Fix/mesh work

.gitignore

@@ -20,3 +20,4 @@ canvases
 *.class
 *.java-version
 *dockerfile
+/meshes

pom.xml

@@ -44,7 +44,7 @@
 
 		<!-- kotlin -->
 		<kotlin.compiler.jvmTarget>11</kotlin.compiler.jvmTarget>
-		<kotlin.version>1.8.0</kotlin.version>
+		<kotlin.version>1.9.20</kotlin.version>
 		<kotlin.compiler.incremental>true</kotlin.compiler.incremental>
 
 		<!-- NB: Convert README.md to html during compilation. -->
@@ -88,6 +88,11 @@
 
 
 	<dependencies>
+		<dependency>
+			<groupId>javax.xml.bind</groupId>
+			<artifactId>jaxb-api</artifactId>
+			<version>2.2.2</version>
+		</dependency>
 		<dependency>
 			<groupId>dev.dirs</groupId>
 			<artifactId>directories</artifactId>
@@ -151,6 +156,11 @@
 			<groupId>org.jetbrains.kotlin</groupId>
 			<artifactId>kotlin-stdlib</artifactId>
 		</dependency>
+		<dependency>
+			<groupId>io.github.oshai</groupId>
+			<artifactId>kotlin-logging-jvm</artifactId>
+			<version>5.1.0</version>
+		</dependency>
 		<dependency>
 			<groupId>org.scijava</groupId>
 			<artifactId>scijava-common</artifactId>
@@ -541,7 +551,7 @@
 		<dependency>
 			<groupId>org.jetbrains.kotlinx</groupId>
 			<artifactId>kotlinx-coroutines-core</artifactId>
-			<version>1.6.4</version>
+			<version>1.7.3</version>
 			<scope>compile</scope>
 		</dependency>
 	</dependencies>

src/main/java/org/janelia/saalfeldlab/paintera/meshes/ManagedMeshSettings.java

@@ -23,7 +23,7 @@
 import java.util.function.Predicate;
 import java.util.stream.Collectors;
 
-public class ManagedMeshSettings {
+public class ManagedMeshSettings<K> {
 
 	public static final String MESH_SETTINGS_KEY = "meshSettings";
 
@@ -35,9 +35,9 @@ public class ManagedMeshSettings {
 
 	private final MeshSettings globalSettings;
 
-	private final Map<Long, MeshSettings> individualSettings = new HashMap<>();
+	private final Map<K, MeshSettings> individualSettings = new HashMap<>();
 
-	private final HashMap<Long, SimpleBooleanProperty> isManagedProperties = new HashMap<>();
+	private final HashMap<K, SimpleBooleanProperty> isManagedProperties = new HashMap<>();
 
 	private final SimpleBooleanProperty isMeshListEnabled = new SimpleBooleanProperty(DEFAULT_IS_MESH_LIST_ENABLED);
 
@@ -53,7 +53,18 @@ public ManagedMeshSettings(final MeshSettings globalSettings) {
 		this.globalSettings = globalSettings;
 	}
 
-	public MeshSettings getOrAddMesh(final Long id, final boolean isManaged) {
+	/**
+	 * Retrieves a MeshSettings object for the given id.
+	 * If the mesh settings are managed, the existing managed settings will be returned.
+	 * Otherwise, a new MeshSettings object will be created based on the global settings.
+	 * <p>
+	 * The resulting MeshSettings will be added to the `individualSettings` for this `id`, either `isManaged` or not.
+	 *
+	 * @param id        The id of the mesh to retrieve the settings for.
+	 * @param isManaged True if the individual mesh settings should be used.
+	 * @return The mesh settings for the given id, or a new MeshSettings object if the id is not found.
+	 */
+	public MeshSettings getMeshSettings(final K id, final boolean isManaged) {
 
 		if (!isManagedProperties.containsKey(id)) {
 			final SimpleBooleanProperty isManagedProperty = new SimpleBooleanProperty(isManaged);
@@ -69,25 +80,44 @@ public MeshSettings getOrAddMesh(final Long id, final boolean isManaged) {
 		return individualSettings.get(id);
 	}
 
-	public MeshSettings getOrAddMesh(final Long id) {
+	/**
+	 * Retrieves a MeshSettings for the given key.
+	 * If the mesh settings are managed, then the managed settings will be returned.
+	 * Otherwise, a new MeshSettings object will be created based on global settings.
+	 *
+	 * @param meshKey the key of the mesh to retrieve the settings for
+	 * @return the mesh settings for the given mesh key, or a new MeshSettings object if the key is not found
+	 */
+	public MeshSettings getMeshSettings(final K meshKey) {
+
+		final var isManagedProperty = isManagedProperties.get(meshKey);
+
+		final boolean isManaged;
+		if (isManagedProperty != null)
+			isManaged = isManagedProperty.get();
+		else
+			isManaged = false;
 
