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/*
* 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 hdf.hdf5lib.exceptions.HDF5JavaException;
/**
* An object representing the storage features that are to be used for a data set.
* <p>
* The available storage layouts are {@link HDF5StorageLayout#COMPACT},
* {@link HDF5StorageLayout#CONTIGUOUS} or {@link HDF5StorageLayout#CHUNKED} can be chosen. Only
* {@link HDF5StorageLayout#CHUNKED} is extendable and can be compressed.
* <p>
* Two types of compressions are supported: <i>deflation</i> (the method used by <code>gzip</code>)
* and <i>scaling</i>, which can be used if the accuracy of the values are smaller than what the
* atomic data type can store. Note that <i>scaling</i> in general can be a lossy compression while
* <i>deflation</i> is always lossless. <i>Scaling</i> compression is only available with HDF5 1.8
* and newer. Trying to use <i>scaling</i> in strict HDF5 1.6 compatibility mode will throw an
* {@link IllegalStateException}.
* <p>
* For <i>deflation</i> the deflation level can be chosen to get the right balance between speed of
* compression and compression ratio. Often the {@link #DEFAULT_DEFLATION_LEVEL} will be the right
* choice.
* <p>
* For <i>scaling</i>, the scaling factor can be chosen that determines the accuracy of the values
* saved. What exactly the scaling factor means, differs between float and integer values.
*
* @author Bernd Rinn
*/
abstract class HDF5AbstractStorageFeatures
{
/**
* A constant that specifies that no deflation should be used.
*/
public final static byte NO_DEFLATION_LEVEL = 0;
/**
* A constant that specifies the default deflation level (gzip compression).
*/
public final static byte DEFAULT_DEFLATION_LEVEL = 6;
/**
* A constant that specifies the maximal deflation level (gzip compression).
*/
public final static byte MAX_DEFLATION_LEVEL = 9;
/**
* The policy on how to deal with write access to existing datasets. "Keeping the dataset" means
* to overwrite the content of the dataset, while "replacing the dataset" refers to deleting the
* existing dataset and create a new one.
*/
public enum DataSetReplacementPolicy
{
/** Use the default behavior as specified when the writer was created. */
USE_WRITER_DEFAULT,
/** Enforce to keep the existing dataset, overwriting the writer's default. */
ENFORCE_KEEP_EXISTING,
/** Enforce to replace the existing dataset, overwriting the writer's default. */
ENFORCE_REPLACE_WITH_NEW
}
/**
* Do not perform any scaling on the data.
*/
final static byte NO_SCALING_FACTOR = -1;
static byte toByte(int i)
{
final byte b = (byte) i;
if (b != i)
{
throw new HDF5JavaException("Value " + i + " cannot be casted to type byte");
}
return b;
}
private final byte deflateLevel;
private final byte scalingFactor;
private final DataSetReplacementPolicy datasetReplacementPolicy;
private final HDF5StorageLayout proposedLayoutOrNull;
private final boolean shuffleBeforeDeflate;
public abstract static class HDF5AbstractStorageFeatureBuilder
{
private byte deflateLevel;
private byte scalingFactor;
private HDF5StorageLayout storageLayout;
private DataSetReplacementPolicy datasetReplacementPolicy =
DataSetReplacementPolicy.USE_WRITER_DEFAULT;
private boolean shuffleBeforeDeflate;
HDF5AbstractStorageFeatureBuilder()
{
}
public HDF5AbstractStorageFeatureBuilder(HDF5AbstractStorageFeatures template)
{
deflateLevel(template.getDeflateLevel());
scalingFactor(template.getScalingFactor());
storageLayout(template.tryGetProposedLayout());
datasetReplacementPolicy(template.getDatasetReplacementPolicy());
shuffleBeforeDeflate(template.isShuffleBeforeDeflate());
}
byte getDeflateLevel()
{
return deflateLevel;
}
byte getScalingFactor()
{
return scalingFactor;
}
HDF5StorageLayout getStorageLayout()
{
return storageLayout;
}
DataSetReplacementPolicy getDatasetReplacementPolicy()
{
return datasetReplacementPolicy;
}
boolean isShuffleBeforeDeflate()
{
return shuffleBeforeDeflate;
}
public HDF5AbstractStorageFeatureBuilder compress(boolean compress)
{
this.deflateLevel = compress ? DEFAULT_DEFLATION_LEVEL : NO_DEFLATION_LEVEL;
return this;
}
public HDF5AbstractStorageFeatureBuilder compress()
{
this.deflateLevel = DEFAULT_DEFLATION_LEVEL;
return this;
}
public HDF5AbstractStorageFeatureBuilder deflateLevel(@SuppressWarnings("hiding")
byte deflateLevel)
{
this.deflateLevel = deflateLevel;
return this;
}
public HDF5AbstractStorageFeatureBuilder scalingFactor(@SuppressWarnings("hiding")
byte scalingFactor)
{
this.scalingFactor = scalingFactor;
return this;
}
public HDF5AbstractStorageFeatureBuilder noScaling()
{
this.scalingFactor = (byte) -1;
return this;
}
public HDF5AbstractStorageFeatureBuilder shuffleBeforeDeflate(@SuppressWarnings("hiding")
