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Remove obsolete check for UnsignedShortType when exporting to HDF5 #173

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merged 1 commit into from
Mar 1, 2024
Merged

Remove obsolete check for UnsignedShortType when exporting to HDF5 #173

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60 changes: 24 additions & 36 deletions src/main/java/bdv/export/WriteSequenceToHdf5.java
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Original file line number Diff line number Diff line change
Expand Up @@ -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;
Expand All @@ -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;
Expand All @@ -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
Expand Down Expand Up @@ -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() )
Expand Down
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