Merge pull request #549 from saalfeldlab/feat/1.5.0

Feat/1.5.0

pom.xml

@@ -10,7 +10,7 @@
 
 	<groupId>org.janelia.saalfeldlab</groupId>
 	<artifactId>paintera</artifactId>
-	<version>1.4.4-SNAPSHOT</version>
+	<version>1.5.0-SNAPSHOT</version>
 
 	<name>Paintera</name>
 	<description>New Era Painting and annotation tool</description>
@@ -68,7 +68,7 @@
 		<main-class>org.janelia.saalfeldlab.paintera.Paintera</main-class>
 		<app.name>Paintera</app.name>
 		<app.package>paintera</app.package>
-		<app.version>1.4.1</app.version>
+		<app.version>1.5.0</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>
@@ -81,7 +81,9 @@
 		<n5-aws-s3.version>4.2.1</n5-aws-s3.version>
 		<n5-google-cloud>4.1.1</n5-google-cloud>
 		<n5-zarr.version>1.3.5</n5-zarr.version>
-		<imglib2-label-multisets.version>0.15.0</imglib2-label-multisets.version>
+		<imglib2-label-multisets.version>0.15.1</imglib2-label-multisets.version>
+		<imglib2.version>6.1.0</imglib2.version>
+		<imglib2-realtransform.version>4.0.1</imglib2-realtransform.version>
 
 		<maven-compiler-plugin.version>3.13.0</maven-compiler-plugin.version>
 		<enforcer.skip>true</enforcer.skip>
@@ -185,7 +187,6 @@
 		<dependency>
 			<groupId>net.imglib2</groupId>
 			<artifactId>imglib2</artifactId>
-			<version>6.1.0</version>
 		</dependency>
 		<dependency>
 			<groupId>net.imglib2</groupId>
@@ -194,7 +195,6 @@
 		<dependency>
 			<groupId>net.imglib2</groupId>
 			<artifactId>imglib2-realtransform</artifactId>
-			<version>4.0.1</version>
 		</dependency>
 		<dependency>
 			<groupId>net.imglib2</groupId>
@@ -687,7 +687,7 @@
 					<artifactId>maven-surefire-plugin</artifactId>
 					<configuration>
 						<forkCount>1</forkCount>
-						<argLine>-Dtestfx.robot=glass -Dglass.platform=Monocle -Dmonocle.platform=Headless -Dprism.order=sw --enable-preview</argLine>
+						<argLine>-Dtestfx.robot=glass -Dglass.platform=Monocle -Dmonocle.platform=Headless -Dprism.order=sw</argLine>
 					</configuration>
 				</plugin>
 			</plugins>
@@ -709,7 +709,6 @@
 					</annotationProcessors>
 					<source>21</source>
 					<target>21</target>
-					<compilerArgs>--enable-preview</compilerArgs>
 				</configuration>
 			</plugin>
 			<plugin>
@@ -919,7 +918,6 @@
 				<version>${kotlin.version}</version>
 				<configuration>
 					<javacOptions>
-						<javacOption>--enable-preview</javacOption>
 					</javacOptions>
 				</configuration>
 			</plugin>

src/main/java/org/janelia/saalfeldlab/bdv/fx/viewer/render/MultiResolutionRendererGeneric.java

@@ -256,7 +256,7 @@ public interface ImageGenerator<T> {
 	/**
 	 * @param display                    The canvas that will display the images we render.
 	 * @param painterThread              Thread that triggers repainting of the display. Requests for repainting are send there.
-	 * @param screenScales               Scale factors from the viewer canvas to screen images of different resolutions. A scale factor of 1 means 1
+	 * @param initialScreenScales               Scale factors from the viewer canvas to screen images of different resolutions. A scale factor of 1 means 1
 	 *                                   pixel in the screen image is displayed as 1 pixel on the canvas, a scale factor of 0.5 means 1 pixel in the
 	 *                                   screen image is displayed as 2 pixel on the canvas, etc.
 	 * @param targetRenderNanos          Target rendering time in nanoseconds. The rendering time for the coarsest rendered scale should be below
@@ -271,7 +271,7 @@ public interface ImageGenerator<T> {
 	MultiResolutionRendererGeneric(
 			final TransformAwareRenderTargetGeneric<T> display,
 			final PainterThreadFx painterThread,
-			final double[] screenScales,
+			final double[] initialScreenScales,
 			final long targetRenderNanos,
 			final boolean doubleBuffered,
 			final TaskExecutor renderingTaskExecutor,
@@ -287,7 +287,7 @@ public interface ImageGenerator<T> {
 		this.painterThread = painterThread;
 		projector = null;
 		currentScreenScaleIndex = -1;
-		this.screenScales = screenScales.clone();
+		this.screenScales = initialScreenScales.clone();
 		this.doubleBuffered = doubleBuffered;
 		createVariables();
 

