diff --git a/pom.xml b/pom.xml
index a61c695cb201a0c2e026602af9233a204b449420..410704e7b097c36eb3b6c599801e19c2ca191865 100644
--- a/pom.xml
+++ b/pom.xml
@@ -5,7 +5,7 @@
<parent>
<groupId>org.scijava</groupId>
<artifactId>pom-scijava</artifactId>
- <version>26.0.0</version>
+ <version>28.0.0</version>
<relativePath />
</parent>
@@ -87,8 +87,10 @@
<stringtemplate.version>3.2.1</stringtemplate.version>
<!-- TODO: Remove these version pins and update the code. -->
- <bigdataviewer-core.version>3.0.3</bigdataviewer-core.version>
- <imglib2.version>3.3.0</imglib2.version>
+ <bigdataviewer-core.version>9.0.3</bigdataviewer-core.version>
+ <imglib2.version>5.9.0</imglib2.version>
+ <imglib2-cache.version>1.0.0-beta-13</imglib2-cache.version>
+ <spim_data.version>2.2.4</spim_data.version>
</properties>
<repositories>
diff --git a/src/main/java/bdv/server/CellHandler.java b/src/main/java/bdv/server/CellHandler.java
index 1cb8682b2b339e9bfbf79896e1582f7c478cab24..9777bf3bd1b9185ab14536897b517c6443f6edaf 100644
--- a/src/main/java/bdv/server/CellHandler.java
+++ b/src/main/java/bdv/server/CellHandler.java
@@ -10,10 +10,15 @@ import java.nio.file.Files;
import java.nio.file.Path;
import java.nio.file.Paths;
+import java.util.concurrent.ExecutionException;
import javax.imageio.ImageIO;
import javax.servlet.http.HttpServletRequest;
import javax.servlet.http.HttpServletResponse;
+import net.imglib2.cache.CacheLoader;
+import net.imglib2.cache.LoaderCache;
+import net.imglib2.cache.ref.SoftRefLoaderCache;
+import net.imglib2.img.cell.Cell;
import org.eclipse.jetty.server.Request;
import org.eclipse.jetty.server.handler.ContextHandler;
import org.eclipse.jetty.util.log.Log;
@@ -26,12 +31,7 @@ import org.jdom2.output.XMLOutputter;
import com.google.gson.GsonBuilder;
import bdv.BigDataViewer;
-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.remote.AffineTransform3DJsonSerializer;
@@ -49,11 +49,74 @@ public class CellHandler extends ContextHandler
{
private static final org.eclipse.jetty.util.log.Logger LOG = Log.getLogger( CellHandler.class );
- private final VolatileGlobalCellCache cache;
+ /**
+ * Key for a cell identified by timepoint, setup, level, and index
+ * (flattened spatial coordinate).
+ */
+ public static class Key
+ {
+ private final int timepoint;
+
+ private final int setup;
+
+ private final int level;
+
+ private final long index;
+
+ private final String[] parts;
+
+ /**
+ * Create a Key for the specified cell. Note that {@code cellDims} and
+ * {@code cellMin} are not used for {@code hashcode()/equals()}.
+ *
+ * @param timepoint
+ * timepoint coordinate of the cell
+ * @param setup
+ * setup coordinate of the cell
+ * @param level
+ * level coordinate of the cell
+ * @param index
+ * index of the cell (flattened spatial coordinate of the
+ * cell)
+ */
+ public Key( final int timepoint, final int setup, final int level, final long index, final String[] parts )
+ {
+ this.timepoint = timepoint;
+ this.setup = setup;
+ this.level = level;
+ this.index = index;
+ this.parts = parts;
+
+ int value = Long.hashCode( index );
+ value = 31 * value + level;
+ value = 31 * value + setup;
+ value = 31 * value + timepoint;
+ hashcode = value;
+ }
+
+ @Override
+ public boolean equals( final Object other )
+ {
+ if ( this == other )
+ return true;
+ if ( !( other instanceof VolatileGlobalCellCache.Key ) )
+ return false;
+ final Key that = ( Key ) other;
+ return ( this.index == that.index ) && ( this.timepoint == that.timepoint ) && ( this.setup == that.setup ) && ( this.level == that.level );
+ }
- private final Hdf5VolatileShortArrayLoader loader;
+ final int hashcode;
- private final CacheHints cacheHints;
+ @Override
+ public int hashCode()
+ {
+ return hashcode;
+ }
+ }
+
+ private final CacheLoader< Key, Cell< ? > > loader;
+
+ private final LoaderCache< Key, Cell< ? > > cache;
/**
* Full path of the dataset xml file this {@link CellHandler} is serving.
