5Dget_space, FAIL) H5TRACE1("i","i",dset_id); /* Check args */ if (NULL==(dset=H5I_object_verify(dset_id, H5I_DATASET))) HGOTO_ERROR (H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset") /* Read the data space message and return a data space object */ if (NULL==(space=H5S_copy (dset->space))) HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to get data space") /* Create an atom */ if ((ret_value=H5I_register (H5I_DATASPACE, space))<0) HGOTO_ERROR (H5E_ATOM, H5E_CANTREGISTER, FAIL, "unable to register data space") done: if(ret_value<0) { if(space!=NULL) { if(H5S_close(space)<0) HDONE_ERROR(H5E_DATASET, H5E_CLOSEERROR, FAIL, "unable to release dataspace"); } /* end if */ } /* end if */ FUNC_LEAVE_API(ret_value) } /*------------------------------------------------------------------------- * Function: H5Dget_space_status * * Purpose: Returns the status of data space allocation. * * Return: * Success: Non-negative * * Failture: Negative * * Programmer: Raymond Lu * * Modification: * *------------------------------------------------------------------------- */ herr_t H5Dget_space_status(hid_t dset_id, H5D_space_status_t *allocation) { H5D_t *dset = NULL; herr_t ret_value = SUCCEED; FUNC_ENTER_API(H5Dget_space_status, FAIL) /* Check arguments */ if(NULL==(dset=H5I_object_verify(dset_id, H5I_DATASET))) HGOTO_ERROR (H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset") /* Read data space address and return */ if(FAIL==(ret_value=H5D_get_space_status(dset, allocation, H5AC_ind_dxpl_id))) HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to get space status") done: FUNC_LEAVE_API(ret_value) } /*------------------------------------------------------------------------- * Function: H5D_get_space_status * * Purpose: Returns the status of data space allocation. * * Return: * Success: Non-negative * * Failture: Negative * * Programmer: Raymond Lu * * Modification: * *------------------------------------------------------------------------- */ static herr_t H5D_get_space_status(const H5D_t *dset, H5D_space_status_t *allocation, hid_t dxpl_id) { H5S_t *space; /* Dataset's dataspace */ hsize_t space_allocated; /* The number of bytes allocated for chunks */ hssize_t total_elem; /* The total number of elements in dataspace */ size_t type_size; /* The size of the datatype for the dataset */ hsize_t full_size; /* The number of bytes in the dataset when fully populated */ herr_t ret_value = SUCCEED; FUNC_ENTER_NOINIT(H5D_get_space_status) assert(dset); /* Get the dataset's dataspace */ space=dset->space; assert(space); /* Get the total number of elements in dataset's dataspace */ if((total_elem=H5S_get_simple_extent_npoints(space))<0) HGOTO_ERROR(H5E_DATASET, H5E_CANTCOUNT, FAIL, "unable to get # of dataspace elements") /* Get the size of the dataset's datatype */ if((type_size=H5T_get_size(dset->type))==0) HGOTO_ERROR(H5E_DATASET, H5E_CANTCOUNT, FAIL, "unable to get size of datatype") /* Compute the maximum size of the dataset in bytes */ H5_CHECK_OVERFLOW(total_elem,hssize_t,hsize_t); full_size=((hsize_t)total_elem)*type_size; /* Difficult to error check, since the error value is 0 and 0 is a valid value... :-/ */ space_allocated=H5D_get_storage_size(dset,dxpl_id); /* Decide on how much of the space is allocated */ if(space_allocated==0) *allocation = H5D_SPACE_STATUS_NOT_ALLOCATED; else if(space_allocated==full_size) *allocation = H5D_SPACE_STATUS_ALLOCATED; else { /* Should only happen for chunked datasets currently */ assert(dset->layout.type==H5D_CHUNKED); *allocation = H5D_SPACE_STATUS_PART_ALLOCATED; } /* end else */ done: FUNC_LEAVE_NOAPI(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: * * Robb Matzke, 1 Jun 1998 * If the dataset has a named data type then a handle to the opened data * type is returned. Otherwise the returned data type is read-only. If * atomization of the data type fails then the data type is closed. * *------------------------------------------------------------------------- */ hid_t H5Dget_type(hid_t dset_id) { H5D_t *dset = NULL; H5T_t *copied_type = NULL; hid_t ret_value = FAIL; FUNC_ENTER_API(H5Dget_type, FAIL) H5TRACE1("i","i",dset_id); /* Check args */ if (NULL==(dset=H5I_object_verify(dset_id, H5I_DATASET))) HGOTO_ERROR (H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset") /* Copy the data type and mark it read-only */ if (NULL==(copied_type=H5T_copy (dset->type, H5T_COPY_REOPEN))) HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to copy the data type") /* Mark any datatypes as being in memory now */ if (H5T_set_loc(copied_type, NULL, H5T_LOC_MEMORY)<0) HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "invalid datatype location") /* Unlock copied type */ if (H5T_lock (copied_type, FALSE)<0) HGOTO_ERROR (H5E_DATATYPE, H5E_CANTINIT, FAIL, "unable to lock transient data type") /* Create an atom */ if ((ret_value=H5I_register (H5I_DATATYPE, copied_type))<0) HGOTO_ERROR (H5E_ATOM, H5E_CANTREGISTER, FAIL, "unable to register data type") done: if(ret_value<0) { if(copied_type!=NULL) { if(H5T_close (copied_type)<0) HDONE_ERROR(H5E_DATASET, H5E_CLOSEERROR, FAIL, "unable to release datatype"); } /* end if */ } /* end if */ FUNC_LEAVE_API(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 H5P_close(). * * Failure: FAIL * * Programmer: Robb Matzke * Tuesday, February 3, 1998 * * Modifications: * * Raymond Lu * Tuesday, October 2, 2001 * The way to retrieve and set property is changed for the * generic property list. * *------------------------------------------------------------------------- */ hid_t H5Dget_create_plist(hid_t dset_id) { H5D_t *dset = NULL; H5O_fill_t copied_fill={NULL,0,NULL}; H5P_genplist_t *dcpl_plist; H5P_genplist_t *new_plist; hid_t new_dcpl_id = FAIL; hid_t ret_value = FAIL; FUNC_ENTER_API(H5Dget_create_plist, FAIL) H5TRACE1("i","i",dset_id); /* Check args */ if (NULL==(dset=H5I_object_verify(dset_id, H5I_DATASET))) HGOTO_ERROR (H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset") if (NULL == (dcpl_plist = H5I_object(dset->dcpl_id))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "can't get property list") /* Copy the creation property list */ if((new_dcpl_id = H5P_copy_plist(dcpl_plist)) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "unable to copy the creation property list") if (NULL == (new_plist = H5I_object(new_dcpl_id))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "can't get property list") /* Get the fill value property */ if(H5P_get(new_plist, H5D_CRT_FILL_VALUE_NAME, &copied_fill) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't get fill value") /* Copy the dataset type into the fill value message */ if(copied_fill.type==NULL) if(NULL==(copied_fill.type=H5T_copy(dset->type, H5T_COPY_TRANSIENT))) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to copy dataset data type for fill value") /* Set back the fill value property to property list */ if(H5P_set(new_plist, H5D_CRT_FILL_VALUE_NAME, &copied_fill) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "unable to set property list fill value") /* Set the return value */ ret_value=new_dcpl_id; done: if(ret_value<0) { if(new_dcpl_id>0) (void)H5I_dec_ref(new_dcpl_id); } /* end if */ FUNC_LEAVE_API(ret_value) } /*------------------------------------------------------------------------- * 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: Non-negative on success/Negative on failure * * Programmer: Robb Matzke * Friday, January 30, 1998 * * Modifications: * *------------------------------------------------------------------------- */ herr_t H5Dextend(hid_t dset_id, const hsize_t *size) { H5D_t *dset = NULL; herr_t ret_value=SUCCEED; /* Return value */ FUNC_ENTER_API(H5Dextend, FAIL) H5TRACE2("e","i*h",dset_id,size); /* Check args */ if (NULL==(dset=H5I_object_verify(dset_id, H5I_DATASET))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset") if (!size) HGOTO_ERROR (H5E_ARGS, H5E_BADVALUE, FAIL, "no size specified") /* Increase size */ if (H5D_extend (dset, size, H5AC_dxpl_id)<0) HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to extend dataset") done: FUNC_LEAVE_API(ret_value) } /*------------------------------------------------------------------------- * Function: H5D_new * * Purpose: Creates a new, empty dataset structure * * Return: Success: Pointer to a new dataset descriptor. * * Failure: NULL * * Errors: * * Programmer: Quincey Koziol * Monday, October 12, 1998 * * Modifications: * * Raymond Lu * Tuesday, October 2, 2001 * Changed the way to query and inialization for generic * property list. * *------------------------------------------------------------------------- */ static H5D_t * H5D_new(hid_t dcpl_id, hbool_t creating, hbool_t vl_type) { H5P_genplist_t *plist; /* Property list created */ H5D_t *new_dset = NULL; /* New dataset object */ H5D_t *ret_value; /* Return value */ FUNC_ENTER_NOAPI(H5D_new, NULL) if (NULL==(new_dset = H5FL_MALLOC(H5D_t))) HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed") /* If we are using the default dataset creation property list, during creation * don't bother to copy it, just increment the reference count */ if(!vl_type && creating && dcpl_id == H5P_DATASET_CREATE_DEFAULT) { /* Copy the default dataset information */ HDmemcpy(new_dset,&H5D_def_dset,sizeof(H5D_t)); if(H5I_inc_ref(dcpl_id)<0) HGOTO_ERROR (H5E_DATASET, H5E_CANTINC, NULL, "Can't increment default DCPL ID") new_dset->dcpl_id = dcpl_id; } /* end if */ else { /* Reset the dataset information */ HDmemset(new_dset,0,sizeof(H5D_t)); /* Get the property list */ if (NULL == (plist = H5I_object(dcpl_id))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, NULL, "not a property list") new_dset->dcpl_id = H5P_copy_plist(plist); } /* end else */ new_dset->ent.header = HADDR_UNDEF; /* Set return value */ ret_value=new_dset; done: if(ret_value==NULL) { if(new_dset!=NULL) { if(new_dset->dcpl_id!