Controller tracking

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")
@@ -67,9 +68,6 @@ dependencies {
 
     // 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")
@@ -135,6 +133,8 @@ dependencies {
     // OME
     implementation("ome:formats-bsd")
     implementation("ome:formats-gpl")
+
+    implementation("org.mastodon:mastodon:1.0.0-beta-34")
 }
 
 //kapt {
@@ -148,6 +148,19 @@ 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()

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/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/OpenN5.kt

@@ -139,6 +139,7 @@ class OpenN5 : DynamicCommand() {
                 DataType.FLOAT64 -> N5Utils.openVolatile<DoubleType>(reader, dataset)
                 DataType.OBJECT -> TODO()
                 null -> TODO()
+                DataType.STRING -> TODO()
             }
 
             val wrapped = VolatileViews.wrapAsVolatile(img)

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 );
+    }
+}