kspaceFirstOrder3D-CUDA  1.1
The CUDA/C++ implementation of the k-wave toolbox for the time-domain simulation of acoustic wave fields in 3D
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HDF5_File.h
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1 /**
2  * @file HDF5_File.h
3  *
4  * @author Jiri Jaros \n
5  * Faculty of Information Technology \n
6  * Brno University of Technology \n
7  * jarosjir@fit.vutbr.cz
8  *
9  * @brief The header file containing the HDF5 related classes.
10  *
11  * @version kspaceFirstOrder3D 3.4
12  *
13  * @date 27 July 2012, 14:14 (created) \n
14  * 10 August 2016, 10:49 (revised)
15  *
16  *
17  * @section HDF HDF5 File Structure
18  *
19  * The CUDA/C++ code has been designed as a standalone application which is not dependent on MATLAB
20  * libraries or a MEX interface. This is of particular importance when using servers and
21  * supercomputers without MATLAB support. For this reason, simulation data must be transferred
22  * between the CUDA/C++ code and MATLAB using external input and output files. These files are
23  * stored using the Hierarchical Data Format HDF5 (http://www.hdfgroup.org/HDF5/). This is a data
24  * model, library, and file format for storing and managing data. It supports a variety of
25  * datatypes, and is designed for flexible and efficient I/O and for high volume and complex data.
26  * The HDF5 technology suite includes tools and applications for managing, manipulating, viewing,
27  * and analysing data in the HDF5 format.
28  *
29  *
30  * Each HDF5 file is a container for storing a variety of scientific data and is composed of two
31  * primary types of objects: groups and datasets. An HDF5 group is a structure containing zero or
32  * more HDF5 objects, together with supporting metadata. A HDF5 group can be seen as a disk folder.
33  * An HDF5 dataset is a multidimensional array of data elements, together with supporting metadata.
34  * A HDF5 dataset can be seen as a disk file. Any HDF5 group or dataset may also have an associated
35  * attribute list. An HDF5 attribute is a user-defined HDF5 structure that provides extra
36  * information about an HDF5 object. More information can be obtained from the HDF5 documentation
37  * (http://www.hdfgroup.org/HDF5/doc/index.html).
38  *
39  *
40  * kspaceFirstOrder3D-CUDA v1.1 introduces a new version of the HDF5 input and output file format.
41  * The code is happy to work with both versions (1.0 and 1.1), however when working with an input
42  * file of version 1.0, some features are not supported, namely the cuboid sensor mask, and
43  * u_non_staggered_raw. When running from within the actual MATLAB K-Wave Toolbox, the files will
44  * always be generated in version 1.1
45  *
46  * The HDF5 input file for the CUDA/C++ simulation code contains a file header with brief
47  * description of the simulation stored in string attributes, and the root group `/' which stores
48  * all the simulation properties in the form of 3D datasets (a complete list of input datasets is
49  * given bellow).
50  * The HDF5 checkpoint file contains the same file header as the input file and the root group `/'
51  * with a few datasets keeping the actual simulation state.
52  * The HDF5 output file contains a file header with the simulation description as well as
53  * performance statistics, such as the simulation time and memory consumption, stored in string
54  * attributes.
55 
56  * The results of the simulation are stored in the root group `/' in the form of 3D datasets. If the
57  * linear sensor mask is used, all output quantities are stored as datasets in the root group. If
58  * the cuboid corners sensor mask is used, the sampled quantities form private groups containing
59  * datasets on per cuboid basis.
60  *
61  *
62  * \verbatim
63 ==============================================================================================================
64  Input File/Checkpoint File Header
65 =============================================================================================================
66 created_by Short description of the tool that created this file
67 creation_date Date when the file was created
68 file_description Short description of the content of the file (e.g. simulation name)
69 file_type Type of the file (input)
70 major_version Major version of the file definition (1)
71 minor_version Minor version of the file definition (1)
72 ==============================================================================================================
73  \endverbatim
74  *
75  * \verbatim
76 ==============================================================================================================
77  Output File Header
78 ==============================================================================================================
79 created_by Short description of the tool that created this file
80 creation_date Date when the file was created
81 file_description Short description of the content of the file (e.g. simulation name)
82 file_type Type of the file (output)
83 major_version Major version of the file definition (1)
84 minor_version Minor version of the file definition (1)
85 -------------------------------------------------------------------------------------------------------------
86 host_names List of hosts (computer names) the simulation was executed on
87 number_of_cpu_cores Number of CPU cores used for the simulation
88 data_loading_phase_execution_time Time taken to load data from the file
89 pre-processing_phase_execution_time Time taken to pre-process data
90 simulation_phase_execution_time Time taken to run the simulation
91 post-processing_phase_execution_time Time taken to complete the post-processing phase
92 total_execution_time Total execution time
93 peak_core_memory_in_use Peak memory required per core during the simulation
94 total_memory_in_use Total Peak memory in use
95 ==============================================================================================================
96  \endverbatim
97  *
98  *
99  *
100  * The input and checkpoint file stores all quantities as three dimensional datasets with dimension
101  * sizes designed by <tt>(Nx, Ny, Nz)</tt>. In order to support scalars and 1D and 2D arrays, the
102  * unused dimensions are set to 1. For example, scalar variables are stored with a dimension size of
103  * <tt>(1,1,1)</tt>, 1D vectors oriented in y-direction are stored with a dimension size of
104  * <tt>(1, Ny, 1)</tt>, and so on. If the dataset stores a complex variable, the real and imaginary
105  * parts are stored in an interleaved layout and the lowest used dimension size is doubled (i.e.,
106  * Nx for a 3D matrix, Ny for a 1D vector oriented in the y-direction). The datasets are physically
107  * stored in row-major order (in contrast to column-major order used by MATLAB) using either the
108  * <tt>`H5T_IEEE_F32LE'</tt> data type for floating point datasets or <tt>`H5T_STD_U64LE'</tt> for
109  * integer based datasets. All the datasets are store under the root group.
110  *
111  *
112  * The output file of version 1.0 could only store recorded quantities as 3D datasets under the
113  * root group. However, with version 1.1 and the new cuboid corner sensor mask, the sampled
114  * quantities may be laid out as 4D quantities stored under specific groups. The dimensions are
115  * always <tt>(Nx, Ny, Nz, Nt)</tt>, every sampled cuboid is stored as a distinct dataset and the
116  * datasets are grouped under a group named by the quantity stored. This makes the file
117  * clearly readable and easy to parse.
