From 61094aebb570232632f8584ac8fd470819c5b37b Mon Sep 17 00:00:00 2001
From: Christian Tischer <tischitischer@gmail.com>
Date: Thu, 6 Aug 2020 19:58:27 +0200
Subject: [PATCH] Handle missing n5 blocks (#104)
handle missing n5 blocks by creating empty arrays
TODO consider handling this in the CachedCellImg or possibly re-using
arrays to reduce RAM consumption/ better utilize cache
Co-authored-by: Christian Tischer <christian.tischer@embl.de>
---
src/main/java/bdv/img/n5/N5ImageLoader.java | 40 +++++++++++++++++----
1 file changed, 34 insertions(+), 6 deletions(-)
diff --git a/src/main/java/bdv/img/n5/N5ImageLoader.java b/src/main/java/bdv/img/n5/N5ImageLoader.java
index 00eb8c60..e3d6db5a 100644
--- a/src/main/java/bdv/img/n5/N5ImageLoader.java
+++ b/src/main/java/bdv/img/n5/N5ImageLoader.java
@@ -89,11 +89,7 @@ import net.imglib2.type.volatiles.VolatileUnsignedLongType;
import net.imglib2.type.volatiles.VolatileUnsignedShortType;
import net.imglib2.util.Cast;
import net.imglib2.view.Views;
-import org.janelia.saalfeldlab.n5.DataBlock;
-import org.janelia.saalfeldlab.n5.DataType;
-import org.janelia.saalfeldlab.n5.DatasetAttributes;
-import org.janelia.saalfeldlab.n5.N5FSReader;
-import org.janelia.saalfeldlab.n5.N5Reader;
+import org.janelia.saalfeldlab.n5.*;
import static bdv.img.n5.BdvN5Format.DATA_TYPE_KEY;
import static bdv.img.n5.BdvN5Format.DOWNSAMPLING_FACTORS_KEY;
@@ -352,7 +348,39 @@ public class N5ImageLoader implements ViewerImgLoader, MultiResolutionImgLoader
@Override
public A loadArray( final long[] gridPosition ) throws IOException
{
- return createArray.apply( n5.readBlock( pathName, attributes, gridPosition ) );
+ final DataBlock< ? > dataBlock = n5.readBlock( pathName, attributes, gridPosition );
+
+ if ( dataBlock == null )
+ return createEmptyArray( gridPosition );
+ else
+ return createArray.apply( dataBlock );
+ }
+
+ private A createEmptyArray( long[] gridPosition )
+ {
+ final int[] blockSize = attributes.getBlockSize();
+ final int n = blockSize[ 0 ] * blockSize[ 1 ] * blockSize[ 2 ];
+ switch ( attributes.getDataType() )
+ {
+ case UINT8:
+ case INT8:
+ return createArray.apply( new ByteArrayDataBlock( blockSize, gridPosition, new byte[ n ] ) );
+ case UINT16:
+ case INT16:
+ return createArray.apply( new ShortArrayDataBlock( blockSize, gridPosition, new short[ n ] ) );
+ case UINT32:
+ case INT32:
+ return createArray.apply( new IntArrayDataBlock( blockSize, gridPosition, new int[ n ] ) );
+ case UINT64:
+ case INT64:
+ return createArray.apply( new LongArrayDataBlock( blockSize, gridPosition, new long[ n ] ) );
+ case FLOAT32:
+ return createArray.apply( new FloatArrayDataBlock( blockSize, gridPosition, new float[ n ] ) );
+ case FLOAT64:
+ return createArray.apply( new DoubleArrayDataBlock( blockSize, gridPosition, new double[ n ] ) );
+ default:
+ throw new UnsupportedOperationException("Data type not supported: " + attributes.getDataType());
+ }
}
}
--
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