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Commit 5981d62f authored by Vojtech Moravec's avatar Vojtech Moravec
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Fixed imports.

parent 48a98ca8
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pom.xml
+ 7
− 1
View file @ 5981d62f
......@@ -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
+ 35
− 5
View file @ 5981d62f
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 &lt;tobias.pietzsch@gmail.com&gt;
* @author HongKee Moon &lt;moon@mpi-cbg.de&gt;
* @author HongKee Moon &lt;moon@mpi-cbg.quantization.de&gt;
*/
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
+ 22
− 7
View file @ 5981d62f
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
+ 1
− 1
View file @ 5981d62f
......@@ -16,7 +16,7 @@ import java.net.URISyntaxException;
/**
* Provides a list of available datasets on this {@link BigDataServer}
*
* @author HongKee Moon &lt;moon@mpi-cbg.de&gt;
* @author HongKee Moon &lt;moon@mpi-cbg.quantization.de&gt;
*/
public class JsonDatasetListHandler extends ContextHandler
{
......
src/main/java/bdv/server/ManagerHandler.java
+ 2
− 2
View file @ 5981d62f
......@@ -24,7 +24,7 @@ import java.net.URISyntaxException;
import java.text.DecimalFormat;
/**
* @author HongKee Moon &lt;moon@mpi-cbg.de&gt;
* @author HongKee Moon &lt;moon@mpi-cbg.quantization.de&gt;
* @author Tobias Pietzsch &lt;tobias.pietzsch@gmail.com&gt;
*/
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 )
{
......
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