Merge pull request #542 from saalfeldlab/1.3.3

1.3.3

pom.xml

@@ -58,7 +58,7 @@
 
 		<!-- JavaFx Version-->
 		<javafx.version>22.0.1</javafx.version>
-		<saalfx.version>1.4.1</saalfx.version>
+		<saalfx.version>1.4.2</saalfx.version>
 		<testfx.version>4.0.16-alpha</testfx.version>
 
 		<alphanumeric-comparator.version>1.4.1</alphanumeric-comparator.version>

src/main/kotlin/org/janelia/saalfeldlab/paintera/BindingKeys.kt

@@ -156,6 +156,29 @@ enum class LabelSourceStateKeys(lateInitNamedKeyCombo : LateInitNamedKeyCombinat
     }
 }
 
+enum class RawSourceStateKeys(lateInitNamedKeyCombo : LateInitNamedKeyCombination) : NamedKeyBinding by lateInitNamedKeyCombo {
+    RESET_MIN_MAX_INTENSITY_THRESHOLD                 ( SHIFT_DOWN + Y, "Reset Min / Max Intensity Threshold"),
+    AUTO_MIN_MAX_INTENSITY_THRESHOLD                  ( Y, "Auto Min / Max Intensity Threshold"),
+    ;
+
+
+    private val formattedName = name.lowercase()
+        .replace("__", ": ")
+        .replace("_", " ")
+
+    constructor(keys : KeyCombination, name : String? = null) : this(LateInitNamedKeyCombination(keys, name))
+    constructor(key : KeyCode, name : String? = null) : this(LateInitNamedKeyCombination(key.asCombination(), name))
+    constructor(key : Modifier, name : String? = null) : this(LateInitNamedKeyCombination(key.asCombination(), name))
+
+    init {
+        lateInitNamedKeyCombo.setName(formattedName)
+    }
+
+    companion object {
+        fun namedCombinationsCopy() = NamedKeyCombination.CombinationMap(*entries.map { it.deepCopy }.toTypedArray())
+    }
+}
+
 object NavigationKeys {
     const val BUTTON_TRANSLATE_ALONG_NORMAL_FORWARD       = "translate along normal forward"
     const val BUTTON_TRANSLATE_ALONG_NORMAL_FORWARD_FAST  = "translate along normal forward fast"

src/main/kotlin/org/janelia/saalfeldlab/paintera/control/modes/RawSourceMode.kt

@@ -28,6 +28,7 @@ import org.janelia.saalfeldlab.fx.actions.painteraActionSet
 import org.janelia.saalfeldlab.fx.ortho.OrthogonalViews
 import org.janelia.saalfeldlab.fx.ui.ScaleView
 import org.janelia.saalfeldlab.net.imglib2.converter.ARGBColorConverter
+import org.janelia.saalfeldlab.paintera.RawSourceStateKeys
 import org.janelia.saalfeldlab.paintera.control.actions.AllowedActions
 import org.janelia.saalfeldlab.paintera.control.tools.Tool
 import org.janelia.saalfeldlab.paintera.paintera
@@ -46,14 +47,14 @@ object RawSourceMode : AbstractToolMode() {
 
 	private val minMaxIntensityThreshold = painteraActionSet("Min/Max Intensity Threshold") {
 		verifyAll(KEY_PRESSED, "Source State is Raw Source State ") { activeSourceStateProperty.get() is ConnectomicsRawState<*, *> }
-		KEY_PRESSED(KeyCode.SHIFT, KeyCode.Y) {
+		KEY_PRESSED(RawSourceStateKeys.RESET_MIN_MAX_INTENSITY_THRESHOLD) {
 			graphic = { ScaleView().apply { styleClass += "intensity-reset-min-max" } }
 			onAction {
 				val rawSource = activeSourceStateProperty.get() as ConnectomicsRawState<*, *>
 				resetIntensityMinMax(rawSource)
 			}
 		}
-		KEY_PRESSED(KeyCode.Y) {
+		KEY_PRESSED(RawSourceStateKeys.AUTO_MIN_MAX_INTENSITY_THRESHOLD) {
 			lateinit var viewer: ViewerPanelFX
 			graphic = { ScaleView().apply { styleClass += "intensity-auto-min-max" } }
 			verify("Last focused viewer found") { paintera.baseView.lastFocusHolder.value?.viewer()?.also { viewer = it } != null }

src/main/kotlin/org/janelia/saalfeldlab/paintera/control/modes/ShapeInterpolationMode.kt

