Add mechanism for updating Java

pom.xml

@@ -192,6 +192,7 @@
 		<dependency>
 			<groupId>org.scijava</groupId>
 			<artifactId>scijava-common</artifactId>
+			<version>2.98.1-SNAPSHOT</version>
 		</dependency>
 		<dependency>
 			<groupId>org.scijava</groupId>
@@ -207,6 +208,10 @@
 			<groupId>com.miglayout</groupId>
 			<artifactId>miglayout-swing</artifactId>
 		</dependency>
+		<dependency>
+			<groupId>org.apache.commons</groupId>
+			<artifactId>commons-compress</artifactId>
+		</dependency>
 		<dependency>
 			<groupId>org.jfree</groupId>
 			<artifactId>jfreechart</artifactId>

src/main/java/net/imagej/ui/swing/SwingColorBar.java

@@ -2,17 +2,17 @@
  * #%L
  * ImageJ software for multidimensional image processing and analysis.
  * %%
- * Copyright (C) 2009 - 2023 ImageJ developers.
+ * Copyright (C) 2009 - 2024 ImageJ developers.
  * %%
  * Redistribution and use in source and binary forms, with or without
  * modification, are permitted provided that the following conditions are met:
- * 
+ *
  * 1. Redistributions of source code must retain the above copyright notice,
  *    this list of conditions and the following disclaimer.
  * 2. Redistributions in binary form must reproduce the above copyright notice,
  *    this list of conditions and the following disclaimer in the documentation
  *    and/or other materials provided with the distribution.
- * 
+ *
  * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
  * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
  * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
@@ -47,7 +47,7 @@
 
 /**
  * A widget for displaying a {@link ColorTable} as a bar.
- * 
+ *
  * @author Curtis Rueden
  * @author Grant Harris
  */
@@ -81,7 +81,7 @@ public SwingColorBar(final ColorTable lut, final int height) {
 
 	/** Sets the {@link ColorTable} displayed by this color bar. */
 	public void setColorTable(final ColorTable colorTable) {
-		
+
 		if (bar == null || bar.getWidth() != colorTable.getLength()) {
 			// create compatible image
 			bar = AWTImageTools.createImage(colorTable.getLength(), 1);
@@ -94,7 +94,7 @@ public void setColorTable(final ColorTable colorTable) {
 			gfx.setColor(new Color(argb, false));
 			gfx.drawLine(i, 0, i, 1);
 		}
-		gfx.dispose();		
+		gfx.dispose();
 	}
 
 	// -- JComponent methods --
@@ -124,11 +124,11 @@ public void paintComponent(final Graphics g) {
 	// -- Main method --
 
 	public static void main(final String[] args) {
-		final ColorTable[] luts =
-			{ ColorTables.FIRE, ColorTables.ICE, ColorTables.SPECTRUM,
-				ColorTables.RED, ColorTables.GREEN, ColorTables.BLUE, ColorTables.CYAN,
-				ColorTables.MAGENTA, ColorTables.YELLOW, ColorTables.GRAYS,
-				ColorTables.REDGREEN, ColorTables.RGB332 };
+		final ColorTable[] luts = { ColorTables.FIRE, ColorTables.ICE,
+			ColorTables.SPECTRUM, ColorTables.RED, ColorTables.GREEN,
+			ColorTables.BLUE, ColorTables.CYAN, ColorTables.MAGENTA,
+			ColorTables.YELLOW, ColorTables.GRAYS, ColorTables.REDGREEN,
+			ColorTables.RGB332 };
 
 		final JFrame frame = new JFrame();
 		frame.setTitle("LUTs");

src/main/java/net/imagej/ui/swing/commands/OverlayManager.java

@@ -2,17 +2,17 @@
  * #%L
  * ImageJ software for multidimensional image processing and analysis.
  * %%
- * Copyright (C) 2009 - 2023 ImageJ developers.
+ * Copyright (C) 2009 - 2024 ImageJ developers.
  * %%
  * Redistribution and use in source and binary forms, with or without
  * modification, are permitted provided that the following conditions are met:
- * 
+ *
  * 1. Redistributions of source code must retain the above copyright notice,
  *    this list of conditions and the following disclaimer.
  * 2. Redistributions in binary form must reproduce the above copyright notice,
  *    this list of conditions and the following disclaimer in the documentation
  *    and/or other materials provided with the distribution.
- * 
+ *
  * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
  * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
  * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
@@ -39,7 +39,7 @@
 
