mirror of
https://github.com/HDFGroup/hdf5.git
synced 2026-09-29 04:09:39 +03:00
Binh-Minh Ribler
daa61b5986
Description:
Wrappers of H5Rcreate had incorrect prototypes.
Solution:
Added these overloaded functions for H5Rcreate wrapper to IdComponent:
void reference(void* ref, const char* name, DataSpace& dataspace,
H5R_type_t ref_type = H5R_DATASET_REGION) const;
void reference(void* ref, const char* name) const;
void reference(void* ref, const H5std_string& name) const;
Added these overloaded functions for H5Rdereference:
void dereference(IdComponent& obj, void* ref);
DataSet(IdComponent& obj, void* ref);
Group(IdComponent& obj, void* ref);
DataType(IdComponent& obj, void* ref);
The incorrect wrappers will be removed after announcing.
Platform tested:
Linux 2.4 (heping)
AIX 5.1 (copper)
SunOS 5.8 64-bit (sol)
567 lines
22 KiB
C++
567 lines
22 KiB
C++
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
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* Copyright by the Board of Trustees of the University of Illinois. *
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* All rights reserved. *
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* *
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* This file is part of HDF5. The full HDF5 copyright notice, including *
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* terms governing use, modification, and redistribution, is contained in *
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* the files COPYING and Copyright.html. COPYING can be found at the root *
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* of the source code distribution tree; Copyright.html can be found at the *
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* root level of an installed copy of the electronic HDF5 document set and *
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* is linked from the top-level documents page. It can also be found at *
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* http://hdf.ncsa.uiuc.edu/HDF5/doc/Copyright.html. If you do not have *
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* access to either file, you may request a copy from hdfhelp@ncsa.uiuc.edu. *
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* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
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#ifdef OLD_HEADER_FILENAME
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#include <iostream.h>
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#else
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#include <iostream>
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#endif
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#include <string>
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#include "H5Include.h"
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#include "H5Exception.h"
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#include "H5IdComponent.h"
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#include "H5PropList.h"
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#include "H5Object.h"
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#include "H5PropList.h"
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#include "H5DxferProp.h"
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#include "H5DcreatProp.h"
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#include "H5CommonFG.h"
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#include "H5DataType.h"
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#include "H5DataSpace.h"
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#include "H5AbstractDs.h"
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#include "H5DataSet.h"
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#ifndef H5_NO_NAMESPACE
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namespace H5 {
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#ifndef H5_NO_STD
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using std::cerr;
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using std::endl;
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#endif // H5_NO_STD
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#endif
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//--------------------------------------------------------------------------
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// Function: DataSet default constructor
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///\brief Default constructor: creates a stub DataSet.
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// Programmer Binh-Minh Ribler - 2000
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//--------------------------------------------------------------------------
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DataSet::DataSet() : AbstractDs() {}
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//--------------------------------------------------------------------------
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// Function: DataSet overloaded constructor
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///\brief Creates an DataSet object using the id of an existing dataset.
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///\param existing_id - IN: Id of an existing dataset
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// Programmer Binh-Minh Ribler - 2000
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//--------------------------------------------------------------------------
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DataSet::DataSet(const hid_t existing_id) : AbstractDs(existing_id) {}
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//--------------------------------------------------------------------------
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// Function: DataSet copy constructor
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///\brief Copy constructor: makes a copy of the original DataSet object.
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///\param original - IN: DataSet instance to copy
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// Programmer Binh-Minh Ribler - 2000
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//--------------------------------------------------------------------------
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DataSet::DataSet( const DataSet& original ) : AbstractDs( original ) {}
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//--------------------------------------------------------------------------
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// Function: DataSet overload constructor - dereference
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///\brief Given a reference to some object, returns that dataset
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/// obj - IN: Dataset reference object is in or location of
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/// object that the dataset is located within.
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///\param ref - IN: Reference pointer
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///\exception H5::DataSetIException
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///\parDescription
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/// \c obj can be DataSet, Group, H5File, or named DataType, that
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/// is a datatype that has been named by DataType::commit.
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// Programmer Binh-Minh Ribler - Oct, 2006
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//--------------------------------------------------------------------------
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DataSet::DataSet(IdComponent& obj, void* ref) : AbstractDs()
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{
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IdComponent::dereference(obj, ref);
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}
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//--------------------------------------------------------------------------
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// Function: DataSet::getSpace
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///\brief Gets a copy of the dataspace of this dataset.
