diff --git a/pom.xml b/pom.xml
index a46ee15faad93b93668b9d0c18b72d03ba4c8454..e437b06707a7d74f8b8ecb591dc3fa376dac47c5 100644
--- a/pom.xml
+++ b/pom.xml
@@ -5,41 +5,47 @@
<parent>
<groupId>sc.fiji</groupId>
<artifactId>pom-bigdataviewer</artifactId>
- <version>2.1.6</version>
+ <version>4.0.1</version>
</parent>
<artifactId>bigdataviewer-server</artifactId>
- <version>1.0.5-SNAPSHOT</version>
+ <version>2.1.1-SNAPSHOT</version>
<name>BigDataServer</name>
<description>A web server for BigDataViewer datasets</description>
+ <scm>
+ <connection>scm:git:git://github.com/bigdataviewer/bigdataviewer-server</connection>
+ <developerConnection>scm:git:git@github.com:bigdataviewer/bigdataviewer-server</developerConnection>
+ <tag>HEAD</tag>
+ <url>https://github.com/bigdataviewer/bigdataviewer-server</url>
+ </scm>
+ <issueManagement>
+ <system>GitHub Issues</system>
+ <url>https://github.com/bigdataviewer/bigdataviewer-server/issues</url>
+ </issueManagement>
+ <ciManagement>
+ <system>Jenkins</system>
+ <url>http://jenkins.imagej.net/job/bigdataviewer-server/</url>
+ </ciManagement>
+
<properties>
- <scijava.jvm.version>1.7</scijava.jvm.version>
- <jetty.version>9.2.10.v20150310</jetty.version>
+ <enforcer.skip>true</enforcer.skip>
+ <!-- <jetty.version>9.2.10.v20150310</jetty.version> -->
</properties>
- <build>
- <plugins>
- <plugin>
- <artifactId>maven-compiler-plugin</artifactId>
- <configuration>
- <source>1.7</source>
- <target>1.7</target>
- </configuration>
- </plugin>
- </plugins>
- </build>
+ <repositories>
+ <repository>
+ <id>imagej.public</id>
+ <url>http://maven.imagej.net/content/groups/public</url>
+ </repository>
+ </repositories>
<dependencies>
<dependency>
<groupId>sc.fiji</groupId>
<artifactId>bigdataviewer-core</artifactId>
</dependency>
- <dependency>
- <groupId>sc.fiji</groupId>
- <artifactId>spim_data</artifactId>
- </dependency>
<dependency>
<groupId>org.eclipse.jetty</groupId>
<artifactId>jetty-server</artifactId>
@@ -73,15 +79,16 @@
<developer>
<id>tpietzsch</id>
<name>Tobias Pietzsch</name>
- <email>pietzsch@mpi-cbg.de</email>
- <url/>
- <organization>MPI-CBG</organization>
- <organizationUrl>http://www.mpi-cbg.de/</organizationUrl>
+ <url>http://imagej.net/User:Pietzsch</url>
<roles>
- <role>architect</role>
+ <role>founder</role>
+ <role>lead</role>
<role>developer</role>
+ <role>debugger</role>
+ <role>reviewer</role>
+ <role>support</role>
+ <role>maintainer</role>
</roles>
- <timezone>+1</timezone>
</developer>
<developer>
<id>hkmoon</id>
@@ -94,21 +101,6 @@
<role>architect</role>
<role>developer</role>
</roles>
- <timezone>+1</timezone>
</developer>
</developers>
-
- <repositories>
- <repository>
- <id>imagej.public</id>
- <url>http://maven.imagej.net/content/groups/public</url>
- </repository>
- </repositories>
-
- <scm>
- <connection>scm:git:git://github.com/bigdataviewer/bigdataviewer-server</connection>
- <developerConnection>scm:git:git@github.com:bigdataviewer/bigdataviewer-server</developerConnection>
- <tag>HEAD</tag>
- <url>https://github.com/bigdataviewer/bigdataviewer-server</url>
- </scm>
</project>
diff --git a/src/main/java/bdv/server/CellHandler.java b/src/main/java/bdv/server/CellHandler.java
index e9024c67fcd25671f262097b5c5ec09b26ce577a..e432f9c77bb702f45c890a433db2095edbf6e50f 100644
--- a/src/main/java/bdv/server/CellHandler.java
+++ b/src/main/java/bdv/server/CellHandler.java
@@ -1,11 +1,40 @@
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.nio.file.Files;
+import java.nio.file.Path;
+import java.nio.file.Paths;
+
+import javax.imageio.ImageIO;
+import javax.servlet.http.HttpServletRequest;
+import javax.servlet.http.HttpServletResponse;
+
+import org.eclipse.jetty.server.Request;
+import org.eclipse.jetty.server.handler.ContextHandler;
+import org.eclipse.jetty.util.log.Log;
+import org.jdom2.Document;
+import org.jdom2.JDOMException;
+import org.jdom2.input.SAXBuilder;
+import org.jdom2.output.Format;
