CellTrackingBase: add "merge selected" button, reorder button menus

src/main/kotlin/sc/iview/commands/analysis/CellTrackingBase.kt

@@ -39,7 +39,8 @@ import kotlin.concurrent.thread
  * @param [sciview] The [SciView] instance to use
  */
 open class CellTrackingBase(
-    open var sciview: SciView
+    open var sciview: SciView,
+    val resolutionScale: Float = 1f
 ) {
     val logger by lazyLogger(System.getProperty("scenery.LogLevel", "info"))
 
@@ -130,6 +131,14 @@ open class CellTrackingBase(
     var setVolumeVisCallback: ((Boolean) -> Unit)? = null
     /** Merges overlapping spots in a given timepoint. */
     var mergeOverlapsCallback: ((Int) -> Unit)? = null
+    /** Merges selected spots. */
+    var mergeSelectedCallback: (() -> Unit)? = null
+    /** Deletes the whole graph. */
+    var deleteGraphCallback: (() -> Unit)? = null
+    /** Deletes all annotations from this timepoint. */
+    var deleteTimepointCallback: (() -> Unit)? = null
+    /** Recenter and set default scaling for volume, then center camera on volume. */
+    var resetViewCallback: (() -> Unit)? = null
 
     enum class HedgehogVisibility { Hidden, PerTimePoint, Visible }
 
@@ -146,12 +155,8 @@ open class CellTrackingBase(
 
     var cursor = CursorTool
     var leftElephantColumn: Column? = null
-    var leftColumnPredict: Column? = null
-    var leftColumnLink: Column? = null
-    var leftUndoMenu: Column? = null
-
+    var generalMenu: Column? = null
     var enableTrackingPreview = true
-
     val leftMenuList = mutableListOf<Column>()
     var leftMenuIndex = 0
 
@@ -163,7 +168,7 @@ open class CellTrackingBase(
     private val observers = mutableListOf<TimepointObserver>()
 
     open fun run() {
-        sciview.toggleVRRendering()
+        sciview.toggleVRRendering(resolutionScale = resolutionScale)
         hmd = sciview.hub.getWorkingHMD() as? OpenVRHMD ?: throw IllegalStateException("Could not find headset")
 
         // Try to load the correct button mapping corresponding to the controller layout
@@ -226,6 +231,7 @@ open class CellTrackingBase(
         inputSetup()
 
         cellTrackingActive = true
+        rebuildGeometryCallback?.invoke()
         launchUpdaterThread()
     }
 
@@ -284,7 +290,7 @@ open class CellTrackingBase(
     val trackCellsWithController = ClickBehaviour { _, _ ->
         if (!controllerTrackingActive) {
             controllerTrackingActive = true
-            cursor.setTrackingColor()
+            cursor.activateTrackingColor()
             // we dont want animation, because we track step by step
             playing = false
             // Assume the user didn't click on an existing spot to start the track.
@@ -299,7 +305,7 @@ open class CellTrackingBase(
             // If this is the first spot we track, and its a valid existing spot, mark it as such
             if (isValidSelection && controllerTrackList.size == 0) {
                 startWithExistingSpot = selected
-                logger.info("Set startWithExistingPost to $startWithExistingSpot")
+                logger.debug("Set startWithExistingPost to $startWithExistingSpot")
             } else {
                 controllerTrackList.add(p)
             }
@@ -361,12 +367,8 @@ open class CellTrackingBase(
             color = unpressedColor, touchingColor = touchingColor, pressedColor = pressedColor)
 
         leftElephantColumn =
-            createWristMenuColumn(stageSpotsButton, name = "Stage Menu")
+            createWristMenuColumn(stageSpotsButton, trainAllButton, predictTPButton, predictAllButton, linkingButton, name = "Stage Menu")
         leftElephantColumn?.visible = false
-        leftColumnPredict = createWristMenuColumn(trainAllButton, predictTPButton, predictAllButton, name = "Train/Predict Menu")
-        leftColumnPredict?.visible = false
-        leftColumnLink = createWristMenuColumn(linkingButton, name = "Linking Menu")
-        leftColumnLink?.visible = false
     }
 
     var lastButtonTime = System.currentTimeMillis()
@@ -477,14 +479,17 @@ open class CellTrackingBase(
             color = color, pressedColor = pressedColor, touchingColor = touchingColor
         )
 
-        val timeControlRow = Row(goToFirstBtn, playSlowerBtn, togglePlaybackDirBtn, playFasterBtn, goToLastBtn)
+        val resetViewButton = Button(
+            "Recenter", command = {
+                resetViewCallback?.invoke()
+            }, byTouch = true, depressDelay = 250,
+            color = color, pressedColor = pressedColor, touchingColor = touchingColor
+        )
 
