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hdf5/src/H5D.c

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/****************************************************************************
* NCSA HDF *
* Software Development Group *
* National Center for Supercomputing Applications *
* University of Illinois at Urbana-Champaign *
* 605 E. Springfield, Champaign IL 61820 *
* *
* For conditions of distribution and use, see the accompanying *
* hdf/COPYING file. *
* *
****************************************************************************/
#ifdef RCSID
static char RcsId[] = "@(#)$Revision$";
#endif
/* $Id$ */
#include <H5private.h> /* Generic Functions */
#include <H5Iprivate.h> /* IDs */
#include <H5ACprivate.h> /* Cache */
#include <H5Dprivate.h> /* Dataset functions */
#include <H5Eprivate.h> /* Error handling */
#include <H5Gprivate.h> /* Group headers */
#include <H5HLprivate.h> /* Name heap */
#include <H5MFprivate.h> /* File space allocation header */
#include <H5MMprivate.h> /* Memory management */
#include <H5Oprivate.h> /* Object headers */
#include <H5Pprivate.h> /* Property lists */
#include <H5Sprivate.h> /* Dataspace functions rky 980813 */
#include <H5TBprivate.h> /* Temporary buffers */
#include <H5Vprivate.h> /* Vector and array functions */
#include <H5Zprivate.h> /* Data filters */
#define PABLO_MASK H5D_mask
/*
* A dataset is the following struct.
*/
struct H5D_t {
H5G_entry_t ent; /*cached object header stuff */
H5T_t *type; /*datatype of this dataset */
H5D_create_t *create_parms; /*creation parameters */
H5O_layout_t layout; /*data layout */
};
/* Default dataset creation property list */
const H5D_create_t H5D_create_dflt = {
H5D_CONTIGUOUS, /* Layout */
1, /* Chunk dimensions */
{1, 1, 1, 1, 1, 1, 1, 1, /* Chunk size. These default values....*/
1, 1, 1, 1, 1, 1, 1, 1, /*...are quite useless. Larger chunks..*/
1, 1, 1, 1, 1, 1, 1, 1, /*...produce fewer, but larger I/O......*/
1, 1, 1, 1, 1, 1, 1, 1}, /*...requests. */
/* Fill value */
{NULL, 0, NULL}, /* No fill value */
/* External file list */
{H5F_ADDR_UNDEF, /* External file list heap address */
0, /*...slots allocated */
0, /*...slots used */
NULL}, /*...slot array */
/* Filters */
{0, 0, NULL} /* No filters in pipeline */
};
/* Default dataset transfer property list */
const H5D_xfer_t H5D_xfer_dflt = {
1024*1024, /* Temporary buffer size */
NULL, /* Type conversion buffer or NULL */
NULL, /* Background buffer or NULL */
H5T_BKG_NO, /* Type of background buffer needed */
{0.1, 0.5, 0.9}, /* B-tree node splitting ratios */
#ifndef HAVE_PARALLEL
1, /* Cache the hyperslab blocks by default*/
#else
0, /*
* Don't cache the hyperslab blocks by
* default (for parallel)
*/
#endif /* HAVE_PARALLEL */
0, /*
* Default to no upper limit on hyperslab
* block size to cache
*/
#ifdef HAVE_PARALLEL
H5D_XFER_DFLT, /* Independent data transfer */
#endif
};
/* Interface initialization? */
static hbool_t interface_initialize_g = FALSE;
#define INTERFACE_INIT H5D_init_interface
static herr_t H5D_init_interface(void);
static void H5D_term_interface(void);
static herr_t H5D_init_storage(H5D_t *dataset, const H5S_t *space);
/*--------------------------------------------------------------------------
NAME
H5D_init_interface -- Initialize interface-specific information
USAGE
herr_t H5D_init_interface()
RETURNS
SUCCEED/FAIL
DESCRIPTION
Initializes any interface-specific data or routines.
--------------------------------------------------------------------------*/
static herr_t
H5D_init_interface(void)
{
herr_t ret_value = SUCCEED;
FUNC_ENTER(H5D_init_interface, FAIL);
/* Initialize the atom group for the dataset IDs */
if ((ret_value = H5I_init_group(H5I_DATASET, H5I_DATASETID_HASHSIZE,
H5D_RESERVED_ATOMS,
(herr_t (*)(void *)) H5D_close)) != FAIL) {
ret_value = H5_add_exit(H5D_term_interface);
}
FUNC_LEAVE(ret_value);
}
/*--------------------------------------------------------------------------
NAME
H5D_term_interface
PURPOSE
Terminate various H5D objects
USAGE
void H5D_term_interface()
RETURNS
SUCCEED/FAIL
DESCRIPTION
Release the atom group and any other resources allocated.
GLOBAL VARIABLES
COMMENTS, BUGS, ASSUMPTIONS
Can't report errors...
EXAMPLES
REVISION LOG
--------------------------------------------------------------------------*/
static void
H5D_term_interface(void)
{
H5I_destroy_group(H5I_DATASET);
}
/*-------------------------------------------------------------------------
* 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 (PLIST_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 plist_id)
{
H5G_entry_t *loc = NULL;
H5T_t *type = NULL;
H5S_t *space = NULL;
H5D_t *new_dset = NULL;
hid_t ret_value = FAIL;
const H5D_create_t *create_parms = NULL;
FUNC_ENTER(H5Dcreate, FAIL);
H5TRACE5("i","isiii",loc_id,name,type_id,space_id,plist_id);
/* Check arguments */
if (NULL == (loc = H5G_loc(loc_id))) {
HRETURN_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a location");
}
if (!name || !*name) {
HRETURN_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "no name");
}
if (H5I_DATATYPE != H5I_get_type(type_id) ||
NULL == (type = H5I_object(type_id))) {
HRETURN_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a type");
}
if (H5I_DATASPACE != H5I_get_type(space_id) ||
NULL == (space = H5I_object(space_id))) {
HRETURN_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a data space");
}
if (H5P_DEFAULT==plist_id) {
create_parms = &H5D_create_dflt;
} else if (H5P_DATASET_CREATE != H5P_get_class(plist_id) ||
NULL == (create_parms = H5I_object(plist_id))) {
HRETURN_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL,
"not a dataset creation property list");
}
/* build and open the new dataset */
if (NULL == (new_dset = H5D_create(loc, name, type, space,
create_parms))) {
HRETURN_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) {
H5D_close(new_dset);
HRETURN_ERROR(H5E_DATASET, H5E_CANTREGISTER, FAIL,
"unable to register dataset");
}
FUNC_LEAVE(ret_value);
}
/*-------------------------------------------------------------------------
* Function: H5Dopen
*
* Purpose: Finds a dataset named NAME 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 */
H5D_t *dataset = NULL; /*the dataset */
hid_t ret_value = FAIL;
FUNC_ENTER(H5Dopen, FAIL);
H5TRACE2("i","is",loc_id,name);
/* Check args */
if (NULL == (loc = H5G_loc(loc_id))) {
HRETURN_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a location");
}
if (!name || !*name) {
HRETURN_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "no name");
}
/* Find the dataset */
if (NULL == (dataset = H5D_open(loc, name))) {
HRETURN_ERROR(H5E_DATASET, H5E_NOTFOUND, FAIL, "dataset not found");
}
/* Create an atom for the dataset */
if ((ret_value = H5I_register(H5I_DATASET, dataset)) < 0) {
H5D_close(dataset);
HRETURN_ERROR(H5E_DATASET, H5E_CANTREGISTER, FAIL,
"can't register dataset");
}
FUNC_LEAVE(ret_value);
}
/*-------------------------------------------------------------------------
* Function: H5Dclose
*
* Purpose: Closes access to a dataset (DATASET_ID) and releases
* resources used by it. It is illegal to subsequently use that
* same dataset ID in calls to other dataset functions.
*
* Return: Success: SUCCEED
*
* Failure: FAIL
*
* Errors:
* ARGS BADTYPE Not a dataset.
* DATASET CANTINIT Can't free.
*
* Programmer: Robb Matzke
* Thursday, December 4, 1997
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
herr_t
H5Dclose(hid_t dset_id)
{
H5D_t *dset = NULL; /* dataset object to release */
FUNC_ENTER(H5Dclose, FAIL);
H5TRACE1("e","i",dset_id);
/* Check args */
if (H5I_DATASET != H5I_get_type(dset_id) ||
NULL == (dset = H5I_object(dset_id)) ||
NULL == dset->ent.file) {
HRETURN_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset");
}
/*
* Decrement the counter on the dataset. It will be freed if the count
* reaches zero.