src/main/java/org/janelia/saalfeldlab/fx/ortho/OrthogonalViews.java

@@ -211,6 +211,10 @@ public void requestRepaint(final RealInterval intervalInGlobalSpace) {
 		this.applyToAll(v -> v.requestRepaint(intervalInGlobalSpace));
 	}
 
+	public void drawOverlays() {
+		applyToAll(it -> it.getDisplay().drawOverlays());
+	}
+
 	/**
 	 * {@link ViewerPanelFX#setAllSources(Collection)}} for all {@link ViewerPanelFX viewer children} (top left, top right, bottom left)
 	 *

src/main/java/org/janelia/saalfeldlab/paintera/PainteraConfigYaml.java

@@ -1,6 +1,7 @@
 package org.janelia.saalfeldlab.paintera;
 
 import com.pivovarit.function.ThrowingSupplier;
+import org.janelia.saalfeldlab.paintera.config.PainteraDirectoriesConfig;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.yaml.snakeyaml.Yaml;
@@ -14,50 +15,63 @@
 import java.nio.file.Paths;
 import java.util.HashMap;
 import java.util.Map;
+import java.util.function.Function;
 import java.util.function.Supplier;
 
 public class PainteraConfigYaml {
 
 	private static final Logger LOG = LoggerFactory.getLogger(MethodHandles.lookup().lookupClass());
 
-	private static final String USER_HOME = System.getProperty("user.home");
+	private static final String PAINTERA_YAML = "paintera.yml";
 
-	private static final Path PAINTERA_YAML = Paths.get(USER_HOME, ".config", "paintera.yml");
+	public static <T> T getConfig(final Supplier<T> fallBack, final String... segments) {
 
-	public static Object getConfig(final Supplier<Object> fallBack, final String... segments) {
 
-		Object currentConfig = getConfig();
-		for (final String segment : segments) {
-			if (!(currentConfig instanceof Map<?, ?>))
-				return fallBack.get();
-			final Map<?, ?> map = (Map<?, ?>)currentConfig;
-			if (!map.containsKey(segment))
+		Map<?, ?> currentConfig = getConfig();
+
+		final Function<Object, T> getOrFallback = (config) -> {
+			try {
+				return (T) config;
+			} catch (ClassCastException e) {
 				return fallBack.get();
-			currentConfig = map.get(segment);
+			}
+		};
+
+		for (int i = 0; i < segments.length; i++) {
+			final String segment = segments[i];
+			if (currentConfig.containsKey(segment)) {
+				final Object config = currentConfig.get(segment);
+				if (i == segments.length - 1)
+					return getOrFallback.apply(config);
+				if (config instanceof Map<?, ?>)
+					currentConfig = (Map<?, ?>) config;
+				else
+					return fallBack.get();
+			}
 		}
-		return currentConfig;
+		return fallBack.get();
 	}
 
-	// TODO should this return copy?
 	public static Map<?, ?> getConfig() {
 
-		return CONFIG;
+		String appConfigDir;
+		try {
+			appConfigDir = Paintera.getPaintera().getProperties().getPainteraDirectoriesConfig().getAppConfigDir();
+		} catch (Exception e) {
+			appConfigDir = PainteraDirectoriesConfig.APPLICATION_DIRECTORIES.configDir;
+		}
+		return readConfigUnchecked(Paths.get(appConfigDir, PAINTERA_YAML));
 	}
 
