From 020a185ead3a2e124eca8dd648ea6816dc011ef3 Mon Sep 17 00:00:00 2001
From: tpietzsch <tobias.pietzsch@gmail.com>
Date: Fri, 1 Mar 2024 10:03:01 +0100
Subject: [PATCH] Remove obsolete check for UnsignedShortType when exporting to
 HDF5

---
 .../java/bdv/export/WriteSequenceToHdf5.java  | 60 ++++++++-----------
 1 file changed, 24 insertions(+), 36 deletions(-)

diff --git a/src/main/java/bdv/export/WriteSequenceToHdf5.java b/src/main/java/bdv/export/WriteSequenceToHdf5.java
index 13b90b61..298714e9 100644
--- a/src/main/java/bdv/export/WriteSequenceToHdf5.java
+++ b/src/main/java/bdv/export/WriteSequenceToHdf5.java
@@ -28,6 +28,30 @@
  */
 package bdv.export;
 
+import java.io.File;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.Map;
+import java.util.Map.Entry;
+import java.util.concurrent.ExecutorService;
+import java.util.concurrent.Executors;
+import java.util.function.Function;
+
+import org.janelia.saalfeldlab.n5.ByteArrayDataBlock;
+import org.janelia.saalfeldlab.n5.Compression;
+import org.janelia.saalfeldlab.n5.DataBlock;
+import org.janelia.saalfeldlab.n5.DataType;
+import org.janelia.saalfeldlab.n5.DatasetAttributes;
+import org.janelia.saalfeldlab.n5.DoubleArrayDataBlock;
+import org.janelia.saalfeldlab.n5.FloatArrayDataBlock;
+import org.janelia.saalfeldlab.n5.GzipCompression;
+import org.janelia.saalfeldlab.n5.IntArrayDataBlock;
+import org.janelia.saalfeldlab.n5.LongArrayDataBlock;
+import org.janelia.saalfeldlab.n5.RawCompression;
+import org.janelia.saalfeldlab.n5.ShortArrayDataBlock;
+
 import bdv.export.ExportScalePyramid.AfterEachPlane;
 import bdv.export.ExportScalePyramid.Block;
 import bdv.export.ExportScalePyramid.DatasetIO;
@@ -38,19 +62,8 @@
 import bdv.img.n5.DataTypeProperties;
 import bdv.spimdata.SequenceDescriptionMinimal;
 import ch.systemsx.cisd.hdf5.HDF5Factory;
-import ch.systemsx.cisd.hdf5.HDF5IntStorageFeatures;
 import ch.systemsx.cisd.hdf5.IHDF5Reader;
 import ch.systemsx.cisd.hdf5.IHDF5Writer;
-import java.io.File;
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.Collections;
-import java.util.HashMap;
-import java.util.Map;
-import java.util.Map.Entry;
-import java.util.concurrent.ExecutorService;
-import java.util.concurrent.Executors;
-import java.util.function.Function;
 import mpicbg.spim.data.XmlHelpers;
 import mpicbg.spim.data.generic.sequence.AbstractSequenceDescription;
 import mpicbg.spim.data.generic.sequence.BasicImgLoader;
@@ -61,28 +74,11 @@
 import mpicbg.spim.data.sequence.ViewId;
 import net.imglib2.Dimensions;
 import net.imglib2.RandomAccessibleInterval;
-import net.imglib2.cache.img.SingleCellArrayImg;
 import net.imglib2.img.cell.CellImg;
 import net.imglib2.type.NativeType;
 import net.imglib2.type.numeric.RealType;
 import net.imglib2.type.numeric.integer.UnsignedShortType;
 import net.imglib2.util.Cast;
-import net.imglib2.util.Intervals;
-import org.janelia.saalfeldlab.n5.ByteArrayDataBlock;
-import org.janelia.saalfeldlab.n5.Compression;
-import org.janelia.saalfeldlab.n5.DataBlock;
-import org.janelia.saalfeldlab.n5.DataType;
-import org.janelia.saalfeldlab.n5.DatasetAttributes;
-import org.janelia.saalfeldlab.n5.DoubleArrayDataBlock;
-import org.janelia.saalfeldlab.n5.FloatArrayDataBlock;
-import org.janelia.saalfeldlab.n5.GzipCompression;
-import org.janelia.saalfeldlab.n5.IntArrayDataBlock;
-import org.janelia.saalfeldlab.n5.LongArrayDataBlock;
-import org.janelia.saalfeldlab.n5.N5Writer;
-import org.janelia.saalfeldlab.n5.RawCompression;
-import org.janelia.saalfeldlab.n5.ShortArrayDataBlock;
-
-import static net.imglib2.util.Util.long2int;
 
 /**
  * Create a hdf5 files containing image data from all views and all timepoints
@@ -398,14 +394,6 @@ public static void writeHdf5PartitionFile(
 		// get the BasicImgLoader that supplies the images
 		final BasicImgLoader imgLoader = seq.getImgLoader();
 
-		for ( final BasicViewSetup setup : seq.getViewSetupsOrdered() ) {
-			final Object type = imgLoader.getSetupImgLoader( setup.getId() ).getImageType();
-			if ( !( type instanceof UnsignedShortType ) )
-				throw new IllegalArgumentException( "Expected BasicImgLoader<UnsignedShortTyp> but your dataset has BasicImgLoader<"
-						+ type.getClass().getSimpleName() + ">.\nCurrently writing to HDF5 is only supported for UnsignedShortType." );
-		}
-
-
 		// open HDF5 partition output file
 		final File hdf5File = new File( partition.getPath() );
 		if ( hdf5File.exists() )