=0) (void)H5I_dec_ref(new_dset->dcpl_id); H5FL_FREE(H5D_t,new_dset); } /* end if */ } /* end if */ FUNC_LEAVE_NOAPI(ret_value) } /*------------------------------------------------------------------------- * Function: H5D_update_entry_info * * Purpose: Create and fill an H5G_entry_t object for insertion into * the group LOC. * * This code was originally found at the end of H5D_create() * but was placed here for general use. * * Return: Success: SUCCEED * Failure: FAIL * * Errors: * * Programmer: Bill Wendling * Thursday, October 31, 2002 * * Modifications: * *------------------------------------------------------------------------- */ static herr_t H5D_update_entry_info(H5F_t *file, hid_t dxpl_id, H5D_t *dset, H5P_genplist_t *plist) { size_t ohdr_size = H5D_MINHDR_SIZE; /* Size of dataset's object header */ H5G_entry_t *ent=NULL; /* Dataset's group entry */ H5O_layout_t *layout; /* Dataset's layout information */ H5T_t *type; /* Dataset's datatype */ H5S_t *space; /* Dataset's dataspace */ H5D_alloc_time_t alloc_time;/* Dataset's allocation time */ H5O_efl_t *efl; /* Dataset's external file list */ /* fill value variables */ H5D_fill_time_t fill_time; H5O_fill_t *fill_prop; /* Pointer to dataset's fill value information */ H5O_fill_new_t fill = { NULL, 0, NULL, H5D_ALLOC_TIME_LATE, H5D_FILL_TIME_ALLOC, TRUE }; H5D_fill_value_t fill_status; struct H5O_t *oh=NULL; /* Pointer to dataset's object header */ /* return code */ herr_t ret_value = SUCCEED; FUNC_ENTER_NOAPI(H5D_update_entry_info, FAIL) /* Sanity checking */ assert(file); assert(dset); /* Pick up former parameters */ ent=&dset->ent; layout=&dset->layout; type=dset->type; space=dset->space; alloc_time=dset->alloc_time; efl=&dset->efl; /* Add the dataset's raw data size to the size of the header, if the raw data will be stored as compact */ if (layout->type == H5D_COMPACT) ohdr_size += layout->size; /* Create (open for write access) an object header */ if (H5O_create(file, dxpl_id, ohdr_size, ent) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to create dataset object header") /* Get a pointer to the object header itself */ if((oh=H5O_protect(ent, dxpl_id))==NULL) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to protect dataset object header") /* Point at dataset's copy, to cache it for later */ fill_prop=&dset->fill; fill_time=dset->fill_time; /* Check if dataset has non-default creation property list */ if(dset->dcpl_id!=H5P_DATASET_CREATE_DEFAULT) { /* * Retrieve properties of fill value and others. Copy them into new fill * value struct. Convert the fill value to the dataset type and write * the message */ if (H5P_get(plist, H5D_CRT_FILL_TIME_NAME, &fill_time) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't retrieve fill time") dset->fill_time=fill_time; /* Cache this for later */ /* Get the fill value information from the property list */ if (H5P_get(plist, H5D_CRT_FILL_VALUE_NAME, fill_prop) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't retrieve fill value") } /* end if */ if (H5P_is_fill_value_defined(fill_prop, &fill_status) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't tell if fill value defined") /* Special case handling for variable-length types */ if(H5T_detect_class(type, H5T_VLEN)) { /* If the default fill value is chosen for variable-length types, always write it */ if(fill_time==H5D_FILL_TIME_IFSET && fill_status==H5D_FILL_VALUE_DEFAULT) { dset->fill_time=fill_time=H5D_FILL_TIME_ALLOC; /* Update dataset creation property */ assert(dset->dcpl_id!=H5P_DATASET_CREATE_DEFAULT); if (H5P_set(plist, H5D_CRT_FILL_TIME_NAME, &fill_time) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTSET, FAIL, "can't set fill time") } /* end if */ /* Don't allow never writing fill values with variable-length types */ if(fill_time==H5D_FILL_TIME_NEVER) HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, FAIL, "Dataset doesn't support VL datatype when fill value is not defined") } /* end if */ if (fill_status == H5D_FILL_VALUE_DEFAULT || fill_status == H5D_FILL_VALUE_USER_DEFINED) { if (H5O_copy(H5O_FILL_ID, fill_prop, &fill) == NULL) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT,FAIL, "unable to copy fill value") if (fill_prop->buf && fill_prop->size > 0 && H5O_fill_convert(&fill, type, dxpl_id) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to convert fill value to dataset type") fill.fill_defined = TRUE; } else if (fill_status == H5D_FILL_VALUE_UNDEFINED) { fill.size = -1; fill.type = fill.buf = NULL; fill.fill_defined = FALSE; } else { HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "unable to determine if fill value is defined") } fill.alloc_time = alloc_time; fill.fill_time = fill_time; if (fill.fill_defined == FALSE && fill_time == H5D_FILL_TIME_ALLOC) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT,FAIL, "unable to create dataset") /* Write new fill value message */ if (H5O_append(file, dxpl_id, oh, H5O_FILL_NEW_ID, H5O_FLAG_CONSTANT, &fill) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to update fill value header message") /* If there is valid information for the old fill value struct, update it */ if (fill.buf) { /* Clear any previous values */ if(H5O_reset(H5O_FILL_ID, fill_prop)<0) HGOTO_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "can't release fill info") /* Copy new fill value information to old fill value struct */ if(H5O_copy(H5O_FILL_ID, &fill, fill_prop) == NULL) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT,FAIL,"unable to copy fill value") /* Write old fill value */ if (fill_prop->buf && H5O_append(file, dxpl_id, oh, H5O_FILL_ID, H5O_FLAG_CONSTANT, fill_prop) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to update fill value header message") /* Update dataset creation property */ assert(dset->dcpl_id!=H5P_DATASET_CREATE_DEFAULT); if (H5P_set(plist, H5D_CRT_FILL_VALUE_NAME, fill_prop) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTSET, FAIL, "can't set fill value") } /* end if */ /* Update the type and space header messages */ if (H5O_append(file, dxpl_id, oh, H5O_DTYPE_ID, H5O_FLAG_CONSTANT | H5O_FLAG_SHARED, type) < 0 || H5S_append(file, dxpl_id, oh, space) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to update type or space header messages") /* Update the filters message, if this is a chunked dataset */ if(layout->type==H5D_CHUNKED) { H5O_pline_t pline; /* Chunked data I/O pipeline info */ if (H5P_get(plist, H5D_CRT_DATA_PIPELINE_NAME, &pline) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "Can't retrieve pipeline filter") if (pline.nfilters > 0 && H5O_append(file, dxpl_id, oh, H5O_PLINE_ID, H5O_FLAG_CONSTANT, &pline) < 0) HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to update filter header message") } /* end if */ /* * Allocate storage if space allocate time is early; otherwise delay * allocation until later. */ if (alloc_time == H5D_ALLOC_TIME_EARLY) if (H5D_alloc_storage(file, dxpl_id, dset, H5D_ALLOC_CREATE, FALSE, FALSE) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize storage") /* Update external storage message */ if (efl->nused > 0) { size_t heap_size = H5HL_ALIGN(1); int i; for (i = 0; i < efl->nused; ++i) heap_size += H5HL_ALIGN(HDstrlen(efl->slot[i].name) + 1); if (H5HL_create(file, dxpl_id, heap_size, &efl->heap_addr/*out*/) < 0 || H5HL_insert(file, dxpl_id, efl->heap_addr, 1, "") == (size_t)(-1)) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to create external file list name heap") for (i = 0; i < efl->nused; ++i) { size_t offset = H5HL_insert(file, dxpl_id, efl->heap_addr, HDstrlen(efl->slot[i].name) + 1, efl->slot[i].name); assert(0 == efl->slot[i].name_offset); if (offset == (size_t)(-1)) HGOTO_ERROR(H5E_EFL, H5E_CANTINIT, FAIL, "unable to insert URL into name heap") efl->slot[i].name_offset = offset; } if (H5O_append(file, dxpl_id, oh, H5O_EFL_ID, H5O_FLAG_CONSTANT, efl) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to update external file list message") } /* Update layout message */ /* (Don't make layout message constant unless allocation time is early, since space may not be allocated) */ /* Note: this is relying on H5D_alloc_storage not calling H5O_modify during dataset creation */ if (H5D_COMPACT != layout->type && H5O_append(file, dxpl_id, oh, H5O_LAYOUT_ID, (alloc_time == H5D_ALLOC_TIME_EARLY ? H5O_FLAG_CONSTANT : 0), layout) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to update layout") #ifdef H5O_ENABLE_BOGUS /* * Add a "bogus" message. */ if (H5O_bogus_oh(file, dxpl_id, oh))<0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "unable to update 'bogus' message") #endif /* H5O_ENABLE_BOGUS */ /* Add a modification time message. */ if (H5O_touch_oh(file, oh, TRUE) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to update modification time message") done: /* Release pointer to object header itself */ if(ent!=NULL && oh!=NULL) if(H5O_unprotect(ent,oh, dxpl_id)<0) HDONE_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to unprotect dataset object header"); FUNC_LEAVE_NOAPI(ret_value) } /*------------------------------------------------------------------------- * 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. * DATASET CANTINIT Fail in file space allocation for * chunks * * Programmer: Robb Matzke * Thursday, December 4, 1997 * * Modifications: * Robb Matzke, 9 Jun 1998 * The data space message is no longer cached in the dataset struct. * * Robb Matzke, 27 Jul 1998 * Added the MTIME message to the dataset object header. * * Robb Matzke, 1999-10-14 * The names for the external file list are entered into the heap hear * instead of when the efl message is encoded, preventing a possible * infinite recursion situation. * * Raymond Lu * Tuesday, October 2, 2001 * Changed the way to retrieve and set property for generic property * list. * * Raymond Lu, 26 Feb 2002 * A new fill value message is added. Two properties, space allocation * time and fill value writing time, govern space allocation and fill * value writing. * * Bill Wendling, 1. November 2002 * Removed the cache updating mechanism. This was done so that it * can be called separately from the H5D_create function. There were * two of these mechanisms: one to create and insert into the parent * group the H5G_entry_t object and the other to update based upon * whether we're working with an external file or not. Between the * two, there is a conditional call to allocate space which isn't * part of updating the cache. * *------------------------------------------------------------------------- */ static H5D_t * H5D_create(H5G_entry_t *loc, const char *name, hid_t type_id, const H5S_t *space, hid_t dcpl_id, hid_t dxpl_id) { const H5T_t *type; /* Datatype for dataset */ H5D_t *new_dset = NULL; int i, ndims; hsize_t comp_data_size; unsigned u; hsize_t max_dim[H5O_LAYOUT_NDIMS]={0}; H5F_t *file=NULL; unsigned chunk_ndims = 0; /* Dimensionality of chunk */ hsize_t chunk_size[H5O_LAYOUT_NDIMS]={0}; H5P_genplist_t *dc_plist=NULL; /* New Property list */ hbool_t has_vl_type=FALSE; /* Flag to indicate a VL-type for dataset */ H5D_t *ret_value; /* Return value */ #ifdef H5_HAVE_FPHDF5 hbool_t locked_grp = FALSE; /* The parent group is locked */ hobj_ref_t grp_oid; #endif /* H5_HAVE_FPHDF5 */ FUNC_ENTER_NOAPI(H5D_create, NULL) /* check args */ assert (loc); assert (name && *name); assert (H5I_DATATYPE==H5I_get_type(type_id)); assert (space); assert (H5I_GENPROP_LST==H5I_get_type(dcpl_id)); assert (H5I_GENPROP_LST==H5I_get_type(dxpl_id)); /* Check if the filters in the DCPL can be applied to this dataset */ if(H5Z_can_apply(dcpl_id,type_id)<0) HGOTO_ERROR(H5E_ARGS, H5E_CANTINIT, NULL, "I/O filters can't operate on this dataset") /* Get the dataset's datatype */ if (NULL == (type = H5I_object(type_id))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, NULL, "not a datatype") /* Check if the datatype is "sensible" for use in a dataset */ if(H5T_is_sensible(type)!