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chore: update dependencies to newest alpha release snapshots #43

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chore: update dependencies to newest alpha release snapshots
bogovicj Mar 17, 2026
89e7a62
chore: use latest releases
bogovicj Apr 14, 2026
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19 changes: 14 additions & 5 deletions pom.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,7 @@
<parent>
<groupId>org.scijava</groupId>
<artifactId>pom-scijava</artifactId>
<version>37.0.0</version>
<version>43.0.0</version>
<relativePath />
</parent>

Expand Down Expand Up @@ -96,17 +96,26 @@
<license.organizationName>Saalfeld Lab</license.organizationName>
<license.copyrightOwners>Igor Pisarev, Stephan Saalfeld</license.copyrightOwners>

<scijava.jvm.version>17</scijava.jvm.version>
<scijava.jvm.version>11</scijava.jvm.version>
<maven-compiler-plugin.version>3.13.0</maven-compiler-plugin.version>
<extra-enforcer-rules.version>1.9.0</extra-enforcer-rules.version>


<!-- NB: Deploy releases to the SciJava Maven repository. -->
<releaseProfiles>sign,deploy-to-scijava</releaseProfiles>
<args4j.version>2.33</args4j.version>
<n5.version>3.2.0</n5.version>
<n5-imglib2.version>7.0.0</n5-imglib2.version>
<n5-ij.version>4.1.1</n5-ij.version>

<n5.version>4.0.0-alpha-12</n5.version>
<n5-aws-s3.version>4.4.0-alpha-9</n5-aws-s3.version>
<n5-blosc.version>2.0.0-alpha-4</n5-blosc.version>
<n5-google-cloud.version>5.2.0-alpha-7</n5-google-cloud.version>
<n5-hdf5.version>2.3.0-alpha-7</n5-hdf5.version>
<n5-ij.version>4.5.0-alpha-8-SNAPSHOT</n5-ij.version>
<n5-imglib2.version>7.1.0-alpha-8</n5-imglib2.version>
<n5-universe.version>2.4.0-alpha-9</n5-universe.version>
<n5-zarr.version>2.0.0-alpha-8</n5-zarr.version>
<n5-zstandard.version>2.0.0-alpha-4</n5-zstandard.version>

<bigdataviewer-core.version>10.4.14</bigdataviewer-core.version>

<kryo.version>4.0.2</kryo.version>
Expand Down
5 changes: 3 additions & 2 deletions src/main/java/org/janelia/saalfeldlab/n5/spark/N5MaxIntensityProjectionSpark.java
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Expand Up @@ -55,6 +55,7 @@
import org.janelia.saalfeldlab.n5.DatasetAttributes;
import org.janelia.saalfeldlab.n5.N5FSReader;
import org.janelia.saalfeldlab.n5.N5Reader;
import org.janelia.saalfeldlab.n5.imglib2.N5Utils;
import org.janelia.saalfeldlab.n5.spark.supplier.N5ReaderSupplier;
import org.janelia.saalfeldlab.n5.spark.util.CmdUtils;
import org.janelia.saalfeldlab.n5.spark.util.N5SparkUtils;
Expand Down Expand Up @@ -219,7 +220,7 @@ public static <T extends NativeType<T> & RealType<T>> void createMaxIntensityPro
new BasicNameValuePair("dataset", datasetPath),
new BasicNameValuePair("call", "create-max-intensity-projection")
).toString();
final CachedCellImg<T, ?> cellImg = Singleton.get(readerCacheKey, () -> N5SparkUtils.openWithLoaderCache(n5, datasetPath, new SoftRefLoaderCache<>()));
final CachedCellImg<T, ?> cellImg = Singleton.get(readerCacheKey, () -> (CachedCellImg<T, ?>)N5Utils.open(n5, datasetPath));
final long[] cellGridDimensions = cellImg.getCellGrid().getGridDimensions();
numCells = Intervals.numElements(cellGridDimensions);
type = Util.getTypeFromInterval(cellImg).createVariable();
Expand Down Expand Up @@ -249,7 +250,7 @@ public static <T extends NativeType<T> & RealType<T>> void createMaxIntensityPro
new BasicNameValuePair("dataset", datasetPath),
new BasicNameValuePair("call", "create-max-intensity-projection")
).toString();
final CachedCellImg<T, ?> cellImg = Singleton.get(readerCacheKey, () -> N5SparkUtils.openWithLoaderCache(n5, datasetPath, new SoftRefLoaderCache<>()));
final CachedCellImg<T, ?> cellImg = Singleton.get(readerCacheKey, () -> (CachedCellImg<T, ?>)N5Utils.open(n5, datasetPath));
final RandomAccess<T> cellImgRandomAccess = cellImg.randomAccess();

