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98d1c2d9a9e0e0da02a3bd4367c574bfa3326af7
hdf5/c++/src/H5DataSet.cpp
Binh-Minh Ribler 98d1c2d9a9 [svn-r26655] Purpose: Fixed HDFFV-7947 
Description:
    When copy constructor or constructor that takes an existing id is invoked,
    the C ref counter stays the same but there is an extra C++ object which
    later is destroyed and may cause the HDF5 id to be closed prematurely. The
    C++ library needs to increment the ref counter in these situations, so that
    the C library will not close the id when it is still being referenced.

    However, the incrementing of ref count left some objects opened at the end
    of the program, perhaps, due to compiler's optimization on cons/destructors.    The constructor, that takes an existing id, needs to increment the counter
    but it seems that the matching destructor wasn't invoked.  The workaround
    is to have a function for each class that has "id" that only sets the id
    and not increment the ref count for the library to use in these situations.
    These functions are "friend" and not public.

    The friend functions are:
        void f_Attribute_setId(Attribute *, hid_t)
        void f_DataSet_setId(DataSet *, hid_t)
        void f_DataSpace_setId(DataSpace *, hid_t)
        void f_DataType_setId(DataType *, hid_t)
Platforms tested:
    Linux/64 (platypus)
    Linux/32 2.6 (jam gnu and Intel 15.0)
    SunOS 5.11 (emu)
2015-03-30 12:58:44 -05:00

819 lines
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/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* 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 files COPYING and Copyright.html. COPYING can be found at the root *
* of the source code distribution tree; Copyright.html can be found at the *
* root level of an installed copy of the electronic HDF5 document set and *
* is linked from the top-level documents page. It can also be found at *
* http://hdfgroup.org/HDF5/doc/Copyright.html. 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 "H5Include.h"
#include "H5Exception.h"
#include "H5IdComponent.h"
#include "H5PropList.h"
#include "H5Object.h"
#include "H5PropList.h"
#include "H5DxferProp.h"
#include "H5DcreatProp.h"
#include "H5FaccProp.h"
#include "H5FcreatProp.h"
#include "H5CommonFG.h"
#include "H5DataType.h"
#include "H5DataSpace.h"
#include "H5AbstractDs.h"
#include "H5File.h"
#include "H5Attribute.h"
#include "H5DataSet.h"
#include "H5private.h" // for HDfree
#ifndef H5_NO_NAMESPACE
namespace H5 {
#ifndef H5_NO_STD
using std::cerr;
using std::endl;
#endif // H5_NO_STD
#endif
//--------------------------------------------------------------------------
// 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
//--------------------------------------------------------------------------
DataSet::DataSet(const hid_t existing_id) : H5Object(), AbstractDs()
{
id = existing_id;
}
//--------------------------------------------------------------------------
// Function: DataSet copy constructor
///\brief Copy constructor: makes a copy of the original DataSet object.
///\param original - IN: DataSet instance to copy
// Programmer Binh-Minh Ribler - 2000
//--------------------------------------------------------------------------
DataSet::DataSet(const DataSet& original) : H5Object(), AbstractDs()
{
id = original.getId();
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
// Modification
// Jul, 2008
// Added for application convenience.
//--------------------------------------------------------------------------
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
// Modification
// Jul, 2008
// Added for application convenience.
//--------------------------------------------------------------------------
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(create_plist_id); // ok to use existing id const
return(create_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.
///\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
///\brief 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
//--------------------------------------------------------------------------
hsize_t DataSet::getVlenBufSize( DataType& type, DataSpace& space ) const
{
return(getVlenBufSize((const DataType)type, (const DataSpace)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 = H5Dvlen_reclaim( type_id, space_id, xfer_plist_id, buf );
if( ret_value < 0 )
{
throw DataSetIException("DataSet::vlenReclaim", "H5Dvlen_reclaim 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 = H5Dvlen_reclaim(type_id, space_id, xfer_plist_id, buf);
if (ret_value < 0)
{
throw DataSetIException("DataSet::vlenReclaim", "H5Dvlen_reclaim 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 more information, please see the Description section in
/// C layer Reference Manual at:
///\par
/// http://www.hdfgroup.org/HDF5/doc/RM/RM_H5D.html#Dataset-Extend
// 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
// Modification
// Used the non-const version.
//--------------------------------------------------------------------------
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
///\brief 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
//--------------------------------------------------------------------------
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
///\brief 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
//--------------------------------------------------------------------------
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;
}
#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;
}
}
#ifndef H5_NO_NAMESPACE
} // end namespace
#endif
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