Move to Java 21

.github/workflows/maven.yml

@@ -16,10 +16,10 @@ jobs:
     steps:
     - uses: actions/checkout@v5
 
-    - name: Set up JDK 11
+    - name: Set up JDK 21
       uses: actions/setup-java@v5
       with:
-        java-version: '11'
+        java-version: '21'
         distribution: 'zulu'
         cache: maven
 

Dockerfile

@@ -32,7 +32,7 @@
 # Install library dependencies before actually building source.
 # This caches libraries into an image layer that can be reused when only source code has changed.
 
-FROM azul/zulu-openjdk-debian:11 as build_environment
+FROM azul/zulu-openjdk-debian:21 as build_environment
 LABEL maintainer="Forrest Collman <forrestc@alleninstitute.org>, Eric Trautman <trautmane@janelia.hhmi.org>"
 
 RUN apt-get update && apt-get install -y maven
@@ -85,7 +85,7 @@ RUN mkdir -p /root/render-lib && \
 # Once web service application is built, set up jetty server and deploy application to it.
 
 # NOTE: jetty version should be kept in sync with values in render/render-ws/pom.xml and render/render-ws/src/main/scripts/install.sh
-FROM jetty:10.0.13-jre11 as render-ws
+FROM jetty:10.0.26-jre21 as render-ws
 
 # add packages not included in base image:
 #   curl and coreutils are always needed for gnu readlink, tzdata is needed to set timezone

docs/pom.xml

@@ -6,7 +6,7 @@
     <parent>
         <artifactId>modules-root</artifactId>
         <groupId>org.janelia.render</groupId>
-        <version>4.3.0-SNAPSHOT</version>
+        <version>5.0.0-SNAPSHOT</version>
     </parent>
 
     <name>Render Documents</name>

docs/src/site/markdown/how-to/how-to-local-spark-intellij.md

@@ -1,7 +1,7 @@
 # How To: Run Spark Locally in IntelliJ
 
 It can be useful to run and test render spark clients within an IDE  
-[using a local master URL](https://spark.apache.org/docs/3.4.1/submitting-applications.html#master-urls).  Unfortunately 
+[using a local master URL](https://spark.apache.org/docs/4.0.4/submitting-applications.html#master-urls).  Unfortunately 
 because we need to exclude spark libraries from the render-ws-spark-client fat jar, you'll need to add a 
 few extra settings to your IntelliJ run configuration to get spark clients to run within the IDE.
 
@@ -10,7 +10,7 @@ few extra settings to your IntelliJ run configuration to get spark clients to ru
 The hadoop client runtime library is required to run spark locally.  If you don't already have it in a local directory, 
 an easy way to install it is to: 
 - Comment out the library's exclusion block in the 
-[render-ws-spark-client pom.xml](../../../../../render-ws-spark-client/pom.xml#L213-L216):
+[render-ws-spark-client pom.xml](../../../../../render-ws-spark-client/pom.xml#L267-L270):
 ```
 <!--
   <exclusion>
@@ -21,10 +21,10 @@ an easy way to install it is to:
 ```
 - Run `mvn compile` to pull the library into your local .m2/repository.  The compilation will fail because of 
   the enforcer no-duplicate-classes rule, but the jar will get pulled.
-- Once `${HOME}/.m2/repository/org/apache/hadoop/hadoop-client-runtime/3.3.4/hadoop-client-runtime-3.3.4.jar` exists,
+- Once `${HOME}/.m2/repository/org/apache/hadoop/hadoop-client-runtime/3.4.1/hadoop-client-runtime-3.4.1.jar` exists,
 restore the pom.xml file to its original state by uncommenting the exclusion.
 
-The local hadoop-client-runtime-3.3.4.jar path can then be referenced in all IntelliJ run configurations 
+The local hadoop-client-runtime-3.4.1.jar path can then be referenced in all IntelliJ run configurations 
 that use spark.  This means you'll only need to do this install process once unless you change spark versions 
 or clean out your local `${HOME}/.m2/repository`.  
 
@@ -44,10 +44,13 @@ Select the run drop-down menu and click Edit Configurations...
 
