File: IHDF5DateTimeReader.java

package info (click to toggle)
libsis-jhdf5-java 19.04.0%2Bdfsg-4
  • links: PTS, VCS
  • area: main
  • in suites: bullseye
  • size: 8,668 kB
  • sloc: java: 79,644; ansic: 18,986; sh: 309; makefile: 49; xml: 12
file content (439 lines) | stat: -rw-r--r-- 21,895 bytes parent folder | download | duplicates (2)
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
/*
 * Copyright 2007 - 2018 ETH Zuerich, CISD and SIS.
 *
 * Licensed under the Apache License, Version 2.0 (the "License");
 * you may not use this file except in compliance with the License.
 * You may obtain a copy of the License at
 *
 *      http://www.apache.org/licenses/LICENSE-2.0
 *
 * Unless required by applicable law or agreed to in writing, software
 * distributed under the License is distributed on an "AS IS" BASIS,
 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 * See the License for the specific language governing permissions and
 * limitations under the License.
 */

package ch.systemsx.cisd.hdf5;

import java.util.Date;

import hdf.hdf5lib.exceptions.HDF5JavaException;

import ch.systemsx.cisd.base.mdarray.MDArray;
import ch.systemsx.cisd.base.mdarray.MDLongArray;

/**
 * An interface that provides methods for reading time and date values from HDF5 files.
 * <p>
 * Obtain an object implementing this interface by calling {@link IHDF5Reader#time()}.
 *
 * @author Bernd Rinn
 */
public interface IHDF5DateTimeReader
{

    // /////////////////////
    // Attributes
    // /////////////////////

    /**
     * Returns <code>true</code>, if the attribute <var>attributeName</var> of data set
     * <var>objectPath</var> is a time stamp and <code>false</code> otherwise.
     */
    public boolean isTimeStamp(String objectPath, String attributeName) throws HDF5JavaException;

    /**
     * Reads a time stamp attribute named <var>attributeName</var> from the data set
     * <var>objectPath</var>.
     * 
     * @param objectPath The name (including path information) of the data set object in the file.
     * @param attributeName The name of the attribute to read.
     * @return The time stamp as number of milliseconds since January 1, 1970, 00:00:00 GMT.
     * @throws HDF5JavaException If the attribute <var>attributeName</var> of objct
     *             <var>objectPath</var> is not defined as type variant
     *             {@link HDF5DataTypeVariant#TIMESTAMP_MILLISECONDS_SINCE_START_OF_THE_EPOCH}.
     */
    public long getAttrAsLong(String objectPath, String attributeName);

    /**
     * Reads a time stamp array attribute named <var>attributeName</var> from the data set
     * <var>objectPath</var>.
     * 
     * @param objectPath The name (including path information) of the data set object in the file.
     * @param attributeName The name of the attribute to read.
     * @return The time stamp array; each element is a number of milliseconds since January 1, 1970,
     *         00:00:00 GMT.
     * @throws HDF5JavaException If the attribute <var>attributeName</var> of objct
     *             <var>objectPath</var> is not defined as type variant
     *             {@link HDF5DataTypeVariant#TIMESTAMP_MILLISECONDS_SINCE_START_OF_THE_EPOCH}.
     */
    public long[] getArrayAttrAsLong(String objectPath, String attributeName);

    /**
     * Reads a multi-dimension time stamp array attribute named <var>attributeName</var> from the
     * data set <var>objectPath</var>.
     * 
     * @param objectPath The name (including path information) of the data set object in the file.
     * @param attributeName The name of the attribute to read.
     * @return The time stamp array; each element is a number of milliseconds since January 1, 1970,
     *         00:00:00 GMT.
     * @throws HDF5JavaException If the attribute <var>attributeName</var> of objct
     *             <var>objectPath</var> is not defined as type variant
     *             {@link HDF5DataTypeVariant#TIMESTAMP_MILLISECONDS_SINCE_START_OF_THE_EPOCH}.
     */
    public MDLongArray getMDArrayAttrAsLong(String objectPath, String attributeName);

    /**
     * Reads a time stamp attribute named <var>attributeName</var> from the data set
     * <var>objectPath</var> and returns it as a <code>Date</code>.
     * 
     * @param objectPath The name (including path information) of the data set object in the file.
     * @param attributeName The name of the attribute to read.
     * @return The time stamp as {@link java.util.Date}.
     * @throws HDF5JavaException If the attribute <var>attributeName</var> of objct
     *             <var>objectPath</var> is not defined as type variant
     *             {@link HDF5DataTypeVariant#TIMESTAMP_MILLISECONDS_SINCE_START_OF_THE_EPOCH}.
     */
    public Date getAttr(String objectPath, String attributeName);

