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Fix CellHandler
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Works again for 16bit HDF5.
Other backends / datatypes are still not supported.
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@tpietzsch
tpietzsch committed Nov 21, 2024
1 parent a9c480a commit 9783c52
Showing 1 changed file with 17 additions and 109 deletions.
126 changes: 17 additions & 109 deletions src/main/java/bdv/server/CellHandler.java
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Original file line number Diff line number Diff line change
Expand Up @@ -27,19 +27,15 @@
import java.io.OutputStream;
import java.io.PrintWriter;
import java.io.StringWriter;
import java.nio.ByteBuffer;
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;
Expand All @@ -52,9 +48,8 @@
import com.google.gson.GsonBuilder;

import bdv.BigDataViewer;
import bdv.img.cache.VolatileGlobalCellCache;
import bdv.cache.SharedQueue;
import bdv.img.hdf5.Hdf5ImageLoader;
import bdv.img.hdf5.Hdf5ImageLoader.SetupImgLoader;
import bdv.img.remote.AffineTransform3DJsonSerializer;
import bdv.img.remote.RemoteImageLoader;
import bdv.img.remote.RemoteImageLoaderMetaData;
Expand All @@ -63,82 +58,17 @@
import bdv.spimdata.XmlIoSpimDataMinimal;
import bdv.util.ThumbnailGenerator;
import mpicbg.spim.data.SpimDataException;
import net.imglib2.RandomAccessibleInterval;
import net.imglib2.img.basictypeaccess.volatiles.array.VolatileShortArray;
import net.imglib2.img.cell.AbstractCellImg;
import net.imglib2.img.cell.Cell;
import net.imglib2.realtransform.AffineTransform3D;
import net.imglib2.type.numeric.integer.UnsignedShortType;

public class CellHandler extends ContextHandler
{
private static final org.eclipse.jetty.util.log.Logger LOG = Log.getLogger( CellHandler.class );

/**
* 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 );
}

final int hashcode;

@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.
*/
Expand Down Expand Up @@ -175,27 +105,15 @@ public int hashCode()
*/
private final String thumbnailFilename;

private final Hdf5ImageLoader imgLoader;

public CellHandler( final String baseUrl, final String xmlFilename, final String datasetName, final String thumbnailsDirectory ) 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();

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 ] ) };
SetupImgLoader<?, ?> setupImgLoader = imgLoader.getSetupImgLoader(key.setup);
return new Cell<>( cellDims, cellMin, setupImgLoader.getVolatileImage(key.timepoint, key.level));
};

cache = new SoftRefLoaderCache<>();
imgLoader = ( Hdf5ImageLoader ) seq.getImgLoader();
imgLoader.setCreatedSharedQueue( new SharedQueue( 0 ) );

// dataSetURL property is used for providing the XML file by replace
// SequenceDescription>ImageLoader>baseUrl
Expand Down Expand Up @@ -240,25 +158,15 @@ public void doHandle( final String target, final Request baseRequest, final Http
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 Key( timepoint, setup, level, index, parts );
short[] data;
try
{
final Cell< ? > cell = cache.get( key, loader );
data = ( ( VolatileShortArray ) cell.getData() ).getCurrentStorageArray();
}
catch ( ExecutionException e )
{
data = new short[ 0 ];
}

final RandomAccessibleInterval< ? > image = imgLoader.getSetupImgLoader( setup ).getImage( timepoint, level );
final AbstractCellImg< UnsignedShortType, ?, ?, ? > cellImg = ( AbstractCellImg< UnsignedShortType, ?, ?, ? > ) image;
final long[] gridpos = new long[ cellImg.numDimensions() ];
cellImg.getCellGrid().getCellGridPositionFlat( index, gridpos );
final Cell< ? > cell = cellImg.getCells().getAt( gridpos );
final short[] data = ( ( VolatileShortArray ) cell.getData() ).getCurrentStorageArray();
final byte[] buf = new byte[ 2 * data.length ];
for ( int i = 0, j = 0; i < data.length; i++ )
{
final short s = data[ i ];
buf[ j++ ] = ( byte ) ( ( s >> 8 ) & 0xff );
buf[ j++ ] = ( byte ) ( s & 0xff );
}
ByteBuffer.wrap( buf ).asShortBuffer().put( data );

response.setContentType( "application/octet-stream" );
response.setContentLength( buf.length );
Expand Down

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