Eyetracking utilization

build.gradle.kts

@@ -58,6 +58,7 @@ dependencies {
     }
 
     implementation("net.java.dev.jna:jna-platform:5.14.0")
+//    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")
@@ -148,6 +149,19 @@ dependencies {
 val isRelease: Boolean
     get() = System.getProperty("release") == "true"
 
+//kotlin {
+//    jvmToolchain(21)
+////    compilerOptions {
+////        jvmTarget = JvmTarget.JVM_21
+////        freeCompilerArgs = listOf("-Xinline-classes", "-opt-in=kotlin.RequiresOptIn")
+////    }
+//}
+//
+//java {
+//    targetCompatibility = JavaVersion.VERSION_21
+//    sourceCompatibility = JavaVersion.VERSION_21
+//}
+
 tasks {
     withType<KotlinCompile>().all {
         val version = System.getProperty("java.version").substringBefore('.').toInt()
@@ -414,30 +428,32 @@ tasks {
 
     register<JavaExec>(name = "run") {
         classpath = sourceSets.main.get().runtimeClasspath
-        if (project.hasProperty("target")) {
-            project.property("target")?.let { target ->
-                classpath = sourceSets.test.get().runtimeClasspath
-
-                println("Target is $target")
-                //                if(target.endsWith(".kt")) {
-                //                    main = target.substringAfter("kotlin${File.separatorChar}").replace(File.separatorChar, '.').substringBefore(".kt")
-                //                } else {
-                //                    main = target.substringAfter("java${File.separatorChar}").replace(File.separatorChar, '.').substringBefore(".java")
-                //                }
-
-                mainClass.set("$target")
-                val props = System.getProperties().filter { (k, _) -> k.toString().startsWith("scenery.") }
-
-                val additionalArgs = System.getenv("SCENERY_JVM_ARGS")
-                allJvmArgs = if (additionalArgs != null) {
-                    allJvmArgs + props.flatMap { (k, v) -> listOf("-D$k=$v") } + additionalArgs
-                } else {
-                    allJvmArgs + props.flatMap { (k, v) -> listOf("-D$k=$v") }
-                }
+        var target: Any? = null
+        if (project.hasProperty("target"))
+            target = project.property("target")
+        target = "StartEyeTrackingDirectlyKt"
+        if (target != null) {
+            classpath = sourceSets.test.get().runtimeClasspath
+
+            println("Target is $target")
+            //                if(target.endsWith(".kt")) {
+            //                    main = target.substringAfter("kotlin${File.separatorChar}").replace(File.separatorChar, '.').substringBefore(".kt")
+            //                } else {
+            //                    main = target.substringAfter("java${File.separatorChar}").replace(File.separatorChar, '.').substringBefore(".java")
+            //                }
+
+            mainClass.set("$target")
+            val props = System.getProperties().filter { (k, _) -> k.toString().startsWith("scenery.") }
 
-                println("Will run target $target with classpath $classpath, main=${mainClass.get()}")
-                println("JVM arguments passed to target: $allJvmArgs")
+            val additionalArgs = System.getenv("SCENERY_JVM_ARGS")
+            allJvmArgs = if (additionalArgs != null) {
+                allJvmArgs + props.flatMap { (k, v) -> listOf("-D$k=$v") } + additionalArgs
+            } else {
+                allJvmArgs + props.flatMap { (k, v) -> listOf("-D$k=$v") }
             }
+
+            println("Will run target $target with classpath $classpath, main=${mainClass.get()}")
+            println("JVM arguments passed to target: $allJvmArgs")
         }
     }
 

gradle.properties

@@ -1,7 +1,7 @@
 org.gradle.jvmargs=-XX:MaxMetaspaceSize=2g
 org.gradle.caching=true
 jvmTarget=21
-#useLocalScenery=true
+useLocalScenery=true
 kotlinVersion=1.9.23
 dokkaVersion=1.9.10
 scijavaParentPOMVersion=37.0.0

src/main/java/com/intellij/openapi/diagnostic/DefaultLogger.java

@@ -22,6 +22,8 @@
 import org.jetbrains.annotations.NotNull;
 import org.jetbrains.annotations.Nullable;
 
