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1 /************************************************************************/
2 /* */
3 /* Copyright 2009 by Michael Hanselmann and Ullrich Koethe */
4 /* */
5 /* This file is part of the VIGRA computer vision library. */
6 /* The VIGRA Website is */
7 /* http://hci.iwr.uni-heidelberg.de/vigra/ */
8 /* Please direct questions, bug reports, and contributions to */
9 /* ullrich.koethe@iwr.uni-heidelberg.de or */
10 /* vigra@informatik.uni-hamburg.de */
11 /* */
12 /* Permission is hereby granted, free of charge, to any person */
13 /* obtaining a copy of this software and associated documentation */
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17 /* sell copies of the Software, and to permit persons to whom the */
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19 /* conditions: */
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22 /* included in all copies or substantial portions of the */
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33 /* */
34 /************************************************************************/
35
36 #ifndef VIGRA_HDF5IMPEX_HXX
37 #define VIGRA_HDF5IMPEX_HXX
38
39 #include <string>
40
41 #define H5Gcreate_vers 2
42 #define H5Gopen_vers 2
43 #define H5Dopen_vers 2
44 #define H5Dcreate_vers 2
45 #define H5Acreate_vers 2
46
47 #include <hdf5.h>
48
49 #if (H5_VERS_MAJOR == 1 && H5_VERS_MINOR <= 6)
50 # ifndef H5Gopen
51 # define H5Gopen(a, b, c) H5Gopen(a, b)
52 # endif
53 # ifndef H5Gcreate
54 # define H5Gcreate(a, b, c, d, e) H5Gcreate(a, b, 1)
55 # endif
56 # ifndef H5Dopen
57 # define H5Dopen(a, b, c) H5Dopen(a, b)
58 # endif
59 # ifndef H5Dcreate
60 # define H5Dcreate(a, b, c, d, e, f, g) H5Dcreate(a, b, c, d, f)
61 # endif
62 # ifndef H5Acreate
63 # define H5Acreate(a, b, c, d, e, f) H5Acreate(a, b, c, d, e)
64 # endif
65 # ifndef H5Pset_obj_track_times
66 # define H5Pset_obj_track_times(a, b) do {} while (0)
67 # endif
68 # include <H5LT.h>
69 #else
70 # include <hdf5_hl.h>
71 #endif
72
73 #include "impex.hxx"
74 #include "multi_array.hxx"
75 #include "multi_iterator_coupled.hxx"
76 #include "multi_impex.hxx"
77 #include "utilities.hxx"
78 #include "error.hxx"
79
80 #include <algorithm>
81
82 #if defined(_MSC_VER)
83 # include <io.h>
84 #else
85 # include <unistd.h>
86 #endif
87
88 namespace vigra {
89
90 /** \addtogroup VigraHDF5Impex Import/Export of Images and Arrays in HDF5 Format
91
92 Supports arrays with arbitrary element types and arbitrary many dimensions.
93 See the <a href="http://www.hdfgroup.org/HDF5/">HDF5 Website</a> for more
94 information on the HDF5 file format.
95 */
96 //@{
97
98 /** \brief Check if given filename refers to a HDF5 file.
99 */
100 inline bool isHDF5(char const * filename)
101 {
102 #ifdef _MSC_VER
103 return _access(filename, 0) != -1 && H5Fis_hdf5(filename);
104 #else
105 return access(filename, F_OK) == 0 && H5Fis_hdf5(filename);
106 #endif
107 }
108
109 /** \brief Wrapper for hid_t objects.
110
111 Newly created or opened HDF5 handles are usually stored as objects of type 'hid_t'. When the handle
112 is no longer needed, the appropriate close function must be called. However, if a function is
113 aborted by an exception, this is difficult to ensure. Class HDF5Handle is a smart pointer that
114 solves this problem by calling the close function in the destructor (This is analogous to how
115 VIGRA_UNIQUE_PTR calls 'delete' on the contained pointer). A pointer to the close function must be
116 passed to the constructor, along with an error message that is raised when creation/opening fails.
117
118 Since HDF5Handle objects are convertible to hid_t, they can be used in the code in place
119 of the latter.
120
121 <b>Usage:</b>
122
123 \code
124 HDF5Handle file_id(H5Fopen(filename, H5F_ACC_RDWR, H5P_DEFAULT),
125 &H5Fclose,
126 "Error message.");
127
128 ... // use file_id in the same way as a plain hid_t object
129 \endcode
130
131 <b>\#include</b> <vigra/hdf5impex.hxx><br>
132 Namespace: vigra
133 */
134 class HDF5Handle
135 {
136 public:
137 typedef herr_t (*Destructor)(hid_t);
138
139 private:
140 hid_t handle_;
141 Destructor destructor_;
142
143 public:
144
145 /** \brief Default constructor.
146 Creates a NULL handle.
147 **/
148 HDF5Handle()
149 : handle_( 0 ),
150 destructor_(0)
151 {}
152
153 /** \brief Create a wrapper for a hid_t object.
154
155 The hid_t object \a h is assumed to be the return value of an open or create function.
156 It will be closed with the given close function \a destructor as soon as this
157 HDF5Handle is destructed, except when \a destructor is a NULL pointer (in which
158 case nothing happens at destruction time). If \a h has a value that indicates
159 failed opening or creation (by HDF5 convention, this means if it is a negative number),
160 an exception is raised by calling <tt>vigra_fail(error_message)</tt>.
161
162 <b>Usage:</b>
163
164 \code
165 HDF5Handle file_id(H5Fopen(filename, H5F_ACC_RDWR, H5P_DEFAULT),
166 &H5Fclose,
167 "Error message.");
168
169 ... // use file_id in the same way
170 \endcode
171 */
172 HDF5Handle(hid_t h, Destructor destructor, const char * error_message)
173 : handle_( h ),
174 destructor_(destructor)
175 {
176 if(handle_ < 0)
177 vigra_fail(error_message);
178 }
179
180 /** \brief Copy constructor.
181 Hands over ownership of the RHS handle (analogous to VIGRA_UNIQUE_PTR).
182 */
183 HDF5Handle(HDF5Handle const & h)
184 : handle_( h.handle_ ),
185 destructor_(h.destructor_)
186 {
187 const_cast<HDF5Handle &>(h).handle_ = 0;
188 }
189
190 /** \brief Assignment.
191 Calls close() for the LHS handle and hands over ownership of the
192 RHS handle (analogous to VIGRA_UNIQUE_PTR).
193 */
194 HDF5Handle & operator=(HDF5Handle const & h)
195 {
196 if(h.handle_ != handle_)
197 {
198 close();
199 handle_ = h.handle_;
200 destructor_ = h.destructor_;
201 const_cast<HDF5Handle &>(h).handle_ = 0;
202 }
203 return *this;
204 }
205
206 /** \brief Destructor.
207 Calls close() for the contained handle.
208 */
209 ~HDF5Handle()
210 {
211 close();
212 }
213
214 /** \brief Explicitly call the stored function (if one has been stored within
215 this object) for the contained handle and set the handle to NULL.
216 */
217 herr_t close()
218 {
219 herr_t res = 1;
220 if(handle_ && destructor_)
221 res = (*destructor_)(handle_);
222 handle_ = 0;
223 return res;
224 }
225
226 /** \brief Get a temporary hid_t object for the contained handle.
227 Do not call a close function on the return value - a crash will be likely
228 otherwise.
229 */
230 hid_t get() const
231 {
232 return handle_;
233 }
234
235 /** \brief Convert to a plain hid_t object.
236
237 This function ensures that hid_t objects can be transparently replaced with
238 HDF5Handle objects in user code. Do not call a close function on the return
239 value - a crash will be likely otherwise.
240 */
241 operator hid_t() const
242 {
243 return handle_;
244 }
245
246 /** \brief Equality comparison of the contained handle.
247 */
248 bool operator==(HDF5Handle const & h) const
249 {
250 return handle_ == h.handle_;
251 }
252
253 /** \brief Equality comparison of the contained handle.
254 */
255 bool operator==(hid_t h) const
256 {
257 return handle_ == h;
258 }
259
260 /** \brief Inequality comparison of the contained handle.
261 */
262 bool operator!=(HDF5Handle const & h) const
263 {
264 return handle_ != h.handle_;
265 }
266
267 /** \brief Inequality comparison of the contained handle.
268 */
269 bool operator!=(hid_t h) const
270 {
271 return handle_ != h;
272 }
273 };
274
275 /********************************************************/
276 /* */
277 /* HDF5ImportInfo */
278 /* */
279 /********************************************************/
280
281 /** \brief Argument object for the function readHDF5().
282
283 See \ref readHDF5() for a usage example. This object must be
284 used to read an image or array from an HDF5 file
285 and enquire about its properties.
286
287 <b>\#include</b> <vigra/hdf5impex.hxx><br>
288 Namespace: vigra
289 */
290 class HDF5ImportInfo
291 {
292 public:
293 enum PixelType { UINT8, UINT16, UINT32, UINT64,
294 INT8, INT16, INT32, INT64,
295 FLOAT, DOUBLE };
296
297 /** Construct HDF5ImportInfo object.
298
299 The dataset \a pathInFile in the HDF5 file \a filename is accessed to
300 read its properties. \a pathInFile may contain '/'-separated group
301 names, but must end with the name of the desired dataset:
302
303 \code
304 HDF5ImportInfo info(filename, "/group1/group2/my_dataset");
305 \endcode
306 */
307 VIGRA_EXPORT HDF5ImportInfo( const char* filePath, const char* pathInFile );
308
309 VIGRA_EXPORT ~HDF5ImportInfo();
310
311 /** Get the filename of this HDF5 object.
312 */
313 VIGRA_EXPORT const std::string& getFilePath() const;
314
315 /** Get the dataset's full name in the HDF5 file.
316 */
317 VIGRA_EXPORT const std::string& getPathInFile() const;
318
319 /** Get a handle to the file represented by this info object.
320 */
321 VIGRA_EXPORT hid_t getH5FileHandle() const;
322
323 /** Get a handle to the dataset represented by this info object.
324 */
325 VIGRA_EXPORT hid_t getDatasetHandle() const;
326
327 /** Get the number of dimensions of the dataset represented by this info object.
328 */
329 VIGRA_EXPORT MultiArrayIndex numDimensions() const;
330
331 /** Get the shape of the dataset represented by this info object.
332
333 Note that the memory order between VIGRA and HDF5 files differs: VIGRA uses
334 Fortran-order, while HDF5 uses C-order. This function therefore reverses the axis
335 order relative to the file contents. That is, when the axes in the file are
336 ordered as 'z', 'y', 'x', this function will return the shape in the order
337 'x', 'y', 'z'.
338 */
339 VIGRA_EXPORT ArrayVector<hsize_t> const & shape() const
340 {
341 return m_dims;
342 }
343
344 /** Get the shape (length) of the dataset along dimension \a dim.
345
346 Note that the memory order between VIGRA and HDF5 files differs: VIGRA uses
347 Fortran-order, while HDF5 uses C-order. This function therefore reverses the axis
348 order relative to the file contents. That is, when the axes in the file are
349 ordered as 'z', 'y', 'x', this function will return the shape in the order
350 'x', 'y', 'z'.
351 */
352 VIGRA_EXPORT MultiArrayIndex shapeOfDimension(const int dim) const;
353
354 /** Query the pixel type of the dataset.
355
356 Possible values are:
357 <DL>
358 <DT>"INT8"<DD> 8-bit signed integer (unsigned char)
359 <DT>"UINT8"<DD> 8-bit unsigned integer (unsigned char)
360 <DT>"INT16"<DD> 16-bit signed integer (short)
361 <DT>"UINT16"<DD> 16-bit unsigned integer (unsigned short)
362 <DT>"INT32"<DD> 32-bit signed integer (long)
363 <DT>"UINT32"<DD> 32-bit unsigned integer (unsigned long)
364 <DT>"INT64"<DD> 64-bit signed integer (long long)
365 <DT>"UINT64"<DD> 64-bit unsigned integer (unsigned long long)
366 <DT>"FLOAT"<DD> 32-bit floating point (float)
367 <DT>"DOUBLE"<DD> 64-bit floating point (double)
368 </DL>
369 */
370 VIGRA_EXPORT const char * getPixelType() const;
371
372 /** Query the pixel type of the dataset.
373
374 Same as getPixelType(), but the result is returned as a
375 ImageImportInfo::PixelType enum. This is useful to implement
376 a switch() on the pixel type.
377
378 Possible values are:
379 <DL>
380 <DT>UINT8<DD> 8-bit unsigned integer (unsigned char)
381 <DT>INT16<DD> 16-bit signed integer (short)
382 <DT>UINT16<DD> 16-bit unsigned integer (unsigned short)
383 <DT>INT32<DD> 32-bit signed integer (long)
384 <DT>UINT32<DD> 32-bit unsigned integer (unsigned long)
385 <DT>FLOAT<DD> 32-bit floating point (float)
386 <DT>DOUBLE<DD> 64-bit floating point (double)
387 </DL>
388 */
389 VIGRA_EXPORT PixelType pixelType() const;
390
391 private:
392 HDF5Handle m_file_handle, m_dataset_handle;
393 std::string m_filename, m_path, m_pixeltype;
394 hssize_t m_dimensions;
395 ArrayVector<hsize_t> m_dims;
396 };
397
398
399 namespace detail {
400
401 template<class type>
402 inline hid_t getH5DataType()
403 {
404 std::runtime_error("getH5DataType(): invalid type");
405 return 0;
406 }
407
408 #define VIGRA_H5_DATATYPE(type, h5type) \
409 template<> \
410 inline hid_t getH5DataType<type>() \
411 { return h5type;}
412
413 VIGRA_H5_DATATYPE(char, H5T_NATIVE_CHAR)
414 VIGRA_H5_DATATYPE(float, H5T_NATIVE_FLOAT)
415 VIGRA_H5_DATATYPE(double, H5T_NATIVE_DOUBLE)
416 VIGRA_H5_DATATYPE(long double, H5T_NATIVE_LDOUBLE)
417
418 // char arrays with flexible length require 'handcrafted' H5 datatype
419 template<>
420 inline hid_t getH5DataType<char*>()
421 {
422 hid_t stringtype = H5Tcopy (H5T_C_S1);
423 H5Tset_size(stringtype, H5T_VARIABLE);
424 return stringtype;
425 }
426 template<>
427 inline hid_t getH5DataType<const char*>()
428 {
429 hid_t stringtype = H5Tcopy (H5T_C_S1);
430 H5Tset_size(stringtype, H5T_VARIABLE);
431 return stringtype;
432 }
433 #undef VIGRA_H5_DATATYPE
434
435 template <unsigned int SIZE>
436 struct HDF5TypeBySize;
437
438 template <>
439 struct HDF5TypeBySize<1>
440 {
441 static hid_t signed_type() { return H5T_NATIVE_INT8; }
442 static hid_t unsigned_type() { return H5T_NATIVE_UINT8; }
443 };
444
445 template <>
446 struct HDF5TypeBySize<2>
447 {
448 static hid_t signed_type() { return H5T_NATIVE_INT16; }
449 static hid_t unsigned_type() { return H5T_NATIVE_UINT16; }
450 };
451
452 template <>
453 struct HDF5TypeBySize<4>
454 {
455 static hid_t signed_type() { return H5T_NATIVE_INT32; }
456 static hid_t unsigned_type() { return H5T_NATIVE_UINT32; }
457 };
458
459 template <>
460 struct HDF5TypeBySize<8>
461 {
462 static hid_t signed_type() { return H5T_NATIVE_INT64; }
463 static hid_t unsigned_type() { return H5T_NATIVE_UINT64; }
464 };
465
466 #define VIGRA_H5_SIGNED_DATATYPE(type) \
467 template<> \
468 inline hid_t getH5DataType<type>() \
469 { return HDF5TypeBySize<sizeof(type)>::signed_type(); }
470
471 VIGRA_H5_SIGNED_DATATYPE(signed char)
472 VIGRA_H5_SIGNED_DATATYPE(signed short)
473 VIGRA_H5_SIGNED_DATATYPE(signed int)
474 VIGRA_H5_SIGNED_DATATYPE(signed long)
475 VIGRA_H5_SIGNED_DATATYPE(signed long long)
476
477 #undef VIGRA_H5_SIGNED_DATATYPE
478
479 #define VIGRA_H5_UNSIGNED_DATATYPE(type) \
480 template<> \
481 inline hid_t getH5DataType<type>() \
482 { return HDF5TypeBySize<sizeof(type)>::unsigned_type(); }
483
484 VIGRA_H5_UNSIGNED_DATATYPE(unsigned char)
485 VIGRA_H5_UNSIGNED_DATATYPE(unsigned short)
486 VIGRA_H5_UNSIGNED_DATATYPE(unsigned int)
487 VIGRA_H5_UNSIGNED_DATATYPE(unsigned long)
488 VIGRA_H5_UNSIGNED_DATATYPE(unsigned long long)
489
490 #undef VIGRA_H5_UNSIGNED_DATATYPE
491
492 #if 0
493 template<>
494 inline hid_t getH5DataType<FFTWComplex<float> >()
495 {
496 hid_t complex_id = H5Tcreate (H5T_COMPOUND, sizeof (FFTWComplex<float>));
497 H5Tinsert (complex_id, "real", 0, H5T_NATIVE_FLOAT);
498 H5Tinsert (complex_id, "imaginary", sizeof(float), H5T_NATIVE_FLOAT);
499 return complex_id;
500 }
501
502 template<>
503 inline hid_t getH5DataType<FFTWComplex<double> >()
504 {
505 hid_t complex_id = H5Tcreate (H5T_COMPOUND, sizeof (FFTWComplex<double>));
506 H5Tinsert (complex_id, "real", 0, H5T_NATIVE_DOUBLE);
507 H5Tinsert (complex_id, "imaginary", sizeof(double), H5T_NATIVE_DOUBLE);
508 return complex_id;
509 }
510 #endif
511
512
513 } // namespace detail
514
515 // helper friend function for callback HDF5_ls_inserter_callback()
516 void HDF5_ls_insert(void*, const std::string &);
517 // callback function for ls(), called via HDF5File::H5Literate()
518 // see http://www.parashift.com/c++-faq-lite/pointers-to-members.html#faq-33.2
519 // for as to why.