@@ -1,7 +1,6 @@
 package org.janelia.saalfeldlab.paintera.control.modes
 
 import bdv.fx.viewer.render.RenderUnitState
-import bdv.util.BdvFunctions
 import de.jensd.fx.glyphs.fontawesome.FontAwesomeIconView
 import io.github.oshai.kotlinlogging.KotlinLogging
 import javafx.beans.value.ChangeListener
@@ -18,39 +17,45 @@ import net.imglib2.loops.LoopBuilder
 import net.imglib2.realtransform.AffineTransform3D
 import net.imglib2.type.logic.BoolType
 import net.imglib2.type.numeric.IntegerType
-import net.imglib2.type.numeric.integer.UnsignedIntType
 import net.imglib2.type.numeric.integer.UnsignedLongType
-import net.imglib2.type.volatiles.VolatileUnsignedIntType
 import net.imglib2.util.Intervals
 import net.imglib2.view.IntervalView
 import net.imglib2.view.Views
 import org.janelia.saalfeldlab.control.mcu.MCUButtonControl
-import org.janelia.saalfeldlab.fx.actions.*
+import org.janelia.saalfeldlab.fx.actions.ActionSet
 import org.janelia.saalfeldlab.fx.actions.ActionSet.Companion.installActionSet
 import org.janelia.saalfeldlab.fx.actions.ActionSet.Companion.removeActionSet
+import org.janelia.saalfeldlab.fx.actions.NamedKeyBinding
+import org.janelia.saalfeldlab.fx.actions.painteraActionSet
+import org.janelia.saalfeldlab.fx.actions.painteraMidiActionSet
+import org.janelia.saalfeldlab.fx.extensions.addTriggeredWithListener
 import org.janelia.saalfeldlab.fx.midi.MidiButtonEvent
 import org.janelia.saalfeldlab.fx.midi.MidiToggleEvent
 import org.janelia.saalfeldlab.fx.midi.ToggleAction
 import org.janelia.saalfeldlab.fx.ortho.OrthogonalViews
 import org.janelia.saalfeldlab.fx.ui.GlyphScaleView
 import org.janelia.saalfeldlab.fx.util.InvokeOnJavaFXApplicationThread
 import org.janelia.saalfeldlab.labels.Label
+import org.janelia.saalfeldlab.net.imglib2.view.BundleView
 import org.janelia.saalfeldlab.paintera.DeviceManager
 import org.janelia.saalfeldlab.paintera.LabelSourceStateKeys.*
 import org.janelia.saalfeldlab.paintera.cache.HashableTransform.Companion.hashable
+import org.janelia.saalfeldlab.paintera.cache.SamEmbeddingLoaderCache
+import org.janelia.saalfeldlab.paintera.cache.SamEmbeddingLoaderCache.calculateTargetSamScreenScaleFactor
 import org.janelia.saalfeldlab.paintera.control.ShapeInterpolationController
 import org.janelia.saalfeldlab.paintera.control.ShapeInterpolationController.ControllerState.Moving
 import org.janelia.saalfeldlab.paintera.control.ShapeInterpolationController.EditSelectionChoice
 import org.janelia.saalfeldlab.paintera.control.actions.AllowedActions
 import org.janelia.saalfeldlab.paintera.control.actions.MenuActionType
 import org.janelia.saalfeldlab.paintera.control.actions.NavigationActionType
 import org.janelia.saalfeldlab.paintera.control.actions.PaintActionType
-import org.janelia.saalfeldlab.paintera.cache.SamEmbeddingLoaderCache
-import org.janelia.saalfeldlab.paintera.cache.SamEmbeddingLoaderCache.calculateTargetSamScreenScaleFactor
 import org.janelia.saalfeldlab.paintera.control.paint.ViewerMask
 import org.janelia.saalfeldlab.paintera.control.paint.ViewerMask.Companion.createViewerMask
 import org.janelia.saalfeldlab.paintera.control.tools.Tool
-import org.janelia.saalfeldlab.paintera.control.tools.paint.*
+import org.janelia.saalfeldlab.paintera.control.tools.paint.Fill2DTool
+import org.janelia.saalfeldlab.paintera.control.tools.paint.PaintBrushTool
+import org.janelia.saalfeldlab.paintera.control.tools.paint.SamPredictor
+import org.janelia.saalfeldlab.paintera.control.tools.paint.SamTool
 import org.janelia.saalfeldlab.paintera.control.tools.shapeinterpolation.ShapeInterpolationFillTool
 import org.janelia.saalfeldlab.paintera.control.tools.shapeinterpolation.ShapeInterpolationPaintBrushTool
 import org.janelia.saalfeldlab.paintera.control.tools.shapeinterpolation.ShapeInterpolationSAMTool
@@ -59,8 +64,6 @@ import org.janelia.saalfeldlab.paintera.data.mask.MaskInfo
 import org.janelia.saalfeldlab.paintera.data.mask.MaskedSource
 import org.janelia.saalfeldlab.paintera.paintera
 import org.janelia.saalfeldlab.util.*
-import org.janelia.saalfeldlab.net.imglib2.view.BundleView
-import kotlin.collections.forEach
 import kotlin.collections.set
 
