Bump pom-scijava to 45

pom.xml

@@ -5,7 +5,7 @@
     <parent>
         <groupId>org.scijava</groupId>
         <artifactId>pom-scijava</artifactId>
-        <version>39.0.0</version> <!-- 39.0.0 was released on 2024-10-15, see https://mvnrepository.com/artifact/org.scijava/pom-scijava -->
+        <version>45.1.0</version> <!-- 45.1.0 was released on 2026-07-19, see https://mvnrepository.com/artifact/org.scijava/pom-scijava -->
         <relativePath />
     </parent>
 
@@ -138,10 +138,18 @@
           NOTE: To prevent attributes.json read errors the render n5 version should be kept in-sync with
                 the hot-knife n5 version if you need to run concurrent code from both repos on the same n5 group.
         -->
-        <n5-version>3.3.0</n5-version>
-
-        <imglib2.version>7.1.4</imglib2.version>
-        <imglib2-algorithm.version>0.17.2</imglib2-algorithm.version>
+        <n5-version>4.0.1</n5-version>
+
+        <!-- pom-scijava 45 bumps Descriptor_based_registration to 3.0.1, whose SPIM_Registration replacement
+             (net.preibisch:multiview-reconstruction) drops the point-descriptor / DoG API render's geometric
+             descriptor matcher is built on (mpicbg.pointdescriptor.matcher.*, mpicbg.spim.segmentation.*). Porting
+             that matcher is a separate effort, so keep the 2.x line reactor-wide (render-app also pins 2.1.3). -->
+        <Descriptor_based_registration.version>2.1.3</Descriptor_based_registration.version>
+
+        <!-- pom-scijava 45 bumps Stitching_ to 3.1.10, which is compiled for JDK 21 and trips the
+             EnforceBytecodeVersion enforcer rule (render targets JDK 11). Keep 3.1.9 (pom-scijava 39's version,
+             JDK 8 bytecode); render only uses stable mpicbg.stitching.* / stitching.* APIs. -->
+        <Stitching.version>3.1.9</Stitching.version>
 
         <jackson-version>2.14.3</jackson-version> <!-- NOTE: 2.15.3 causes NullPointerException in maven enforcer plugin -->
 

render-app/src/test/java/org/janelia/alignment/loader/HDF5SliceLoaderTest.java

@@ -1,8 +1,9 @@
 package org.janelia.alignment.loader;
 
+import com.google.common.base.Throwables;
+
 import ij.process.ImageProcessor;
 
-import org.apache.commons.lang.exception.ExceptionUtils;
 import org.junit.Assert;
 import org.junit.Test;
 
@@ -21,7 +22,7 @@ public void testLoad() {
         try {
             ip = loader.load(urlString);
         } catch (final Throwable t) {
-            final String failureMessage = ExceptionUtils.getStackTrace(t);
+            final String failureMessage = Throwables.getStackTraceAsString(t);
             Assert.fail("failed load with following exception: " + failureMessage);
         }
         Assert.assertEquals("invalid width", 5000, ip.getWidth());

render-ws-java-client/pom.xml

@@ -172,6 +172,15 @@
         <dependency>
             <groupId>sc.fiji</groupId>
             <artifactId>bigdataviewer-vistools</artifactId>
+            <!-- pom-scijava 45 no longer manages this artifact; pin the version pom-scijava 39 provided. -->
+            <version>1.0.0-beta-36</version>
+        </dependency>
+
+        <!-- RestartSolverClient uses org.apache.commons.lang.math.DoubleRange (commons-lang 2.x). This used to
+             arrive transitively; declare it directly (version managed by pom-scijava at 2.6). -->
+        <dependency>
+            <groupId>commons-lang</groupId>
+            <artifactId>commons-lang</artifactId>
         </dependency>
 
         <dependency>

render-ws-java-client/src/main/java/org/janelia/render/client/multisem/ThomasCalibrationIntensityCorrectionClient.java

