Update for scenery 0.9.0

build.gradle.kts

@@ -4,7 +4,7 @@ import java.net.URL
 import sciview.*
 
 plugins {
-    val ktVersion = "1.8.20"
+    val ktVersion = "1.8.22"
     val dokkaVersion = "1.8.20"
 
     java
@@ -25,43 +25,47 @@ java {
 }
 
 repositories {
+    if(project.properties["useMavenLocal"] == "true") {
+        logger.warn("Using local Maven repository as source")
+        mavenLocal()
+    }
     mavenCentral()
     maven("https://maven.scijava.org/content/groups/public")
 }
 
 dependencies {
-    val ktVersion = "1.8.20"
-    implementation(platform("org.scijava:pom-scijava:31.1.0"))
+    val ktVersion = "1.8.22"
+    implementation(platform("org.scijava:pom-scijava:35.1.1"))
 
     // Graphics dependencies
 
-    annotationProcessor("org.scijava:scijava-common:2.90.0")
-    kapt("org.scijava:scijava-common:2.90.0") { // MANUAL version increment
+    // Attention! Manual version increment necessary here!
+    val scijavaCommonVersion = "2.94.1"
+    annotationProcessor("org.scijava:scijava-common:$scijavaCommonVersion")
+    kapt("org.scijava:scijava-common:$scijavaCommonVersion") {
         exclude("org.lwjgl")
     }
 
-    val sceneryVersion = "0.8.0"
+    val sceneryVersion = "0.9.0"
     api("graphics.scenery:scenery:$sceneryVersion") {
         version { strictly(sceneryVersion) }
         exclude("org.biojava.thirdparty", "forester")
         exclude("null", "unspecified")
     }
 
-    implementation("com.fasterxml.jackson.core:jackson-databind:2.13.4.2")
-    implementation("com.fasterxml.jackson.module:jackson-module-kotlin:2.13.4")
-    implementation("com.fasterxml.jackson.dataformat:jackson-dataformat-yaml:2.13.4")
-    implementation("org.msgpack:jackson-dataformat-msgpack:0.9.3")
     implementation("net.java.dev.jna:jna-platform:5.11.0")
-    implementation("net.clearvolume:cleargl")
     implementation("org.janelia.saalfeldlab:n5")
     implementation("org.janelia.saalfeldlab:n5-imglib2")
     implementation("org.apache.logging.log4j:log4j-api:2.20.0")
     implementation("org.apache.logging.log4j:log4j-1.2-api:2.20.0")
 
-    implementation("com.formdev:flatlaf:2.6")
+    implementation("com.formdev:flatlaf")
 
     // SciJava dependencies
 
+    implementation("org.yaml:snakeyaml") {
+        version { strictly("1.33") }
+    }
     implementation("org.scijava:scijava-common")
     implementation("org.scijava:ui-behaviour")
     implementation("org.scijava:script-editor")
@@ -110,6 +114,14 @@ dependencies {
 //    implementation(n5.imglib2)
     implementation("org.janelia.saalfeldlab:n5")
     implementation("org.janelia.saalfeldlab:n5-hdf5")
+    implementation("org.janelia.saalfeldlab:n5-ij:3.2.4-SNAPSHOT")
+    implementation("org.janelia.saalfeldlab:n5-imglib2:5.0.0")
+    implementation("org.janelia.saalfeldlab:n5-viewer_fiji:5.3.0")
+    //implementation("com.github.saalfeldlab:n5-viewer:ec0b177")
+    implementation("org.janelia.saalfeldlab:n5-aws-s3")
+    implementation("org.janelia.saalfeldlab:n5-google-cloud")
+    implementation("org.janelia.saalfeldlab:n5-blosc")
+    implementation("org.janelia.saalfeldlab:n5-zarr")
     implementation("sc.fiji:spim_data")
 
     implementation(platform(kotlin("bom")))
@@ -435,5 +447,7 @@ artifacts {
     archives(dokkaHtmlJar)
 }
 
+
+
 java.withSourcesJar()
 

src/main/java/sc/iview/commands/demo/animation/SceneRiggingDemo.java

@@ -113,7 +113,7 @@ public void run() {
         sciView.centerOnNode( sciView.getActiveNode() );
 
         for( PointLight light : sciView.getLights() ) {
-            Icosphere s = new Icosphere(1f, 1);
+            Icosphere s = new Icosphere(1f, 1, false);
             s.getMaterial().setDiffuse(light.getEmissionColor());
             s.getMaterial().setAmbient(light.getEmissionColor());
             s.getMaterial().setSpecular(light.getEmissionColor());

src/main/java/sc/iview/commands/edit/add/AddOrientationCompass.java

@@ -86,7 +86,7 @@ private Node makeAxis( float axisLength, float angleX, float angleY, float angle
             return null;
         });
 