final long[] cellMin = new long[dim], cellMax = new long[dim];
Expand Down
3 changes: 2 additions & 1 deletion src/main/java/org/janelia/saalfeldlab/n5/spark/N5ToSliceTiffSpark.java
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Expand Up @@ -58,6 +58,7 @@
import org.janelia.saalfeldlab.n5.DatasetAttributes;
import org.janelia.saalfeldlab.n5.N5FSReader;
import org.janelia.saalfeldlab.n5.N5Reader;
import org.janelia.saalfeldlab.n5.imglib2.N5Utils;
import org.janelia.saalfeldlab.n5.spark.supplier.N5ReaderSupplier;
import org.janelia.saalfeldlab.n5.spark.util.N5SparkUtils;
import org.janelia.saalfeldlab.n5.spark.util.SliceDimension;
Expand Down Expand Up @@ -261,7 +262,7 @@ public static < T extends NativeType< T > & RealType< T >, U extends NativeType<
new BasicNameValuePair("dataset", datasetPath),
new BasicNameValuePair("call", "create-max-intensity-projection")
).toString();
final CachedCellImg<T, ?> cellImg = Singleton.get(readerCacheKey, () -> N5SparkUtils.openWithLoaderCache(n5, datasetPath, new SoftRefLoaderCache<>()));
final CachedCellImg<T, ?> cellImg = Singleton.get(readerCacheKey, () -> (CachedCellImg<T, ?>)N5Utils.open(n5, datasetPath));

final CellGrid cellGrid = cellImg.getCellGrid();
final long[] slicePos = new long[ cellImg.numDimensions() ], cellPos = new long[ cellImg.numDimensions() ];
Expand Down
2 changes: 1 addition & 1 deletion src/main/java/org/janelia/saalfeldlab/n5/spark/SliceTiffToN5Spark.java
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Expand Up @@ -223,7 +223,7 @@ public static < T extends NativeType< T > > void convert(
new BasicNameValuePair("call", "slice-tiff-to-n5-spark")
).toString();

final RandomAccessibleInterval< T > tmpImg = Singleton.get(tmpReaderCacheKey, () -> N5Utils.open( n5Local, tmpDataset ));
final RandomAccessibleInterval< T > tmpImg = Singleton.get(tmpReaderCacheKey, () -> (RandomAccessibleInterval< T > )N5Utils.open( n5Local, tmpDataset ));

final Interval interval = N5SparkUtils.toInterval( minMaxTuple );
final RandomAccessibleInterval< T > tmpImgCrop = Views.offsetInterval( tmpImg, interval );
Expand Down
2 changes: 1 addition & 1 deletion src/main/java/org/janelia/saalfeldlab/n5/spark/downsample/N5DownsamplerSpark.java
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Expand Up @@ -261,7 +261,7 @@ public static <T extends NativeType<T> & RealType<T>> void downsample(
new BasicNameValuePair("call", "n5-downsample-spark")
).toString();

final RandomAccessibleInterval< T > source = Singleton.get(imgCacheKey, () -> N5Utils.open( n5Writer, inputDatasetPath ));
final RandomAccessibleInterval< T > source = Singleton.get(imgCacheKey, () -> (RandomAccessibleInterval< T > )N5Utils.open( n5Writer, inputDatasetPath ));
final RandomAccessibleInterval<T> sourceBlock = Views.offsetInterval(source, sourceInterval);