118  *
119  *
120  * In order to enable compression and more efficient data processing, big datasets are not stored as
121  * monolithic blocks but broken into chunks that may be compressed by the ZIP library and stored
122  * separately. The chunk size is defined as follows:
123  *
124  * \li <tt> (1M elements, 1, 1) </tt> in the case of 1D variables - index sensor mask (8MB blocks).
125  * \li <tt> (Nx, Ny, 1) </tt> in the case of 3D variables (one 2D slab).
126  * \li <tt> (Nx, Ny, Nz, 1) </tt> in the case of 4D variables (one time step).
127  * \li <tt> (N_sensor_points, 1, 1) </tt> in the case of the output time series (one time step of
128  * the simulation).
129  *
130  *
131  * All datasets have two attributes that specify the content of the dataset. The \c `data_type'
132  * attribute specifies the data type of the dataset. The admissible values are either \c `float' or
133  * \c `long'. The \c `domain_type' attribute specifies the domain of the dataset. The admissible
134  * values are either \c `real' for the real domain or \c `complex' for the complex domain. The
135  * C++ code reads these attributes and checks their values.
136  *
137  *
138  *
139  * \verbatim
140 ==============================================================================================================
141  Input File Datasets
142 ==============================================================================================================
143 Name Size Data type Domain Type Condition of Presence
144 ==============================================================================================================
145  1. Simulation Flags
146 --------------------------------------------------------------------------------------------------------------
147  ux_source_flag (1, 1, 1) long real
148  uy_source_flag (1, 1, 1) long real
149  uz_source_flag (1, 1, 1) long real
150  p_source_flag (1, 1, 1) long real
151  p0_source_flag (1, 1, 1) long real
152  transducer_source_flag (1, 1, 1) long real
153  nonuniform_grid_flag (1, 1, 1) long real must be set to 0
154  nonlinear_flag (1, 1, 1) long real
155  absorbing_flag (1, 1, 1) long real
156 --------------------------------------------------------------------------------------------------------------
157  2. Grid Properties
158 --------------------------------------------------------------------------------------------------------------
159  Nx (1, 1, 1) long real
160  Ny (1, 1, 1) long real
161  Nz (1, 1, 1) long real
162  Nt (1, 1, 1) long real
163  dt (1, 1, 1) float real
164  dx (1, 1, 1) float real
165  dy (1, 1, 1) float real
166  dz (1, 1, 1) float real
167 --------------------------------------------------------------------------------------------------------------
168  3 Medium Properties
169 --------------------------------------------------------------------------------------------------------------
170  3.1 Regular Medium Properties
171  rho0 (Nx, Ny, Nz) float real heterogenous
172  (1, 1, 1) float real homogenous
173  rho0_sgx (Nx, Ny, Nz) float real heterogenous
174  (1, 1, 1) float real homogenous
175  rho0_sgy (Nx, Ny, Nz) float real heterogenous
176  (1, 1, 1) float real homogenous
177  rho0_sgz (Nx, Ny, Nz) float real heterogenous
178  (1, 1, 1) float real homogenous
179  c0 (Nx, Ny, Nz) float real heterogenous
180  (1, 1, 1) float real homogenous
181  c_ref (1, 1, 1) float real
182 
183  3.2 Nonlinear Medium Properties (defined if (nonlinear_flag == 1))
184  BonA (Nx, Ny, Nz) float real heterogenous
185  (1, 1, 1) float real homogenous
186 
187  3.3 Absorbing Medium Properties (defined if (absorbing_flag == 1))
188  alpha_coef (Nx, Ny, Nz) float real heterogenous
189  (1, 1, 1) float real homogenous
190  alpha_power (1, 1, 1) float real
191 --------------------------------------------------------------------------------------------------------------
192  4. Sensor Variables
193 --------------------------------------------------------------------------------------------------------------
194  sensor_mask_type (1, 1, 1) long real file version 1.1 (0 = index, 1 = corners)
195  sensor_mask_index (Nsens, 1, 1) long real file version 1.0 always, File version 1.1 if sensor_mask_type == 0
196  sensor_mask_corners (Ncubes, 6, 1) long real file version 1.1, if sensor_mask_type == 1
197 --------------------------------------------------------------------------------------------------------------
198  5 Source Properties
199 --------------------------------------------------------------------------------------------------------------
200  5.1 Velocity Source Terms (defined if (ux_source_flag == 1 || uy_source_flag == 1 || uz_source_flag == 1))
201  u_source_mode (1, 1, 1) long real
202  u_source_many (1, 1, 1) long real
203  u_source_index (Nsrc, 1, 1) long real
204  ux_source_input (1, Nt_src, 1) float real u_source_many == 0
205  (Nsrc, Nt_src, 1) float real u_source_many == 1
206  uy_source_input (1, Nt_src, 1) float real u_source_many == 0
207  (Nsrc, Nt_src, 1) float real u_source_many == 1
208  uz_source_input (1, Nt_src, 1) float real u_source_many == 0
209  (Nt_src, Nsrc, 1) float real u_source_many == 1
210 
211  5.2 Pressure Source Terms (defined if (p_source_flag == 1))
212  p_source_mode (1, 1, 1) long real
213  p_source_many (1, 1, 1) long real
214  p_source_index (Nsrc, 1, 1) long real
215  p_source_input (Nsrc, Nt_src, 1) float real p_source_many == 1
216  (1, Nt_src, 1) float real p_source_many == 0
217 
218  5.3 Transducer Source Terms (defined if (transducer_source_flag == 1))
219  u_source_index (Nsrc, 1, 1) long real
220  transducer_source_input (Nt_src, 1, 1) float real
221  delay_mask (Nsrc, 1, 1) float real
222 
223  5.4 IVP Source Terms (defined if ( p0_source_flag ==1))
224  p0_source_input (Nx, Ny, Nz) float real
225 --------------------------------------------------------------------------------------------------------------
226  6. K-space and Shift Variables
227 --------------------------------------------------------------------------------------------------------------
228  ddx_k_shift_pos_r (Nx/2 + 1, 1, 1) float complex
229  ddx_k_shift_neg_r (Nx/2 + 1, 1, 1) float complex
230  ddy_k_shift_pos (1, Ny, 1) float complex
231  ddy_k_shift_neg (1, Ny, 1) float complex
232  ddz_k_shift_pos (1, 1, Nz) float complex
233  ddz_k_shift_neg (1, 1, Nz) float complex
234  x_shift_neg_r (Nx/2 + 1, 1, 1) float complex file version 1.1
235  y_shift_neg_r (1, Ny/2 + 1, 1) float complex file version 1.1
236  z_shift_neg_r (1, 1, Nz/2) float complex file version 1.1
237 --------------------------------------------------------------------------------------------------------------
238  7. PML Variables
239 --------------------------------------------------------------------------------------------------------------
240  pml_x_size (1, 1, 1) long real
241  pml_y_size (1, 1, 1) long real
242  pml_z_size (1, 1, 1) long real
243  pml_x_alpha (1, 1, 1) float real
244  pml_y_alpha (1, 1, 1) float real
245  pml_z_alpha (1, 1, 1) float real
246 
247  pml_x (Nx, 1, 1) float real
