/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* Copyright by The HDF Group. *
* 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 COPYING file, which can be found at the root of the source code *
* distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. *
* If you do not have access to either file, you may request a copy from *
* help@hdfgroup.org. *
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
#ifdef OLD_HEADER_FILENAME
#include <iostream.h>
#else
#include <iostream>
#endif
#include <string>
#include "H5private.h" // for HDfree
#include "H5Include.h"
#include "H5Exception.h"
#include "H5IdComponent.h"
#include "H5PropList.h"
#include "H5FaccProp.h"
#include "H5FcreatProp.h"
#include "H5OcreatProp.h"
#include "H5DxferProp.h"
#include "H5DcreatProp.h"
#include "H5LcreatProp.h"
#include "H5LaccProp.h"
#include "H5DaccProp.h"
#include "H5Location.h"
#include "H5Object.h"
#include "H5DataType.h"
#include "H5DataSpace.h"
#include "H5AbstractDs.h"
#include "H5Attribute.h"
#include "H5DataSet.h"
namespace H5 {
using std::cerr;
using std::endl;
//--------------------------------------------------------------------------
// Function: DataSet default constructor
///\brief Default constructor: creates a stub DataSet.
// Programmer Binh-Minh Ribler - 2000
//--------------------------------------------------------------------------
DataSet::DataSet() : H5Object(), AbstractDs(), id(H5I_INVALID_HID) {}
//--------------------------------------------------------------------------
// Function: DataSet overloaded constructor
///\brief Creates an DataSet object using the id of an existing dataset.
///\param existing_id - IN: Id of an existing dataset
// Programmer Binh-Minh Ribler - 2000
// Description
// incRefCount() is needed here to prevent the id from being closed
// prematurely. That is, when application uses the id of an
// existing DataSet object to create another DataSet object. So,
// when one of those objects is deleted, the id will be closed if
// the reference counter is only 1.
//--------------------------------------------------------------------------
DataSet::DataSet(const hid_t existing_id) : H5Object(), AbstractDs(), id(existing_id)
{
incRefCount(); // increment number of references to this id
}
//--------------------------------------------------------------------------
// Function: DataSet copy constructor
///\brief Copy constructor: same HDF5 object as \a original
///\param original - IN: DataSet instance to copy
// Programmer Binh-Minh Ribler - 2000
//--------------------------------------------------------------------------
DataSet::DataSet(const DataSet &original) : H5Object(), AbstractDs(), id(original.id)
{
incRefCount(); // increment number of references to this id
}
//--------------------------------------------------------------------------
// Function: DataSet overload constructor - dereference
///\brief Given a reference, ref, to an hdf5 location, creates a
/// DataSet object
///\param loc - IN: Dataset reference object is in or location of
/// object that the dataset is located within.
///\param ref - IN: Reference pointer
///\param ref_type - IN: Reference type - default to H5R_OBJECT
///\param plist - IN: Property list - default to PropList::DEFAULT
///\exception H5::DataSetIException
///\par Description
/// \c loc can be DataSet, Group, H5File, or named DataType, that
/// is a datatype that has been named by DataType::commit.
// Programmer Binh-Minh Ribler - Oct, 2006
//--------------------------------------------------------------------------
DataSet::DataSet(const H5Location &loc, const void *ref, H5R_type_t ref_type, const PropList &plist)
: H5Object(), AbstractDs(), id(H5I_INVALID_HID)
{
id = H5Location::p_dereference(loc.getId(), ref, ref_type, plist, "constructor - by dereferenced");
}
//--------------------------------------------------------------------------
// Function: DataSet overload constructor - dereference
///\brief Given a reference, ref, to an hdf5 attribute, creates a
/// DataSet object
///\param attr - IN: Specifying location where the referenced object is in
///\param ref - IN: Reference pointer
///\param ref_type - IN: Reference type - default to H5R_OBJECT
///\param plist - IN: Property list - default to PropList::DEFAULT
///\exception H5::ReferenceException
// Programmer Binh-Minh Ribler - Oct, 2006
//--------------------------------------------------------------------------
DataSet::DataSet(const Attribute &attr, const void *ref, H5R_type_t ref_type, const PropList &plist)
: H5Object(), AbstractDs(), id(H5I_INVALID_HID)
{
id = H5Location::p_dereference(attr.getId(), ref, ref_type, plist, "constructor - by dereference");
}
//--------------------------------------------------------------------------
// Function: DataSet::getSpace
///\brief Gets a copy of the dataspace of this dataset.