+import org.jdom2.output.XMLOutputter;
+
+import com.google.gson.GsonBuilder;
+import com.google.gson.stream.JsonWriter;
+
import bdv.BigDataViewer;
-import bdv.img.cache.CacheHints;
-import bdv.img.cache.LoadingStrategy;
+import bdv.cache.CacheHints;
+import bdv.cache.LoadingStrategy;
import bdv.img.cache.VolatileCell;
import bdv.img.cache.VolatileGlobalCellCache;
+import bdv.img.cache.VolatileGlobalCellCache.Key;
+import bdv.img.cache.VolatileGlobalCellCache.VolatileCellLoader;
import bdv.img.hdf5.Hdf5ImageLoader;
+import bdv.img.hdf5.Hdf5VolatileShortArrayLoader;
import bdv.img.hdf5.Partition;
import bdv.img.remote.AffineTransform3DJsonSerializer;
import bdv.img.remote.RemoteImageLoader;
@@ -15,39 +44,17 @@ import bdv.spimdata.SequenceDescriptionMinimal;
import bdv.spimdata.SpimDataMinimal;
import bdv.spimdata.XmlIoSpimDataMinimal;
import bdv.util.ThumbnailGenerator;
-
-import com.google.gson.GsonBuilder;
-
-import com.google.gson.stream.JsonWriter;
import mpicbg.spim.data.SpimDataException;
import net.imglib2.img.basictypeaccess.volatiles.array.VolatileShortArray;
import net.imglib2.realtransform.AffineTransform3D;
-import org.eclipse.jetty.server.Handler;
-import org.eclipse.jetty.server.Request;
-import org.eclipse.jetty.server.handler.ContextHandler;
-import org.eclipse.jetty.util.log.Log;
-import org.jdom2.Document;
-import org.jdom2.JDOMException;
-import org.jdom2.input.SAXBuilder;
-import org.jdom2.output.Format;
-import org.jdom2.output.XMLOutputter;
-
-import javax.imageio.ImageIO;
-import javax.servlet.http.HttpServletRequest;
-import javax.servlet.http.HttpServletResponse;
-
-import java.awt.image.BufferedImage;
-import java.io.*;
-import java.nio.file.Files;
-import java.nio.file.Path;
-import java.nio.file.Paths;
-
public class CellHandler extends ContextHandler
{
private static final org.eclipse.jetty.util.log.Logger LOG = Log.getLogger( CellHandler.class );
- private VolatileGlobalCellCache< VolatileShortArray > cache;
+ private VolatileGlobalCellCache cache;
+
+ private final Hdf5VolatileShortArrayLoader loader;
private final CacheHints cacheHints;
@@ -82,11 +89,11 @@ public class CellHandler extends ContextHandler
private boolean active = false;
- private SequenceDescriptionMinimal seq;
+ private final SequenceDescriptionMinimal seq;
private Hdf5ImageLoader imgLoader;
- private String baseUrl;
+ private final String baseUrl;
/**
* DataSet information holder
@@ -104,7 +111,8 @@ public class CellHandler extends ContextHandler
seq = spimData.getSequenceDescription();
imgLoader = ( Hdf5ImageLoader ) seq.getImgLoader();
- cache = imgLoader.getCache();
+ cache = imgLoader.getCacheControl();
+ loader = imgLoader.getShortArrayLoader();
cacheHints = new CacheHints( LoadingStrategy.BLOCKING, 0, false );
// dataSetURL property is used for providing the XML file by replace
@@ -122,7 +130,7 @@ public class CellHandler extends ContextHandler
long size = new File( xmlFilename.replace( ".xml", ".h5" ) ).length();
if ( imgLoader.getPartitions().size() > 0 )
- for ( Partition partition : imgLoader.getPartitions() )
+ for ( final Partition partition : imgLoader.getPartitions() )
{
size += new File( partition.getPath() ).length();
}
@@ -170,7 +178,8 @@ public class CellHandler extends ContextHandler
final int timepoint = Integer.parseInt( parts[ 2 ] );
final int setup = Integer.parseInt( parts[ 3 ] );
final int level = Integer.parseInt( parts[ 4 ] );
- VolatileCell< VolatileShortArray > cell = cache.getGlobalIfCached( timepoint, setup, level, index, cacheHints );
+ final Key key = new VolatileGlobalCellCache.Key( timepoint, setup, level, index );
+ VolatileCell< ? > cell = cache.getLoadingVolatileCache().getIfPresent( key, cacheHints );
if ( cell == null )
{
final int[] cellDims = new int[] {
@@ -181,10 +190,11 @@ public class CellHandler extends ContextHandler
Long.parseLong( parts[ 8 ] ),
Long.parseLong( parts[ 9 ] ),