@@ -4,7 +4,6 @@
 import com.beust.jcommander.ParametersDelegate;
 import com.google.gson.JsonObject;
 import com.google.gson.JsonParser;
-import com.google.gson.JsonPrimitive;
 
 import java.io.IOException;
 import java.nio.file.Files;
@@ -21,6 +20,7 @@
 import net.imglib2.RandomAccess;
 import net.imglib2.RandomAccessibleInterval;
 import net.imglib2.img.basictypeaccess.AccessFlags;
+import net.imglib2.type.NativeType;
 import net.imglib2.type.numeric.RealType;
 import net.imglib2.type.numeric.real.FloatType;
 
@@ -34,13 +34,9 @@
 import org.janelia.render.client.parameter.CommandLineParameters;
 import org.janelia.render.client.parameter.RenderWebServiceParameters;
 import org.janelia.render.client.parameter.ZRangeParameters;
-import org.janelia.saalfeldlab.n5.DataBlock;
-import org.janelia.saalfeldlab.n5.DataType;
 import org.janelia.saalfeldlab.n5.N5Reader;
 import org.janelia.saalfeldlab.n5.imglib2.N5Utils;
 import org.janelia.saalfeldlab.n5.universe.N5Factory;
-import org.janelia.saalfeldlab.n5.zarr.ZarrDatasetAttributes;
-import org.janelia.saalfeldlab.n5.zarr.ZarrKeyValueReader;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
@@ -417,117 +413,31 @@ private int[] readOptionalIntArray(final N5Reader reader, final String dataset)
 	}
 
 	/**
-	 * Reads all values of a 1D coordinate array as doubles, or returns null if the array's metadata is not present.
+	 * Reads all values of a 1D coordinate array as doubles, or returns null if the dataset is not present.
 	 * <p>
-	 * n5-zarr 1.3.5 fails to parse a {@code .zarray} whose {@code fill_value} is JSON {@code null} (which is how
-	 * xarray writes coordinate arrays), so {@link N5Utils#open} cannot be used here. Instead the {@code .zarray}
-	 * JSON is read directly, its {@code fill_value} is patched to a parseable value (it is irrelevant for chunks
-	 * that are physically present), the resulting {@link ZarrDatasetAttributes} is built via the reader, and the
-	 * chunks are read with {@link N5Reader#readBlock} (which honors the zarr little-endian byte order).
+	 * Uses the same {@link N5Utils#open} overload as {@link #openHomogenizationArray} (see there for why).
+	 * The imglib2 type handles unsigned promotion, so uint8/uint16 labels come out as their unsigned values.
 	 */
-	private double[] readCoordinateValues(final N5Reader reader, final String dataset) {
-		final JsonObject zArray = readZArrayJson(dataset);
-		if (zArray == null) {
+	private <T extends RealType<T> & NativeType<T>> double[] readCoordinateValues(final N5Reader reader,
+																				  final String dataset) {
+		if (!reader.datasetExists(dataset)) {
 			return null;
 		}
-		if (!zArray.has("fill_value") || zArray.get("fill_value").isJsonNull()) {
-			zArray.add("fill_value", new JsonPrimitive("0"));
-		}
-		if (!(reader instanceof ZarrKeyValueReader)) {
-			throw new IllegalArgumentException("expected a zarr reader but got " + reader.getClass().getName());
-		}
-		final ZarrDatasetAttributes attributes = ((ZarrKeyValueReader) reader).createDatasetAttributes(zArray);
-		if (attributes == null) {
-			throw new IllegalArgumentException("could not parse .zarray for coordinate dataset " + dataset);
-		}
-		if (attributes.getNumDimensions() != 1) {
+		final Consumer<IterableInterval<T>> noMissingBlockHandler = blocks -> { };
+		final RandomAccessibleInterval<T> rai = N5Utils.open(reader, dataset, noMissingBlockHandler, AccessFlags.setOf());
+		if (rai.numDimensions() != 1) {
 			throw new IllegalArgumentException("coordinate array " + dataset + " is expected to be 1-dimensional but has "
-					+ attributes.getNumDimensions() + " dimensions");
+					+ rai.numDimensions() + " dimensions");
 		}
 