///\return DataSpace instance
///\exception H5::DataSetIException
// Programmer Binh-Minh Ribler - 2000
//--------------------------------------------------------------------------
DataSpace
DataSet::getSpace() const
{
// Calls C function H5Dget_space to get the id of the dataspace
hid_t dataspace_id = H5Dget_space(id);
// If the dataspace id is invalid, throw an exception
if (dataspace_id < 0) {
throw DataSetIException("DataSet::getSpace", "H5Dget_space failed");
}
// create dataspace object using the existing id then return the object
DataSpace data_space;
f_DataSpace_setId(&data_space, dataspace_id);
return (data_space);
}
// This private member function calls the C API to get the identifier
// of the datatype that is used by this dataset. It is used
// by the various AbstractDs functions to get the specific datatype.
hid_t
DataSet::p_get_type() const
{
hid_t type_id = H5Dget_type(id);
if (type_id > 0)
return (type_id);
else {
throw DataSetIException("", "H5Dget_type failed");
}
}
//--------------------------------------------------------------------------
// Function: DataSet::getCreatePlist
///\brief Gets the dataset creation property list.
///\return DSetCreatPropList instance
///\exception H5::DataSetIException
// Programmer Binh-Minh Ribler - 2000
//--------------------------------------------------------------------------
DSetCreatPropList
DataSet::getCreatePlist() const
{
hid_t create_plist_id = H5Dget_create_plist(id);
if (create_plist_id < 0) {
throw DataSetIException("DataSet::getCreatePlist", "H5Dget_create_plist failed");
}
// create and return the DSetCreatPropList object
DSetCreatPropList create_plist;
f_PropList_setId(&create_plist, create_plist_id);
return (create_plist);
}
//--------------------------------------------------------------------------
// Function: DataSet::getAccessPlist
///\brief Gets the dataset access property list.
///\return DSetAccPropList instance
///\exception H5::DataSetIException
// July 2018
//--------------------------------------------------------------------------
DSetAccPropList
DataSet::getAccessPlist() const
{
hid_t access_plist_id = H5Dget_access_plist(id);
if (access_plist_id < 0) {
throw DataSetIException("DataSet::getAccessPlist", "H5Dget_access_plist failed");
}
// create and return the DSetCreatPropList object
DSetAccPropList access_plist;
f_PropList_setId(&access_plist, access_plist_id);
return (access_plist);
}
//--------------------------------------------------------------------------
// Function: DataSet::getStorageSize
///\brief Returns the amount of storage required for a dataset.
///\return Size of the storage or 0, for no data
///\exception H5::DataSetIException
// Note: H5Dget_storage_size returns 0 when there is no data. This
// function should have no failure. (from SLU)
// Programmer Binh-Minh Ribler - Mar, 2005
//--------------------------------------------------------------------------
hsize_t
DataSet::getStorageSize() const
{
hsize_t storage_size = H5Dget_storage_size(id);
return (storage_size);
}
//--------------------------------------------------------------------------
// Function: DataSet::getInMemDataSize
///\brief Gets the size in memory of the dataset's data.