 /**
  * Command to pop up the {@link SwingOverlayManager}.
- * 
+ *
  * @author Adam Fraser
  */
 @Plugin(type = Command.class, menu = { //
@@ -51,7 +51,8 @@ public class OverlayManager extends ContextCommand {
 
 	@Override
 	public void run() {
-		final SwingOverlayManager overlaymgr = new SwingOverlayManager(getContext());
+		final SwingOverlayManager overlaymgr = new SwingOverlayManager(
+			getContext());
 		overlaymgr.setVisible(true);
 	}
 

src/main/java/net/imagej/ui/swing/mdi/viewer/SwingMdiImageDisplayViewer.java

@@ -2,17 +2,17 @@
  * #%L
  * ImageJ software for multidimensional image processing and analysis.
  * %%
- * Copyright (C) 2009 - 2023 ImageJ developers.
+ * Copyright (C) 2009 - 2024 ImageJ developers.
  * %%
  * Redistribution and use in source and binary forms, with or without
  * modification, are permitted provided that the following conditions are met:
- * 
+ *
  * 1. Redistributions of source code must retain the above copyright notice,
  *    this list of conditions and the following disclaimer.
  * 2. Redistributions in binary form must reproduce the above copyright notice,
  *    this list of conditions and the following disclaimer in the documentation
  *    and/or other materials provided with the distribution.
- * 
+ *
  * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
  * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
  * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
@@ -44,14 +44,15 @@
 /**
  * Multiple Document Interface implementation of Swing image display viewer. The
  * MDI display is housed in a {@link JInternalFrame}.
- * 
+ *
  * @author Grant Harris
  * @author Curtis Rueden
  * @author Lee Kamentsky
  * @see SwingImageDisplayViewer
  */
 @Plugin(type = DisplayViewer.class)
-public class SwingMdiImageDisplayViewer extends AbstractSwingImageDisplayViewer
+public class SwingMdiImageDisplayViewer extends
+	AbstractSwingImageDisplayViewer
 {
 
 	// -- DisplayViewer methods --

src/main/java/net/imagej/ui/swing/overlay/AbstractJHotDrawAdapter.java

@@ -2,17 +2,17 @@
  * #%L
  * ImageJ software for multidimensional image processing and analysis.
  * %%
- * Copyright (C) 2009 - 2023 ImageJ developers.
+ * Copyright (C) 2009 - 2024 ImageJ developers.
  * %%
  * Redistribution and use in source and binary forms, with or without
  * modification, are permitted provided that the following conditions are met:
- * 
+ *
  * 1. Redistributions of source code must retain the above copyright notice,
  *    this list of conditions and the following disclaimer.
  * 2. Redistributions in binary form must reproduce the above copyright notice,
  *    this list of conditions and the following disclaimer in the documentation
  *    and/or other materials provided with the distribution.
- * 
+ *
  * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
  * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
  * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
@@ -55,7 +55,7 @@
 /**
  * An abstract class that gives default behavior for the {@link JHotDrawAdapter}
  * interface.
- * 
+ *
  * @author Lee Kamentsky
  */
 public abstract class AbstractJHotDrawAdapter<O extends Overlay, F extends Figure>

src/main/java/net/imagej/ui/swing/overlay/AngleJHotDrawAdapter.java

@@ -2,17 +2,17 @@
  * #%L
  * ImageJ software for multidimensional image processing and analysis.
  * %%
- * Copyright (C) 2009 - 2023 ImageJ developers.
+ * Copyright (C) 2009 - 2024 ImageJ developers.
  * %%
  * Redistribution and use in source and binary forms, with or without
  * modification, are permitted provided that the following conditions are met:
- * 
+ *
  * 1. Redistributions of source code must retain the above copyright notice,
  *    this list of conditions and the following disclaimer.
  * 2. Redistributions in binary form must reproduce the above copyright notice,
  *    this list of conditions and the following disclaimer in the documentation
  *    and/or other materials provided with the distribution.
- * 
+ *
  * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
  * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
  * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
@@ -46,7 +46,7 @@
 