 class ShapeInterpolationMode<D : IntegerType<D>>(val controller: ShapeInterpolationController<D>, private val previousMode: ControlMode) : AbstractToolMode() {
@@ -165,7 +168,7 @@ class ShapeInterpolationMode<D : IntegerType<D>>(val controller: ShapeInterpolat
 				with(controller) {
 					verifyAll(KEY_PRESSED, "Shape Interpolation Controller is Active ") { isControllerActive }
 					verifyAll(Event.ANY, "Shape Interpolation Tool is Active") { activeTool is ShapeInterpolationTool }
-					val exitMode = { _ : Event? ->
+					val exitMode = { _: Event? ->
 						exitShapeInterpolation(false)
 						paintera.baseView.changeMode(previousMode)
 					}
@@ -190,7 +193,12 @@ class ShapeInterpolationMode<D : IntegerType<D>>(val controller: ShapeInterpolat
 					filter = true
 					verify("Fill2DTool is active") { activeTool is Fill2DTool }
 					onAction {
-						switchTool(shapeInterpolationTool)
+						fill2DTool.fillIsRunningProperty.addTriggeredWithListener { obs, _, isRunning ->
+							if (!isRunning) {
+								switchTool(shapeInterpolationTool)
+								obs?.removeListener(this)
+							}
+						}
 					}
 				}
 			},
@@ -202,7 +210,7 @@ class ShapeInterpolationMode<D : IntegerType<D>>(val controller: ShapeInterpolat
 				}
 				KEY_PRESSED(fill2DTool.keyTrigger) {
 					name = "switch to fill2d tool"
-					verify("Active source is MaskedSource")  { activeSourceStateProperty.get()?.dataSource is MaskedSource<*, *> }
+					verify("Active source is MaskedSource") { activeSourceStateProperty.get()?.dataSource is MaskedSource<*, *> }
 					onAction { switchTool(fill2DTool) }
 				}
 				KEY_PRESSED(samTool.keyTrigger) {
@@ -343,7 +351,7 @@ class ShapeInterpolationMode<D : IntegerType<D>>(val controller: ShapeInterpolat
 
 	private fun ActionSet.keyPressEditSelectionAction(choice: EditSelectionChoice, namedKey: NamedKeyBinding) =
 		with(controller) {
-			KEY_PRESSED ( namedKey) {
+			KEY_PRESSED(namedKey) {
 				graphic = when (choice) {
 					EditSelectionChoice.First -> {
 						{ GlyphScaleView(FontAwesomeIconView().also { it.styleClass += "interpolation-first-slice" }) }
@@ -398,7 +406,7 @@ class ShapeInterpolationMode<D : IntegerType<D>>(val controller: ShapeInterpolat
 				.toList()
 