 Then make the following changes to the run configuration (and save the changes):
 - A: Add `SPARK_LOCAL_IP=127.0.0.1` to the environment variables so that runs will work when you are connected via VPN. 
+     Also make sure the configuration's JDK is 21: spark 4 supports java 17 and 21 only, and on java 24+ every
+     spark client dies in `new JavaSparkContext(...)` with `UnsupportedOperationException: getSubject is not supported`
+     (hadoop's `UserGroupInformation` uses the security manager API that JEP 486 removed). 
 - B: Select the `Modify options` drop-down menu.
 - C: Select `Modify classpath`. 
 - D: Select `Add dependencies with "provided" scope to classpath` and close the drop-down menu.
-- E: Click the `+` button below `Modify classpath:` and use the dialog to add the hadoop-client-runtime-3.3.4.jar 
+- E: Click the `+` button below `Modify classpath:` and use the dialog to add the hadoop-client-runtime-3.4.1.jar 
      path from your local .m2/repository.  This can be a little tricky on Macs because the .m2 directory is usually 
      hidden from Finder windows.  On Macs you can use `⌘⇧.` to reveal dot files or use `⌘⇧G` to open a 
      Go dialog and paste in a path. 

pom.xml

@@ -12,7 +12,7 @@
     <name>Janelia Render Tools And Services</name>
     <groupId>org.janelia.render</groupId>
     <artifactId>modules-root</artifactId>
-    <version>4.3.0-SNAPSHOT</version>
+    <version>5.0.0-SNAPSHOT</version>
 
     <description>A collection of tools and HTTP services (APIs) for rendering transformed image tiles.</description>
     <url>https://github.com/saalfeldlab/render</url>
@@ -150,18 +150,13 @@
         -->
         <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 -->
+        <!--
+          Keep this in sync with the jackson version bundled with the spark version in
+          render-ws-spark-client/pom.xml: spark refuses to start when its jackson-module-scala does not
+          match the jackson-databind on the classpath.  Overriding pom-scijava's jackson.version keeps
+          jackson-databind, jackson-core, jackson-annotations and jackson-jaxrs-json-provider aligned with each other.
+        -->
+        <jackson.version>2.18.6</jackson.version>
 
         <swagger-version>1.6.2</swagger-version>
 
@@ -173,9 +168,9 @@
         <license.licenseName>gpl_v2</license.licenseName>
         <license.copyrightOwners>Howard Hughes Medical Institute</license.copyrightOwners>
 
-        <!-- Override JDK 8 settings in pom-scijava-base now that Jetty 10 has forced us to JDK 11  -->
-        <scijava.jvm.version>11</scijava.jvm.version>
-        <scijava.jvm.build.version>[11,]</scijava.jvm.build.version>
+        <!-- render targets JDK 21; try to not lag behind scijava too much -->
+        <scijava.jvm.version>21</scijava.jvm.version>
+        <scijava.jvm.build.version>[21,]</scijava.jvm.build.version>
 
         <!-- only print test summaries for failures and avoid warnings for skipped tests -->
         <surefire.printSummary>false</surefire.printSummary>
@@ -189,7 +184,20 @@
                 <plugin>
                     <artifactId>maven-compiler-plugin</artifactId>
                     <configuration>
-                        <release>11</release>
+                        <release>21</release>
+                        <!--
+                            Render has no annotation processors of its own and no scijava annotations
+                            (no @Plugin, no org.scijava.annotations usage), but scijava-common puts
+                            org.scijava.annotations.AnnotationProcessor on the class path where javac
+                            discovers it automatically.  That processor still declares
+                            @SupportedSourceVersion(SourceVersion.RELEASE_8) as of scijava-common 2.100.1,
+                            so every module compile prints:
+                              [WARNING] Supported source version 'RELEASE_8' from annotation processor
+                                        'org.scijava.annotations.AnnotationProcessor' less than -source '21'
+                            That warning is not covered by -Xlint:processing, so turn processing off
+                            instead.  Remove this if render ever needs a compile time annotation processor.
+                        -->
+                        <proc>none</proc>
                     </configuration>
                 </plugin>
                 <plugin>

render-app/pom.xml

@@ -5,7 +5,7 @@
     <parent>
         <groupId>org.janelia.render</groupId>
         <artifactId>modules-root</artifactId>
-        <version>4.3.0-SNAPSHOT</version>
+        <version>5.0.0-SNAPSHOT</version>
     </parent>
 