*/
if (H5I_dec_ref(dset_id) < 0) {
HRETURN_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "can't free");
}
FUNC_LEAVE(SUCCEED);
}
/*-------------------------------------------------------------------------
* Function: H5Dget_space
*
* Purpose: Returns a copy of the file data space for a dataset.
*
* Return: Success: ID for a copy of the data space. The data
* space should be released by calling
* H5Sclose().
*
* Failure: FAIL
*
* Programmer: Robb Matzke
* Wednesday, January 28, 1998
*
* Modifications:
* 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 = FAIL;
FUNC_ENTER (H5Dget_space, FAIL);
H5TRACE1("i","i",dset_id);
/* Check args */
if (H5I_DATASET!=H5I_get_type (dset_id) ||
NULL==(dset=H5I_object (dset_id))) {
HRETURN_ERROR (H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset");
}
/* Read the data space message and return a data space object */
if (NULL==(space=H5D_get_space (dset))) {
HRETURN_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL,
"unable to get data space");
}
/* Create an atom */
if ((ret_value=H5I_register (H5I_DATASPACE, space))<0) {
H5S_close (space);
HRETURN_ERROR (H5E_ATOM, H5E_CANTREGISTER, FAIL,
"unable to register data space");
}
FUNC_LEAVE (ret_value);
}
/*-------------------------------------------------------------------------
* Function: H5D_get_space
*
* Purpose: Returns the data space associated with the dataset.
*
* Return: Success: Ptr to a copy of the data space.
*
* Failure: NULL
*
* Programmer: Robb Matzke
* Tuesday, August 25, 1998
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
H5S_t *
H5D_get_space(H5D_t *dset)
{
H5S_t *space = NULL;
FUNC_ENTER(H5D_get_space, NULL);
assert(dset);
if (NULL==(space=H5S_read(&(dset->ent)))) {
HRETURN_ERROR(H5E_DATASET, H5E_CANTINIT, NULL,
"unable to load space info from dataset header");
}
FUNC_LEAVE(space);
}
/*-------------------------------------------------------------------------
* 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 (H5Dget_type, FAIL);
H5TRACE1("i","i",dset_id);
/* Check args */
if (H5I_DATASET!=H5I_get_type (dset_id) ||
NULL==(dset=H5I_object (dset_id))) {
HRETURN_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))) {
HRETURN_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL,
"unable to copy the data type");
}
if (H5T_lock (copied_type, FALSE)<0) {
H5T_close (copied_type);
HRETURN_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) {
H5T_close (copied_type);
HRETURN_ERROR (H5E_ATOM, H5E_CANTREGISTER, FAIL,
"unable to register data type");
}
FUNC_LEAVE (ret_value);
}
/*-------------------------------------------------------------------------
* Function: H5Dget_create_plist
*
* Purpose: Returns a copy of the dataset creation property list.
*
* Return: Success: ID for a copy of the dataset creation
* property list. The template should be
* released by calling H5Pclose().
*
* Failure: FAIL
*
* Programmer: Robb Matzke
* Tuesday, February 3, 1998
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
hid_t
H5Dget_create_plist(hid_t dset_id)
{
H5D_t *dset = NULL;
H5D_create_t *copied_parms = NULL;
hid_t ret_value = FAIL;
FUNC_ENTER (H5Dget_create_plist, FAIL);
H5TRACE1("i","i",dset_id);
/* Check args */
if (H5I_DATASET!=H5I_get_type (dset_id) ||
NULL==(dset=H5I_object (dset_id))) {
HRETURN_ERROR (H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset");
}
/* Copy the creation property list */
if (NULL==(copied_parms=H5P_copy (H5P_DATASET_CREATE,
dset->create_parms))) {
HRETURN_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL,
"unable to copy the creation property list");
}
/* Copy the dataset type into the fill value message */
if (!copied_parms->fill.type &&
NULL==(copied_parms->fill.type=H5T_copy(dset->type,
H5T_COPY_TRANSIENT))) {
HRETURN_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL,
"unable to copy dataset data type for fill value");
}
/* Create an atom */
if ((ret_value=H5I_register ((H5I_type_t)(H5I_TEMPLATE_0+
H5P_DATASET_CREATE),
copied_parms))<0) {
HRETURN_ERROR (H5E_ATOM, H5E_CANTREGISTER, FAIL,
"unable to register creation property list");
}
FUNC_LEAVE (ret_value);
}
/*-------------------------------------------------------------------------
* Function: H5Dread
*
* Purpose: Reads (part of) a DSET from the file into application
* memory BUF. The part of the dataset to read is defined with
* MEM_SPACE_ID and FILE_SPACE_ID. The data points are
* converted from their file type to the MEM_TYPE_ID specified.
* Additional miscellaneous data transfer properties can be
* passed to this function with the PLIST_ID argument.
*
* The FILE_SPACE_ID can be the constant H5S_ALL which indicates
* that the entire file data space is to be referenced.
*
* The MEM_SPACE_ID can be the constant H5S_ALL in which case
* the memory data space is the same as the file data space
* defined when the dataset was created.
*
* The number of elements in the memory data space must match
* the number of elements in the file data space.
*
* The PLIST_ID can be the constant H5P_DEFAULT in which
* case the default data transfer properties are used.
*
* Return: Success: SUCCEED
*
* Failure: FAIL
*
* Errors:
* ARGS BADTYPE Not a data space.
* ARGS BADTYPE Not a data type.
* ARGS BADTYPE Not a dataset.
* ARGS BADTYPE Not xfer parms.
* ARGS BADVALUE No output buffer.
* DATASET READERROR Can't read data.
*
* Programmer: Robb Matzke
* Thursday, December 4, 1997
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
herr_t
H5Dread(hid_t dset_id, hid_t mem_type_id, hid_t mem_space_id,
hid_t file_space_id, hid_t plist_id, void *buf/*out*/)
{
H5D_t *dset = NULL;
const H5T_t *mem_type = NULL;
const H5S_t *mem_space = NULL;
const H5S_t *file_space = NULL;
const H5D_xfer_t *xfer_parms = NULL;
FUNC_ENTER(H5Dread, FAIL);
H5TRACE6("e","iiiiix",dset_id,mem_type_id,mem_space_id,file_space_id,
plist_id,buf);
/* check arguments */
if (H5I_DATASET != H5I_get_type(dset_id) ||
NULL == (dset = H5I_object(dset_id)) ||
NULL == dset->ent.file) {
HRETURN_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset");
}
if (H5I_DATATYPE != H5I_get_type(mem_type_id) ||
NULL == (mem_type = H5I_object(mem_type_id))) {
HRETURN_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a data type");
}
if (H5S_ALL != mem_space_id) {
if (H5I_DATASPACE != H5I_get_type(mem_space_id) ||
NULL == (mem_space = H5I_object(mem_space_id))) {
HRETURN_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a data space");
}
/* Check for valid selection */
if(H5S_select_valid(mem_space)!=TRUE) {
HRETURN_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL,
"selection+offset not within extent");
}
}
if (H5S_ALL != file_space_id) {
if (H5I_DATASPACE != H5I_get_type(file_space_id) ||
NULL == (file_space = H5I_object(file_space_id))) {
HRETURN_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a data space");
}
/* Check for valid selection */
if(H5S_select_valid(file_space)!=TRUE) {
HRETURN_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL,
"selection+offset not within extent");
}
}
if (H5P_DEFAULT == plist_id) {
xfer_parms = &H5D_xfer_dflt;
} else if (H5P_DATASET_XFER != H5P_get_class(plist_id) ||
NULL == (xfer_parms = H5I_object(plist_id))) {
HRETURN_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not xfer parms");
}
if (!buf) {
HRETURN_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "no output buffer");
}
/* read raw data */
if (H5D_read(dset, mem_type, mem_space, file_space, xfer_parms,
buf/*out*/) < 0) {
HRETURN_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "can't read data");
}
FUNC_LEAVE(SUCCEED);
}
/*-------------------------------------------------------------------------
* Function: H5Dwrite
*
* Purpose: Writes (part of) a DSET from application memory BUF to the
* file. The part of the dataset to write is defined with the
* MEM_SPACE_ID and FILE_SPACE_ID arguments. The data points
* are converted from their current type (MEM_TYPE_ID) to their
* file data type. Additional miscellaneous data transfer
* properties can be passed to this function with the
* PLIST_ID argument.
*
* The FILE_SPACE_ID can be the constant H5S_ALL which indicates
* that the entire file data space is to be referenced.
*
* The MEM_SPACE_ID can be the constant H5S_ALL in which case
* the memory data space is the same as the file data space
* defined when the dataset was created.
*
* The number of elements in the memory data space must match
* the number of elements in the file data space.