 			val renderState = RenderUnitState(mask.initialGlobalToViewerTransform.copy(), mask.info.time, sources, width.toLong(), height.toLong())
-			val predictionRequest = SamPredictor.SparsePrediction(maxDistancePositions.map { (x,y) -> renderState.getSamPoint(x,y, SamPredictor.SparseLabel.IN) })
+			val predictionRequest = SamPredictor.SparsePrediction(maxDistancePositions.map { (x, y) -> renderState.getSamPoint(x, y, SamPredictor.SparseLabel.IN) })
 
 			SamSliceInfo(renderState, mask, predictionRequest, null, false).also {
 				SamEmbeddingLoaderCache.load(renderState)
@@ -465,7 +473,7 @@ class ShapeInterpolationMode<D : IntegerType<D>>(val controller: ShapeInterpolat
 		selectionIntervalOverMask: Interval,
 		globalTransform: AffineTransform3D = paintera.baseView.manager().transform,
 		viewerMask: ViewerMask = controller.currentViewerMask!!,
-		replaceExistingSlice : Boolean = false
+		replaceExistingSlice: Boolean = false
 	): SamSliceInfo? {
 		val globalToViewerTransform = viewerMask.initialGlobalToMaskTransform
 		val sliceDepth = controller.depthAt(globalToViewerTransform)
@@ -527,7 +535,7 @@ internal fun IntervalView<UnsignedLongType>.getComponentMaxDistancePosition(): L
 
 	DistanceTransform.binaryTransform(invertedBinaryImg, distances, DistanceTransform.DISTANCE_TYPE.EUCLIDIAN)
 
-	val distancePerComponent  = mutableMapOf<Int, Pair<Double, LongArray>>()
+	val distancePerComponent = mutableMapOf<Int, Pair<Double, LongArray>>()
 
 	var backgroundId = -1;
 
@@ -601,7 +609,7 @@ internal data class SamSliceInfo(val renderState: RenderUnitState, val mask: Vie
 		prediction = SamPredictor.SparsePrediction(listOf(renderState.getSamPoint(viewerX, viewerY, label)))
 	}
 
-	fun updatePrediction(viewerPositions : List<DoubleArray>, label: SamPredictor.SparseLabel = SamPredictor.SparseLabel.IN) {
-		prediction = SamPredictor.SparsePrediction(viewerPositions.map { (x,y) -> renderState.getSamPoint(x,y, label) })
+	fun updatePrediction(viewerPositions: List<DoubleArray>, label: SamPredictor.SparseLabel = SamPredictor.SparseLabel.IN) {
+		prediction = SamPredictor.SparsePrediction(viewerPositions.map { (x, y) -> renderState.getSamPoint(x, y, label) })
 	}
 }

src/main/kotlin/org/janelia/saalfeldlab/paintera/control/tools/paint/Fill2DTool.kt

@@ -8,6 +8,7 @@ import javafx.beans.property.SimpleObjectProperty
 import javafx.beans.value.ObservableValue
 import javafx.scene.Cursor
 import javafx.scene.input.*
+import javafx.util.Subscription
 import net.imglib2.Interval
 import net.imglib2.util.Intervals
 import org.janelia.saalfeldlab.fx.UtilityTask
@@ -110,14 +111,16 @@ open class Fill2DTool(activeSourceStateProperty: SimpleObjectProperty<SourceStat
 					graphic = { GlyphScaleView(FontAwesomeIconView().apply { styleClass += "reject" }).apply { styleClass += "ignore-disable"} }
 					filter = true
 					onAction {
-						fillTask?.run { if (!isCancelled) cancel() } ?: mode?.switchTool(mode.defaultTool)
+						cancelFloodFill() ?: mode?.switchTool(mode.defaultTool)
 					}
 				}
 			}
 		)
 	}
 
