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
|
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* 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 "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 "H5DcreatProp.h"
#include "H5LaccProp.h"
#include "H5Location.h"
#include "H5Object.h"
#include "H5AbstractDs.h"
#include "H5DataType.h"
#include "H5DataSpace.h"
#include "H5Attribute.h"
namespace H5 {
#ifndef H5_NO_STD
using std::cerr;
using std::endl;
#endif // H5_NO_STD
//class H5_DLLCPP H5Object; // forward declaration for UserData4Aiterate
//--------------------------------------------------------------------------
// Function: Attribute default constructor
///\brief Default constructor: Creates a stub attribute
// Programmer Binh-Minh Ribler - May, 2004
//--------------------------------------------------------------------------
Attribute::Attribute() : AbstractDs(), H5Location(), id(H5I_INVALID_HID) {}
//--------------------------------------------------------------------------
// Function: Attribute copy constructor
///\brief Copy constructor: makes a copy of the original Attribute object.
///\param original - IN: Original Attribute object to copy
// Programmer Binh-Minh Ribler - 2000
//--------------------------------------------------------------------------
Attribute::Attribute(const Attribute& original) : AbstractDs(), H5Location(), id(original.id)
{
incRefCount(); // increment number of references to this id
}
//--------------------------------------------------------------------------
// Function: Attribute overloaded constructor
///\brief Creates an Attribute object using the id of an existing
/// attribute.
///\param existing_id - IN: Id of an existing attribute
///\exception H5::AttributeIException
// Programmer Binh-Minh Ribler - 2000
//--------------------------------------------------------------------------
Attribute::Attribute(const hid_t existing_id) : AbstractDs(), H5Location(), id(existing_id)
{
incRefCount(); // increment number of references to this id
}
//--------------------------------------------------------------------------
// Function: Attribute::write
///\brief Writes data to this attribute.
///\param mem_type - IN: Attribute datatype (in memory)
///\param buf - IN: Data to be written
///\exception H5::AttributeIException
// Programmer Binh-Minh Ribler - 2000
//--------------------------------------------------------------------------
void Attribute::write(const DataType& mem_type, const void *buf) const
{
herr_t ret_value = H5Awrite(id, mem_type.getId(), buf);
if(ret_value < 0)
{
throw AttributeIException("Attribute::write", "H5Awrite failed");
}
}
//--------------------------------------------------------------------------
// Function: Attribute::write
///\brief This is an overloaded member function, provided for convenience.
/// It writes a \a H5std_string to this attribute.
///\param mem_type - IN: Attribute datatype (in memory)
///\param strg - IN: Data to be written
///\exception H5::AttributeIException
// Programmer Binh-Minh Ribler - Apr, 2003
//--------------------------------------------------------------------------
void Attribute::write(const DataType& mem_type, const H5std_string& strg) 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 AttributeIException("Attribute::write", "H5Tis_variable_str failed");
}
// 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 = H5Awrite(id, mem_type.getId(), strg_C);
}
else
{
// passing third argument by address
ret_value = H5Awrite(id, mem_type.getId(), &strg_C);
}
if (ret_value < 0)
{
throw AttributeIException("Attribute::write", "H5Awrite failed");
}
}
//--------------------------------------------------------------------------
// Function: Attribute::read
///\brief Reads data from this attribute.
///\param mem_type - IN: Attribute datatype (in memory)
///\param buf - OUT: Buffer for read data
///\exception H5::AttributeIException
// Programmer Binh-Minh Ribler - 2000
//--------------------------------------------------------------------------
void Attribute::read(const DataType& mem_type, void *buf) const
{
herr_t ret_value = H5Aread(id, mem_type.getId(), buf);
if(ret_value < 0)
{
throw AttributeIException("Attribute::read", "H5Aread failed");
}
}
//--------------------------------------------------------------------------
// Function: Attribute::read
///\brief This is an overloaded member function, provided for convenience.
/// It reads a \a H5std_string from this attribute.