*
* The PLIST_ID can be the constant H5P_DEFAULT in which
* case the default data transfer properties are used.
*
* Return: Success: SUCCEED
*
* Failure: FAIL
*
* Errors:
*
* Programmer: Robb Matzke
* Thursday, December 4, 1997
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
herr_t
H5Dwrite(hid_t dset_id, hid_t mem_type_id, hid_t mem_space_id,
hid_t file_space_id, hid_t plist_id, const void *buf)
{
H5D_t *dset = NULL;
const H5T_t *mem_type = NULL;
const H5S_t *mem_space = NULL;
const H5S_t *file_space = NULL;
const H5D_xfer_t *xfer_parms = NULL;
FUNC_ENTER(H5Dwrite, FAIL);
H5TRACE6("e","iiiiix",dset_id,mem_type_id,mem_space_id,file_space_id,
plist_id,buf);
/* check arguments */
if (H5I_DATASET != H5I_get_type(dset_id) ||
NULL == (dset = H5I_object(dset_id)) ||
NULL == dset->ent.file) {
HRETURN_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset");
}
if (H5I_DATATYPE != H5I_get_type(mem_type_id) ||
NULL == (mem_type = H5I_object(mem_type_id))) {
HRETURN_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a data type");
}
if (H5S_ALL != mem_space_id) {
if (H5I_DATASPACE != H5I_get_type(mem_space_id) ||
NULL == (mem_space = H5I_object(mem_space_id))) {
HRETURN_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a data space");
}
/* Check for valid selection */
if (H5S_select_valid(mem_space)!=TRUE) {
HRETURN_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL,
"selection+offset not within extent");
}
}
if (H5S_ALL != file_space_id) {
if (H5I_DATASPACE != H5I_get_type(file_space_id) ||
NULL == (file_space = H5I_object(file_space_id))) {
HRETURN_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a data space");
}
/* Check for valid selection */
if (H5S_select_valid(file_space)!=TRUE) {
HRETURN_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL,
"selection+offset not within extent");
}
}
if (H5P_DEFAULT == plist_id) {
xfer_parms = &H5D_xfer_dflt;
} else if (H5P_DATASET_XFER != H5P_get_class(plist_id) ||
NULL == (xfer_parms = H5I_object(plist_id))) {
HRETURN_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not xfer parms");
}
if (!buf) {
HRETURN_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "no output buffer");
}
/* write raw data */
if (H5D_write(dset, mem_type, mem_space, file_space, xfer_parms,
buf) < 0) {
HRETURN_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "can't write data");
}
FUNC_LEAVE(SUCCEED);
}
/*-------------------------------------------------------------------------
* Function: H5Dextend
*
* Purpose: This function makes sure that the dataset is at least of size
* SIZE. The dimensionality of SIZE is the same as the data
* space of the dataset being changed.
*
* Return: Success: SUCCEED
*
* Failure: FAIL
*
* Programmer: Robb Matzke
* Friday, January 30, 1998
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
herr_t
H5Dextend(hid_t dset_id, const hsize_t *size)
{
H5D_t *dset = NULL;
FUNC_ENTER (H5Dextend, FAIL);
H5TRACE2("e","i*h",dset_id,size);
/* Check args */
if (H5I_DATASET!=H5I_get_type (dset_id) ||
NULL==(dset=H5I_object (dset_id))) {
HRETURN_ERROR (H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset");
}
if (!size) {
HRETURN_ERROR (H5E_ARGS, H5E_BADVALUE, FAIL, "no size specified");
}
/* Increase size */
if (H5D_extend (dset, size)<0) {
HRETURN_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL,
"unable to extend dataset");
}
FUNC_LEAVE (SUCCEED);
}
/*-------------------------------------------------------------------------
* 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:
*
*-------------------------------------------------------------------------
*/
H5D_t *
H5D_new(const H5D_create_t *create_parms)
{
H5D_t *ret_value = NULL; /*return value */
FUNC_ENTER(H5D_new, NULL);
/* check args */
/* Nothing to check */
if (NULL==(ret_value = H5MM_calloc(sizeof(H5D_t)))) {
HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, NULL,
"memory allocation failed");
}
if(create_parms!=NULL) {
ret_value->create_parms = H5P_copy (H5P_DATASET_CREATE, create_parms);
} else {
ret_value->create_parms = H5P_copy (H5P_DATASET_CREATE,
&H5D_create_dflt);
}
H5F_addr_undef(&(ret_value->ent.header));
/* Success */
done:
FUNC_LEAVE(ret_value);
} /* end H5D_new() */
/*-------------------------------------------------------------------------
* 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.
*
*-------------------------------------------------------------------------
*/
H5D_t *
H5D_create(H5G_entry_t *loc, const char *name, const H5T_t *type,
const H5S_t *space, const H5D_create_t *create_parms)
{
H5D_t *new_dset = NULL;
H5D_t *ret_value = NULL;
intn i, ndims;
hsize_t max_dim[H5O_LAYOUT_NDIMS];
H5O_efl_t *efl = NULL;
H5F_t *f = NULL;
FUNC_ENTER(H5D_create, NULL);
/* check args */
assert (loc);
assert (name && *name);
assert (type);
assert (space);
assert (create_parms);
if (create_parms->pline.nfilters>0 &&
H5D_CHUNKED!=create_parms->layout) {
HGOTO_ERROR (H5E_DATASET, H5E_BADVALUE, NULL,
"filters can only be used with chunked layout");
}
/* What file is the dataset being added to? */
if (NULL==(f=H5G_insertion_file(loc, name))) {
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL,
"unable to locate insertion point");
}
#ifdef HAVE_PARALLEL
/* If MPIO is used, no filter support yet. */
if (f->shared->access_parms->driver == H5F_LOW_MPIO &&
create_parms->pline.nfilters>0) {
HGOTO_ERROR (H5E_DATASET, H5E_UNSUPPORTED, NULL,
"Parallel IO does not support filters yet");
}
#endif
/* Initialize the dataset object */
if (NULL==(new_dset = H5D_new(create_parms))) {
HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, NULL,
"memory allocation failed");
}
new_dset->type = H5T_copy(type, H5T_COPY_ALL);
efl = &(new_dset->create_parms->efl);
/* Total raw data size */
new_dset->layout.type = new_dset->create_parms->layout;
new_dset->layout.ndims = H5S_get_simple_extent_ndims(space) + 1;
assert((unsigned)(new_dset->layout.ndims) <= NELMTS(new_dset->layout.dim));
new_dset->layout.dim[new_dset->layout.ndims-1] = H5T_get_size(type);
switch (new_dset->create_parms->layout) {
case H5D_CONTIGUOUS:
/*
* The maximum size of the dataset cannot exceed the storage size.
* Also, only the slowest varying dimension of a simple data space
* can be extendible.
*/
if ((ndims=H5S_get_simple_extent_dims(space, new_dset->layout.dim,
max_dim))<0) {
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL,
"unable to initialize contiguous storage");
}
for (i=1; i<ndims; i++) {
if (max_dim[i]>new_dset->layout.dim[i]) {
HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, NULL,
"only the first dimension can be extendible");
}
}
if (efl->nused>0) {
hsize_t max_points = H5S_get_npoints_max (space);
hsize_t max_storage = H5O_efl_total_size (efl);
if (H5S_UNLIMITED==max_points) {
if (H5O_EFL_UNLIMITED!=max_storage) {
HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, NULL,
"unlimited data space but finite storage");
}
} else if (max_points * H5T_get_size (type) < max_points) {
HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, NULL,
"data space * type size overflowed");
} else if (max_points * H5T_get_size (type) > max_storage) {
HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, NULL,
"data space size exceeds external storage size");
}
} else if (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 (new_dset->create_parms->chunk_ndims !=
H5S_get_simple_extent_ndims(space)) {
HGOTO_ERROR(H5E_DATASET, H5E_BADVALUE, NULL,
"dimensionality of chunks doesn't match the data space");
}
if (efl->nused>0) {
HGOTO_ERROR (H5E_DATASET, H5E_BADVALUE, NULL,
"external storage not supported with chunked layout");
}
for (i=0; i<new_dset->layout.ndims-1; i++) {
new_dset->layout.dim[i] = new_dset->create_parms->chunk_size[i];
}
break;
default:
HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, NULL, "not implemented yet");
}
/* Create (open for write access) an object header */
if (H5O_create(f, 96, &(new_dset->ent)) < 0) {
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL,
"unable to create dataset object header");
}
/* Convert the fill value to the dataset type and write the message */
if (H5O_fill_convert(&(new_dset->create_parms->fill), new_dset->type)<0) {
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL,
"unable to convert fill value to dataset type");
}
if (new_dset->create_parms->fill.buf &&
H5O_modify(&(new_dset->ent), H5O_FILL, 0, H5O_FLAG_CONSTANT,
&(new_dset->create_parms->fill))<0) {
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL,
"unable to update fill value header message");
}
/* Update the type and space header messages */
if (H5O_modify(&(new_dset->ent), H5O_DTYPE, 0,
H5O_FLAG_CONSTANT|H5O_FLAG_SHARED, new_dset->type)<0 ||
H5S_modify(&(new_dset->ent), space) < 0) {
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL,
"unable to update type or space header messages");
}
/* Update the filters message */
if (new_dset->create_parms->pline.nfilters>0 &&
H5O_modify (&(new_dset->ent), H5O_PLINE, 0, H5O_FLAG_CONSTANT,
&(new_dset->create_parms->pline))<0) {
HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, NULL,
"unable to update filter header message");
}
/*
* Add a modification time message.