-		final int length = (int) attributes.getDimensions()[0];
-		final int chunkSize = attributes.getBlockSize()[0];
-		final DataType dataType = attributes.getDataType();
-		final double[] values = new double[length];
-		final int numChunks = (int) Math.ceil((double) length / chunkSize);
-		for (int chunk = 0; chunk < numChunks; chunk++) {
-			final DataBlock<?> block = reader.readBlock(dataset, attributes, (long) chunk);
-			if (block == null) {
-				throw new IllegalArgumentException("missing chunk " + chunk + " of coordinate array " + dataset);
-			}
-			copyBlockValues(block.getData(), dataType, values, chunk * chunkSize);
+		final double[] values = new double[(int) rai.dimension(0)];
+		final RandomAccess<T> access = rai.randomAccess();
+		for (int i = 0; i < values.length; i++) {
+			values[i] = access.setPositionAndGet(i).getRealDouble();
 		}
 		return values;
 	}
 
-	/** Reads the raw .zarray JSON for a dataset from the per-array file, falling back to consolidated .zmetadata. */
-	private JsonObject readZArrayJson(final String dataset) {
-		final Path perArray = Paths.get(params.zarrPath, dataset, ".zarray");
-		try {
-			if (Files.isRegularFile(perArray)) {
-				return JsonParser.parseString(Files.readString(perArray)).getAsJsonObject();
-			}
-		} catch (final Exception e) {
-			LOG.warn("readZArrayJson: failed to read {} ({})", perArray, e.getMessage());
-		}
-		try {
-			final Path zMetadata = Paths.get(params.zarrPath, ".zmetadata");
-			if (Files.isRegularFile(zMetadata)) {
-				final JsonObject root = JsonParser.parseString(Files.readString(zMetadata)).getAsJsonObject();
-				final JsonObject metadata = root.getAsJsonObject("metadata");
-				if (metadata != null) {
-					final JsonObject zArray = metadata.getAsJsonObject(dataset + "/.zarray");
-					if (zArray != null) {
-						return zArray.deepCopy();
-					}
-				}
-			}
-		} catch (final Exception e) {
-			LOG.warn("readZArrayJson: failed to read .zmetadata for {} ({})", dataset, e.getMessage());
-		}
-		return null;
-	}
-
-	/** Copies a decoded data block into dst[offset...], applying unsigned promotion based on the data type. */
-	private static void copyBlockValues(final Object data, final DataType dataType, final double[] dst, final int offset) {
-		if (data instanceof byte[]) {
-			final byte[] a = (byte[]) data;
-			final boolean unsigned = dataType == DataType.UINT8;
-			for (int i = 0; i < a.length && offset + i < dst.length; i++) {
-				dst[offset + i] = unsigned ? (a[i] & 0xFF) : a[i];
-			}
-		} else if (data instanceof short[]) {
-			final short[] a = (short[]) data;
-			final boolean unsigned = dataType == DataType.UINT16;
-			for (int i = 0; i < a.length && offset + i < dst.length; i++) {
-				dst[offset + i] = unsigned ? (a[i] & 0xFFFF) : a[i];
-			}
-		} else if (data instanceof int[]) {
-			final int[] a = (int[]) data;
-			final boolean unsigned = dataType == DataType.UINT32;
-			for (int i = 0; i < a.length && offset + i < dst.length; i++) {
-				dst[offset + i] = unsigned ? (a[i] & 0xFFFFFFFFL) : a[i];
-			}
-		} else if (data instanceof long[]) {
-			final long[] a = (long[]) data;
-			for (int i = 0; i < a.length && offset + i < dst.length; i++) {
-				dst[offset + i] = a[i];
-			}
-		} else if (data instanceof float[]) {
-			final float[] a = (float[]) data;
-			for (int i = 0; i < a.length && offset + i < dst.length; i++) {
-				dst[offset + i] = a[i];
-			}
-		} else if (data instanceof double[]) {
-			final double[] a = (double[]) data;
-			for (int i = 0; i < a.length && offset + i < dst.length; i++) {
-				dst[offset + i] = a[i];
-			}
-		} else {
-			throw new IllegalArgumentException("unsupported coordinate block data type " + data.getClass());
-		}
-	}
-
 	/**
 	 * Opens the (float32) homogenization array lazily.
 	 * <p>

render-ws-java-client/src/main/java/org/janelia/render/client/tile/RenderTilesClient.java

