Merge pull request #538 from saalfeldlab/feat/sam_si_connected_compon…

…ents

Multi-point prompt for auto-sam, create scalar label source, fixes

pom.xml

@@ -10,7 +10,7 @@
 
 	<groupId>org.janelia.saalfeldlab</groupId>
 	<artifactId>paintera</artifactId>
-	<version>1.2.4-SNAPSHOT</version>
+	<version>1.3.0-SNAPSHOT</version>
 
 	<name>Paintera</name>
 	<description>New Era Painting and annotation tool</description>
@@ -66,7 +66,8 @@
 
 		<main-class>org.janelia.saalfeldlab.paintera.Paintera</main-class>
 		<app.name>Paintera</app.name>
-		<app.version>1.2.4</app.version>
+		<app.package>paintera</app.package>
+		<app.version>1.3.0</app.version>
 		<jvm.modules>javafx.base,javafx.controls,javafx.fxml,javafx.media,javafx.swing,javafx.web,javafx.graphics,java.naming,java.management,java.sql</jvm.modules>
 		<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
 		<windows.upgrade.uuid>f918b6f9-8685-4b50-9fbd-9be7a1209249</windows.upgrade.uuid>

src/main/java/org/janelia/saalfeldlab/paintera/ui/dialogs/create/MipMapLevel.java

@@ -18,6 +18,7 @@
 
 public class MipMapLevel {
 
+	final public SimpleBooleanProperty isLabelMultisetProperty = new SimpleBooleanProperty(true);
 
 	final SpatialField<LongProperty> baseDimensions;
 	final SpatialField<IntegerProperty> relativeDownsamplingFactors;
@@ -80,7 +81,14 @@ public Node makeNode() {
 			mipMapRow.getChildren().add(new VBox(resolutionHeader, resolution.getNode()));
 			mipMapRow.getChildren().add(new VBox(dimensionHeader, dimensions.getNode()));
 		}
-		mipMapRow.getChildren().add(new VBox(maxEntriesHeader, maxNumberOfEntriesPerSet.getTextField()));
+		final VBox numEntriesRow = new VBox(maxEntriesHeader, maxNumberOfEntriesPerSet.getTextField());
+
+		isLabelMultisetProperty.subscribe(isLabelMultiset -> {
+			if (isLabelMultiset)
+				mipMapRow.getChildren().add(numEntriesRow);
+			else
+				mipMapRow.getChildren().remove(numEntriesRow);
+		});
 
 		mipMapRow.setPadding(new Insets(0, 10.0, 0, 10.0));
 		mipMapRow.spacingProperty().setValue(10.0);

src/main/java/org/janelia/saalfeldlab/util/n5/N5Data.java

@@ -50,6 +50,7 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
+import javax.annotation.Nullable;
 import java.io.IOException;
 import java.lang.invoke.MethodHandles;
 import java.util.ArrayList;
@@ -749,9 +750,10 @@ public static void createEmptyLabelDataset(
 			final double[] resolution,
 			final double[] offset,
 			final double[][] relativeScaleFactors,
-			final int[] maxNumEntries) throws IOException {
+			@Nullable final int[] maxNumEntries,
+			final boolean labelMultiset) throws IOException {
 
-		createEmptyLabelDataset(container, group, dimensions, blockSize, resolution, offset, relativeScaleFactors, maxNumEntries, false);
+		createEmptyLabelDataset(container, group, dimensions, blockSize, resolution, offset, relativeScaleFactors, maxNumEntries, labelMultiset, false);
 	}
 
 	/**
@@ -776,7 +778,8 @@ public static void createEmptyLabelDataset(
 			final double[] resolution,
 			final double[] offset,
 			final double[][] relativeScaleFactors,
-			final int[] maxNumEntries,
+			@Nullable final int[] maxNumEntries,
+			final boolean labelMultisetType,
 			final boolean ignoreExisiting) throws IOException {
 
 		final Map<String, String> pd = new HashMap<>();
@@ -806,7 +809,7 @@ public static void createEmptyLabelDataset(
 		n5.setAttribute(dataGroup, N5Helpers.MULTI_SCALE_KEY, true);
 		n5.setAttribute(dataGroup, N5Helpers.OFFSET_KEY, offset);
 		n5.setAttribute(dataGroup, N5Helpers.RESOLUTION_KEY, resolution);
-		n5.setAttribute(dataGroup, N5Helpers.IS_LABEL_MULTISET_KEY, true);
+		n5.setAttribute(dataGroup, N5Helpers.IS_LABEL_MULTISET_KEY, labelMultisetType);
 
 		n5.createGroup(uniqueLabelsGroup);
 		n5.setAttribute(uniqueLabelsGroup, N5Helpers.MULTI_SCALE_KEY, true);
@@ -825,12 +828,14 @@ public static void createEmptyLabelDataset(
 
 			final String dataset = String.format(scaleDatasetPattern, scaleLevel);
 			final String uniqeLabelsDataset = String.format(scaleUniqueLabelsPattern, scaleLevel);
-			final int maxNum = downscaledLevel < 0 ? -1 : maxNumEntries[downscaledLevel];
 			n5.createDataset(dataset, scaledDimensions, blockSize, DataType.UINT8, new GzipCompression());
 			n5.createDataset(uniqeLabelsDataset, scaledDimensions, blockSize, DataType.UINT64, new GzipCompression());
 