-        leftUndoMenu = createWristMenuColumn(undoButton, redoButton, name = "Left Undo Menu")
-        leftUndoMenu?.visible = false
-        val previewMenu = createWristMenuColumn(toggleTrackingPreviewBtn, name = "Preview Menu")
-        previewMenu.visible = false
-        val timeMenu = createWristMenuColumn(timeControlRow, name = "Time Menu")
-        timeMenu.visible = false
+        val timeControlRow = Row(goToFirstBtn, playSlowerBtn, togglePlaybackDirBtn, playFasterBtn, goToLastBtn)
+        val undoRedoRow = Row(undoButton, redoButton, resetViewButton)
+        generalMenu = createWristMenuColumn(timeControlRow, undoRedoRow, name = "Left Undo Menu")
+        generalMenu?.visible = false
 
         val toggleVolume = ToggleButton(
             "Volume off", "Volume on", command = {
@@ -509,15 +514,33 @@ open class CellTrackingBase(
             },
             byTouch = true, color = color, pressedColor = pressedColor, touchingColor = touchingColor, default = true
         )
-        val toggleVisMenu = createWristMenuColumn(toggleVolume, toggleTracks, toggleSpots)
+        val toggleVisMenu = createWristMenuColumn(toggleVolume, toggleTracks, toggleSpots, toggleTrackingPreviewBtn)
         toggleVisMenu.visible = false
 
-        val mergeButton = Button(
+        val mergeOverlapsButton = Button(
             "Merge overlaps", command = {
                 mergeOverlapsCallback?.invoke(volume.currentTimepoint)
             }, byTouch = true, depressDelay = 250, color = color, pressedColor = pressedColor, touchingColor = touchingColor
         )
-        val cleanupMenu = createWristMenuColumn(mergeButton)
+        val mergeSelectedButton = Button(
+            "Merge selected", command = {
+                mergeSelectedCallback?.invoke()
+            }, byTouch = true, depressDelay = 250, color = color, pressedColor = pressedColor, touchingColor = touchingColor
+        )
+
+        val deleteGraphButton = Button(
+            "Delete Graph", command = {
+                deleteGraphCallback?.invoke()
+            }, byTouch = true, depressDelay = 250, color = color, pressedColor = pressedColor, touchingColor = touchingColor
+        )
+        val deleteTimepointButton = Button(
+            "Delete TP", command = {
+                deleteTimepointCallback?.invoke()
+            }, byTouch = true, depressDelay = 250, color = color, pressedColor = pressedColor, touchingColor = touchingColor
+        )
+        val mergeRow = Row(mergeOverlapsButton, mergeSelectedButton)
+        val deleteRow = Row(deleteGraphButton, deleteTimepointButton)
+        val cleanupMenu = createWristMenuColumn(mergeRow, deleteRow)
         cleanupMenu.visible = false
     }
 
@@ -567,7 +590,7 @@ open class CellTrackingBase(
     /** Object that represents the 3D cursor in form of a sphere. It needs to be attached to a VR controller via [attachCursor].
      * The current cursor position can be obtained with [getPosition]. The current radius is stored in [radius].
      * The tool can be scaled up and down with [scaleByFactor].
-     * [resetColor], [setSelectColor] and [setTrackingColor] allow changing the cursor's color to reflect the currently active operation. */
+     * [resetColor], [activateSelectColor] and [activateTrackingColor] allow changing the cursor's color to reflect the currently active operation. */
     object CursorTool {
         private val logger by lazyLogger()
         var radius: Float = 0.007f
@@ -611,11 +634,12 @@ open class CellTrackingBase(
             cursor.material().diffuse = Vector3f(0.15f, 0.2f, 1f)
         }
 
-        fun setSelectColor() {
+        // TODO rename to activate
+        fun activateSelectColor() {
             cursor.material().diffuse = Vector3f(1f, 0.25f, 0.25f)
         }
 
-        fun setTrackingColor() {
+        fun activateTrackingColor() {
             cursor.material().diffuse = Vector3f(0.65f, 1f, 0.22f)
         }
 