520
521 VIGRA_EXPORT H5O_type_t HDF5_get_type(hid_t, const char*);
522 extern "C" VIGRA_EXPORT herr_t HDF5_ls_inserter_callback(hid_t, const char*, const H5L_info_t*, void*);
523
524 /********************************************************/
525 /* */
526 /* HDF5File */
527 /* */
528 /********************************************************/
529
530
531 /** \brief Access to HDF5 files
532
533 HDF5File provides a convenient way of accessing data in HDF5 files. vigra::MultiArray
534 structures of any dimension can be stored to / loaded from HDF5 files. Typical
535 HDF5 features like subvolume access, chunks and data compression are available,
536 string attributes can be attached to any dataset or group. Group- or dataset-handles
537 are encapsulated in the class and managed automatically. The internal file-system like
538 structure can be accessed by functions like "cd()" or "mkdir()".
539
540 Note that the memory order between VIGRA and HDF5 files differs: VIGRA uses
541 Fortran-order, while HDF5 uses C-order. This means that a VIGRA MultiArray,
542 whose indices represent the 'x'-, 'y'-, and 'z'-axis in that order, is reversed
543 upon writing to an HDF5 file, i.e. in the file the axis order is 'z', 'y', 'x'.
544 Likewise, the order is reversed upon reading.
545
546 <b>Example:</b>
547 Write the MultiArray out_multi_array to file. Change the current directory to
548 "/group" and read in the same MultiArray as in_multi_array.
549 \code
550 HDF5File file("/path/to/file",HDF5File::New);
551 file.mkdir("group");
552 file.write("/group/dataset", out_multi_array);
553
554 file.cd("/group");
555 file.read("dataset", in_multi_array);
556
557 \endcode
558
559 <b>\#include</b> <vigra/hdf5impex.hxx><br>
560 Namespace: vigra
561 */
562 class HDF5File
563 {
564 protected:
565 HDF5Handle fileHandle_;
566
567 // current group handle
568 HDF5Handle cGroupHandle_;
569
570 private:
571 // time tagging of datasets, turned off (= 0) by default.
572 int track_time;
573
574 // helper class for ls()
575 struct ls_closure
576 {
577 virtual void insert(const std::string &) = 0;
578 virtual ~ls_closure() {}
579 };
580 // datastructure to hold a list of dataset and group names
581 struct lsOpData : public ls_closure
582 {
583 std::vector<std::string> & objects;
584 lsOpData(std::vector<std::string> & o) : objects(o) {}
585 void insert(const std::string & x)
586 {
587 objects.push_back(x);
588 }
589 };
590 // (associative-)container closure
591 template<class Container>
592 struct ls_container_data : public ls_closure
593 {
594 Container & objects;
595 ls_container_data(Container & o) : objects(o) {}
596 void insert(const std::string & x)
597 {
598 objects.insert(std::string(x));
599 }
600 };
601
602 public:
603
604 // helper for callback HDF5_ls_inserter_callback(), used by ls()
605 friend void HDF5_ls_insert(void*, const std::string &);
606
607 /** \brief Set how a file is opened.
608
609 OpenMode::New creates a new file. If the file already exists, overwrite it.
610
611 OpenMode::Open opens a file for reading/writing. The file will be created,
612 if necessary.
613 */
614 enum OpenMode {
615 New, // Create new empty file (existing file will be deleted).
616 Open, // Open file. Create if not existing.
617 OpenReadOnly // Open file in read-only mode.
618 };
619
620 /** \brief Default constructor.
621
622 A file can later be opened via the open() function.
623
624 If \a track_creation_times is non-zero, time tagging of datasets will be enabled (it is disabled
625 by default).
626 */
627 HDF5File(int track_creation_times = 0)
628 : track_time(track_creation_times)
629 {}
630
631 /** \brief Open or create an HDF5File object.
632
633 Creates or opens HDF5 file with given filename.
634 The current group is set to "/".
635
636 Note that the HDF5File class is not copyable (the copy constructor is
637 private to enforce this).
638 */
639 HDF5File(std::string filename, OpenMode mode, int track_creation_times = 0)
640 : track_time(track_creation_times)
641 {
642 open(filename, mode);
643 }
644
645 /** \brief The destructor flushes and closes the file.
646 */
647 ~HDF5File()
648 {
649 // The members fileHandle_ and cGroupHandle_ are automatically closed
650 // as they are of type HDF5Handle and are properly initialised.
651 // The closing of fileHandle_ implies flushing the file to
652 // the operating system, see
653 // http://www.hdfgroup.org/HDF5/doc/RM/RM_H5F.html#File-Close .
654 }
655
656 // copying is not permitted.
657 private:
658 HDF5File(const HDF5File &);
659 void operator=(const HDF5File &);
660
661 public:
662
663 /** \brief Open or create the given file in the given mode and set the group to "/".
664 If another file is currently open, it is first closed.
665 */
666 void open(std::string filename, OpenMode mode)
667 {
668 close();
669
670 std::string errorMessage = "HDF5File.open(): Could not open or create file '" + filename + "'.";
671 fileHandle_ = HDF5Handle(createFile_(filename, mode), &H5Fclose, errorMessage.c_str());
672 cGroupHandle_ = HDF5Handle(openCreateGroup_("/"), &H5Gclose, "HDF5File.open(): Failed to open root group.");
673 }
674
675 /** \brief Close the current file.
676 */
677 void close()
678 {
679 bool success = cGroupHandle_.close() >= 0 && fileHandle_.close() >= 0;
680 vigra_postcondition(success, "HDF5File.close() failed.");
681 }
682
683 /** \brief Change current group to "/".
684 */
685 inline void root()
686 {
687 std::string message = "HDF5File::root(): Could not open group '/'.";
688 cGroupHandle_ = HDF5Handle(H5Gopen(fileHandle_, "/", H5P_DEFAULT),&H5Gclose,message.c_str());
689 }
690
691 /** \brief Change the current group.
692 Both absolute and relative group names are allowed.
693 */
694 inline void cd(std::string groupName)
695 {
696 cGroupHandle_ = getGroupHandle(groupName, "HDF5File::cd()");
697 }
698
699 /** \brief Change the current group to its parent group.
700 Returns true if successful, false otherwise. If unsuccessful,
701 the group will not change.
702 */
703 inline bool cd_up()
704 {
705 std::string groupName = currentGroupName_();
706
707 //do not try to move up if we already in "/"
708 if(groupName == "/"){
709 return false;
710 }
711
712 size_t lastSlash = groupName.find_last_of('/');
713
714 std::string parentGroup (groupName.begin(), groupName.begin()+lastSlash+1);
715
716 cd(parentGroup);
717
718 return true;
719 }
720
721 /** \brief Change the current group to its parent group.
722 Returns true if successful, false otherwise. If unsuccessful,
723 the group will not change.
724 */
725 inline bool cd_up(int levels)
726 {
727 std::string groupName = currentGroupName_();
728
729 for(int i = 0; i<levels; i++)
730 {
731 if(!cd_up())
732 {
733 // restore old group if neccessary
734 if(groupName != currentGroupName_())
735 cd(groupName);
736 return false;
737 }
738 }
739 return true;
740 }
741
742 /** \brief Create a new group.
743 If the first character is a "/", the path will be interpreted as absolute path,
744 otherwise it will be interpreted as path relative to the current group.
745 */
746 inline void mkdir(std::string groupName)
747 {
748 std::string message = "HDF5File::mkdir(): Could not create group '" + groupName + "'.\n";
749
750 // make groupName clean
751 groupName = get_absolute_path(groupName);
752
753 HDF5Handle(openCreateGroup_(groupName.c_str()),&H5Gclose,message.c_str());
754 }
755
756 /** \brief Change the current group; create it if necessary.
757 If the first character is a "/", the path will be interpreted as absolute path,
758 otherwise it will be interpreted as path relative to the current group.
759 */
760 inline void cd_mk(std::string groupName)
761 {
762 std::string message = "HDF5File::cd_mk(): Could not create group '" + groupName + "'.";
763
764 // make groupName clean
765 groupName = get_absolute_path(groupName);
766
767 cGroupHandle_ = HDF5Handle(openCreateGroup_(groupName.c_str()),&H5Gclose,message.c_str());
768 }
769
770 // helper function for the various ls() variants.
771 void ls_H5Literate(ls_closure & data) const
772 {
773 H5Literate(cGroupHandle_, H5_INDEX_NAME, H5_ITER_NATIVE, NULL,
774 HDF5_ls_inserter_callback, static_cast<void*>(&data));
775 }
776
777 /** \brief List the contents of the current group.
778 The function returns a vector of strings holding the entries of the
779 current group. Only datasets and groups are listed, other objects
780 (e.g. datatypes) are ignored. Group names always have a trailing "/".
781 */
782 inline std::vector<std::string> ls() const
783 {
784 std::vector<std::string> list;
785 lsOpData data(list);
786 ls_H5Literate(data);
787 return list;
788 }
789
790 /** \brief List the contents of the current group into a container-like
791 object via insert().
792
793 Only datasets and groups are inserted, other objects (e.g., datatypes) are ignored.
794 Group names always have a trailing "/".
795
796 The argument cont is presumably an associative container, however,
797 only its member function <tt>cont.insert(std::string)</tt> will be
798 called.
799 \param cont reference to a container supplying a member function
800 <tt>insert(const i_type &)</tt>, where <tt>i_type</tt>
801 is convertible to <tt>std::string</tt>.
802 */
803 template<class Container>
804 void ls(Container & cont) const
805 {
806 ls_container_data<Container> data(cont);
807 ls_H5Literate(data);
808 }
809
810 /** \brief Get the path of the current group.
811 */
812 inline std::string pwd() const
813 {
814 return currentGroupName_();
815 }
816
817 /** \brief Get the name of the associated file.
818 */
819 inline std::string filename() const
820 {
821 return fileName_();
822 }
823
824 /** \brief Check if given datasetName exists.
825 */
826 inline bool existsDataset(std::string datasetName)
827 {
828 // make datasetName clean
829 datasetName = get_absolute_path(datasetName);
830 return (H5Lexists(fileHandle_, datasetName.c_str(), H5P_DEFAULT) > 0);
831 }
832
833 /** \brief Get the number of dimensions of a certain dataset
834 If the first character is a "/", the path will be interpreted as absolute path,
835 otherwise it will be interpreted as path relative to the current group.
836 */
837 hssize_t getDatasetDimensions(std::string datasetName)
838 {
839 // make datasetName clean
840 datasetName = get_absolute_path(datasetName);
841
842 //Open dataset and dataspace
843 std::string errorMessage = "HDF5File::getDatasetDimensions(): Unable to open dataset '" + datasetName + "'.";
844 HDF5Handle datasetHandle = HDF5Handle(getDatasetHandle_(datasetName), &H5Dclose, errorMessage.c_str());
845
846 errorMessage = "HDF5File::getDatasetDimensions(): Unable to access dataspace.";
847 HDF5Handle dataspaceHandle(H5Dget_space(datasetHandle), &H5Sclose, errorMessage.c_str());
848
849 //return dimension information
850 return H5Sget_simple_extent_ndims(dataspaceHandle);
851 }
852
853 /** \brief Get the shape of each dimension of a certain dataset.
854
855 Normally, this function is called after determining the dimension of the
856 dataset using \ref getDatasetDimensions().
857 If the first character is a "/", the path will be interpreted as absolute path,
858 otherwise it will be interpreted as path relative to the current group.
859
860 Note that the memory order between VIGRA and HDF5 files differs: VIGRA uses
861 Fortran-order, while HDF5 uses C-order. This function therefore reverses the axis
862 order relative to the file contents. That is, when the axes in the file are
863 ordered as 'z', 'y', 'x', this function will return the shape in the order
864 'x', 'y', 'z'.
865 */
866 ArrayVector<hsize_t> getDatasetShape(std::string datasetName)
867 {
868 // make datasetName clean
869 datasetName = get_absolute_path(datasetName);
870
871 //Open dataset and dataspace
872 std::string errorMessage = "HDF5File::getDatasetShape(): Unable to open dataset '" + datasetName + "'.";
873 HDF5Handle datasetHandle = HDF5Handle(getDatasetHandle_(datasetName), &H5Dclose, errorMessage.c_str());
874
875 errorMessage = "HDF5File::getDatasetShape(): Unable to access dataspace.";
876 HDF5Handle dataspaceHandle(H5Dget_space(datasetHandle), &H5Sclose, errorMessage.c_str());
877
878 //get dimension information
879 ArrayVector<hsize_t>::size_type dimensions = H5Sget_simple_extent_ndims(dataspaceHandle);
880
881 ArrayVector<hsize_t> shape(dimensions);
882 ArrayVector<hsize_t> maxdims(dimensions);
883 H5Sget_simple_extent_dims(dataspaceHandle, shape.data(), maxdims.data());
884
885 // invert the dimensions to guarantee VIGRA-compatible order.
886 std::reverse(shape.begin(), shape.end());
887 return shape;
888 }
889
890 /** Query the pixel type of the dataset.
891
892 Possible values are:
893 <DL>
894 <DT>"INT8"<DD> 8-bit signed integer (unsigned char)
895 <DT>"UINT8"<DD> 8-bit unsigned integer (unsigned char)
896 <DT>"INT16"<DD> 16-bit signed integer (short)
897 <DT>"UINT16"<DD> 16-bit unsigned integer (unsigned short)
898 <DT>"INT32"<DD> 32-bit signed integer (long)
899 <DT>"UINT32"<DD> 32-bit unsigned integer (unsigned long)
900 <DT>"INT64"<DD> 64-bit signed integer (long long)
901 <DT>"UINT64"<DD> 64-bit unsigned integer (unsigned long long)
902 <DT>"FLOAT"<DD> 32-bit floating point (float)
903 <DT>"DOUBLE"<DD> 64-bit floating point (double)
904 <DT>"UNKNOWN"<DD> any other type
905 </DL>
906 */
907 std::string getDatasetType(std::string const & datasetName)
908 {
909 HDF5Handle datasetHandle = getDatasetHandle(datasetName);
910
911 hid_t datatype = H5Dget_type(datasetHandle);
912 H5T_class_t dataclass = H5Tget_class(datatype);
913 size_t datasize = H5Tget_size(datatype);
914 H5T_sign_t datasign = H5Tget_sign(datatype);
915
916 if(dataclass == H5T_FLOAT)
917 {
918 if(datasize == 4)
919 return "FLOAT";
920 else if(datasize == 8)
921 return "DOUBLE";
922 }
923 else if(dataclass == H5T_INTEGER)
924 {
925 if(datasign == H5T_SGN_NONE)
926 {
927 if(datasize == 1)
928 return "UINT8";
929 else if(datasize == 2)
930 return "UINT16";
931 else if(datasize == 4)
932 return "UINT32";
933 else if(datasize == 8)
934 return "UINT64";
935 }
936 else
937 {
938 if(datasize == 1)
939 return "INT8";
940 else if(datasize == 2)
941 return "INT16";
942 else if(datasize == 4)
943 return "INT32";
944 else if(datasize == 8)
945 return "INT64";
946 }
947 }
948 return "UNKNOWN";
949 }
950
951 /** \brief Obtain the HDF5 handle of a dataset.
952 */
953 inline HDF5Handle getDatasetHandle(std::string const & datasetName)
954 {
955 std::string errorMessage = "HDF5File::getDatasetHandle(): Unable to open dataset '" + datasetName + "'.";
956 return HDF5Handle(getDatasetHandle_(get_absolute_path(datasetName)), &H5Dclose, errorMessage.c_str());
957 }
958
959 /** \brief Obtain the HDF5 handle of a group.
960 */
961 inline HDF5Handle getGroupHandle(std::string group_name, std::string function_name = "HDF5File::getGroupHandle()")
962 {
963 std::string errorMessage = function_name + ": Group '" + group_name + "' not found.";
964
965 // make group_name clean
966 group_name = get_absolute_path(group_name);
967
968 // group must exist
969 vigra_precondition(group_name == "/" || H5Lexists(fileHandle_, group_name.c_str(), H5P_DEFAULT) != 0,
970 errorMessage.c_str());
971
972 // open group and return group handle
973 return HDF5Handle(openCreateGroup_(group_name), &H5Gclose, "Internal error");
974 }
975
976 /** \brief Obtain the HDF5 handle of a attribute.
977 */
978 inline HDF5Handle getAttributeHandle(std::string dataset_name, std::string attribute_name)
979 {
980 std::string message = "HDF5File::getAttributeHandle(): Attribute '" + attribute_name + "' not found.";
981 return HDF5Handle(H5Aopen(getDatasetHandle(dataset_name), attribute_name.c_str(), H5P_DEFAULT),
982 &H5Aclose, message.c_str());
983 }
984
985 /* Writing Attributes */
986
987 /** \brief Write MultiArray Attributes.
988 * In contrast to datasets, subarray access, chunks and compression are not available.