=TRUE) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, NULL, "datatype is not sensible") /* Check if the datatype is/contains a VL-type */ if(H5T_detect_class(type, H5T_VLEN)) has_vl_type=TRUE; /* Initialize the dataset object */ if(NULL == (new_dset = H5D_new(dcpl_id,TRUE,has_vl_type))) HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed") /* Make the "set local" filter callbacks for this dataset */ if(H5Z_set_local(new_dset->dcpl_id,type_id)<0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "unable to set local filter parameters") /* What file is the dataset being added to? */ if (NULL==(file=H5G_insertion_file(loc, name, dxpl_id))) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "unable to locate insertion point") #ifdef H5_HAVE_FPHDF5 #error "This is not the right place for this code, see comment in code - QAK" /* This code ought to be somewhere in H5G_insert (or one of the functions that * it calls), not here. All the routines which create objects in the file * (H5Dcreate, H5Gcreate, H5Tcommit, H5Glink, etc.) all prepare an object in * memory and then call H5G_insert to actually insert the object into the group * that contains it. * * Looking through the H5G_insert code, it calls H5G_namei which calls * H5G_stab_insert to actually insert the object into the symbol table, so * H5G_stab_insert would probably be the best place to do this sort of locking. * (I think it would be better to do it there than in H5G_insert because the * H5Glink code doesn't end up calling H5G_insert for creating soft links, but * it does end up calling H5G_stab_insert). * * Otherwise, you are going to have to duplicate this chunk of code into far * too many places in the library... - QAK */ if (H5FD_is_fphdf5_driver(file->shared->lf)) { unsigned file_id = H5FD_fphdf5_file_id(file->shared->lf); char *tmp_name = H5MM_xstrdup(name); char *last = HDstrrchr(tmp_name, '/'); hid_t gid; H5G_t *grp = NULL; H5G_entry_t *grp_loc = NULL; H5FP_status_t status; unsigned req_id; /* Chop off the dataset name (we only want to lock the group) */ if (last) last[1] = '\0'; /* Open the group */ if ((grp = H5G_open(loc, tmp_name, dxpl_id)) == NULL) HGOTO_ERROR(H5E_SYM, H5E_CANTOPENOBJ, NULL, "unable to open group"); /* Register the group so we can grab information about it */ if ((gid = H5I_register(H5I_GROUP, grp)) < 0) { H5G_close(grp); HGOTO_ERROR(H5E_ATOM, H5E_CANTREGISTER, NULL, "unable to register group"); } /* Grab the location of the group */ if ((grp_loc = H5G_loc(gid)) == NULL) { H5I_dec_ref(gid); HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, NULL, "not a location ID") } grp_oid = grp_loc->header; if (H5FP_request_lock(file_id, grp_oid, H5FP_LOCK_WRITE, TRUE, &req_id, &status) != SUCCEED) { /* FIXME: This is bad. We should check the "status" variable */ H5I_dec_ref(gid); H5MM_xfree(tmp_name); HGOTO_ERROR(H5E_FPHDF5, H5E_CANTLOCK, NULL, "unable to lock group"); } if (H5I_dec_ref(gid) != SUCCEED) HGOTO_ERROR(H5E_SYM, H5E_CANTINIT, NULL, "unable to close group"); locked_grp = TRUE; H5MM_xfree(tmp_name); } #endif /* H5_HAVE_FPHDF5 */ /* Copy datatype for dataset */ if((new_dset->type = H5T_copy(type, H5T_COPY_ALL))==NULL) HGOTO_ERROR(H5E_DATATYPE, H5E_CANTCOPY, NULL, "can't copy datatype") /* Mark any datatypes as being on disk now */ if (H5T_set_loc(new_dset->type, file, H5T_LOC_DISK)<0) HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, NULL, "invalid datatype location") /* Copy dataspace for dataset */ if((new_dset->space = H5S_copy(space))==NULL) HGOTO_ERROR(H5E_DATASPACE, H5E_CANTCOPY, NULL, "can't copy dataspace") /* Set the dataset's dataspace to 'all' selection */ if(H5S_select_all(new_dset->space,1)<0) HGOTO_ERROR (H5E_DATASPACE, H5E_CANTSET, NULL, "unable to set all selection") /* Check if the dataset has a non-default DCPL & get important values, if so */ if(new_dset->dcpl_id!=H5P_DATASET_CREATE_DEFAULT) { H5D_layout_t dcpl_layout; /* Dataset's layout information */ H5O_pline_t dcpl_pline; /* Dataset's I/O pipeline information */ H5D_alloc_time_t alloc_time; /* Dataset's allocation time */ /* Get new dataset's property list object */ if (NULL == (dc_plist = H5I_object(new_dset->dcpl_id))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, NULL, "can't get dataset creation property list") if(H5P_get(dc_plist, H5D_CRT_DATA_PIPELINE_NAME, &dcpl_pline) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, NULL, "can't retrieve pipeline filter") if(H5P_get(dc_plist, H5D_CRT_LAYOUT_NAME, &dcpl_layout) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, NULL, "can't retrieve layout") if(dcpl_pline.nfilters > 0 && H5D_CHUNKED != dcpl_layout) HGOTO_ERROR(H5E_DATASET, H5E_BADVALUE, NULL, "filters can only be used with chunked layout") if(H5P_get(dc_plist, H5D_CRT_ALLOC_TIME_NAME, &alloc_time) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, NULL, "can't retrieve space allocation time") /* Check if the alloc_time is the default and set it accordingly */ if(alloc_time==H5D_ALLOC_TIME_DEFAULT) { switch(dcpl_layout) { case H5D_COMPACT: alloc_time=H5D_ALLOC_TIME_EARLY; break; case H5D_CONTIGUOUS: alloc_time=H5D_ALLOC_TIME_LATE; break; case H5D_CHUNKED: alloc_time=H5D_ALLOC_TIME_INCR; break; default: HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, NULL, "not implemented yet") } /* end switch */ } /* end if */ /* Don't allow compact datasets to allocate space later */ if(dcpl_layout==H5D_COMPACT && alloc_time!=H5D_ALLOC_TIME_EARLY) HGOTO_ERROR(H5E_DATASET, H5E_BADVALUE, NULL, "compact dataset doesn't support late space allocation") /* Set the alloc_time for the dataset, in case the default was used */ new_dset->alloc_time=alloc_time; /* If MPI VFD is used, no filter support yet. */ if(IS_H5FD_MPI(file) && dcpl_pline.nfilters > 0) HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, NULL, "Parallel I/O does not support filters yet") /* Chunked datasets are non-default, so retrieve their info here */ if(H5P_get(dc_plist, H5D_CRT_CHUNK_DIM_NAME, &chunk_ndims) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, NULL, "can't retrieve chunk dimensions") /* Get the dataset's external file list information */ if(H5P_get(dc_plist, H5D_CRT_EXT_FILE_LIST_NAME, &new_dset->efl) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, NULL, "can't retrieve external file list") /* Get the dataset's data storage method */ if(H5P_get(dc_plist, H5D_CRT_LAYOUT_NAME, &(new_dset->layout.type)) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, NULL, "can't retrieve layout") } /* end if */ /* Check if this dataset is going into a parallel file and set space allocation time */ if(IS_H5FD_MPI(file)) new_dset->alloc_time=H5D_ALLOC_TIME_EARLY; /* Set up layout information */ if((ndims=H5S_get_simple_extent_ndims(new_dset->space))<0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, NULL, "unable to get rank") new_dset->layout.ndims = (unsigned)ndims + 1; assert((unsigned)(new_dset->layout.ndims) <= NELMTS(new_dset->layout.dim)); new_dset->layout.dim[new_dset->layout.ndims-1] = H5T_get_size(new_dset->type); new_dset->layout.addr = HADDR_UNDEF; /* Initialize to no address */ switch (new_dset->layout.type) { 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_simple_extent_dims(new_dset->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 (new_dset->efl.nused>0) { hsize_t max_points = H5S_get_npoints_max (new_dset->space); hsize_t max_storage = H5O_efl_total_size (&new_dset->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 (ndims>0 && 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(chunk_ndims != (unsigned)H5S_get_simple_extent_ndims(new_dset->space)) HGOTO_ERROR(H5E_DATASET, H5E_BADVALUE, NULL, "dimensionality of chunks doesn't match the data space") if (new_dset->efl.nused>0) HGOTO_ERROR (H5E_DATASET, H5E_BADVALUE, NULL, "external storage not supported with chunked layout") /* * The chunk size of a dimension with a fixed size cannot exceed * the maximum dimension size */ if(H5P_get(dc_plist, H5D_CRT_CHUNK_SIZE_NAME, chunk_size) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, NULL, "can't retrieve chunk size") if (H5S_get_simple_extent_dims(new_dset->space, NULL, max_dim)<0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "unable to query maximum dimensions") for (u=0; ulayout.ndims-1; u++) { if(max_dim[u] != H5S_UNLIMITED && max_dim[u] < chunk_size[u]) HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, NULL, "chunk size must be <= maximum dimension size for fixed-sized dimensions") } /* Set the dataset's chunk sizes from the property list's chunk sizes */ for (u=0; ulayout.ndims-1; u++) new_dset->layout.dim[u] = chunk_size[u]; break; case H5D_COMPACT: { hssize_t tmp_size; /* Temporary holder for raw data size */ /* * Compact dataset is stored in dataset object header message of * layout. */ tmp_size = H5S_get_simple_extent_npoints(space) * H5T_get_size(new_dset->type); H5_ASSIGN_OVERFLOW(new_dset->layout.size,tmp_size,hssize_t,size_t); /* Verify data size is smaller than maximum header message size * (64KB) minus other layout message fields. */ comp_data_size=H5O_MAX_SIZE-H5O_layout_meta_size(file, &(new_dset->layout)); if(new_dset->layout.size > comp_data_size) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "compact dataset size is bigger than header message maximum size") if ((ndims=H5S_get_simple_extent_dims(space, new_dset->layout.dim, max_dim))<0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "unable to initialize dimension size of compact dataset storage") /* remember to check if size is small enough to fit header message */ } break; default: HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, NULL, "not implemented yet") } /* end switch */ /* * Update the dataset's entry info. */ if (H5D_update_entry_info(file, dxpl_id, new_dset, dc_plist) != SUCCEED) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "can't update the metadata cache") /* * Give the dataset a name. That is, create and add a new * "H5G_entry_t" object to the group this dataset is being initially * created in. */ if (H5G_insert(loc, name, &new_dset->ent, dxpl_id) < 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->space) { if(H5S_close(new_dset->space)<0) HDONE_ERROR(H5E_DATASET, H5E_CLOSEERROR, NULL, "unable to release dataspace"); } /* end if */ if (new_dset->type) { if(H5T_close(new_dset->type)<0) HDONE_ERROR(H5E_DATASET, H5E_CLOSEERROR, NULL, "unable to release datatype"); } /* end if */ if (H5F_addr_defined(new_dset->ent.header)) { if(H5O_close(&(new_dset->ent))<0) HDONE_ERROR(H5E_DATASET, H5E_CLOSEERROR, NULL, "unable to release object header"); if(file) { if(H5O_delete(file, dxpl_id,new_dset->ent.header)<0) HDONE_ERROR(H5E_DATASET, H5E_CANTDELETE, NULL, "unable to delete object header"); } /* end if */ } /* end if */ if(new_dset->dcpl_id!=0) { if(H5I_dec_ref(new_dset->dcpl_id)<0) HDONE_ERROR(H5E_DATASET, H5E_CANTDEC, NULL, "unable to decrement ref count on property list"); } /* end if */ new_dset->ent.file = NULL; H5FL_FREE(H5D_t,new_dset); } #ifdef H5_HAVE_FPHDF5 if (locked_grp) { unsigned file_id = H5FD_fphdf5_file_id(file->shared->lf); H5FP_status_t status; unsigned req_id; /* Request a release of the lock */ if (H5FP_request_release_lock(file_id, grp_oid, TRUE, &req_id, &status)) { /* FIXME: This is bad. We should check the "status" variable */ HGOTO_ERROR(H5E_FPHDF5, H5E_CANTLOCK, NULL, "unable to lock group"); } } #endif /* H5_HAVE_FPHDF5 */ FUNC_LEAVE_NOAPI(ret_value) } /*------------------------------------------------------------------------- * Function: H5D_isa * * Purpose: Determines if an object has the requisite messages for being * a dataset. * * Return: Success: TRUE if the required dataset messages are * present; FALSE otherwise. * * Failure: FAIL if the existence of certain messages * cannot be determined. * * Programmer: Robb Matzke * Monday, November 2, 1998 * * Modifications: * *------------------------------------------------------------------------- */ htri_t H5D_isa(H5G_entry_t *ent, hid_t dxpl_id) { htri_t exists; htri_t ret_value=TRUE; /* Return value */ FUNC_ENTER_NOAPI(H5D_isa, FAIL) assert(ent); /* Data type */ if ((exists=H5O_exists(ent, H5O_DTYPE_ID, 0, dxpl_id))<0) { HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to read object header") } else if (!exists) { HGOTO_DONE(FALSE) } /* Layout */ if ((exists=H5O_exists(ent, H5O_LAYOUT_ID, 0, dxpl_id))<0) { HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to read object header") } else if (!exists) { HGOTO_DONE(FALSE) } done: FUNC_LEAVE_NOAPI(ret_value) } /* *------------------------------------------------------------------------- * Function: H5D_open * * Purpose: Checks if dataset is already open, or opens a dataset for * access. * * Return: Success: Dataset ID * Failure: FAIL * * Errors: * * Programmer: Quincey Koziol * Friday, December 20, 2002 * * Modifications: * *------------------------------------------------------------------------- */ hid_t H5D_open(H5G_entry_t *ent, hid_t dxpl_id) { hid_t ret_value; /* Return value */ FUNC_ENTER_NOAPI(H5D_open, FAIL) /* check args */ assert (ent); /* Check if dataset was already open */ if((ret_value=H5FO_opened(ent->file,ent->header))<0) { H5D_t *dataset; /*the dataset which was found */ /* Clear any errors from H5FO_opened() */ H5E_clear(NULL); /* Open the dataset object */ if ((dataset=H5D_open_oid(ent, dxpl_id)) ==NULL) HGOTO_ERROR(H5E_DATASET, H5E_NOTFOUND, FAIL, "not found") /* Create an atom for the dataset */ if ((ret_value = H5I_register(H5I_DATASET, dataset)) < 0) { (void)H5D_close(dataset); HGOTO_ERROR(H5E_DATASET, H5E_CANTREGISTER, FAIL, "can't register dataset") } /* end if */ /* Add the dataset to the list of opened objects in the file */ if(H5FO_insert(ent->file,ent->header,ret_value)<0) { (void)H5I_dec_ref(ret_value); HGOTO_ERROR(H5E_DATASET, H5E_CANTINSERT, FAIL, "can't insert dataset into list of open objects") } /* end if */ } /* end if */ else { /* Dataset is already open, increment the reference count on the ID */ if(H5I_inc_ref(ret_value)<0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINC, FAIL, "Can't increment dataset ID") /* Release the dataset entry we located earlier (in H5Dopen()) */ if(H5G_free_ent_name(ent)<0) { (void)H5I_dec_ref(ret_value); HGOTO_ERROR(H5E_DATASET, H5E_CANTRELEASE, FAIL, "can't release group entry") } /* end if */ } /* end else */ done: FUNC_LEAVE_NOAPI(ret_value) } /*------------------------------------------------------------------------- * Function: H5D_open_oid * * Purpose: Opens a dataset for access. * * Return: Dataset pointer on success, NULL on failure * * Errors: * * Programmer: Quincey Koziol * Monday, October 12, 1998 * * Modifications: * * Raymond Lu * Tuesday, October 2, 2001 * Changed the way to set property for generic property list. * * Raymond Lu * Feb 26, 2002 * A new fill value message and two new properties are added. * * Pedro Vicente, 22 Aug 2002 * Added a deep copy of the symbol table entry * *------------------------------------------------------------------------- */ static H5D_t * H5D_open_oid(const H5G_entry_t *ent, hid_t dxpl_id) { H5D_t *dataset = NULL; /*new dataset struct */ H5O_fill_new_t fill = {NULL, 0, NULL, H5D_ALLOC_TIME_LATE, H5D_CRT_FILL_TIME_DEF, TRUE}; H5O_fill_t *fill_prop; /* Pointer to dataset's fill value area */ H5O_pline_t pline; /* I/O pipeline information */ H5D_layout_t layout; /* Dataset layout */ H5P_genplist_t *plist; /* Property list */ H5D_t *ret_value = NULL; /*return value */ FUNC_ENTER_NOAPI(H5D_open_oid, NULL) /* check args */ assert (ent); /* Allocate the dataset structure */ /* (Set the 'vl_type' parameter to FALSE since it doesn't matter from here) */ if(NULL==(dataset = H5D_new(H5P_DATASET_CREATE_DEFAULT,FALSE,FALSE))) HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed") /* Shallow copy (take ownership) of the group entry object */ if(H5G_ent_copy(&(dataset->ent),ent,H5G_COPY_SHALLOW)<0) HGOTO_ERROR (H5E_DATASET, H5E_CANTCOPY, NULL, "can't copy group entry") /* Find the dataset object */ if (H5O_open(&(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_ID, 0, NULL, dxpl_id))) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "unable to load type info from dataset header") if (NULL==(dataset->space=H5S_read(&(dataset->ent),dxpl_id))) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "unable to load space info from dataset header") /* Get dataset creation property list object */ if (NULL == (plist = H5I_object(dataset->dcpl_id))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, NULL, "can't get dataset creation property list") /* Get the optional filters message */ if(NULL == H5O_read(&(dataset->ent), H5O_PLINE_ID, 0, &pline, dxpl_id)) { H5E_clear(NULL); HDmemset(&pline, 0, sizeof(pline)); } if(H5P_set(plist, H5D_CRT_DATA_PIPELINE_NAME, &pline) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, NULL, "can't set pipeline") /* If MPI VFD is used, no filter support yet. */ if(IS_H5FD_MPI(dataset->ent.file) && pline.nfilters > 0) HGOTO_ERROR (H5E_DATASET, H5E_UNSUPPORTED, NULL, "Parallel IO does not support filters yet") /* * 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_ID, 0, &(dataset->layout), dxpl_id)) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "unable to read data layout message") switch (dataset->layout.type) { case H5D_CONTIGUOUS: layout = H5D_CONTIGUOUS; if(H5P_set(plist, H5D_CRT_LAYOUT_NAME, &layout) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, NULL, "can't set layout") 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. */ { unsigned chunk_ndims; /* Dimensionality of chunk */ layout = H5D_CHUNKED; chunk_ndims = dataset->layout.ndims - 1; if(H5P_set(plist, H5D_CRT_LAYOUT_NAME, &layout) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, NULL, "can't set layout") if(H5P_set(plist, H5D_CRT_CHUNK_DIM_NAME, &chunk_ndims) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, NULL, "can't set chunk dimensions") if(H5P_set(plist, H5D_CRT_CHUNK_SIZE_NAME, dataset->layout.dim) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, NULL, "can't set chunk size") } break; case H5D_COMPACT: layout = H5D_COMPACT; if(H5P_set(plist, H5D_CRT_LAYOUT_NAME, &layout) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, NULL, "can't set layout") break; default: HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, NULL, "not implemented yet") } /* end switch */ /* Point at dataset's copy, to cache it for later */ fill_prop=&dataset->fill; /* Retrieve & release the previous fill-value settings */ if(H5P_get(plist, H5D_CRT_FILL_VALUE_NAME, fill_prop) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, NULL, "can't get fill value") if(H5O_reset(H5O_FILL_ID, fill_prop)<0) HGOTO_ERROR(H5E_DATASET, H5E_CANTFREE, NULL, "can't release fill info") /* Get the new fill value message */ if(NULL == H5O_read(&(dataset->ent), H5O_FILL_NEW_ID, 0, &fill, dxpl_id)) { H5E_clear(NULL); HDmemset(&fill, 0, sizeof(fill)); /* Set the space allocation time appropriately, based on the type of dataset storage */ switch (dataset->layout.type) { case H5D_COMPACT: fill.alloc_time=H5D_ALLOC_TIME_EARLY; break; case H5D_CONTIGUOUS: fill.alloc_time=H5D_ALLOC_TIME_LATE; break; case H5D_CHUNKED: fill.alloc_time=H5D_ALLOC_TIME_INCR; break; default: HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, NULL, "not implemented yet") } /* end switch */ /* Set the default fill time */ fill.fill_time=H5D_CRT_FILL_TIME_DEF; } /* end if */ if(fill.fill_defined) { if(NULL==H5O_copy(H5O_FILL_ID, &fill, fill_prop)) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "can't copy fill value") } else { /* For compatibility with v1.4. Retrieve the old fill value message. * If size is 0, make it -1 for undefined. */ if(NULL == H5O_read(&(dataset->ent), H5O_FILL_ID, 0, fill_prop, dxpl_id)) { H5E_clear(NULL); HDmemset(fill_prop, 0, sizeof(H5O_fill_t)); } if(fill_prop->size == 0) { fill_prop->type = fill_prop->buf = NULL; fill_prop->size = (size_t)-1; } } /* end else */ /* Set revised fill value properties */ if(H5P_set(plist, H5D_CRT_FILL_VALUE_NAME, fill_prop) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, NULL, "can't set fill value") dataset->alloc_time=fill.alloc_time; /* Cache this for later */ if(H5P_set(plist, H5D_CRT_ALLOC_TIME_NAME, &fill.alloc_time) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, NULL, "can't set fill value") dataset->fill_time=fill.fill_time; /* Cache this for later */ if(H5P_set(plist, H5D_CRT_FILL_TIME_NAME, &fill.fill_time) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, NULL, "can't set fill value") /* Get the external file list message, which might not exist. Space is * also undefined when space allocate time is H5D_ALLOC_TIME_LATE. */ if( !H5F_addr_defined(dataset->layout.addr)) { HDmemset(&dataset->efl,0,sizeof(H5O_efl_t)); if(NULL != H5O_read(&(dataset->ent), H5O_EFL_ID, 0, &dataset->efl, dxpl_id)) if(H5P_set(plist, H5D_CRT_EXT_FILE_LIST_NAME, &dataset->efl) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, NULL, "can't set external file list") } /* * Make sure all storage is properly initialized. * This is important only for parallel I/O where the space must * be fully allocated before I/O can happen. */ if ((H5F_get_intent(dataset->ent.file) & H5F_ACC_RDWR) && (dataset->layout.type!=H5D_COMPACT && dataset->layout.addr==HADDR_UNDEF) && IS_H5FD_MPI(dataset->ent.file)) { if (H5D_alloc_storage(dataset->ent.file, dxpl_id, dataset,H5D_ALLOC_OPEN, TRUE, FALSE)<0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "unable to initialize file storage") } /* Success */ ret_value = dataset; done: if (ret_value==NULL && dataset) { if (H5F_addr_defined(dataset->ent.header)) { if(H5O_close(&(dataset->ent))<0) HDONE_ERROR(H5E_DATASET, H5E_CLOSEERROR, NULL, "unable to release object header"); } /* end if */ if (dataset->space) { if(H5S_close(dataset->space)<0) HDONE_ERROR(H5E_DATASET, H5E_CLOSEERROR, NULL, "unable to release dataspace"); } /* end if */ if (dataset->type) { if(H5T_close(dataset->type)<0) HDONE_ERROR(H5E_DATASET, H5E_CLOSEERROR, NULL, "unable to release datatype"); } /* end if */ dataset->ent.file = NULL; H5FL_FREE(H5D_t,dataset); } /* end if */ FUNC_LEAVE_NOAPI(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: Non-negative on success/Negative on failure * * Errors: * DATASET CANTINIT Couldn't free the type or space, * but the dataset was freed anyway. * * Programmer: Robb Matzke * Thursday, December 4, 1997 * * Modifications: * Robb Matzke, 9 Jun 1998 * The data space message is no longer cached in the dataset struct. * *------------------------------------------------------------------------- */ static herr_t H5D_close(H5D_t *dataset) { unsigned free_failed; herr_t ret_value=SUCCEED; /* Return value */ FUNC_ENTER_NOAPI(H5D_close, FAIL) /* check args */ assert(dataset && dataset->ent.file); /* * Release datatype, dataspace and creation property list -- 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 || H5I_dec_ref(dataset->dcpl_id) < 0); /* Update header message of layout for compact dataset. */ if(dataset->layout.type==H5D_COMPACT && dataset->layout.dirty) { if(H5O_modify(&(dataset->ent), H5O_LAYOUT_ID, 0, 0, 1, &(dataset->layout), H5AC_dxpl_id)<0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to update layout message") dataset->layout.dirty = FALSE; } /* end if */ /* Remove the dataset from the list of opened objects in the file */ if(H5FO_delete(dataset->ent.file, H5AC_dxpl_id, dataset->ent.header)<0) HGOTO_ERROR(H5E_DATASET, H5E_CANTRELEASE, FAIL, "can't remove dataset from list of open objects") /* Close the dataset object */ /* (This closes the file, if this is the last object open) */ if(H5O_close(&(dataset->ent))<0) HGOTO_ERROR(H5E_DATASET, H5E_CLOSEERROR, FAIL, "unable to release object header"); /* * 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; /* Free the buffer for the raw data for compact datasets */ if(dataset->layout.type==H5D_COMPACT) dataset->layout.buf=H5MM_xfree(dataset->layout.buf); H5FL_FREE(H5D_t,dataset); if (free_failed) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "couldn't free the type or creation property list, but the dataset was freed anyway.") done: FUNC_LEAVE_NOAPI(ret_value) } /*------------------------------------------------------------------------- * Function: H5D_extend * * Purpose: Increases the size of a dataset. * * Return: Non-negative on success/Negative on failure * * Programmer: Robb Matzke * Friday, January 30, 1998 * * Modifications: * * Raymond Lu * Tuesday, October 2, 2001 * Changed the way to retrieve property for generic property * list. * *------------------------------------------------------------------------- */ static herr_t H5D_extend (H5D_t *dataset, const hsize_t *size, hid_t dxpl_id) { int changed; /* Flag to indicate that the dataspace was successfully extended */ H5S_t *space = NULL; /* Dataset's dataspace */ herr_t ret_value=SUCCEED; /* Return value */ FUNC_ENTER_NOAPI(H5D_extend, FAIL) /* Check args */ assert (dataset); assert (size); /* * NOTE: Restrictions on extensions were checked when the dataset was * created. All extensions are allowed here since none should be * able to muck things up. */ /* Increase the size of the data space */ space=dataset->space; if ((changed=H5S_extend (space, size))<0) HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to increase size of data space") if (changed>0){ /* Save the new dataspace in the file if necessary */ if (H5S_modify (&(dataset->ent), space, TRUE, dxpl_id)<0) HGOTO_ERROR (H5E_DATASET, H5E_WRITEERROR, FAIL, "unable to update file with new dataspace") /* Allocate space for the new parts of the dataset, if appropriate */ if(dataset->alloc_time==H5D_ALLOC_TIME_EARLY) if (H5D_alloc_storage(dataset->ent.file, dxpl_id, dataset, H5D_ALLOC_EXTEND, TRUE, FALSE)<0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize dataset with fill value") } /* end if */ done: FUNC_LEAVE_NOAPI(ret_value) } /*------------------------------------------------------------------------- * Function: H5D_entof * * Purpose: Returns a pointer to the entry for a dataset. * * Return: Success: Ptr to entry * * Failure: NULL * * Programmer: Robb Matzke * Friday, April 24, 1998 * * Modifications: * *------------------------------------------------------------------------- */ H5G_entry_t * H5D_entof (H5D_t *dataset) { /* Use FUNC_ENTER_NOINIT here to avoid performance issues */ FUNC_ENTER_NOINIT(H5D_entof) FUNC_LEAVE_NOAPI( dataset ? &(dataset->ent) : (H5G_entry_t *)NULL) } /*------------------------------------------------------------------------- * Function: H5D_typeof * * Purpose: Returns a pointer to the dataset's data type. The data type * is not copied. * * Return: Success: Ptr to the dataset's data type, uncopied. * * Failure: NULL * * Programmer: Robb Matzke * Thursday, June 4, 1998 * * Modifications: * *------------------------------------------------------------------------- */ H5T_t * H5D_typeof (const H5D_t *dset) { /* Use FUNC_ENTER_NOINIT here to avoid performance issues */ FUNC_ENTER_NOINIT(H5D_typeof) assert (dset); assert (dset->type); FUNC_LEAVE_NOAPI(dset->type) } /*------------------------------------------------------------------------- * Function: H5D_get_file * * Purpose: Returns the dataset's file pointer. * * Return: Success: Ptr to the dataset's file pointer. * * Failure: NULL * * Programmer: Quincey Koziol * Thursday, October 22, 1998 * * Modifications: * *------------------------------------------------------------------------- */ static H5F_t * H5D_get_file (const H5D_t *dset) { /* Use FUNC_ENTER_NOINIT here to avoid performance issues */ FUNC_ENTER_NOINIT(H5D_get_file) assert (dset); assert (dset->ent.file); FUNC_LEAVE_NOAPI(dset->ent.file) } /*------------------------------------------------------------------------- * Function: H5D_alloc_storage * * Purpose: Allocate storage for the raw data of a dataset. * * Return: Non-negative on success/Negative on failure * * Programmer: Robb Matzke * Friday, January 16, 1998 * * Modifications: * Quincey Koziol * Thursday, August 22, 2002 * Moved here from H5F_arr_create and moved more logic into * this function from places where it was being called. * *------------------------------------------------------------------------- */ herr_t H5D_alloc_storage (H5F_t *f, hid_t dxpl_id, H5D_t *dset/*in,out*/, H5D_time_alloc_t time_alloc, hbool_t update_time, hbool_t full_overwrite) { struct H5O_layout_t *layout; /* The dataset's layout information */ unsigned init_space=0; /* Flag to indicate that space should be initialized */ unsigned addr_set=0; /* Flag to indicate that the dataset's storage address was set */ herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_NOINIT(H5D_alloc_storage) /* check args */ assert (f); assert (dset); /* If the data is stored in external files, don't set an address for the layout * We assume that external storage is already * allocated by the caller, or at least will be before I/O is performed. */ if(dset->efl.nused==0) { /* Get a pointer to the dataset's layout information */ layout=&(dset->layout); switch (layout->type) { case H5D_CONTIGUOUS: if(layout->addr==HADDR_UNDEF) { /* Reserve space in the file for the entire array */ if (H5F_contig_create (f, dxpl_id, layout/*out*/)<0) HGOTO_ERROR (H5E_IO, H5E_CANTINIT, FAIL, "unable to initialize contiguous storage") /* Indicate that we set the storage addr */ addr_set=1; /* Indicate that we should initialize storage space */ init_space=1; } /* end if */ break; case H5D_CHUNKED: if(layout->addr==HADDR_UNDEF) { /* Create the root of the B-tree that describes chunked storage */ if (H5F_istore_create (f, dxpl_id, layout/*out*/)<0) HGOTO_ERROR (H5E_IO, H5E_CANTINIT, FAIL, "unable to initialize chunked storage") /* Indicate that we set