Fixed imports.

pom.xml

@@ -117,5 +117,11 @@
 			<artifactId>commons-cli</artifactId>
 			<version>${commons-cli.version}</version>
 		</dependency>
-	</dependencies>
+        <dependency>
+            <groupId>org.scijava</groupId>
+            <artifactId>DataCompressor</artifactId>
+            <version>1.0-SNAPSHOT</version>
+            <scope>compile</scope>
+        </dependency>
+    </dependencies>
 </project>

src/main/java/bdv/server/BigDataServer.java

 package bdv.server;
 
+import compression.quantization.scalar.LloydMaxU16ScalarQuantization;
+import gnu.trove.impl.sync.TSynchronizedShortByteMap;
 import mpicbg.spim.data.SpimDataException;
 
 import org.apache.commons.cli.*;
@@ -49,12 +51,14 @@ import java.util.Map.Entry;
  * {@link Constants#ENABLE_EXPERIMENTAL_FEATURES} set to {@code true}.
  *
  * @author Tobias Pietzsch <tobias.pietzsch@gmail.com>
- * @author HongKee Moon <moon@mpi-cbg.de>
+ * @author HongKee Moon <moon@mpi-cbg.quantization.de>
  */
 public class BigDataServer
 {
 	private static final org.eclipse.jetty.util.log.Logger LOG = Log.getLogger( BigDataServer.class );
 
+	private static LloydMaxU16ScalarQuantization quantizer;
+
 	static Parameters getDefaultParameters()
 	{
 		final int port = 8080;
@@ -69,7 +73,7 @@ public class BigDataServer
 		}
 		final String thumbnailDirectory = null;
 		final boolean enableManagerContext = false;
-		return new Parameters( port, hostname, new HashMap< String, String >(), thumbnailDirectory, enableManagerContext );
+		return new Parameters( port, hostname, new HashMap< String, String >(), thumbnailDirectory, enableManagerContext, CellHandler.DumpFile);
 	}
 
 	public static void main( final String[] args ) throws Exception
@@ -80,6 +84,8 @@ public class BigDataServer
 		if ( params == null )
 			return;
 
+		CellHandler.DumpFile = params.getDumpFile();
+
 		final String thumbnailsDirectoryName = getThumbnailDirectoryPath( params );
 
 		// Threadpool for multiple connections
@@ -93,6 +99,10 @@ public class BigDataServer
 		server.setConnectors( new Connector[] { connector } );
 		final String baseURL = "http://" + server.getURI().getHost() + ":" + params.getPort();
 
+
+		quantizer = new LloydMaxU16ScalarQuantization("D:\\tmp\\server-dump\\initial_load.bin",8);
+		quantizer.train(true);
+
 		// Handler initialization
 		final HandlerCollection handlers = new HandlerCollection();
 
@@ -114,6 +124,8 @@ public class BigDataServer
 			handler = statHandler;
 		}
 
+
+
 		LOG.info( "Set handler: " + handler );
 		server.setHandler( handler );
 		LOG.info( "Server Base URL: " + baseURL );
@@ -138,15 +150,18 @@ public class BigDataServer
 
 		private final String thumbnailDirectory;
 
+		private final String dumpFile;
+
 		private final boolean enableManagerContext;
 
-		Parameters( final int port, final String hostname, final Map< String, String > datasetNameToXml, final String thumbnailDirectory, final boolean enableManagerContext )
+		Parameters( final int port, final String hostname, final Map< String, String > datasetNameToXml, final String thumbnailDirectory, final boolean enableManagerContext, final String dumpFile)
 		{
 			this.port = port;
 			this.hostname = hostname;
 			this.datasetNameToXml = datasetNameToXml;
 			this.thumbnailDirectory = thumbnailDirectory;
 			this.enableManagerContext = enableManagerContext;
+			this.dumpFile = dumpFile;
 		}
 
 		public int getPort()
@@ -178,6 +193,10 @@ public class BigDataServer
 		{
 			return enableManagerContext;
 		}
+
+		public String getDumpFile() {
+			return dumpFile;
+		}
 	}
 
 	@SuppressWarnings( "static-access" )
@@ -217,6 +236,13 @@ public class BigDataServer
 				.withArgName( "DIRECTORY" )
 				.create( "t" ) );
 
+
+		options.addOption( OptionBuilder
+				.withDescription( "File in which to store data dump" )
+				.hasArg()
+				.withArgName( "DUMP" )
+				.create( "dump" ) );
+
 		if ( Constants.ENABLE_EXPERIMENTAL_FEATURES )
 		{
 			options.addOption( OptionBuilder
@@ -233,12 +259,16 @@ public class BigDataServer
 			final String portString = cmd.getOptionValue( "p", Integer.toString( defaultParameters.getPort() ) );
 			final int port = Integer.parseInt( portString );
 
+			final String dumpFile = cmd.getOptionValue("dump", defaultParameters.getDumpFile());
+
 			// Getting server name option
 			final String serverName = cmd.getOptionValue( "s", defaultParameters.getHostname() );
 
 			// Getting thumbnail directory option
 			final String thumbnailDirectory = cmd.getOptionValue( "t", defaultParameters.getThumbnailDirectory() );
 
+
+
 			final HashMap< String, String > datasets = new HashMap< String, String >( defaultParameters.getDatasets() );
 
 			boolean enableManagerContext = false;
@@ -294,7 +324,7 @@ public class BigDataServer
 			if ( datasets.isEmpty() )
 				throw new IllegalArgumentException( "Dataset list is empty." );
 