248  pml_x_sgx (Nx, 1, 1) float real
249  pml_y (1, Ny, 1) float real
250  pml_y_sgy (1, Ny, 1) float real
251  pml_z (1, 1, Nz) float real
252  pml_z_sgz (1, 1, Nz) float real
253 ==============================================================================================================
254  \endverbatim
255 
256 \verbatim
257 ==============================================================================================================
258  Checkpoint File Datasets
259 ==============================================================================================================
260 Name Size Data type Domain Type Condition of Presence
261 ==============================================================================================================
262  1. Grid Properties
263 --------------------------------------------------------------------------------------------------------------
264  Nx (1, 1, 1) long real
265  Ny (1, 1, 1) long real
266  Nz (1, 1, 1) long real
267  Nt (1, 1, 1) long real
268  t_index (1, 1, 1) long real
269 --------------------------------------------------------------------------------------------------------------
270  2. Simulation State
271 --------------------------------------------------------------------------------------------------------------
272  p (Nx, Ny, Nz) float real
273  ux_sgx (Nx, Ny, Nz) float real
274  uy_sgy (Nx, Ny, Nz) float real
275  uz_sgz (Nx, Ny, Nz) float real
276  rhox (Nx, Ny, Nz) float real
277  rhoy (Nx, Ny, Nz) float real
278  rhoz (Nx, Ny, Nz) float real
279 --------------------------------------------------------------------------------------------------------------
280 \endverbatim
281 
282 
283  \verbatim
284 ==============================================================================================================
285  Output File Datasets
286 ==============================================================================================================
287 Name Size Data type Domain Type Condition of Presence
288 ==============================================================================================================
289  1. Simulation Flags
290 --------------------------------------------------------------------------------------------------------------
291  ux_source_flag (1, 1, 1) long real
292  uy_source_flag (1, 1, 1) long real
293  uz_source_flag (1, 1, 1) long real
294  p_source_flag (1, 1, 1) long real
295  p0_source_flag (1, 1, 1) long real
296  transducer_source_flag (1, 1, 1) long real
297  nonuniform_grid_flag (1, 1, 1) long real
298  nonlinear_flag (1, 1, 1) long real
299  absorbing_flag (1, 1, 1) long real
300  u_source_mode (1, 1, 1) long real if u_source
301  u_source_many (1, 1, 1) long real if u_source
302  p_source_mode (1, 1, 1) long real if p_source
303  p_source_many (1, 1, 1) long real if p_source
304 --------------------------------------------------------------------------------------------------------------
305  2. Grid Properties
306 --------------------------------------------------------------------------------------------------------------
307  Nx (1, 1, 1) long real
308  Ny (1, 1, 1) long real
309  Nz (1, 1, 1) long real
310  Nt (1, 1, 1) long real
311  dt (1, 1, 1) float real
312  dx (1, 1, 1) float real
313  dy (1, 1, 1) float real
314  dz (1, 1, 1) float real
315 -------------------------------------------------------------------------------------------------------------
316  3. PML Variables
317 --------------------------------------------------------------------------------------------------------------
318  pml_x_size (1, 1, 1) long real
319  pml_y_size (1, 1, 1) long real
320  pml_z_size (1, 1, 1) long real
321  pml_x_alpha (1, 1, 1) float real
322  pml_y_alpha (1, 1, 1) float real
323  pml_z_alpha (1, 1, 1) float real
324 
325  pml_x (Nx, 1, 1) float real
326  pml_x_sgx (Nx, 1, 1) float real
327  pml_y (1, Ny, 1) float real
328  pml_y_sgy (1, Ny, 1) float real
329  pml_z (1, 1, Nz) float real
330  pml_z_sgz (1, 1, Nz) float real
331 --------------------------------------------------------------------------------------------------------------
332  4. Sensor Variables (present if --copy_sensor_mask)
333 --------------------------------------------------------------------------------------------------------------
334  sensor_mask_type (1, 1, 1) long real file version 1.1 and --copy_sensor_mask
335  sensor_mask_index (Nsens, 1, 1) long real file version 1.1 and if sensor_mask_type == 0
336  sensor_mask_corners (Ncubes, 6, 1) long real file version 1.1 and if sensor_mask_type == 1
337 --------------------------------------------------------------------------------------------------------------
338  5a. Simulation Results: if sensor_mask_type == 0 (index), or File version == 1.0
339 --------------------------------------------------------------------------------------------------------------
340  p (Nsens, Nt - s, 1) float real -p or --p_raw
341  p_rms (Nsens, 1, 1) float real --p_rms
342  p_max (Nsens, 1, 1) float real --p_max
343  p_min (Nsens, 1, 1) float real --p_min
344  p_max_all (Nx, Ny, Nz) float real --p_max_all
345  p_min_all (Nx, Ny, Nz) float real --p_min_all
346  p_final (Nx, Ny, Nz) float real --p_final
347 
348 
349  ux (Nsens, Nt - s, 1) float real -u or --u_raw
350  uy (Nsens, Nt - s, 1) float real -u or --u_raw
351  uz (Nsens, Nt - s, 1) float real -u or --u_raw
352 
353  ux_non_staggered (Nsens, Nt - s, 1) float real --u_non_staggered_raw (File version ==1.1)
354  uy_non_staggered (Nsens, Nt - s, 1) float real --u_non_staggered_raw (File version ==1.1)
355  uz_non_staggered (Nsens, Nt - s, 1) float real --u_non_staggered_raw (File version ==1.1)
356 
357  ux_rms (Nsens, 1, 1) float real --u_rms
358  uy_rms (Nsens, 1, 1) float real --u_rms
359  uz_rms (Nsens, 1, 1) float real --u_rms
360 
361  ux_max (Nsens, 1, 1) float real --u_max
362  uy_max (Nsens, 1, 1) float real --u_max
363  uz_max (Nsens, 1, 1) float real --u_max
364 
365  ux_min (Nsens, 1, 1) float real --u_min
366  uy_min (Nsens, 1, 1) float real --u_min
367  uz_min (Nsens, 1, 1) float real --u_min
368 
369  ux_max_all (Nx, Ny, Nz) float real --u_max_all
370  uy_max_all (Nx, Ny, Nz) float real --u_max_all
371  uz_max_all (Nx, Ny, Nz) float real --u_max_all
372 
373  ux_min_all (Nx, Ny, Nz) float real --u_min_all
374  uy_min_all (Nx, Ny, Nz) float real --u_min_all
375  uz_min_all (Nx, Ny, Nz) float real --u_min_all
376 
377  ux_final (Nx, Ny, Nz) float real --u_final
378  uy_final (Nx, Ny, Nz) float real --u_final
379  uz_final (Nx, Ny, Nz) float real --u_final
380 --------------------------------------------------------------------------------------------------------------
381  5b. Simulation Results: if sensor_mask_type == 1 (corners) and file version == 1.1
382 --------------------------------------------------------------------------------------------------------------
383  /p group of datasets, one per cuboid -p or --p_raw
384  /p/1 (Cx, Cy, Cz, Nt-s) float real 1st sampled cuboid
385  /p/2 (Cx, Cy, Cz, Nt-s) float real 2nd sampled cuboid, etc.