-		if (!isManagedProperties.containsKey(id)) {
-			return new MeshSettings(globalSettings.getNumScaleLevels());
-		}
-		return individualSettings.get(id);
+		return getMeshSettings(meshKey, isManaged);
 	}
 
 	public MeshSettings getGlobalSettings() {
 
 		return globalSettings;
 	}
 
-	public boolean isPresent(final Long t) {
+	/**
+	 * Checks if the given mesh key is managed.
+	 *
+	 * @param meshKey the mesh key
+	 * @return true if the mesh key is managed, false otherwise
+	 */
+	public boolean isManaged(final K meshKey) {
 
-		return this.isManagedProperties.containsKey(t);
+		return this.isManagedProperties.containsKey(meshKey);
 	}
 
-	public BooleanProperty isManagedProperty(final Long t) {
+	public BooleanProperty isManagedProperty(final K t) {
 
 		return this.isManagedProperties.get(t);
 	}
@@ -108,9 +138,9 @@ public void clearSettings() {
 		this.individualSettings.clear();
 	}
 
-	public void keepOnlyMatching(final Predicate<Long> filter) {
+	public void keepOnlyMatching(final Predicate<K> filter) {
 
-		final Set<Long> toBeRemoved = isManagedProperties
+		final Set<K> toBeRemoved = isManagedProperties
 				.keySet()
 				.stream()
 				.filter(filter.negate())
@@ -125,16 +155,16 @@ public static Serializer jsonSerializer() {
 		return new Serializer();
 	}
 
-	public void set(final ManagedMeshSettings that) {
+	public void set(final ManagedMeshSettings<K> that) {
 
 		clearSettings();
 		globalSettings.setTo(that.globalSettings);
 		isMeshListEnabled.set(that.isMeshListEnabled.get());
 		meshesEnabled.set(that.meshesEnabled.get());
-		for (final Entry<Long, MeshSettings> entry : that.individualSettings.entrySet()) {
-			final Long id = entry.getKey();
+		for (final Entry<K, MeshSettings> entry : that.individualSettings.entrySet()) {
+			final K id = entry.getKey();
 			final boolean isManaged = that.isManagedProperties.get(id).get();
-			this.getOrAddMesh(id, isManaged);
+			this.getMeshSettings(id, isManaged);
 			if (!isManaged)
 				this.individualSettings.get(id).setTo(entry.getValue());
 		}
@@ -188,24 +218,26 @@ public ManagedMeshSettings deserialize(
 					if (!settingsMap.has(ID_KEY)) {
 						continue;
 					}
+					//TODO Caleb: This needs to store and deserialize based on generic key type, not just Long
+					//  Necessary to share logic for meshes across segment and virtual sources
 					final Long id = context.deserialize(settingsMap.get(ID_KEY), Long.class);
 					final MeshSettings settings = Optional
 							.ofNullable(settingsMap.get(SETTINGS_KEY))
-							.map(el -> (MeshSettings)context.deserialize(el, MeshSettings.class))
+							.map(el -> (MeshSettings) context.deserialize(el, MeshSettings.class))
 							.orElseGet(globalSettings::copy);
 					final boolean isManaged = Optional
 							.ofNullable(settingsMap.get(IS_MANAGED_KEY))
 							.map(JsonElement::getAsBoolean)
 							.orElse(true);
 					LOG.debug("{} is managed? {}", id, isManaged);
 					if (!isManaged)
-						managedSettings.getOrAddMesh(id, false).setTo(settings);
+						managedSettings.getMeshSettings(id, false).setTo(settings);
 					else
-						managedSettings.getOrAddMesh(id, true);
+						managedSettings.getMeshSettings(id, true);
 				}
 				return managedSettings;
 			} catch (final Exception e) {
-				throw e instanceof JsonParseException ? (JsonParseException)e : new JsonParseException(e);
+				throw e instanceof JsonParseException ? (JsonParseException) e : new JsonParseException(e);
 			}
 		}
 
@@ -215,19 +247,22 @@ public JsonElement serialize(
 				final Type typeOfSrc,
 				final JsonSerializationContext context) {
 
+			//TODO Caleb: This also needs to serialize the generic type, instead of casting to Object
+			ManagedMeshSettings<Object> managedMeshSettings = (ManagedMeshSettings<Object>) src;
+
 			final JsonObject map = new JsonObject();
-			map.add(GLOBAL_SETTINGS_KEY, context.serialize(src.globalSettings));
+			map.add(GLOBAL_SETTINGS_KEY, context.serialize(managedMeshSettings.globalSettings));
 