    /**
     * Reads a time stamp array attribute named <var>attributeName</var> from the data set
     * <var>objectPath</var> and returns it as a <code>Date[]</code>.
     * 
     * @param objectPath The name (including path information) of the data set object in the file.
     * @param attributeName The name of the attribute to read.
     * @return The time stamp as {@link java.util.Date}.
     * @throws HDF5JavaException If the attribute <var>attributeName</var> of objct
     *             <var>objectPath</var> is not defined as type variant
     *             {@link HDF5DataTypeVariant#TIMESTAMP_MILLISECONDS_SINCE_START_OF_THE_EPOCH}.
     */
    public Date[] getArrayAttr(String objectPath, String attributeName);

    /**
     * Reads a multi-dimension time stamp array attribute named <var>attributeName</var> from the
     * data set <var>objectPath</var>.
     * 
     * @param objectPath The name (including path information) of the data set object in the file.
     * @param attributeName The name of the attribute to read.
     * @return The time stamp as {@link java.util.Date}.
     * @throws HDF5JavaException If the attribute <var>attributeName</var> of objct
     *             <var>objectPath</var> is not defined as type variant
     *             {@link HDF5DataTypeVariant#TIMESTAMP_MILLISECONDS_SINCE_START_OF_THE_EPOCH}.
     */
    public MDArray<Date> getMDArrayAttr(String objectPath, String attributeName);

    // /////////////////////
    // Data Sets
    // /////////////////////

    /**
     * Returns <code>true</code>, if the data set given by <var>objectPath</var> is a time stamp and
     * <code>false</code> otherwise.
     */
    public boolean isTimeStamp(String objectPath) throws HDF5JavaException;

    /**
     * Reads a time stamp value from the data set <var>objectPath</var>. The time stamp is stored as
     * a <code>long</code> value in the HDF5 file. It needs to be tagged as type variant
     * {@link HDF5DataTypeVariant#TIMESTAMP_MILLISECONDS_SINCE_START_OF_THE_EPOCH}.
     * <p>
     * This tagging is done by the writer when using
     * {@link IHDF5Writer#writeTimeDuration(String, HDF5TimeDuration)} or can be done by calling
     * {@link IHDF5ObjectReadWriteInfoProviderHandler#setTypeVariant(String, HDF5DataTypeVariant)},
     * most conveniently by code like
     * 
     * <pre>
     * writer.addTypeVariant(&quot;/dataSetPath&quot;, HDF5TimeUnit.SECONDS.getTypeVariant());
     * </pre>
     * 
     * @param objectPath The name (including path information) of the data set object in the file.
     * @return The time stamp as number of milliseconds since January 1, 1970, 00:00:00 GMT.
     * @throws HDF5JavaException If the <var>objectPath</var> is not defined as type variant
     *             {@link HDF5DataTypeVariant#TIMESTAMP_MILLISECONDS_SINCE_START_OF_THE_EPOCH}.
     */
    public long readTimeStamp(String objectPath) throws HDF5JavaException;

    /**
     * Reads a time stamp array from the data set <var>objectPath</var>. The time stamp is stored as
     * a <code>long</code> value in the HDF5 file. It needs to be tagged as type variant
     * {@link HDF5DataTypeVariant#TIMESTAMP_MILLISECONDS_SINCE_START_OF_THE_EPOCH}.
     * <p>
     * This tagging is done by the writer when using
     * {@link IHDF5Writer#writeTimeDuration(String, HDF5TimeDuration)} or can be done by calling
     * {@link IHDF5ObjectReadWriteInfoProviderHandler#setTypeVariant(String, HDF5DataTypeVariant)},
     * most conveniently by code like
     * 
     * <pre>
     * writer.addTypeVariant(&quot;/dataSetPath&quot;, HDF5TimeUnit.SECONDS.getTypeVariant());
     * </pre>
     * 
     * @param objectPath The name (including path information) of the data set object in the file.
     * @return The time stamp as number of milliseconds since January 1, 1970, 00:00:00 GMT.
     * @throws HDF5JavaException If the <var>objectPath</var> is not defined as type variant
     *             {@link HDF5DataTypeVariant#TIMESTAMP_MILLISECONDS_SINCE_START_OF_THE_EPOCH}.
     */
    public long[] readTimeStampArray(String objectPath) throws HDF5JavaException;