///\return Size of data (in memory)
///\exception H5::DataSetIException
// Programmer Binh-Minh Ribler - Apr 2009
//--------------------------------------------------------------------------
size_t
DataSet::getInMemDataSize() const
{
const char *func = "DataSet::getInMemDataSize";
// Get the data type of this dataset
hid_t mem_type_id = H5Dget_type(id);
if (mem_type_id < 0) {
throw DataSetIException(func, "H5Dget_type failed");
}
// Get the data type's size by first getting its native type then getting
// the native type's size.
hid_t native_type = H5Tget_native_type(mem_type_id, H5T_DIR_DEFAULT);
if (native_type < 0) {
throw DataSetIException(func, "H5Tget_native_type failed");
}
size_t type_size = H5Tget_size(native_type);
if (type_size == 0) {
throw DataSetIException(func, "H5Tget_size failed");
}
// Close the native type and the datatype of this dataset.
if (H5Tclose(native_type) < 0) {
throw DataSetIException(func, "H5Tclose(native_type) failed");
}
if (H5Tclose(mem_type_id) < 0) {
throw DataSetIException(func, "H5Tclose(mem_type_id) failed");
}
// Get number of elements of the dataset by first getting its dataspace,
// then getting the number of elements in the dataspace
hid_t space_id = H5Dget_space(id);
if (space_id < 0) {
throw DataSetIException(func, "H5Dget_space failed");
}
hssize_t num_elements = H5Sget_simple_extent_npoints(space_id);
if (num_elements < 0) {
throw DataSetIException(func, "H5Sget_simple_extent_npoints failed");
}
// Close the dataspace
if (H5Sclose(space_id) < 0) {
throw DataSetIException(func, "H5Sclose failed");
}
// Calculate and return the size of the data
size_t data_size = type_size * num_elements;
return (data_size);
}
//--------------------------------------------------------------------------
// Function: DataSet::getOffset
///\brief Returns the address of this dataset in the file.
///\return Address of dataset
///\exception H5::DataSetIException
// Programmer Binh-Minh Ribler - 2000
//--------------------------------------------------------------------------
haddr_t
DataSet::getOffset() const
{
haddr_t ds_addr; // for address of dataset
ds_addr = H5Dget_offset(id);
if (ds_addr == HADDR_UNDEF) {
throw DataSetIException("DataSet::getOffset", "H5Dget_offset returned HADDR_UNDEF");
}
return (ds_addr);
}
//--------------------------------------------------------------------------
// Function: DataSet::getSpaceStatus
///\brief Determines whether space has been allocated for a dataset.
///\param status - OUT: Space allocation status
///\exception H5::DataSetIException
// Programmer Binh-Minh Ribler - 2000
//--------------------------------------------------------------------------
void
DataSet::getSpaceStatus(H5D_space_status_t &status) const
{
herr_t ret_value = H5Dget_space_status(id, &status);
if (ret_value < 0) {
throw DataSetIException("DataSet::getSpaceStatus", "H5Dget_space_status failed");
}
}
//--------------------------------------------------------------------------
// Function: DataSet::getVlenBufSize
///\brief Returns the number of bytes required to store VL data.
///\param type - IN: Datatype, which is the datatype for the buffer
///\param space - IN: Selection for the memory buffer
///\return Amount of storage
///\exception H5::DataSetIException
// Programmer Binh-Minh Ribler - 2000
//--------------------------------------------------------------------------
hsize_t
DataSet::getVlenBufSize(const DataType &type, const DataSpace &space) const
{
// Obtain identifiers for C API
hid_t type_id = type.getId();
hid_t space_id = space.getId();
hsize_t size; // for amount of storage
herr_t ret_value = H5Dvlen_get_buf_size(id, type_id, space_id, &size);
if (ret_value < 0) {
throw DataSetIException("DataSet::getVlenBufSize", "H5Dvlen_get_buf_size failed");
}
return (size);
}
//--------------------------------------------------------------------------
// Function: DataSet::getVlenBufSize
// Purpose This is an overloaded member function, kept for backward
// compatibility. It differs from the above function in that it
// misses const's. This wrapper will be removed in future release.