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///\return DataSpace instance
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///\exception H5::DataSetIException
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// Programmer Binh-Minh Ribler - 2000
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//--------------------------------------------------------------------------
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DataSpace DataSet::getSpace() const
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{
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// Calls C function H5Dget_space to get the id of the dataspace
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hid_t dataspace_id = H5Dget_space( id );
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// If the dataspace id is invalid, throw an exception
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if( dataspace_id < 0 )
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{
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throw DataSetIException("DataSet::getSpace", "H5Dget_space failed");
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}
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//create dataspace object using the existing id then return the object
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DataSpace data_space( dataspace_id );
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return( data_space );
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}
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// This private member function calls the C API to get the identifier
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// of the datatype that is used by this dataset. It is used
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// by the various AbstractDs functions to get the specific datatype.
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hid_t DataSet::p_get_type() const
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{
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hid_t type_id = H5Dget_type( id );
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if( type_id > 0 )
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return( type_id );
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else
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{
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throw DataSetIException("", "H5Dget_type failed");
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}
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}
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//--------------------------------------------------------------------------
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// Function: DataSet::getCreatePlist
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///\brief Gets the dataset creation property list.
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///\return DSetCreatPropList instance
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///\exception H5::DataSetIException
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// Programmer Binh-Minh Ribler - 2000
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//--------------------------------------------------------------------------
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DSetCreatPropList DataSet::getCreatePlist() const
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{
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hid_t create_plist_id = H5Dget_create_plist( id );
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if( create_plist_id < 0 )
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{
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throw DataSetIException("DataSet::getCreatePlist", "H5Dget_create_plist failed");
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}
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// create and return the DSetCreatPropList object
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DSetCreatPropList create_plist( create_plist_id );
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return( create_plist );
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}
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//--------------------------------------------------------------------------
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// Function: DataSet::getStorageSize
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///\brief Returns the amount of storage required for a dataset.
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///\return Size of the storage or 0, for no data
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///\exception H5::DataSetIException
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// Note: H5Dget_storage_size returns 0 when there is no data. This
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// function should have no failure. (from SLU)
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// Programmer Binh-Minh Ribler - Mar, 2005
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//--------------------------------------------------------------------------
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hsize_t DataSet::getStorageSize() const
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{
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hsize_t storage_size = H5Dget_storage_size(id);
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return(storage_size);
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}
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//--------------------------------------------------------------------------
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// Function: DataSet::getOffset
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///\brief Returns the address of this dataset in the file.
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///\return Address of dataset
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///\exception H5::DataSetIException
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// Programmer Binh-Minh Ribler - 2000
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//--------------------------------------------------------------------------
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haddr_t DataSet::getOffset() const
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{
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haddr_t ds_addr; // for address of dataset
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ds_addr = H5Dget_offset(id);
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if( ds_addr == HADDR_UNDEF )
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{
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throw DataSetIException("DataSet::getOffset", "H5Dget_offset returned HADDR_UNDEF");
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}
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return(ds_addr);
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}
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//--------------------------------------------------------------------------
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// Function: DataSet::getSpaceStatus
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///\brief Determines whether space has been allocated for a dataset.
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///\param status - OUT: Space allocation status
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///\exception H5::DataSetIException
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// Programmer Binh-Minh Ribler - 2000
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//--------------------------------------------------------------------------
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void DataSet::getSpaceStatus(H5D_space_status_t& status) const
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{
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herr_t ret_value = H5Dget_space_status(id, &status);
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if( ret_value < 0 )
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{
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throw DataSetIException("DataSet::getSpaceStatus", "H5Dget_space_status failed");
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}
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}
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//--------------------------------------------------------------------------
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// Function: DataSet::getVlenBufSize
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///\brief Returns the number of bytes required to store VL data.
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///\return Amount of storage
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///\exception H5::DataSetIException
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// Programmer Binh-Minh Ribler - 2000
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//--------------------------------------------------------------------------
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hsize_t DataSet::getVlenBufSize( DataType& type, DataSpace& space ) const
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{
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// Obtain identifiers for C API
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hid_t type_id = type.getId();
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hid_t space_id = space.getId();
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hsize_t size; // for amount of storage
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herr_t ret_value = H5Dvlen_get_buf_size( id, type_id, space_id, &size );
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if( ret_value < 0 )
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{
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throw DataSetIException("DataSet::getVlenBufSize", "H5Dvlen_get_buf_size failed");
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}
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return( size );
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}
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//--------------------------------------------------------------------------
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// Function: DataSet::vlenReclaim
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///\brief Reclaims VL datatype memory buffers.
