1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 481
|
/*
* 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.BitSet;
import java.util.Date;
import java.util.List;
import hdf.hdf5lib.exceptions.HDF5JavaException;
/**
* A class for writing HDF5 files (HDF5 1.6.x or HDF5 1.8.x).
* <p>
* The class focuses on ease of use instead of completeness. As a consequence not all valid HDF5
* files can be generated using this class, but only a subset.
* <p>
* Usage:
*
* <pre>
* float[] f = new float[100];
* ...
* HDF5Writer writer = new HDF5WriterConfig("test.h5").writer();
* writer.writeFloatArray("/some/path/dataset", f);
* writer.addAttribute("some key", "some value");
* writer.close();
* </pre>
*
* @author Bernd Rinn
*/
final class HDF5Writer extends HDF5Reader implements IHDF5Writer
{
private final HDF5BaseWriter baseWriter;
private final IHDF5FileLevelReadWriteHandler fileHandler;
private final IHDF5ObjectReadWriteInfoProviderHandler objectHandler;
private final IHDF5ByteWriter byteWriter;
private final IHDF5ByteWriter ubyteWriter;
private final IHDF5ShortWriter shortWriter;
private final IHDF5ShortWriter ushortWriter;
private final IHDF5IntWriter intWriter;
private final IHDF5IntWriter uintWriter;
private final IHDF5LongWriter longWriter;
private final IHDF5LongWriter ulongWriter;
private final IHDF5FloatWriter floatWriter;
private final IHDF5DoubleWriter doubleWriter;
private final IHDF5BooleanWriter booleanWriter;
private final IHDF5StringWriter stringWriter;
private final IHDF5EnumWriter enumWriter;
private final IHDF5CompoundWriter compoundWriter;
private final IHDF5DateTimeWriter dateTimeWriter;
private final HDF5TimeDurationWriter timeDurationWriter;
private final IHDF5ReferenceWriter referenceWriter;
private final IHDF5OpaqueWriter opaqueWriter;
HDF5Writer(HDF5BaseWriter baseWriter)
{
super(baseWriter);
this.baseWriter = baseWriter;
// Ensure the finalizer of this HDF5Writer doesn't close the file behind the back of the
// specialized writers when they are still in operation.
baseWriter.setMyReader(this);
this.fileHandler = new HDF5FileLevelReadWriteHandler(baseWriter);
this.objectHandler = new HDF5ObjectReadWriteInfoProviderHandler(baseWriter);
this.byteWriter = new HDF5ByteWriter(baseWriter);
this.ubyteWriter = new HDF5UnsignedByteWriter(baseWriter);
this.shortWriter = new HDF5ShortWriter(baseWriter);
this.ushortWriter = new HDF5UnsignedShortWriter(baseWriter);
this.intWriter = new HDF5IntWriter(baseWriter);
this.uintWriter = new HDF5UnsignedIntWriter(baseWriter);
this.longWriter = new HDF5LongWriter(baseWriter);
this.ulongWriter = new HDF5UnsignedLongWriter(baseWriter);
this.floatWriter = new HDF5FloatWriter(baseWriter);
this.doubleWriter = new HDF5DoubleWriter(baseWriter);
this.booleanWriter = new HDF5BooleanWriter(baseWriter);
this.stringWriter = new HDF5StringWriter(baseWriter);
this.enumWriter = new HDF5EnumWriter(baseWriter);
this.compoundWriter = new HDF5CompoundWriter(baseWriter, enumWriter);
this.dateTimeWriter = new HDF5DateTimeWriter(baseWriter, (HDF5LongReader) longReader);
this.timeDurationWriter =
new HDF5TimeDurationWriter(baseWriter, (HDF5LongReader) longReader);
this.referenceWriter = new HDF5ReferenceWriter(baseWriter);
this.opaqueWriter = new HDF5OpaqueWriter(baseWriter);
}
HDF5BaseWriter getBaseWriter()
{
return baseWriter;
}
// /////////////////////
// File
// /////////////////////
@Override
public IHDF5FileLevelReadWriteHandler file()
{
return fileHandler;
}
// /////////////////////////////////
// Objects, links, groups and types
// /////////////////////////////////
@Override
public IHDF5ObjectReadWriteInfoProviderHandler object()
{
return objectHandler;
}
@Override
public boolean exists(String objectPath)
{
return objectHandler.exists(objectPath);
}
@Override
public boolean isGroup(String objectPath)
{
return objectHandler.isGroup(objectPath);
}
@Override
public void delete(String objectPath)
{
objectHandler.delete(objectPath);
}
@Override
public HDF5DataSetInformation getDataSetInformation(String dataSetPath)
{
return objectHandler.getDataSetInformation(dataSetPath);
}
@Override
public List<String> getGroupMembers(String groupPath)
{
return objectHandler.getGroupMembers(groupPath);
}
// /////////////////////////////
// Data Set Reading and Writing
// /////////////////////////////
//
// Boolean
//
@Override
public IHDF5BooleanWriter bool()
{
return booleanWriter;
}
@Override
public void writeBitField(String objectPath, BitSet data)
{
booleanWriter.writeBitField(objectPath, data);
}
@Override
public void writeBoolean(String objectPath, boolean value)
{
booleanWriter.write(objectPath, value);
}
//