    /**
     * Reads a block of a time stamp array (of rank 1) from the data set <var>objectPath</var>. The
     * time stamp is stored as a <code>long</code> value in the HDF5 file. It needs to be tagged as
     * type variant {@link HDF5DataTypeVariant#TIMESTAMP_MILLISECONDS_SINCE_START_OF_THE_EPOCH}.
     * <p>
     * This tagging is done by the writer when using
     * {@link IHDF5Writer#writeTimeDuration(String, HDF5TimeDuration)} or can be done by calling
     * {@link IHDF5ObjectReadWriteInfoProviderHandler#setTypeVariant(String, HDF5DataTypeVariant)},
     * most conveniently by code like
     * 
     * <pre>
     * writer.addTypeVariant(&quot;/dataSetPath&quot;, HDF5TimeUnit.SECONDS.getTypeVariant());
     * </pre>
     * 
     * @param objectPath The name (including path information) of the data set object in the file.
     * @param blockSize The block size (this will be the length of the <code>long[]</code> returned
     *            if the data set is long enough).
     * @param blockNumber The number of the block to read (starting with 0, offset: multiply with
     *            <var>blockSize</var>).
     * @return The data read from the data set. The length will be min(size - blockSize*blockNumber,
     *         blockSize).
     */
    public long[] readTimeStampArrayBlock(String objectPath, int blockSize, long blockNumber);

    /**
     * Reads a block of a time stamp array (of rank 1) from the data set <var>objectPath</var>. The
     * time stamp is stored as a <code>long</code> value in the HDF5 file. It needs to be tagged as
     * type variant {@link HDF5DataTypeVariant#TIMESTAMP_MILLISECONDS_SINCE_START_OF_THE_EPOCH}.
     * <p>
     * This tagging is done by the writer when using
     * {@link IHDF5Writer#writeTimeDuration(String, HDF5TimeDuration)} or can be done by calling
     * {@link IHDF5ObjectReadWriteInfoProviderHandler#setTypeVariant(String, HDF5DataTypeVariant)},
     * most conveniently by code like
     * 
     * <pre>
     * writer.addTypeVariant(&quot;/dataSetPath&quot;, HDF5TimeUnit.SECONDS.getTypeVariant());
     * </pre>
     * 
     * @param objectPath The name (including path information) of the data set object in the file.
     * @param blockSize The block size (this will be the length of the <code>long[]</code>
     *            returned).
     * @param offset The offset of the block in the data set to start reading from (starting with
     *            0).
     * @return The data block read from the data set.
     */
    public long[] readTimeStampArrayBlockWithOffset(String objectPath, int blockSize, long offset);

    /**
     * Provides all natural blocks of this one-dimensional data set of time stamps to iterate over.
     * 
     * @see HDF5DataBlock
     * @throws HDF5JavaException If the data set is not of rank 1.
     */
    public Iterable<HDF5DataBlock<long[]>> getTimeStampArrayNaturalBlocks(String dataSetPath)
            throws HDF5JavaException;

    /**
     * Reads a time stamp value from the data set <var>objectPath</var> and returns it as a
     * {@link Date}. The time stamp is stored as a <code>long</code> value in the HDF5 file. It
     * needs to be tagged as type variant
     * {@link HDF5DataTypeVariant#TIMESTAMP_MILLISECONDS_SINCE_START_OF_THE_EPOCH}.
     * <p>
     * This tagging is done by the writer when using
     * {@link IHDF5Writer#writeTimeDuration(String, HDF5TimeDuration)} or can be done by calling
     * {@link IHDF5ObjectReadWriteInfoProviderHandler#setTypeVariant(String, HDF5DataTypeVariant)},
     * most conveniently by code like
     * 
     * <pre>
     * writer.addTypeVariant(&quot;/dataSetPath&quot;, HDF5TimeUnit.SECONDS.getTypeVariant());
     * </pre>
     * 
     * @param objectPath The name (including path information) of the data set object in the file.
     * @return The time stamp as {@link Date}.
     * @throws HDF5JavaException If the <var>objectPath</var> does not denote a time stamp.
     */
    public Date readDate(String objectPath) throws HDF5JavaException;