// Return Amount of storage
// Exception H5::DataSetIException
// Programmer Binh-Minh Ribler - 2000
// Modification
// Modified to call its replacement. -BMR, 2014/04/16
// Removed from documentation. -BMR, 2016/03/07 1.8.17 and 1.10.0
// Removed from code. -BMR, 2016/08/11 1.8.18 and 1.10.1
//--------------------------------------------------------------------------
// hsize_t DataSet::getVlenBufSize(DataType& type, DataSpace& space) const
//{
// return(getVlenBufSize(type, space));
//}
//--------------------------------------------------------------------------
// Function: DataSet::vlenReclaim
///\brief Reclaims VL datatype memory buffers.
///\param type - IN: Datatype, which is the datatype stored in the buffer
///\param space - IN: Selection for the memory buffer to free the
/// VL datatypes within
///\param xfer_plist - IN: Property list used to create the buffer
///\param buf - IN: Pointer to the buffer to be reclaimed
///\exception H5::DataSetIException
// Programmer Binh-Minh Ribler - 2000
//--------------------------------------------------------------------------
void
DataSet::vlenReclaim(const DataType &type, const DataSpace &space, const DSetMemXferPropList &xfer_plist,
void *buf)
{
// Obtain identifiers for C API
hid_t type_id = type.getId();
hid_t space_id = space.getId();
hid_t xfer_plist_id = xfer_plist.getId();
herr_t ret_value = H5Treclaim(type_id, space_id, xfer_plist_id, buf);
if (ret_value < 0) {
throw DataSetIException("DataSet::vlenReclaim", "H5Treclaim failed");
}
}
//--------------------------------------------------------------------------
// Function: DataSet::vlenReclaim
///\brief Reclaims VL datatype memory buffers.
///\param type - IN: Datatype, which is the datatype stored in the buffer
///\param space - IN: Selection for the memory buffer to free the
/// VL datatypes within
///\param xfer_plist - IN: Property list used to create the buffer
///\param buf - IN: Pointer to the buffer to be reclaimed
///\exception H5::DataSetIException
// Programmer Binh-Minh Ribler - 2000
//\parDescription
// This function has better prototype for the users than the
// other, which might be removed at some point. BMR - 2006/12/20
//--------------------------------------------------------------------------
void
DataSet::vlenReclaim(void *buf, const DataType &type, const DataSpace &space,
const DSetMemXferPropList &xfer_plist)
{
// Obtain identifiers for C API
hid_t type_id = type.getId();
hid_t space_id = space.getId();
hid_t xfer_plist_id = xfer_plist.getId();
herr_t ret_value = H5Treclaim(type_id, space_id, xfer_plist_id, buf);
if (ret_value < 0) {
throw DataSetIException("DataSet::vlenReclaim", "H5Treclaim failed");
}
}
//--------------------------------------------------------------------------
// Function: DataSet::read
///\brief Reads raw data from the specified dataset.
///\param buf - IN: Buffer for read data
///\param mem_type - IN: Memory datatype
///\param mem_space - IN: Memory dataspace
///\param file_space - IN: Dataset's dataspace in the file
///\param xfer_plist - IN: Transfer property list for this I/O operation
///\exception H5::DataSetIException
///\par Description
/// This function reads raw data from this dataset into the
/// buffer \a buf, converting from file datatype and dataspace
/// to memory datatype \a mem_type and dataspace \a mem_space.
// Programmer Binh-Minh Ribler - 2000
//--------------------------------------------------------------------------
void
DataSet::read(void *buf, const DataType &mem_type, const DataSpace &mem_space, const DataSpace &file_space,
const DSetMemXferPropList &xfer_plist) const
{
// Obtain identifiers for C API
hid_t mem_type_id = mem_type.getId();
hid_t mem_space_id = mem_space.getId();
hid_t file_space_id = file_space.getId();
hid_t xfer_plist_id = xfer_plist.getId();
herr_t ret_value = H5Dread(id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, buf);
if (ret_value < 0) {
throw DataSetIException("DataSet::read", "H5Dread failed");
}
}
//--------------------------------------------------------------------------
// Function: DataSet::read
///\brief This is an overloaded member function, provided for convenience.
/// It takes a reference to a \c H5std_string for the buffer.