boolean shuffleBeforeDeflate)
{
this.shuffleBeforeDeflate = shuffleBeforeDeflate;
return this;
}
public HDF5AbstractStorageFeatureBuilder shuffleBeforeDeflate()
{
this.shuffleBeforeDeflate = true;
return this;
}
public HDF5AbstractStorageFeatureBuilder noShuffleBeforeDeflate()
{
this.shuffleBeforeDeflate = true;
return this;
}
public HDF5AbstractStorageFeatureBuilder storageLayout(@SuppressWarnings("hiding")
HDF5StorageLayout storageLayout)
{
this.storageLayout = storageLayout;
return this;
}
public HDF5AbstractStorageFeatureBuilder compactStorageLayout()
{
this.storageLayout = HDF5StorageLayout.COMPACT;
return this;
}
public HDF5AbstractStorageFeatureBuilder contiguousStorageLayout()
{
this.storageLayout = HDF5StorageLayout.CONTIGUOUS;
return this;
}
public HDF5AbstractStorageFeatureBuilder chunkedStorageLayout()
{
this.storageLayout = HDF5StorageLayout.CHUNKED;
return this;
}
public HDF5AbstractStorageFeatureBuilder defaultStorageLayout()
{
this.storageLayout = null;
return this;
}
public HDF5AbstractStorageFeatureBuilder datasetReplacementPolicy(
@SuppressWarnings("hiding")
DataSetReplacementPolicy datasetReplacementPolicy)
{
this.datasetReplacementPolicy = datasetReplacementPolicy;
return this;
}
public HDF5AbstractStorageFeatureBuilder datasetReplacementUseWriterDefault()
{
this.datasetReplacementPolicy = DataSetReplacementPolicy.USE_WRITER_DEFAULT;
return this;
}
public HDF5AbstractStorageFeatureBuilder datasetReplacementEnforceKeepExisting()
{
this.datasetReplacementPolicy = DataSetReplacementPolicy.ENFORCE_KEEP_EXISTING;
return this;
}
public HDF5AbstractStorageFeatureBuilder datasetReplacementEnforceReplaceWithNew()
{
this.datasetReplacementPolicy = DataSetReplacementPolicy.ENFORCE_REPLACE_WITH_NEW;
return this;
}
abstract public HDF5AbstractStorageFeatures features();
}
HDF5AbstractStorageFeatures(final HDF5StorageLayout proposedLayoutOrNull,
final DataSetReplacementPolicy datasetReplacementPolicy, final byte deflateLevel,
final byte scalingFactor)
{
this(proposedLayoutOrNull, datasetReplacementPolicy, false, deflateLevel, scalingFactor);
}
HDF5AbstractStorageFeatures(final HDF5StorageLayout proposedLayoutOrNull,
final DataSetReplacementPolicy datasetReplacementPolicy,
final boolean shuffleBeforeDeflate, final byte deflateLevel, final byte scalingFactor)
{
if (deflateLevel < 0)
{
throw new IllegalArgumentException("Invalid deflateLevel " + deflateLevel);
}
this.proposedLayoutOrNull = proposedLayoutOrNull;
this.datasetReplacementPolicy = datasetReplacementPolicy;
this.shuffleBeforeDeflate = shuffleBeforeDeflate;
this.deflateLevel = deflateLevel;
this.scalingFactor = scalingFactor;
}
/**
* Returns true, if this compression setting can be applied on the given <var>dataClassId</var>.
*/
abstract boolean isCompatibleWithDataClass(int dataClassId);
/**
* Returns the proposed storage layout, or <code>null</code>, if no particular storage layout
* should be proposed.
*/
public HDF5StorageLayout tryGetProposedLayout()
{
return proposedLayoutOrNull;
}
/**
* Returns the policy of this storage feature object regarding replacing or keeping already
* existing datasets.
*/
public DataSetReplacementPolicy getDatasetReplacementPolicy()
{
return datasetReplacementPolicy;
}
boolean requiresChunking()
{
return isDeflating() || isScaling() || proposedLayoutOrNull == HDF5StorageLayout.CHUNKED;
}
boolean allowsCompact()
{
return proposedLayoutOrNull == null || proposedLayoutOrNull == HDF5StorageLayout.COMPACT;
}
/**
* Returns <code>true</code>, if this storage feature object deflates data.
*/
public boolean isDeflating()
{
return (deflateLevel != NO_DEFLATION_LEVEL);
}
/**
* Returns <code>true</code>, if this storage feature object scales data.
*/
public boolean isScaling()
{
return scalingFactor >= 0;
}
/**
* Returns <code>true</code>, if this storage feature object performs shuffling before deflating
* the data.
*/
public boolean isShuffleBeforeDeflate()
{
return shuffleBeforeDeflate;
}
/**
* Returns the deflate level of this storage feature object. 0 means no deflate.
*/
public byte getDeflateLevel()
{
return deflateLevel;
}
/**
* Returns the scaling factor of this storage feature object. -1 means no scaling, 0 means
* auto-scaling.
*/
public byte getScalingFactor()
{
return scalingFactor;
}
static DataSetReplacementPolicy getDataSetReplacementPolicy(boolean keepDataSetIfExists,
boolean deleteDataSetIfExists)
{
return keepDataSetIfExists ? DataSetReplacementPolicy.ENFORCE_KEEP_EXISTING
: (deleteDataSetIfExists ? DataSetReplacementPolicy.ENFORCE_REPLACE_WITH_NEW
: DataSetReplacementPolicy.USE_WRITER_DEFAULT);
}
}
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