-			n5.setAttribute(dataset, N5Helpers.MAX_NUM_ENTRIES_KEY, maxNum);
-			n5.setAttribute(dataset, N5Helpers.IS_LABEL_MULTISET_KEY, true);
+			if (labelMultisetType) {
+				final int maxNum = downscaledLevel < 0 ? -1 : maxNumEntries[downscaledLevel];
+				n5.setAttribute(dataset, N5Helpers.MAX_NUM_ENTRIES_KEY, maxNum);
+				n5.setAttribute(dataset, N5Helpers.IS_LABEL_MULTISET_KEY, true);
+			}
 
 			if (scaleLevel != 0) {
 				n5.setAttribute(dataset, N5Helpers.DOWNSAMPLING_FACTORS_KEY, accumulatedFactors);

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

@@ -1,6 +1,5 @@
 package org.janelia.saalfeldlab.paintera
 
-import org.janelia.saalfeldlab.bdv.fx.viewer.ViewerPanelFX
 import bdv.viewer.ViewerOptions
 import com.google.gson.Gson
 import com.google.gson.JsonElement
@@ -16,6 +15,7 @@ import javafx.scene.image.Image
 import javafx.stage.Stage
 import net.imglib2.realtransform.AffineTransform3D
 import org.controlsfx.control.Notifications
+import org.janelia.saalfeldlab.bdv.fx.viewer.ViewerPanelFX
 import org.janelia.saalfeldlab.fx.event.KeyTracker
 import org.janelia.saalfeldlab.fx.event.MouseTracker
 import org.janelia.saalfeldlab.fx.extensions.createNullableValueBinding
@@ -239,7 +239,13 @@ class PainteraMainWindow(val gateway: PainteraGateway = PainteraGateway()) {
 		.toFile()
 
 	private fun deserialize(json: JsonObject?, gson: Gson, indexToState: MutableMap<Int, SourceState<*, *>>) {
-		initProperties(gson.get<Properties>(json) ?: Properties())
+		/* Clear any errant null values from the properties. It shouldn't happen, but also is recoverable in case is does (did). */
+		json?.entrySet()
+			?.filter { (_, value) -> value == null || value.isJsonNull }?.toList()
+			?.forEach { (key, _) -> json.remove(key) }
+
+		val properties = gson.get<Properties>(json) ?: Properties()
+		initProperties(properties)
 		json?.get<JsonObject>(SOURCES_KEY)?.let { sourcesJson ->
 			SourceInfoSerializer.populate(
 				{ baseView.addState(it) },
@@ -273,7 +279,7 @@ class PainteraMainWindow(val gateway: PainteraGateway = PainteraGateway()) {
 		stage.onHiding = EventHandler { if (!doSaveAndQuit()) it.consume() }
 	}
 
-	internal fun askSaveAndQuit() : Boolean {
+	internal fun askSaveAndQuit(): Boolean {
 		return when {
 			wasQuit -> false
 			!isSaveNecessary() -> true
@@ -337,6 +343,7 @@ class PainteraMainWindow(val gateway: PainteraGateway = PainteraGateway()) {
 	class Serializer : PainteraSerialization.PainteraSerializer<PainteraMainWindow> {
 		override fun serialize(mainWindow: PainteraMainWindow, typeOfSrc: Type, context: JsonSerializationContext): JsonElement {
 			val map = context[mainWindow.properties].asJsonObject
+			map.entrySet().filter { (_, value) -> value == null || value.isJsonNull }.toList().forEach { (key, _) -> map.remove(key) }
 			map.add(SOURCES_KEY, context[mainWindow.baseView.sourceInfo()])
 			map.addProperty(VERSION_KEY, VERSION_STRING)
 			map.add(GLOBAL_TRANSFORM_KEY, context[AffineTransform3D().also { mainWindow.baseView.manager().getTransform(it) }])