*/
if (H5O_touch(&(new_dset->ent), TRUE)<0) {
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL,
"unable to update modification time message");
}
/*
* Initialize storage. We assume that external storage is already
* initialized by the caller, or at least will be before I/O is
* performed.
*/
if (0==efl->nused) {
if (H5F_arr_create(f, &(new_dset->layout)) < 0) {
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL,
"unable to initialize storage");
}
} else {
H5F_addr_undef (&(new_dset->layout.addr));
}
/* Update layout message */
if (H5O_modify (&(new_dset->ent), H5O_LAYOUT, 0, H5O_FLAG_CONSTANT,
&(new_dset->layout)) < 0) {
HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, NULL,
"unable to update layout message");
}
/* Update external storage message */
if (efl->nused>0) {
size_t heap_size = H5HL_ALIGN (1);
for (i=0; i<efl->nused; i++) {
heap_size += H5HL_ALIGN (HDstrlen (efl->slot[i].name)+1);
}
if (H5HL_create (f, heap_size, &(efl->heap_addr))<0 ||
(size_t)(-1)==H5HL_insert (f, &(efl->heap_addr), 1, "")) {
HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, NULL,
"unable to create external file list name heap");
}
if (H5O_modify (&(new_dset->ent), H5O_EFL, 0, H5O_FLAG_CONSTANT,
efl)<0) {
HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, NULL,
"unable to update external file list message");
}
}
/* Initialize the raw data */
if (H5D_init_storage(new_dset, space)<0) {
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL,
"unable to initialize storage");
}
/* Give the dataset a name */
if (H5G_insert(loc, name, &(new_dset->ent)) < 0) {
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "unable to name dataset");
}
/* Success */
ret_value = new_dset;
done:
if (!ret_value && new_dset) {
if (new_dset->type) H5T_close(new_dset->type);
if (new_dset->create_parms) {
H5P_close (H5P_DATASET_CREATE, new_dset->create_parms);
new_dset->create_parms = NULL;
}
if (H5F_addr_defined(&(new_dset->ent.header))) {
H5O_close(&(new_dset->ent));
}
new_dset->ent.file = NULL;
H5MM_xfree(new_dset);
}
FUNC_LEAVE(ret_value);
}
/*-------------------------------------------------------------------------
* Function: H5D_open
*
* Purpose: Finds a dataset named NAME in file F and builds a descriptor
* for it, opening it for access.
*
* Return: Success: Pointer to a new dataset descriptor.
*
* Failure: NULL
*
* Errors:
*
* Programmer: Robb Matzke
* Thursday, December 4, 1997
*
* Modifications:
* Robb Matzke, 9 Jun 1998
* The data space message is no longer cached in the dataset struct.
*
* Quincey Koziol, 12 Oct 1998
* Moved guts of function into H5D_open_oid
*
*-------------------------------------------------------------------------
*/
H5D_t *
H5D_open(H5G_entry_t *loc, const char *name)
{
H5D_t *dataset = NULL; /*the dataset which was found */
H5D_t *ret_value = NULL; /*return value */
FUNC_ENTER(H5D_open, NULL);
/* check args */
assert (loc);
assert (name && *name);
if (NULL==(dataset = H5D_new(NULL))) {
HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, NULL,
"memory allocation failed");
}
/* Find the dataset object */
if (H5G_find(loc, name, NULL, &(dataset->ent)) < 0) {
HGOTO_ERROR(H5E_DATASET, H5E_NOTFOUND, NULL, "not found");
}
/* Open the dataset object */
if (H5D_open_oid(dataset, NULL) < 0) {
HGOTO_ERROR(H5E_DATASET, H5E_NOTFOUND, NULL, "not found");
}
/* Success */
ret_value = dataset;
done:
FUNC_LEAVE(ret_value);
} /* end H5D_open() */
/*-------------------------------------------------------------------------
* Function: H5D_open_oid
*
* Purpose: Opens a dataset for access.
*
* Return: SUCCEED/FAIL
*
* Errors:
*
* Programmer: Quincey Koziol
* Monday, October 12, 1998
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
herr_t
H5D_open_oid(H5D_t *dataset, H5G_entry_t *ent)
{
herr_t ret_value = FAIL; /*return value */
intn i;
H5S_t *space = NULL;
FUNC_ENTER(H5D_open_oid, FAIL);
/* check args */
assert (dataset);
/* Copy over the symbol table information if it's provided */
if(ent!=NULL)
HDmemcpy(&(dataset->ent),ent,sizeof(H5G_entry_t));
/* Find the dataset object */
if (H5O_open(&(dataset->ent)) < 0) {
HGOTO_ERROR(H5E_DATASET, H5E_CANTOPENOBJ, FAIL, "unable to open");
}
/* Get the type and space */
if (NULL==(dataset->type=H5O_read(&(dataset->ent), H5O_DTYPE, 0, NULL))) {
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL,
"unable to load type info from dataset header");
}
if (NULL==(space=H5S_read (&(dataset->ent)))) {
HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL,
"unable to read data space info from dataset header");
}
/* Get the optional fill value message */
if (NULL==H5O_read(&(dataset->ent), H5O_FILL, 0,
&(dataset->create_parms->fill))) {
H5E_clear();
HDmemset(&(dataset->create_parms->fill), 0,
sizeof(dataset->create_parms->fill));
}
/* Get the optional filters message */
if (NULL==H5O_read (&(dataset->ent), H5O_PLINE, 0,
&(dataset->create_parms->pline))) {
H5E_clear ();
HDmemset (&(dataset->create_parms->pline), 0,
sizeof(dataset->create_parms->pline));
}
#ifdef HAVE_PARALLEL
/* If MPIO is used, no filter support yet. */
if (dataset->ent.file->shared->access_parms->driver == H5F_LOW_MPIO &&
dataset->create_parms->pline.nfilters>0){
HGOTO_ERROR (H5E_DATASET, H5E_UNSUPPORTED, FAIL,
"Parallel IO does not support filters yet");
}
#endif
/*
* Get the raw data layout info. It's actually stored in two locations:
* the storage message of the dataset (dataset->storage) and certain
* values are copied to the dataset create plist so the user can query
* them.
*/
if (NULL==H5O_read(&(dataset->ent), H5O_LAYOUT, 0, &(dataset->layout))) {
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL,
"unable to read data layout message");
}
switch (dataset->layout.type) {
case H5D_CONTIGUOUS:
dataset->create_parms->layout = H5D_CONTIGUOUS;
break;
case H5D_CHUNKED:
/*
* Chunked storage. The creation plist's dimension is one less than
* the chunk dimension because the chunk includes a dimension for the
* individual bytes of the data type.
*/
dataset->create_parms->layout = H5D_CHUNKED;
dataset->create_parms->chunk_ndims = dataset->layout.ndims - 1;
for (i = 0; i < dataset->layout.ndims - 1; i++) {
dataset->create_parms->chunk_size[i] = dataset->layout.dim[i];
}
break;
default:
HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, FAIL,
"not implemented yet");
}
/* Get the external file list message, which might not exist */
if (NULL==H5O_read (&(dataset->ent), H5O_EFL, 0,
&(dataset->create_parms->efl)) &&
!H5F_addr_defined (&(dataset->layout.addr))) {
HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL,
"storage address is undefined an no external file list");
}
/*
* Make sure all storage is properly initialized for chunked datasets.
* This is especially important for parallel I/O where the B-tree must
* be fully populated before I/O can happen.