    /**
     * Reads a time stamp array (of rank 1) from the data set <var>objectPath</var> and returns it
     * as an array of {@link Date}s. The time stamp array is stored as a an array of
     * <code>long</code> values in the HDF5 file. It needs to be tagged as type variant
     * {@link HDF5DataTypeVariant#TIMESTAMP_MILLISECONDS_SINCE_START_OF_THE_EPOCH}.
     * <p>
     * This tagging is done by the writer when using
     * {@link IHDF5Writer#writeTimeDuration(String, HDF5TimeDuration)} or can be done by calling
     * {@link IHDF5ObjectReadWriteInfoProviderHandler#setTypeVariant(String, HDF5DataTypeVariant)},
     * most conveniently by code like
     * 
     * <pre>
     * writer.addTypeVariant(&quot;/dataSetPath&quot;, HDF5TimeUnit.SECONDS.getTypeVariant());
     * </pre>
     * 
     * @param objectPath The name (including path information) of the data set object in the file.
     * @return The time stamp as {@link Date}.
     * @throws HDF5JavaException If the <var>objectPath</var> does not denote a time stamp.
     */
    public Date[] readDateArray(String objectPath) throws HDF5JavaException;

    /**
     * Reads a block of a {@link Date} array (of rank 1) from the data set <var>objectPath</var>.
     * The time stamp is stored as a <code>long</code> value in the HDF5 file. It needs to be tagged
     * as type variant {@link HDF5DataTypeVariant#TIMESTAMP_MILLISECONDS_SINCE_START_OF_THE_EPOCH}.
     * <p>
     * This tagging is done by the writer when using
     * {@link IHDF5Writer#writeTimeDuration(String, HDF5TimeDuration)} or can be done by calling
     * {@link IHDF5ObjectReadWriteInfoProviderHandler#setTypeVariant(String, HDF5DataTypeVariant)},
     * most conveniently by code like
     * 
     * <pre>
     * writer.addTypeVariant(&quot;/dataSetPath&quot;, HDF5TimeUnit.SECONDS.getTypeVariant());
     * </pre>
     * 
     * @param objectPath The name (including path information) of the data set object in the file.
     * @param blockSize The block size (this will be the length of the <code>long[]</code> returned
     *            if the data set is long enough).
     * @param blockNumber The number of the block to read (starting with 0, offset: multiply with
     *            <var>blockSize</var>).
     * @return The data read from the data set. The length will be min(size - blockSize*blockNumber,
     *         blockSize).
     */
    public Date[] readDateArrayBlock(String objectPath, int blockSize, long blockNumber);

    /**
     * Reads a block of a {@link Date} array (of rank 1) from the data set <var>objectPath</var>.
     * The time stamp is stored as a <code>long</code> value in the HDF5 file. It needs to be tagged
     * as type variant {@link HDF5DataTypeVariant#TIMESTAMP_MILLISECONDS_SINCE_START_OF_THE_EPOCH}.
     * <p>
     * This tagging is done by the writer when using
     * {@link IHDF5Writer#writeTimeDuration(String, HDF5TimeDuration)} or can be done by calling
     * {@link IHDF5ObjectReadWriteInfoProviderHandler#setTypeVariant(String, HDF5DataTypeVariant)},
     * most conveniently by code like
     * 
     * <pre>
     * writer.addTypeVariant(&quot;/dataSetPath&quot;, HDF5TimeUnit.SECONDS.getTypeVariant());
     * </pre>
     * 
     * @param objectPath The name (including path information) of the data set object in the file.
     * @param blockSize The block size (this will be the length of the <code>long[]</code>
     *            returned).
     * @param offset The offset of the block in the data set to start reading from (starting with
     *            0).
     * @return The data block read from the data set.
     */
    public Date[] readDateArrayBlockWithOffset(String objectPath, int blockSize, long offset);

    /**
     * Provides all natural blocks of this one-dimensional data set of {@link Date}s to iterate
     * over.
     * 
     * @see HDF5DataBlock
     * @throws HDF5JavaException If the data set is not of rank 1.
     */
    public Iterable<HDF5DataBlock<Date[]>> getDateArrayNaturalBlocks(String dataSetPath)
            throws HDF5JavaException;