 /**
  * JHotDraw adapter for angle overlays.
- * 
+ *
  * @author Lee Kamentsky
  * @author Barry DeZonia
  * @see SwingAngleTool

src/main/java/net/imagej/ui/swing/overlay/BezierPathFunctions.java

@@ -2,17 +2,17 @@
  * #%L
  * ImageJ software for multidimensional image processing and analysis.
  * %%
- * Copyright (C) 2009 - 2023 ImageJ developers.
+ * Copyright (C) 2009 - 2024 ImageJ developers.
  * %%
  * Redistribution and use in source and binary forms, with or without
  * modification, are permitted provided that the following conditions are met:
- * 
+ *
  * 1. Redistributions of source code must retain the above copyright notice,
  *    this list of conditions and the following disclaimer.
  * 2. Redistributions in binary form must reproduce the above copyright notice,
  *    this list of conditions and the following disclaimer in the documentation
  *    and/or other materials provided with the distribution.
- * 
+ *
  * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
  * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
  * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
@@ -47,7 +47,7 @@
 
 /**
  * Utility functions for {@link GeneralPathJHotDrawAdapter}.
- * 
+ *
  * @author Johannes Schindelin
  */
 public class BezierPathFunctions {
@@ -115,11 +115,10 @@ public static void addToRegionOfInterest(final PathIterator iterator,
 	}
 
 	public enum OP {
-		ADD, XOR, INTERSECT, SUBTRACT
+			ADD, XOR, INTERSECT, SUBTRACT
 	}
 
-	public static BezierPath add(final BezierPath path1, final BezierPath path2)
-	{
+	public static BezierPath add(final BezierPath path1, final BezierPath path2) {
 		return op(path1, path2, OP.ADD);
 	}
 

src/main/java/net/imagej/ui/swing/overlay/DefaultJHotDrawAdapter.java

@@ -2,17 +2,17 @@
  * #%L
  * ImageJ software for multidimensional image processing and analysis.
  * %%
- * Copyright (C) 2009 - 2023 ImageJ developers.
+ * Copyright (C) 2009 - 2024 ImageJ developers.
  * %%
  * Redistribution and use in source and binary forms, with or without
  * modification, are permitted provided that the following conditions are met:
- * 
+ *
  * 1. Redistributions of source code must retain the above copyright notice,
  *    this list of conditions and the following disclaimer.
  * 2. Redistributions in binary form must reproduce the above copyright notice,
  *    this list of conditions and the following disclaimer in the documentation
  *    and/or other materials provided with the distribution.
- * 
+ *
  * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
  * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
  * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
@@ -60,7 +60,7 @@
  * The default adapter handles any kind of overlay. It uses the fill color and
  * alpha of the overlay to draw the mask and leaves the rest of the figure
  * transparent.
- * 
+ *
  * @author Lee Kamentsky
  */
 @Plugin(type = JHotDrawAdapter.class,
@@ -95,8 +95,8 @@ public Figure createDefaultFigure() {
 	}
 
 	@Override
-	public void
-		updateFigure(final OverlayView overlay, final ImageFigure figure)
+	public void updateFigure(final OverlayView overlay,
+		final ImageFigure figure)
 	{
 		super.updateFigure(overlay, figure);
 