the storage addr */ addr_set=1; /* Indicate that we should initialize storage space */ init_space=1; } /* end if */ /* If space allocation is set to 'early' and we are extending * the dataset, indicate that space should be allocated, so the * B-tree gets expanded. -QAK */ if(dset->alloc_time==H5D_ALLOC_TIME_EARLY && time_alloc==H5D_ALLOC_EXTEND) init_space=1; break; case H5D_COMPACT: /* Check if space is already allocated */ if(layout->buf==NULL) { /* Reserve space in layout header message for the entire array. */ assert(layout->size>0); if (NULL==(layout->buf=H5MM_malloc(layout->size))) HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, "unable to allocate memory for compact dataset") layout->dirty = TRUE; /* Indicate that we set the storage addr */ addr_set=1; /* Indicate that we should initialize storage space */ init_space=1; } /* end if */ break; default: assert ("not implemented yet" && 0); #ifdef NDEBUG HGOTO_ERROR (H5E_IO, H5E_UNSUPPORTED, FAIL, "unsupported storage layout") #endif /* NDEBUG */ } /* end switch */ /* Check if we need to initialize the space */ if(init_space) { if (layout->type==H5D_CHUNKED) { /* If we are doing incremental allocation and the B-tree got * created during a H5Dwrite call, don't initialize the storage * now, wait for the actual writes to each block and let the * low-level chunking routines handle initialize the fill-values. * Otherwise, pass along the space initialization call and let * the low-level chunking routines sort out whether to write * fill values to the chunks they allocate space for. Yes, * this is icky. -QAK */ if(!(dset->alloc_time==H5D_ALLOC_TIME_INCR && time_alloc==H5D_ALLOC_WRITE)) { if(H5D_init_storage(dset, full_overwrite, dxpl_id) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize dataset with fill value") } /* end if */ } /* end if */ else { H5D_fill_value_t fill_status; /* The fill value status */ /* Check the dataset's fill-value status */ if (H5P_is_fill_value_defined(&(dset->fill), &fill_status) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't tell if fill value defined") /* If we are filling the dataset on allocation or "if set" and * the fill value _is_ set, do that now */ if(dset->fill_time==H5D_FILL_TIME_ALLOC || (dset->fill_time==H5D_FILL_TIME_IFSET && fill_status==H5D_FILL_VALUE_USER_DEFINED)) { if(H5D_init_storage(dset, full_overwrite, dxpl_id) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize dataset with fill value") } /* end if */ } /* end else */ } /* end if */ /* Also update header message for layout with new address, if we * set the address. (this is improves forward compatibility). */ if(time_alloc!=H5D_ALLOC_CREATE && addr_set) if (H5O_modify (&(dset->ent), H5O_LAYOUT_ID, 0, H5O_FLAG_CONSTANT, update_time, &(dset->layout), dxpl_id) < 0) HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to update layout message") } /* end if */ done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D_alloc_storage() */ /*------------------------------------------------------------------------- * Function: H5D_init_storage * * Purpose: Initialize the data for a new dataset. If a selection is * defined for SPACE then initialize only that part of the * dataset. * * Return: Non-negative on success/Negative on failure * * Programmer: Robb Matzke * Monday, October 5, 1998 * * Modifications: * * Raymond Lu * Tuesday, October 2, 2001 * Changed the way to retrieve property for generic property * list. * *------------------------------------------------------------------------- */ static herr_t H5D_init_storage(H5D_t *dset, hbool_t full_overwrite, hid_t dxpl_id) { hssize_t snpoints; /* Number of points in space (for error checking) */ size_t npoints; /* Number of points in space */ H5S_t *space; /* Dataset's dataspace */ H5P_genplist_t *plist; /* Property list */ herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_NOINIT(H5D_init_storage) assert(dset); /* Get the dataset's dataspace */ space=dset->space; /* Get the number of elements in the dataset's dataspace */ snpoints = H5S_get_simple_extent_npoints(space); assert(snpoints>=0); H5_ASSIGN_OVERFLOW(npoints,snpoints,hssize_t,size_t); switch (dset->layout.type) { case H5D_COMPACT: /* If we will be immediately overwriting the values, don't bother to clear them */ if(!full_overwrite) { /* If the fill value is defined, initialize the data buffer with it */ if(dset->fill.buf) /* Initialize the cached data buffer with the fill value */ H5V_array_fill(dset->layout.buf, dset->fill.buf, dset->fill.size, npoints); else /* If the fill value is default, zero set data buf. */ HDmemset(dset->layout.buf, 0, dset->layout.size); } /* end if */ break; case H5D_CONTIGUOUS: /* Don't write default fill values to external files */ /* If we will be immediately overwriting the values, don't bother to clear them */ if((dset->efl.nused==0 || dset->fill.buf) && !full_overwrite) { /* Get dataset's creation property list */ if (NULL == (plist = H5I_object(dset->dcpl_id))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset creation property list") if (H5F_contig_fill(dset->ent.file, dxpl_id, &(dset->layout), plist, space, &dset->fill, H5T_get_size(dset->type))<0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to allocate all chunks of dataset") } /* end if */ break; case H5D_CHUNKED: /* * Allocate file space * for all chunks now and initialize each chunk with the fill value. */ { /* We only handle simple data spaces so far */ int ndims; hsize_t dim[H5O_LAYOUT_NDIMS]; /* Get dataset's creation property list */ if (NULL == (plist = H5I_object(dset->dcpl_id))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset creation property list") if ((ndims=H5S_get_simple_extent_dims(space, dim, NULL))<0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to get simple data space info") dim[ndims] = dset->layout.dim[ndims]; if (H5F_istore_allocate(dset->ent.file, dxpl_id, &(dset->layout), dim, plist, full_overwrite)<0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to allocate all chunks of dataset") } /* end if */ break; default: assert ("not implemented yet" && 0); #ifdef NDEBUG HGOTO_ERROR (H5E_IO, H5E_UNSUPPORTED, FAIL, "unsupported storage layout") #endif /* NDEBUG */ } /* end switch */ done: FUNC_LEAVE_NOAPI(ret_value) } /*------------------------------------------------------------------------- * Function: H5Dget_storage_size * * Purpose: Returns the amount of storage that is required for the * dataset. For chunked datasets this is the number of allocated * chunks times the chunk size. * * Return: Success: The amount of storage space allocated for the * dataset, not counting meta data. The return * value may be zero if no data has been stored. * * Failure: Zero * * Programmer: Robb Matzke * Wednesday, April 21, 1999 * * Modifications: * *------------------------------------------------------------------------- */ hsize_t H5Dget_storage_size(hid_t dset_id) { H5D_t *dset=NULL; hsize_t ret_value; /* Return value */ FUNC_ENTER_API(H5Dget_storage_size, 0) H5TRACE1("h","i",dset_id); /* Check args */ if (NULL==(dset=H5I_object_verify(dset_id, H5I_DATASET))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, 0, "not a dataset") /* Set return value */ ret_value = H5D_get_storage_size(dset,H5AC_ind_dxpl_id); done: FUNC_LEAVE_API(ret_value) } /*------------------------------------------------------------------------- * Function: H5D_get_storage_size * * Purpose: Determines how much space has been reserved to store the raw * data of a dataset. * * Return: Success: Number of bytes reserved to hold raw data. * * Failure: 0 * * Programmer: Robb Matzke * Wednesday, April 21, 1999 * * Modifications: * *------------------------------------------------------------------------- */ static hsize_t H5D_get_storage_size(const H5D_t *dset, hid_t dxpl_id) { unsigned u; /* Index variable */ hsize_t ret_value; FUNC_ENTER_NOAPI(H5D_get_storage_size, 0) switch(dset->layout.type) { case H5D_CHUNKED: if(dset->layout.addr == HADDR_UNDEF) ret_value=0; else ret_value = H5F_istore_allocated(dset->ent.file, dxpl_id, dset->layout.ndims, dset->layout.addr); break; case H5D_CONTIGUOUS: /* Datasets which are not allocated yet are using no space on disk */ if(dset->layout.addr == HADDR_UNDEF) ret_value=0; else { for (u=0, ret_value=1; ulayout.ndims; u++) ret_value *= dset->layout.dim[u]; } /* end else */ break; case H5D_COMPACT: ret_value = dset->layout.size; break; default: HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, 0, "not a dataset type") } done: FUNC_LEAVE_NOAPI(ret_value) } /*------------------------------------------------------------------------- * Function: H5Dget_offset * * Purpose: Returns the address of dataset in file. * * Return: Success: the address of dataset * * Failure: HADDR_UNDEF * * Programmer: Raymond Lu * November 6, 2002 * * Modifications: * *------------------------------------------------------------------------- */ haddr_t H5Dget_offset(hid_t dset_id) { H5D_t *dset=NULL; haddr_t ret_value; /* Return value */ FUNC_ENTER_API(H5Dget_offset, HADDR_UNDEF) H5TRACE1("a","i",dset_id); /* Check args */ if (NULL==(dset=H5I_object_verify(dset_id, H5I_DATASET))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, HADDR_UNDEF, "not a dataset") /* Set return value */ ret_value = H5D_get_offset(dset); done: FUNC_LEAVE_API(ret_value) } /*------------------------------------------------------------------------- * Function: H5D_get_offset * * Purpose: Private function for H5D_get_offset. Returns the address * of dataset in file. * * Return: Success: the address of dataset * * Failure: HADDR_UNDEF * * Programmer: Raymond Lu * November 6, 2002 * * Modifications: * *------------------------------------------------------------------------- */ static haddr_t H5D_get_offset(const H5D_t *dset) { haddr_t ret_value; haddr_t base_addr; H5F_t *f; FUNC_ENTER_NOAPI(H5D_get_offset, HADDR_UNDEF) assert(dset); switch(dset->layout.type) { case H5D_CHUNKED: case H5D_COMPACT: ret_value = HADDR_UNDEF; break; case H5D_CONTIGUOUS: /* If dataspace hasn't been allocated or dataset is stored in * an external file, the value will be HADDR_UNDEF. */ f = H5D_get_file(dset); base_addr = H5F_get_base_addr(f); /* If there's user block in file, returns the absolute dataset offset * from the beginning of file. */ if(base_addr!