386 
387  /p_rms group of datasets, one per cuboid --p_rms
388  /p_rms/1 (Cx, Cy, Cz, Nt-s) float real 1st sampled cuboid
389 
390  /p_max group of datasets, one per cuboid --p_max
391  /p_max/1 (Cx, Cy, Cz, Nt-s) float real 1st sampled cuboid
392 
393  /p_min group of datasets, one per cuboid --p_min
394  /p_min/1 (Cx, Cy, Cz, Nt-s) float real 1st sampled cuboid
395 
396  p_max_all (Nx, Ny, Nz) float real --p_max_all
397  p_min_all (Nx, Ny, Nz) float real --p_min_all
398  p_final (Nx, Ny, Nz) float real --p_final
399 
400 
401  /ux group of datasets, one per cuboid -u or --u_raw
402  /ux/1 (Cx, Cy, Cz, Nt-s) float real 1st sampled cuboid
403  /uy group of datasets, one per cuboid -u or --u_raw
404  /uy/1 (Cx, Cy, Cz, Nt-s) float real 1st sampled cuboid
405  /uz group of datasets, one per cuboid -u or --u_raw
406  /uz/1 (Cx, Cy, Cz, Nt-s) float real 1st sampled cuboid
407 
408  /ux_non_staggered group of datasets, one per cuboid --u_non_staggered_raw
409  /ux_non_staggered/1 (Cx, Cy, Cz, Nt-s) float real 1st sampled cuboid
410  /uy_non_staggered group of datasets, one per cuboid --u_non_staggered_raw
411  /uy_non_staggered/1 (Cx, Cy, Cz, Nt-s) float real 1st sampled cuboid
412  /uz_non_staggered group of datasets, one per cuboid --u_non_staggered_raw
413  /uz_non_staggered/1 (Cx, Cy, Cz, Nt-s) float real 1st sampled cuboid
414 
415  /ux_rms group of datasets, one per cuboid --u_rms
416  /ux_rms/1 (Cx, Cy, Cz, Nt-s) float real 1st sampled cuboid
417  /uy_rms group of datasets, one per cuboid --u_rms
418  /uy_rms/1 (Cx, Cy, Cz, Nt-s) float real 1st sampled cuboid
419  /uz_rms group of datasets, one per cuboid --u_rms
420  /uy_rms/1 (Cx, Cy, Cz, Nt-s) float real 1st sampled cuboid
421 
422  /ux_max group of datasets, one per cuboid --u_max
423  /ux_max/1 (Cx, Cy, Cz, Nt-s) float real 1st sampled cuboid
424  /uy_max group of datasets, one per cuboid --u_max
425  /ux_max/1 (Cx, Cy, Cz, Nt-s) float real 1st sampled cuboid
426  /uz_max group of datasets, one per cuboid --u_max
427  /ux_max/1 (Cx, Cy, Cz, Nt-s) float real 1st sampled cuboid
428 
429  /ux_min group of datasets, one per cuboid --u_min
430  /ux_min/1 (Cx, Cy, Cz, Nt-s) float real 1st sampled cuboid
431  /uy_min group of datasets, one per cuboid --u_min
432  /ux_min/1 (Cx, Cy, Cz, Nt-s) float real 1st sampled cuboid
433  /uz_min group of datasets, one per cuboid --u_min
434  /ux_min/1 (Cx, Cy, Cz, Nt-s) float real 1st sampled cuboid
435 
436  ux_max_all (Nx, Ny, Nz) float real --u_max_all
437  uy_max_all (Nx, Ny, Nz) float real --u_max_all
438  uz_max_all (Nx, Ny, Nz) float real --u_max_all
439 
440  ux_min_all (Nx, Ny, Nz) float real --u_min_all
441  uy_min_all (Nx, Ny, Nz) float real --u_min_all
442  uz_min_all (Nx, Ny, Nz) float real --u_min_all
443 
444  ux_final (Nx, Ny, Nz) float real --u_final
445  uy_final (Nx, Ny, Nz) float real --u_final
446  uz_final (Nx, Ny, Nz) float real --u_final
447 ==============================================================================================================
448 \endverbatim
449  *
450  *
451  *
452  * @section License
453  * This file is part of the C++ extension of the k-Wave Toolbox
454  * (http://www.k-wave.org).\n Copyright (C) 2016 Jiri Jaros and Bradley Treeby.
455  *
456  * This file is part of the k-Wave. k-Wave is free software: you can redistribute it and/or modify
457  * it under the terms of the GNU Lesser General Public License as published by the Free Software
458  * Foundation, either version 3 of the License, or (at your option) any later version.
459  *
460  * k-Wave is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even
461  * the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser
462  * General Public License for more details.
463  *
464  * You should have received a copy of the GNU Lesser General Public License along with k-Wave.
465  * If not, see http://www.gnu.org/licenses/.