-	private val fillIsRunningProperty = SimpleBooleanProperty(false, "Fill2D is Running")
+	fun cancelFloodFill() = fillTask?.run { if (!isCancelled) cancel() }
+
+	val fillIsRunningProperty = SimpleBooleanProperty(false, "Fill2D is Running")
 
 	internal fun executeFill2DAction(x: Double, y: Double, afterFill: (Interval) -> Unit = {}): UtilityTask<*>? {
 

src/main/kotlin/org/janelia/saalfeldlab/paintera/control/tools/paint/SamTool.kt

@@ -26,6 +26,7 @@ import javafx.scene.layout.Pane
 import javafx.scene.shape.Circle
 import javafx.scene.shape.Rectangle
 import kotlinx.coroutines.*
+import kotlinx.coroutines.channels.Channel
 import net.imglib2.FinalInterval
 import net.imglib2.Interval
 import net.imglib2.RandomAccessibleInterval
@@ -92,7 +93,6 @@ import org.janelia.saalfeldlab.paintera.util.IntervalHelpers.Companion.smallestC
 import org.janelia.saalfeldlab.paintera.util.algorithms.otsuThresholdPrediction
 import org.janelia.saalfeldlab.util.*
 import java.util.concurrent.CancellationException
-import java.util.concurrent.LinkedBlockingQueue
 import kotlin.collections.List
 import kotlin.collections.MutableList
 import kotlin.collections.addAll
@@ -204,7 +204,7 @@ open class SamTool(activeSourceStateProperty: SimpleObjectProperty<SourceState<*
 			originalWritableVolatileBackingImage = field?.volatileViewerImg?.writableSource
 		}
 
-	private var predictionJob : Job = Job().apply { complete() }
+	private var predictionJob: Job = Job().apply { complete() }
 
 	internal val lastPredictionProperty = SimpleObjectProperty<SamTaskInfo?>(null)
 	var lastPrediction by lastPredictionProperty.nullable()
@@ -232,13 +232,13 @@ open class SamTool(activeSourceStateProperty: SimpleObjectProperty<SourceState<*
 
 	private var screenScale by Delegates.notNull<Double>()
 
-	private val predictionQueue = LinkedBlockingQueue<Pair<SamPredictor.PredictionRequest, Boolean>>(1)
+	private val predictionChannel = Channel<Pair<SamPredictor.PredictionRequest, Boolean>>(1)
 
 	private var currentPredictionRequest: Pair<SamPredictor.PredictionRequest, Boolean>? = null
-		set(value) = synchronized(predictionQueue) {
-			predictionQueue.clear()
+		set(value) = runBlocking {
+			predictionChannel.tryReceive() /* capacity 1, so this will always either do nothing, or empty the channel */
 			value?.let { (request, _) ->
-				predictionQueue.put(value)
+				predictionChannel.send(value)
 				if (!temporaryPrompt)
 					request.drawPrompt()
 			}
@@ -297,6 +297,7 @@ open class SamTool(activeSourceStateProperty: SimpleObjectProperty<SourceState<*
 		clearPromptDrawings()
 		currentLabelToPaint = Label.INVALID
 		predictionJob.cancel()
+		predictionChannel.tryReceive() /*clear the channel if not empty */
 		if (unwrapResult) {
 			if (!maskProvided) {
 				maskedSource?.resetMasks()
@@ -560,7 +561,7 @@ open class SamTool(activeSourceStateProperty: SimpleObjectProperty<SourceState<*
 				KEY_PRESSED(CANCEL) {
 					name = "exit SAM tool"
 					graphic = { GlyphScaleView(FontAwesomeIconView().apply { styleClass += "reject" }).apply { styleClass += "ignore-disable" } }
-					onAction { cancelAction() }
+					onAction { mode?.switchTool(mode.defaultTool) }
 				}
 			},
 
@@ -651,10 +652,6 @@ open class SamTool(activeSourceStateProperty: SimpleObjectProperty<SourceState<*
 		)
 	}
 