*/
if ((dataset->ent.file->intent & H5F_ACC_RDWR) &&
H5D_CHUNKED==dataset->layout.type) {
if (H5D_init_storage(dataset, space)<0) {
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL,
"unable to initialize file storage");
}
}
/* Success */
ret_value = SUCCEED;
done:
if (space)
H5S_close (space);
if (ret_value==FAIL && dataset) {
if (H5F_addr_defined(&(dataset->ent.header))) {
H5O_close(&(dataset->ent));
}
if (dataset->type) {
H5T_close(dataset->type);
}
if (dataset->create_parms) {
H5P_close (H5P_DATASET_CREATE, dataset->create_parms);
}
dataset->ent.file = NULL;
H5MM_xfree(dataset);
}
FUNC_LEAVE(ret_value);
} /* end H5D_open_oid() */
/*-------------------------------------------------------------------------
* Function: H5D_close
*
* Purpose: Insures that all data has been saved to the file, closes the
* dataset object header, and frees all resources used by the
* descriptor.
*
* Return: Success: SUCCEED
*
* Failure: FAIL
*
* Errors:
* DATASET CANTINIT Couldn't free the type or space,
* but the dataset was freed anyway.
*
* Programmer: Robb Matzke
* Thursday, December 4, 1997
*
* Modifications:
* Robb Matzke, 9 Jun 1998
* The data space message is no longer cached in the dataset struct.
*
*-------------------------------------------------------------------------
*/
herr_t
H5D_close(H5D_t *dataset)
{
uintn free_failed;
FUNC_ENTER(H5D_close, FAIL);
/* check args */
assert(dataset && dataset->ent.file);
/*
* Release data type 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 ||
H5P_close (H5P_DATASET_CREATE, dataset->create_parms));
/* Close the dataset object */
H5O_close(&(dataset->ent));
/*
* Free memory. Before freeing the memory set the file pointer to NULL.
* We always check for a null file pointer in other H5D functions to be
* sure we're not accessing an already freed dataset (see the assert()
* above).
*/
dataset->ent.file = NULL;
H5MM_xfree(dataset);
if (free_failed) {
HRETURN_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL,
"couldn't free the type or creation property list, "
"but the dataset was freed anyway.");
}
FUNC_LEAVE(SUCCEED);
}
/*-------------------------------------------------------------------------
* Function: H5D_read
*
* Purpose: Reads (part of) a DATASET into application memory BUF. See
* H5Dread() for complete details.
*
* Return: Success: SUCCEED
*
* Failure: FAIL
*
* Programmer: Robb Matzke
* Thursday, December 4, 1997
*
* Modifications:
* Robb Matzke, 9 Jun 1998
* The data space is no longer cached in the dataset struct.
*
* Robb Matzke, 11 Aug 1998
* Added timing calls around all the data space I/O functions.
*
* rky 980918
* Added must_convert to do non-optimized read when necessary.
*
*-------------------------------------------------------------------------
*/
herr_t
H5D_read(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space,
const H5S_t *file_space, const H5D_xfer_t *xfer_parms,
void *buf/*out*/)
{
hsize_t nelmts; /*number of elements */
size_t smine_start; /*strip mine start loc */
size_t n, smine_nelmts; /*elements per strip */
hid_t tconv_id=FAIL, bkg_id=FAIL; /* Conversion buffer IDs */
uint8 *tconv_buf = NULL; /*data type conv buffer */
uint8 *bkg_buf = NULL; /*background buffer */
H5T_conv_t tconv_func = NULL; /*conversion function */
hid_t src_id = -1, dst_id = -1;/*temporary type atoms */
H5S_conv_t *sconv=NULL; /*space conversion funcs*/
H5S_sel_iter_t mem_iter; /* mem selection iteration info*/
H5S_sel_iter_t bkg_iter; /*background iteration info*/
H5S_sel_iter_t file_iter; /*file selection iter info*/
H5T_cdata_t *cdata = NULL; /*type conversion data */
herr_t ret_value = FAIL;
herr_t status;
size_t src_type_size; /*size of source type */
size_t dst_type_size; /*size of destination type*/
size_t target_size; /*desired buffer size */
size_t request_nelmts; /*requested strip mine */
H5T_bkg_t need_bkg; /*type of background buf*/
H5S_t *free_this_space=NULL; /*data space to free */
hbool_t must_convert; /*have to xfer the slow way */
#ifdef H5T_DEBUG
H5_timer_t timer;
#endif
FUNC_ENTER(H5D_read, FAIL);
/* check args */
assert(dataset && dataset->ent.file);
assert(mem_type);
assert(xfer_parms);
assert(buf);
/* Initialize these before any errors can occur */
HDmemset(&mem_iter,0,sizeof(H5S_sel_iter_t));
HDmemset(&bkg_iter,0,sizeof(H5S_sel_iter_t));
HDmemset(&file_iter,0,sizeof(H5S_sel_iter_t));
if (!file_space) {
if (NULL==(free_this_space=H5S_read (&(dataset->ent)))) {
HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL,
"unable to read data space from dataset header");
}
file_space = free_this_space;
}
if (!mem_space) mem_space = file_space;
nelmts = H5S_get_select_npoints(mem_space);
#ifdef HAVE_PARALLEL
/*
* Check if collective data transfer requested.
*/
if (xfer_parms->xfer_mode == H5D_XFER_COLLECTIVE){
/*
* Verify that the file can support collective access. The check may
* not be necessarily since collective access can always be simulated
* by independent access. Nevertheless, must check driver is MPIO
* before using those access_mode which exists only for MPIO case.
*/
if (dataset->ent.file->shared->access_parms->driver != H5F_LOW_MPIO)
HGOTO_ERROR (H5E_DATASET, H5E_UNSUPPORTED, FAIL,
"collective access not permissible");
}
#endif
/*
* Locate the type conversion function and data space conversion
* functions, and set up the element numbering information. If a data
* type conversion is necessary then register data type atoms. Data type
* conversion is necessary if the user has set the `need_bkg' to a high
* enough value in xfer_parms since turning off data type conversion also
* turns off background preservation.
*/
if (nelmts!=H5S_get_select_npoints (file_space)) {
HGOTO_ERROR (H5E_ARGS, H5E_BADVALUE, FAIL,
"src and dest data spaces have different sizes");
}
if (NULL == (tconv_func = H5T_find(dataset->type, mem_type,
xfer_parms->need_bkg, &cdata))) {
HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, FAIL,
"unable to convert between src and dest data types");
} else if (H5T_conv_noop!=tconv_func) {
if ((src_id=H5I_register(H5I_DATATYPE,
H5T_copy(dataset->type, H5T_COPY_ALL)))<0 ||
(dst_id=H5I_register(H5I_DATATYPE,
H5T_copy(mem_type, H5T_COPY_ALL)))<0) {
HGOTO_ERROR(H5E_DATASET, H5E_CANTREGISTER, FAIL,
"unable to register types for conversion");
}
}
if (NULL==(sconv=H5S_find(mem_space, file_space))) {
HGOTO_ERROR (H5E_DATASET, H5E_UNSUPPORTED, FAIL,
"unable to convert from file to memory data space");
}
#ifdef HAVE_PARALLEL
/* rky 980813 This is a temporary KLUGE.
* The sconv functions should be set by H5S_find,
* or we should use a different way to call the MPI-IO
* mem-and-file-dataspace-xfer functions
* (the latter in case the arguments to sconv_funcs
* turn out to be inappropriate for MPI-IO). */
if (H5_mpi_opt_types_g &&
H5F_LOW_MPIO==dataset->ent.file->shared->access_parms->driver) {
sconv->read = H5S_mpio_spaces_read;
}
#endif /*HAVE_PARALLEL*/
/*
* If there is no type conversion then try reading directly into the
* application's buffer. This saves at least one mem-to-mem copy.
*/
if (H5T_conv_noop==tconv_func && sconv->read) {
status = (sconv->read)(dataset->ent.file, &(dataset->layout),
&(dataset->create_parms->pline),
&(dataset->create_parms->efl),
H5T_get_size (dataset->type), file_space,
mem_space, xfer_parms->xfer_mode,
buf/*out*/, &must_convert );
if (status<0) {
/* Supports only no conversion, type or space, for now. */
HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL,
"optimized read failed");
}
if (must_convert) {
/* sconv->read cannot do a direct transfer;
* fall through and xfer the data in the more roundabout way */
} else {
/* direct xfer accomplished successfully */
goto succeed;
}
#ifdef H5D_DEBUG
if (H5DEBUG(D)) {
fprintf (H5DEBUG(D), "H5D: data space conversion could not be "
"optimized for this case (using general method "
"instead)\n");
}
#endif
H5E_clear ();
}
/*
* This is the general case. Figure out the strip mine size.