///\param mem_type - IN: Attribute datatype (in memory)
///\param strg - IN: Buffer for read string
///\exception H5::AttributeIException
// Programmer Binh-Minh Ribler - Apr, 2003
// Modification
// Mar 2008
// Corrected a misunderstanding that H5Aread would allocate
// space for the buffer. Obtained the attribute size and
// allocated memory properly. -BMR
// Apr 2009
// Used getInMemDataSize to get attribute data size. -BMR
// Jul 2009
// Divided into specific private functions for fixed- and
// variable-len string data: p_read_fixed_len and
// p_read_variable_len. This should improve readability. -BMR
//--------------------------------------------------------------------------
void Attribute::read(const DataType& mem_type, H5std_string& strg) 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 AttributeIException("Attribute::read", "H5Tis_variable_str failed");
}
if (!is_variable_len) // only allocate for fixed-len string
{
p_read_fixed_len(mem_type, strg);
}
else
{
p_read_variable_len(mem_type, strg);
}
}
//--------------------------------------------------------------------------
// Function: Attribute::getInMemDataSize
///\brief Gets the size in memory of the attribute's data.
///\return Size of data (in memory)
///\exception H5::AttributeIException
// Programmer Binh-Minh Ribler - Apr 2009
//--------------------------------------------------------------------------
size_t Attribute::getInMemDataSize() const
{
const char *func = "Attribute::getInMemDataSize";
// Get the data type of this attribute
hid_t mem_type_id = H5Aget_type(id);
if(mem_type_id < 0)
{
throw AttributeIException(func, "H5Aget_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 AttributeIException(func, "H5Tget_native_type failed");
}
size_t type_size = H5Tget_size(native_type);
if (type_size == 0)
{
throw AttributeIException(func, "H5Tget_size failed");
}
// Close the native type and the datatype of this attribute.
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 attribute by first getting its dataspace
// then getting the number of elements in the dataspace
hid_t space_id = H5Aget_space(id);
if (space_id < 0)
{
throw AttributeIException(func, "H5Aget_space failed");
}
hssize_t num_elements = H5Sget_simple_extent_npoints(space_id);
if (num_elements < 0)
{
throw AttributeIException(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: Attribute::getSpace
///\brief Gets a copy of the dataspace for this attribute.
///\return Dataspace instance
///\exception H5::AttributeIException
// Programmer Binh-Minh Ribler - 2000
//--------------------------------------------------------------------------
DataSpace Attribute::getSpace() const
{
// Calls C function H5Aget_space to get the id of the dataspace
hid_t dataspace_id = H5Aget_space(id);
// If the dataspace id is valid, create and return the DataSpace object
if(dataspace_id > 0)
{
DataSpace dataspace;
f_DataSpace_setId(&dataspace, dataspace_id);
return(dataspace);
}
else
{
throw AttributeIException("Attribute::getSpace", "H5Aget_space failed");
}
}
//--------------------------------------------------------------------------
// Function: Attribute::getFileName
///\brief Gets the name of the file, in which this attribute belongs.
///\return File name
///\exception H5::IdComponentException
// Programmer Binh-Minh Ribler - Jul, 2004
//--------------------------------------------------------------------------
H5std_string Attribute::getFileName() const
{
try {
return(p_get_file_name());
}
catch (IdComponentException& E) {
throw FileIException("Attribute::getFileName", E.getDetailMsg());
}
}
//--------------------------------------------------------------------------
// Function: Attribute::getName
///\brief Gets the name of this attribute, returning its length.
///\param attr_name - OUT: Buffer for the name string as char*
///\param buf_size - IN: Length of the buffer, default to 0
///\return Actual length of the attribute name
///\exception H5::AttributeIException
///\par Description
/// This function retrieves \a buf_size chars of the attribute's
/// name including null termination. Thus, if the actual length
/// of the name is more than buf_size-1, the retrieved name will
/// be truncated to accommodate the null terminator.
/// To get length of the attribute's name for buffer allocation,
/// an application can call this function passing in NULL for the
/// first argument and ignore the second argument.
// Programmer Binh-Minh Ribler - Mar, 2014
//--------------------------------------------------------------------------
ssize_t Attribute::getName(char* attr_name, size_t buf_size) const
{
// H5Aget_name will get buf_size-1 chars of the name to null terminate it
ssize_t name_size = H5Aget_name(id, buf_size, attr_name);
// If H5Aget_name returns a negative value, raise an exception
if (name_size < 0)
{
throw AttributeIException("Attribute::getName", "H5Aget_name failed");
}
else if (name_size == 0)
{
throw AttributeIException("Attribute::getName", "Attribute must have a name, name length is 0");
}
// Return length of the name
return(name_size);
}
//--------------------------------------------------------------------------
// Function: Attribute::getName
///\brief Returns the name of this attribute as an \a H5std_string.