+
+
 public class DefaultLogger extends Logger {
   @SuppressWarnings("UnusedParameters")
   public DefaultLogger(String category) { }

src/main/java/sc/iview/commands/file/OpenDirofTif.java

@@ -0,0 +1,85 @@
+/*-
+ * #%L
+ * Scenery-backed 3D visualization package for ImageJ.
+ * %%
+ * Copyright (C) 2016 - 2021 SciView developers.
+ * %%
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions are met:
+ *
+ * 1. Redistributions of source code must retain the above copyright notice,
+ *    this list of conditions and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above copyright notice,
+ *    this list of conditions and the following disclaimer in the documentation
+ *    and/or other materials provided with the distribution.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+ * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
+ * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+ * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+ * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+ * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+ * POSSIBILITY OF SUCH DAMAGE.
+ * #L%
+ */
+package sc.iview.commands.file;
+
+import org.scijava.command.Command;
+import org.scijava.io.IOService;
+import org.scijava.log.LogService;
+import org.scijava.plugin.Menu;
+import org.scijava.plugin.Parameter;
+import org.scijava.plugin.Plugin;
+import sc.iview.SciView;
+
+import java.io.File;
+import java.io.IOException;
+
+import static sc.iview.commands.MenuWeights.FILE;
+import static sc.iview.commands.MenuWeights.FILE_OPEN;
+
+/**
+ * Command to open a file in SciView
+ *
+ * @author Kyle Harrington
+ *
+ */
+@Plugin(type = Command.class, menuRoot = "SciView", //
+        menu = { @Menu(label = "File", weight = FILE), //
+                @Menu(label = "Open Directory of tif...", weight = FILE_OPEN) })
+public class OpenDirofTif implements Command {
+
+    @Parameter
+    private IOService io;
+
+    @Parameter
+    private LogService log;
+
+    @Parameter
+    private SciView sciView;
+
+    // TODO: Find a more extensible way than hard-coding the extensions.
+    @Parameter(style = "directory")
+    private File file;
+
+    @Parameter
+    private int onlyFirst = 0;
+
+    @Override
+    public void run() {
+        try {
+            if(onlyFirst > 0) {
+                sciView.openDirTiff(file.toPath(), onlyFirst);
+            } else {
+                sciView.openDirTiff(file.toPath(), null);
+            }
+        }
+        catch (final IOException | IllegalArgumentException exc) {
+            log.error( exc );
+        }
+    }
+}

src/main/java/sc/iview/commands/file/OpenTrackFile.java

@@ -0,0 +1,79 @@
+/*-
+ * #%L
+ * Scenery-backed 3D visualization package for ImageJ.
+ * %%
+ * Copyright (C) 2016 - 2021 SciView developers.
+ * %%
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions are met:
+ *
+ * 1. Redistributions of source code must retain the above copyright notice,
+ *    this list of conditions and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above copyright notice,
+ *    this list of conditions and the following disclaimer in the documentation
+ *    and/or other materials provided with the distribution.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+ * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
+ * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+ * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+ * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+ * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+ * POSSIBILITY OF SUCH DAMAGE.
+ * #L%
+ */
+package sc.iview.commands.file;
+
+import org.scijava.command.Command;
+import org.scijava.io.IOService;
+import org.scijava.log.LogService;
+import org.scijava.plugin.Menu;
+import org.scijava.plugin.Parameter;
+import org.scijava.plugin.Plugin;
+import sc.iview.SciView;
+
+import java.io.File;
+import java.io.IOException;
+
+import static sc.iview.commands.MenuWeights.FILE;
+import static sc.iview.commands.MenuWeights.FILE_OPEN;
+
+/**
+ * Command to open a file in SciView
+ *
+ * @author Kyle Harrington
+ *
+ */
+@Plugin(type = Command.class, menuRoot = "SciView", //
+        menu = { @Menu(label = "File", weight = FILE), //
+                @Menu(label = "Open Track File", weight = FILE_OPEN) })
+public class OpenTrackFile implements Command {
+
+    @Parameter
+    private IOService io;
+
+    @Parameter
+    private LogService log;
+
+    @Parameter
+    private SciView sciView;
+
+    // TODO: Find a more extensible way than hard-coding the extensions.
+    @Parameter(style = "open,extensions:csv")
+    private File file;
+
+    @Override
+    public void run() {
+        try {
+            sciView.openTrackFile(file);
+
+        }
+        catch (final IOException | IllegalArgumentException exc) {
+            log.error( exc );
+        }
+    }
+}

src/main/java/sc/iview/event/NodeTaggedEvent.java

@@ -0,0 +1,10 @@
+package sc.iview.event;
+
+import graphics.scenery.Node;
+
+
+public class NodeTaggedEvent extends NodeEvent {
+    public NodeTaggedEvent(final Node node ) {
+        super( node );
+    }
+}