     <name>Render Application</name>
@@ -164,11 +164,11 @@
             <artifactId>n5-hdf5</artifactId>
         </dependency>
 
-        <!-- Use older version of jackson to keep consistent with render-ws jackson-jaxrs-json-provider version. -->
+        <!-- Version comes from the jackson.version property in the root pom, which keeps jackson-databind
+             in sync with jackson-core, jackson-annotations and the jaxrs provider. -->
         <dependency>
             <groupId>com.fasterxml.jackson.core</groupId>
             <artifactId>jackson-databind</artifactId>
-            <version>${jackson-version}</version>
         </dependency>
 
         <!-- Dependencies not defined in SciJava -->
@@ -182,7 +182,6 @@
         <dependency>
             <groupId>sc.fiji</groupId>
             <artifactId>Descriptor_based_registration</artifactId>
-            <version>2.1.3</version>
             <exclusions>
                 <!-- filter out slf4j jar so that it does not conflict with jetty version -->
                 <exclusion>

render-app/src/main/java/org/janelia/alignment/match/CanvasPeakMatcher.java

@@ -7,8 +7,8 @@
 import mpicbg.imglib.type.numeric.real.FloatType;
 import mpicbg.models.Model;
 import mpicbg.models.PointMatch;
-import mpicbg.pointdescriptor.matcher.Matcher;
-import mpicbg.pointdescriptor.matcher.SubsetMatcher;
+import net.preibisch.mvrecon.process.pointcloud.pointdescriptor.matcher.Matcher;
+import net.preibisch.mvrecon.process.pointcloud.pointdescriptor.matcher.SubsetMatcher;
 import mpicbg.util.Timer;
 
 import org.janelia.alignment.match.parameters.GeometricDescriptorParameters;

render-app/src/main/java/org/janelia/alignment/match/parameters/GeometricDescriptorParameters.java

@@ -5,7 +5,7 @@
 import java.io.Serializable;
 import java.util.Objects;
 
-import mpicbg.spim.segmentation.InteractiveDoG;
+import net.preibisch.mvrecon.fiji.plugin.interestpointdetection.interactive.HelperFunctions;
 
 import plugin.DescriptorParameters;
 
@@ -149,7 +149,7 @@ public DescriptorParameters toDescriptorParameters() {
         dp.redundancy = redundancy;
         dp.significance = significance;
         dp.sigma1 = sigma;
-        dp.sigma2 = InteractiveDoG.computeSigma2(sigma.floatValue(), InteractiveDoG.standardSensitivity );
+        dp.sigma2 = HelperFunctions.computeSigma2(sigma, 4); // 4 = former InteractiveDoG.standardSensitivity
         dp.threshold = threshold;
         dp.localization = localization.code;
         dp.lookForMinima = lookForMinima;

render-app/src/main/java/process/GeometricDescriptorMatcher.java

@@ -7,7 +7,7 @@
 import mpicbg.imglib.type.numeric.real.FloatType;
 import mpicbg.models.Model;
 import mpicbg.models.PointMatch;
-import mpicbg.pointdescriptor.matcher.Matcher;
+import net.preibisch.mvrecon.process.pointcloud.pointdescriptor.matcher.Matcher;
 
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;

render-app/src/test/java/org/janelia/alignment/match/GeometricDescriptorSIFTMatcherTest.java