@@ -63,6 +63,7 @@
 import org.janelia.saalfeldlab.googlecloud.GoogleCloudUtils;
 import org.janelia.saalfeldlab.n5.KeyValueAccess;
 import org.janelia.saalfeldlab.n5.LockedChannel;
+import org.janelia.saalfeldlab.n5.N5Exception;
 import org.janelia.saalfeldlab.n5.googlecloud.GoogleCloudStorageKeyValueAccess;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
@@ -659,7 +660,7 @@ void ensureWritableDirectory(final URI uri) {
             if (!keyValueAccess.exists(uri.getPath())) {
                 try {
                     keyValueAccess.createDirectories(uri.getPath());
-                } catch (final IOException e) {
+                } catch (final N5Exception e) {
                     throw new RuntimeException("Could not create directory " + uri, e);
                 }
             }

render-ws-spark-client/src/main/java/org/janelia/render/client/spark/multisem/Wafer6061Inpainter.java

@@ -24,6 +24,7 @@
 import org.janelia.saalfeldlab.n5.N5Writer;
 import org.janelia.saalfeldlab.n5.imglib2.N5Utils;
 import org.janelia.saalfeldlab.n5.universe.N5Factory;
+import org.janelia.saalfeldlab.n5.universe.StorageFormat;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
@@ -106,7 +107,7 @@ public void run() {
 
 		// Read and cache some metadata of the tissue and mask datasets
 		// Assume that the tissue is a multiscale pyramid / mask is a standalone dataset
-		try (final N5Reader n5 = new N5Factory().openReader(N5Factory.StorageFormat.N5, param.n5Path)) {
+		try (final N5Reader n5 = new N5Factory().openReader(StorageFormat.N5, param.n5Path)) {
 			LOG.info("Reading metadata from {}", param.n5Path);
 			tissueAttributes = ExtendedAttributes.read(n5, param.fullDataset(), param.dataset);
 			maskAttributes = ExtendedAttributes.read(n5, param.mask, param.mask);
@@ -118,7 +119,7 @@ public void run() {
 				throw new IllegalArgumentException("Dataset '" + param.output + "' is different from the input dataset and already exists. Stopping.");
 			} else {
 				LOG.info("Output dataset is '{}'. Creating new dataset.", param.output);
-				try (final N5Writer n5Writer = new N5Factory().openWriter(N5Factory.StorageFormat.N5, param.n5Path)) {
+				try (final N5Writer n5Writer = new N5Factory().openWriter(StorageFormat.N5, param.n5Path)) {
 					n5Writer.createDataset(param.output, tissueAttributes.attrs);
 				}
 			}
@@ -179,7 +180,7 @@ private static Grid.Block translateAndCheckHomogeneity(
 
 		// Read the mask block and check if it is homogeneous
 		boolean isHomogeneous = true;
-		try (final N5Reader n5 = new N5Factory().openReader(N5Factory.StorageFormat.N5, param.n5Path)) {
+		try (final N5Reader n5 = new N5Factory().openReader(StorageFormat.N5, param.n5Path)) {
 			final Img<UnsignedByteType> mask = N5Utils.open(n5, param.mask);
 			final Interval interval = Intervals.intersect(mask, block);
 			final RandomAccessibleInterval<UnsignedByteType> maskPixels = Views.interval(mask, interval);
@@ -240,7 +241,7 @@ private static void inpaintBlock(
 		// Preallocate the inpainted block
 		final Img<UnsignedByteType> inpaintedBlock = ArrayImgs.unsignedBytes(block.dimensions);
 
-		try (final N5Reader n5 = new N5Factory().openReader(N5Factory.StorageFormat.N5, param.n5Path)) {
+		try (final N5Reader n5 = new N5Factory().openReader(StorageFormat.N5, param.n5Path)) {
 			// Load and translate the tissue and mask data
 			LOG.info("Loading data at {}", block.offset);
 			final Img<UnsignedByteType> rawTissue = N5Utils.open(n5, param.fullDataset());
@@ -265,7 +266,7 @@ private static void inpaintBlock(
 			LOG.info("Finished inpainting in {} ms", System.currentTimeMillis() - start);
 		}
 
