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chore: remove license header; don't update license header
Signed-off-by: Caleb Hulbert <cmhulbert@gmail.com>
1 parent 04a38d6 commit b7f4d69

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‎LICENSE.txt‎

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‎pom.xml‎

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<properties>
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<package-name>org.janelia.saalfeldlab.n5</package-name>
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<license.licenseName>bsd_2</license.licenseName>
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<license.projectName>Not HDF5</license.projectName>
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<license.organizationName>Saalfeld Lab</license.organizationName>
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<license.copyrightOwners>Stephan Saalfeld</license.copyrightOwners>
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<license.excludes>**/*.json</license.excludes>
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<license.skipUpdateLicense>true</license.skipUpdateLicense>
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<license.skipUpdateProjectLicense>true</license.skipUpdateProjectLicense>
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<!-- NB: Deploy releases to the SciJava Maven repository. -->
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<releaseProfiles>sign,deploy-to-scijava</releaseProfiles>

‎src/main/java/org/janelia/saalfeldlab/n5/AbstractDataBlock.java‎

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/*-
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* #%L
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* Not HDF5
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* %%
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* Copyright (C) 2017 - 2025 Stephan Saalfeld
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* %%
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* Redistribution and use in source and binary forms, with or without
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* modification, are permitted provided that the following conditions are met:
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*
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* 1. Redistributions of source code must retain the above copyright notice,
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* this list of conditions and the following disclaimer.
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* 2. Redistributions in binary form must reproduce the above copyright notice,
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* this list of conditions and the following disclaimer in the documentation
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* and/or other materials provided with the distribution.
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*
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* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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* AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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* IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
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* ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
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* LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
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* CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
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* SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
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* INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
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* CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
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* ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
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* POSSIBILITY OF SUCH DAMAGE.
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* #L%
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*/
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package org.janelia.saalfeldlab.n5;
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import java.util.function.ToIntFunction;
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/**
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* Abstract base class for {@link DataBlock} implementations.
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*
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* @param <T>
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* the block data type
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*
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* @author Stephan Saalfeld
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*/
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public abstract class AbstractDataBlock<T> implements DataBlock<T> {
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protected final int[] size;

‎src/main/java/org/janelia/saalfeldlab/n5/ByteArrayDataBlock.java‎

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/*-
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* #%L
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* Not HDF5
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* %%
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* Copyright (C) 2017 - 2025 Stephan Saalfeld
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* %%
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* Redistribution and use in source and binary forms, with or without
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* modification, are permitted provided that the following conditions are met:
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*
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* 1. Redistributions of source code must retain the above copyright notice,
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* this list of conditions and the following disclaimer.
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* 2. Redistributions in binary form must reproduce the above copyright notice,
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* this list of conditions and the following disclaimer in the documentation
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* and/or other materials provided with the distribution.
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*
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* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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* AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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* IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
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* ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
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* LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
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* CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
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* SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
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* INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
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* CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
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* ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
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* POSSIBILITY OF SUCH DAMAGE.
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* #L%
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*/
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package org.janelia.saalfeldlab.n5;
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public class ByteArrayDataBlock extends AbstractDataBlock<byte[]> {

‎src/main/java/org/janelia/saalfeldlab/n5/Bzip2Compression.java‎

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/*-
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* #%L
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* Not HDF5
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* %%
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* Copyright (C) 2017 - 2025 Stephan Saalfeld
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* %%
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* Redistribution and use in source and binary forms, with or without
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* modification, are permitted provided that the following conditions are met:
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*
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* 1. Redistributions of source code must retain the above copyright notice,
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* this list of conditions and the following disclaimer.
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* 2. Redistributions in binary form must reproduce the above copyright notice,
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* this list of conditions and the following disclaimer in the documentation
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* and/or other materials provided with the distribution.
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*
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* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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* AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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* IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
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* ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
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* LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
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* CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
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* SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
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* INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
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* CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
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* ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
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* POSSIBILITY OF SUCH DAMAGE.
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* #L%
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*/
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package org.janelia.saalfeldlab.n5;
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import java.io.IOException;

‎src/main/java/org/janelia/saalfeldlab/n5/CachedGsonKeyValueN5Reader.java‎

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/*-
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* #%L
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* Not HDF5
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* %%
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* Copyright (C) 2017 - 2025 Stephan Saalfeld
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* %%
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* Redistribution and use in source and binary forms, with or without
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* modification, are permitted provided that the following conditions are met:
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*
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* 1. Redistributions of source code must retain the above copyright notice,
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* this list of conditions and the following disclaimer.
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* 2. Redistributions in binary form must reproduce the above copyright notice,
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* this list of conditions and the following disclaimer in the documentation
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* and/or other materials provided with the distribution.
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*
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* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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* AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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* IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
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* ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
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* LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
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* CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
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* SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
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* INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
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* CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
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* ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
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* POSSIBILITY OF SUCH DAMAGE.
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* #L%
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*/
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package org.janelia.saalfeldlab.n5;
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import java.lang.reflect.Type;
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import com.google.gson.Gson;
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import com.google.gson.JsonElement;
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import com.google.gson.JsonObject;
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/**
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* {@link N5Reader} implementation through {@link KeyValueAccess} with JSON
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* attributes parsed with {@link Gson}.
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*
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*/
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public interface CachedGsonKeyValueN5Reader extends GsonKeyValueN5Reader, N5JsonCacheableContainer {
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default N5JsonCache newCache() {

