bump to pom-scijava-37.0.0

# Conflicts: # src/main/java/org/janelia/saalfeldlab/View.java # src/main/java/org/janelia/saalfeldlab/cosem/ViewCosem.java
saalfeldlab · May 2, 2024 · c74a73a · c74a73a
1 parent 062e22a
commit c74a73a
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Showing 8 changed files with 274 additions and 613 deletions.
diff --git a/pom.xml b/pom.xml
@@ -1,19 +1,22 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+<project xmlns="http://maven.apache.org/POM/4.0.0"
+	xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+	xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
 	<modelVersion>4.0.0</modelVersion>
 
 	<parent>
 		<groupId>org.scijava</groupId>
 		<artifactId>pom-scijava</artifactId>
-		<version>33.2.0</version>
+		<version>37.0.0</version>
 	</parent>
 
 	<groupId>org.janelia.saalfeldlab</groupId>
 	<artifactId>n5-utils</artifactId>
 	<version>0.0.7-SNAPSHOT</version>
 
 	<name>N5 Utils</name>
-	<description>simple standalone BigDataViewer for multiple N5 (or HDF5) datasets.</description>
+	<description>simple standalone BigDataViewer for multiple N5 (or HDF5)
+		datasets.</description>
 	<url>https://github.com/saalfeldlab/n5-utils</url>
 	<inceptionYear>2017</inceptionYear>
 	<organization>
@@ -48,27 +51,37 @@
 		<contributor>
 			<name>Jan Funke</name>
 			<url>https://imagej.net/User:Funke</url>
-			<properties><id>funkey</id></properties>
+			<properties>
+				<id>funkey</id>
+			</properties>
 		</contributor>
 		<contributor>
 			<name>Kyle Harrington</name>
 			<url>https://imagej.net/User:Kharrington</url>
-			<properties><id>kephale</id></properties>
+			<properties>
+				<id>kephale</id>
+			</properties>
 		</contributor>
 		<contributor>
 			<name>Gregory Jefferis</name>
 			<url>https://imagej.net/User:Jefferis</url>
-			<properties><id>jefferis</id></properties>
+			<properties>
+				<id>jefferis</id>
+			</properties>
 		</contributor>
 		<contributor>
 			<name>Tobias Pietzsch</name>
 			<url>https://imagej.net/User:Pietzsch</url>
-			<properties><id>tpietzsch</id></properties>
+			<properties>
+				<id>tpietzsch</id>
+			</properties>
 		</contributor>
 		<contributor>
 			<name>Igor Pisarev</name>
 			<url>https://imagej.net/User:Pisarevi</url>
-			<properties><id>igorpisarev</id></properties>
+			<properties>
+				<id>igorpisarev</id>
+			</properties>
 		</contributor>
 		<contributor>
 			<name>Greg Fleishman</name>
@@ -107,13 +120,6 @@
 		<!-- NB: Deploy releases to the SciJava Maven repository. -->
 		<releaseProfiles>sign,deploy-to-scijava</releaseProfiles>
 
-		<!-- TODO remove when pom-scijava-base is updated -->
-		<scijava.jvm.version>8</scijava.jvm.version>
-		<scijava.jvm.build.version>[1.8.0-101,)</scijava.jvm.build.version>
-
-		<maven-enforcer-plugin.version>3.0.0-M3</maven-enforcer-plugin.version>
-		<jacoco-maven-plugin.version>0.8.6</jacoco-maven-plugin.version>
-
 		<n5-jpeg.version>0.0.1-beta1</n5-jpeg.version>
 	</properties>
 
@@ -147,6 +153,11 @@
 			<groupId>org.janelia.saalfeldlab</groupId>
 			<artifactId>n5-hdf5</artifactId>
 		</dependency>
+		<dependency>
+			<groupId>net.imglib2</groupId>
+			<artifactId>imglib2-algorithm-gpl</artifactId>
+		</dependency>
+
 		<dependency>
 			<groupId>org.janelia.saalfeldlab</groupId>
 			<artifactId>n5-aws-s3</artifactId>
@@ -200,11 +211,13 @@
 			<artifactId>n5-jpeg</artifactId>
 			<version>${n5-jpeg.version}</version>
 		</dependency>
-
+		<dependency>
+			<groupId>org.janelia.saalfeldlab</groupId>
+			<artifactId>n5-universe</artifactId>
+		</dependency>
 		<dependency>
 			<groupId>cisd</groupId>
 			<artifactId>jhdf5</artifactId>
-			<version>${cisd.jhdf5.version}</version>
 		</dependency>
 	</dependencies>
 

diff --git a/src/main/java/org/janelia/saalfeldlab/Copy.java b/src/main/java/org/janelia/saalfeldlab/Copy.java
@@ -119,7 +119,6 @@
  */
 package org.janelia.saalfeldlab;
 
-import java.io.IOException;
 import java.util.HashSet;
 import java.util.List;
 import java.util.Map;
@@ -129,12 +128,12 @@
 import java.util.concurrent.ExecutorService;
 import java.util.concurrent.Executors;
 