989 */
990 template<unsigned int N, class T, class Stride>
991 inline void writeAttribute(std::string object_name,
992 std::string attribute_name,
993 const MultiArrayView<N, T, Stride> & array)
994 {
995 // make object_name clean
996 object_name = get_absolute_path(object_name);
997
998 write_attribute_(object_name, attribute_name, array, detail::getH5DataType<T>(), 1);
999 }
1000
1001 template<unsigned int N, class T, int SIZE, class Stride>
1002 inline void writeAttribute(std::string datasetName,
1003 std::string attributeName,
1004 const MultiArrayView<N, TinyVector<T, SIZE>, Stride> & array)
1005 {
1006 // make datasetName clean
1007 datasetName = get_absolute_path(datasetName);
1008
1009 write_attribute_(datasetName, attributeName, array, detail::getH5DataType<T>(), SIZE);
1010 }
1011
1012 template<unsigned int N, class T, class Stride>
1013 inline void writeAttribute(std::string datasetName,
1014 std::string attributeName,
1015 const MultiArrayView<N, RGBValue<T>, Stride> & array)
1016 {
1017 // make datasetName clean
1018 datasetName = get_absolute_path(datasetName);
1019
1020 write_attribute_(datasetName, attributeName, array, detail::getH5DataType<T>(), 3);
1021 }
1022
1023 /** \brief Write a single value.
1024 Specialization of the write function for simple datatypes
1025 */
1026 inline void writeAttribute(std::string object_name, std::string attribute_name, char data)
1027 { writeAtomicAttribute(object_name,attribute_name,data); }
1028 inline void writeAttribute(std::string datasetName, std::string attributeName, signed char data)
1029 { writeAtomicAttribute(datasetName,attributeName,data); }
1030 inline void writeAttribute(std::string datasetName, std::string attributeName, signed short data)
1031 { writeAtomicAttribute(datasetName,attributeName,data); }
1032 inline void writeAttribute(std::string datasetName, std::string attributeName, signed int data)
1033 { writeAtomicAttribute(datasetName,attributeName,data); }
1034 inline void writeAttribute(std::string datasetName, std::string attributeName, signed long data)
1035 { writeAtomicAttribute(datasetName,attributeName,data); }
1036 inline void writeAttribute(std::string datasetName, std::string attributeName, signed long long data)
1037 { writeAtomicAttribute(datasetName,attributeName,data); }
1038 inline void writeAttribute(std::string datasetName, std::string attributeName, unsigned char data)
1039 { writeAtomicAttribute(datasetName,attributeName,data); }
1040 inline void writeAttribute(std::string datasetName, std::string attributeName, unsigned short data)
1041 { writeAtomicAttribute(datasetName,attributeName,data); }
1042 inline void writeAttribute(std::string datasetName, std::string attributeName, unsigned int data)
1043 { writeAtomicAttribute(datasetName,attributeName,data); }
1044 inline void writeAttribute(std::string datasetName, std::string attributeName, unsigned long data)
1045 { writeAtomicAttribute(datasetName,attributeName,data); }
1046 inline void writeAttribute(std::string datasetName, std::string attributeName, unsigned long long data)
1047 { writeAtomicAttribute(datasetName,attributeName,data); }
1048 inline void writeAttribute(std::string datasetName, std::string attributeName, float data)
1049 { writeAtomicAttribute(datasetName,attributeName,data); }
1050 inline void writeAttribute(std::string datasetName, std::string attributeName, double data)
1051 { writeAtomicAttribute(datasetName,attributeName,data); }
1052 inline void writeAttribute(std::string datasetName, std::string attributeName, long double data)
1053 { writeAtomicAttribute(datasetName,attributeName,data); }
1054 inline void writeAttribute(std::string datasetName, std::string attributeName, const char* data)
1055 { writeAtomicAttribute(datasetName,attributeName,data); }
1056 inline void writeAttribute(std::string datasetName, std::string attributeName, std::string const & data)
1057 { writeAtomicAttribute(datasetName,attributeName,data.c_str()); }
1058
1059 /** \brief Test if attribute exists.
1060 */
1061 bool existsAttribute(std::string object_name, std::string attribute_name)
1062 {
1063 std::string obj_path = get_absolute_path(object_name);
1064 htri_t exists = H5Aexists_by_name(fileHandle_, obj_path.c_str(),
1065 attribute_name.c_str(), H5P_DEFAULT);
1066 vigra_precondition(exists >= 0, "HDF5File::existsAttribute(): "
1067 "object '" + object_name + "' "
1068 "not found.");
1069 return exists != 0;
1070 }
1071
1072 // Reading Attributes
1073
1074 /** \brief Read MultiArray Attributes.
1075 * In contrast to datasets, subarray access is not available.
1076 */
1077 template<unsigned int N, class T, class Stride>
1078 inline void readAttribute(std::string object_name,
1079 std::string attribute_name,
1080 MultiArrayView<N, T, Stride> array)
1081 {
1082 // make object_name clean
1083 object_name = get_absolute_path(object_name);
1084
1085 read_attribute_(object_name, attribute_name, array, detail::getH5DataType<T>(), 1);
1086 }
1087
1088 template<unsigned int N, class T, int SIZE, class Stride>
1089 inline void readAttribute(std::string datasetName,
1090 std::string attributeName,
1091 MultiArrayView<N, TinyVector<T, SIZE>, Stride> array)
1092 {
1093 // make datasetName clean
1094 datasetName = get_absolute_path(datasetName);
1095
1096 read_attribute_(datasetName, attributeName, array, detail::getH5DataType<T>(), SIZE);
1097 }
1098
1099 template<unsigned int N, class T, class Stride>
1100 inline void readAttribute(std::string datasetName,
1101 std::string attributeName,
1102 MultiArrayView<N, RGBValue<T>, Stride> array)
1103 {
1104 // make datasetName clean
1105 datasetName = get_absolute_path(datasetName);
1106
1107 read_attribute_(datasetName, attributeName, array, detail::getH5DataType<T>(), 3);
1108 }
1109
1110 /** \brief Read a single value.
1111 Specialization of the read function for simple datatypes
1112 */
1113 inline void readAttribute(std::string object_name, std::string attribute_name, char &data)
1114 { readAtomicAttribute(object_name,attribute_name,data); }
1115 inline void readAttribute(std::string datasetName, std::string attributeName, signed char &data)
1116 { readAtomicAttribute(datasetName,attributeName,data); }
1117 inline void readAttribute(std::string datasetName, std::string attributeName, signed short &data)
1118 { readAtomicAttribute(datasetName,attributeName,data); }
1119 inline void readAttribute(std::string datasetName, std::string attributeName, signed int &data)
1120 { readAtomicAttribute(datasetName,attributeName,data); }
1121 inline void readAttribute(std::string datasetName, std::string attributeName, signed long &data)
1122 { readAtomicAttribute(datasetName,attributeName,data); }
1123 inline void readAttribute(std::string datasetName, std::string attributeName, signed long long &data)
1124 { readAtomicAttribute(datasetName,attributeName,data); }
1125 inline void readAttribute(std::string datasetName, std::string attributeName, unsigned char &data)
1126 { readAtomicAttribute(datasetName,attributeName,data); }
1127 inline void readAttribute(std::string datasetName, std::string attributeName, unsigned short &data)
1128 { readAtomicAttribute(datasetName,attributeName,data); }
1129 inline void readAttribute(std::string datasetName, std::string attributeName, unsigned int &data)
1130 { readAtomicAttribute(datasetName,attributeName,data); }
1131 inline void readAttribute(std::string datasetName, std::string attributeName, unsigned long &data)
1132 { readAtomicAttribute(datasetName,attributeName,data); }
1133 inline void readAttribute(std::string datasetName, std::string attributeName, unsigned long long &data)
1134 { readAtomicAttribute(datasetName,attributeName,data); }
1135 inline void readAttribute(std::string datasetName, std::string attributeName, float &data)
1136 { readAtomicAttribute(datasetName,attributeName,data); }
1137 inline void readAttribute(std::string datasetName, std::string attributeName, double &data)
1138 { readAtomicAttribute(datasetName,attributeName,data); }
1139 inline void readAttribute(std::string datasetName, std::string attributeName, long double &data)
1140 { readAtomicAttribute(datasetName,attributeName,data); }
1141 inline void readAttribute(std::string datasetName, std::string attributeName, std::string &data)
1142 { readAtomicAttribute(datasetName,attributeName,data); }
1143
1144 // Writing data
1145
1146 /** \brief Write multi arrays.
1147
1148 Chunks can be activated by setting
1149 \code iChunkSize = size; //size > 0
1150 \endcode .
1151 The chunks will be hypercubes with edge length size. When <tt>iChunkSize == 0</tt>
1152 (default), the behavior depends on the <tt>compression</tt> setting: If no
1153 compression is requested, the data is written without chunking. Otherwise,
1154 chuning is required, and the chunk size is automatically selected such that
1155 each chunk contains about 300k pixels.
1156
1157 Compression can be activated by setting
1158 \code compression = parameter; // 0 < parameter <= 9
1159 \endcode
1160 where 0 stands for no compression and 9 for maximum compression.
1161
1162 If the first character of datasetName is a "/", the path will be interpreted as absolute path,
1163 otherwise it will be interpreted as path relative to the current group.
1164
1165 Note that the memory order between VIGRA and HDF5 files differs: VIGRA uses
1166 Fortran-order, while HDF5 uses C-order. This means that a VIGRA MultiArray,
1167 whose indices represent the 'x'-, 'y'-, and 'z'-axis in that order, is reversed
1168 upon writing to an HDF5 file, i.e. in the file the axis order is 'z', 'y', 'x'.
1169 */
1170 template<unsigned int N, class T, class Stride>
1171 inline void write(std::string datasetName,
1172 const MultiArrayView<N, T, Stride> & array,
1173 int iChunkSize = 0, int compression = 0)
1174 {
1175 // make datasetName clean
1176 datasetName = get_absolute_path(datasetName);
1177
1178 typename MultiArrayShape<N>::type chunkSize;
1179 for(unsigned int i = 0; i < N; i++){
1180 chunkSize[i] = iChunkSize;
1181 }
1182 write_(datasetName, array, detail::getH5DataType<T>(), 1, chunkSize, compression);
1183 }
1184
1185 /** \brief Write multi arrays.
1186 Chunks can be activated by providing a MultiArrayShape as chunkSize.
1187 chunkSize must have equal dimension as array.
1188
1189 Compression can be activated by setting
1190 \code compression = parameter; // 0 < parameter <= 9
1191 \endcode
1192 where 0 stands for no compression and 9 for maximum compression.
1193
1194 If the first character of datasetName is a "/", the path will be interpreted as absolute path,
1195 otherwise it will be interpreted as path relative to the current group.
1196
1197 Note that the memory order between VIGRA and HDF5 files differs: VIGRA uses
1198 Fortran-order, while HDF5 uses C-order. This means that a VIGRA MultiArray,
1199 whose indices represent the 'x'-, 'y'-, and 'z'-axis in that order, is reversed
1200 upon writing to an HDF5 file, i.e. in the file the axis order is 'z', 'y', 'x'.
1201 */
1202 template<unsigned int N, class T, class Stride>
1203 inline void write(std::string datasetName,
1204 const MultiArrayView<N, T, Stride> & array,
1205 typename MultiArrayShape<N>::type chunkSize, int compression = 0)
1206 {
1207 // make datasetName clean
1208 datasetName = get_absolute_path(datasetName);
1209
1210 write_(datasetName, array, detail::getH5DataType<T>(), 1, chunkSize, compression);
1211 }
1212
1213 /** \brief Write a multi array into a larger volume.
1214 blockOffset determines the position, where array is written.
1215
1216 If the first character of datasetName is a "/", the path will be interpreted as absolute path,
1217 otherwise it will be interpreted as path relative to the current group.
1218
1219 Note that the memory order between VIGRA and HDF5 files differs: VIGRA uses
1220 Fortran-order, while HDF5 uses C-order. This means that a VIGRA MultiArray,
1221 whose indices represent the 'x'-, 'y'-, and 'z'-axis in that order, is reversed
1222 upon writing to an HDF5 file, i.e. in the file the axis order is 'z', 'y', 'x'.
1223 */
1224 template<unsigned int N, class T, class Stride>
1225 inline void writeBlock(std::string datasetName,
1226 typename MultiArrayShape<N>::type blockOffset,
1227 const MultiArrayView<N, T, Stride> & array)
1228 {
1229 // make datasetName clean
1230 datasetName = get_absolute_path(datasetName);
1231
1232 writeBlock_(datasetName, blockOffset, array, detail::getH5DataType<T>(), 1);
1233 }
1234
1235 // non-scalar (TinyVector) and unstrided multi arrays
1236 template<unsigned int N, class T, int SIZE, class Stride>
1237 inline void write(std::string datasetName,
1238 const MultiArrayView<N, TinyVector<T, SIZE>, Stride> & array,
1239 int iChunkSize = 0, int compression = 0)
1240 {
1241 // make datasetName clean
1242 datasetName = get_absolute_path(datasetName);
1243
1244 typename MultiArrayShape<N>::type chunkSize;
1245 for(int i = 0; i < N; i++){
1246 chunkSize[i] = iChunkSize;
1247 }
1248 write_(datasetName, array, detail::getH5DataType<T>(), SIZE, chunkSize, compression);
1249 }
1250
1251 template<unsigned int N, class T, int SIZE, class Stride>
1252 inline void write(std::string datasetName,
1253 const MultiArrayView<N, TinyVector<T, SIZE>, Stride> & array,
1254 typename MultiArrayShape<N>::type chunkSize, int compression = 0)
1255 {
1256 // make datasetName clean
1257 datasetName = get_absolute_path(datasetName);
1258
1259 write_(datasetName, array, detail::getH5DataType<T>(), SIZE, chunkSize, compression);
1260 }
1261
1262 /** \brief Write array vectors.
1263
1264 Compression can be activated by setting
1265 \code compression = parameter; // 0 < parameter <= 9
1266 \endcode
1267 where 0 stands for no compression and 9 for maximum compression.
1268
1269 If the first character of datasetName is a "/", the path will be interpreted as absolute path,
1270 otherwise it will be interpreted as path relative to the current group.
1271 */
1272 template<class T>
1273 void write(const std::string & datasetName,
1274 const ArrayVectorView<T> & array,
1275 int compression = 0)
1276 {
1277 // convert to a (trivial) MultiArrayView and forward.
1278 MultiArrayShape<1>::type shape(array.size());
1279 const MultiArrayView<1, T> m_array(shape, const_cast<T*>(array.data()));
1280 write(datasetName, m_array, compression);
1281 }
1282
1283 template<unsigned int N, class T, int SIZE, class Stride>
1284 inline void writeBlock(std::string datasetName,
1285 typename MultiArrayShape<N>::type blockOffset,
1286 const MultiArrayView<N, TinyVector<T, SIZE>, Stride> & array)
1287 {
1288 // make datasetName clean
1289 datasetName = get_absolute_path(datasetName);
1290
1291 writeBlock_(datasetName, blockOffset, array, detail::getH5DataType<T>(), SIZE);
1292 }
1293
1294 // non-scalar (RGBValue) and unstrided multi arrays
1295 template<unsigned int N, class T, class Stride>
1296 inline void write(std::string datasetName,
1297 const MultiArrayView<N, RGBValue<T>, Stride> & array,
1298 int iChunkSize = 0, int compression = 0)
1299 {
1300 // make datasetName clean
1301 datasetName = get_absolute_path(datasetName);
1302
1303 typename MultiArrayShape<N>::type chunkSize;
1304 for(int i = 0; i < N; i++){
1305 chunkSize[i] = iChunkSize;
1306 }
1307 write_(datasetName, array, detail::getH5DataType<T>(), 3, chunkSize, compression);
1308 }
1309
1310 template<unsigned int N, class T, class Stride>
1311 inline void write(std::string datasetName,
1312 const MultiArrayView<N, RGBValue<T>, Stride> & array,
1313 typename MultiArrayShape<N>::type chunkSize, int compression = 0)
1314 {
1315 // make datasetName clean
1316 datasetName = get_absolute_path(datasetName);
1317
1318 write_(datasetName, array, detail::getH5DataType<T>(), 3, chunkSize, compression);
1319 }
1320
1321 template<unsigned int N, class T, class Stride>
1322 inline void writeBlock(std::string datasetName,
1323 typename MultiArrayShape<N>::type blockOffset,
1324 const MultiArrayView<N, RGBValue<T>, Stride> & array)
1325 {
1326 // make datasetName clean
1327 datasetName = get_absolute_path(datasetName);
1328
1329 writeBlock_(datasetName, blockOffset, array, detail::getH5DataType<T>(), 3);
1330 }
1331
1332 /** \brief Write a single value.
1333 Specialization of the write function for simple datatypes
1334 */
1335 inline void write(std::string datasetName, char data) { writeAtomic(datasetName,data); }
1336 inline void write(std::string datasetName, signed char data) { writeAtomic(datasetName,data); }
1337 inline void write(std::string datasetName, signed short data) { writeAtomic(datasetName,data); }
1338 inline void write(std::string datasetName, signed int data) { writeAtomic(datasetName,data); }
1339 inline void write(std::string datasetName, signed long data) { writeAtomic(datasetName,data); }
1340 inline void write(std::string datasetName, signed long long data) { writeAtomic(datasetName,data); }
1341 inline void write(std::string datasetName, unsigned char data) { writeAtomic(datasetName,data); }
1342 inline void write(std::string datasetName, unsigned short data) { writeAtomic(datasetName,data); }
1343 inline void write(std::string datasetName, unsigned int data) { writeAtomic(datasetName,data); }
1344 inline void write(std::string datasetName, unsigned long data) { writeAtomic(datasetName,data); }
1345 inline void write(std::string datasetName, unsigned long long data) { writeAtomic(datasetName,data); }
1346 inline void write(std::string datasetName, float data) { writeAtomic(datasetName,data); }
1347 inline void write(std::string datasetName, double data) { writeAtomic(datasetName,data); }
1348 inline void write(std::string datasetName, long double data) { writeAtomic(datasetName,data); }
1349 inline void write(std::string datasetName, const char* data) { writeAtomic(datasetName,data); }
1350 inline void write(std::string datasetName, std::string const & data) { writeAtomic(datasetName,data.c_str()); }
1351
1352 // Reading data
1353
1354 /** \brief Read data into a multi array.