‎src/main/java/org/janelia/saalfeldlab/n5/CachedGsonKeyValueN5Writer.java‎

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/*-
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* #%L
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* Not HDF5
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* %%
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* Copyright (C) 2017 - 2025 Stephan Saalfeld
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* %%
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* Redistribution and use in source and binary forms, with or without
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* modification, are permitted provided that the following conditions are met:
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*
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* 1. Redistributions of source code must retain the above copyright notice,
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* this list of conditions and the following disclaimer.
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* 2. Redistributions in binary form must reproduce the above copyright notice,
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* this list of conditions and the following disclaimer in the documentation
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* and/or other materials provided with the distribution.
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*
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* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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* AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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* IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
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* ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
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* LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
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* CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
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* SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
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* INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
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* CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
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* ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
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* POSSIBILITY OF SUCH DAMAGE.
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* #L%
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*/
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package org.janelia.saalfeldlab.n5;
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import org.janelia.saalfeldlab.n5.N5Exception.N5IOException;
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import com.google.gson.Gson;
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import com.google.gson.JsonElement;
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/**
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* Cached default implementation of {@link N5Writer} with JSON attributes parsed
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* with {@link Gson}.
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*/
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public interface CachedGsonKeyValueN5Writer extends CachedGsonKeyValueN5Reader, GsonKeyValueN5Writer {
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@Override

‎src/main/java/org/janelia/saalfeldlab/n5/ChannelLock.java‎

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import java.nio.file.Files;
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import java.nio.file.Path;
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import java.nio.file.StandardOpenOption;
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/**
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* Holds a channel and system-level file lock (shared for writing, non-shared
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* for reading) and keeps it open until this {@code ChannelLock} is {@link
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* #close() closed}.
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*/
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class ChannelLock implements Closeable {
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private final FileChannel channel;

‎src/main/java/org/janelia/saalfeldlab/n5/Compression.java‎

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/*-
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* #%L
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* Not HDF5
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* %%
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* Copyright (C) 2017 - 2025 Stephan Saalfeld
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* %%
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* Redistribution and use in source and binary forms, with or without
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* modification, are permitted provided that the following conditions are met:
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*
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* 1. Redistributions of source code must retain the above copyright notice,
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* this list of conditions and the following disclaimer.
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* 2. Redistributions in binary form must reproduce the above copyright notice,
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* this list of conditions and the following disclaimer in the documentation
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* and/or other materials provided with the distribution.
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*
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* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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* AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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* IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
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* ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
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* LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
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* CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
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* SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
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* INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
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* CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
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* ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
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* POSSIBILITY OF SUCH DAMAGE.
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* #L%
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*/
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package org.janelia.saalfeldlab.n5;
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import java.io.Serializable;
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import org.janelia.saalfeldlab.n5.codec.CodecInfo;
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import org.janelia.saalfeldlab.n5.codec.DataCodecInfo;
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import org.scijava.annotations.Indexable;
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/**
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* This interface is used to indicate that a {@link DataCodec} can be
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* serialized as a "compression" for the N5 format (using the N5 API).
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* <p>
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* N5Readers and N5Writers for the N5 format can declare DataCodecs that
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* implement this interface so that the {@link CompressionAdapter} is used for
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* serialization.
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* <p>
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* See also: an alternative method for serializing general {@link CodecInfo}s is
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* with the {@link NameConfigAdapter}. This interface remains for legacy
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* (de)serialization.
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*
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* @author Stephan Saalfeld
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*/
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public interface Compression extends Serializable, DataCodec, DataCodecInfo {
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/**

‎src/main/java/org/janelia/saalfeldlab/n5/CompressionAdapter.java‎

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/*-
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* #%L
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* Not HDF5
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* %%
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* Copyright (C) 2017 - 2025 Stephan Saalfeld
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* %%
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* Redistribution and use in source and binary forms, with or without
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* modification, are permitted provided that the following conditions are met:
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*
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* 1. Redistributions of source code must retain the above copyright notice,
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* this list of conditions and the following disclaimer.
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* 2. Redistributions in binary form must reproduce the above copyright notice,
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* this list of conditions and the following disclaimer in the documentation
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* and/or other materials provided with the distribution.
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*
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* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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* AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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* IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
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* ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
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* LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
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* CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
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* SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
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* INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
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* CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
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* ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
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* POSSIBILITY OF SUCH DAMAGE.
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* #L%
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*/
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package org.janelia.saalfeldlab.n5;
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import java.lang.reflect.Constructor;
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import com.google.gson.JsonParseException;
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import com.google.gson.JsonSerializationContext;
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import com.google.gson.JsonSerializer;
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/**
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* Compression adapter, auto-discovers annotated compression implementations
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* in the classpath.
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*
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* @author Stephan Saalfeld
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*/
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public class CompressionAdapter implements JsonDeserializer<Compression>, JsonSerializer<Compression> {
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private static CompressionAdapter instance = null;

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