-import org.janelia.saalfeldlab.N5Factory.N5Options;
 import org.janelia.saalfeldlab.n5.Bzip2Compression;
 import org.janelia.saalfeldlab.n5.Compression;
 import org.janelia.saalfeldlab.n5.DatasetAttributes;
 import org.janelia.saalfeldlab.n5.GzipCompression;
 import org.janelia.saalfeldlab.n5.Lz4Compression;
+import org.janelia.saalfeldlab.n5.N5Exception;
 import org.janelia.saalfeldlab.n5.N5Reader;
 import org.janelia.saalfeldlab.n5.N5Writer;
 import org.janelia.saalfeldlab.n5.RawCompression;
@@ -143,6 +142,7 @@
 import org.janelia.saalfeldlab.n5.hdf5.N5HDF5Writer;
 import org.janelia.saalfeldlab.n5.imglib2.N5Utils;
 import org.janelia.saalfeldlab.n5.jpeg.JPEGCompression;
+import org.janelia.saalfeldlab.n5.universe.N5Factory;
 
 import net.imglib2.RandomAccessibleInterval;
 import net.imglib2.type.NativeType;
@@ -236,7 +236,7 @@ protected void reorderIfNecessary(final long[] array) {
 			reorder(array);
 	}
 
-	protected <T extends NativeType<T>> void copyDataset(final String datasetName) throws IOException, InterruptedException, ExecutionException {
+	protected <T extends NativeType<T>> void copyDataset(final String datasetName) throws InterruptedException, ExecutionException {
 
 		System.out.println(datasetName);
 
@@ -272,8 +272,7 @@ protected <T extends NativeType<T>> void copyDataset(final String datasetName) t
 		copyAttributes(datasetName);
 	}
 
-	protected void copyAttributes(final String groupName)
-			throws IOException {
+	protected void copyAttributes(final String groupName) {
 
 		System.out.println("  attributes:");
 
@@ -291,14 +290,14 @@ protected void copyAttributes(final String groupName)
 
 				try {
 					n5Writer.setAttribute(groupName, key, n5Reader.getAttribute(groupName, key, clazz));
-				} catch (final IOException e) {
+				} catch (final N5Exception e) {
 					e.printStackTrace(System.err);
 				}
 			}
 		});
 	}
 
-	protected <T extends NativeType<T>> void copyGroup(final String groupName) throws IOException, InterruptedException, ExecutionException {
+	protected <T extends NativeType<T>> void copyGroup(final String groupName) throws InterruptedException, ExecutionException {
 
 		System.out.println(groupName);
 
@@ -315,7 +314,7 @@ protected <T extends NativeType<T>> void copyGroup(final String groupName) throw
 	}
 
 	@Override
-	public Void call() throws IOException, InterruptedException, ExecutionException {
+	public Void call() throws InterruptedException, ExecutionException {
 
 		blockSize = blockSizeString == null ? null : parseCSIntArray(blockSizeString);
 
@@ -349,8 +348,14 @@ public Void call() throws IOException, InterruptedException, ExecutionException
 			}
 		}
 
-		n5Reader = N5Factory.createN5Reader(new N5Options(inputContainerPath, blockSize, compression));
-		n5Writer = N5Factory.createN5Writer(new N5Options(outputContainerPath, blockSize, compression));
+		final N5Factory n5Factory = new N5Factory()
+				.hdf5DefaultBlockSize(blockSize)
+				.zarrDimensionSeparator(".")
+				.zarrMapN5Attributes(false)
+				.zarrMergeAttributes(false);
+
+		n5Reader = n5Factory.openReader(inputContainerPath);
+		n5Writer = n5Factory.openWriter(outputContainerPath);
 
 		if (groupNames == null)
 			copyGroup("");

diff --git a/src/main/java/org/janelia/saalfeldlab/Equals.java b/src/main/java/org/janelia/saalfeldlab/Equals.java
@@ -119,15 +119,15 @@
  */
 package org.janelia.saalfeldlab;
 
-import java.io.IOException;
 import java.util.Arrays;
 import java.util.concurrent.Callable;
 import java.util.concurrent.ExecutionException;
 
-import org.janelia.saalfeldlab.N5Factory.N5Options;
 import org.janelia.saalfeldlab.n5.DatasetAttributes;
+import org.janelia.saalfeldlab.n5.N5Exception;
 import org.janelia.saalfeldlab.n5.N5Reader;
 import org.janelia.saalfeldlab.n5.imglib2.N5Utils;
+import org.janelia.saalfeldlab.n5.universe.N5Factory;
 
 import net.imglib2.Cursor;
 import net.imglib2.RandomAccessibleInterval;
@@ -179,18 +179,18 @@ protected <T extends Type<T>> Boolean datasetEquals() {
 
 			return equals;
 		}
-		catch (final IOException e) {
+		catch (final N5Exception e) {
 
 			return false;
 		}
 	}
 
 
 	@Override
-	public Boolean call() throws IOException, InterruptedException, ExecutionException {
+	public Boolean call() throws InterruptedException, ExecutionException {
 
-		n5Reader1 = N5Factory.createN5Reader(new N5Options(inputContainerPath1, null, null));
-		n5Reader2 = N5Factory.createN5Reader(new N5Options(inputContainerPath2, null, null));
+		n5Reader1 = new N5Factory().openReader(inputContainerPath1);
+		n5Reader2 = new N5Factory().openReader(inputContainerPath2);
 
 		return datasetEquals();
 	}