Eyetracking utilization

build.gradle.kts

@@ -22,6 +22,7 @@ java {
 }
 
 repositories {
+    mavenCentral()
     if(project.properties["useMavenLocal"] == "true") {
         logger.warn("Using local Maven repository as source")
         mavenLocal()
@@ -44,7 +45,7 @@ dependencies {
         exclude("org.lwjgl")
     }
 
-    val sceneryVersion = "0.11.2"
+    val sceneryVersion = "0.12.0"
     api("graphics.scenery:scenery:$sceneryVersion") {
         version { strictly(sceneryVersion) }
         exclude("org.biojava.thirdparty", "forester")

src/main/java/sc/iview/commands/file/OpenDirOfTIFF.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 OpenDirOfTIFF 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/kotlin/sc/iview/SciView.kt

@@ -55,9 +55,9 @@ import graphics.scenery.utils.ExtractsNatives.Companion.getPlatform
 import graphics.scenery.utils.LogbackUtils
 import graphics.scenery.utils.SceneryPanel
 import graphics.scenery.utils.Statistics
-import graphics.scenery.utils.extensions.times
 import graphics.scenery.volumes.Colormap
 import graphics.scenery.volumes.RAIVolume
+import graphics.scenery.volumes.TransferFunction
 import graphics.scenery.volumes.Volume
 import graphics.scenery.volumes.Volume.Companion.fromXML
 import graphics.scenery.volumes.Volume.Companion.setupId
@@ -85,6 +85,7 @@ import net.imglib2.type.numeric.integer.UnsignedByteType
 import net.imglib2.view.Views
 import org.joml.Quaternionf
 import org.joml.Vector3f
+import org.joml.Vector4f
 import org.scijava.Context
 import org.scijava.`object`.ObjectService
 import org.scijava.display.Display
@@ -100,6 +101,7 @@ import org.scijava.thread.ThreadService
 import org.scijava.util.ColorRGB
 import org.scijava.util.Colors
 import org.scijava.util.VersionUtils
+import sc.iview.commands.demo.animation.ParticleDemo
 import sc.iview.commands.edit.InspectorInteractiveCommand
 import sc.iview.event.NodeActivatedEvent
 import sc.iview.event.NodeAddedEvent
@@ -110,14 +112,14 @@ import sc.iview.ui.CustomPropertyUI
 import sc.iview.ui.MainWindow
 import sc.iview.ui.SwingMainWindow
 import sc.iview.ui.TaskManager
-import ucar.units.ConversionException
 import java.awt.event.WindowListener
 import java.io.File
 import java.io.IOException
 import java.net.JarURLConnection
 import java.net.URL
 import java.nio.ByteBuffer
 import java.nio.FloatBuffer
+import java.nio.file.Path
 import java.time.LocalDate
 import java.time.format.DateTimeFormatter
 import java.util.*
@@ -134,6 +136,7 @@ import kotlin.concurrent.thread
 import javax.swing.JOptionPane
 import kotlin.math.cos
 import kotlin.math.sin
+import kotlin.system.measureTimeMillis
 
 /**
  * Main SciView class.
@@ -784,6 +787,25 @@ class SciView : SceneryBase, CalibratedRealInterval<CalibratedAxis> {
         }
     }
 
+    @Throws(IOException::class)
+    fun openDirTiff(source: Path, onlyFirst: Int? = null)
+    {
+        val v = Volume.fromPath(source, hub, onlyFirst)
+        v.name = "volume"
+        v.spatial().position = Vector3f(-3.0f, 10.0f, 0.0f)
+        v.colormap = Colormap.get("jet")
+        v.spatial().scale = Vector3f(15.0f, 15.0f,45.0f)
+        v.transferFunction = TransferFunction.ramp(0.05f, 0.8f)
+        v.metadata["animating"] = true
+        v.converterSetups.firstOrNull()?.setDisplayRange(0.0, 1500.0)
+        v.visible = true
+
+        v.spatial().wantsComposeModel = true
+        v.spatial().updateWorld(true)
+        addNode(v)
+    }
+
+
     /**
      * Open a file specified by the source path. The file can be anything that SciView knows about: mesh, volume, point cloud
      * @param source string of a data source
@@ -1697,28 +1719,41 @@ class SciView : SceneryBase, CalibratedRealInterval<CalibratedAxis> {
         val cam = scene.activeObserver as? DetachedHeadCamera ?: return
         var ti: TrackerInput? = null
         var hmdAdded = false
-        if (!hub.has(SceneryElement.HMDInput)) {
-            try {
-                val hmd = OpenVRHMD(false, true)
-                if (hmd.initializedAndWorking()) {
-                    hub.add(SceneryElement.HMDInput, hmd)
-                    ti = hmd
-                } else {
-                    logger.warn("Could not initialise VR headset, just activating stereo rendering.")
+
+        if (vrActive) {
+
+            // VR activation logic
+            if (!hub.has(SceneryElement.HMDInput)) {
+                try {
+                    val hmd = OpenVRHMD(false, true)
+                    if (hmd.initializedAndWorking()) {
+                        hub.add(SceneryElement.HMDInput, hmd)
+                        ti = hmd
+                    } else {
+                        logger.warn("Could not initialise VR headset, just activating stereo rendering.")
+                    }
+                } catch (e: Exception) {
+                    logger.error("Could not add OpenVRHMD: $e")
                 }
                 hmdAdded = true
-            } catch (e: Exception) {
-                logger.error("Could not add OpenVRHMD: $e")
+            } else {
+                ti = hub.getWorkingHMD()
+            }
+
+            // Set tracker on the DetachedHeadCamera
+            if (ti != null) {
+                cam.tracker = ti
+                logger.info("tracker set")
             }
         } else {
-            ti = hub.getWorkingHMD()
-        }
-        if (vrActive && ti != null) {
-            cam.tracker = ti
-        } else {
+            // VR deactivation logic
+            // Convert back to normal Camera
+            logger.info("Shutting down VR")
             cam.tracker = null
         }
-        renderer.pushMode = false
+
+        // Enable push mode if VR is inactive, and the other way round
+        renderer.pushMode = !vrActive
 
         // we need to force reloading the renderer as the HMD might require device or instance extensions
         if (renderer is VulkanRenderer && hmdAdded) {
@@ -1732,8 +1767,17 @@ class SciView : SceneryBase, CalibratedRealInterval<CalibratedAxis> {
                     e.printStackTrace()
                 }
             }
-
-            renderer.toggleVR()
+        }
+        logger.debug("Replaced renderer.")
+        renderer.toggleVR()
+        // Cleanup HMD after VR has been toggled off
+        if (!vrActive) {
+            if (hub.has(SceneryElement.HMDInput)) {
+                val hmd = hub.get(SceneryElement.HMDInput) as? OpenVRHMD
+                hmd?.close()
+                // TODO hub.remove(hmd)
+                logger.debug("Closed HMD.")
+            }
         }
     }