@@ -15,7 +15,7 @@
 import mpicbg.models.AffineModel2D;
 import mpicbg.models.Point;
 import mpicbg.models.PointMatch;
-import mpicbg.spim.io.IOFunctions;
+import net.preibisch.legacy.io.IOFunctions;
 import mpicbg.trakem2.transform.TransformMeshMappingWithMasks.ImageProcessorWithMasks;
 
 import org.janelia.alignment.RenderParameters;

render-app/src/test/java/org/janelia/alignment/spec/TileSpecTest.java

@@ -34,19 +34,19 @@ public void testJsonProcessing() {
         final Map.Entry<Integer, ImageAndMask> firstMipMap = tileSpec.getFirstMipmapEntry();
         Assert.assertNotNull("first mipmap entry is null", firstMipMap);
         Assert.assertEquals("mipmap sorting failed, unexpected first entry returned",
-                            new Integer(0), firstMipMap.getKey());
+                            Integer.valueOf(0), firstMipMap.getKey());
 
-        final ChannelSpec channelSpec = tileSpec.getAllChannels().get(0);
+        final ChannelSpec channelSpec = tileSpec.getAllChannels().getFirst();
 
         Map.Entry<Integer, ImageAndMask> floorMipMap = channelSpec.getFloorMipmapEntry(3);
         Assert.assertNotNull("floor 3 mipmap entry is null", floorMipMap);
         Assert.assertEquals("invalid key for floor 3 mipmap entry",
-                            new Integer(3), floorMipMap.getKey());
+                            Integer.valueOf(3), floorMipMap.getKey());
 
         floorMipMap = channelSpec.getFloorMipmapEntry(4);
         Assert.assertNotNull("floor 4 mipmap entry is null", floorMipMap);
         Assert.assertEquals("invalid key for floor 3 mipmap entry",
-                            new Integer(3), floorMipMap.getKey());
+                            Integer.valueOf(3), floorMipMap.getKey());
 
         final FilterSpec filterSpec = channelSpec.getFilterSpec();
         Assert.assertNotNull("filterSpec is null", filterSpec);

render-ws-java-client/Dockerfile

@@ -14,7 +14,7 @@
 #       so I switched to use the same zulu image used for the final image
 #       rather than try to debug alpine issues.
 
-FROM azul/zulu-openjdk-debian:11 as builder
+FROM azul/zulu-openjdk-debian:21 as builder
 
 RUN apt-get update && apt-get install -y git maven
 
@@ -34,7 +34,7 @@ RUN git clone --branch $GIT_TAG https://github.com/saalfeldlab/render.git . \
 # ---------------------------------------------------------------------
 # Stage 2: Create slimmed down final image that only contains client jar and scripts.
 
-FROM azul/zulu-openjdk-debian:11
+FROM azul/zulu-openjdk-debian:21
 
 # ARGs need to be re-declared for each stage in multi-stage builds - who knew?
 ARG GIT_COMMIT

render-ws-java-client/pom.xml

@@ -5,7 +5,7 @@
     <parent>
         <artifactId>modules-root</artifactId>
         <groupId>org.janelia.render</groupId>
-        <version>4.3.0-SNAPSHOT</version>
+        <version>5.0.0-SNAPSHOT</version>
     </parent>
 
     <name>Render Web Service Java Client</name>
@@ -111,7 +111,7 @@
                                     </excludes>
                                 </filter>
                                 <filter>
-                                    <artifact>sc.fiji:SPIM_Registration</artifact>
+                                    <artifact>net.preibisch:multiview-reconstruction</artifact>
                                     <excludes>
                                         <exclude>META-INF/json/**</exclude>
                                     </excludes>
@@ -270,11 +270,11 @@
             <version>${n5-version}</version>
         </dependency>
 
-        <!-- Use older version of jackson to keep consistent with render-ws jackson-jaxrs-json-provider version. -->
+        <!-- Version comes from the jackson.version property in the root pom, which keeps jackson-databind
+             in sync with jackson-core, jackson-annotations and the jaxrs provider. -->
         <dependency>
             <groupId>com.fasterxml.jackson.core</groupId>
             <artifactId>jackson-databind</artifactId>
-            <version>${jackson-version}</version>
         </dependency>
 