@@ -814,7 +838,7 @@ open class CellTrackingBase(
             override fun init(x: Int, y: Int) {
                 time = System.currentTimeMillis()
                 val p = cursor.getPosition()
-                cursor.setSelectColor()
+                cursor.activateSelectColor()
                 spotSelectCallback?.invoke(p, volume.currentTimepoint, cursor.radius, false)
             }
             override fun drag(x: Int, y: Int) {
@@ -1073,19 +1097,26 @@ open class CellTrackingBase(
     open fun stop() {
         logger.info("Objects in the scene: ${sciview.allSceneNodes.map { it.name }}")
         cellTrackingActive = false
-        lightTetrahedron.forEach { sciview.deleteNode(it) }
+        if (::lightTetrahedron.isInitialized) {
+            lightTetrahedron.forEach { sciview.deleteNode(it) }
+        }
         // Try to find and delete possibly existing VR objects
         listOf("Shell", "leftHand", "rightHand").forEach {
             val n = sciview.find(it)
             n?.let { sciview.deleteNode(n) }
         }
-        sciview.deleteNode(rightVRController?.model)
-        sciview.deleteNode(leftVRController?.model)
+        rightVRController?.model?.let {
+            sciview.deleteNode(it)
+        }
+        leftVRController?.model?.let {
+            sciview.deleteNode(it)
+        }
 
         logger.info("Cleaned up basic VR objects. Objects left: ${sciview.allSceneNodes.map { it.name }}")
 
         sciview.toggleVRRendering()
         logger.info("Shut down and disabled VR environment.")
+        rebuildGeometryCallback?.invoke()
     }
 
 }

src/main/kotlin/sc/iview/commands/analysis/EyeTracking.kt

@@ -11,6 +11,8 @@ import graphics.scenery.ui.Column
 import graphics.scenery.ui.ToggleButton
 import graphics.scenery.utils.SystemHelpers
 import graphics.scenery.utils.extensions.*
+import kotlinx.coroutines.runBlocking
+import kotlinx.coroutines.withTimeoutOrNull
 import net.imglib2.type.numeric.integer.UnsignedByteType
 import org.apache.commons.math3.ml.clustering.Clusterable
 import org.apache.commons.math3.ml.clustering.DBSCANClusterer
@@ -21,6 +23,9 @@ import java.awt.image.DataBufferByte
 import java.io.ByteArrayInputStream
 import java.nio.file.Files
 import java.nio.file.Paths
+import java.util.concurrent.CompletableFuture
+import java.util.concurrent.TimeUnit
+import java.util.concurrent.TimeoutException
 import javax.imageio.ImageIO
 import kotlin.concurrent.thread
 import kotlin.math.PI
@@ -32,13 +37,11 @@ import kotlin.time.TimeSource
  * [trackCreationCallback], which is called on every spine graph vertex that is extracted
  */
 class EyeTracking(
-    sciview: SciView
-): CellTrackingBase(sciview) {
+    sciview: SciView,
+    resolutionScale: Float = 1f,
+): CellTrackingBase(sciview, resolutionScale) {
 
-    val pupilTracker = PupilEyeTracker(
-        calibrationType = PupilEyeTracker.CalibrationType.WorldSpace,
-        port = System.getProperty("PupilPort", "50020").toInt()
-    )
+    lateinit var pupilTracker: PupilEyeTracker
     val calibrationTarget = Icosphere(0.02f, 2)
     val laser = Cylinder(0.005f, 0.2f, 10)
 
@@ -52,7 +55,35 @@ class EyeTracking(
 
     private var currentTrackingType = TrackingType.Follow
 
+    fun establishEyeTrackerConnection(): Boolean {
+        return try {
+            val future = CompletableFuture.supplyAsync {
+                PupilEyeTracker(
+                    calibrationType = PupilEyeTracker.CalibrationType.WorldSpace,
+                    port = System.getProperty("PupilPort", "50020").toInt()
+                )
+            }
+            pupilTracker = future.get(4, TimeUnit.SECONDS)
+            true
+        } catch (e: TimeoutException) {
+            logger.warn("Eye tracker initialization timed out after 2 seconds. Resuming with default VR.")
+            false
+        } catch (e: Exception) {
+            logger.error("Eye tracker initialization failed with ${e.message}")
+            false
+        }
+    }
+
     override fun run() {
+        // Check whether we already initialized the pupilTracker or not
+        if (!::pupilTracker.isInitialized) {
+            if (!establishEyeTrackerConnection()) {
+                logger.error("Failed to initialize eye tracker")
+                // Handle the failure - maybe throw an exception or set a flag
+                return
+            }
+        }
+
         // Do all the things for general VR startup before setting up the eye tracking environment
         super.run()
 
@@ -471,9 +502,13 @@ class EyeTracking(
         n?.let { sciview.deleteNode(it) }
         // Delete definitely existing objects
         listOf(referenceTarget, calibrationTarget, laser, debugBoard, hedgehogs).forEach {
-            sciview.deleteNode(it)
+            try {
+                sciview.deleteNode(it)
+            } catch (e: Exception) {
+                logger.warn("Failed to delete $it")
+            }
         }
-        logger.info("Successfully cleaned up eye tracking environemt.")
+        logger.info("Successfully cleaned up eye tracking environment.")
         super.stop()
     }