*/
src_type_size = H5T_get_size(dataset->type);
dst_type_size = H5T_get_size(mem_type);
target_size = xfer_parms->buf_size;
request_nelmts = target_size / MAX(src_type_size, dst_type_size);
if (request_nelmts<=0) {
HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL,
"temporary buffer max size is too small");
}
if ((sconv->f->init)(&(dataset->layout), file_space, &file_iter)<0) {
HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL,
"unable to initialize file selection information");
}
if ((sconv->m->init)(&(dataset->layout), mem_space, &mem_iter)<0) {
HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL,
"unable to initialize memory selection information");
}
if ((sconv->m->init)(&(dataset->layout), mem_space, &bkg_iter)<0) {
HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL,
"unable to initialize background selection information");
}
#ifdef QAK
printf("%s: check 3.0, request_nelmts=%d\n",FUNC,(int)request_nelmts);
#endif
/*
* Get a temporary buffer for type conversion unless the app has already
* supplied one through the xfer properties. Instead of allocating a
* buffer which is the exact size, we allocate the target size. The
* malloc() is usually less resource-intensive if we allocate/free the
* same size over and over.
*/
if (cdata->need_bkg) {
need_bkg = MAX (cdata->need_bkg, xfer_parms->need_bkg);
} else {
need_bkg = H5T_BKG_NO; /*never needed even if app says yes*/
}
if (NULL==(tconv_buf=xfer_parms->tconv_buf)) {
/* Allocate temporary buffer */
if (FAIL==(tconv_id = H5TB_get_buf(target_size, 1,
(void **)&tconv_buf))) {
HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL,
"memory allocation failed for type conversion");
}
}
if (need_bkg && NULL==(bkg_buf=xfer_parms->bkg_buf)) {
/* Allocate temporary buffer */
if (FAIL==(bkg_id = H5TB_get_buf(request_nelmts*dst_type_size, 1,
(void **)&bkg_buf))) {
HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL,
"memory allocation failed for type conversion");
}
}
#ifdef QAK
printf("%s: check 4.0, nelmts=%d, need_bkg=%d\n",
FUNC,(int)nelmts,(int)need_bkg);
#endif
/* Start strip mining... */
for (smine_start=0; smine_start<nelmts; smine_start+=smine_nelmts) {
/* Go figure out how many elements to read from the file */
smine_nelmts = (sconv->f->avail)(file_space,&file_iter,
MIN(request_nelmts,
(nelmts-smine_start)));
#ifdef QAK
printf("%s: check 5.0, nelmts=%d, smine_start=%d, smine_nelmts=%d\n",
FUNC,(int)nelmts,(int)smine_start,(int)smine_nelmts);
#endif
/*
* Gather the data from disk into the data type conversion
* buffer. Also gather data from application to background buffer
* if necessary.
*/
#ifdef H5S_DEBUG
H5_timer_begin(&timer);
#endif
n = (sconv->f->gath)(dataset->ent.file, &(dataset->layout),
&(dataset->create_parms->pline),
&(dataset->create_parms->fill),
&(dataset->create_parms->efl), src_type_size,
file_space, &file_iter, smine_nelmts,
xfer_parms, tconv_buf/*out*/);
#ifdef H5S_DEBUG
H5_timer_end(&(sconv->stats[1].gath_timer), &timer);
sconv->stats[1].gath_nbytes += n * src_type_size;
sconv->stats[1].gath_ncalls++;
#endif
if (n!=smine_nelmts) {
HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "file gather failed");
}
#ifdef QAK
printf("%s: check 6.0\n",FUNC);
printf("%s: check 6.5\n",FUNC);
{
int i;
uint16 *b;
if(qak_debug) {
b=tconv_buf;
printf("\ntconv_buf:");
for (i=0; i<smine_nelmts; i++,b++) {
printf("(%d)%u ",i,(unsigned)*b);
}
printf("\n");
}
}
#endif
if (H5T_BKG_YES==need_bkg) {
#ifdef H5S_DEBUG
H5_timer_begin(&timer);
#endif
n = (sconv->m->gath)(buf, dst_type_size, mem_space, &bkg_iter,
smine_nelmts, bkg_buf/*out*/);
#ifdef H5S_DEBUG
H5_timer_end(&(sconv->stats[1].bkg_timer), &timer);
sconv->stats[1].bkg_nbytes += n * dst_type_size;
sconv->stats[1].bkg_ncalls++;
#endif
if (n!=smine_nelmts) {
HGOTO_ERROR (H5E_IO, H5E_READERROR, FAIL, "mem gather failed");
}
}
#ifdef QAK
printf("%s: check 7.0\n",FUNC);
#endif
/*
* Perform data type conversion.
*/
#ifdef H5T_DEBUG
H5T_timer_begin (&timer, cdata);
#endif
cdata->command = H5T_CONV_CONV;
status = (tconv_func)(src_id, dst_id, cdata, smine_nelmts, tconv_buf,
bkg_buf);
#ifdef H5T_DEBUG
H5T_timer_end (&timer, cdata, smine_nelmts);
#endif
if (status<0) {
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL,
"data type conversion failed");
}
#ifdef QAK
printf("%s: check 8.0\n",FUNC);
#endif
/*
* Scatter the data into memory.
*/
#ifdef H5S_DEBUG
H5_timer_begin(&timer);
#endif
status = (sconv->m->scat)(tconv_buf, dst_type_size, mem_space,
&mem_iter, smine_nelmts, buf/*out*/);
#ifdef H5S_DEBUG
H5_timer_end(&(sconv->stats[1].scat_timer), &timer);
sconv->stats[1].scat_nbytes += smine_nelmts * dst_type_size;
sconv->stats[1].scat_ncalls++;
#endif
if (status<0) {
HGOTO_ERROR (H5E_IO, H5E_READERROR, FAIL, "scatter failed");
}
#ifdef QAK
printf("%s: check 9.0\n",FUNC);
#endif /* QAK */
}
succeed:
ret_value = SUCCEED;
done:
/* Release selection iterators */
H5S_sel_iter_release(file_space,&file_iter);
H5S_sel_iter_release(mem_space,&mem_iter);
H5S_sel_iter_release(mem_space,&bkg_iter);
if (src_id >= 0) H5I_dec_ref(src_id);
if (dst_id >= 0) H5I_dec_ref(dst_id);
if (tconv_buf && NULL==xfer_parms->tconv_buf) H5TB_release_buf(tconv_id);
if (bkg_buf && NULL==xfer_parms->bkg_buf) H5TB_release_buf (bkg_id);
if (free_this_space) H5S_close (free_this_space);
FUNC_LEAVE(ret_value);
}
/*-------------------------------------------------------------------------
* Function: H5D_write
*
* Purpose: Writes (part of) a DATASET to a file from application memory
* BUF. See H5Dwrite() for complete details.
*
* Return: Success: SUCCEED
*
* Failure: FAIL
*
* Programmer: Robb Matzke
* Thursday, December 4, 1997
*
* Modifications:
* Robb Matzke, 9 Jun 1998
* The data space is no longer cached in the dataset struct.
*
* rky 980918
* Added must_convert to do non-optimized read when necessary.
*
*-------------------------------------------------------------------------
*/
herr_t
H5D_write(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space,
const H5S_t *file_space, const H5D_xfer_t *xfer_parms,
const void *buf)
{
hsize_t nelmts; /*total number of elmts */
size_t smine_start; /*strip mine start loc */
size_t n, smine_nelmts; /*elements per strip */
hid_t tconv_id=FAIL, bkg_id=FAIL; /* Conversion buffer IDs */
uint8 *tconv_buf = NULL; /*data type conv buffer */
uint8 *bkg_buf = NULL; /*background buffer */
H5T_conv_t tconv_func = NULL; /*conversion function */
hid_t src_id = -1, dst_id = -1;/*temporary type atoms */
H5S_conv_t *sconv=NULL; /*space conversion funcs*/
H5S_sel_iter_t mem_iter; /*memory selection iteration info*/
H5S_sel_iter_t bkg_iter; /*background iteration info*/
H5S_sel_iter_t file_iter; /*file selection iteration info*/
H5T_cdata_t *cdata = NULL; /*type conversion data */
herr_t ret_value = FAIL, status;
size_t src_type_size; /*size of source type */
size_t dst_type_size; /*size of destination type*/
size_t target_size; /*desired buffer size */
size_t request_nelmts; /*requested strip mine */
H5T_bkg_t need_bkg; /*type of background buf*/
H5S_t *free_this_space=NULL; /*data space to free */
hbool_t must_convert; /*have to xfer the slow way */
#ifdef H5T_DEBUG
H5_timer_t timer;
#endif
FUNC_ENTER(H5D_write, FAIL);
/* check args */
assert(dataset && dataset->ent.file);
assert(mem_type);
assert(xfer_parms);
assert(buf);
/* Initialize these before any errors can occur */
HDmemset(&mem_iter,0,sizeof(H5S_sel_iter_t));
HDmemset(&bkg_iter,0,sizeof(H5S_sel_iter_t));
HDmemset(&file_iter,0,sizeof(H5S_sel_iter_t));
if (0==(dataset->ent.file->intent & H5F_ACC_RDWR)) {
HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL,
"no write intent on file");
}
if (!file_space) {
if (NULL==(free_this_space=H5S_read (&(dataset->ent)))) {
HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL,
"unable to read data space from dataset header");
}
file_space = free_this_space;
}
if (!mem_space) mem_space = file_space;
nelmts = H5S_get_select_npoints(mem_space);
#ifdef HAVE_PARALLEL
/*
* Check if collective data transfer requested.