///\return Name of the attribute
///\exception H5::AttributeIException
// Programmer Binh-Minh Ribler - May, 2004
// Modification
// Mar 2014 - BMR
// Revised to use the modified getName() above
//--------------------------------------------------------------------------
H5std_string Attribute::getName() const
{
H5std_string attr_name(""); // attribute name to return
// Preliminary call to get the size of the attribute name
ssize_t name_size = H5Aget_name(id, static_cast<size_t>(0), NULL);
// If H5Aget_name failed, throw exception
if (name_size < 0)
{
throw AttributeIException("Attribute::getName", "H5Aget_name failed");
}
else if (name_size == 0)
{
throw AttributeIException("Attribute::getName", "Attribute must have a name, name length is 0");
}
// Attribute's name exists, retrieve it
else if (name_size > 0)
{
char* name_C = new char[name_size+1]; // temporary C-string
HDmemset(name_C, 0, name_size+1); // clear buffer
// Use overloaded function
name_size = getName(name_C, name_size+1);
// Convert the C attribute name to return
attr_name = name_C;
// Clean up resource
delete []name_C;
}
// Return attribute's name
return(attr_name);
}
//--------------------------------------------------------------------------
// Function: Attribute::getName
///\brief This is an overloaded member function, provided for convenience.
/// It differs from the above function in that it takes an integer
/// specifying a desired length to be retrieved of the name.
///\return Name (or part of name) of the attribute
///\param len - IN: Desired length of the name
///\exception H5::AttributeIException
// Programmer Binh-Minh Ribler - 2000
// Modification
// Mar 2014 - BMR
// Revised to use the new getName() below
//--------------------------------------------------------------------------
H5std_string Attribute::getName(size_t len) const
{
H5std_string attr_name;
ssize_t name_size = getName(attr_name, len);
if (name_size < 0)
return("");
else
return(attr_name);
}
//--------------------------------------------------------------------------
// Function: Attribute::getName
///\brief Gets the name of this attribute, returning its length.
///\param attr_name - OUT: Buffer for the name string as \a H5std_string
///\param len - IN: Desired length of the name, default to 0
///\return Actual length of the attribute name
///\exception H5::AttributeIException
///\par Description
/// This function retrieves the attribute's name as a string. The
/// buf_size can specify a specific length or default to 0, in
/// which case the entire name will be retrieved.
// Programmer Binh-Minh Ribler - Nov, 2001
// Modification
// Mar 2014 - BMR
// Added to replace getName(size_t, H5std_string&) so that it'll
// allow the argument "len" to be skipped.
//--------------------------------------------------------------------------
ssize_t Attribute::getName(H5std_string& attr_name, size_t len) const
{
ssize_t name_size = 0;
// If no length is provided, get the entire attribute name
if (len == 0)
{
attr_name = getName();
name_size = attr_name.length();
}
// If length is provided, get that number of characters in name
else
{
char* name_C = new char[len+1]; // temporary C-string
HDmemset(name_C, 0, len+1); // clear buffer
// Use overloaded function
name_size = getName(name_C, len+1);
// Convert the C attribute name to return
attr_name = name_C;
// Clean up resource
delete []name_C;
}
// Otherwise, keep attr_name intact
// Return name size
return(name_size);
}
//--------------------------------------------------------------------------
// Function: Attribute::getName
// Purpose This function is replaced by the previous function, which
// provides more convenient prototype. It will be removed
// in future release.
// Param len - IN: Desired length of the name
// Param attr_name - OUT: Buffer for the name string
// Return Actual length of the attribute name
// Exception H5::AttributeIException
// Programmer Binh-Minh Ribler - Nov, 2001
// 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
//--------------------------------------------------------------------------
//ssize_t Attribute::getName(size_t len, H5std_string& attr_name) const
//{
// return (getName(attr_name, len));
//}
//--------------------------------------------------------------------------
// Function: Attribute::getStorageSize
///\brief Returns the amount of storage size required for this attribute.
///\return Size of the storage or 0, for no data
///\exception H5::AttributeIException
// 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 Attribute::getStorageSize() const
{
hsize_t storage_size = H5Aget_storage_size(id);
return (storage_size);
}
//--------------------------------------------------------------------------
// Function: Attribute::flush
///\brief Flushes all buffers associated with a file specified by
/// this attribute, to disk.
///\param scope - IN: Specifies the scope of the flushing action,
/// which can be either of these values:
/// \li \c H5F_SCOPE_GLOBAL - Flushes the entire virtual file
/// \li \c H5F_SCOPE_LOCAL - Flushes only the specified file
///\exception H5::AttributeIException
///\par Description
/// This attribute is used to identify the file to be flushed.
