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Add NIOService for working with NIO classes
Migrated from the NIOService of SCIFIO, which was previously adapted from the NIOByteBufferProvider class of Bio-Formats.
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‎src/main/java/org/scijava/io/nio/DefaultNIOService.java‎

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/*
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* #%L
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* SciJava Common shared library for SciJava software.
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* %%
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* Copyright (C) 2009 - 2016 Board of Regents of the University of
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* Wisconsin-Madison, Broad Institute of MIT and Harvard, and Max Planck
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* Institute of Molecular Cell Biology and Genetics.
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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.scijava.io.nio;
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import java.io.IOException;
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import java.nio.ByteBuffer;
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import java.nio.channels.FileChannel;
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import java.nio.channels.FileChannel.MapMode;
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import org.scijava.log.LogService;
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import org.scijava.plugin.Parameter;
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import org.scijava.plugin.Plugin;
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import org.scijava.service.AbstractService;
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import org.scijava.service.Service;
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/**
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* Default service for working with the {@link java.nio} package, particularly
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* NIO {@link ByteBuffer} objects.
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*
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* @author Chris Allan
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* @author Curtis Rueden
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*/
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@Plugin(type = Service.class)
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public class DefaultNIOService extends AbstractService implements NIOService {
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// -- Fields --
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@Parameter
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private LogService log;
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/** Whether or not we are to use memory mapped I/O. */
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private final boolean useMappedByteBuffer = Boolean.parseBoolean(System
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.getProperty("mappedBuffers"));
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// -- NIOService API methods --
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@Override
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public ByteBuffer allocate(final FileChannel channel, final MapMode mapMode,
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final long bufferStartPosition, final int newSize) throws IOException
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{
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log.debug("NIO: allocate: mapped=" + useMappedByteBuffer + ", start=" +
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bufferStartPosition + ", size=" + newSize);
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if (useMappedByteBuffer) {
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return allocateMappedByteBuffer(channel, mapMode, bufferStartPosition,
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newSize);
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}
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return allocateDirect(channel, bufferStartPosition, newSize);
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}
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// -- Helper methods --
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/**
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* Allocates memory and copies the desired file data into it.
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*
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* @param channel File channel to allocate or map byte buffers from.
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* @param bufferStartPosition The absolute position of the start of the
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* buffer.
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* @param newSize The buffer size.
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* @return A newly allocated NIO byte buffer.
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* @throws IOException If there is an issue aligning or allocating the buffer.
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*/
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private ByteBuffer allocateDirect(final FileChannel channel,
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final long bufferStartPosition, final int newSize) throws IOException
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{
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final ByteBuffer buffer = ByteBuffer.allocate(newSize);
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channel.read(buffer, bufferStartPosition);
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return buffer;
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}
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/**
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* Memory maps the desired file data into memory.
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*
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* @param channel File channel to allocate or map byte buffers from.
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* @param mapMode The map mode. Required but only used if memory mapped I/O is
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* to occur.
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* @param bufferStartPosition The absolute position of the start of the
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* buffer.
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* @param newSize The buffer size.
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* @return A newly mapped NIO byte buffer.
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* @throws IOException If there is an issue mapping, aligning or allocating
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* the buffer.
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*/
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private ByteBuffer allocateMappedByteBuffer(final FileChannel channel,
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final MapMode mapMode, final long bufferStartPosition, final int newSize)
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throws IOException
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{
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return channel.map(mapMode, bufferStartPosition, newSize);
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}
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}

‎src/main/java/org/scijava/io/nio/NIOService.java‎

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/*
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* #%L
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* SciJava Common shared library for SciJava software.
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* %%
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* Copyright (C) 2009 - 2016 Board of Regents of the University of
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* Wisconsin-Madison, Broad Institute of MIT and Harvard, and Max Planck
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* Institute of Molecular Cell Biology and Genetics.
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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.scijava.io.nio;
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import java.io.IOException;
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import java.nio.ByteBuffer;
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import java.nio.channels.FileChannel;
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import java.nio.channels.FileChannel.MapMode;
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import org.scijava.service.SciJavaService;
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/**
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* Interface for services that work with the {@link java.nio} package,
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* particularly NIO {@link ByteBuffer} objects.
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*
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* @author Chris Allan
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* @author Curtis Rueden
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*/
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public interface NIOService extends SciJavaService {
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/**
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* Allocates or maps the desired file data into memory.
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* <p>
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* This method provides a facade to byte buffer allocation that enables
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* <code>FileChannel.map()</code> usage on platforms where it's unlikely to
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* give us problems and heap allocation where it is.
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* </p>
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*
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* @param channel File channel to allocate or map byte buffers from.
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* @param mapMode The map mode. Required but only used if memory mapped I/O is
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* to occur.
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* @param bufferStartPosition The absolute position of the start of the
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* buffer.
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* @param newSize The buffer size.
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* @return A newly allocated or mapped NIO byte buffer.
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* @see "http://bugs.sun.com/bugdatabase/view_bug.do?bug_id=5092131"
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* @see "http://bugs.sun.com/bugdatabase/view_bug.do?bug_id=6417205"
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* @throws IOException If there is an issue mapping, aligning or allocating
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* the buffer.
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*/
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ByteBuffer allocate(FileChannel channel, MapMode mapMode,
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long bufferStartPosition, int newSize) throws IOException;
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}

‎src/test/java/org/scijava/ContextCreationTest.java‎

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org.scijava.io.DefaultDataHandleService.class,
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org.scijava.io.DefaultIOService.class,
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org.scijava.io.DefaultRecentFileService.class,
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org.scijava.io.nio.DefaultNIOService.class,
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org.scijava.main.DefaultMainService.class,
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org.scijava.menu.DefaultMenuService.class,
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org.scijava.module.DefaultModuleService.class,

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