466  */
467 
468 #ifndef THDF5_FILE_H
469 #define THDF5_FILE_H
470 
471 
472 #include <hdf5.h>
473 #include <hdf5_hl.h>
474 #include <cstring>
475 #include <map>
476 
477 // Linux build
478 #ifdef __linux__
479  #include <unistd.h>
480 #endif
481 // Windows build
482 #ifdef _WIN64
483  #include <io.h>
484 #endif
485 
486 #include <Utils/DimensionSizes.h>
487 #include <Utils/MatrixNames.h>
488 
489 
490 // Class with File header
491 class THDF5_FileHeader;
492 
493 /**
494  * @class THDF5_File
495  * @brief Class wrapping the HDF5 routines.
496  * @details This class is responsible for working with HDF5 files. It offers routines to manage
497  * files (create, open, close) as well as creating, reading and modifying the contents
498  * (groups and datasets).
499  */
501 {
502  public:
503 
504  /**
505  * @enum TMatrixDataType
506  * @brief HDF5 matrix data type (float or uint64).
507  * @details HDF5 matrix data type (float or uint64).
508  */
510  {
511  FLOAT = 0,
512  LONG = 1
513  };
514 
515  /**
516  * @enum TMatrixDomainType
517  * @brief HDF5 Matrix domain type (real or complex).
518  * @details HDF5 Matrix domain type (real or complex).
519  */
521  {
522  REAL = 0,
523  COMPLEX = 1
524  };
525 
526 
527  /// Constructor of the class.
528  THDF5_File();
529  /// Destructor.
530  virtual ~THDF5_File();
531 
532  //----------------------- Basic file operations --------------------------//
533  /// Create a file.
534  void Create(const std::string& fileName,
535  unsigned int flags = H5F_ACC_TRUNC);
536 
537  /// Open a file.
538  void Open(const std::string& fileName,
539  unsigned int flags = H5F_ACC_RDONLY);
540  /**
541  * @brief Is the file opened?
542  * @details Is the file opened?
543  * @return true if the file is opened.
544  */
545  bool IsOpen() const {return file != H5I_BADID;};
546 
547  /**
548  * @brief Does the file exist?
549  * @details Check if the file exist.
550  * @param [in] fileName
551  * @return true if the file exists.
552  */
553  static bool IsHDF5(const std::string& fileName);
554 
555  /// Close file.
556  void Close();
557 
558  //----------------------------------- Group manipulators -------------------------------------//
559  /// Create a HDF5 group at a specified place in the file tree.
560  hid_t CreateGroup(const hid_t parentGroup,
561  TMatrixName& groupName);
562  /// Open a HDF5 group at a specified place in the file tree.
563  hid_t OpenGroup(const hid_t parentGroup,
564  TMatrixName& groupName);
565  /// Close group.
566  void CloseGroup(const hid_t group);
567 
568  /**
569  * @brief Get handle to the root group.
570  * @details Get handle to the root group.
571  * @return handle to the root group
572  */
573  hid_t GetRootGroup() const {return file;};
574 
575 
576  //---------------------------------- Dataset manipulators -------------------------------------//
577  /// Open the HDF5 dataset at a specified place in the file tree.
578  hid_t OpenDataset(const hid_t parentGroup,
579  TMatrixName& datasetName);
580 
581  /// Create a float HDF5 dataset at a specified place in the file tree (3D/4D).
582  hid_t CreateFloatDataset(const hid_t parentGroup,
583  TMatrixName& datasetName,
584  const TDimensionSizes& dimensionSizes,
585  const TDimensionSizes& chunkSizes,
586  const size_t compressionLevel);
587 
588  /// Create an index HDF5 dataset at a specified place in the file tree (3D only).
589  hid_t CreateIndexDataset(const hid_t parentGroup,
590  TMatrixName& datasetName,
591  const TDimensionSizes& dimensionSizes,
592  const TDimensionSizes& chunkSizes,
593  const size_t compressionLevel);
594 
595  /// Close the HDF5 dataset.
596  void CloseDataset (const hid_t dataset);
597 
598 
599  //----------------------------- Dataset Read/Write operations --------------------------------//
600  /// Write a hyper-slab into the dataset - float dataset.
601  void WriteHyperSlab(const hid_t dataset,
602  const TDimensionSizes& position,
603  const TDimensionSizes& size,
604  const float* data);
605  /// Write a hyper-slab into the dataset - long dataset.
606  void WriteHyperSlab(const hid_t dataset,
607  const TDimensionSizes& position,
608  const TDimensionSizes& size,
609  const size_t* data);
610 
611  /// Write a cuboid selected within the matrixData into a hyperslab.
612  void WriteCuboidToHyperSlab(const hid_t dataset,
613  const TDimensionSizes& hyperslabPosition,
614  const TDimensionSizes& cuboidPosition,
615  const TDimensionSizes& cuboidSize,
616  const TDimensionSizes& matrixDimensions,
617  const float* mMatrixData);
618 
619  /// Write sensor data selected by the sensor mask - Occasionally very slow, do not use!
620  void WriteDataByMaskToHyperSlab(const hid_t dataset,
621  const TDimensionSizes& hyperslabPosition,
622  const size_t indexSensorSize,
623  const size_t* indexSensorData,
624  const TDimensionSizes& matrixDimensions,
625  const float* matrixData);
626 
627  /// Write the scalar value under a specified group, float value.
628  void WriteScalarValue(const hid_t parentGroup,
629  TMatrixName& datasetName,
630  const float value);
631  /// Write the scalar value under a specified group, index value.
632  void WriteScalarValue(const hid_t parentGroup,
633  TMatrixName& datasetName,
634  const size_t value);
635 
636  /// Read the scalar value under a specified group, float value.
637  void ReadScalarValue(const hid_t parentGroup,
638  TMatrixName& datasetName,
639  float& value);
640  /// Read the scalar value under a specified group, index value.
641  void ReadScalarValue(const hid_t parentGroup,
642  TMatrixName& datasetName,
643  size_t& value);
644 
645  /// Read data from the dataset under a specified group, float dataset.
646  void ReadCompleteDataset(const hid_t parentGroup,
647  TMatrixName& datasetName,
648  const TDimensionSizes& dimensionSizes,
649  float* data);
650  /// Read data from the dataset under a specified group, index dataset.
