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
|
/*
* 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 static ch.systemsx.cisd.hdf5.HDF5Utils.OPAQUE_PREFIX;
import static ch.systemsx.cisd.hdf5.HDF5Utils.createDataTypePath;
import static hdf.hdf5lib.H5.H5Dwrite;
import static hdf.hdf5lib.HDF5Constants.H5P_DEFAULT;
import static hdf.hdf5lib.HDF5Constants.H5S_ALL;
import ch.systemsx.cisd.hdf5.cleanup.ICallableWithCleanUp;
import ch.systemsx.cisd.hdf5.cleanup.ICleanUpRegistry;
/**
* Implementation of {@link IHDF5OpaqueWriter}.
*
* @author Bernd Rinn
*/
public class HDF5OpaqueWriter extends HDF5OpaqueReader implements IHDF5OpaqueWriter
{
private final HDF5BaseWriter baseWriter;
HDF5OpaqueWriter(HDF5BaseWriter baseWriter)
{
super(baseWriter);
assert baseWriter != null;
this.baseWriter = baseWriter;
}
@Override
public void writeArray(final String objectPath, final String tag, final byte[] data)
{
writeArray(objectPath, tag, data,
HDF5GenericStorageFeatures.GENERIC_NO_COMPRESSION);
}
@Override
public void writeArray(final String objectPath, final String tag, final byte[] data,
final HDF5GenericStorageFeatures features)
{
assert objectPath != null;
assert tag != null;
assert data != null;
baseWriter.checkOpen();
final ICallableWithCleanUp<Void> writeRunnable = new ICallableWithCleanUp<Void>()
{
@Override
public Void call(ICleanUpRegistry registry)
{
final long dataTypeId = getOrCreateOpaqueTypeId(tag);
final long dataSetId =
baseWriter.getOrCreateDataSetId(objectPath, dataTypeId, new long[]
{ data.length }, 1, features, registry);
H5Dwrite(dataSetId, dataTypeId, H5S_ALL, H5S_ALL, H5P_DEFAULT, data);
return null; // Nothing to return.
}
};
baseWriter.runner.call(writeRunnable);
}
@Override
public HDF5OpaqueType createArray(String objectPath, String tag, int size)
{
return createArray(objectPath, tag, size,
HDF5GenericStorageFeatures.GENERIC_NO_COMPRESSION);
}
@Override
public HDF5OpaqueType createArray(final String objectPath, final String tag,
final long size, final int blockSize)
{
return createArray(objectPath, tag, size, blockSize,
HDF5GenericStorageFeatures.GENERIC_NO_COMPRESSION);
}
@Override
public HDF5OpaqueType createArray(final String objectPath, final String tag,
final int size, final HDF5GenericStorageFeatures features)
{
assert objectPath != null;
assert tag != null;
assert size >= 0;
baseWriter.checkOpen();
final long dataTypeId = getOrCreateOpaqueTypeId(tag);
final ICallableWithCleanUp<Void> createRunnable = new ICallableWithCleanUp<Void>()
{
@Override
public Void call(ICleanUpRegistry registry)
{
if (features.requiresChunking())
{
baseWriter.createDataSet(objectPath, dataTypeId, features, new long[]
{ 0 }, new long[]
{ size }, 1, registry);
} else
{
baseWriter.createDataSet(objectPath, dataTypeId, features, new long[]
{ size }, null, 1, registry);
}
return null; // Nothing to return.
}
};
baseWriter.runner.call(createRunnable);
return new HDF5OpaqueType(baseWriter.fileId, dataTypeId, tag, baseWriter);
}
@Override
public HDF5OpaqueType createArray(final String objectPath, final String tag,
final long size, final int blockSize, final HDF5GenericStorageFeatures features)
{
assert objectPath != null;
assert tag != null;
assert size >= 0;
assert blockSize >= 0 && (blockSize <= size || size == 0);
baseWriter.checkOpen();
final long dataTypeId = getOrCreateOpaqueTypeId(tag);
final ICallableWithCleanUp<Void> createRunnable = new ICallableWithCleanUp<Void>()
{
@Override
public Void call(ICleanUpRegistry registry)
{
baseWriter.createDataSet(objectPath, dataTypeId, features, new long[]
{ size }, new long[]
{ blockSize }, 1, registry);
return null; // Nothing to return.