*/
if (xfer_parms->xfer_mode == H5D_XFER_COLLECTIVE){
/*
* Verify that the file can support collective access. The check may
* not be necessarily since collective access can always be simulated
* by independent access. Nevertheless, must check driver is MPIO
* before using those access_mode which exists only for MPIO case.
*/
if (dataset->ent.file->shared->access_parms->driver != H5F_LOW_MPIO)
HGOTO_ERROR (H5E_DATASET, H5E_UNSUPPORTED, FAIL,
"collective access not permissible");
}
#endif
/*
* Locate the type conversion function and data space conversion
* functions, and set up the element numbering information. If a data
* type conversion is necessary then register data type atoms. Data type
* conversion is necessary if the user has set the `need_bkg' to a high
* enough value in xfer_parms since turning off data type conversion also
* turns off background preservation.
*/
#ifdef QAK
printf("%s: check 0.5, nelmts=%d, mem_space->rank=%d\n", FUNC,
(int)nelmts, mem_space->extent.u.simple.rank);
#endif /* QAK */
if (nelmts!=H5S_get_select_npoints (file_space)) {
HGOTO_ERROR (H5E_ARGS, H5E_BADVALUE, FAIL,
"src and dest data spaces have different sizes");
}
if (NULL == (tconv_func = H5T_find(mem_type, dataset->type,
xfer_parms->need_bkg, &cdata))) {
HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, FAIL,
"unable to convert between src and dest data types");
} else if (H5T_conv_noop!=tconv_func) {
if ((src_id = H5I_register(H5I_DATATYPE,
H5T_copy(mem_type, H5T_COPY_ALL)))<0 ||
(dst_id = H5I_register(H5I_DATATYPE,
H5T_copy(dataset->type, H5T_COPY_ALL)))<0) {
HGOTO_ERROR(H5E_DATASET, H5E_CANTREGISTER, FAIL,
"unable to register types for conversion");
}
}
#ifdef QAK
printf("%s: after H5T_find, tconv_func=%p\n",FUNC,tconv_func);
#endif /* QAK */
if (NULL==(sconv=H5S_find(mem_space, file_space))) {
HGOTO_ERROR (H5E_DATASET, H5E_UNSUPPORTED, FAIL,
"unable to convert from memory to file data space");
}
#ifdef HAVE_PARALLEL
/* rky 980813 This is a temporary KLUGE.
* The sconv functions should be set by H5S_find,
* or we should use a different way to call the MPI-IO
* mem-and-file-dataspace-xfer functions
* (the latter in case the arguments to sconv_funcs
* turn out to be inappropriate for MPI-IO). */
if (H5_mpi_opt_types_g &&
H5F_LOW_MPIO==dataset->ent.file->shared->access_parms->driver) {
sconv->write = H5S_mpio_spaces_write;
}
#endif /*HAVE_PARALLEL*/
/*
* If there is no type conversion then try writing directly from
* application buffer to file.
*/
if (H5T_conv_noop==tconv_func && sconv->write) {
status = (sconv->write)(dataset->ent.file, &(dataset->layout),
&(dataset->create_parms->pline),
&(dataset->create_parms->efl),
H5T_get_size (dataset->type), file_space,
mem_space, xfer_parms->xfer_mode, buf,
&must_convert /*out*/ );
if (status<0) {
/* Supports only no conversion, type or space, for now. */
HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL,
"optimized write failed");
}
if (must_convert) {
/* sconv->write cannot do a direct transfer;
* fall through and xfer the data in the more roundabout way */
} else {
/* direct xfer accomplished successfully */
goto succeed;
}
#ifdef H5D_DEBUG
if (H5DEBUG(D)) {
fprintf (H5DEBUG(D), "H5D: data space conversion could not be "
"optimized for this case (using general method "
"instead)\n");
}
#endif
H5E_clear ();
}
/*
* This is the general case. Figure out the strip mine size.
*/
src_type_size = H5T_get_size(mem_type);
dst_type_size = H5T_get_size(dataset->type);
target_size = xfer_parms->buf_size;
request_nelmts = target_size / MAX (src_type_size, dst_type_size);
if (request_nelmts<=0) {
HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL,
"temporary buffer max size is too small");
}
if ((sconv->f->init)(&(dataset->layout), file_space, &file_iter)<0) {
HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL,
"unable to initialize file selection information");
}
if ((sconv->m->init)(&(dataset->layout), mem_space, &mem_iter)<0) {
HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL,
"unable to initialize memory selection information");
}
if ((sconv->f->init)(&(dataset->layout), file_space, &bkg_iter)<0) {
HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL,
"unable to initialize memory selection information");
}
#ifdef QAK
printf("%s: check 3.0, request_nelmts=%d\n",FUNC,(int)request_nelmts);
#endif
/*
* Get a temporary buffer for type conversion unless the app has already
* supplied one through the xfer properties. Instead of allocating a
* buffer which is the exact size, we allocate the target size. The
* malloc() is usually less resource-intensive if we allocate/free the
* same size over and over.
*/
if (cdata->need_bkg) {
need_bkg = MAX (cdata->need_bkg, xfer_parms->need_bkg);
} else {
need_bkg = H5T_BKG_NO; /*never needed even if app says yes*/
}
if (NULL==(tconv_buf=xfer_parms->tconv_buf)) {
/* Allocate temporary buffer */
if (FAIL==(tconv_id = H5TB_get_buf(target_size, 1,
(void **)&tconv_buf))) {
HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL,
"memory allocation failed for type conversion");
}
}
if (need_bkg && NULL==(bkg_buf=xfer_parms->bkg_buf)) {
/* Allocate temporary buffer */
if (FAIL==(bkg_id = H5TB_get_buf(request_nelmts*dst_type_size, 1,
(void **)&bkg_buf))) {
HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL,
"memory allocation failed for type conversion");
}
}
#ifdef QAK
printf("%s: check 4.0, nelmts=%d, need_bkg=%d\n",
FUNC,(int)nelmts,(int)need_bkg);
#endif
/* Start strip mining... */
for (smine_start=0; smine_start<nelmts; smine_start+=smine_nelmts) {
/* Go figure out how many elements to read from the file */
smine_nelmts = (sconv->f->avail)(file_space,&file_iter,
MIN(request_nelmts,
(nelmts-smine_start)));
#ifdef QAK
printf("%s: check 5.0, nelmts=%d, smine_start=%d, smine_nelmts=%d\n",
FUNC,(int)nelmts,(int)smine_start,(int)smine_nelmts);
#endif
/*
* Gather data from application buffer into the data type conversion
* buffer. Also gather data from the file into the background buffer
* if necessary.
*/
#ifdef H5S_DEBUG
H5_timer_begin(&timer);
#endif
n = (sconv->m->gath)(buf, src_type_size, mem_space, &mem_iter,
smine_nelmts, tconv_buf/*out*/);
#ifdef H5S_DEBUG
H5_timer_end(&(sconv->stats[0].gath_timer), &timer);
sconv->stats[0].gath_nbytes += n * src_type_size;
sconv->stats[0].gath_ncalls++;
#endif
if (n!=smine_nelmts) {
HGOTO_ERROR (H5E_IO, H5E_WRITEERROR, FAIL, "mem gather failed");
}
#ifdef QAK
{
int i;
uint16 *b;
if(qak_debug) {
b=tconv_buf;
printf("\ntconv_buf:");
for (i=0; i<smine_nelmts; i++,b++) {
printf("(%d)%d ",i,(int)*b);
}
printf("\n");
}
}
printf("%s: check 6.0\n",FUNC);
#endif
if (H5T_BKG_YES==need_bkg) {
#ifdef H5S_DEBUG
H5_timer_begin(&timer);
#endif
n = (sconv->f->gath)(dataset->ent.file, &(dataset->layout),
&(dataset->create_parms->pline),
&(dataset->create_parms->fill),
&(dataset->create_parms->efl), dst_type_size,
file_space, &bkg_iter, smine_nelmts,
xfer_parms, bkg_buf/*out*/);
#ifdef H5S_DEBUG
H5_timer_end(&(sconv->stats[0].bkg_timer), &timer);
sconv->stats[0].bkg_nbytes += n * dst_type_size;
sconv->stats[0].bkg_ncalls++;
#endif
if (n!=smine_nelmts) {
HGOTO_ERROR (H5E_IO, H5E_WRITEERROR, FAIL,
"file gather failed");
}
}
/*
* Perform data type conversion.