=HADDR_UNDEF) ret_value = dset->layout.addr + base_addr; else ret_value = dset->layout.addr; break; default: assert ("not implemented yet" && 0); #ifdef NDEBUG HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, HADDR_UNDEF, "unknown dataset layout type") #endif /* NDEBUG */ } done: FUNC_LEAVE_NOAPI(ret_value) } /*------------------------------------------------------------------------- * Function: H5Diterate * * Purpose: This routine iterates over all the elements selected in a memory * buffer. The callback function is called once for each element selected * in the dataspace. The selection in the dataspace is modified so * that any elements already iterated over are removed from the selection * if the iteration is interrupted (by the H5D_operator_t function * returning non-zero) in the "middle" of the iteration and may be * re-started by the user where it left off. * * NOTE: Until "subtracting" elements from a selection is implemented, * the selection is not modified. * * Parameters: * void *buf; IN/OUT: Pointer to the buffer in memory containing * the elements to iterate over. * hid_t type_id; IN: Datatype ID for the elements stored in BUF. * hid_t space_id; IN: Dataspace ID for BUF, also contains the * selection to iterate over. * H5D_operator_t op; IN: Function pointer to the routine to be * called for each element in BUF iterated over. * void *operator_data; IN/OUT: Pointer to any user-defined data * associated with the operation. * * Operation information: * H5D_operator_t is defined as: * typedef herr_t (*H5D_operator_t)(void *elem, hid_t type_id, * hsize_t ndim, hssize_t *point, void *operator_data); * * H5D_operator_t parameters: * void *elem; IN/OUT: Pointer to the element in memory containing * the current point. * hid_t type_id; IN: Datatype ID for the elements stored in ELEM. * hsize_t ndim; IN: Number of dimensions for POINT array * hssize_t *point; IN: Array containing the location of the element * within the original dataspace. * void *operator_data; IN/OUT: Pointer to any user-defined data * associated with the operation. * * The return values from an operator are: * Zero causes the iterator to continue, returning zero when all * elements have been processed. * Positive causes the iterator to immediately return that positive * value, indicating short-circuit success. The iterator can be * restarted at the next element. * Negative causes the iterator to immediately return that value, * indicating failure. The iterator can be restarted at the next * element. * * Return: Returns the return value of the last operator if it was non-zero, * or zero if all elements were processed. Otherwise returns a * negative value. * * Programmer: Quincey Koziol * Friday, June 11, 1999 * * Modifications: * *------------------------------------------------------------------------- */ herr_t H5Diterate(void *buf, hid_t type_id, hid_t space_id, H5D_operator_t op, void *operator_data) { H5S_t *space = NULL; herr_t ret_value; FUNC_ENTER_API(H5Diterate, FAIL) H5TRACE5("e","xiixx",buf,type_id,space_id,op,operator_data); /* Check args */ if (NULL==op) HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "invalid operator") if (buf==NULL) HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "invalid buffer") if (H5I_DATATYPE != H5I_get_type(type_id)) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "invalid datatype") if (NULL == (space = H5I_object_verify(space_id, H5I_DATASPACE))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "invalid dataspace") ret_value=H5S_select_iterate(buf,type_id,space,op,operator_data); done: FUNC_LEAVE_API(ret_value) } /* end H5Diterate() */ /*------------------------------------------------------------------------- * Function: H5Dvlen_reclaim * * Purpose: Frees the buffers allocated for storing variable-length data * in memory. Only frees the VL data in the selection defined in the * dataspace. The dataset transfer property list is required to find the * correct allocation/free methods for the VL data in the buffer. * * Return: Non-negative on success, negative on failure * * Programmer: Quincey Koziol * Thursday, June 10, 1999 * * Modifications: * *------------------------------------------------------------------------- */ herr_t H5Dvlen_reclaim(hid_t type_id, hid_t space_id, hid_t plist_id, void *buf) { herr_t ret_value; FUNC_ENTER_API(H5Dvlen_reclaim, FAIL) H5TRACE4("e","iiix",type_id,space_id,plist_id,buf); /* Check args */ if (H5I_DATATYPE!=H5I_get_type(type_id) || H5I_DATASPACE!=H5I_get_type(space_id) || buf==NULL) HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "invalid argument") /* Get the default dataset transfer property list if the user didn't provide one */ if (H5P_DEFAULT == plist_id) plist_id= H5P_DATASET_XFER_DEFAULT; else if (TRUE!=H5P_isa_class(plist_id,H5P_DATASET_XFER)) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not xfer parms") /* Call H5Diterate with args, etc. */ ret_value=H5Diterate(buf,type_id,space_id,H5T_vlen_reclaim,&plist_id); done: FUNC_LEAVE_API(ret_value) } /* end H5Dvlen_reclaim() */ /*------------------------------------------------------------------------- * Function: H5D_vlen_get_buf_size_alloc * * Purpose: This routine makes certain there is enough space in the temporary * buffer for the new data to read in. All the VL data read in is actually * placed in this buffer, overwriting the previous data. Needless to say, * this data is not actually usable. * * Return: Non-negative on success, negative on failure * * Programmer: Quincey Koziol * Tuesday, August 17, 1999 * * Modifications: * *------------------------------------------------------------------------- */ static void * H5D_vlen_get_buf_size_alloc(size_t size, void *info) { H5D_vlen_bufsize_t *vlen_bufsize=(H5D_vlen_bufsize_t *)info; void *ret_value; /* Return value */ FUNC_ENTER_NOAPI(H5D_vlen_get_buf_size_alloc, NULL) /* Get a temporary pointer to space for the VL data */ if ((vlen_bufsize->vl_tbuf=H5FL_BLK_REALLOC(vlen_vl_buf,vlen_bufsize->vl_tbuf,size))!=NULL) vlen_bufsize->size+=size; /* Set return value */ ret_value=vlen_bufsize->vl_tbuf; done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D_vlen_get_buf_size_alloc() */ /*------------------------------------------------------------------------- * Function: H5D_vlen_get_buf_size * * Purpose: This routine checks the number of bytes required to store a single * element from a dataset in memory, creating a selection with just the * single element selected to read in the element and using a custom memory * allocator for any VL data encountered. * The *size value is modified according to how many bytes are * required to store the element in memory. * * Implementation: This routine actually performs the read with a custom * memory manager which basically just counts the bytes requested and * uses a temporary memory buffer (through the H5FL API) to make certain * enough space is available to perform the read. Then the temporary * buffer is released and the number of bytes allocated is returned. * Kinda kludgy, but easier than the other method of trying to figure out * the sizes without actually reading the data in... - QAK * * Return: Non-negative on success, negative on failure * * Programmer: Quincey Koziol * Tuesday, August 17, 1999 * * Modifications: * *------------------------------------------------------------------------- */ static herr_t H5D_vlen_get_buf_size(void UNUSED *elem, hid_t type_id, hsize_t UNUSED ndim, hssize_t *point, void *op_data) { H5D_vlen_bufsize_t *vlen_bufsize=(H5D_vlen_bufsize_t *)op_data; H5T_t *dt = NULL; herr_t ret_value=0; /* The correct return value, if this function succeeds */ FUNC_ENTER_NOAPI(H5D_vlen_get_buf_size, FAIL) assert(op_data); assert(H5I_DATATYPE == H5I_get_type(type_id)); /* Check args */ if (NULL==(dt=H5I_object(type_id))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a data type") /* Make certain there is enough fixed-length buffer available */ if ((vlen_bufsize->fl_tbuf=H5FL_BLK_REALLOC(vlen_fl_buf,vlen_bufsize->fl_tbuf,H5T_get_size(dt)))==NULL) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "can't resize tbuf") /* Select point to read in */ if (H5Sselect_elements(vlen_bufsize->fspace_id,H5S_SELECT_SET,1,(const hssize_t **)point)<0) HGOTO_ERROR(H5E_DATASPACE, H5E_CANTCREATE, FAIL, "can't select point") /* Read in the point (with the custom VL memory allocator) */ if(H5Dread(vlen_bufsize->dataset_id,type_id,vlen_bufsize->mspace_id,vlen_bufsize->fspace_id,vlen_bufsize->xfer_pid,vlen_bufsize->fl_tbuf)<0) HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "can't read point") done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D_vlen_get_buf_size() */ /*lint !e715 !e818 Make lint ignore unused parameters */ /*------------------------------------------------------------------------- * Function: H5Dvlen_get_buf_size * * Purpose: This routine checks the number of bytes required to store the VL * data from the dataset, using the space_id for the selection in the * dataset on disk and the type_id for the memory representation of the * VL data, in memory. The *size value is modified according to how many * bytes are required to store the VL data in memory. * * Implementation: This routine actually performs the read with a custom * memory manager which basically just counts the bytes requested and * uses a temporary memory buffer (through the H5FL API) to make certain * enough space is available to perform the read. Then the temporary * buffer is released and the number of bytes allocated is returned. * Kinda kludgy, but easier than the other method of trying to figure out * the sizes without actually reading the data in... - QAK * * Return: Non-negative on success, negative on failure * * Programmer: Quincey Koziol * Wednesday, August 11, 1999 * * Modifications: * *------------------------------------------------------------------------- */ herr_t H5Dvlen_get_buf_size(hid_t dataset_id, hid_t type_id, hid_t space_id, hsize_t *size) { H5D_vlen_bufsize_t vlen_bufsize = {0, 0, 0, 0, 0, 0, 0}; char bogus; /* bogus value to pass to H5Diterate() */ H5P_genclass_t *pclass; /* Property class */ H5P_genplist_t *plist; /* Property list */ herr_t ret_value=FAIL; FUNC_ENTER_API(H5Dvlen_get_buf_size, FAIL) H5TRACE4("e","iii*h",dataset_id,type_id,space_id,size); /* Check args */ if (H5I_DATASET!