}
};
baseWriter.runner.call(createRunnable);
return new HDF5OpaqueType(baseWriter.fileId, dataTypeId, tag, baseWriter);
}
@Override
public void writeArrayBlock(final String objectPath, final HDF5OpaqueType dataType,
final byte[] data, final long blockNumber)
{
assert objectPath != null;
assert dataType != null;
assert data != null;
baseWriter.checkOpen();
dataType.check(baseWriter.fileId);
final ICallableWithCleanUp<Void> writeRunnable = new ICallableWithCleanUp<Void>()
{
@Override
public Void call(ICleanUpRegistry registry)
{
final long[] blockDimensions = new long[]
{ data.length };
final long[] slabStartOrNull = new long[]
{ data.length * blockNumber };
final long dataSetId =
baseWriter.h5.openAndExtendDataSet(baseWriter.fileId, objectPath,
baseWriter.fileFormat, new long[]
{ data.length * (blockNumber + 1) }, false, registry);
final long dataSpaceId =
baseWriter.h5.getDataSpaceForDataSet(dataSetId, registry);
baseWriter.h5.setHyperslabBlock(dataSpaceId, slabStartOrNull, blockDimensions);
final long memorySpaceId =
baseWriter.h5.createSimpleDataSpace(blockDimensions, registry);
H5Dwrite(dataSetId, dataType.getNativeTypeId(), memorySpaceId, dataSpaceId,
H5P_DEFAULT, data);
return null; // Nothing to return.
}
};
baseWriter.runner.call(writeRunnable);
}
@Override
public void writeArrayBlockWithOffset(final String objectPath,
final HDF5OpaqueType dataType, final byte[] data, final int dataSize, final long offset)
{
assert objectPath != null;
assert dataType != null;
assert data != null;
baseWriter.checkOpen();
dataType.check(baseWriter.fileId);
final ICallableWithCleanUp<Void> writeRunnable = new ICallableWithCleanUp<Void>()
{
@Override
public Void call(ICleanUpRegistry registry)
{
final long[] blockDimensions = new long[]
{ dataSize };
final long[] slabStartOrNull = new long[]
{ offset };
final long dataSetId =
baseWriter.h5.openAndExtendDataSet(baseWriter.fileId, objectPath,
baseWriter.fileFormat, new long[]
{ offset + dataSize }, false, registry);
final long dataSpaceId =
baseWriter.h5.getDataSpaceForDataSet(dataSetId, registry);
baseWriter.h5.setHyperslabBlock(dataSpaceId, slabStartOrNull, blockDimensions);
final long memorySpaceId =
baseWriter.h5.createSimpleDataSpace(blockDimensions, registry);
H5Dwrite(dataSetId, dataType.getNativeTypeId(), memorySpaceId, dataSpaceId,
H5P_DEFAULT, data);
return null; // Nothing to return.
}
};
baseWriter.runner.call(writeRunnable);
}
private long getOrCreateOpaqueTypeId(final String tag)
{
final String dataTypePath =
createDataTypePath(OPAQUE_PREFIX, baseWriter.houseKeepingNameSuffix, tag);
long dataTypeId = baseWriter.getDataTypeId(dataTypePath);
if (dataTypeId < 0)
{
dataTypeId = baseWriter.h5.createDataTypeOpaque(1, tag, baseWriter.fileRegistry);
baseWriter.commitDataType(dataTypePath, dataTypeId);
}
return dataTypeId;
}
}
|