-		try (final N5Writer n5Writer = new N5Factory().openWriter(N5Factory.StorageFormat.N5, param.n5Path)) {
+		try (final N5Writer n5Writer = new N5Factory().openWriter(StorageFormat.N5, param.n5Path)) {
 			N5Utils.saveBlock(inpaintedBlock, n5Writer, param.output, targetAttributes, block.gridPosition);
 			LOG.info("Wrote tissue block to '{}'", param.output);
 		} catch (final Exception e) {

render-ws-spark-client/src/main/java/org/janelia/render/client/spark/n5/DownsampleHelper.java

@@ -19,6 +19,7 @@
 import org.janelia.saalfeldlab.n5.spark.downsample.N5DownsamplerSpark;
 import org.janelia.saalfeldlab.n5.spark.supplier.N5WriterSupplier;
 import org.janelia.saalfeldlab.n5.universe.N5Factory;
+import org.janelia.saalfeldlab.n5.universe.StorageFormat;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
@@ -96,7 +97,7 @@ public void run(final JavaSparkContext sparkContext)
                  basePathOrStorageUrl, sZeroDatasetPath, Arrays.toString(downsampleFactors), requiredSLevel, retryParameters);
 
         final N5WriterSupplier n5Supplier = () ->
-                new N5Factory().openWriter(N5Factory.StorageFormat.N5, basePathOrStorageUrl);
+                new N5Factory().openWriter(StorageFormat.N5, basePathOrStorageUrl);
 
         final N5Writer n5 = n5Supplier.get();
         final DatasetAttributes fullScaleAttributes = n5.getDatasetAttributes(sZeroDatasetPath);

render-ws-spark-client/src/main/java/org/janelia/render/client/spark/n5/N5Client.java

@@ -40,7 +40,7 @@
 import org.janelia.saalfeldlab.n5.N5Writer;
 import org.janelia.saalfeldlab.n5.imglib2.N5Utils;
 import org.janelia.saalfeldlab.n5.universe.N5Factory;
-import org.janelia.saalfeldlab.n5.universe.N5Factory.StorageFormat;
+import org.janelia.saalfeldlab.n5.universe.StorageFormat;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 

render-ws-spark-client/src/main/java/org/janelia/render/client/spark/n5/Util.java

@@ -5,6 +5,7 @@
 import org.janelia.saalfeldlab.n5.N5Writer;
 import org.janelia.saalfeldlab.n5.spark.supplier.N5WriterSupplier;
 import org.janelia.saalfeldlab.n5.universe.N5Factory;
+import org.janelia.saalfeldlab.n5.universe.StorageFormat;
 
 /**
  * Utilities for N5 operations.
@@ -22,7 +23,7 @@ public N5PathSupplier(final String path) {
         @Override
         public N5Writer get()
                 throws IOException {
-            return new N5Factory().openWriter(N5Factory.StorageFormat.N5, path);
+            return new N5Factory().openWriter(StorageFormat.N5, path);
         }
     }
 

render-ws/pom.xml

@@ -124,6 +124,12 @@
                     <groupId>jakarta.validation</groupId>
                     <artifactId>jakarta.validation-api</artifactId>
                 </exclusion>
+                <!-- javax.annotation classes covered by javax.annotation:javax.annotation-api;
+                     the newer resteasy BOM (pom-scijava 45) adds this spec jar, causing duplicate classes -->
+                <exclusion>
+                    <groupId>org.jboss.spec.javax.annotation</groupId>
+                    <artifactId>jboss-annotations-api_1.3_spec</artifactId>
+                </exclusion>
             </exclusions>
         </dependency>
 
@@ -141,6 +147,12 @@
                     <groupId>jakarta.validation</groupId>
                     <artifactId>jakarta.validation-api</artifactId>
                 </exclusion>
+                <!-- javax.annotation classes covered by javax.annotation:javax.annotation-api;
+                     the newer resteasy BOM (pom-scijava 45) adds this spec jar, causing duplicate classes -->
+                <exclusion>
+                    <groupId>org.jboss.spec.javax.annotation</groupId>
+                    <artifactId>jboss-annotations-api_1.3_spec</artifactId>
+                </exclusion>
             </exclusions>
         </dependency>