///\param strg - IN: Buffer for read data string
///\param mem_type - IN: Memory datatype
///\param mem_space - IN: Memory dataspace
///\param file_space - IN: Dataset's dataspace in the file
///\param xfer_plist - IN: Transfer property list for this I/O operation
///\exception H5::DataSetIException
// Programmer Binh-Minh Ribler - 2000
// Modification
// Jul 2009
// Follow the change to Attribute::read and use the following
// private functions to read datasets with fixed- and
// variable-length string:
// DataSet::p_read_fixed_len and
// DataSet::p_read_variable_len
//--------------------------------------------------------------------------
void
DataSet::read(H5std_string &strg, const DataType &mem_type, const DataSpace &mem_space,
const DataSpace &file_space, const DSetMemXferPropList &xfer_plist) const
{
// Check if this dataset has variable-len string or fixed-len string and
// proceed appropriately.
htri_t is_variable_len = H5Tis_variable_str(mem_type.getId());
if (is_variable_len < 0) {
throw DataSetIException("DataSet::read", "H5Tis_variable_str failed");
}
// Obtain identifiers for C API
hid_t mem_type_id = mem_type.getId();
hid_t mem_space_id = mem_space.getId();
hid_t file_space_id = file_space.getId();
hid_t xfer_plist_id = xfer_plist.getId();
if (!is_variable_len) // only allocate for fixed-len string
{
p_read_fixed_len(mem_type_id, mem_space_id, file_space_id, xfer_plist_id, strg);
}
else {
p_read_variable_len(mem_type_id, mem_space_id, file_space_id, xfer_plist_id, strg);
}
}
//--------------------------------------------------------------------------
// Function: DataSet::write
///\brief Writes raw data from an application buffer to a dataset.
///\param buf - IN: Buffer containing data to be written
///\param mem_type - IN: Memory datatype
///\param mem_space - IN: Memory dataspace
///\param file_space - IN: Dataset's dataspace in the file
///\param xfer_plist - IN: Transfer property list for this I/O operation
///\exception H5::DataSetIException
///\par Description
/// This function writes raw data from an application buffer
/// \a buf to a dataset, converting from memory datatype
/// \a mem_type and dataspace \a mem_space to file datatype
/// and dataspace.
// Programmer Binh-Minh Ribler - 2000
//--------------------------------------------------------------------------
void
DataSet::write(const void *buf, const DataType &mem_type, const DataSpace &mem_space,
const DataSpace &file_space, const DSetMemXferPropList &xfer_plist) const
{
// Obtain identifiers for C API
hid_t mem_type_id = mem_type.getId();
hid_t mem_space_id = mem_space.getId();
hid_t file_space_id = file_space.getId();
hid_t xfer_plist_id = xfer_plist.getId();
herr_t ret_value = H5Dwrite(id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, buf);
if (ret_value < 0) {
throw DataSetIException("DataSet::write", "H5Dwrite failed");
}
}
//--------------------------------------------------------------------------
// Function: DataSet::write
///\brief This is an overloaded member function, provided for convenience.
/// It takes a reference to a \c H5std_string for the buffer.
// Programmer Binh-Minh Ribler - 2000
// Modification
// Jul 2009
// Modified to pass the buffer into H5Dwrite properly depending
// whether the dataset has variable- or fixed-length string.
//--------------------------------------------------------------------------
void
DataSet::write(const H5std_string &strg, const DataType &mem_type, const DataSpace &mem_space,
const DataSpace &file_space, const DSetMemXferPropList &xfer_plist) const
{
// Check if this attribute has variable-len string or fixed-len string and
// proceed appropriately.
htri_t is_variable_len = H5Tis_variable_str(mem_type.getId());
if (is_variable_len < 0) {
throw DataSetIException("DataSet::write", "H5Tis_variable_str failed");
}
// Obtain identifiers for C API
hid_t mem_type_id = mem_type.getId();
hid_t mem_space_id = mem_space.getId();
hid_t file_space_id = file_space.getId();
hid_t xfer_plist_id = xfer_plist.getId();
// Convert string to C-string
const char *strg_C;
strg_C = strg.c_str(); // strg_C refers to the contents of strg as a C-str
herr_t ret_value = 0;
// Pass string in differently depends on variable or fixed length
if (!is_variable_len) {
ret_value = H5Dwrite(id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, strg_C);
}
else {
// passing string argument by address
ret_value = H5Dwrite(id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, &strg_C);
}
if (ret_value < 0) {
throw DataSetIException("DataSet::write", "H5Dwrite failed");
}
}
//--------------------------------------------------------------------------
// Function: DataSet::iterateElems
///\brief Iterates over all selected elements in a dataspace.