1355 If the first character of datasetName is a "/", the path will be interpreted as absolute path,
1356 otherwise it will be interpreted as path relative to the current group.
1357
1358 Note that the memory order between VIGRA and HDF5 files differs: VIGRA uses
1359 Fortran-order, while HDF5 uses C-order. This means that a HDF5 dataset,
1360 whose indices represent the 'z'-, 'y'-, and 'x'-axis in that order, is reversed
1361 upon reading into a MultiArrayView, i.e. in the array axis order must be 'x', 'y', 'z'.
1362 */
1363 template<unsigned int N, class T, class Stride>
1364 inline void read(std::string datasetName, MultiArrayView<N, T, Stride> array)
1365 {
1366 // make datasetName clean
1367 datasetName = get_absolute_path(datasetName);
1368
1369 read_(datasetName, array, detail::getH5DataType<T>(), 1);
1370 }
1371
1372 /** \brief Read data into a MultiArray. Resize MultiArray to the correct size.
1373 If the first character of datasetName is a "/", the path will be interpreted as absolute path,
1374 otherwise it will be interpreted as path relative to the current group.
1375
1376 Note that the memory order between VIGRA and HDF5 files differs: VIGRA uses
1377 Fortran-order, while HDF5 uses C-order. This means that a HDF5 dataset,
1378 whose indices represent the 'z'-, 'y'-, and 'x'-axis in that order, is reversed
1379 upon reading into a MultiArray, i.e. in the array axis order will be 'x', 'y', 'z'.
1380 */
1381 template<unsigned int N, class T, class Alloc>
1382 inline void readAndResize(std::string datasetName, MultiArray<N, T, Alloc> & array)
1383 {
1384 // make datasetName clean
1385 datasetName = get_absolute_path(datasetName);
1386
1387 // get dataset dimension
1388 ArrayVector<hsize_t> dimshape = getDatasetShape(datasetName);
1389
1390 // check if dimensions are correct
1391 vigra_precondition(N == MultiArrayIndex(dimshape.size()), // the object in the HDF5 file may have one additional dimension which we then interpret as the pixel type bands
1392 "HDF5File::readAndResize(): Array dimension disagrees with dataset dimension.");
1393
1394 // reshape target MultiArray
1395 typename MultiArrayShape<N>::type shape;
1396 for(int k=0; k < (int)dimshape.size(); ++k)
1397 shape[k] = (MultiArrayIndex)dimshape[k];
1398 array.reshape(shape);
1399
1400 read_(datasetName, array, detail::getH5DataType<T>(), 1);
1401 }
1402
1403 /** \brief Read data into an array vector.
1404 If the first character of datasetName is a "/", the path will be interpreted as absolute path,
1405 otherwise it will be interpreted as path relative to the current group.
1406 */
1407 template<class T>
1408 inline void read(const std::string & datasetName, ArrayVectorView<T> array)
1409 {
1410 // convert to a (trivial) MultiArrayView and forward.
1411 MultiArrayShape<1>::type shape(array.size());
1412 MultiArrayView<1, T> m_array(shape, (array.data()));
1413 read(datasetName, m_array);
1414 }
1415
1416 /** \brief Read data into an array vector. Resize the array vector to the correct size.
1417 If the first character of datasetName is a "/", the path will be interpreted as absolute path,
1418 otherwise it will be interpreted as path relative to the current group.
1419 */
1420 template<class T>
1421 inline void readAndResize(std::string datasetName,
1422 ArrayVector<T> & array)
1423 {
1424 // make dataset name clean
1425 datasetName = get_absolute_path(datasetName);
1426
1427 // get dataset dimension
1428 ArrayVector<hsize_t> dimshape = getDatasetShape(datasetName);
1429
1430 // check if dimensions are correct
1431 vigra_precondition(1 == MultiArrayIndex(dimshape.size()),
1432 "HDF5File::readAndResize(): Array dimension disagrees with Dataset dimension must equal one for vigra::ArrayVector.");
1433
1434 // resize target array vector
1435 array.resize((typename ArrayVector<T>::size_type)dimshape[0]);
1436 // convert to a (trivial) MultiArrayView and forward.
1437 MultiArrayShape<1>::type shape(array.size());
1438 MultiArrayView<1, T> m_array(shape, (array.data()));
1439
1440 read_(datasetName, m_array, detail::getH5DataType<T>(), 1);
1441 }
1442
1443 /** \brief Read a block of data into a multi array.
1444 This function allows to read a small block out of a larger volume stored
1445 in an HDF5 dataset.
1446
1447 blockOffset determines the position of the block.
1448 blockSize determines the size in each dimension of the block.
1449
1450 If the first character of datasetName is a "/", the path will be interpreted as absolute path,
1451 otherwise it will be interpreted as path relative to the current group.
1452
1453 Note that the memory order between VIGRA and HDF5 files differs: VIGRA uses
1454 Fortran-order, while HDF5 uses C-order. This means that a HDF5 dataset,
1455 whose indices represent the 'z'-, 'y'-, and 'x'-axis in that order, is reversed
1456 upon reading into a MultiArray, i.e. in the array axis order will be 'x', 'y', 'z'.
1457 */
1458 template<unsigned int N, class T, class Stride>
1459 inline void readBlock(std::string datasetName,
1460 typename MultiArrayShape<N>::type blockOffset,
1461 typename MultiArrayShape<N>::type blockShape,
1462 MultiArrayView<N, T, Stride> array)
1463 {
1464 // make datasetName clean
1465 datasetName = get_absolute_path(datasetName);
1466
1467 readBlock_(datasetName, blockOffset, blockShape, array, detail::getH5DataType<T>(), 1);
1468 }
1469
1470 // non-scalar (TinyVector) and unstrided target MultiArrayView
1471 template<unsigned int N, class T, int SIZE, class Stride>
1472 inline void read(std::string datasetName, MultiArrayView<N, TinyVector<T, SIZE>, Stride> array)
1473 {
1474 // make datasetName clean
1475 datasetName = get_absolute_path(datasetName);
1476
1477 read_(datasetName, array, detail::getH5DataType<T>(), SIZE);
1478 }
1479
1480 // non-scalar (TinyVector) MultiArray
1481 template<unsigned int N, class T, int SIZE, class Alloc>
1482 inline void readAndResize(std::string datasetName, MultiArray<N, TinyVector<T, SIZE>, Alloc> & array)
1483 {
1484 // make datasetName clean
1485 datasetName = get_absolute_path(datasetName);
1486
1487 // get dataset dimension
1488 ArrayVector<hsize_t> dimshape = getDatasetShape(datasetName);
1489
1490 // check if dimensions are correct
1491 vigra_precondition((N+1) == MultiArrayIndex(dimshape.size()) &&
1492 SIZE == dimshape[0], // the object in the HDF5 file must have one additional dimension which we interpret as the pixel type bands
1493 "HDF5File::readAndResize(): Array dimension disagrees with dataset dimension.");
1494
1495 // reshape target MultiArray
1496 typename MultiArrayShape<N>::type shape;
1497 for(int k=1; k < (int)dimshape.size(); ++k)
1498 shape[k-1] = (MultiArrayIndex)dimshape[k];
1499 array.reshape(shape);
1500
1501 read_(datasetName, array, detail::getH5DataType<T>(), SIZE);
1502 }
1503
1504 template<unsigned int N, class T, int SIZE, class Stride>
1505 inline void readBlock(std::string datasetName,
1506 typename MultiArrayShape<N>::type blockOffset,
1507 typename MultiArrayShape<N>::type blockShape,
1508 MultiArrayView<N, TinyVector<T, SIZE>, Stride> array)
1509 {
1510 // make datasetName clean
1511 datasetName = get_absolute_path(datasetName);
1512
1513 readBlock_(datasetName, blockOffset, blockShape, array, detail::getH5DataType<T>(), SIZE);
1514 }
1515
1516 // non-scalar (RGBValue) and unstrided target MultiArrayView
1517 template<unsigned int N, class T, class Stride>
1518 inline void read(std::string datasetName, MultiArrayView<N, RGBValue<T>, Stride> array)
1519 {
1520 // make datasetName clean
1521 datasetName = get_absolute_path(datasetName);
1522
1523 read_(datasetName, array, detail::getH5DataType<T>(), 3);
1524 }
1525
1526 // non-scalar (RGBValue) MultiArray
1527 template<unsigned int N, class T, class Alloc>
1528 inline void readAndResize(std::string datasetName, MultiArray<N, RGBValue<T>, Alloc> & array)
1529 {
1530 // make datasetName clean
1531 datasetName = get_absolute_path(datasetName);
1532
1533 // get dataset dimension
1534 ArrayVector<hsize_t> dimshape = getDatasetShape(datasetName);
1535
1536 // check if dimensions are correct
1537 vigra_precondition((N+1) == MultiArrayIndex(dimshape.size()) &&
1538 3 == dimshape[0], // the object in the HDF5 file must have one additional dimension which we interpret as the pixel type bands
1539 "HDF5File::readAndResize(): Array dimension disagrees with dataset dimension.");
1540
1541 // reshape target MultiArray
1542 typename MultiArrayShape<N>::type shape;
1543 for(int k=1; k < (int)dimshape.size(); ++k)
1544 shape[k-1] = (MultiArrayIndex)dimshape[k];
1545 array.reshape(shape);
1546
1547 read_(datasetName, array, detail::getH5DataType<T>(), 3);
1548 }
1549
1550 template<unsigned int N, class T, class Stride>
1551 inline void readBlock(std::string datasetName,
1552 typename MultiArrayShape<N>::type blockOffset,
1553 typename MultiArrayShape<N>::type blockShape,
1554 MultiArrayView<N, RGBValue<T>, Stride> array)
1555 {
1556 // make datasetName clean
1557 datasetName = get_absolute_path(datasetName);
1558
1559 readBlock_(datasetName, blockOffset, blockShape, array, detail::getH5DataType<T>(), 3);
1560 }
1561
1562 /** \brief Read a single value.
1563 Specialization of the read function for simple datatypes
1564 */
1565 inline void read(std::string datasetName, char &data) { readAtomic(datasetName,data); }
1566 inline void read(std::string datasetName, signed char &data) { readAtomic(datasetName,data); }
1567 inline void read(std::string datasetName, signed short &data) { readAtomic(datasetName,data); }
1568 inline void read(std::string datasetName, signed int &data) { readAtomic(datasetName,data); }
1569 inline void read(std::string datasetName, signed long &data) { readAtomic(datasetName,data); }
1570 inline void read(std::string datasetName, signed long long &data) { readAtomic(datasetName,data); }
1571 inline void read(std::string datasetName, unsigned char &data) { readAtomic(datasetName,data); }
1572 inline void read(std::string datasetName, unsigned short &data) { readAtomic(datasetName,data); }
1573 inline void read(std::string datasetName, unsigned int &data) { readAtomic(datasetName,data); }
1574 inline void read(std::string datasetName, unsigned long &data) { readAtomic(datasetName,data); }
1575 inline void read(std::string datasetName, unsigned long long &data) { readAtomic(datasetName,data); }
1576 inline void read(std::string datasetName, float &data) { readAtomic(datasetName,data); }
1577 inline void read(std::string datasetName, double &data) { readAtomic(datasetName,data); }
1578 inline void read(std::string datasetName, long double &data) { readAtomic(datasetName,data); }
1579 inline void read(std::string datasetName, std::string &data) { readAtomic(datasetName,data); }
1580
1581 /** \brief Create a new dataset.
1582 This function can be used to create a dataset filled with a default value,
1583 for example before writing data into it using \ref writeBlock().
1584 Attention: only atomic datatypes are provided. For spectral data, add an
1585 dimension (case RGB: add one dimension of size 3).
1586
1587 shape determines the dimension and the size of the dataset.
1588
1589 Chunks can be activated by providing a MultiArrayShape as chunkSize.
1590 chunkSize must have equal dimension as array.
1591
1592 Compression can be activated by setting
1593 \code compression = parameter; // 0 < parameter <= 9
1594 \endcode
1595 where 0 stands for no compression and 9 for maximum compression.
1596
1597 If the first character of datasetName is a "/", the path will be interpreted as absolute path,
1598 otherwise it will be interpreted as path relative to the current group.
1599
1600 Note that the memory order between VIGRA and HDF5 files differs: VIGRA uses
1601 Fortran-order, while HDF5 uses C-order. This means that a VIGRA MultiArray,
1602 whose indices represent the 'x'-, 'y'-, and 'z'-axis in that order, is reversed
1603 upon writing to an HDF5 file, i.e. in the file the axis order is 'z', 'y', 'x'.
1604 */
1605 template<unsigned int N, class T>
1606 inline void createDataset(std::string datasetName,
1607 typename MultiArrayShape<N>::type shape,
1608 T init = T(),
1609 int iChunkSize = 0,
1610 int compressionParameter = 0)
1611 {
1612 // make datasetName clean
1613 datasetName = get_absolute_path(datasetName);
1614
1615 typename MultiArrayShape<N>::type chunkSize;
1616 for(int i = 0; i < N; i++){
1617 chunkSize[i] = iChunkSize;
1618 }
1619 createDataset<N,T>(datasetName, shape, init, chunkSize, compressionParameter);
1620 }
1621
1622 template<unsigned int N, class T>
1623 inline void createDataset(std::string datasetName,
1624 typename MultiArrayShape<N>::type shape,
1625 T init,
1626 typename MultiArrayShape<N>::type chunkSize,
1627 int compressionParameter = 0)
1628 {
1629 // make datasetName clean
1630 datasetName = get_absolute_path(datasetName);
1631
1632 std::string groupname = SplitString(datasetName).first();
1633 std::string setname = SplitString(datasetName).last();
1634
1635 hid_t parent = openCreateGroup_(groupname);
1636
1637 // delete the dataset if it already exists
1638 deleteDataset_(parent, setname);
1639
1640 // create dataspace
1641 // add an extra dimension in case that the data is non-scalar
1642 HDF5Handle dataspaceHandle;
1643
1644 // invert dimensions to guarantee c-order
1645 hsize_t shape_inv[N];
1646 for(unsigned int k=0; k<N; ++k)
1647 shape_inv[N-1-k] = shape[k];
1648
1649 // create dataspace
1650 dataspaceHandle = HDF5Handle(H5Screate_simple(N, shape_inv, NULL),
1651 &H5Sclose, "HDF5File::createDataset(): unable to create dataspace for scalar data.");
1652
1653 // set fill value
1654 HDF5Handle plist ( H5Pcreate(H5P_DATASET_CREATE), &H5Pclose, "HDF5File::createDataset(): unable to create property list." );
1655 H5Pset_fill_value(plist,detail::getH5DataType<T>(), &init);
1656
1657 // turn off time tagging of datasets by default.
1658 H5Pset_obj_track_times(plist, track_time);
1659
1660 // enable chunks
1661 ArrayVector<hsize_t> chunks(defineChunks(chunkSize, shape, 1, compressionParameter));
1662 if(chunks.size() > 0)
1663 {
1664 std::reverse(chunks.begin(), chunks.end());
1665 H5Pset_chunk (plist, chunks.size(), chunks.begin());
1666 }
1667
1668 // enable compression
1669 if(compressionParameter > 0)
1670 {
1671 H5Pset_deflate(plist, compressionParameter);
1672 }
1673
1674 //create the dataset.
1675 HDF5Handle datasetHandle ( H5Dcreate(parent, setname.c_str(), detail::getH5DataType<T>(), dataspaceHandle, H5P_DEFAULT, plist, H5P_DEFAULT),
1676 &H5Dclose, "HDF5File::createDataset(): unable to create dataset.");
1677 if(parent != cGroupHandle_)
1678 H5Gclose(parent);
1679 }
1680
1681 /** \brief Immediately write all data to disk
1682 */
1683 inline void flushToDisk()
1684 {
1685 H5Fflush(fileHandle_, H5F_SCOPE_GLOBAL);
1686 }
1687
1688 private:
1689
1690 /* Simple extension of std::string for splitting into two parts
1691 *
1692 * Strings (in particular: file/dataset paths) will be split into two
1693 * parts. The split is made at the last occurrence of the delimiter.
1694 *
1695 * For example, "/path/to/some/file" will be split (delimiter = "/") into
1696 * first() = "/path/to/some" and last() = "file".