// Opaque
//
@Override
public IHDF5OpaqueWriter opaque()
{
return opaqueWriter;
}
//
// Date
//
@Override
public IHDF5DateTimeWriter time()
{
return dateTimeWriter;
}
@Override
public IHDF5TimeDurationWriter duration()
{
return timeDurationWriter;
}
@Override
public void writeDate(String objectPath, Date date)
{
dateTimeWriter.write(objectPath, date);
}
@Override
public void writeDateArray(String objectPath, Date[] dates)
{
dateTimeWriter.writeArray(objectPath, dates);
}
//
// Duration
//
@Override
public void writeTimeDuration(String objectPath, HDF5TimeDuration timeDuration)
{
timeDurationWriter.write(objectPath, timeDuration);
}
@Override
public void writeTimeDurationArray(String objectPath, HDF5TimeDurationArray timeDurations)
{
timeDurationWriter.writeArray(objectPath, timeDurations);
}
//
// References
//
@Override
public IHDF5ReferenceWriter reference()
{
return referenceWriter;
}
//
// String
//
@Override
public IHDF5StringWriter string()
{
return stringWriter;
}
@Override
public void writeString(String objectPath, String data)
{
stringWriter.write(objectPath, data);
}
@Override
public void writeStringArray(String objectPath, String[] data)
{
stringWriter.writeArray(objectPath, data);
}
//
// Enum
//
@Override
public IHDF5EnumWriter enumeration()
{
return enumWriter;
}
@Override
public <T extends Enum<T>> void writeEnum(String objectPath, Enum<T> value)
throws HDF5JavaException
{
enumWriter.write(objectPath, value);
}
@Override
public <T extends Enum<T>> void writeEnumArray(String objectPath, Enum<T>[] data)
{
enumWriter.writeArray(objectPath, enumWriter.newAnonArray(data));
}
@Override
public void writeEnumArray(String objectPath, String[] options, String[] data)
{
enumWriter.writeArray(objectPath, enumWriter.newAnonArray(options, data));
}
//
// Compound
//
@Override
public IHDF5CompoundWriter compound()
{
return compoundWriter;
}
@Override
public <T> void writeCompound(String objectPath, T data)
{
compoundWriter.write(objectPath, data);
}
@Override
public <T> void writeCompoundArray(String objectPath, T[] data)
{
compoundWriter.writeArray(objectPath, data);
}
// ------------------------------------------------------------------------------
// Primitive types - START
// ------------------------------------------------------------------------------
@Override
public void writeByteArray(String objectPath, byte[] data)
{
byteWriter.writeArray(objectPath, data);
}
@Override
public void writeDouble(String objectPath, double value)
{
doubleWriter.write(objectPath, value);
}
@Override
public void writeDoubleArray(String objectPath, double[] data)
{
doubleWriter.writeArray(objectPath, data);
}
@Override
public void writeDoubleMatrix(String objectPath, double[][] data)
{
doubleWriter.writeMatrix(objectPath, data);
}
@Override
public void writeFloat(String objectPath, float value)
{
floatWriter.write(objectPath, value);
}
@Override
public void writeFloatArray(String objectPath, float[] data)
{
floatWriter.writeArray(objectPath, data);
}
@Override
public void writeFloatMatrix(String objectPath, float[][] data)
{
floatWriter.writeMatrix(objectPath, data);
}
@Override
public void writeInt(String objectPath, int value)
{
intWriter.write(objectPath, value);
}
@Override
public void writeIntArray(String objectPath, int[] data)
{
intWriter.writeArray(objectPath, data);
}
@Override
public void writeIntMatrix(String objectPath, int[][] data)
{
intWriter.writeMatrix(objectPath, data);
}
@Override
public void writeLong(String objectPath, long value)
{
longWriter.write(objectPath, value);
}
@Override
public void writeLongArray(String objectPath, long[] data)
{
longWriter.writeArray(objectPath, data);
}
@Override
public void writeLongMatrix(String objectPath, long[][] data)
{
longWriter.writeMatrix(objectPath, data);
}
@Override
public IHDF5ByteWriter int8()
{
return byteWriter;
}
@Override
public IHDF5ByteWriter uint8()
{
return ubyteWriter;
}
@Override
public IHDF5ShortWriter int16()
{
return shortWriter;
}
@Override
public IHDF5ShortWriter uint16()
{
return ushortWriter;
}
@Override
public IHDF5IntWriter int32()
{
return intWriter;
}
@Override
public IHDF5IntWriter uint32()
{
return uintWriter;
}
@Override
public IHDF5LongWriter int64()
{
return longWriter;
}
@Override
public IHDF5LongWriter uint64()
{
return ulongWriter;
}
@Override
public IHDF5FloatWriter float32()
{
return floatWriter;
}
@Override
public IHDF5DoubleWriter float64()
{
return doubleWriter;
}
// ------------------------------------------------------------------------------
// Primitive Types - END
// ------------------------------------------------------------------------------
}
|