@@ -98,9 +161,20 @@ public class CellHandler extends ContextHandler
final SequenceDescriptionMinimal seq = spimData.getSequenceDescription();
final Hdf5ImageLoader imgLoader = ( Hdf5ImageLoader ) seq.getImgLoader();
- cache = imgLoader.getCacheControl();
- loader = imgLoader.getShortArrayLoader();
- cacheHints = new CacheHints( LoadingStrategy.BLOCKING, 0, false );
+ final Hdf5VolatileShortArrayLoader cacheArrayLoader = imgLoader.getShortArrayLoader();
+ loader = key -> {
+ final int[] cellDims = new int[] {
+ Integer.parseInt( key.parts[ 5 ] ),
+ Integer.parseInt( key.parts[ 6 ] ),
+ Integer.parseInt( key.parts[ 7 ] ) };
+ final long[] cellMin = new long[] {
+ Long.parseLong( key.parts[ 8 ] ),
+ Long.parseLong( key.parts[ 9 ] ),
+ Long.parseLong( key.parts[ 10 ] ) };
+ return new Cell<>( cellDims, cellMin, cacheArrayLoader.loadArray( key.timepoint, key.setup, key.level, cellDims, cellMin ) );
+ };
+
+ cache = new SoftRefLoaderCache<>();
// dataSetURL property is used for providing the XML file by replace
// SequenceDescription>ImageLoader>baseUrl
@@ -145,23 +219,18 @@ 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 ] );
- final Key key = new VolatileGlobalCellCache.Key( timepoint, setup, level, index );
- VolatileCell< ? > cell = cache.getLoadingVolatileCache().getIfPresent( key, cacheHints );
- if ( cell == null )
+ final Key key = new Key( timepoint, setup, level, index, parts );
+ short[] data;
+ try
+ {
+ final Cell< ? > cell = cache.get( key, loader );
+ data = ( ( VolatileShortArray ) cell.getData() ).getCurrentStorageArray();
+ }
+ catch ( ExecutionException e )
{
- final int[] cellDims = new int[] {
- Integer.parseInt( parts[ 5 ] ),
- Integer.parseInt( parts[ 6 ] ),
- Integer.parseInt( parts[ 7 ] ) };
- final long[] cellMin = new long[] {
- Long.parseLong( parts[ 8 ] ),
- Long.parseLong( parts[ 9 ] ),
- Long.parseLong( parts[ 10 ] ) };
- cell = cache.getLoadingVolatileCache().get( key, cacheHints, new VolatileCellLoader<>( loader, timepoint, setup, level, cellDims, cellMin ) );
+ data = new short[ 0 ];
}
- @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++ )
{
diff --git a/src/main/java/bdv/util/ThumbnailGenerator.java b/src/main/java/bdv/util/ThumbnailGenerator.java
index 92c0f322bce7e29f9406fd1d063dba49b65e25f5..f8d64a61efc32e9f4be13b7bee888a998077ea9a 100644
--- a/src/main/java/bdv/util/ThumbnailGenerator.java
+++ b/src/main/java/bdv/util/ThumbnailGenerator.java
@@ -114,7 +114,7 @@ public class ThumbnailGenerator
final int numGroups = 10;
final ArrayList< SourceGroup > groups = new ArrayList< SourceGroup >( numGroups );
for ( int i = 0; i < numGroups; ++i )
- groups.add( new SourceGroup( "", null ) );
+ groups.add( new SourceGroup( "" ) );
state = new ViewerState( sources, groups, numTimePoints );
if ( !sources.isEmpty() )