///\param buf - IN/OUT: Pointer to the buffer in memory containing the
/// elements to iterate over
///\param type - IN: Datatype for the elements stored in \a buf
///\param space - IN: Dataspace for \a buf. Also contains the selection
/// to iterate over.
///\param op - IN: Function pointer to the routine to be called for
/// each element in \a buf iterated over
///\param op_data - IN/OUT: Pointer to any user-defined data associated
/// with the operation
///\exception H5::DataSetIException
///\note This function may not work correctly yet - it's still
/// under development.
// Programmer Binh-Minh Ribler - 2000
//--------------------------------------------------------------------------
int
DataSet::iterateElems(void *buf, const DataType &type, const DataSpace &space, H5D_operator_t op,
void *op_data)
{
// Obtain identifiers for C API
hid_t type_id = type.getId();
hid_t space_id = space.getId();
herr_t ret_value = H5Diterate(buf, type_id, space_id, op, op_data);
if (ret_value >= 0)
return (ret_value);
else // raise exception when H5Diterate returns a negative value
{
throw DataSetIException("DataSet::iterateElems", "H5Diterate failed");
}
}
//--------------------------------------------------------------------------
// Function: DataSet::extend
///\brief Extends a dataset with unlimited dimension.
///\param size - IN: Array containing the new magnitude of each dimension
///\exception H5::DataSetIException
///\par Description
/// For information, please refer to the H5Dset_extent API in
/// the HDF5 C Reference Manual.
// Programmer Binh-Minh Ribler - 2000
//--------------------------------------------------------------------------
void
DataSet::extend(const hsize_t *size) const
{
herr_t ret_value = H5Dset_extent(id, size);
if (ret_value < 0) // raise exception when H5Dset_extent returns a neg value
throw DataSetIException("DataSet::extend", "H5Dset_extent failed");
}
//--------------------------------------------------------------------------
// Function: DataSet::fillMemBuf
///\brief Fills a selection in memory with a value.
///\param fill - IN: Pointer to fill value to use - default NULL
///\param fill_type - IN: Datatype of the fill value
///\param buf - IN/OUT: Memory buffer to fill selection within
///\param buf_type - IN: Datatype of the elements in buffer
///\param space - IN: Dataspace describing memory buffer & containing selection to use
///\exception H5::DataSetIException
// Programmer Binh-Minh Ribler - 2014
//--------------------------------------------------------------------------
void
DataSet::fillMemBuf(const void *fill, const DataType &fill_type, void *buf, const DataType &buf_type,
const DataSpace &space) const
{
hid_t fill_type_id = fill_type.getId();
hid_t buf_type_id = buf_type.getId();
hid_t space_id = space.getId();
herr_t ret_value = H5Dfill(fill, fill_type_id, buf, buf_type_id, space_id);
if (ret_value < 0) {
throw DataSetIException("DataSet::fillMemBuf", "H5Dfill failed");
}
}
//--------------------------------------------------------------------------
// Function: DataSet::fillMemBuf
// Purpose This is an overloaded member function, kept for backward
// compatibility. It differs from the above function in that it
// misses const's. This wrapper will be removed in future release.