@@ -109,18 +109,16 @@ public Figure createDefaultFigure() {
 			final long minY = (long) Math.floor(roi.realMin(1));
 			final long maxY = (long) Math.ceil(roi.realMax(1)) + 1;
 			final ColorRGB color = overlay.getData().getFillColor();
-			final IndexColorModel cm =
-				new IndexColorModel(1, 2, new byte[] { 0, (byte) color.getRed() },
-					new byte[] { 0, (byte) color.getGreen() }, new byte[] { 0,
-						(byte) color.getBlue() }, new byte[] { 0,
-						(byte) overlay.getData().getAlpha() });
+			final IndexColorModel cm = new IndexColorModel(1, 2, new byte[] { 0,
+				(byte) color.getRed() }, new byte[] { 0, (byte) color.getGreen() },
+				new byte[] { 0, (byte) color.getBlue() }, new byte[] { 0, (byte) overlay
+					.getData().getAlpha() });
 			final int w = (int) (maxX - minX);
 			final int h = (int) (maxY - minY);
-			final BufferedImage img =
-				new BufferedImage(w, h, BufferedImage.TYPE_BYTE_INDEXED, cm);
-			final SampleModel sm =
-				new SinglePixelPackedSampleModel(DataBuffer.TYPE_BYTE, w, h,
-					new int[] { 1 });
+			final BufferedImage img = new BufferedImage(w, h,
+				BufferedImage.TYPE_BYTE_INDEXED, cm);
+			final SampleModel sm = new SinglePixelPackedSampleModel(
+				DataBuffer.TYPE_BYTE, w, h, new int[] { 1 });
 			final DataBuffer dbuncast = sm.createDataBuffer();
 			assert dbuncast instanceof DataBufferByte;
 			final DataBufferByte db = (DataBufferByte) dbuncast;
@@ -140,8 +138,8 @@ public Figure createDefaultFigure() {
 					index++;
 				}
 			}
-			final Raster raster =
-				Raster.createRaster(sm, db, new java.awt.Point(0, 0));
+			final Raster raster = Raster.createRaster(sm, db, new java.awt.Point(0,
+				0));
 			img.setData(raster);
 			figure.setBounds(new Rectangle2D.Double(minX, minY, w, h));
 			figure.setBufferedImage(img);

src/main/java/net/imagej/ui/swing/overlay/EllipseJHotDrawAdapter.java

@@ -2,17 +2,17 @@
  * #%L
  * ImageJ software for multidimensional image processing and analysis.
  * %%
- * Copyright (C) 2009 - 2023 ImageJ developers.
+ * Copyright (C) 2009 - 2024 ImageJ developers.
  * %%
  * Redistribution and use in source and binary forms, with or without
  * modification, are permitted provided that the following conditions are met:
- * 
+ *
  * 1. Redistributions of source code must retain the above copyright notice,
  *    this list of conditions and the following disclaimer.
  * 2. Redistributions in binary form must reproduce the above copyright notice,
  *    this list of conditions and the following disclaimer in the documentation
  *    and/or other materials provided with the distribution.
- * 
+ *
  * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
  * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
  * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
@@ -50,7 +50,7 @@
 
 /**
  * JHotDraw adapter for ellipse overlays.
- * 
+ *
  * @author Lee Kamentsky
  * @author Barry DeZonia
  * @see SwingEllipseTool
@@ -99,8 +99,7 @@ public Figure createDefaultFigure() {
 	}
 
 	@Override
-	public void updateFigure(final OverlayView view, final EllipseFigure figure)
-	{
+	public void updateFigure(final OverlayView view, final EllipseFigure figure) {
 		super.updateFigure(view, figure);
 		final EllipseOverlay overlay = downcastOverlay(view.getData());
 		final double centerX = overlay.getOrigin(0);
@@ -113,8 +112,8 @@ public void updateFigure(final OverlayView view, final EllipseFigure figure)
 	}
 
 	@Override
-	public void
-		updateOverlay(final EllipseFigure figure, final OverlayView view)
+	public void updateOverlay(final EllipseFigure figure,
+		final OverlayView view)
 	{
 		super.updateOverlay(figure, view);
 		final EllipseOverlay overlay = downcastOverlay(view.getData());