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///\param type - IN: Datatype, which is the datatype stored in the buffer
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///\param space - IN: Selection for the memory buffer to free the
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/// VL datatypes within
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///\param xfer_plist - IN: Property list used to create the buffer
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///\param buf - IN: Pointer to the buffer to be reclaimed
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///\exception H5::DataSetIException
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// Programmer Binh-Minh Ribler - 2000
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//--------------------------------------------------------------------------
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void DataSet::vlenReclaim( DataType& type, DataSpace& space, DSetMemXferPropList& xfer_plist, void* buf ) const
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{
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// Obtain identifiers for C API
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hid_t type_id = type.getId();
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hid_t space_id = space.getId();
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hid_t xfer_plist_id = xfer_plist.getId();
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herr_t ret_value = H5Dvlen_reclaim( type_id, space_id, xfer_plist_id, buf );
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if( ret_value < 0 )
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{
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throw DataSetIException("DataSet::vlenReclaim", "H5Dvlen_reclaim failed");
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}
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}
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//--------------------------------------------------------------------------
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// Function: DataSet::read
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///\brief Reads raw data from the specified dataset.
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///\param buf - IN: Buffer for read data
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///\param mem_type - IN: Memory datatype
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///\param mem_space - IN: Memory dataspace
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///\param file_space - IN: Dataset's dataspace in the file
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///\param xfer_plist - IN: Transfer property list for this I/O operation
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///\exception H5::DataSetIException
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///\par Description
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/// This function reads raw data from this dataset into the
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/// buffer \a buf, converting from file datatype and dataspace
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/// to memory datatype \a mem_type and dataspace \a mem_space.
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// Programmer Binh-Minh Ribler - 2000
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//--------------------------------------------------------------------------
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void DataSet::read( void* buf, const DataType& mem_type, const DataSpace& mem_space, const DataSpace& file_space, const DSetMemXferPropList& xfer_plist ) const
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{
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// Obtain identifiers for C API
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hid_t mem_type_id = mem_type.getId();
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hid_t mem_space_id = mem_space.getId();
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hid_t file_space_id = file_space.getId();
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hid_t xfer_plist_id = xfer_plist.getId();
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herr_t ret_value = H5Dread( id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, buf );
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if( ret_value < 0 )
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{
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throw DataSetIException("DataSet::read", "H5Dread failed");
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}
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}
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//--------------------------------------------------------------------------
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// Function: DataSet::read
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///\brief This is an overloaded member function, provided for convenience.
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/// It takes a reference to a \c std::string for the buffer.
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// Programmer Binh-Minh Ribler - 2000
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//--------------------------------------------------------------------------
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void DataSet::read( H5std_string& strg, const DataType& mem_type, const DataSpace& mem_space, const DataSpace& file_space, const DSetMemXferPropList& xfer_plist ) const
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{
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// Allocate C character string for reading
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size_t size = mem_type.getSize();
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char* strg_C = new char[size+1]; // temporary C-string for C API
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// Use the overloaded member to read
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read(strg_C, mem_type, mem_space, file_space, xfer_plist);
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// Get the String and clean up
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strg = strg_C;
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delete []strg_C;
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}
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//--------------------------------------------------------------------------
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// Function: DataSet::write
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///\brief Writes raw data from an application buffer to a dataset.
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///\param buf - IN: Buffer containing data to be written
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///\param mem_type - IN: Memory datatype
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///\param mem_space - IN: Memory dataspace
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///\param file_space - IN: Dataset's dataspace in the file
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///\param xfer_plist - IN: Transfer property list for this I/O operation
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///\exception H5::DataSetIException
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///\par Description
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/// This function writes raw data from an application buffer
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/// \a buf to a dataset, converting from memory datatype
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/// \a mem_type and dataspace \a mem_space to file datatype
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/// and dataspace.
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// Programmer Binh-Minh Ribler - 2000
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//--------------------------------------------------------------------------
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void DataSet::write( const void* buf, const DataType& mem_type, const DataSpace& mem_space, const DataSpace& file_space, const DSetMemXferPropList& xfer_plist ) const
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{
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// Obtain identifiers for C API
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hid_t mem_type_id = mem_type.getId();
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hid_t mem_space_id = mem_space.getId();
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hid_t file_space_id = file_space.getId();
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hid_t xfer_plist_id = xfer_plist.getId();
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herr_t ret_value = H5Dwrite( id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, buf );
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if( ret_value < 0 )
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{
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throw DataSetIException("DataSet::write", "H5Dwrite failed");
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}
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}
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//--------------------------------------------------------------------------
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// Function: DataSet::write
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///\brief This is an overloaded member function, provided for convenience.
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/// It takes a reference to a \c std::string for the buffer.