-        Icosphere axisCap = new Icosphere(AXESBARRADIUS, 2);
+        Icosphere axisCap = new Icosphere(AXESBARRADIUS, 2, false);
         axisCap.ifSpatial(spatial -> {
             spatial.setPosition(new Vector3f(0, axisLength, 0));
             return null;

src/main/java/sc/iview/io/N5IO.java

@@ -29,6 +29,7 @@
 package sc.iview.io;
 
 import bdv.util.AxisOrder;
+import bvv.core.VolumeViewerOptions;
 import graphics.scenery.Group;
 import graphics.scenery.Node;
 import graphics.scenery.primitives.PointCloud;
@@ -46,7 +47,6 @@
 import sc.iview.SciView;
 import sc.iview.SciViewService;
 import sc.iview.process.MeshConverter;
-import tpietzsch.example2.VolumeViewerOptions;
 
 import java.io.File;
 import java.io.IOException;

src/main/java/sc/iview/ui/REPLPane.java

@@ -75,7 +75,7 @@ public REPLPane(final Context context) {
     final JScrollPane outputScroll = new JScrollPane(output);
     outputScroll.setPreferredSize(new Dimension(440, 400));
 
-    repl = new ScriptREPL(context, output.getOutputStream());
+    repl = new ScriptREPL(context, "Python (Jython)", output.getOutputStream());
     repl.initialize();
 
     final Writer writer = output.getOutputWriter();
@@ -89,7 +89,7 @@ public REPLPane(final Context context) {
     //prompt = new REPLEditor(repl, vars, output);
     prompt = new REPLEditor(repl, null, output);
     context.inject(prompt);
-    prompt.setREPLLanguage("Python");
+
     final JScrollPane promptScroll = new JScrollPane(prompt);
 
     final JPanel bottomPane = new JPanel();

src/main/kotlin/sc/iview/SciView.kt

@@ -37,11 +37,11 @@ import bdv.util.RandomAccessibleIntervalSource4D
 import bdv.util.volatiles.VolatileView
 import bdv.viewer.Source
 import bdv.viewer.SourceAndConverter
+import bvv.core.VolumeViewerOptions
 import dev.dirs.ProjectDirectories
 import graphics.scenery.*
 import graphics.scenery.Scene.RaycastResult
 import graphics.scenery.backends.Renderer
-import graphics.scenery.backends.opengl.OpenGLRenderer
 import graphics.scenery.backends.vulkan.VulkanRenderer
 import graphics.scenery.controls.InputHandler
 import graphics.scenery.controls.OpenVRHMD
@@ -110,7 +110,6 @@ import sc.iview.ui.CustomPropertyUI
 import sc.iview.ui.MainWindow
 import sc.iview.ui.SwingMainWindow
 import sc.iview.ui.TaskManager
-import tpietzsch.example2.VolumeViewerOptions
 import java.awt.event.WindowListener
 import java.io.IOException
 import java.net.URL
@@ -388,10 +387,9 @@ class SciView : SceneryBase, CalibratedRealInterval<CalibratedAxis> {
                 versionString = versionString.substring(0, 5)
                 val launcherVersion = Version(versionString)
                 val nonWorkingVersion = Version("4.0.5")
-                if (launcherVersion.compareTo(nonWorkingVersion) <= 0
+                if (launcherVersion <= nonWorkingVersion
                         && !java.lang.Boolean.parseBoolean(System.getProperty("sciview.DisableLauncherVersionCheck", "false"))) {
-                    logger.info("imagej-launcher version smaller or equal to non-working version ($versionString vs. 4.0.5), disabling Vulkan as rendering backend. Disable check by setting 'scenery.DisableLauncherVersionCheck' system property to 'true'.")
-                    System.setProperty("scenery.Renderer", "OpenGLRenderer")
+                    throw IllegalStateException("imagej-launcher version is outdated, please update your Fiji installation.")
                 } else {
                     logger.info("imagej-launcher version bigger that non-working version ($versionString vs. 4.0.5), all good.")
                 }