1697 */
1698 class SplitString: public std::string {
1699 public:
1700 SplitString(std::string &sstring): std::string(sstring) {};
1701
1702 // return the part of the string before the delimiter
1703 std::string first(char delimiter = '/')
1704 {
1705 size_t last = find_last_of(delimiter);
1706 if(last == std::string::npos) // delimiter not found --> no first
1707 return "";
1708
1709 return std::string(begin(), begin()+last+1);
1710 }
1711
1712 // return the part of the string after the delimiter
1713 std::string last(char delimiter = '/')
1714 {
1715 size_t last = find_last_of(delimiter);
1716 if(last == std::string::npos) // delimiter not found --> only last
1717 return std::string(*this);
1718 return std::string(begin()+last+1, end());
1719 }
1720 };
1721
1722 template <class Shape>
1723 ArrayVector<hsize_t>
1724 defineChunks(Shape const & chunks, Shape const & shape, int numBands, int compression = 0)
1725 {
1726 if(chunks[0] > 0)
1727 {
1728 ArrayVector<hsize_t> res(chunks.begin(), chunks.end());
1729 if(numBands > 1)
1730 res.insert(res.begin(), numBands);
1731 return res;
1732 }
1733 else if(compression > 0)
1734 {
1735 // set default chunks to enable compression
1736 // (arbitrarily include about 300k pixels into each chunk, but make sure
1737 // that the chunk size doesn't exceed the shape)
1738 ArrayVector<hsize_t> res(shape.begin(), shape.end());
1739 hsize_t chunk_length = (hsize_t)std::pow(300000.0, 1.0 / shape.size());
1740 for(unsigned int k=0; k < shape.size(); ++k)
1741 if(res[k] > chunk_length)
1742 res[k] = chunk_length;
1743 if(numBands > 1)
1744 res.insert(res.begin(), numBands);
1745 return res;
1746 }
1747 else
1748 {
1749 return ArrayVector<hsize_t>();
1750 }
1751 }
1752
1753 public:
1754
1755 /** \brief takes any path and converts it into an absolute path
1756 in the current file.
1757
1758 Elements like "." and ".." are treated as expected.
1759 Links are not supported or resolved.
1760 */
1761 inline std::string get_absolute_path(std::string path) const {
1762 // check for empty input or "." and return the current folder
1763 if(path.length() == 0 || path == "."){
1764 return currentGroupName_();
1765 }
1766
1767 std::string str;
1768 // convert to absolute path
1769 if(relativePath_(path)){
1770 std::string cname = currentGroupName_();
1771 if (cname == "/")
1772 str = currentGroupName_()+path;
1773 else
1774 str = currentGroupName_()+"/"+path;
1775 }else{
1776 str = path;
1777 }
1778
1779 // cut out "./"
1780 std::string::size_type startpos = 0;
1781 while(str.find(std::string("./"), startpos) != std::string::npos){
1782 std::string::size_type pos = str.find(std::string("./"), startpos);
1783 startpos = pos+1;
1784 // only cut if "./" is not part of "../" (see below)
1785 if(str.substr(pos-1,3) != "../"){
1786 // cut out part of the string
1787 str = str.substr(0,pos) + str.substr(pos+2,str.length()-pos-2);
1788 startpos = pos;
1789 }
1790 }
1791
1792 // cut out pairs of "bla/../"
1793 while(str.find(std::string("..")) != std::string::npos){
1794 std::string::size_type pos = str.find(std::string(".."));
1795
1796 // find first slash after ".."
1797 std::string::size_type end = str.find("/",pos);
1798 if(end != std::string::npos){
1799 // also include slash
1800 end++;
1801 }else{
1802 // no "/" after ".." --> this is a group, add a "/"
1803 str = str + "/";
1804 end = str.length();
1805 }
1806
1807 // find first slash before ".."
1808 std::string::size_type prev_slash = str.rfind("/",pos);
1809 // if the root slash is the first before ".." --> Error
1810 vigra_invariant(prev_slash != 0 && prev_slash != std::string::npos,
1811 "Error parsing path: "+str);
1812 // find second slash before ".."
1813 std::string::size_type begin = str.rfind("/",prev_slash-1);
1814
1815 // cut out part of the string
1816 str = str.substr(0,begin+1) + str.substr(end,str.length()-end);
1817 }
1818
1819 return str;
1820 }
1821
1822 protected:
1823
1824 /* checks if the given path is a relative path.
1825 */
1826 inline bool relativePath_(std::string & path) const
1827 {
1828 std::string::size_type pos = path.find('/') ;
1829 if(pos == 0)
1830 return false;
1831
1832 return true;
1833 }
1834
1835 /* return the name of the current group
1836 */
1837 inline std::string currentGroupName_() const
1838 {
1839 int len = H5Iget_name(cGroupHandle_,NULL,1000);
1840 ArrayVector<char> name (len+1,0);
1841 H5Iget_name(cGroupHandle_,name.begin(),len+1);
1842
1843 return std::string(name.begin());
1844 }
1845
1846 /* return the name of the current file
1847 */
1848 inline std::string fileName_() const
1849 {
1850 int len = H5Fget_name(fileHandle_,NULL,1000);
1851 ArrayVector<char> name (len+1,0);
1852 H5Fget_name(fileHandle_,name.begin(),len+1);
1853
1854 return std::string(name.begin());
1855 }
1856
1857 /* create an empty file and open is
1858 */
1859 inline hid_t createFile_(std::string filePath, OpenMode mode = Open)
1860 {
1861 // try to open file
1862 FILE * pFile;
1863 pFile = fopen ( filePath.c_str(), "r" );
1864 hid_t fileId;
1865
1866 // check if opening was successful (= file exists)
1867 if ( pFile == NULL )
1868 {
1869 fileId = H5Fcreate(filePath.c_str(), H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
1870 }
1871 else if(mode == Open)
1872 {
1873 fclose( pFile );
1874 fileId = H5Fopen(filePath.c_str(), H5F_ACC_RDWR, H5P_DEFAULT);
1875 }
1876 else if(mode == OpenReadOnly) {
1877 fclose( pFile );
1878 fileId = H5Fopen(filePath.c_str(), H5F_ACC_RDONLY, H5P_DEFAULT);
1879 }
1880 else
1881 {
1882 fclose(pFile);
1883 std::remove(filePath.c_str());
1884 fileId = H5Fcreate(filePath.c_str(), H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
1885 }
1886 return fileId;
1887 }
1888
1889 /* open a group and subgroups. Create if necessary.
1890 */
1891 inline hid_t openCreateGroup_(std::string groupName)
1892 {
1893 // make groupName clean
1894 groupName = get_absolute_path(groupName);
1895
1896 // open root group
1897 hid_t parent = H5Gopen(fileHandle_, "/", H5P_DEFAULT);
1898 if(groupName == "/")
1899 {
1900 return parent;
1901 }
1902
1903 // remove leading /
1904 groupName = std::string(groupName.begin()+1, groupName.end());
1905
1906 // check if the groupName has finishing slash
1907 if( groupName.size() != 0 && *groupName.rbegin() != '/')
1908 {
1909 groupName = groupName + '/';
1910 }
1911
1912 // open or create subgroups one by one
1913 std::string::size_type begin = 0, end = groupName.find('/');
1914 while (end != std::string::npos)
1915 {
1916 std::string group(groupName.begin()+begin, groupName.begin()+end);
1917 hid_t prevParent = parent;
1918
1919 if(H5LTfind_dataset(parent, group.c_str()) == 0)
1920 {
1921 parent = H5Gcreate(prevParent, group.c_str(), H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
1922 } else {
1923 parent = H5Gopen(prevParent, group.c_str(), H5P_DEFAULT);
1924 }
1925 H5Gclose(prevParent);
1926
1927 if(parent < 0)
1928 {
1929 return parent;
1930 }
1931 begin = end + 1;
1932 end = groupName.find('/', begin);
1933 }
1934
1935 return parent;
1936 }
1937
1938 /* delete a dataset by unlinking it from the file structure. This does not
1939 delete the data!
1940 */
1941 inline void deleteDataset_(hid_t parent, std::string datasetName)
1942 {
1943 // delete existing data and create new dataset
1944 if(H5LTfind_dataset(parent, datasetName.c_str()))
1945 {
1946
1947 #if (H5_VERS_MAJOR == 1 && H5_VERS_MINOR <= 6)
1948 if(H5Gunlink(parent, datasetName.c_str()) < 0)
1949 {
1950 vigra_postcondition(false, "HDF5File::deleteDataset_(): Unable to delete existing data.");
1951 }
1952 #else
1953 if(H5Ldelete(parent, datasetName.c_str(), H5P_DEFAULT ) < 0)
1954 {
1955 vigra_postcondition(false, "HDF5File::deleteDataset_(): Unable to delete existing data.");
1956 }
1957 #endif
1958 }
1959 }
1960
1961 /* get the handle of a dataset specified by a string
1962 */
1963 inline hid_t getDatasetHandle_(std::string datasetName)
1964 {
1965 // make datasetName clean
1966 datasetName = get_absolute_path(datasetName);
1967
1968 std::string groupname = SplitString(datasetName).first();
1969 std::string setname = SplitString(datasetName).last();
1970
1971 if(H5Lexists(fileHandle_, datasetName.c_str(), H5P_DEFAULT) <= 0)
1972 {
1973 std::cerr << "HDF5File::getDatasetHandle_(): Dataset '" << datasetName << "' does not exist.\n";
1974 return -1;
1975 }
1976
1977 // Open parent group
1978 HDF5Handle groupHandle(openCreateGroup_(groupname), &H5Gclose, "HDF5File::getDatasetHandle_(): Internal error");
1979
1980 return H5Dopen(groupHandle, setname.c_str(), H5P_DEFAULT);
1981 }
1982
1983 /* get the type of an object specified by a string
1984 */
1985 H5O_type_t get_object_type_(std::string name)
1986 {
1987 name = get_absolute_path(name);
1988 std::string group_name = SplitString(name).first();
1989 std::string object_name = SplitString(name).last();
1990 if (!object_name.size())
1991 return H5O_TYPE_GROUP;
1992
1993 htri_t exists = H5Lexists(fileHandle_, name.c_str(), H5P_DEFAULT);
1994 vigra_precondition(exists > 0, "HDF5File::get_object_type_(): "
1995 "object \"" + name + "\" "
1996 "not found.");
1997 // open parent group
1998 HDF5Handle group_handle(openCreateGroup_(group_name), &H5Gclose, "Internal error");
1999 return HDF5_get_type(group_handle, name.c_str());
2000 }
2001
2002 /* low-level write function to write vigra MultiArray data as an attribute
2003 */
2004 template<unsigned int N, class T, class Stride>
2005 void write_attribute_(std::string name,
2006 const std::string & attribute_name,
2007 const MultiArrayView<N, T, Stride> & array,
2008 const hid_t datatype,
2009 const int numBandsOfType);
2010
2011 /* Write single value attribute
2012 This function allows to write data of atomic datatypes (int, long, double)
2013 as an attribute in the HDF5 file. So it is not necessary to create a MultiArray
2014 of size 1 to write a single number.
2015 */
2016 template<class T>
2017 inline void writeAtomicAttribute(std::string datasetName, std::string attributeName, const T data)
2018 {
2019 // make datasetName clean
2020 datasetName = get_absolute_path(datasetName);
2021
2022 typename MultiArrayShape<1>::type chunkSize;
2023 chunkSize[0] = 0;
2024 MultiArray<1,T> array(MultiArrayShape<1>::type(1));
2025 array[0] = data;
2026 write_attribute_(datasetName, attributeName, array, detail::getH5DataType<T>(), 1);
2027 }
2028
2029 /* low-level read function to read vigra MultiArray data from attributes
2030 */
2031 template<unsigned int N, class T, class Stride>
2032 void read_attribute_(std::string datasetName,
2033 std::string attributeName,
2034 MultiArrayView<N, T, Stride> array,
2035 const hid_t datatype, const int numBandsOfType);
2036
2037 /* Read a single value attribute.
2038 This functions allows to read a single value attribute of atomic datatype (int, long, double)
2039 from the HDF5 file. So it is not necessary to create a MultiArray
2040 of size 1 to read a single number.
2041 */
2042 template<class T>
2043 inline void readAtomicAttribute(std::string datasetName, std::string attributeName, T & data)
2044 {
2045 // make datasetName clean
2046 datasetName = get_absolute_path(datasetName);
2047
2048 MultiArray<1,T> array(MultiArrayShape<1>::type(1));
2049 read_attribute_(datasetName, attributeName, array, detail::getH5DataType<T>(), 1);
2050 data = array[0];
2051 }
2052
2053 inline void readAtomicAttribute(std::string datasetName, std::string attributeName, std::string & data)
2054 {
2055 // make datasetName clean
2056 datasetName = get_absolute_path(datasetName);
2057
2058 MultiArray<1,const char *> array(MultiArrayShape<1>::type(1));
2059 read_attribute_(datasetName, attributeName, array, detail::getH5DataType<const char *>(), 1);
2060 data = std::string(array[0]);
2061 }
2062
2063 /* low-level write function to write vigra unstrided MultiArray data
2064 */
2065 template<unsigned int N, class T, class Stride>
2066 void write_(std::string &datasetName,
2067 const MultiArrayView<N, T, Stride> & array,
2068 const hid_t datatype,
2069 const int numBandsOfType,
2070 typename MultiArrayShape<N>::type &chunkSize,
2071 int compressionParameter = 0);
2072
2073 /* Write single value as dataset.
2074 This functions allows to write data of atomic datatypes (int, long, double)
2075 as a dataset in the HDF5 file. So it is not necessary to create a MultiArray
2076 of size 1 to write a single number.
2077
2078 If the first character of datasetName is a "/", the path will be interpreted as absolute path,
2079 otherwise it will be interpreted as path relative to the current group.
2080 */
2081 template<class T>
2082 inline void writeAtomic(std::string datasetName, const T data)
2083 {
2084 // make datasetName clean
2085 datasetName = get_absolute_path(datasetName);
2086
2087 typename MultiArrayShape<1>::type chunkSize;
2088 chunkSize[0] = 0;
2089 MultiArray<1,T> array(MultiArrayShape<1>::type(1));
2090 array[0] = data;
2091 write_(datasetName, array, detail::getH5DataType<T>(), 1, chunkSize,0);
2092 }
2093
2094 /* low-level read function to read vigra unstrided MultiArray data
2095 */
2096 template<unsigned int N, class T, class Stride>
2097 void read_(std::string datasetName,
2098 MultiArrayView<N, T, Stride> array,
2099 const hid_t datatype, const int numBandsOfType);
2100
2101 /* Read a single value.
2102 This functions allows to read a single datum of atomic datatype (int, long, double)
2103 from the HDF5 file. So it is not necessary to create a MultiArray
2104 of size 1 to read a single number.
2105
2106 If the first character of datasetName is a "/", the path will be interpreted as absolute path,
2107 otherwise it will be interpreted as path relative to the current group.
2108 */
2109 template<class T>
2110 inline void readAtomic(std::string datasetName, T & data)
2111 {
2112 // make datasetName clean
2113 datasetName = get_absolute_path(datasetName);
2114
2115 MultiArray<1,T> array(MultiArrayShape<1>::type(1));
2116 read_(datasetName, array, detail::getH5DataType<T>(), 1);
2117 data = array[0];
2118 }
2119
2120 inline void readAtomic(std::string datasetName, std::string & data)
2121 {
2122 // make datasetName clean
2123 datasetName = get_absolute_path(datasetName);
2124
2125 MultiArray<1,const char *> array(MultiArrayShape<1>::type(1));
2126 read_(datasetName, array, detail::getH5DataType<const char *>(), 1);
2127 data = std::string(array[0]);
2128 }
2129
2130 /* low-level write function to write vigra unstrided MultiArray data into a sub-block of a dataset
2131 */
2132 template<unsigned int N, class T, class Stride>
2133 void writeBlock_(std::string datasetName,
2134 typename MultiArrayShape<N>::type &blockOffset,
2135 const MultiArrayView<N, T, Stride> & array,
2136 const hid_t datatype,
2137 const int numBandsOfType);
2138
2139 /* low-level read function to read vigra unstrided MultiArray data from a sub-block of a dataset.
2140
2141 The array must have the same shape as the block.
2142 */
2143 template<unsigned int N, class T, class Stride>
2144 void readBlock_(std::string datasetName,
2145 typename MultiArrayShape<N>::type &blockOffset,
2146 typename MultiArrayShape<N>::type &blockShape,
2147 MultiArrayView<N, T, Stride> &array,
2148 const hid_t datatype, const int numBandsOfType);
2149 }; /* class HDF5File */
2150
2151 /********************************************************************/
2152
2153 template<unsigned int N, class T, class Stride>
2154 void HDF5File::write_(std::string &datasetName,
2155 const MultiArrayView<N, T, Stride> & array,
2156 const hid_t datatype,
2157 const int numBandsOfType,
2158 typename MultiArrayShape<N>::type &chunkSize,
2159 int compressionParameter)
2160 {
2161 std::string groupname = SplitString(datasetName).first();
2162 std::string setname = SplitString(datasetName).last();
2163
2164 // shape of the array. Add one dimension, if array contains non-scalars.
2165 ArrayVector<hsize_t> shape(array.shape().begin(), array.shape().end());
2166 std::reverse(shape.begin(), shape.end());
2167
2168 if(numBandsOfType > 1)
2169 shape.push_back(numBandsOfType);
2170
2171 HDF5Handle dataspace(H5Screate_simple(shape.size(), shape.begin(), NULL), &H5Sclose,
2172 "HDF5File::write(): Can not create dataspace.");
2173
2174 // create and open group:
2175 std::string errorMessage ("HDF5File::write(): can not create group '" + groupname + "'.");
2176 HDF5Handle groupHandle(openCreateGroup_(groupname), &H5Gclose, errorMessage.c_str());
2177
2178 // delete dataset, if it already exists
2179 deleteDataset_(groupHandle, setname.c_str());
2180
2181 // set up properties list
2182 HDF5Handle plist(H5Pcreate(H5P_DATASET_CREATE), &H5Pclose,
2183 "HDF5File::write(): unable to create property list." );
2184
2185 // turn off time tagging of datasets by default.