-	protected open fun cancelAction() {
-		mode?.switchTool(mode.defaultTool)
-	}
-
 	private fun resetPromptAndPrediction() {
 		clearPromptDrawings()
 		currentPredictionRequest = null
@@ -797,7 +794,7 @@ open class SamTool(activeSourceStateProperty: SimpleObjectProperty<SourceState<*
 				maskedSource.applyMask(currentMask, sourceInterval.smallestContainingInterval, MaskedSource.VALID_LABEL_CHECK)
 				viewerMask = null
 			} else {
-				val predictionMaxInterval = originalWritableBackingImage!!.intersect( maskInterval)
+				val predictionMaxInterval = originalWritableBackingImage!!.intersect(maskInterval)
 				LoopBuilder
 					.setImages(originalWritableBackingImage!!.interval(predictionMaxInterval), currentMask.viewerImg.wrappedSource.interval(predictionMaxInterval))
 					.multiThreaded()
@@ -829,6 +826,9 @@ open class SamTool(activeSourceStateProperty: SimpleObjectProperty<SourceState<*
 	}
 
 	open fun requestPrediction(promptPoints: List<SamPoint>, estimateThreshold: Boolean = true) {
+		if (promptPoints.isEmpty())
+			temporaryPrompt = true
+
 		if (!predictionJob.isActive) {
 			startPredictionJob()
 		}
@@ -845,9 +845,24 @@ open class SamTool(activeSourceStateProperty: SimpleObjectProperty<SourceState<*
 	private var embeddingRequest: Deferred<OnnxTensor>? = null
 
 	private var currentPrediction: SamPredictor.SamPrediction? = null
+
+	private val resetSAMTaskOnException = CoroutineExceptionHandler { _, exception ->
+		LOG.error(exception) { "Error during SAM Prediction " }
+		isBusy = false
+		deactivate()
+		mode?.apply {
+			InvokeOnJavaFXApplicationThread {
+				switchTool(defaultTool)
+			}
+		}
+		SAM_TASK_SCOPE = CoroutineScope(Dispatchers.IO + Job())
+	}
+
+	protected open var currentDisplay = false
+
 	private fun startPredictionJob() {
 		val maskSource = maskedSource ?: return
-		predictionJob = SAM_TASK_SCOPE.launch {
+		predictionJob = SAM_TASK_SCOPE.launch(resetSAMTaskOnException) {
 			val session = createOrtSessionTask.get()
 			val imageEmbedding = try {
 				runBlocking {
@@ -863,9 +878,8 @@ open class SamTool(activeSourceStateProperty: SimpleObjectProperty<SourceState<*
 				isBusy = false
 			}
 			val predictor = SamPredictor(ortEnv, session, imageEmbedding, imgWidth to imgHeight)
-			while (coroutineContext.isActive) {
-				val predictionPair = predictionQueue.take()
-				val (predictionRequest, estimateThreshold) = predictionPair
+			while (predictionJob.isActive) {
+				val (predictionRequest, estimateThreshold) =  predictionChannel.receive()
 				val points = (predictionRequest as SparsePrediction).points
 
 				val newPredictionRequest = estimateThreshold || currentPrediction == null
@@ -929,7 +943,7 @@ open class SamTool(activeSourceStateProperty: SimpleObjectProperty<SourceState<*
 				} catch (e: InterruptedException) {
 					System.setErr(stdErr)
 					LOG.debug(e) { "Connected Components Interrupted During SAM" }
-					cancel("Connected Components Interrupted During SAM" )
+					cancel("Connected Components Interrupted During SAM")
 					continue
 				} finally {
 					System.setErr(stdErr)
@@ -1134,7 +1148,7 @@ open class SamTool(activeSourceStateProperty: SimpleObjectProperty<SourceState<*
 
 		private val LOG = KotlinLogging.logger { }
 
-		internal val SAM_TASK_SCOPE = CoroutineScope(Dispatchers.IO + Job())
+		private var SAM_TASK_SCOPE = CoroutineScope(Dispatchers.IO + Job())
 
 
 		private fun calculateTargetScreenScaleFactor(viewer: ViewerPanelFX): Double {