-			return new Parameters( port, serverName, datasets, thumbnailDirectory, enableManagerContext );
+			return new Parameters( port, serverName, datasets, thumbnailDirectory, enableManagerContext, dumpFile );
 		}
 		catch ( final ParseException | IllegalArgumentException e )
 		{
@@ -360,7 +390,7 @@ public class BigDataServer
 			final String name = entry.getKey();
 			final String xmlpath = entry.getValue();
 			final String context = "/" + name;
-			final CellHandler ctx = new CellHandler( baseURL + context + "/", xmlpath, name, thumbnailsDirectoryName );
+			final CellHandler ctx = new CellHandler( baseURL + context + "/", xmlpath, name, thumbnailsDirectoryName, quantizer );
 			ctx.setContextPath( context );
 			handlers.addHandler( ctx );
 		}

src/main/java/bdv/server/CellHandler.java

 package bdv.server;
 
 import java.awt.image.BufferedImage;
-import java.io.File;
-import java.io.IOException;
-import java.io.OutputStream;
-import java.io.PrintWriter;
-import java.io.StringWriter;
+import java.io.*;
 import java.nio.file.Files;
 import java.nio.file.Path;
 import java.nio.file.Paths;
@@ -14,6 +10,7 @@ import javax.imageio.ImageIO;
 import javax.servlet.http.HttpServletRequest;
 import javax.servlet.http.HttpServletResponse;
 
+import compression.quantization.scalar.LloydMaxU16ScalarQuantization;
 import org.eclipse.jetty.server.Request;
 import org.eclipse.jetty.server.handler.ContextHandler;
 import org.eclipse.jetty.util.log.Log;
@@ -51,6 +48,8 @@ public class CellHandler extends ContextHandler
 
 	private static final org.eclipse.jetty.util.log.Logger LOG = Log.getLogger( CellHandler.class );
 
+	public static String DumpFile = "";
+	private int counter = 0;
 	private final VolatileGlobalCellCache cache;
 
 	private final Hdf5VolatileShortArrayLoader loader;
@@ -93,12 +92,15 @@ public class CellHandler extends ContextHandler
 	 */
 	private final String thumbnailFilename;
 
-	public CellHandler( final String baseUrl, final String xmlFilename, final String datasetName, final String thumbnailsDirectory ) throws SpimDataException, IOException
+	private LloydMaxU16ScalarQuantization quantizer;
+
+	public CellHandler(final String baseUrl, final String xmlFilename, final String datasetName, final String thumbnailsDirectory, final LloydMaxU16ScalarQuantization quantizer) throws SpimDataException, IOException
 	{
 		final XmlIoSpimDataMinimal io = new XmlIoSpimDataMinimal();
 		final SpimDataMinimal spimData = io.load( xmlFilename );
 		final SequenceDescriptionMinimal seq = spimData.getSequenceDescription();
 		final Hdf5ImageLoader imgLoader = ( Hdf5ImageLoader ) seq.getImgLoader();
+		this.quantizer = quantizer;
 
 		cache = imgLoader.getCacheControl();
 		loader = imgLoader.getShortArrayLoader();
@@ -162,8 +164,12 @@ public class CellHandler extends ContextHandler
 				cell = cache.getLoadingVolatileCache().get( key, cacheHints, new VolatileCellLoader<>( loader, timepoint, setup, level, cellDims, cellMin ) );
 			}
 
+
 			@SuppressWarnings( "unchecked" )
-			final short[] data = ( ( VolatileCell< VolatileShortArray > ) cell ).getData().getCurrentStorageArray();
+			short[] data = ((VolatileCell<VolatileShortArray>) cell).getData().getCurrentStorageArray();
+			if (quantizer != null) {
+				data = quantizer.quantize(data);
+			}
 
 			/*
 			* NOTE(Moravec): This is possible place, where to compress data. Image data are inside data array, but we access only part of the image.
@@ -181,6 +187,15 @@ public class CellHandler extends ContextHandler
 				buf[ j++ ] = ( byte ) ( s & 0xff );
 			}
 
+			if (!DumpFile.equals("")) {
+				//String requestLog = String.format("%s\\request_%d_%d.data", DumpFile, buf.length, counter++);
+				FileOutputStream dumpStream = new FileOutputStream(DumpFile, true);
+				dumpStream.write(buf);
+				dumpStream.flush();
+				dumpStream.close();
+			}
+
+
 			transferedDataSize += buf.length;
 			LOG.info(String.format("Total transfered data: [%d KB] [%d MB]", (transferedDataSize/1000), ((transferedDataSize/1000)/1000)));
 

src/main/java/bdv/server/JsonDatasetListHandler.java

@@ -16,7 +16,7 @@ import java.net.URISyntaxException;
 /**
  * Provides a list of available datasets on this {@link BigDataServer}
  *
- * @author HongKee Moon <moon@mpi-cbg.de>
+ * @author HongKee Moon <moon@mpi-cbg.quantization.de>
  */
 public class JsonDatasetListHandler extends ContextHandler
 {

src/main/java/bdv/server/ManagerHandler.java

@@ -24,7 +24,7 @@ import java.net.URISyntaxException;
 import java.text.DecimalFormat;
 
 /**
- * @author HongKee Moon <moon@mpi-cbg.de>
+ * @author HongKee Moon <moon@mpi-cbg.quantization.de>
  * @author Tobias Pietzsch <tobias.pietzsch@gmail.com>
  */
 public class ManagerHandler extends ContextHandler
@@ -175,7 +175,7 @@ public class ManagerHandler extends ContextHandler
 			CellHandler ctx = null;
 			try
 			{
-				ctx = new CellHandler( baseURL + context + "/", fileLocation, datasetName, thumbnailsDirectoryName );
+				ctx = new CellHandler( baseURL + context + "/", fileLocation, datasetName, thumbnailsDirectoryName, null );
 			}
 			catch ( final SpimDataException e )
 			{