2186 H5Pset_obj_track_times(plist, track_time);
2187
2188 // enable chunks
2189 ArrayVector<hsize_t> chunks(defineChunks(chunkSize, array.shape(), numBandsOfType, compressionParameter));
2190 if(chunks.size() > 0)
2191 {
2192 std::reverse(chunks.begin(), chunks.end());
2193 H5Pset_chunk (plist, chunks.size(), chunks.begin());
2194 }
2195
2196 // enable compression
2197 if(compressionParameter > 0)
2198 {
2199 H5Pset_deflate(plist, compressionParameter);
2200 }
2201
2202 // create dataset
2203 HDF5Handle datasetHandle(H5Dcreate(groupHandle, setname.c_str(), datatype, dataspace,H5P_DEFAULT, plist, H5P_DEFAULT),
2204 &H5Dclose, "HDF5File::write(): Can not create dataset.");
2205
2206 herr_t status = 0;
2207 if(array.isUnstrided())
2208 {
2209 // Write the data directly from the array data buffer
2210 status = H5Dwrite(datasetHandle, datatype, H5S_ALL, H5S_ALL, H5P_DEFAULT, array.data());
2211 }
2212 else
2213 {
2214 // otherwise, we need an intermediate buffer
2215 // FIXME: right now, the buffer has the same size as the array to be read
2216 // incomplete code for better solutions is below
2217 // MultiArray<N, T> buffer(array);
2218 // status = H5Dwrite(datasetHandle, datatype, H5S_ALL, H5S_ALL, H5P_DEFAULT, buffer.data());
2219
2220 int offset = numBandsOfType > 1 ? 1 : 0;
2221 std::reverse(shape.begin(), shape.end());
2222 if(chunks.size() > 0)
2223 {
2224 // if the file is chunked, we use a buffer that matches the chunk size.
2225 std::reverse(chunks.begin(), chunks.end());
2226 }
2227 else
2228 {
2229 // otherwise, we compute a suitable chunk size.
2230 ArrayVector<hsize_t>(shape.size(), 1).swap(chunks);
2231 chunks[0] = numBandsOfType;
2232 MultiArrayIndex prod = 1;
2233 for(unsigned int k=0; k<N; ++k)
2234 {
2235 chunks[k+offset] = array.shape(k);
2236 prod *= array.shape(k);
2237 if(prod > 300000)
2238 break;
2239 }
2240 }
2241
2242 ArrayVector<hsize_t> null(shape.size(), 0),
2243 start(shape.size(), 0),
2244 count(shape.size(), 1);
2245
2246 count[N-1-offset] = numBandsOfType;
2247
2248 typedef typename MultiArrayShape<N>::type Shape;
2249 Shape chunkCount, chunkMaxShape;
2250 for(unsigned int k=offset; k<chunks.size(); ++k)
2251 {
2252 chunkMaxShape[k-offset] = chunks[k];
2253 chunkCount[k-offset] = (MultiArrayIndex)std::ceil(double(shape[k]) / chunks[k]);
2254 }
2255
2256 typename CoupledIteratorType<N>::type chunkIter = createCoupledIterator(chunkCount),
2257 chunkEnd = chunkIter.getEndIterator();
2258 for(; chunkIter != chunkEnd; ++chunkIter)
2259 {
2260 Shape chunkStart(chunkIter.point() * chunkMaxShape),
2261 chunkStop(min(chunkStart + chunkMaxShape, array.shape()));
2262 MultiArray<N, T> buffer(array.subarray(chunkStart, chunkStop));
2263
2264 for(unsigned int k=0; k<N; ++k)
2265 {
2266 start[N-1-k] = chunkStart[k];
2267 count[N-1-k] = buffer.shape(k);
2268 }
2269 if(offset == 1)
2270 {
2271 start[N] = 0;
2272 count[N] = numBandsOfType;
2273 }
2274 HDF5Handle filespace(H5Dget_space(datasetHandle),
2275 &H5Sclose, "HDF5File::write(): unable to create hyperslabs.");
2276 status = H5Sselect_hyperslab(filespace, H5S_SELECT_SET, start.data(), NULL, count.data(), NULL);
2277 if(status < 0)
2278 break;
2279
2280 HDF5Handle dataspace(H5Screate_simple(count.size(), count.data(), NULL),
2281 &H5Sclose, "HDF5File::write(): unable to create hyperslabs.");
2282 status = H5Sselect_hyperslab(dataspace, H5S_SELECT_SET, null.data(), NULL, count.data(), NULL);
2283 if(status < 0)
2284 break;
2285
2286 status = H5Dwrite(datasetHandle, datatype, dataspace, filespace, H5P_DEFAULT, buffer.data());
2287 if(status < 0)
2288 break;
2289 }
2290 }
2291 vigra_postcondition(status >= 0,
2292 "HDF5File::write(): write to dataset '" + datasetName + "' via H5Dwrite() failed.");
2293 }
2294
2295 /********************************************************************/
2296
2297 template<unsigned int N, class T, class Stride>
2298 void HDF5File::writeBlock_(std::string datasetName,
2299 typename MultiArrayShape<N>::type &blockOffset,
2300 const MultiArrayView<N, T, Stride> & array,
2301 const hid_t datatype,
2302 const int numBandsOfType)
2303 {
2304 // open dataset if it exists
2305 std::string errorMessage = "HDF5File::writeBlock(): Error opening dataset '" + datasetName + "'.";
2306 HDF5Handle datasetHandle (getDatasetHandle_(datasetName), &H5Dclose, errorMessage.c_str());
2307
2308 // hyperslab parameters for position, size, ...
2309 hsize_t boffset [N];
2310 hsize_t bshape [N];
2311 hsize_t bones [N];
2312
2313 for(int i = 0; i < N; i++){
2314 boffset[i] = blockOffset[N-1-i];
2315 bshape[i] = array.size(N-1-i);
2316 bones[i] = 1;
2317 }
2318
2319 // create a target dataspace in memory with the shape of the desired block
2320 HDF5Handle memspace_handle (H5Screate_simple(N,bshape,NULL),&H5Sclose,"Unable to get origin dataspace");
2321
2322 // get file dataspace and select the desired block
2323 HDF5Handle dataspaceHandle (H5Dget_space(datasetHandle),&H5Sclose,"Unable to create target dataspace");
2324 H5Sselect_hyperslab(dataspaceHandle, H5S_SELECT_SET, boffset, bones, bones, bshape);
2325
2326 herr_t status = 0;
2327 if(array.isUnstrided())
2328 {
2329 // when the array is unstrided, we can read the data directly from the array buffer
2330 status = H5Dwrite( datasetHandle, datatype, memspace_handle, dataspaceHandle, H5P_DEFAULT, array.data());
2331 }
2332 else
2333 {
2334 // otherwise, we must copy the data into an unstrided extra buffer
2335 MultiArray<N, T> buffer(array);
2336 status = H5Dwrite( datasetHandle, datatype, memspace_handle, dataspaceHandle, H5P_DEFAULT, buffer.data());
2337 }
2338 vigra_postcondition(status >= 0,
2339 "HDF5File::writeBlock(): write to dataset '" + datasetName + "' via H5Dwrite() failed.");
2340 }
2341
2342 /********************************************************************/
2343
2344 template<unsigned int N, class T, class Stride>
2345 void HDF5File::write_attribute_(std::string name,
2346 const std::string & attribute_name,
2347 const MultiArrayView<N, T, Stride> & array,
2348 const hid_t datatype,
2349 const int numBandsOfType)
2350 {
2351 // shape of the array. Add one dimension, if array contains non-scalars.
2352 ArrayVector<hsize_t> shape(array.shape().begin(), array.shape().end());
2353 std::reverse(shape.begin(), shape.end());
2354 if(numBandsOfType > 1)
2355 shape.push_back(numBandsOfType);
2356
2357 HDF5Handle dataspace(H5Screate_simple(shape.size(),
2358 shape.begin(), NULL),
2359 &H5Sclose, "HDF5File::writeAttribute(): Can not"
2360 " create dataspace.");
2361
2362 std::string errorMessage ("HDF5File::writeAttribute(): can not find "
2363 "object '" + name + "'.");
2364
2365 H5O_type_t h5_type = get_object_type_(name);
2366 bool is_group = h5_type == H5O_TYPE_GROUP;
2367 if (!is_group && h5_type != H5O_TYPE_DATASET)
2368 vigra_precondition(0, "HDF5File::writeAttribute(): object \""
2369 + name + "\" is neither a group nor a "
2370 "dataset.");
2371 // get parent object handle
2372 HDF5Handle object_handle(is_group
2373 ? openCreateGroup_(name)
2374 : getDatasetHandle_(name),
2375 is_group
2376 ? &H5Gclose
2377 : &H5Dclose,
2378 errorMessage.c_str());
2379 // create / open attribute
2380 bool exists = existsAttribute(name, attribute_name);
2381 HDF5Handle attributeHandle(exists
2382 ? H5Aopen(object_handle,
2383 attribute_name.c_str(),
2384 H5P_DEFAULT)
2385 : H5Acreate(object_handle,
2386 attribute_name.c_str(), datatype,
2387 dataspace, H5P_DEFAULT,
2388 H5P_DEFAULT),
2389 &H5Aclose,
2390 "HDF5File::writeAttribute(): Can not create"
2391 " attribute.");
2392 herr_t status = 0;
2393 if(array.isUnstrided())
2394 {
2395 // write the data directly from the array data buffer
2396 status = H5Awrite(attributeHandle, datatype, array.data());
2397 }
2398 else
2399 {
2400 // write the data via an unstrided copy
2401 // (we assume that attributes are small arrays, so that the wasted memory is uncritical)
2402 MultiArray<N, T> buffer(array);
2403 status = H5Awrite(attributeHandle, datatype, buffer.data());
2404 }
2405 vigra_postcondition(status >= 0,
2406 "HDF5File::writeAttribute(): write to attribute '" + attribute_name + "' via H5Awrite() failed.");
2407 }
2408
2409 /********************************************************************/
2410
2411 template<unsigned int N, class T, class Stride>
2412 void HDF5File::read_(std::string datasetName,
2413 MultiArrayView<N, T, Stride> array,
2414 const hid_t datatype, const int numBandsOfType)
2415 {
2416 //Prepare to read without using HDF5ImportInfo
2417 ArrayVector<hsize_t> dimshape = getDatasetShape(datasetName);
2418
2419 std::string errorMessage ("HDF5File::read(): Unable to open dataset '" + datasetName + "'.");
2420 HDF5Handle datasetHandle(getDatasetHandle_(datasetName), &H5Dclose, errorMessage.c_str());
2421
2422 // the object in the HDF5 file may have one additional dimension which we
2423 // interprete as the pixel type's bands
2424 int offset = (numBandsOfType > 1)
2425 ? 1
2426 : 0;
2427
2428 vigra_precondition((N + offset ) == MultiArrayIndex(dimshape.size()),
2429 "HDF5File::read(): Array dimension disagrees with dataset dimension.");
2430
2431 typename MultiArrayShape<N>::type shape;
2432 for(int k=offset; k < (int)dimshape.size(); ++k)
2433 shape[k-offset] = (MultiArrayIndex)dimshape[k];
2434
2435 vigra_precondition(shape == array.shape(),
2436 "HDF5File::read(): Array shape disagrees with dataset shape.");
2437 if (offset)
2438 vigra_precondition(dimshape[0] == static_cast<hsize_t>(numBandsOfType),
2439 "HDF5File::read(): Band count doesn't match destination array compound type.");
2440
2441 herr_t status = 0;
2442 if(array.isUnstrided())
2443 {
2444 // when the array is unstrided, we can read the data directly into the array buffer
2445 status = H5Dread(datasetHandle, datatype, H5S_ALL, H5S_ALL, H5P_DEFAULT, array.data() );
2446 }
2447 else
2448 {
2449 // otherwise, we need an intermediate buffer
2450
2451 ArrayVector<hsize_t> null(dimshape.size(), 0),
2452 chunks(dimshape.size(), 1),
2453 start(dimshape.size(), 0),
2454 count(dimshape.size(), 1);
2455
2456 HDF5Handle properties(H5Dget_create_plist(datasetHandle),
2457 &H5Pclose, "HDF5File::read(): failed to get property list");
2458 if(H5D_CHUNKED == H5Pget_layout(properties))
2459 {
2460 // if the file is chunked, we use a buffer that matches the chunk size.
2461 H5Pget_chunk(properties, chunks.size(), chunks.data());
2462 std::reverse(chunks.begin(), chunks.end());
2463 }
2464 else
2465 {
2466 // otherwise, we compute a suitable chunk size.
2467 chunks[0] = numBandsOfType;
2468 MultiArrayIndex prod = 1;
2469 for(unsigned int k=0; k<N; ++k)
2470 {
2471 chunks[k+offset] = array.shape(k);
2472 prod *= array.shape(k);
2473 if(prod > 300000)
2474 break;
2475 }
2476 }
2477
2478 count[N-1-offset] = numBandsOfType;
2479
2480 typedef typename MultiArrayShape<N>::type Shape;
2481 Shape chunkCount, chunkMaxShape;
2482 for(unsigned int k=offset; k<chunks.size(); ++k)
2483 {
2484 chunkMaxShape[k-offset] = chunks[k];
2485 chunkCount[k-offset] = (MultiArrayIndex)std::ceil(double(dimshape[k]) / chunks[k]);
2486 }
2487
2488 typename CoupledIteratorType<N>::type chunkIter = createCoupledIterator(chunkCount),
2489 chunkEnd = chunkIter.getEndIterator();
2490 for(; chunkIter != chunkEnd; ++chunkIter)
2491 {
2492 Shape chunkStart(chunkIter.point() * chunkMaxShape),
2493 chunkStop(min(chunkStart + chunkMaxShape, array.shape()));
2494 MultiArray<N, T> buffer(chunkStop - chunkStart);
2495
2496 for(unsigned int k=0; k<N; ++k)
2497 {
2498 start[N-1-k] = chunkStart[k];
2499 count[N-1-k] = buffer.shape(k);
2500 }
2501 if(offset == 1)
2502 {
2503 start[N] = 0;
2504 count[N] = numBandsOfType;
2505 }
2506 HDF5Handle filespace(H5Dget_space(datasetHandle),
2507 &H5Sclose, "HDF5File::read(): unable to create hyperslabs.");
2508 status = H5Sselect_hyperslab(filespace, H5S_SELECT_SET, start.data(), NULL, count.data(), NULL);
2509 if(status < 0)
2510 break;
2511
2512 HDF5Handle dataspace(H5Screate_simple(count.size(), count.data(), NULL),
2513 &H5Sclose, "HDF5File::read(): unable to create hyperslabs.");
2514 status = H5Sselect_hyperslab(dataspace, H5S_SELECT_SET, null.data(), NULL, count.data(), NULL);
2515 if(status < 0)
2516 break;
2517
2518 status = H5Dread(datasetHandle, datatype, dataspace, filespace, H5P_DEFAULT, buffer.data());
2519 if(status < 0)
2520 break;
2521
2522 array.subarray(chunkStart, chunkStop) = buffer;
2523 }
2524 }
2525 vigra_postcondition(status >= 0,
2526 "HDF5File::read(): read from dataset '" + datasetName + "' via H5Dread() failed.");
2527 }
2528
2529 /********************************************************************/
2530
2531 template<unsigned int N, class T, class Stride>
2532 void HDF5File::readBlock_(std::string datasetName,
2533 typename MultiArrayShape<N>::type &blockOffset,
2534 typename MultiArrayShape<N>::type &blockShape,
2535 MultiArrayView<N, T, Stride> &array,
2536 const hid_t datatype, const int numBandsOfType)
2537 {
2538 //Prepare to read without using HDF5ImportInfo
2539 //ArrayVector<hsize_t> dimshape = getDatasetShape(datasetName) ;
2540 hssize_t dimensions = getDatasetDimensions(datasetName);
2541
2542 std::string errorMessage ("HDF5File::readBlock(): Unable to open dataset '" + datasetName + "'.");
2543 HDF5Handle datasetHandle (getDatasetHandle_(datasetName), &H5Dclose, errorMessage.c_str());
2544
2545 int offset = (numBandsOfType > 1)
2546 ? 1
2547 : 0;
2548
2549 vigra_precondition(( (N + offset ) == MultiArrayIndex(dimensions)), // the object in the HDF5 file may have one additional dimension which we then interpret as the pixel type bands
2550 "HDF5File::readBlock(): Array dimension disagrees with data dimension.");
2551
2552 vigra_precondition(blockShape == array.shape(),
2553 "HDF5File::readBlock(): Array shape disagrees with block size.");
2554
2555 // hyperslab parameters for position, size, ...
2556 hsize_t boffset [N];
2557 hsize_t bshape [N];
2558 hsize_t bones [N];
2559
2560 for(int i = 0; i < N; i++){
2561 // vigra and hdf5 use different indexing
2562 boffset[i] = blockOffset[N-1-i];
2563 //bshape[i] = blockShape[i];
2564 bshape[i] = blockShape[N-1-i];
2565 //boffset[i] = blockOffset[N-1-i];
2566 bones[i] = 1;
2567 }
2568
2569 // create a target dataspace in memory with the shape of the desired block
2570 HDF5Handle memspace_handle(H5Screate_simple(N,bshape,NULL),&H5Sclose,
2571 "Unable to create target dataspace");
2572
2573 // get file dataspace and select the desired block
2574 HDF5Handle dataspaceHandle(H5Dget_space(datasetHandle),&H5Sclose,
2575 "Unable to get dataspace");
2576 H5Sselect_hyperslab(dataspaceHandle, H5S_SELECT_SET, boffset, bones, bones, bshape);
2577
2578 herr_t status = 0;
2579 if(array.isUnstrided())
2580 {
2581 // when the array is unstrided, we can read the data directly into the array buffer
2582 status = H5Dread( datasetHandle, datatype, memspace_handle, dataspaceHandle, H5P_DEFAULT, array.data());
2583 }
2584 else
2585 {
2586 // otherwise, we need an unstrided extra buffer ...