/* test if empty */
Expand Down
2 changes: 1 addition & 1 deletion src/main/java/org/janelia/saalfeldlab/n5/spark/downsample/N5LabelDownsamplerSpark.java
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Expand Up @@ -235,7 +235,7 @@ public static <T extends NativeType<T> & IntegerType<T>> void downsampleLabel(
new BasicNameValuePair("call", "n5-downsample-spark")
).toString();

final RandomAccessibleInterval< T > source = Singleton.get(imgCacheKey, () -> N5Utils.open( n5Writer, inputDatasetPath ));
final RandomAccessibleInterval< T > source = Singleton.get(imgCacheKey, () -> (RandomAccessibleInterval< T >)N5Utils.open( n5Writer, inputDatasetPath ));
final RandomAccessibleInterval<T> sourceBlock = Views.offsetInterval(source, sourceInterval);

/* test if empty */
Expand Down
2 changes: 1 addition & 1 deletion src/main/java/org/janelia/saalfeldlab/n5/spark/downsample/N5OffsetDownsamplerSpark.java
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Expand Up @@ -202,7 +202,7 @@ public static < T extends NativeType< T > & RealType< T > > void downsampleWithO
new BasicNameValuePair("call", "n5-downsample-spark")
).toString();

final RandomAccessibleInterval< T > source = Singleton.get(imgCacheKey, () -> N5Utils.open( n5Writer, inputDatasetPath ));
final RandomAccessibleInterval< T > source = Singleton.get(imgCacheKey, () -> (RandomAccessibleInterval< T >)N5Utils.open( n5Writer, inputDatasetPath ));

// apply offset to source to align it with respect to the target block
final RandomAccessibleInterval< T > translatedSource = Views.translate( source, offset );
Expand Down
123 changes: 0 additions & 123 deletions src/main/java/org/janelia/saalfeldlab/n5/spark/util/N5SparkUtils.java
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Expand Up @@ -28,41 +28,12 @@
*/
package org.janelia.saalfeldlab.n5.spark.util;

import java.io.IOException;
import java.util.ArrayList;
import java.util.List;
import java.util.Set;
import java.util.stream.Collectors;

import org.janelia.saalfeldlab.n5.DatasetAttributes;
import org.janelia.saalfeldlab.n5.N5Reader;
import org.janelia.saalfeldlab.n5.imglib2.N5CellLoader;

import net.imglib2.FinalInterval;
import net.imglib2.Interval;
import net.imglib2.cache.Cache;
import net.imglib2.cache.CacheLoader;
import net.imglib2.cache.LoaderCache;
import net.imglib2.cache.img.CachedCellImg;
import net.imglib2.cache.img.LoadedCellCacheLoader;
import net.imglib2.cache.ref.BoundedSoftRefLoaderCache;
import net.imglib2.img.basictypeaccess.AccessFlags;
import net.imglib2.img.basictypeaccess.ArrayDataAccessFactory;
import net.imglib2.img.cell.Cell;
import net.imglib2.img.cell.CellGrid;
import net.imglib2.img.cell.LazyCellImg;
import net.imglib2.type.NativeType;
import net.imglib2.type.PrimitiveType;
import net.imglib2.type.numeric.integer.ByteType;
import net.imglib2.type.numeric.integer.IntType;
import net.imglib2.type.numeric.integer.LongType;
import net.imglib2.type.numeric.integer.ShortType;
import net.imglib2.type.numeric.integer.UnsignedByteType;
import net.imglib2.type.numeric.integer.UnsignedIntType;
import net.imglib2.type.numeric.integer.UnsignedLongType;
import net.imglib2.type.numeric.integer.UnsignedShortType;
import net.imglib2.type.numeric.real.DoubleType;
import net.imglib2.type.numeric.real.FloatType;
import net.imglib2.util.Intervals;
import scala.Tuple2;

Expand Down Expand Up @@ -93,98 +64,4 @@ public static Interval toInterval( final Tuple2< long[], long[] > minMaxTuple )
);
}