// Programmer Binh-Minh Ribler - 2013
// Modification
// Mar 2013 - BMR
// Duplicated from H5Location
//--------------------------------------------------------------------------
void Attribute::flush(H5F_scope_t scope) const
{
herr_t ret_value = H5Fflush(getId(), scope);
if(ret_value < 0)
{
throw AttributeIException("Attribute::flush", "H5Fflush failed");
}
}
//--------------------------------------------------------------------------
// Function: Attribute::getId
///\brief Get the id of this attribute
///\return Attribute 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 Attribute::getId() const
{
return(id);
}
//--------------------------------------------------------------------------
// Function: Attribute::p_get_type (private)
// Purpose Gets the datatype of this attribute.
// Return Id of the datatype
// Exception H5::AttributeIException
// Description
// This private function is used in AbstractDs.
// Programmer Binh-Minh Ribler - 2000
//--------------------------------------------------------------------------
hid_t Attribute::p_get_type() const
{
hid_t type_id = H5Aget_type(id);
if(type_id > 0)
return(type_id);
else
{
throw AttributeIException("", "H5Aget_type failed");
}
}
//--------------------------------------------------------------------------
// Function: Attribute::p_read_fixed_len (private)
// brief Reads a fixed length \a H5std_string from an attribute.
// param mem_type - IN: Attribute datatype (in memory)
// param strg - IN: Buffer for read string
// exception H5::AttributeIException
// Programmer Binh-Minh Ribler - Jul, 2009
// Modification
// Jul 2009
// Separated the fixed length case from the original
// Attribute::read
//--------------------------------------------------------------------------
void Attribute::p_read_fixed_len(const DataType& mem_type, H5std_string& strg) const
{
// Only allocate for fixed-len string.
// Get the size of the attribute's data
size_t attr_size = getInMemDataSize();
// If there is data, allocate buffer and read it.
if (attr_size > 0)
{
char *strg_C = new char[attr_size+1];
herr_t ret_value = H5Aread(id, mem_type.getId(), strg_C);
if(ret_value < 0)
{
delete []strg_C; // de-allocate for fixed-len string
throw AttributeIException("Attribute::read", "H5Aread failed");
}
// Get string from the C char* and release resource allocated locally
strg_C[attr_size] = '\0';
strg = strg_C;
delete []strg_C;
}
}
//--------------------------------------------------------------------------
// Function: Attribute::p_read_variable_len (private)
// brief Reads a variable length \a H5std_string from an attribute.
// param mem_type - IN: Attribute datatype (in memory)
// param strg - IN: Buffer for read string
// exception H5::AttributeIException
// Programmer Binh-Minh Ribler - Jul, 2009
// Modification
// Jul 2009
// Separated the variable length case from the original
// Attribute::read. -BMR
//--------------------------------------------------------------------------
void Attribute::p_read_variable_len(const DataType& mem_type, H5std_string& strg) const
{
// Prepare and call C API to read attribute.
char *strg_C;
// Read attribute, no allocation for variable-len string; C library will
herr_t ret_value = H5Aread(id, mem_type.getId(), &strg_C);
if(ret_value < 0)
{
throw AttributeIException("Attribute::read", "H5Aread failed");
}
// 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: Attribute::p_setId
///\brief Sets the identifier of this object 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 Attribute::p_setId(const hid_t new_id)
{
// handling references to this old id
try {
close();
}
catch (Exception& close_error) {
throw AttributeIException("Attribute::p_setId", close_error.getDetailMsg());
}
// reset object's id to the given id
id = new_id;
}
#endif // DOXYGEN_SHOULD_SKIP_THIS
//--------------------------------------------------------------------------
// Function: Attribute::close
///\brief Closes this attribute.
///
///\exception H5::AttributeIException
// Programmer Binh-Minh Ribler - Mar 9, 2005
//--------------------------------------------------------------------------
void Attribute::close()
{
if (p_valid_id(id))
{
herr_t ret_value = H5Aclose(id);
if(ret_value < 0)
{
throw AttributeIException("Attribute::close", "H5Aclose failed");
}
// reset the id
id = H5I_INVALID_HID;
}
}
//--------------------------------------------------------------------------
// Function: Attribute destructor
///\brief Properly terminates access to this attribute.
// 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
//--------------------------------------------------------------------------
Attribute::~Attribute()
{
try {
close();
}
catch (Exception& close_error) {
cerr << "Attribute::~Attribute - " << close_error.getDetailMsg() << endl;
}
}
} // end namespace
|