path: root/c++/src/H5DataSet.cpp

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 * Copyright by The HDF Group.                                               *
 * Copyright by the Board of Trustees of the University of Illinois.         *
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#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 "H5LaccProp.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: 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.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
// 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;
   f_PropList_setId(&create_plist, create_plist_id);
   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.
///\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 = 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
//--------------------------------------------------------------------------
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;
    }
}

} // end namespace