-			if (DEFAULT_IS_MESH_LIST_ENABLED != src.isMeshListEnabledProperty().get())
-				map.addProperty(IS_MESH_LIST_ENABLED_KEY, src.isMeshListEnabledProperty().get());
+			if (DEFAULT_IS_MESH_LIST_ENABLED != managedMeshSettings.isMeshListEnabledProperty().get())
+				map.addProperty(IS_MESH_LIST_ENABLED_KEY, managedMeshSettings.isMeshListEnabledProperty().get());
 
-			if (DEFAULT_ARE_MESHES_ENABLED != src.getMeshesEnabledProperty().get())
-				map.addProperty(MESHES_ENABLED_KEY, src.getMeshesEnabledProperty().get());
+			if (DEFAULT_ARE_MESHES_ENABLED != managedMeshSettings.getMeshesEnabledProperty().get())
+				map.addProperty(MESHES_ENABLED_KEY, managedMeshSettings.getMeshesEnabledProperty().get());
 
 			final JsonArray meshSettingsList = new JsonArray();
-			for (final Entry<Long, MeshSettings> entry : src.individualSettings.entrySet()) {
-				final Long id = entry.getKey();
-				final Boolean isManaged = Optional.ofNullable(src.isManagedProperty(id)).map(BooleanProperty::get).orElse(true);
+			for (final Entry<?, MeshSettings> entry : managedMeshSettings.individualSettings.entrySet()) {
+				final Object id = entry.getKey();
+				final Boolean isManaged = Optional.ofNullable(managedMeshSettings.isManagedProperty(id)).map(BooleanProperty::get).orElse(true);
 				if (!isManaged) {
 					final JsonObject settingsMap = new JsonObject();
 					settingsMap.addProperty(IS_MANAGED_KEY, false);

src/main/java/org/janelia/saalfeldlab/paintera/meshes/MarchingCubes.java

@@ -1,18 +1,14 @@
 package org.janelia.saalfeldlab.paintera.meshes;
 
 import gnu.trove.list.array.TFloatArrayList;
-import net.imglib2.FinalInterval;
 import net.imglib2.Interval;
-import net.imglib2.RandomAccess;
 import net.imglib2.RandomAccessible;
 import net.imglib2.loops.LoopBuilder;
 import net.imglib2.type.BooleanType;
-import net.imglib2.util.Intervals;
-import paintera.net.imglib2.view.BundleView;
-import net.imglib2.view.IntervalView;
 import net.imglib2.view.Views;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
+import paintera.net.imglib2.view.BundleView;
 
 /**
  * This class implements the marching cubes algorithm. Based on http://paulbourke.net/geometry/polygonise/
@@ -381,67 +377,59 @@ public float[] generateMesh() {
 		// This way, we need to remap the cube vertices.
 		// @formatter:on
 
-		final FinalInterval expandedInterval = new FinalInterval(
-				new long[]{
-						interval.min(0) - 1,
-						interval.min(1) - 1,
-						interval.min(2) - 1},
-				Intervals.maxAsLongArray(interval));
-
 		final TFloatArrayList vertices = new TFloatArrayList();
 		final float[][] interpolationPoints = new float[12][3];
 
 		final boolean[] vertexVals = new boolean[8];
 		final int[] idxRemap = new int[]{5, 7, 3, 1, 4, 6, 2, 0};
 		final long[] prevPos = new long[]{Long.MIN_VALUE, 0, 0};
 		final long[] curPos = new long[3];
-		final BundleView<B> bundledInput = new BundleView<>(Views.interval(input, interval));
-		final IntervalView<RandomAccess<B>> expandedBundle = Views.interval(bundledInput, expandedInterval);
-
-		LoopBuilder.setImages(expandedBundle).forEachPixel(pixelAccess -> {
-			pixelAccess.localize(curPos);
-			if (prevPos[0] != Long.MIN_VALUE && curPos[0] - prevPos[0] == 1 && curPos[1] - prevPos[1] == 0 && curPos[2] - prevPos[2] == 0) {
-				vertexVals[0] = vertexVals[1];
-				vertexVals[2] = vertexVals[3];
-				vertexVals[4] = vertexVals[5];
-				vertexVals[6] = vertexVals[7];
-			} else {
-				vertexVals[0] = pixelAccess.get().get();
-				pixelAccess.move(1, 1); //move to offset (0, 1, 0)
-				vertexVals[2] = pixelAccess.get().get();
-				pixelAccess.move(1, 2); //move to offset (0, 1, 1)
-				vertexVals[6] = pixelAccess.get().get();
-				pixelAccess.move(-1, 1); //move to offset (0, 0, 1)
-				vertexVals[4] = pixelAccess.get().get();
-				pixelAccess.move(-1, 2);
-			}
-			pixelAccess.move(1, 0); //move to offset (1, 0, 0)
-			vertexVals[1] = pixelAccess.get().get();
-			pixelAccess.move(1, 1); //move to offset (1, 1, 0)
-			vertexVals[3] = pixelAccess.get().get();
-			pixelAccess.move(1, 2); //move to offset (1, 1, 1)
-			vertexVals[7] = pixelAccess.get().get();
-			pixelAccess.move(-1, 1); //move to offset (1, 0, 1)
-			vertexVals[5] = pixelAccess.get().get();
-
-			/* setup for next loop*/
-			pixelAccess.setPosition(curPos);
-			System.arraycopy(curPos, 0, prevPos, 0, 3);
-
-			var vertexIn = 0b00000000;
-			for (int i = 0; i < vertexVals.length; i++) {
-				vertexIn |= (vertexVals[idxRemap[i]] ? 1 : 0) << i;
-			}
 