src/main/kotlin/org/janelia/saalfeldlab/paintera/cache/AsyncCacheWithLoader.kt

@@ -45,12 +45,16 @@ open class AsyncCacheWithLoader<K : Any, V>(
 		cache.get(key) {
 			if (clear) cancelUnsubmittedLoadRequests()
 			async(loaderContext) {  loader(key) }
-		}
+		}.also { if (it.isCancelled) cache.invalidate(key) }
 	}
 
 	open fun load(key: K) : Job {
-		/* If it's already in the cache, deferred or not, just return a completed job and skipp the loader queue */
-		if (cache.getIfPresent(key) != null) return Job().apply { complete() }
+		/* If it's already in the cache, deferred or not, just return a completed job and skip the loader queue */
+		cache.getIfPresent(key)?.let {
+			if (it.isCancelled)
+				cache.invalidate(key)
+			else return Job().apply { complete() }
+		}
 
 		return runBlocking {
 			async(loaderQueueContext) {

src/main/kotlin/org/janelia/saalfeldlab/paintera/control/ShapeInterpolationController.kt

@@ -1,6 +1,5 @@
 package org.janelia.saalfeldlab.paintera.control
 
-import org.janelia.saalfeldlab.bdv.fx.viewer.ViewerPanelFX
 import bdv.viewer.TransformListener
 import io.github.oshai.kotlinlogging.KotlinLogging
 import javafx.application.Platform
@@ -25,7 +24,6 @@ import net.imglib2.img.array.ArrayImgFactory
 import net.imglib2.img.array.ArrayImgs
 import net.imglib2.interpolation.randomaccess.NLinearInterpolatorFactory
 import net.imglib2.loops.LoopBuilder
-import org.janelia.saalfeldlab.net.imglib2.outofbounds.RealOutOfBoundsConstantValueFactory
 import net.imglib2.realtransform.AffineTransform3D
 import net.imglib2.realtransform.Translation3D
 import net.imglib2.type.BooleanType
@@ -41,10 +39,12 @@ import net.imglib2.util.*
 import net.imglib2.view.ExtendedRealRandomAccessibleRealInterval
 import net.imglib2.view.IntervalView
 import net.imglib2.view.Views
-import org.checkerframework.common.reflection.qual.Invoke
+import org.janelia.saalfeldlab.bdv.fx.viewer.ViewerPanelFX
 import org.janelia.saalfeldlab.fx.Tasks
 import org.janelia.saalfeldlab.fx.extensions.*
 import org.janelia.saalfeldlab.fx.util.InvokeOnJavaFXApplicationThread
+import org.janelia.saalfeldlab.net.imglib2.outofbounds.RealOutOfBoundsConstantValueFactory
+import org.janelia.saalfeldlab.net.imglib2.view.BundleView
 import org.janelia.saalfeldlab.paintera.Paintera
 import org.janelia.saalfeldlab.paintera.PainteraBaseView
 import org.janelia.saalfeldlab.paintera.control.assignment.FragmentSegmentAssignment
@@ -61,7 +61,6 @@ import org.janelia.saalfeldlab.paintera.util.IntervalHelpers
 import org.janelia.saalfeldlab.paintera.util.IntervalHelpers.Companion.extendBy
 import org.janelia.saalfeldlab.paintera.util.IntervalHelpers.Companion.smallestContainingInterval
 import org.janelia.saalfeldlab.util.*
-import org.janelia.saalfeldlab.net.imglib2.view.BundleView
 import java.math.BigDecimal
 import java.math.RoundingMode
 import java.util.Collections
@@ -192,19 +191,16 @@ class ShapeInterpolationController<D : IntegerType<D>>(
 	@JvmOverloads
 	fun addSelection(
 		maskIntervalOverSelection: Interval,
-		keepInterpolation: Boolean = true,
+		replaceExistingSlice: Boolean = false,
 		globalTransform: AffineTransform3D,
 		viewerMask: ViewerMask
 	): SliceInfo? {
 		if (controllerState == ControllerState.Off) return null
 		isBusy = true
 		val selectionDepth = depthAt(globalTransform)
-		if (!keepInterpolation && slicesAndInterpolants.getSliceAtDepth(selectionDepth) != null) {
+		if (replaceExistingSlice && slicesAndInterpolants.getSliceAtDepth(selectionDepth) != null)
 			slicesAndInterpolants.removeSliceAtDepth(selectionDepth)
-			updateSliceAndInterpolantsCompositeMask()
-			val slice = SliceInfo(viewerMask, globalTransform, maskIntervalOverSelection)
-			slicesAndInterpolants.add(selectionDepth, slice)
-		}
+
 		if (slicesAndInterpolants.getSliceAtDepth(selectionDepth) == null) {
 			val slice = SliceInfo(viewerMask, globalTransform, maskIntervalOverSelection)
 			slicesAndInterpolants.add(selectionDepth, slice)
@@ -280,6 +276,7 @@ class ShapeInterpolationController<D : IntegerType<D>>(
 	}
 
 	fun togglePreviewMode() {
+		freezeInterpolation = false
 		preview = !preview
 		if (preview) interpolateBetweenSlices(false)
 		else updateSliceAndInterpolantsCompositeMask()
@@ -302,6 +299,7 @@ class ShapeInterpolationController<D : IntegerType<D>>(
 