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// Programmer Binh-Minh Ribler - 2000
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//--------------------------------------------------------------------------
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void DataSet::write( const H5std_string& strg, const DataType& mem_type, const DataSpace& mem_space, const DataSpace& file_space, const DSetMemXferPropList& xfer_plist ) const
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{
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// Convert string to C-string
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const char* strg_C;
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strg_C = strg.c_str(); // strg_C refers to the contents of strg as a C-str
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// Use the overloaded member
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write(strg_C, mem_type, mem_space, file_space, xfer_plist);
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}
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//--------------------------------------------------------------------------
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// Function: DataSet::iterateElems
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///\brief Iterates over all selected elements in a dataspace.
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///\param buf - IN/OUT: Pointer to the buffer in memory containing the
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/// elements to iterate over
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///\param type - IN: Datatype for the elements stored in \a buf
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///\param space - IN: Dataspace for \a buf. Also contains the selection
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/// to iterate over.
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///\param op - IN: Function pointer to the routine to be called for
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/// each element in \a buf iterated over
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///\param op_data - IN/OUT: Pointer to any user-defined data associated
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/// with the operation
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///\exception H5::DataSetIException
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///\note This function may not work correctly yet - it's still
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/// under development.
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// Programmer Binh-Minh Ribler - 2000
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//--------------------------------------------------------------------------
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int DataSet::iterateElems( void* buf, const DataType& type, const DataSpace& space, H5D_operator_t op, void* op_data )
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{
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// Obtain identifiers for C API
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hid_t type_id = type.getId();
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hid_t space_id = space.getId();
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herr_t ret_value = H5Diterate( buf, type_id, space_id, op, op_data );
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if( ret_value >= 0 )
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return( ret_value );
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else // raise exception when H5Diterate returns a negative value
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{
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throw DataSetIException("DataSet::iterateElems", "H5Diterate failed");
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}
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}
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//--------------------------------------------------------------------------
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// Function: DataSet::extend
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///\brief Extends a dataset with unlimited dimension.
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///\param size - IN: Array containing the new magnitude of each dimension
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///\exception H5::DataSetIException
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///\par Description
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/// For more information, please see the Description section in
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/// C layer Reference Manual at:
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///\par
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/// http://hdf.ncsa.uiuc.edu/HDF5/doc/RM_H5D.html#Dataset-Extend
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// Programmer Binh-Minh Ribler - 2000
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//--------------------------------------------------------------------------
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void DataSet::extend( const hsize_t* size ) const
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{
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herr_t ret_value = H5Dextend( id, size );
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if( ret_value < 0 ) // raise exception when H5Dextend returns a neg value
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{
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throw DataSetIException("DataSet::extend", "H5Dextend failed");
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}
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}
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//--------------------------------------------------------------------------
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// Function: DataSet::fillMemBuf
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///\brief Fills a selection in memory with a value.
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///\param fill - IN: Pointer to fill value to use - default NULL
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///\param fill_type - IN: Datatype of the fill value
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///\param buf - IN/OUT: Memory buffer to fill selection within
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///\param buf_type - IN: Datatype of the elements in buffer
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///\param space - IN: Dataspace describing memory buffer & containing selection to use
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///\exception H5::DataSetIException
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// Programmer Binh-Minh Ribler - 2000
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//--------------------------------------------------------------------------
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void DataSet::fillMemBuf(const void *fill, DataType& fill_type, void *buf, DataType& buf_type, DataSpace& space)
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{
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hid_t fill_type_id = fill_type.getId();
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hid_t buf_type_id = buf_type.getId();
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hid_t space_id = space.getId();
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herr_t ret_value = H5Dfill(fill, fill_type_id, buf, buf_type_id, space_id);
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if( ret_value < 0 )
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{
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throw DataSetIException("DataSet::fillMemBuf", "H5Dfill failed");
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}
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}
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//--------------------------------------------------------------------------
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// Function: DataSet::fillMemBuf
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///\brief This is an overloaded member function, provided for convenience.
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/// It differs from the above function in that it only takes the
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/// the last three arguments.
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///\param buf - IN/OUT: Memory buffer to fill selection within
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///\param buf_type - IN: Datatype of the elements in buffer
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///\param space - IN: Dataspace describing memory buffer & containing selection to use
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///\exception H5::DataSetIException
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// Programmer Binh-Minh Ribler - 2000
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//--------------------------------------------------------------------------
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void DataSet::fillMemBuf(void *buf, DataType& buf_type, DataSpace& space)
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{
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hid_t buf_type_id = buf_type.getId();
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hid_t space_id = space.getId();
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herr_t ret_value = H5Dfill(NULL, buf_type_id, buf, buf_type_id, space_id);
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if( ret_value < 0 )
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{
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throw DataSetIException("DataSet::fillMemBuf", "H5Dfill failed");
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}
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}
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//--------------------------------------------------------------------------
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// Function: DataSet::Reference
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///\brief Important!!! - This functions may not work correctly, it
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/// will be removed in the near future. Please use
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/// DataSet::reference instead!