    /**
     * Reads a multi-dimensional array of time stamps from the data set <var>objectPath</var>.
     * 
     * @param objectPath The name (including path information) of the data set object in the file.
     * @return The data read from the data set.
     * @throws HDF5JavaException If the <var>objectPath</var> is not tagged as a type variant that
     *             corresponds to a time duration.
     */
    public MDLongArray readTimeStampMDArray(String objectPath);

    /**
     * Reads a multi-dimensional array of time stamps from the data set <var>objectPath</var>.
     * 
     * @param objectPath The name (including path information) of the data set object in the file.
     * @param blockDimensions The extent of the block in each dimension.
     * @param blockNumber The block number in each dimension (offset: multiply with the
     *            <var>blockDimensions</var> in the according dimension).
     * @return The data block read from the data set.
     */
    public MDLongArray readTimeStampMDArrayBlock(String objectPath, int[] blockDimensions,
            long[] blockNumber);

    /**
     * Reads a multi-dimensional array of time stamps from the data set <var>objectPath</var>.
     * 
     * @param objectPath The name (including path information) of the data set object in the file.
     * @param blockDimensions The extent of the block in each dimension.
     * @param offset The offset in the data set to start reading from in each dimension.
     * @return The data block read from the data set.
     */
    public MDLongArray readTimeStampMDArrayBlockWithOffset(String objectPath,
            int[] blockDimensions, long[] offset);

    /**
     * Reads a multi-dimensional array data set <var>objectPath</var> of type time stamp into a
     * given <var>array</var> in memory.
     * 
     * @param objectPath The name (including path information) of the data set object in the file.
     * @param array The array to read the data into.
     * @param memoryOffset The offset in the array to write the data to.
     * @return The effective dimensions of the block in <var>array</var> that was filled.
     */
    public int[] readToMDArrayWithOffset(String objectPath, MDLongArray array, int[] memoryOffset);

    /**
     * Reads a block of the multi-dimensional array data set <var>objectPath</var> of type time
     * stamp into a given <var>array</var> in memory.
     * 
     * @param objectPath The name (including path information) of the data set object in the file.
     * @param array The array to read the data into.
     * @param blockDimensions The size of the block to read along each axis.
     * @param offset The offset of the block in the data set.
     * @param memoryOffset The offset of the block in the array to write the data to.
     * @return The effective dimensions of the block in <var>array</var> that was filled.
     */
    public int[] readToMDArrayBlockWithOffset(String objectPath, MDLongArray array,
            int[] blockDimensions, long[] offset, int[] memoryOffset);

    /**
     * Provides all natural blocks of this multi-dimensional data set to iterate over.
     * 
     * @see HDF5MDDataBlock
     */
    public Iterable<HDF5MDDataBlock<MDLongArray>> getTimeStampMDArrayNaturalBlocks(
            String dataSetPath);

    /**
     * Reads a multi-dimensional array of {@link Date}s from the data set <var>objectPath</var>.
     * 
     * @param objectPath The name (including path information) of the data set object in the file.
     * @return The data read from the data set.
     * @throws HDF5JavaException If the <var>objectPath</var> is not tagged as a type variant that
     *             corresponds to a time duration.
     */
    public MDArray<Date> readDateMDArray(String objectPath);

    /**
     * Reads a multi-dimensional array of {@link Date}s from the data set <var>objectPath</var>.
     * 
     * @param objectPath The name (including path information) of the data set object in the file.
     * @param blockDimensions The extent of the block in each dimension.
     * @param blockNumber The block number in each dimension (offset: multiply with the
     *            <var>blockDimensions</var> in the according dimension).
     * @return The data block read from the data set.
     */
    public MDArray<Date> readDateMDArrayBlock(String objectPath, int[] blockDimensions,
            long[] blockNumber);

    /**
     * Reads a multi-dimensional array of {@link Date}s from the data set <var>objectPath</var>.
     * 
     * @param objectPath The name (including path information) of the data set object in the file.
     * @param blockDimensions The extent of the block in each dimension.
     * @param offset The offset in the data set to start reading from in each dimension.
     * @return The data block read from the data set.
     */
    public MDArray<Date> readDateMDArrayBlockWithOffset(String objectPath, int[] blockDimensions,
            long[] offset);

    /**
     * Provides all natural blocks of this multi-dimensional data set to iterate over.
     * 
     * @see HDF5MDDataBlock
     */
    public Iterable<HDF5MDDataBlock<MDArray<Date>>> getDateMDArrayNaturalBlocks(String dataSetPath);

}