perf: Don't use Files.copy for Unsafe. It's much slower than writing via FileChannel.

fix: ensure parent directories exist before writing file for Unsafe
Signed-off-by: Caleb Hulbert <cmhulbert@gmail.com>

Author: cmhulbert

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

@@ -6,9 +6,7 @@
 import java.nio.channels.FileChannel;
 import java.nio.channels.FileLock;
 import java.nio.channels.OverlappingFileLockException;
-import java.nio.file.Files;
 import java.nio.file.Path;
-import java.nio.file.StandardOpenOption;
 
 /**
  * Holds a channel and system-level file lock (shared for writing, non-shared
@@ -56,7 +54,7 @@ FileChannel getChannel() {
 	 */
 	static ChannelLock lock(final Path path, final boolean forWriting) throws IOException {
 
-		final FileChannel channel = openFileChannel(path, forWriting);
+		final FileChannel channel = FsIoPolicy.openFileChannel(path, forWriting);
 		try {
 			while (true) {
 				try {
@@ -94,7 +92,7 @@ static ChannelLock tryLock(final Path path, final boolean forWriting) throws IOE
 
 		FileChannel channel = null;
 		try {
-			channel = openFileChannel(path, forWriting);
+			channel = FsIoPolicy.openFileChannel(path, forWriting);
 			final FileLock lock = channel.tryLock(0, Long.MAX_VALUE, !forWriting);
 			return lock == null ? null : new ChannelLock(channel, lock);
 		} catch (Exception e) {
@@ -103,26 +101,6 @@ static ChannelLock tryLock(final Path path, final boolean forWriting) throws IOE
 		}
 	}
 
-	/**
-	 * Opens a file channel. If the channel is opened {@code forWriting},
-	 * then this may create the file and the parent directories as needed.
-	 *
-	 * @throws IOException
-	 * 		if the channel cannot be opened
-	 */
-	private static FileChannel openFileChannel(final Path path, final boolean forWriting) throws IOException {
-
-		if (forWriting) {
-			final Path parent = path.getParent();
-			if (parent != null) {
-				Files.createDirectories(parent);
-			}
-			return FileChannel.open(path, StandardOpenOption.READ, StandardOpenOption.WRITE, StandardOpenOption.CREATE);
-		} else {
-			return FileChannel.open(path, StandardOpenOption.READ);
-		}
-	}
-
 	private static void closeQuietly(final FileChannel fileChannel) {
 		if (fileChannel != null) {
 			try {

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

@@ -6,8 +6,10 @@
 
 import java.io.Closeable;
 import java.io.IOException;
+import java.io.OutputStream;
 import java.io.UncheckedIOException;
 import java.nio.ByteBuffer;
+import java.nio.channels.Channels;
 import java.nio.channels.FileChannel;
 import java.nio.file.*;
 
@@ -29,11 +31,36 @@ else if (length >= 0 && offset + length > channelSize)
         return true;
     }
 
+    /**
+     * Opens a file channel. If the channel is opened {@code forWriting},
+     * then this may create the file and the parent directories as needed.
+     *
+     * @throws IOException
+     * 		if the channel cannot be opened
+     */
+    static FileChannel openFileChannel(final Path path, final boolean forWriting) throws IOException {
+
+        if (forWriting) {
+            final Path parent = path.getParent();
+            if (parent != null) {
+                Files.createDirectories(parent);
+            }
+            return FileChannel.open(path, StandardOpenOption.READ, StandardOpenOption.WRITE, StandardOpenOption.CREATE);
+        } else {
+            return FileChannel.open(path, StandardOpenOption.READ);
+        }
+    }
+
     public static class Unsafe implements IoPolicy {
         @Override
         public void write(String key, ReadData readData) throws IOException {
             final Path path = Paths.get(key);
-            Files.copy(readData.inputStream(), path, StandardCopyOption.REPLACE_EXISTING);
+            try (
+                    FileChannel channel = openFileChannel(path, true);
+                    OutputStream os = Channels.newOutputStream(channel);
+            ) {
+                readData.writeTo(os);
+            }
         }
 
         @Override