         <!-- Dependencies not defined in SciJava -->

render-ws-java-client/src/main/java/org/janelia/render/client/FixMaskClient.java

@@ -98,7 +98,7 @@ public void runClient(final String[] args)
                 client.setUpDerivedStack();
 
                 for (final String z : parameters.zValues) {
-                    client.fixStackDataForZ(new Double(z));
+                    client.fixStackDataForZ(Double.valueOf(z));
                 }
 
                 if (parameters.completeTargetStack) {
@@ -128,7 +128,7 @@ private FixMaskClient(final Parameters parameters)
                 .filter(path -> path.toString().endsWith(".png"))
                 .forEach(path -> fixedMaskNamesToUrls.put(path.getFileName().toString(), "file:" + path));
 
-        if (this.fixedMaskNamesToUrls.size() == 0) {
+        if (this.fixedMaskNamesToUrls.isEmpty()) {
             throw new IOException(fixedMasksDirectoryPath + " does not contain any fixed .png mask files");
         }
     }

render-ws-java-client/src/main/java/org/janelia/render/client/MontageOutlierDiagnosticsClient.java

@@ -160,7 +160,7 @@ private void run()
                     // Z,Max PM Residual,Tile 1,Tile 2,PM X,PM Y,Mean Tile Pair Residual Is Outlier
                     final String[] v = line.split(",");
                     if (v.length > 3) {
-                        final Double z = new Double(v[0]);
+                        final Double z = Double.valueOf(v[0]);
                         if ((zValues == null) || (zValues.contains(z))) {
                             final List<OutlierPair> pairList =
                                     zToOutlierPairsMap.computeIfAbsent(z,

render-ws-java-client/src/main/java/org/janelia/render/client/StackClient.java

@@ -241,7 +241,7 @@ private void cloneStackVersion()
         if (parameters.zValues != null) {
             zValues = new ArrayList<>(parameters.zValues.size());
             for (final String zString : parameters.zValues) {
-                zValues.add(new Double(zString));
+                zValues.add(Double.valueOf(zString));
             }
         }
 
@@ -304,9 +304,9 @@ private void deleteStack()
                 renderDataClient.deleteStackSection(stack, parameters.sectionId);
             }
         } else {
-            Double z;
+            double z;
             for (final String zString : parameters.zValues) {
-                z = new Double(zString);
+                z = Double.parseDouble(zString);
                 renderDataClient.deleteStack(stack, z);
             }
             if (parameters.sectionId != null) {

render-ws-java-client/src/main/java/org/janelia/render/client/TerraceLayersClient.java

@@ -104,7 +104,7 @@ public static class Parameters extends CommandLineParameters {
         public String roughMatchCollection;
 
         public String getTargetStack() {
-            if ((targetStack == null) || (targetStack.trim().length() == 0)) {
+            if ((targetStack == null) || (targetStack.trim().isEmpty())) {
                 targetStack = stack;
             }
             return targetStack;
@@ -147,7 +147,7 @@ private TerraceLayersClient(final Parameters parameters)
         this.sourceRenderDataClient = parameters.renderWeb.getDataClient();
 
         if ((parameters.targetProject == null) ||
-            (parameters.targetProject.trim().length() == 0) ||
+            (parameters.targetProject.trim().isEmpty()) ||
             (parameters.targetProject.equals(parameters.renderWeb.project))) {
             this.targetRenderDataClient = sourceRenderDataClient;
         } else {
@@ -254,14 +254,14 @@ private void mapMinCoordinatesByConnectedCluster(final List<Double> sortedZs,
         for (final Set<String> connectedGroupIdSet : connectedGroupIdSets) {
             Bounds connectedBounds = null;
             for (final String groupId : connectedGroupIdSet) {
-                final Double z = new Double(groupId);
+                final Double z = Double.valueOf(groupId);
                 final Bounds layerBounds = zToBoundsMap.get(z);
                 connectedBounds = connectedBounds == null ? layerBounds : connectedBounds.union(layerBounds);
                 connectedLayerCount++;
             }
 
             for (final String groupId : connectedGroupIdSet) {
-                final Double z = new Double(groupId);
+                final Double z = Double.valueOf(groupId);
                 zToBoundsMap.put(z, connectedBounds);
                 zToMinCoordinateMap.put(z, minCoordinate);
             }