*/
#ifdef H5T_DEBUG
H5T_timer_begin (&timer, cdata);
#endif
cdata->command = H5T_CONV_CONV;
status = (tconv_func) (src_id, dst_id, cdata, smine_nelmts, tconv_buf,
bkg_buf);
#ifdef H5T_DEBUG
H5T_timer_end (&timer, cdata, smine_nelmts);
#endif
if (status<0) {
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL,
"data type conversion failed");
}
#ifdef QAK
printf("%s: check 6.3\n",FUNC);
#endif
/*
* Scatter the data out to the file.
*/
#ifdef H5S_DEBUG
H5_timer_begin(&timer);
#endif
status = (sconv->f->scat)(dataset->ent.file, &(dataset->layout),
&(dataset->create_parms->pline),
&(dataset->create_parms->fill),
&(dataset->create_parms->efl), dst_type_size,
file_space, &file_iter, smine_nelmts,
xfer_parms, tconv_buf);
#ifdef QAK
printf("%s: check 6.35\n",FUNC);
#endif
#ifdef H5S_DEBUG
H5_timer_end(&(sconv->stats[0].scat_timer), &timer);
sconv->stats[0].scat_nbytes += smine_nelmts * dst_type_size;
sconv->stats[0].scat_ncalls++;
#endif
if (status<0) {
HGOTO_ERROR (H5E_DATASET, H5E_WRITEERROR, FAIL, "scatter failed");
}
}
#ifdef QAK
printf("%s: check 6.4\n",FUNC);
#endif
/*
* Update modification time. We have to do this explicitly because
* writing to a dataset doesn't necessarily change the object header.
*/
if (H5O_touch(&(dataset->ent), FALSE)<0) {
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL,
"unable to update modification time");
}
succeed:
ret_value = SUCCEED;
done:
/* Release selection iterators */
H5S_sel_iter_release(file_space,&file_iter);
H5S_sel_iter_release(mem_space,&mem_iter);
H5S_sel_iter_release(file_space,&bkg_iter);
if (src_id >= 0) H5I_dec_ref(src_id);
if (dst_id >= 0) H5I_dec_ref(dst_id);
if (tconv_buf && NULL==xfer_parms->tconv_buf) H5TB_release_buf(tconv_id);
if (bkg_buf && NULL==xfer_parms->bkg_buf) H5TB_release_buf (bkg_id);
if (free_this_space) H5S_close (free_this_space);
FUNC_LEAVE(ret_value);
}
/*-------------------------------------------------------------------------
* Function: H5D_extend
*
* Purpose: Increases the size of a dataset.
*
* Return: Success: SUCCEED
*
* Failure: FAIL
*
* Programmer: Robb Matzke
* Friday, January 30, 1998
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
herr_t
H5D_extend (H5D_t *dataset, const hsize_t *size)
{
herr_t changed, ret_value=FAIL;
H5S_t *space = NULL;
FUNC_ENTER (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 */
if (NULL==(space=H5S_read (&(dataset->ent)))) {
HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL,
"unable to read data space info from dataset header");
}
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)<0) {
HGOTO_ERROR (H5E_DATASET, H5E_WRITEERROR, FAIL,
"unable to update file with new dataspace");
}
/* Initialize the new parts of the dataset */
#ifdef LATER
if (H5S_select_all(space)<0 ||
H5S_select_hyperslab(space, H5S_SELECT_DIFF, zero, NULL,
old_dims, NULL)<0) {
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL,
"unable to select new extents for fill value");
}
#else
/*
* We don't have the H5S_SELECT_DIFF operator yet. We really only
* need it for contiguous datasets because the chunked datasets will
* either fill on demand during I/O or attempt a fill of all chunks.
*/
if (H5D_CONTIGUOUS==dataset->layout.type &&
dataset->create_parms->fill.buf) {
HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, FAIL,
"unable to select fill value region");
}
#endif
if (H5D_init_storage(dataset, space)<0) {
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL,
"unable to initialize dataset with fill value");
}
}
ret_value = SUCCEED;
done:
H5S_close (space);
FUNC_LEAVE (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)
{
return dataset ? &(dataset->ent) : 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 (H5D_t *dset)
{
FUNC_ENTER (H5D_typeof, NULL);
assert (dset);
assert (dset->type);
FUNC_LEAVE (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:
*
*-------------------------------------------------------------------------
*/
H5F_t *
H5D_get_file (const H5D_t *dset)
{
FUNC_ENTER (H5D_get_file, NULL);
assert (dset);
assert (dset->ent.file);
FUNC_LEAVE (dset->ent.file);
}
/*-------------------------------------------------------------------------
* 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: Success: SUCCEED
*
* Failure: FAIL
*
* Programmer: Robb Matzke
* Monday, October 5, 1998
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
static herr_t
H5D_init_storage(H5D_t *dset, const H5S_t *space)
{
intn ndims;
hsize_t dim[H5O_LAYOUT_NDIMS];
hsize_t npoints, ptsperbuf;
size_t size, bufsize=8*1024;
hid_t buf_id = -1;
haddr_t addr;
herr_t ret_value = FAIL;
void *buf = NULL;
FUNC_ENTER(H5D_init_storage, FAIL);
assert(dset);
assert(space);
switch (dset->layout.type) {
case H5D_CONTIGUOUS:
/*
* If the fill value is set then write it to the specified selection
* even if it is all zero. This allows the application to force
* filling when the underlying storage isn't initialized to zero.
*/
npoints = H5S_get_simple_extent_npoints(space);
if (dset->create_parms->fill.buf &&
npoints==H5S_get_select_npoints(space)) {
/*
* Fill the entire current extent with the fill value. We can do
* this quite efficiently by making sure we copy the fill value
* in relatively large pieces.
*/
ptsperbuf = MAX(1, bufsize/dset->create_parms->fill.size);
bufsize = ptsperbuf * dset->create_parms->fill.size;
if ((buf_id=H5TB_get_buf(bufsize, TRUE, &buf))<0) {
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL,
"unable to get buffer for fill value");
}
H5V_array_fill(buf, dset->create_parms->fill.buf,
dset->create_parms->fill.size, ptsperbuf);
if (dset->create_parms->efl.nused) {
H5F_addr_reset(&addr);
} else {
addr = dset->layout.addr;
}
while (npoints>0) {
size = MIN(ptsperbuf, npoints) * dset->create_parms->fill.size;
if (dset->create_parms->efl.nused) {
if (H5O_efl_write(dset->ent.file,
&(dset->create_parms->efl),
&addr, size, buf)<0) {
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL,
"unable to write fill value to dataset");
}
} else {
if (H5F_block_write(dset->ent.file, &addr, size,
H5D_XFER_DFLT, buf)<0) {
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL,
"unable to write fill value to dataset");
}
}
npoints -= MIN(ptsperbuf, npoints);
H5F_addr_inc(&addr, size);
}
} else if (dset->create_parms->fill.buf) {
/*
* Fill the specified selection with the fill value.
*/
HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, FAIL,
"unable to initialize dataset with fill value");
}
break;
case H5D_CHUNKED:
/*
* If the dataset is accessed via parallel I/O, allocate file space
* for all chunks now and initialize each chunk with the fill value.
*/
if (H5F_LOW_MPIO==dset->ent.file->shared->access_parms->driver) {
/* We only handle simple data spaces so far */
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];
ndims++;
if (H5F_istore_allocate(dset->ent.file, &(dset->layout),
dim, H5D_xfer_dflt.split_ratios,
&(dset->create_parms->pline),
&(dset->create_parms->fill))<0) {
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL,
"unable to allocate all chunks of dataset");
}
}
break;
}
ret_value = SUCCEED;
done:
if (buf_id>=0 && H5TB_release_buf(buf_id)<0) {
HRETURN_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL,
"unable to release fill value temporary buffer");
}
FUNC_LEAVE(ret_value);
}
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