2587 MultiArray<N, T> buffer(array.shape());
2588 status = H5Dread( datasetHandle, datatype, memspace_handle, dataspaceHandle, H5P_DEFAULT, buffer.data());
2589 // ... and must copy the values
2590 if(status >= 0)
2591 array = buffer;
2592 }
2593 vigra_postcondition(status >= 0,
2594 "HDF5File::readBlock(): read from dataset '" + datasetName + "' via H5Dread() failed.");
2595 }
2596
2597 /********************************************************************/
2598
2599 template<unsigned int N, class T, class Stride>
2600 void HDF5File::read_attribute_(std::string datasetName,
2601 std::string attributeName,
2602 MultiArrayView<N, T, Stride> array,
2603 const hid_t datatype, const int numBandsOfType)
2604 {
2605 std::string dataset_path = get_absolute_path(datasetName);
2606 // open Attribute handle
2607 std::string message = "HDF5File::readAttribute(): could not get handle for attribute '"+attributeName+"'' of object '"+dataset_path+"'.";
2608 HDF5Handle attr_handle (H5Aopen_by_name(fileHandle_,dataset_path.c_str(),attributeName.c_str(),H5P_DEFAULT,H5P_DEFAULT),&H5Aclose, message.c_str());
2609
2610 // get Attribute dataspace
2611 message = "HDF5File::readAttribute(): could not get dataspace for attribute '"+attributeName+"'' of object '"+dataset_path+"'.";
2612 HDF5Handle attr_dataspace_handle (H5Aget_space(attr_handle),&H5Sclose,message.c_str());
2613
2614 // obtain Attribute shape
2615 int raw_dims = H5Sget_simple_extent_ndims(attr_dataspace_handle);
2616 int dims = std::max(raw_dims, 1); // scalar attributes may be stored with raw_dims==0
2617 ArrayVector<hsize_t> dimshape(dims);
2618 if(raw_dims > 0)
2619 H5Sget_simple_extent_dims(attr_dataspace_handle, dimshape.data(), NULL);
2620 else
2621 dimshape[0] = 1;
2622
2623 // invert the dimensions to guarantee VIGRA-compatible order
2624 std::reverse(dimshape.begin(), dimshape.end());
2625
2626 int offset = (numBandsOfType > 1)
2627 ? 1
2628 : 0;
2629 message = "HDF5File::readAttribute(): Array dimension disagrees with dataset dimension.";
2630 // the object in the HDF5 file may have one additional dimension which we then interpret as the pixel type bands
2631 vigra_precondition((N + offset) == MultiArrayIndex(dims), message);
2632
2633 for(int k=offset; k < (int)dimshape.size(); ++k)
2634 vigra_precondition(array.shape()[k-offset] == (MultiArrayIndex)dimshape[k],
2635 "HDF5File::readAttribute(): Array shape disagrees with dataset shape");
2636
2637 herr_t status = 0;
2638 if(array.isUnstrided())
2639 {
2640 // when the array is unstrided, we can read the data directly into the array buffer
2641 status = H5Aread( attr_handle, datatype, array.data());
2642 }
2643 else
2644 {
2645 // otherwise, we need an unstrided extra buffer ...
2646 // (we assume that attributes are small arrays, so that the wasted memory is uncritical)
2647 MultiArray<N, T> buffer(array.shape());
2648 status = H5Aread( attr_handle, datatype, buffer.data() );
2649 // ... and must copy the values
2650 if(status >= 0)
2651 array = buffer;
2652 }
2653 vigra_postcondition(status >= 0,
2654 "HDF5File::readAttribute(): read from attribute '" + attributeName + "' via H5Aread() failed.");
2655 }
2656
2657 /********************************************************************/
2658
2659 /** \brief Read the data specified by the given \ref vigra::HDF5ImportInfo object
2660 and write the into the given 'array'.
2661
2662 The array must have the correct number of dimensions and shape for the dataset
2663 represented by 'info'. When the element type of 'array' differs from the stored element
2664 type, HDF5 will convert the type on the fly (except when the HDF5 version is 1.6 or below,
2665 in which case an error will result). Multi-channel element types (i.e. \ref vigra::RGBValue,
2666 \ref vigra::TinyVector, and \ref vigra::FFTWComplex) are recognized and handled correctly.
2667
2668 <b> Declaration:</b>
2669
2670 \code
2671 namespace vigra {
2672 template<unsigned int N, class T, class StrideTag>
2673 void
2674 readHDF5(const HDF5ImportInfo &info, MultiArrayView<N, T, StrideTag> array);
2675 }
2676 \endcode
2677
2678 <b> Usage:</b>
2679
2680 <b>\#include</b> <vigra/hdf5impex.hxx><br>
2681 Namespace: vigra
2682
2683 \code
2684
2685 HDF5ImportInfo info(filename, dataset_name);
2686 vigra_precondition(info.numDimensions() == 3, "Dataset must be 3-dimensional.");
2687
2688 MultiArrayShape<3>::type shape(info.shape().begin());
2689 MultiArray<3, int> array(shape);
2690
2691 readHDF5(info, array);
2692 \endcode
2693 */
2694 doxygen_overloaded_function(template <...> void readHDF5)
2695
2696 template<unsigned int N, class T, class StrideTag>
2697 inline void readHDF5(const HDF5ImportInfo &info, MultiArrayView<N, T, StrideTag> array)
2698 {
2699 readHDF5(info, array, 0, 0); // last two arguments are not used
2700 }
2701
2702 template<unsigned int N, class T, class StrideTag>
2703 void readHDF5(const HDF5ImportInfo &info, MultiArrayView<N, T, StrideTag> array, const hid_t datatype, const int numBandsOfType)
2704 {
2705 HDF5File file(info.getFilePath(), HDF5File::OpenReadOnly);
2706 file.read(info.getPathInFile(), array);
2707 file.close();
2708 }
2709
2710 inline hid_t openGroup(hid_t parent, std::string group_name)
2711 {
2712 //std::cout << group_name << std::endl;
2713 size_t last_slash = group_name.find_last_of('/');
2714 if (last_slash == std::string::npos || last_slash != group_name.size() - 1)
2715 group_name = group_name + '/';
2716 std::string::size_type begin = 0, end = group_name.find('/');
2717 int ii = 0;
2718 while (end != std::string::npos)
2719 {
2720 std::string group(group_name.begin()+begin, group_name.begin()+end);
2721 hid_t prev_parent = parent;
2722 parent = H5Gopen(prev_parent, group.c_str(), H5P_DEFAULT);
2723
2724 if(ii != 0) H5Gclose(prev_parent);
2725 if(parent < 0) return parent;
2726 ++ii;
2727 begin = end + 1;
2728 end = group_name.find('/', begin);
2729 }
2730 return parent;
2731 }
2732
2733 inline hid_t createGroup(hid_t parent, std::string group_name)
2734 {
2735 if(group_name.size() == 0 ||*group_name.rbegin() != '/')
2736 group_name = group_name + '/';
2737 if(group_name == "/")
2738 return H5Gopen(parent, group_name.c_str(), H5P_DEFAULT);
2739
2740 std::string::size_type begin = 0, end = group_name.find('/');
2741 int ii = 0;
2742 while (end != std::string::npos)
2743 {
2744 std::string group(group_name.begin()+begin, group_name.begin()+end);
2745 hid_t prev_parent = parent;
2746
2747 if(H5LTfind_dataset(parent, group.c_str()) == 0)
2748 {
2749 parent = H5Gcreate(prev_parent, group.c_str(), H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
2750 } else {
2751 parent = H5Gopen(prev_parent, group.c_str(), H5P_DEFAULT);
2752 }
2753
2754 if(ii != 0) H5Gclose(prev_parent);
2755 if(parent < 0) return parent;
2756 ++ii;
2757 begin = end + 1;
2758 end = group_name.find('/', begin);
2759 }
2760 return parent;
2761 }
2762
2763 inline void deleteDataset(hid_t parent, std::string dataset_name)
2764 {
2765 // delete existing data and create new dataset
2766 if(H5LTfind_dataset(parent, dataset_name.c_str()))
2767 {
2768 //std::cout << "dataset already exists" << std::endl;
2769 #if (H5_VERS_MAJOR == 1 && H5_VERS_MINOR <= 6)
2770 if(H5Gunlink(parent, dataset_name.c_str()) < 0)
2771 {
2772 vigra_postcondition(false, "writeToHDF5File(): Unable to delete existing data.");
2773 }
2774 #else
2775 if(H5Ldelete(parent, dataset_name.c_str(), H5P_DEFAULT ) < 0)
2776 {
2777 vigra_postcondition(false, "createDataset(): Unable to delete existing data.");
2778 }
2779 #endif
2780 }
2781 }
2782
2783 inline hid_t createFile(std::string filePath, bool append_ = true)
2784 {
2785 FILE * pFile;
2786 pFile = fopen ( filePath.c_str(), "r" );
2787 hid_t file_id;
2788 if ( pFile == NULL )
2789 {
2790 file_id = H5Fcreate(filePath.c_str(), H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
2791 }
2792 else if(append_)
2793 {
2794 fclose( pFile );
2795 file_id = H5Fopen(filePath.c_str(), H5F_ACC_RDWR, H5P_DEFAULT);
2796 }
2797 else
2798 {
2799 fclose(pFile);
2800 std::remove(filePath.c_str());
2801 file_id = H5Fcreate(filePath.c_str(), H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
2802 }
2803 return file_id;
2804 }
2805
2806 template<unsigned int N, class T, class Tag>
2807 void createDataset(const char* filePath, const char* pathInFile, const MultiArrayView<N, T, Tag> & array, const hid_t datatype, const int numBandsOfType, HDF5Handle & file_handle, HDF5Handle & dataset_handle)
2808 {
2809 std::string path_name(pathInFile), group_name, data_set_name, message;
2810 std::string::size_type delimiter = path_name.rfind('/');
2811
2812 //create or open file
2813 file_handle = HDF5Handle(createFile(filePath), &H5Fclose,
2814 "createDataset(): unable to open output file.");
2815
2816 // get the groupname and the filename
2817 if(delimiter == std::string::npos)
2818 {
2819 group_name = "/";
2820 data_set_name = path_name;
2821 }
2822 else
2823 {
2824 group_name = std::string(path_name.begin(), path_name.begin()+delimiter);
2825 data_set_name = std::string(path_name.begin()+delimiter+1, path_name.end());
2826 }
2827
2828 // create all groups
2829 HDF5Handle group(createGroup(file_handle, group_name), &H5Gclose,
2830 "createDataset(): Unable to create and open group. generic v");
2831
2832 // delete the dataset if it already exists
2833 deleteDataset(group, data_set_name);
2834
2835 // create dataspace
2836 // add an extra dimension in case that the data is non-scalar
2837 HDF5Handle dataspace_handle;
2838 if(numBandsOfType > 1) {
2839 // invert dimensions to guarantee c-order
2840 hsize_t shape_inv[N+1]; // one additional dimension for pixel type channel(s)
2841 for(unsigned int k=0; k<N; ++k) {
2842 shape_inv[N-1-k] = array.shape(k); // the channels (eg of an RGB image) are represented by the first dimension (before inversion)
2843 //std::cout << shape_inv[N-k] << " (" << N << ")";
2844 }
2845 shape_inv[N] = numBandsOfType;
2846
2847 // create dataspace
2848 dataspace_handle = HDF5Handle(H5Screate_simple(N+1, shape_inv, NULL),
2849 &H5Sclose, "createDataset(): unable to create dataspace for non-scalar data.");
2850 } else {
2851 // invert dimensions to guarantee c-order
2852 hsize_t shape_inv[N];
2853 for(unsigned int k=0; k<N; ++k)
2854 shape_inv[N-1-k] = array.shape(k);
2855
2856 // create dataspace
2857 dataspace_handle = HDF5Handle(H5Screate_simple(N, shape_inv, NULL),
2858 &H5Sclose, "createDataset(): unable to create dataspace for scalar data.");
2859 }
2860
2861 //alloc memory for dataset.
2862 dataset_handle = HDF5Handle(H5Dcreate(group,
2863 data_set_name.c_str(),
2864 datatype,
2865 dataspace_handle,
2866 H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT),
2867 &H5Dclose, "createDataset(): unable to create dataset.");
2868 }
2869
2870
2871
2872
2873 /** \brief Store array data in an HDF5 file.
2874
2875 The number of dimensions, shape and element type of the stored dataset is automatically
2876 determined from the properties of the given \a array. Strided arrays are stored in an
2877 unstrided way, i.e. in contiguous scan-order. Multi-channel element types
2878 (i.e. \ref vigra::RGBValue, \ref vigra::TinyVector and \ref vigra::FFTWComplex)
2879 are recognized and handled correctly
2880 (in particular, the will form the innermost dimension of the stored dataset).
2881 \a pathInFile may contain '/'-separated group names, but must end with the name
2882 of the dataset to be created.
2883
2884 <b> Declaration:</b>
2885
2886 \code
2887 namespace vigra {
2888 template<unsigned int N, class T, class StrideTag>
2889 void
2890 writeHDF5(const char* filePath, const char* pathInFile,
2891 MultiArrayView<N, T, StrideTag>const & array);
2892 }
2893 \endcode
2894
2895 <b> Usage:</b>
2896
2897 <b>\#include</b> <vigra/hdf5impex.hxx><br>
2898 Namespace: vigra
2899
2900 \code
2901 MultiArrayShape<3>::type shape(100, 200, 20);
2902 MultiArray<3, int> array(shape);
2903 ... // fill array with data
2904
2905 writeHDF5("mydata.h5", "/group1/my_dataset", array);
2906 \endcode
2907 */
2908 doxygen_overloaded_function(template <...> void writeHDF5)
2909
2910 template<unsigned int N, class T, class StrideTag>
2911 inline void writeHDF5(const char* filePath, const char* pathInFile, const MultiArrayView<N, T, StrideTag> & array)
2912 {
2913 //last two arguments are not used
2914 writeHDF5(filePath, pathInFile, array, 0, 0);
2915 }
2916
2917 template<unsigned int N, class T, class StrideTag>
2918 void writeHDF5(const char* filePath, const char* pathInFile, const MultiArrayView<N, T, StrideTag> & array, const hid_t datatype, const int numBandsOfType)
2919 {
2920 HDF5File file(filePath, HDF5File::Open);
2921 file.write(pathInFile, array);
2922 file.close();
2923 }
2924
2925
2926 namespace detail
2927 {
2928 struct MaxSizeFnc
2929 {
2930 size_t size;
2931
2932 MaxSizeFnc()
2933 : size(0)
2934 {}
2935
2936 void operator()(std::string const & in)
2937 {
2938 size = in.size() > size ?
2939 in.size() :
2940 size;
2941 }
2942 };
2943 }
2944
2945
2946 #if (H5_VERS_MAJOR == 1 && H5_VERS_MINOR == 8) || DOXYGEN
2947 /** Write a numeric MultiArray as an attribute with name \a name
2948 of the dataset specified by the handle \a loc.
2949
2950 <b>\#include</b> <vigra/hdf5impex.hxx><br>
2951 Namespace: vigra
2952 */
2953 template<size_t N, class T, class C>
2954 void writeHDF5Attr(hid_t loc,
2955 const char* name,
2956 MultiArrayView<N, T, C> const & array)
2957 {
2958 if(H5Aexists(loc, name) > 0)
2959 H5Adelete(loc, name);
2960
2961 ArrayVector<hsize_t> shape(array.shape().begin(),
2962 array.shape().end());
2963 HDF5Handle
2964 dataspace_handle(H5Screate_simple(N, shape.data(), NULL),
2965 &H5Sclose,
2966 "writeToHDF5File(): unable to create dataspace.");
2967
2968 HDF5Handle attr(H5Acreate(loc,
2969 name,
2970 detail::getH5DataType<T>(),
2971 dataspace_handle,
2972 H5P_DEFAULT ,H5P_DEFAULT ),
2973 &H5Aclose,
2974 "writeHDF5Attr: unable to create Attribute");
2975
2976 //copy data - since attributes are small - who cares!
2977 ArrayVector<T> buffer;
2978 for(int ii = 0; ii < array.size(); ++ii)
2979 buffer.push_back(array[ii]);
2980 H5Awrite(attr, detail::getH5DataType<T>(), buffer.data());
2981 }
2982
2983 /** Write a string MultiArray as an attribute with name \a name
2984 of the dataset specified by the handle \a loc.
2985
2986 <b>\#include</b> <vigra/hdf5impex.hxx><br>
2987 Namespace: vigra
2988 */
2989 template<size_t N, class C>
2990 void writeHDF5Attr(hid_t loc,
2991 const char* name,
2992 MultiArrayView<N, std::string, C> const & array)
2993 {
2994 if(H5Aexists(loc, name) > 0)
2995 H5Adelete(loc, name);
2996
2997 ArrayVector<hsize_t> shape(array.shape().begin(),
2998 array.shape().end());
2999 HDF5Handle
3000 dataspace_handle(H5Screate_simple(N, shape.data(), NULL),
3001 &H5Sclose,
3002 "writeToHDF5File(): unable to create dataspace.");
3003
3004 HDF5Handle atype(H5Tcopy (H5T_C_S1),
3005 &H5Tclose,
3006 "writeToHDF5File(): unable to create type.");
3007
3008 detail::MaxSizeFnc max_size;
3009 max_size = std::for_each(array.data(),array.data()+ array.size(), max_size);
3010 H5Tset_size (atype, max_size.size);
3011
3012 HDF5Handle attr(H5Acreate(loc,
3013 name,
3014 atype,
3015 dataspace_handle,
3016 H5P_DEFAULT ,H5P_DEFAULT ),
3017 &H5Aclose,
3018 "writeHDF5Attr: unable to create Attribute");
3019
3020 std::string buf ="";
3021 for(int ii = 0; ii < array.size(); ++ii)
3022 {
3023 buf = buf + array[ii]
3024 + std::string(max_size.size - array[ii].size(), ' ');
3025 }
3026 H5Awrite(attr, atype, buf.c_str());
3027 }
3028
3029 /** Write a numeric ArrayVectorView as an attribute with name \a name
3030 of the dataset specified by the handle \a loc.