Long.parseLong( parts[ 10 ] ) };
- cell = cache.createGlobal( cellDims, cellMin, timepoint, setup, level, index, cacheHints );
+ cell = cache.getLoadingVolatileCache().get( key, cacheHints, new VolatileCellLoader<>( loader, timepoint, setup, level, cellDims, cellMin ) );
}
- final short[] data = cell.getData().getCurrentStorageArray();
+ @SuppressWarnings( "unchecked" )
+ final short[] data = ( ( VolatileCell< VolatileShortArray > ) cell ).getData().getCurrentStorageArray();
final byte[] buf = new byte[ 2 * data.length ];
for ( int i = 0, j = 0; i < data.length; i++ )
{
@@ -227,17 +237,17 @@ public class CellHandler extends ContextHandler
}
}
- public void setDescription(String desc)
+ public void setDescription(final String desc)
{
dataSet.setDescription( desc );
}
- public void setCategory(String cate)
+ public void setCategory(final String cate)
{
dataSet.setCategory( cate );
}
- public void setIndex(String idx)
+ public void setIndex(final String idx)
{
dataSet.setIndex( idx );
}
@@ -358,14 +368,14 @@ public class CellHandler extends ContextHandler
* Set the active status
* @param active
*/
- public void setActive( boolean active ) throws SpimDataException
+ public void setActive( final boolean active ) throws SpimDataException
{
this.active = active;
if ( active )
{
imgLoader = ( Hdf5ImageLoader ) seq.getImgLoader();
- cache = imgLoader.getCache();
+ cache = imgLoader.getCacheControl();
}
else
{
diff --git a/src/main/java/bdv/server/JsonDatasetListHandler.java b/src/main/java/bdv/server/JsonDatasetListHandler.java
index e540466b1df3fc84e0c22b62d462efde8640f6d0..59599bb48dd3a31b852ed1cbc3fc5781ad4efbe0 100644
--- a/src/main/java/bdv/server/JsonDatasetListHandler.java
+++ b/src/main/java/bdv/server/JsonDatasetListHandler.java
@@ -21,7 +21,7 @@ import java.util.Comparator;
/**
* Provides a list of available datasets on this {@link BigDataServer}
*
- * @author HongKee Moon <moon@mpi-cbg.de>
+ * @author HongKee Moon <moon@mpi-cbg.de>
*/
public class JsonDatasetListHandler extends ContextHandler
{
diff --git a/src/main/java/bdv/util/ThumbnailGenerator.java b/src/main/java/bdv/util/ThumbnailGenerator.java
index 8f824c63de2d6f27da76bb94cd5cc02d38812fcf..92c0f322bce7e29f9406fd1d063dba49b65e25f5 100644
--- a/src/main/java/bdv/util/ThumbnailGenerator.java
+++ b/src/main/java/bdv/util/ThumbnailGenerator.java
@@ -7,16 +7,12 @@ import java.util.List;
import javax.imageio.ImageIO;
-import net.imglib2.realtransform.AffineTransform3D;
-import net.imglib2.ui.PainterThread;
-import net.imglib2.ui.RenderTarget;
-
import org.jdom2.Document;
import org.jdom2.Element;
import org.jdom2.input.SAXBuilder;
import bdv.BigDataViewer;
-import bdv.img.cache.Cache;
+import bdv.cache.CacheControl;
import bdv.spimdata.SpimDataMinimal;
import bdv.spimdata.XmlIoSpimDataMinimal;
import bdv.tools.InitializeViewerState;
@@ -26,11 +22,15 @@ import bdv.tools.transformation.TransformedSource;
import bdv.tools.transformation.XmlIoTransformedSources;
import bdv.viewer.Source;
import bdv.viewer.SourceAndConverter;
+import bdv.viewer.render.AccumulateProjectorARGB;
import bdv.viewer.render.MultiResolutionRenderer;
import bdv.viewer.state.SourceGroup;
import bdv.viewer.state.SourceState;
import bdv.viewer.state.ViewerState;
import bdv.viewer.state.XmlIoViewerState;
+import net.imglib2.realtransform.AffineTransform3D;
+import net.imglib2.ui.PainterThread;
+import net.imglib2.ui.RenderTarget;
/**
* Created by moon on 2/5/15.
@@ -93,7 +93,7 @@ public class ThumbnailGenerator
}
}
final ThumbnailTarget renderTarget = new ThumbnailTarget();
- new MultiResolutionRenderer( renderTarget, new PainterThread( null ), new double[] { 1 }, 0, false, 1, null, false, new Cache.Dummy() ).paint( state );
+ new MultiResolutionRenderer( renderTarget, new PainterThread( null ), new double[] { 1 }, 0, false, 1, null, false, AccumulateProjectorARGB.factory, new CacheControl.Dummy() ).paint( state );
return renderTarget.bi;
}