651  void ReadCompleteDataset(const hid_t parentGroup,
652  TMatrixName& datasetName,
653  const TDimensionSizes& dimensionSizes,
654  size_t* data);
655 
656  //---------------------------- Attributes Read/Write operations ------------------------------//
657 
658  /// Get dimension sizes of the dataset under a specified group.
659  TDimensionSizes GetDatasetDimensionSizes(const hid_t parentGroup,
660  TMatrixName& datasetName);
661 
662  /// Get number of dimensions of the dataset under a specified group.
663  size_t GetDatasetNumberOfDimensions(const hid_t parentGroup,
664  TMatrixName& datasetName);
665 
666  /// Get dataset element count under a specified group.
667  size_t GetDatasetElementCount(const hid_t parentGroup,
668  TMatrixName& datasetName);
669 
670 
671  /// Write matrix data type into the dataset under a specified group.
672  void WriteMatrixDataType (const hid_t parentGroup,
673  TMatrixName& datasetName,
674  const TMatrixDataType& matrixDataType);
675  /// Write matrix domain type into the dataset under the root group.
676  void WriteMatrixDomainType(const hid_t parentGroup,
677  TMatrixName& datasetName,
678  const TMatrixDomainType& matrixDomainType);
679 
680  /// Read matrix data type from the dataset.
681  THDF5_File::TMatrixDataType ReadMatrixDataType(const hid_t parentGroup,
682  TMatrixName& datasetName);
683  /// Read matrix domain type from the dataset under a specified group.
684  THDF5_File::TMatrixDomainType ReadMatrixDomainType(const hid_t parentGroup,
685  TMatrixName& datasetName);
686 
687 
688  /// Write string attribute into the dataset under the root group.
689  void WriteStringAttribute(const hid_t parentGroup,
690  TMatrixName& datasetName,
691  TMatrixName& attributeName,
692  const std::string& value);
693  /// Read string attribute from the dataset under the root group.
694  std::string ReadStringAttribute(const hid_t parentGroup,
695  TMatrixName& datasetName,
696  TMatrixName& attributeName);
697 
698  protected:
699 
700  /// Copy constructor is not allowed for public.
701  THDF5_File(const THDF5_File& src);
702  /// Operator = is not allowed for public.
703  THDF5_File& operator= (const THDF5_File& src);
704 
705  private:
706  /// String representation of the Domain type in the HDF5 file.
707  static const std::string matrixDomainTypeName;
708  /// String representation of the Data type in the HDF5 file.
709  static const std::string matrixDataTypeName;
710 
711  /// String representation of different domain types.
712  static const std::string matrixDomainTypeNames[];
713  /// String representation of different data types.
714  static const std::string matrixDataTypeNames[];
715 
716  /// HDF file handle.
717  hid_t file;
718  /// File name.
719  std::string fileName;
720 }; // THDF5_File
721 //--------------------------------------------------------------------------------------------------
722 
723 
724 /**
725  * @class THDF5_FileHeader
726  * @brief Class for HDF5 header.
727  * @details This class manages all information that can be stored in the input output or checkpoint
728  * file header.
729  */
731 {
732  public:
733 
734  /**
735  * @enum TFileHeaderItems
736  * @brief List of all header items.
737  * @details List of all header items.
738  * @todo In the future we should add number of GPUs, peak GPU memory.
739  */
741  {
742  CREATED_BY = 0,
743  CREATION_DATA = 1,
744  FILE_DESCRIPTION = 2,
745  MAJOR_VERSION = 3,
746  MINOR_VERSION = 4,
747  FILE_TYPE = 5,
748  HOST_NAME = 6,
749  TOTAL_MEMORY_CONSUMPTION = 7,
750  PEAK_CORE_MEMORY_CONSUMPTION = 8,
751  TOTAL_EXECUTION_TIME = 9,
752  DATA_LOAD_TIME = 10,
753  PREPROCESSING_TIME = 11,
754  SIMULATION_TIME = 12,
755  POST_PROCESSING_TIME = 13,
756  NUMBER_OF_CORES = 14
757  };
758 
759  /**
760  * @enum TFileType
761  * @brief HDF5 file type.
762  * @details HDF5 file type.
763  */
765  {
766  INPUT = 0,
767  OUTPUT = 1,
768  CHECKPOINT = 2,
769  UNKNOWN = 3
770  };
771 
772  /**
773  * @enum TFileVersion
774  * @brief HDF5 file version.
775  * @details HDF5 file version.
776  */
778  {
779  VERSION_10 = 0,
780  VERSION_11 = 1,
781  VERSION_UNKNOWN = 2
782  };
783 
784  /// Constructor.
786  /// Copy constructor.
788  /// Destructor.
790 
791  /// Read header from the input file.
792  void ReadHeaderFromInputFile(THDF5_File& inputFile);
793  /// Read Header from output file (necessary for checkpoint-restart).
794  void ReadHeaderFromOutputFile(THDF5_File& outputFile);
795  /// Read Header from checkpoint file (necessary for checkpoint-restart).
796  void ReadHeaderFromCheckpointFile(THDF5_File& checkpointFile);
797 
798  /// Write header to the output file
799  void WriteHeaderToOutputFile(THDF5_File& outputFile);
800  /// Write header to the output file
801  void WriteHeaderToCheckpointFile(THDF5_File& checkpointFile);
802 
803  /**
804  * @brief Set code name.
805  * @details Set code name to the header.
806  * @param [in] codeName - code version
807  */
808  void SetCodeName(const std::string& codeName)
809  {
810  headerValues[CREATED_BY] = codeName;
811  };
812 
813  /// Set creation time.
814  void SetActualCreationTime();
815 
816  /**
817  * @brief Get string version of current Major version.
818  * @details Get string version of current Major version.
819  * @return Current major version
820  */
821  static std::string GetCurrentHDF5_MajorVersion()
822  {
823  return hdf5_MajorFileVersionsNames[0];
824  };
825 
826  /**
827  * @brief Get string version of current Minor version.
828  * @details Get string version of current Minor version.
829  * @return Current minor version
830  */
831  static std::string GetCurrentHDF5_MinorVersion()
832  {
833  return hdf5_MinorFileVersionsNames[1];
834  };
835 
836  /**
837  * @brief Set major file version.
838  * @details Set major file version.
839  */
841  {
842  headerValues[MAJOR_VERSION] = GetCurrentHDF5_MajorVersion();
843  };
844 
845  /**
846  * @brief Set minor file version.
847  * @details Set minor file version.
