summaryrefslogtreecommitdiffstats
path: root/c++/src/H5DataSet.cpp
blob: c5ecf0a0bbd5c0913e2672b03971e84202f75d39 (plain)
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
 * 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 "H5OcreatProp.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
// 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.
///\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
//--------------------------------------------------------------------------
hsize_t DataSet::getVlenBufSize( DataType& type, DataSpace& space ) const
{
    return(getVlenBufSize(type, space));
    //return(getVlenBufSize(static_cast<const DataType&>(type), static_cast<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
// 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
//--------------------------------------------------------------------------
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
//--------------------------------------------------------------------------
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;
    }
}

#ifndef H5_NO_NAMESPACE
} // end namespace
#endif