// Param fill - IN: Pointer to fill value to use - default NULL
// Param fill_type - IN: Datatype of the fill value
// Param buf - IN/OUT: Memory buffer to fill selection within
// Param buf_type - IN: Datatype of the elements in buffer
// Param space - IN: Dataspace describing memory buffer & containing selection to use
// Exception H5::DataSetIException
// Programmer Binh-Minh Ribler - 2000
// Modification
// Modified to call its replacement. -BMR, 2014/04/16
// Removed from documentation. -BMR, 2016/03/07 1.8.17 and 1.10.0
// Removed from code. -BMR, 2016/08/11 1.8.18 and 1.10.1
//--------------------------------------------------------------------------
// void DataSet::fillMemBuf(const void *fill, DataType& fill_type, void *buf, DataType& buf_type, DataSpace&
// space)
//{
// fillMemBuf(fill, (const DataType)fill_type, buf, (const DataType)buf_type, (const DataSpace)space);
//}
//--------------------------------------------------------------------------
// Function: DataSet::fillMemBuf
///\brief Fills a selection in memory with 0.
///\param buf - IN/OUT: Memory buffer to fill selection within
///\param buf_type - IN: Datatype of the elements in buffer
///\param space - IN: Dataspace describing memory buffer & containing selection to use
///\exception H5::DataSetIException
// Programmer Binh-Minh Ribler - 2000
//--------------------------------------------------------------------------
void
DataSet::fillMemBuf(void *buf, const DataType &buf_type, const DataSpace &space) const
{
hid_t buf_type_id = buf_type.getId();
hid_t space_id = space.getId();
herr_t ret_value = H5Dfill(NULL, buf_type_id, buf, buf_type_id, space_id);
if (ret_value < 0) {
throw DataSetIException("DataSet::fillMemBuf", "H5Dfill failed");
}
}
//--------------------------------------------------------------------------
// Function: DataSet::fillMemBuf
// Purpose This is an overloaded member function, kept for backward
// compatibility. It differs from the above function in that it
// misses const's. This wrapper will be removed in future release.
// Param buf - IN/OUT: Memory buffer to fill selection within
// Param buf_type - IN: Datatype of the elements in buffer
// Param space - IN: Dataspace describing memory buffer & containing selection to use
// Exception H5::DataSetIException
// Programmer Binh-Minh Ribler - 2000
// Modification
// Modified to call its replacement. -BMR, 2014/04/16
// Removed from documentation. -BMR, 2016/03/07 1.8.17 and 1.10.0
// Removed from code. -BMR, 2016/08/11 1.8.18 and 1.10.1
//--------------------------------------------------------------------------
// void DataSet::fillMemBuf(void *buf, DataType& buf_type, DataSpace& space)
//{
// fillMemBuf(buf, (const DataType)buf_type, (const DataSpace)space);
//}
//--------------------------------------------------------------------------
// Function: DataSet::getId
///\brief Get the id of this dataset.
///\return DataSet identifier
// Description:
// Class hierarchy is revised to address bugzilla 1068. Class
// AbstractDs and Attribute are moved out of H5Object. In
// addition, member IdComponent::id is moved into subclasses, and
// IdComponent::getId now becomes pure virtual function.
// Programmer Binh-Minh Ribler - May, 2008
//--------------------------------------------------------------------------
hid_t
DataSet::getId() const
{
return (id);
}
//--------------------------------------------------------------------------
// Function: DataSet::p_read_fixed_len (private)
// brief Reads a fixed length \a H5std_string from a dataset.
// param mem_type - IN: DataSet datatype (in memory)
// param strg - IN: Buffer for read string
// exception H5::DataSetIException
// Programmer Binh-Minh Ribler - Jul, 2009
// Modification
// Jul 2009
// Added in follow to the change in Attribute::read
//--------------------------------------------------------------------------
void
DataSet::p_read_fixed_len(const hid_t mem_type_id, const hid_t mem_space_id, const hid_t file_space_id,
const hid_t xfer_plist_id, H5std_string &strg) const
{
// Only allocate for fixed-len string.