848  */
850  {
851  headerValues[MINOR_VERSION] = GetCurrentHDF5_MinorVersion();
852  };
853 
854  /// Set major file version in a string.
856 
857  /**
858  * @brief Check major file version.
859  * @details Check major file version.
860  * @return true if ok
861  */
863  {
864  return (headerValues[MAJOR_VERSION] == GetCurrentHDF5_MajorVersion());
865  };
866 
867  /**
868  * @brief Check minor file version.
869  * @details Check minor file version.
870  * @return true if ok
871  */
873  {
874  return (headerValues[MINOR_VERSION] <= GetCurrentHDF5_MinorVersion());
875  };
876 
877 
878  /// Get File type.
880  /// Set file type.
881  void SetFileType(const THDF5_FileHeader::TFileType fileType);
882 
883  /// Set host name.
884  void SetHostName();
885  /// Set memory consumption.
886  void SetMemoryConsumption(const size_t totalMemory);
887  /// Set execution times.
888  void SetExecutionTimes(const double totalTime,
889  const double loadTime,
890  const double preProcessingTime,
891  const double simulationTime,
892  const double postprocessingTime);
893 
894  /// Get execution times stored in the output file header.
895  void GetExecutionTimes(double& totalTime,
896  double& loadTime,
897  double& preProcessingTime,
898  double& simulationTime,
899  double& postprocessingTime);
900  /// Set number of cores.
901  void SetNumberOfCores();
902 
903 private:
904  /// Populate the map with the header items.
905  void PopulateHeaderFileMap();
906 
907  /// map for the header values.
908  std::map<TFileHeaderItems, std::string> headerValues;
909  /// map for the header names.
910  std::map<TFileHeaderItems, std::string> headerNames;
911 
912  ///String representation of different file types.
913  static const std::string hdf5_FileTypesNames[];
914  /// String representations of Major file versions.
915  static const std::string hdf5_MajorFileVersionsNames[];
916  /// String representations of Major file versions.
917  static const std::string hdf5_MinorFileVersionsNames[];
918 
919 };// THDF5_FileHeader
920 //--------------------------------------------------------------------------------------------------
921 
922 #endif /* THDF5_FILE_H */
Class for HDF5 header.
Definition: HDF5_File.h:730
size_t GetDatasetNumberOfDimensions(const hid_t parentGroup, TMatrixName &datasetName)
Get number of dimensions of the dataset under a specified group.
Definition: HDF5_File.cpp:982
hid_t CreateFloatDataset(const hid_t parentGroup, TMatrixName &datasetName, const TDimensionSizes &dimensionSizes, const TDimensionSizes &chunkSizes, const size_t compressionLevel)
Create a float HDF5 dataset at a specified place in the file tree (3D/4D).
Definition: HDF5_File.cpp:296
void WriteMatrixDomainType(const hid_t parentGroup, TMatrixName &datasetName, const TMatrixDomainType &matrixDomainType)
Write matrix domain type into the dataset under the root group.
Definition: HDF5_File.cpp:1048
std::string ReadStringAttribute(const hid_t parentGroup, TMatrixName &datasetName, TMatrixName &attributeName)
Read string attribute from the dataset under the root group.
Definition: HDF5_File.cpp:1163
TMatrixDataType
HDF5 matrix data type (float or uint64).
Definition: HDF5_File.h:509
void SetFileType(const THDF5_FileHeader::TFileType fileType)
Set file type.
Definition: HDF5_File.cpp:1491
void SetMinorFileVersion()
Set minor file version.
Definition: HDF5_File.h:849
THDF5_FileHeader()
Constructor.
Definition: HDF5_File.cpp:1205
static const std::string hdf5_MajorFileVersionsNames[]
String representations of Major file versions.
Definition: HDF5_File.h:915
static const std::string matrixDomainTypeName
String representation of the Domain type in the HDF5 file.
Definition: HDF5_File.h:707
void SetMajorFileVersion()
Set major file version.
Definition: HDF5_File.h:840
void Open(const std::string &fileName, unsigned int flags=H5F_ACC_RDONLY)
Open a file.
Definition: HDF5_File.cpp:127
void GetExecutionTimes(double &totalTime, double &loadTime, double &preProcessingTime, double &simulationTime, double &postprocessingTime)
Get execution times stored in the output file header.
Definition: HDF5_File.cpp:1575
TMatrixDomainType
HDF5 Matrix domain type (real or complex).
Definition: HDF5_File.h:520
TFileHeaderItems
List of all header items.
Definition: HDF5_File.h:740
static std::string GetCurrentHDF5_MinorVersion()
Get string version of current Minor version.
Definition: HDF5_File.h:831
std::map< TFileHeaderItems, std::string > headerNames
map for the header names.
Definition: HDF5_File.h:910
static const std::string hdf5_FileTypesNames[]
String representation of different file types.
Definition: HDF5_File.h:913
void SetExecutionTimes(const double totalTime, const double loadTime, const double preProcessingTime, const double simulationTime, const double postprocessingTime)
Set execution times.
Definition: HDF5_File.cpp:1552
hid_t CreateGroup(const hid_t parentGroup, TMatrixName &groupName)
Create a HDF5 group at a specified place in the file tree.
Definition: HDF5_File.cpp:208
THDF5_File::TMatrixDataType ReadMatrixDataType(const hid_t parentGroup, TMatrixName &datasetName)
Read matrix data type from the dataset.
Definition: HDF5_File.cpp:1068
void WriteScalarValue(const hid_t parentGroup, TMatrixName &datasetName, const float value)
Write the scalar value under a specified group, float value.
Definition: HDF5_File.cpp:748
void Close()
Close file.
Definition: HDF5_File.cpp:175
void WriteCuboidToHyperSlab(const hid_t dataset, const TDimensionSizes &hyperslabPosition, const TDimensionSizes &cuboidPosition, const TDimensionSizes &cuboidSize, const TDimensionSizes &matrixDimensions, const float *mMatrixData)
Write a cuboid selected within the matrixData into a hyperslab.
Definition: HDF5_File.cpp:618
void SetCodeName(const std::string &codeName)
Set code name.
Definition: HDF5_File.h:808
bool IsOpen() const
Is the file opened?
Definition: HDF5_File.h:545
void PopulateHeaderFileMap()
Populate the map with the header items.
Definition: HDF5_File.cpp:1609
hid_t file
HDF file handle.
Definition: HDF5_File.h:717
const std::string TMatrixName
Datatype for matrix names.
