From a4a5ac9c46983f500cb81c8f815b2457e6c301f7 Mon Sep 17 00:00:00 2001
From: Mark Kittisopikul <markkitt@gmail.com>
Date: Sun, 3 Dec 2023 09:13:14 -0500
Subject: [PATCH] Add ZstdCompression based on Apache Commons Compress

Note tests will fail since the optional dependency zstd-jni
is not a dependency.
---
 .../saalfeldlab/n5/ZstdCompression.java       | 90 +++++++++++++++++++
 .../saalfeldlab/n5/AbstractN5Test.java        |  3 +-
 2 files changed, 92 insertions(+), 1 deletion(-)
 create mode 100644 src/main/java/org/janelia/saalfeldlab/n5/ZstdCompression.java

diff --git a/src/main/java/org/janelia/saalfeldlab/n5/ZstdCompression.java b/src/main/java/org/janelia/saalfeldlab/n5/ZstdCompression.java
new file mode 100644
index 00000000..a4649442
--- /dev/null
+++ b/src/main/java/org/janelia/saalfeldlab/n5/ZstdCompression.java
@@ -0,0 +1,90 @@
+package org.janelia.saalfeldlab.n5;
+
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.OutputStream;
+
+import org.apache.commons.compress.compressors.zstandard.ZstdCompressorInputStream;
+import org.apache.commons.compress.compressors.zstandard.ZstdCompressorOutputStream;
+import org.janelia.saalfeldlab.n5.Compression.CompressionType;
+
+/**
+ * Zstandard compression for N5
+ * 
+ * Implementation wrapper around Apache Commons Compress
+ * 
+ * Note that zstd-jni is an optional dependency of Apache Commons Compress.
+ * However, it is required for this class, ZstdCompression, to work
+ * https://github.com/luben/zstd-jni
+ * 
+ * Add the following dependency entry under to the Maven pom.xml
+ * 
+ *		<dependency>
+ *		    <groupId>com.github.luben</groupId>
+ *		    <artifactId>zstd-jni</artifactId>
+ *		    <version>1.5.5-10</version>
+ *		</dependency>
+ * 
+ * See the Zstandard manual for details on parameters.
+ * https://facebook.github.io/zstd/zstd_manual.html
+ * 
+ * @author mkitti
+ *
+ */
+@CompressionType("zstd")
+public class ZstdCompression implements DefaultBlockReader, DefaultBlockWriter, Compression {
+	
+	/**
+	 * 
+	 */
+	private static final long serialVersionUID = 8592416400988371189L;
+
+	/*
+	 * Compression level
+	 * 
+	 * Standard compression level is between 1 and 22
+	 * Negative compression levels offer speed
+	 * 
+	 * Note that zarr-developers/numcodecs defaults to 1
+	 * 
+	 * Default: 3 (see ZSTD_CLEVEL_DEFAULT)
+	 */
+	@CompressionParameter
+	private int level = 3;
+	
+	/*
+	 * Default compression level from zstd.h
+	 */
+	public static final int ZSTD_CLEVEL_DEFAULT = 3;
+	
+	public ZstdCompression() {
+		this.level = ZSTD_CLEVEL_DEFAULT;
+	}
+	
+	public ZstdCompression(int level) {
+		this.level = level;
+	}
+
+	@Override
+	public BlockReader getReader() {
+		return this;
+	}
+
+	@Override
+	public BlockWriter getWriter() {
+		return this;
+	}
+
+	@Override
+	public OutputStream getOutputStream(OutputStream out) throws IOException {
+		ZstdCompressorOutputStream zstdOut = new ZstdCompressorOutputStream(out, level);
+		return zstdOut;
+	}
+
+	@Override
+	public InputStream getInputStream(InputStream in) throws IOException {
+		ZstdCompressorInputStream zstdIn = new ZstdCompressorInputStream(in);
+		return zstdIn;
+	}
+
+}
diff --git a/src/test/java/org/janelia/saalfeldlab/n5/AbstractN5Test.java b/src/test/java/org/janelia/saalfeldlab/n5/AbstractN5Test.java
index db3b9a07..f424cb4f 100644
--- a/src/test/java/org/janelia/saalfeldlab/n5/AbstractN5Test.java
+++ b/src/test/java/org/janelia/saalfeldlab/n5/AbstractN5Test.java
@@ -115,7 +115,8 @@ protected Compression[] getCompressions() {
 				new GzipCompression(),
 				new GzipCompression(5, true),
 				new Lz4Compression(),
-				new XzCompression()
+				new XzCompression(),
+				new ZstdCompression()
 		};
 	}