=H5I_get_type(dataset_id) || H5I_DATATYPE!=H5I_get_type(type_id) || H5I_DATASPACE!=H5I_get_type(space_id) || size==NULL) HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "invalid argument") /* Save the dataset ID */ vlen_bufsize.dataset_id=dataset_id; /* Get a copy of the dataspace ID */ if((vlen_bufsize.fspace_id=H5Dget_space(dataset_id))<0) HGOTO_ERROR(H5E_DATASPACE, H5E_CANTCOPY, FAIL, "can't copy dataspace") /* Create a scalar for the memory dataspace */ if((vlen_bufsize.mspace_id=H5Screate(H5S_SCALAR))<0) HGOTO_ERROR(H5E_DATASPACE, H5E_CANTCOPY, FAIL, "can't create dataspace") /* Grab the temporary buffers required */ if((vlen_bufsize.fl_tbuf=H5FL_BLK_MALLOC(vlen_fl_buf,1))==NULL) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "no temporary buffers available") if((vlen_bufsize.vl_tbuf=H5FL_BLK_MALLOC(vlen_vl_buf,1))==NULL) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "no temporary buffers available") /* Get the pointer to the dataset transfer class */ if (NULL == (pclass = H5I_object(H5P_CLS_DATASET_XFER_g))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a property list class") /* Change to the custom memory allocation routines for reading VL data */ if((vlen_bufsize.xfer_pid=H5P_create_id(pclass))<0) HGOTO_ERROR(H5E_PLIST, H5E_CANTCREATE, FAIL, "no dataset xfer plists available") /* Get the property list struct */ if (NULL == (plist = H5I_object(vlen_bufsize.xfer_pid))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset transfer property list") /* Set the memory manager to the special allocation routine */ if(H5P_set_vlen_mem_manager(plist,H5D_vlen_get_buf_size_alloc,&vlen_bufsize,NULL,NULL)<0) HGOTO_ERROR(H5E_PLIST, H5E_CANTINIT, FAIL, "can't set VL data allocation routine") /* Set the initial number of bytes required */ vlen_bufsize.size=0; /* Call H5Diterate with args, etc. */ ret_value=H5Diterate(&bogus,type_id,space_id,H5D_vlen_get_buf_size,&vlen_bufsize); /* Get the size if we succeeded */ if(ret_value>=0) *size=vlen_bufsize.size; done: if(vlen_bufsize.fspace_id>0) { if(H5I_dec_ref(vlen_bufsize.fspace_id)<0) HDONE_ERROR(H5E_DATASET, H5E_CLOSEERROR, FAIL, "unable to release dataspace"); } /* end if */ if(vlen_bufsize.mspace_id>0) { if(H5I_dec_ref(vlen_bufsize.mspace_id)<0) HDONE_ERROR(H5E_DATASET, H5E_CLOSEERROR, FAIL, "unable to release dataspace"); } /* end if */ if(vlen_bufsize.fl_tbuf!=NULL) H5FL_BLK_FREE(vlen_fl_buf,vlen_bufsize.fl_tbuf); if(vlen_bufsize.vl_tbuf!=NULL) H5FL_BLK_FREE(vlen_vl_buf,vlen_bufsize.vl_tbuf); if(vlen_bufsize.xfer_pid>0) { if(H5I_dec_ref(vlen_bufsize.xfer_pid)<0) HDONE_ERROR(H5E_DATASET, H5E_CANTDEC, FAIL, "unable to decrement ref count on property list"); } /* end if */ FUNC_LEAVE_API(ret_value) } /* end H5Dvlen_get_buf_size() */ /*------------------------------------------------------------------------- * Function: H5Dset_extent * * Purpose: Modifies the dimensions of a dataset, based on H5Dextend. * Can change to a lower dimension. * * Return: Success: 0, Failure: -1 * * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu * Robb Matzke * * Date: April 9, 2002 * * Comments: Public function, calls private H5D_set_extent * * Modifications: * *------------------------------------------------------------------------- */ herr_t H5Dset_extent(hid_t dset_id, const hsize_t *size) { H5D_t *dset = NULL; herr_t ret_value=SUCCEED; /* Return value */ FUNC_ENTER_API(H5Dset_extent, FAIL) H5TRACE2("e","i*h",dset_id,size); /* Check args */ if(NULL == (dset = H5I_object_verify(dset_id, H5I_DATASET))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset") if(!size) HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "no size specified") /* Private function */ if(H5D_set_extent(dset, size, H5AC_dxpl_id) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to set extend dataset") done: FUNC_LEAVE_API(ret_value) } /*------------------------------------------------------------------------- * Function: H5D_set_extent * * Purpose: Based in H5D_extend, allows change to a lower dimension, * calls H5S_set_extent and H5F_istore_prune_by_extent instead * * Return: Success: 0, Failure: -1 * * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu * Robb Matzke * * Date: April 9, 2002 * * Comments: Private function * * Modifications: * *------------------------------------------------------------------------- */ static herr_t H5D_set_extent(H5D_t *dset, const hsize_t *size, hid_t dxpl_id) { hsize_t curr_dims[H5O_LAYOUT_NDIMS]; /* Current dimension sizes */ int rank; /* Dataspace # of dimensions */ herr_t ret_value = SUCCEED; /* Return value */ H5S_t *space = NULL; H5P_genplist_t *plist; int u; unsigned shrink = 0; /* Flag to indicate a dimension has shrank */ unsigned expand = 0; /* Flag to indicate a dimension has grown */ int changed = 0; FUNC_ENTER_NOAPI(H5D_set_extent, FAIL) /* Check args */ assert(dset); assert(size); /*------------------------------------------------------------------------- * Get the data space *------------------------------------------------------------------------- */ space = dset->space; /*------------------------------------------------------------------------- * Check if we are shrinking or expanding any of the dimensions *------------------------------------------------------------------------- */ if((rank = H5S_get_simple_extent_dims(space, curr_dims, NULL)) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get dataset dimensions") for(u = 0; u < rank; u++) { if(size[u] < curr_dims[u]) shrink = 1; if(size[u] > curr_dims[u]) expand = 1; } /*------------------------------------------------------------------------- * Modify the size of the data space *------------------------------------------------------------------------- */ if((changed=H5S_set_extent(space, size)) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to modify size of data space") /* Don't bother updating things, unless they've changed */ if(changed) { /*------------------------------------------------------------------------- * Modify the dataset storage *------------------------------------------------------------------------- */ /* Save the new dataspace in the file if necessary */ if(H5S_modify(&(dset->ent), space, TRUE, dxpl_id) < 0) HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "unable to update file with new dataspace") /* Allocate space for the new parts of the dataset, if appropriate */ if(expand && dset->alloc_time==H5D_ALLOC_TIME_EARLY) if(H5D_alloc_storage(dset->ent.file, dxpl_id, dset, H5D_ALLOC_EXTEND, TRUE, FALSE) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize dataset storage") /*------------------------------------------------------------------------- * Remove chunk information in the case of chunked datasets * This removal takes place only in case we are shrinking the dateset *------------------------------------------------------------------------- */ if(shrink && H5D_CHUNKED == dset->layout.type) { /* Get the dataset creation property list */ if(NULL == (plist = H5I_object(dset->dcpl_id))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dset creation property list") /* Remove excess chunks */ if(H5F_istore_prune_by_extent(dset->ent.file, dxpl_id, &dset->layout, space) < 0) HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "unable to remove chunks ") /* Reset the elements outsize the new dimensions, but in existing chunks */ if(H5F_istore_initialize_by_extent(dset->ent.file, dxpl_id, &dset->layout, plist, space) < 0) HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "unable to initialize chunks ") } /* end if */ } /* end if */ done: FUNC_LEAVE_NOAPI(ret_value) } /*------------------------------------------------------------------------- * Function: H5D_flush * * Purpose: Flush any dataset information cached in memory * * Return: Success: Non-negative * Failure: Negative * * * Programmer: Ray Lu * * Date: August 14, 2002 * * Comments: Just flushing the compact data information currently. * * Modifications: * *------------------------------------------------------------------------- */ herr_t H5D_flush(H5F_t *f, hid_t dxpl_id) { int num_dsets; /* Number of datasets in file */ hid_t *id_list=NULL; /* list of dataset IDs */ H5D_t *dataset=NULL; /* Dataset pointer */ herr_t ret_value = SUCCEED; /* Return value */ int j; /* Index variable */ FUNC_ENTER_NOAPI(H5D_flush, FAIL) /* Check args */ assert(f); /* Update layout message for compact dataset */ if((num_dsets=H5F_get_obj_count(f, H5F_OBJ_DATASET))<0) HGOTO_ERROR(H5E_FILE, H5E_CANTINIT, FAIL, "unable to get dataset count") H5_CHECK_OVERFLOW(num_dsets,int,size_t); if(NULL==(id_list=H5MM_malloc((size_t)num_dsets*sizeof(hid_t)))) HGOTO_ERROR(H5E_FILE, H5E_CANTINIT, FAIL, "unable to allocate memory for ID list") if(H5F_get_obj_ids(f, H5F_OBJ_DATASET, -1, id_list)<0) HGOTO_ERROR(H5E_FILE, H5E_CANTINIT, FAIL, "unable to get dataset ID list") for(j=0; jlayout.type==H5D_COMPACT && dataset->layout.dirty) if(H5O_modify(&(dataset->ent), H5O_LAYOUT_ID, 0, 0, 1, &(dataset->layout), dxpl_id)<0) HGOTO_ERROR(H5E_FILE, H5E_CANTINIT, FAIL, "unable to update layout message") dataset->layout.dirty = FALSE; } done: if(id_list!=NULL) H5MM_xfree(id_list); FUNC_LEAVE_NOAPI(ret_value) } /* end H5D_flush() */ /*------------------------------------------------------------------------- * Function: H5Ddebug * * Purpose: Prints various information about a dataset. This function is * not to be documented in the API at this time. * * Return: Success: Non-negative * * Failure: Negative * * Programmer: Robb Matzke * Wednesday, April 28, 1999 * * Modifications: * *------------------------------------------------------------------------- */ herr_t H5Ddebug(hid_t dset_id) { H5D_t *dset=NULL; herr_t ret_value=SUCCEED; /* Return value */ FUNC_ENTER_API(H5Ddebug, FAIL) H5TRACE1("e","i",dset_id); /* Check args */ if (NULL==(dset=H5I_object_verify(dset_id, H5I_DATASET))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset") /* Print B-tree information */ if (H5D_CHUNKED==dset->layout.type) { (void)H5F_istore_dump_btree(dset->ent.file, H5AC_dxpl_id, stdout, dset->layout.ndims, dset->layout.addr); } else if (H5D_CONTIGUOUS==dset->layout.type) { HDfprintf(stdout, " %-10s %a\n", "Address:", dset->layout.addr); } done: FUNC_LEAVE_API(ret_value) }