Definition: MatrixNames.h:45
void ReadHeaderFromCheckpointFile(THDF5_File &checkpointFile)
Read Header from checkpoint file (necessary for checkpoint-restart).
Definition: HDF5_File.cpp:1336
void WriteHeaderToCheckpointFile(THDF5_File &checkpointFile)
Write header to the output file.
Definition: HDF5_File.cpp:1386
TDimensionSizes GetDatasetDimensionSizes(const hid_t parentGroup, TMatrixName &datasetName)
Get dimension sizes of the dataset under a specified group.
Definition: HDF5_File.cpp:949
static std::string GetCurrentHDF5_MajorVersion()
Get string version of current Major version.
Definition: HDF5_File.h:821
void WriteHeaderToOutputFile(THDF5_File &outputFile)
Write header to the output file.
Definition: HDF5_File.cpp:1369
void WriteMatrixDataType(const hid_t parentGroup, TMatrixName &datasetName, const TMatrixDataType &matrixDataType)
Write matrix data type into the dataset under a specified group.
Definition: HDF5_File.cpp:1029
void ReadHeaderFromOutputFile(THDF5_File &outputFile)
Read Header from output file (necessary for checkpoint-restart).
Definition: HDF5_File.cpp:1290
THDF5_File()
Constructor of the class.
Definition: HDF5_File.cpp:82
void SetHostName()
Set host name.
Definition: HDF5_File.cpp:1503
void ReadScalarValue(const hid_t parentGroup, TMatrixName &datasetName, float &value)
Read the scalar value under a specified group, float value.
Definition: HDF5_File.cpp:855
static const std::string matrixDataTypeNames[]
String representation of different data types.
Definition: HDF5_File.h:714
void ReadHeaderFromInputFile(THDF5_File &inputFile)
Read header from the input file.
Definition: HDF5_File.cpp:1241
void WriteStringAttribute(const hid_t parentGroup, TMatrixName &datasetName, TMatrixName &attributeName, const std::string &value)
Write string attribute into the dataset under the root group.
Definition: HDF5_File.cpp:1135
static const std::string hdf5_MinorFileVersionsNames[]
String representations of Major file versions.
Definition: HDF5_File.h:917
static bool IsHDF5(const std::string &fileName)
Does the file exist?
Definition: HDF5_File.cpp:158
hid_t GetRootGroup() const
Get handle to the root group.
Definition: HDF5_File.h:573
TFileVersion
HDF5 file version.
Definition: HDF5_File.h:777
The header file storing names of all variables/matrices/output streams used in the simulation...
~THDF5_FileHeader()
Destructor.
Definition: HDF5_File.cpp:1227
TFileType
HDF5 file type.
Definition: HDF5_File.h:764
The header file containing the structure with 3D dimension sizes.
static const std::string matrixDomainTypeNames[]
String representation of different domain types.
Definition: HDF5_File.h:712
void Create(const std::string &fileName, unsigned int flags=H5F_ACC_TRUNC)
Create a file.
Definition: HDF5_File.cpp:97
void WriteDataByMaskToHyperSlab(const hid_t dataset, const TDimensionSizes &hyperslabPosition, const size_t indexSensorSize, const size_t *indexSensorData, const TDimensionSizes &matrixDimensions, const float *matrixData)
Write sensor data selected by the sensor mask - Occasionally very slow, do not use! ...
Definition: HDF5_File.cpp:686
void SetActualCreationTime()
Set creation time.
Definition: HDF5_File.cpp:1429
bool CheckMajorFileVersion()
Check major file version.
Definition: HDF5_File.h:862
bool CheckMinorFileVersion()
Check minor file version.
Definition: HDF5_File.h:872
THDF5_FileHeader::TFileType GetFileType()
Get File type.
Definition: HDF5_File.cpp:1472
TFileVersion GetFileVersion()
Set major file version in a string.
Definition: HDF5_File.cpp:1447
hid_t CreateIndexDataset(const hid_t parentGroup, TMatrixName &datasetName, const TDimensionSizes &dimensionSizes, const TDimensionSizes &chunkSizes, const size_t compressionLevel)
Create an index HDF5 dataset at a specified place in the file tree (3D only).
Definition: HDF5_File.cpp:392
void SetNumberOfCores()
Set number of cores.
Definition: HDF5_File.cpp:1593
THDF5_File::TMatrixDomainType ReadMatrixDomainType(const hid_t parentGroup, TMatrixName &datasetName)
Read matrix domain type from the dataset under a specified group.
Definition: HDF5_File.cpp:1101
void WriteHyperSlab(const hid_t dataset, const TDimensionSizes &position, const TDimensionSizes &size, const float *data)
Write a hyper-slab into the dataset - float dataset.
Definition: HDF5_File.cpp:473
static const std::string matrixDataTypeName
String representation of the Data type in the HDF5 file.
Definition: HDF5_File.h:709
hid_t OpenGroup(const hid_t parentGroup, TMatrixName &groupName)
Open a HDF5 group at a specified place in the file tree.
Definition: HDF5_File.cpp:232
void CloseGroup(const hid_t group)
Close group.
Definition: HDF5_File.cpp:254
virtual ~THDF5_File()
Destructor.
Definition: HDF5_File.cpp:193
THDF5_File & operator=(const THDF5_File &src)
Operator = is not allowed for public.
size_t GetDatasetElementCount(const hid_t parentGroup, TMatrixName &datasetName)
Get dataset element count under a specified group.
Definition: HDF5_File.cpp:1006
void ReadCompleteDataset(const hid_t parentGroup, TMatrixName &datasetName, const TDimensionSizes &dimensionSizes, float *data)
Read data from the dataset under a specified group, float dataset.
Definition: HDF5_File.cpp:887
std::string fileName
File name.
Definition: HDF5_File.h:719
void CloseDataset(const hid_t dataset)
Close the HDF5 dataset.
Definition: HDF5_File.cpp:457
Class wrapping the HDF5 routines.
Definition: HDF5_File.h:500
std::map< TFileHeaderItems, std::string > headerValues
map for the header values.
Definition: HDF5_File.h:908
Structure with 4D dimension sizes (3 in space and 1 in time).
void SetMemoryConsumption(const size_t totalMemory)
Set memory consumption.
Definition: HDF5_File.cpp:1531
hid_t OpenDataset(const hid_t parentGroup, TMatrixName &datasetName)
Open the HDF5 dataset at a specified place in the file tree.
Definition: HDF5_File.cpp:268