 	@Synchronized
 	fun interpolateBetweenSlices(replaceExistingInterpolants: Boolean) {
+		if (freezeInterpolation) return
 		if (slicesAndInterpolants.slices.size < 2) {
 			updateSliceAndInterpolantsCompositeMask()
 			isBusy = false
@@ -336,7 +334,7 @@ class ShapeInterpolationController<D : IntegerType<D>>(
 						.reduceOrNull(Intervals::union)
 				}
 				updateSliceAndInterpolantsCompositeMask()
- 				requestRepaintAfterTasks(updateInterval)
+				requestRepaintAfterTasks(updateInterval)
 			}
 		}
 			.onCancelled { _, _ -> LOG.debug { "Interpolation Cancelled" } }
@@ -472,9 +470,13 @@ class ShapeInterpolationController<D : IntegerType<D>>(
 		refreshMeshes()
 	}
 
+	private val freezeInterpolationProperty = SimpleBooleanProperty(false)
+	var freezeInterpolation: Boolean by freezeInterpolationProperty.nonnull()
+
 
 	@Throws(MaskInUse::class)
 	private fun setCompositeMask(includeInterpolant: Boolean = preview) {
+		if (freezeInterpolation) return
 		synchronized(source) {
 			source.resetMasks(false)
 			/* If preview is on, hide all except the first and last fill mask */
@@ -620,10 +622,10 @@ class ShapeInterpolationController<D : IntegerType<D>>(
 			activeViewer!!.state.getViewerTransform(it)
 		}
 
-	fun getMask(targetMipMapLevel: Int = currentBestMipMapLevel): ViewerMask {
+	fun getMask(targetMipMapLevel: Int = currentBestMipMapLevel, ignoreExisting: Boolean = false): ViewerMask {
 
 		/* If we have a mask, get it; else create a new one */
-		currentViewerMask = sliceAtCurrentDepth?.let { oldSlice ->
+		currentViewerMask = (if (ignoreExisting) null else sliceAtCurrentDepth)?.let { oldSlice ->
 			val oldSliceBoundingBox = oldSlice.maskBoundingBox ?: let {
 				deleteSliceAt()
 				return@let null
@@ -732,11 +734,13 @@ class ShapeInterpolationController<D : IntegerType<D>>(
 
 		/* get union of adjacent slices bounding boxes */
 		val unionInterval = let {
+
+			val sourceIntervalInMaskSpace = viewerMask.run { currentMaskToSourceTransform.inverse().estimateBounds(source.getSource(0, info.level)) }
 			val interpolantIntervalInMaskSpace = viewerMask.currentGlobalToMaskTransform.estimateBounds(interpolantInterval)
 
 			val minZSlice = interpolantIntervalInMaskSpace.minAsDoubleArray().also { it[2] = 0.0 }
 			val maxZSlice = interpolantIntervalInMaskSpace.maxAsDoubleArray().also { it[2] = 0.0 }
-			val interpolantIntervalSliceInMaskSpace = FinalRealInterval(minZSlice, maxZSlice)
+			val interpolantIntervalSliceInMaskSpace = FinalRealInterval(minZSlice, maxZSlice) intersect sourceIntervalInMaskSpace
 
 
 			val interpolatedMaskView = interpolant.dataInterpolant
@@ -773,7 +777,7 @@ class ShapeInterpolationController<D : IntegerType<D>>(
 	}
 
 	companion object {
-		private val LOG = KotlinLogging.logger {  }
+		private val LOG = KotlinLogging.logger { }
 		private fun paintera(): PainteraBaseView = Paintera.getPaintera().baseView
 
 		private val Long.isInterpolationLabel
@@ -1215,8 +1219,9 @@ class ShapeInterpolationController<D : IntegerType<D>>(
 
 			}
 
+			val sourceInMaskInterval = mask.initialMaskToSourceTransform.inverse().estimateBounds(mask.source.getSource(0, mask.info.level))
 			selectionIntervals
-				.map { BundleView(mask.viewerImg).interval(it) }
+				.map { BundleView(mask.viewerImg).interval(it intersect sourceInMaskInterval) }
 				.map {
 					val shrinkingInterval = ShrinkingInterval(it.numDimensions())
 					LoopBuilder.setImages(it).forEachPixel { access ->