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// Programmer Binh-Minh Ribler - May, 2004
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//--------------------------------------------------------------------------
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void* DataSet::Reference(const char* name, DataSpace& dataspace, H5R_type_t ref_type) const
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{
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try {
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return(p_reference(name, dataspace.getId(), ref_type));
|
|
}
|
|
catch (IdComponentException E) {
|
|
throw DataSetIException("DataSet::Reference", E.getDetailMsg());
|
|
}
|
|
}
|
|
|
|
//--------------------------------------------------------------------------
|
|
// Function: DataSet::Reference
|
|
///\brief Important!!! - This functions may not work correctly, it
|
|
/// will be removed in the near future. Please use similar
|
|
/// DataSet::reference instead!
|
|
// Programmer Binh-Minh Ribler - May, 2004
|
|
//--------------------------------------------------------------------------
|
|
void* DataSet::Reference(const char* name) const
|
|
{
|
|
try {
|
|
return(p_reference(name, -1, H5R_OBJECT));
|
|
}
|
|
catch (IdComponentException E) {
|
|
throw DataSetIException("DataSet::Reference", E.getDetailMsg());
|
|
}
|
|
}
|
|
|
|
//--------------------------------------------------------------------------
|
|
// Function: DataSet::Reference
|
|
///\brief Important!!! - This functions may not work correctly, it
|
|
/// will be removed in the near future. Please use similar
|
|
/// DataSet::reference instead!
|
|
// Programmer Binh-Minh Ribler - May, 2004
|
|
//--------------------------------------------------------------------------
|
|
void* DataSet::Reference(const H5std_string& name) const
|
|
{
|
|
return(Reference(name.c_str()));
|
|
}
|
|
|
|
//--------------------------------------------------------------------------
|
|
// Function: DataSet::getObjType
|
|
///\brief Retrieves the type of object that an object reference points to.
|
|
///\param ref_type - IN: Type of reference to query, valid values are:
|
|
/// \li \c H5R_OBJECT \tReference is an object reference.
|
|
/// \li \c H5R_DATASET_REGION \tReference is a dataset region reference.
|
|
///\param ref - IN: Reference to query
|
|
///\return An object type, which can be one of the following:
|
|
/// \li \c H5G_LINK (0) \tObject is a symbolic link.
|
|
/// \li \c H5G_GROUP (1) \tObject is a group.
|
|
/// \li \c H5G_DATASET (2) \tObject is a dataset.
|
|
/// \li \c H5G_TYPE Object (3) \tis a named datatype
|
|
///\exception H5::DataSetIException
|
|
// Programmer Binh-Minh Ribler - May, 2004
|
|
//--------------------------------------------------------------------------
|
|
H5G_obj_t DataSet::getObjType(void *ref, H5R_type_t ref_type) const
|
|
{
|
|
try {
|
|
return(p_get_obj_type(ref, ref_type));
|
|
}
|
|
catch (IdComponentException E) {
|
|
throw DataSetIException("DataSet::getObjType", E.getDetailMsg());
|
|
}
|
|
}
|
|
|
|
//--------------------------------------------------------------------------
|
|
// Function: DataSet::getRegion
|
|
///\brief Retrieves a dataspace with the region pointed to selected.
|
|
///\param ref_type - IN: Type of reference to get region of - default
|
|
/// to H5R_DATASET_REGION
|
|
///\param ref - IN: Reference to get region of
|
|
///\return DataSpace instance
|
|
///\exception H5::DataSetIException
|
|
// Programmer Binh-Minh Ribler - May, 2004
|
|
//--------------------------------------------------------------------------
|
|
DataSpace DataSet::getRegion(void *ref, H5R_type_t ref_type) const
|
|
{
|
|
try {
|
|
DataSpace dataspace(p_get_region(ref, ref_type));
|
|
return(dataspace);
|
|
}
|
|
catch (IdComponentException E) {
|
|
throw DataSetIException("DataSet::getRegion", E.getDetailMsg());
|
|
}
|
|
}
|
|
|
|
//--------------------------------------------------------------------------
|
|
// 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 because the dataset that it represents is now closed
|
|
id = 0;
|
|
}
|
|
}
|
|
|
|
//--------------------------------------------------------------------------
|
|
// 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
|