-	private static final Map<?, ?> CONFIG = readConfigUnchecked();
-
-	private static Map<?, ?> readConfigUnchecked() {
-
-		return ThrowingSupplier.unchecked(PainteraConfigYaml::readConfig).get();
-	}
+	private static Map<?, ?> readConfigUnchecked(Path painteraYaml) {
+		return ThrowingSupplier.unchecked(() -> readConfig(painteraYaml)).get();
+	};
 
-	private static Map<?, ?> readConfig() throws IOException {
+	private static Map<?, ?> readConfig(Path painteraYaml) throws IOException {
 
 		final Yaml yaml = new Yaml();
-		try (final InputStream fis = new FileInputStream(PAINTERA_YAML.toFile())) {
-			// TODO is this cast always safe?
-			// TODO make this type safe, maybe create config class
-			final Map<?, ?> data = (Map<?, ?>)yaml.load(fis);
+		try (final InputStream fis = new FileInputStream(painteraYaml.toFile())) {
+			final Map<?, ?> data = yaml.load(fis);
 			LOG.debug("Loaded paintera info: {}", data);
 			return data;
 		} catch (final FileNotFoundException e) {

src/main/java/org/janelia/saalfeldlab/paintera/control/actions/MenuActionType.java

@@ -16,7 +16,8 @@ public enum MenuActionType implements ActionType {
 	LoadProject,
 	DetachViewer,
 
-	OpenProject;
+	OpenProject,
+	ExportSource;
 
 	public static EnumSet<MenuActionType> of(final MenuActionType first, final MenuActionType... rest) {
 

src/main/java/org/janelia/saalfeldlab/paintera/control/navigation/CoordinateDisplayListener.java

@@ -10,8 +10,6 @@
 
 import java.util.function.Consumer;
 
-import static java.util.FormatProcessor.FMT;
-
 public class CoordinateDisplayListener {
 
 	private final ViewerPanelFX viewer;
@@ -93,7 +91,7 @@ public static String realPointToString(final RealPoint p) {
 		final double d0 = p.getDoublePosition(0);
 		final double d1 = p.getDoublePosition(1);
 		final double d2 = p.getDoublePosition(2);
-		return FMT."(%8.3f\{d0}, %8.3f\{d1}, %8.3f\{d2})";
+		return String.format("(%8.3f, %8.3f, %8.3f)", d0, d1, d2);
 	}
 
 }

src/main/java/org/janelia/saalfeldlab/paintera/control/navigation/TranslationController.java

@@ -40,23 +40,32 @@ public void translate(final double dX, final double dY, final double dZ, final D
 
 			manager.getTransform(globalTransform);
 			globalToViewerTransformListener.getTransformCopy(globalToViewerTransform);
-			/* undo global transform, left with only scale, rotation, translation in viewer space */
-			globalToViewerTransform.concatenate(globalTransform.inverse());
-			globalToViewerTransform.setTranslation(0.0, 0.0, 0.0);
-
 
 			delta[0] = dX;
 			delta[1] = dY;
 			delta[2] = dZ;
 
-			globalToViewerTransform.applyInverse(delta, delta);
-			globalTransform.translate(delta);
+			translateFromViewer(globalTransform, globalToViewerTransform, delta);
 
 			manager.setTransform(globalTransform, duration != null ? duration : Duration.ZERO);
 		}
 
 	}
 
+	public static void translateFromViewer(
+			final AffineTransform3D globalTransform,
+			final AffineTransform3D globalToViewerTransform,
+			final double[] delta
+	) {
+
+		/* undo global transform, left with only scale, rotation, translation in viewer space */
+		globalToViewerTransform.concatenate(globalTransform.inverse());
+		globalToViewerTransform.setTranslation(0.0, 0.0, 0.0);
+
+		globalToViewerTransform.applyInverse(delta, delta);
+		globalTransform.translate(delta);
+	}
+
 	/*TODO: Move this to somewhere else*/
 	public static final class TransformTracker implements TransformListener<AffineTransform3D> {