// Get the size of the dataset's data
size_t data_size = getInMemDataSize();
// If there is data, allocate buffer and read it.
if (data_size > 0) {
char *strg_C = new char[data_size + 1];
HDmemset(strg_C, 0, data_size + 1); // clear buffer
herr_t ret_value = H5Dread(id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, strg_C);
if (ret_value < 0) {
delete[] strg_C; // de-allocate for fixed-len string
throw DataSetIException("DataSet::read", "H5Dread failed for fixed length string");
}
// Get string from the C char* and release resource allocated locally
strg = strg_C;
delete[] strg_C;
}
}
//--------------------------------------------------------------------------
// Function: DataSet::p_read_variable_len (private)
// brief Reads a variable length \a H5std_string from an dataset.
// param mem_type - IN: DataSet datatype (in memory)
// param strg - IN: Buffer for read string
// exception H5::DataSetIException
// Programmer Binh-Minh Ribler - Jul, 2009
// Modification
// Jul 2009
// Added in follow to the change in Attribute::read
//--------------------------------------------------------------------------
void
DataSet::p_read_variable_len(const hid_t mem_type_id, const hid_t mem_space_id, const hid_t file_space_id,
const hid_t xfer_plist_id, H5std_string &strg) const
{
// Prepare and call C API to read dataset.
char *strg_C;
// Read dataset, no allocation for variable-len string; C library will
herr_t ret_value = H5Dread(id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, &strg_C);
if (ret_value < 0) {
throw DataSetIException("DataSet::read", "H5Dread failed for variable length string");
}
// Get string from the C char* and release resource allocated by C API
strg = strg_C;
HDfree(strg_C);
}
#ifndef DOXYGEN_SHOULD_SKIP_THIS
//--------------------------------------------------------------------------
// Function: DataSet::p_setId (protected)
///\brief Sets the identifier of this dataset to a new value.
///
///\exception H5::IdComponentException when the attempt to close the HDF5
/// object fails
// Description:
// The underlaying reference counting in the C library ensures
// that the current valid id of this object is properly closed.
// Then the object's id is reset to the new id.
// Programmer Binh-Minh Ribler - 2000
//--------------------------------------------------------------------------
void
DataSet::p_setId(const hid_t new_id)
{
// handling references to this old id
try {
close();
}
catch (Exception &close_error) {
throw DataSetIException(inMemFunc("p_setId"), close_error.getDetailMsg());
}
// reset object's id to the given id
id = new_id;
}
//--------------------------------------------------------------------------
// Function: f_PropList_setId - friend
// Purpose: This function is friend to class H5::PropList so that it
// can set PropList::id in order to work around a problem
// described in the JIRA issue HDFFV-7947.
// Applications shouldn't need to use it.
// param dset - IN/OUT: DataSet object to be changed
// param new_id - IN: New id to set
// Programmer Binh-Minh Ribler - 2015
//--------------------------------------------------------------------------
void
f_PropList_setId(PropList *plist, hid_t new_id)
{
plist->p_setId(new_id);
}
#endif // DOXYGEN_SHOULD_SKIP_THIS
//--------------------------------------------------------------------------
// Function: DataSet::close
///\brief Closes this dataset.
///
///\exception H5::DataSetIException
// Programmer Binh-Minh Ribler - Mar 9, 2005
//--------------------------------------------------------------------------
void
DataSet::close()
{
if (p_valid_id(id)) {
herr_t ret_value = H5Dclose(id);
if (ret_value < 0) {
throw DataSetIException("DataSet::close", "H5Dclose failed");
}
// reset the id
id = H5I_INVALID_HID;
}
}
//--------------------------------------------------------------------------
// Function: DataSet destructor
///\brief Properly terminates access to this dataset.
// Programmer Binh-Minh Ribler - 2000
// Modification
// - Replaced resetIdComponent() with decRefCount() to use C
// library ID reference counting mechanism - BMR, Jun 1, 2004
// - Replaced decRefCount with close() to let the C library
// handle the reference counting - BMR, Jun 1, 2006
//--------------------------------------------------------------------------
DataSet::~DataSet()
{
try {
close();
}
catch (Exception &close_error) {
cerr << "DataSet::~DataSet - " << close_error.getDetailMsg() << endl;
}
}
} // namespace H5