-			triangulation(
-					vertexIn,
-					curPos[0], //cursor0.getLongPosition(0),
-					curPos[1], //cursor0.getLongPosition(1),
-					curPos[2], //cursor0.getLongPosition(2),
-					vertices,
-					interpolationPoints
-			);
-		});
+		LoopBuilder.setImages(Views.interval(new BundleView<>(input), interval))
+				.forEachPixel(pixelAccess -> {
+					pixelAccess.localize(curPos);
+					if (prevPos[0] != Long.MIN_VALUE && curPos[0] - prevPos[0] == 1 && curPos[1] - prevPos[1] == 0 && curPos[2] - prevPos[2] == 0) {
+						vertexVals[0] = vertexVals[1];
+						vertexVals[2] = vertexVals[3];
+						vertexVals[4] = vertexVals[5];
+						vertexVals[6] = vertexVals[7];
+					} else {
+						vertexVals[0] = pixelAccess.get().get();
+						pixelAccess.move(1, 1); //move to offset (0, 1, 0)
+						vertexVals[2] = pixelAccess.get().get();
+						pixelAccess.move(1, 2); //move to offset (0, 1, 1)
+						vertexVals[6] = pixelAccess.get().get();
+						pixelAccess.move(-1, 1); //move to offset (0, 0, 1)
+						vertexVals[4] = pixelAccess.get().get();
+						pixelAccess.move(-1, 2);
+					}
+					pixelAccess.move(1, 0); //move to offset (1, 0, 0)
+					vertexVals[1] = pixelAccess.get().get();
+					pixelAccess.move(1, 1); //move to offset (1, 1, 0)
+					vertexVals[3] = pixelAccess.get().get();
+					pixelAccess.move(1, 2); //move to offset (1, 1, 1)
+					vertexVals[7] = pixelAccess.get().get();
+					pixelAccess.move(-1, 1); //move to offset (1, 0, 1)
+					vertexVals[5] = pixelAccess.get().get();
+
+					/* setup for next loop*/
+					pixelAccess.setPosition(curPos);
+					System.arraycopy(curPos, 0, prevPos, 0, 3);
+
+					var vertexIn = 0b00000000;
+					for (int i = 0; i < vertexVals.length; i++) {
+						vertexIn |= (vertexVals[idxRemap[i]] ? 1 : 0) << i;
+					}
+
+					triangulation(
+							vertexIn,
+							curPos[0],
+							curPos[1],
+							curPos[2],
+							vertices,
+							interpolationPoints
+					);
+				});
 		return vertices.toArray();
 	}
 

src/main/java/org/janelia/saalfeldlab/paintera/meshes/Mesh.java

@@ -91,6 +91,10 @@ public FloatLocalizable(float[] position) {
 	 *                                 Of the form [ t1_v0_x, t1_v1_y, t1_v2_z, t2_v0_x, t2_v1_y, t2_v2_z, ..., tn_v0_x, tn_v1_y, tn_v2_z]
 	 */
 	public Mesh(final float[] flatTrianglesAndVertices, final Interval interval, final AffineTransform3D transform) {
+		this(flatTrianglesAndVertices, interval, transform, true);
+	}
+
+	public Mesh(final float[] flatTrianglesAndVertices, final Interval interval, final AffineTransform3D transform, final boolean overlap) {
 
 		assert flatTrianglesAndVertices.length % 9 == 0;
 
@@ -103,9 +107,10 @@ public Mesh(final float[] flatTrianglesAndVertices, final Interval interval, fin
 		final double minX = interval.min(0) - 1;
 		final double minZ = interval.min(2) - 1;
 
-		final double maxX = interval.max(0) + 1; // overlap 1
-		final double maxY = interval.max(1) + 1; // overlap 1
-		final double maxZ = interval.max(2) + 1; // overlap 1
+		final int overlapOffset = overlap ? 1 : 0;
+		final double maxX = interval.max(0) + overlapOffset;
+		final double maxY = interval.max(1) + overlapOffset;
+		final double maxZ = interval.max(2) + overlapOffset;
 
 		final RealInterval vertexBounds = new FinalRealInterval(
 				new double[]{minX, minY, minZ},