3031
3032 <b>\#include</b> <vigra/hdf5impex.hxx><br>
3033 Namespace: vigra
3034 */
3035 template<class T>
3036 inline void writeHDF5Attr( hid_t loc,
3037 const char* name,
3038 ArrayVectorView<T> & array)
3039 {
3040 writeHDF5Attr(loc, name,
3041 MultiArrayView<1, T>(MultiArrayShape<1>::type(array.size()),
3042 array.data()));
3043 }
3044
3045 /** write an Attribute given a file and a path in the file.
3046 the path in the file should have the format
3047 [attribute] or /[subgroups/]dataset.attribute or
3048 /[subgroups/]group.attribute.
3049 The attribute is written to the root group, a dataset or a subgroup
3050 respectively
3051 */
3052 template<class Arr>
3053 inline void writeHDF5Attr( std::string filePath,
3054 std::string pathInFile,
3055 Arr & ar)
3056 {
3057 std::string path_name(pathInFile), group_name, data_set_name, message, attr_name;
3058 std::string::size_type delimiter = path_name.rfind('/');
3059
3060 //create or open file
3061 HDF5Handle file_id(createFile(filePath), &H5Fclose,
3062 "writeToHDF5File(): unable to open output file.");
3063
3064 // get the groupname and the filename
3065 if(delimiter == std::string::npos)
3066 {
3067 group_name = "/";
3068 data_set_name = path_name;
3069 }
3070
3071 else
3072 {
3073 group_name = std::string(path_name.begin(), path_name.begin()+delimiter);
3074 data_set_name = std::string(path_name.begin()+delimiter+1, path_name.end());
3075 }
3076 delimiter = data_set_name.rfind('.');
3077 if(delimiter == std::string::npos)
3078 {
3079 attr_name = path_name;
3080 data_set_name = "/";
3081 }
3082 else
3083 {
3084 attr_name = std::string(data_set_name.begin()+delimiter+1, data_set_name.end());
3085 data_set_name = std::string(data_set_name.begin(), data_set_name.begin()+delimiter);
3086 }
3087
3088 HDF5Handle group(openGroup(file_id, group_name), &H5Gclose,
3089 "writeToHDF5File(): Unable to create and open group. attr ver");
3090
3091 if(data_set_name != "/")
3092 {
3093 HDF5Handle dset(H5Dopen(group, data_set_name.c_str(), H5P_DEFAULT), &H5Dclose,
3094 "writeHDF5Attr():unable to open dataset");
3095 writeHDF5Attr(hid_t(dset), attr_name.c_str(), ar);
3096 }
3097 else
3098 {
3099 writeHDF5Attr(hid_t(group), attr_name.c_str(), ar);
3100 }
3101
3102 }
3103 #endif
3104
3105 //@}
3106
3107 } // namespace vigra
3108
3109 #endif // VIGRA_HDF5IMPEX_HXX
vigra::HDF5File::read
void read(const std::string &datasetName, ArrayVectorView< T > array)
Read data into an array vector. If the first character of datasetName is a "/", the path will be inte...
Definition: hdf5impex.hxx:1408
vigra::HDF5Handle::HDF5Handle
HDF5Handle()
Default constructor. Creates a NULL handle.
Definition: hdf5impex.hxx:148
vigra::HDF5File::write
void write(const std::string &datasetName, const ArrayVectorView< T > &array, int compression=0)
Write array vectors.
Definition: hdf5impex.hxx:1273
vigra::HDF5File::cd_up
bool cd_up(int levels)
Change the current group to its parent group. Returns true if successful, false otherwise. If unsuccessful, the group will not change.
Definition: hdf5impex.hxx:725
vigra::HDF5File::createDataset
void createDataset(std::string datasetName, typename MultiArrayShape< N >::type shape, T init=T(), int iChunkSize=0, int compressionParameter=0)
Create a new dataset. This function can be used to create a dataset filled with a default value...
Definition: hdf5impex.hxx:1606
vigra::HDF5Handle::operator==
bool operator==(HDF5Handle const &h) const
Equality comparison of the contained handle.
Definition: hdf5impex.hxx:248
vigra::HDF5File::HDF5File
HDF5File(std::string filename, OpenMode mode, int track_creation_times=0)
Open or create an HDF5File object.
Definition: hdf5impex.hxx:639
vigra::HDF5Handle
Wrapper for hid_t objects.
Definition: hdf5impex.hxx:134
vigra::writeHDF5Attr
void writeHDF5Attr(std::string filePath, std::string pathInFile, Arr &ar)
Definition: hdf5impex.hxx:3053
vigra::MultiArrayView::shape
const difference_type & shape() const
Definition: multi_array.hxx:1551
vigra::HDF5File::readAttribute
void readAttribute(std::string object_name, std::string attribute_name, MultiArrayView< N, T, Stride > array)
Read MultiArray Attributes. In contrast to datasets, subarray access is not available.
Definition: hdf5impex.hxx:1078
vigra::HDF5File::cd_mk
void cd_mk(std::string groupName)
Change the current group; create it if necessary. If the first character is a "/", the path will be interpreted as absolute path, otherwise it will be interpreted as path relative to the current group.
Definition: hdf5impex.hxx:760
vigra::ArrayVectorView
Definition: array_vector.hxx:76
vigra::HDF5File::getDatasetDimensions
hssize_t getDatasetDimensions(std::string datasetName)
Get the number of dimensions of a certain dataset If the first character is a "/", the path will be interpreted as absolute path, otherwise it will be interpreted as path relative to the current group.
Definition: hdf5impex.hxx:837
vigra::ArrayVectorView::begin
const_iterator begin() const
Definition: array_vector.hxx:223
vigra::MultiArrayView::data
pointer data() const
Definition: multi_array.hxx:1792
vigra::HDF5Handle::HDF5Handle
HDF5Handle(hid_t h, Destructor destructor, const char *error_message)
Create a wrapper for a hid_t object.
Definition: hdf5impex.hxx:172
vigra::HDF5File::get_absolute_path
std::string get_absolute_path(std::string path) const
takes any path and converts it into an absolute path in the current file.
Definition: hdf5impex.hxx:1761
vigra::MultiArray
Main MultiArray class containing the memory management.
Definition: multi_array.hxx:2357
vigra::HDF5File::getDatasetType
std::string getDatasetType(std::string const &datasetName)
Definition: hdf5impex.hxx:907
vigra::MultiArray::reshape
void reshape(const difference_type &shape)
Definition: multi_array.hxx:2738
vigra::HDF5File::mkdir
void mkdir(std::string groupName)
Create a new group. If the first character is a "/", the path will be interpreted as absolute path...
Definition: hdf5impex.hxx:746
vigra::HDF5File::existsAttribute
bool existsAttribute(std::string object_name, std::string attribute_name)
Test if attribute exists.
Definition: hdf5impex.hxx:1061
vigra::HDF5ImportInfo::getFilePath
const std::string & getFilePath() const
vigra::MultiArrayIndex
std::ptrdiff_t MultiArrayIndex
Definition: multi_shape.hxx:55
vigra::HDF5Handle::operator==
bool operator==(hid_t h) const
Equality comparison of the contained handle.
Definition: hdf5impex.hxx:255
vigra
Definition: accessor.hxx:43
vigra::HDF5ImportInfo::getPathInFile
const std::string & getPathInFile() const
vigra::HDF5File::ls
void ls(Container &cont) const
List the contents of the current group into a container-like object via insert(). ...
Definition: hdf5impex.hxx:804
vigra::HDF5File::write
void write(std::string datasetName, const MultiArrayView< N, T, Stride > &array, typename MultiArrayShape< N >::type chunkSize, int compression=0)
Write multi arrays. Chunks can be activated by providing a MultiArrayShape as chunkSize. chunkSize must have equal dimension as array.
Definition: hdf5impex.hxx:1203
vigra::HDF5ImportInfo
Argument object for the function readHDF5().
Definition: hdf5impex.hxx:290
vigra::isHDF5
bool isHDF5(char const *filename)
Check if given filename refers to a HDF5 file.
Definition: hdf5impex.hxx:100
vigra::HDF5Handle::operator!=
bool operator!=(hid_t h) const
Inequality comparison of the contained handle.
Definition: hdf5impex.hxx:269
vigra::HDF5Handle::operator!=
bool operator!=(HDF5Handle const &h) const
Inequality comparison of the contained handle.
Definition: hdf5impex.hxx:262
vigra::MultiArrayView::size
difference_type_1 size() const
Definition: multi_array.hxx:1544
vigra::HDF5File::getDatasetHandle
HDF5Handle getDatasetHandle(std::string const &datasetName)
Obtain the HDF5 handle of a dataset.
Definition: hdf5impex.hxx:953
vigra::ArrayVector< hsize_t >
vigra::HDF5File::filename
std::string filename() const
Get the name of the associated file.
Definition: hdf5impex.hxx:819
vigra::HDF5Handle::operator=
HDF5Handle & operator=(HDF5Handle const &h)
Assignment. Calls close() for the LHS handle and hands over ownership of the RHS handle (analogous to...
Definition: hdf5impex.hxx:194
vigra::HDF5File::~HDF5File
~HDF5File()
The destructor flushes and closes the file.
Definition: hdf5impex.hxx:647
vigra::prod
NumericTraits< V >::Promote prod(TinyVectorBase< V, SIZE, D1, D2 > const &l)
product of the vector&#39;s elements
Definition: tinyvector.hxx:1895
vigra::CoupledScanOrderIterator::getEndIterator
CoupledScanOrderIterator getEndIterator() const
Definition: multi_iterator_coupled.hxx:628
vigra::HDF5File::readAndResize
void readAndResize(std::string datasetName, MultiArray< N, T, Alloc > &array)
Read data into a MultiArray. Resize MultiArray to the correct size. If the first character of dataset...
Definition: hdf5impex.hxx:1382
vigra::readHDF5
void readHDF5(...)
Read the data specified by the given vigra::HDF5ImportInfo object and write the into the given &#39;array...
vigra::HDF5File::readAndResize
void readAndResize(std::string datasetName, ArrayVector< T > &array)
Read data into an array vector. Resize the array vector to the correct size. If the first character o...
Definition: hdf5impex.hxx:1421
vigra::HDF5Handle::~HDF5Handle
~HDF5Handle()
Destructor. Calls close() for the contained handle.
Definition: hdf5impex.hxx:209
vigra::HDF5File::read
void read(std::string datasetName, char &data)
Read a single value. Specialization of the read function for simple datatypes.
Definition: hdf5impex.hxx:1565
vigra::HDF5File::open
void open(std::string filename, OpenMode mode)
Open or create the given file in the given mode and set the group to "/". If another file is currentl...
Definition: hdf5impex.hxx:666
vigra::HDF5File::OpenMode
OpenMode
Set how a file is opened.
Definition: hdf5impex.hxx:614
vigra::HDF5File::readAttribute
void readAttribute(std::string object_name, std::string attribute_name, char &data)
Read a single value. Specialization of the read function for simple datatypes.
Definition: hdf5impex.hxx:1113
vigra::HDF5File::writeBlock
void writeBlock(std::string datasetName, typename MultiArrayShape< N >::type blockOffset, const MultiArrayView< N, T, Stride > &array)
Write a multi array into a larger volume. blockOffset determines the position, where array is written...
Definition: hdf5impex.hxx:1225
vigra::HDF5File::flushToDisk
void flushToDisk()
Immediately write all data to disk.
Definition: hdf5impex.hxx:1683
vigra::HDF5Handle::HDF5Handle
HDF5Handle(HDF5Handle const &h)
Copy constructor. Hands over ownership of the RHS handle (analogous to VIGRA_UNIQUE_PTR).
Definition: hdf5impex.hxx:183
vigra::TinyVector
Class for fixed size vectors.This class contains an array of size SIZE of the specified VALUETYPE...
Definition: accessor.hxx:940
vigra::writeHDF5
void writeHDF5(...)
Store array data in an HDF5 file.
vigra::HDF5File::getAttributeHandle
HDF5Handle getAttributeHandle(std::string dataset_name, std::string attribute_name)
Obtain the HDF5 handle of a attribute.
Definition: hdf5impex.hxx:978
vigra::HDF5File::getGroupHandle
HDF5Handle getGroupHandle(std::string group_name, std::string function_name="HDF5File::getGroupHandle()")
Obtain the HDF5 handle of a group.
Definition: hdf5impex.hxx:961
vigra::HDF5File::pwd
std::string pwd() const
Get the path of the current group.
Definition: hdf5impex.hxx:812
vigra::HDF5File::existsDataset
bool existsDataset(std::string datasetName)
Check if given datasetName exists.
Definition: hdf5impex.hxx:826
vigra::HDF5File::read
void read(std::string datasetName, MultiArrayView< N, T, Stride > array)
Read data into a multi array. If the first character of datasetName is a "/", the path will be interp...
Definition: hdf5impex.hxx:1364
vigra::HDF5File::write
void write(std::string datasetName, char data)
Write a single value. Specialization of the write function for simple datatypes.
Definition: hdf5impex.hxx:1335
vigra::HDF5File::writeAttribute
void writeAttribute(std::string object_name, std::string attribute_name, char data)
Write a single value. Specialization of the write function for simple datatypes.
Definition: hdf5impex.hxx:1026
vigra::HDF5File::writeAttribute
void writeAttribute(std::string object_name, std::string attribute_name, const MultiArrayView< N, T, Stride > &array)
Write MultiArray Attributes. In contrast to datasets, subarray access, chunks and compression are not...
Definition: hdf5impex.hxx:991
vigra::HDF5Handle::close
herr_t close()
Explicitly call the stored function (if one has been stored within this object) for the contained han...
Definition: hdf5impex.hxx:217
vigra::createCoupledIterator
CoupledIteratorType< N >::type createCoupledIterator(TinyVector< MultiArrayIndex, N > const &shape)
Definition: multi_iterator_coupled.hxx:1052
vigra::HDF5File::write
void write(std::string datasetName, const MultiArrayView< N, T, Stride > &array, int iChunkSize=0, int compression=0)
Write multi arrays.
Definition: hdf5impex.hxx:1171
impex.hxx
image import and export functions
vigra::MultiArrayView::isUnstrided
bool isUnstrided(unsigned int dimension=N-1) const
Definition: multi_array.hxx:1201
vigra::HDF5File::close
void close()
Close the current file.
Definition: hdf5impex.hxx:677
vigra::HDF5File::cd_up
bool cd_up()
Change the current group to its parent group. Returns true if successful, false otherwise. If unsuccessful, the group will not change.
Definition: hdf5impex.hxx:703
vigra::MultiArrayView
Base class for, and view to, vigra::MultiArray.
Definition: multi_array.hxx:655
vigra::HDF5File::getDatasetShape
ArrayVector< hsize_t > getDatasetShape(std::string datasetName)
Get the shape of each dimension of a certain dataset.
Definition: hdf5impex.hxx:866
vigra::ArrayVectorView::end
const_iterator end() const
Definition: array_vector.hxx:237
vigra::ArrayVectorView::data
const_pointer data() const
Definition: array_vector.hxx:209
vigra::HDF5ImportInfo::shape
ArrayVector< hsize_t > const & shape() const
Definition: hdf5impex.hxx:339
vigra::ArrayVectorView::size
size_type size() const
Definition: array_vector.hxx:330
vigra::CoupledScanOrderIterator
Iterate over multiple images simultaneously in scan order.
Definition: multi_iterator_coupled.hxx:526
vigra::MultiArrayView::subarray
MultiArrayView subarray(difference_type p, difference_type q) const
Definition: multi_array.hxx:1431
vigra::HDF5File::readBlock
void readBlock(std::string datasetName, typename MultiArrayShape< N >::type blockOffset, typename MultiArrayShape< N >::type blockShape, MultiArrayView< N, T, Stride > array)
Read a block of data into a multi array. This function allows to read a small block out of a larger v...
Definition: hdf5impex.hxx:1459
vigra::RGBValue
Class for a single RGB value.
Definition: accessor.hxx:938
vigra::ceil
int ceil(FixedPoint< IntBits, FracBits > v)
rounding up.
Definition: fixedpoint.hxx:675
vigra::reverse
TinyVector< V, SIZE > reverse(TinyVector< V, SIZE > const &t)
reversed copy
Definition: tinyvector.hxx:2037
vigra::HDF5File::HDF5File
HDF5File(int track_creation_times=0)
Default constructor.
Definition: hdf5impex.hxx:627
vigra::FFTWComplex
Wrapper class for the FFTW complex types &#39;fftw_complex&#39;.
Definition: fftw3.hxx:131
vigra::HDF5File::root
void root()
Change current group to "/".
Definition: hdf5impex.hxx:685
vigra::HDF5File::cd
void cd(std::string groupName)
Change the current group. Both absolute and relative group names are allowed.
Definition: hdf5impex.hxx:694
vigra::HDF5File
Access to HDF5 files.
Definition: hdf5impex.hxx:562
vigra::HDF5File::ls
std::vector< std::string > ls() const
List the contents of the current group. The function returns a vector of strings holding the entries ...
Definition: hdf5impex.hxx:782

© Ullrich Köthe (ullrich.koethe@iwr.uni-heidelberg.de) Heidelberg Collaboratory for Image Processing, University of Heidelberg, Germany | html generated using doxygen and Python vigra 1.10.0