/**
* Open an N5 dataset as a memory cached {@link LazyCellImg} with bounded cache size.
*
* @param n5
* @param dataset
* @param cacheSize
* @return
* @throws IOException
*/
@SuppressWarnings( { "unchecked", "rawtypes" } )
public static final < T extends NativeType< T > > CachedCellImg< T, ? > openWithBoundedCache(
final N5Reader n5,
final String dataset,
final int cacheSize ) throws IOException
{
return openWithLoaderCache( n5, dataset, new BoundedSoftRefLoaderCache<>(cacheSize));
}

public static final < T extends NativeType< T > > CachedCellImg< T, ? > openWithLoaderCache(
final N5Reader n5,
final String dataset,
final LoaderCache<Long, Cell<?>> loaderCache) throws IOException
{
final DatasetAttributes attributes = n5.getDatasetAttributes( dataset );
final long[] dimensions = attributes.getDimensions();
final int[] blockSize = attributes.getBlockSize();

final N5CellLoader< T > loader = new N5CellLoader<>( n5, dataset, blockSize );

final CellGrid grid = new CellGrid( dimensions, blockSize );

final CachedCellImg< T, ? > img;
final T type;
final Cache< Long, Cell< ? > > cache;
final Set< AccessFlags > accessFlags = AccessFlags.setOf();

switch ( attributes.getDataType() )
{
case INT8:
type = ( T )new ByteType();
cache = loaderCache.withLoader( ( CacheLoader )LoadedCellCacheLoader.get( grid, loader, type, accessFlags ) );
img = new CachedCellImg( grid, type, cache, ArrayDataAccessFactory.get( PrimitiveType.BYTE, accessFlags ) );
break;
case UINT8:
type = ( T )new UnsignedByteType();
cache = loaderCache.withLoader( ( CacheLoader )LoadedCellCacheLoader.get( grid, loader, type, accessFlags ) );
img = new CachedCellImg( grid, type, cache, ArrayDataAccessFactory.get( PrimitiveType.BYTE, accessFlags ) );
break;
case INT16:
type = ( T )new ShortType();
cache = loaderCache.withLoader( ( CacheLoader )LoadedCellCacheLoader.get( grid, loader, type, accessFlags ) );
img = new CachedCellImg( grid, type, cache, ArrayDataAccessFactory.get( PrimitiveType.SHORT, accessFlags ) );
break;
case UINT16:
type = ( T )new UnsignedShortType();
cache = loaderCache.withLoader( ( CacheLoader )LoadedCellCacheLoader.get( grid, loader, type, accessFlags ) );
img = new CachedCellImg( grid, type, cache, ArrayDataAccessFactory.get( PrimitiveType.SHORT, accessFlags ) );
break;
case INT32:
type = ( T )new IntType();
cache = loaderCache.withLoader( ( CacheLoader )LoadedCellCacheLoader.get( grid, loader, type, accessFlags ) );
img = new CachedCellImg( grid, type, cache, ArrayDataAccessFactory.get( PrimitiveType.INT, accessFlags ) );
break;
case UINT32:
type = ( T )new UnsignedIntType();
cache = loaderCache.withLoader( ( CacheLoader )LoadedCellCacheLoader.get( grid, loader, type, accessFlags ) );
img = new CachedCellImg( grid, type, cache, ArrayDataAccessFactory.get( PrimitiveType.INT, accessFlags ) );
break;
case INT64:
type = ( T )new LongType();
cache = loaderCache.withLoader( ( CacheLoader )LoadedCellCacheLoader.get( grid, loader, type, accessFlags ) );
img = new CachedCellImg( grid, type, cache, ArrayDataAccessFactory.get( PrimitiveType.LONG, accessFlags ) );
break;
case UINT64:
type = ( T )new UnsignedLongType();
cache = loaderCache.withLoader( ( CacheLoader )LoadedCellCacheLoader.get( grid, loader, type, accessFlags ) );
img = new CachedCellImg( grid, type, cache, ArrayDataAccessFactory.get( PrimitiveType.LONG, accessFlags ) );
break;
case FLOAT32:
type = ( T )new FloatType();
cache = loaderCache.withLoader( ( CacheLoader )LoadedCellCacheLoader.get( grid, loader, type, accessFlags ) );
img = new CachedCellImg( grid, type, cache, ArrayDataAccessFactory.get( PrimitiveType.FLOAT, accessFlags ) );
break;
case FLOAT64:
type = ( T )new DoubleType();
cache = loaderCache.withLoader( ( CacheLoader )LoadedCellCacheLoader.get( grid, loader, type, accessFlags ) );
img = new CachedCellImg( grid, type, cache, ArrayDataAccessFactory.get( PrimitiveType.DOUBLE, accessFlags ) );
break;
default:
img = null;
}

return img;
}
}
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