aherbert bug fixes

pom.xml

@@ -1,5 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+	xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
 	<modelVersion>4.0.0</modelVersion>
 
 	<parent>
@@ -97,6 +98,11 @@
 			<url>https://imagej.net/User:Saalfeld</url>
 			<properties><id>axtimwalde</id></properties>
 		</contributor>
+		<contributor>
+			<name>Alex Herbert</name>
+			<url>https://imagej.net/User:Aherbert</url>
+			<properties><id>aherbert</id></properties>
+		</contributor>
 	</contributors>
 
 	<mailingLists>
@@ -169,5 +175,22 @@
 			<groupId>org.scijava</groupId>
 			<artifactId>vecmath</artifactId>
 		</dependency>
+
+		<!-- Testing -->
+		<dependency>
+			<groupId>junit</groupId>
+			<artifactId>junit</artifactId>
+			<scope>test</scope>
+		</dependency>
+		<dependency>
+			<groupId>org.jogamp.gluegen</groupId>
+			<artifactId>gluegen-rt-main</artifactId>
+			<scope>test</scope>
+		</dependency>
+		<dependency>
+			<groupId>org.jogamp.jogl</groupId>
+			<artifactId>jogl-all-main</artifactId>
+			<scope>test</scope>
+		</dependency>
 	</dependencies>
 </project>

src/main/java/customnode/STLLoader.java

@@ -209,7 +209,6 @@ private CustomMesh createCustomMesh() {
 		cm = new CustomTriangleMesh(vertices);
 		cm.loadedFromName = name;
 		cm.changed = false;
-		cm.changed = false;
 		return cm;
 	}
 

src/main/java/customnode/WavefrontExporter.java

@@ -160,13 +160,13 @@ public static void save(final Map<String, CustomMesh> meshes,
 			objWriter.write(mat.name);
 			objWriter.write('\n');
 			// print faces
-			if (cmesh.getClass() == CustomTriangleMesh.class) writeTriangleFaces(
-				index, objWriter, name);
-			else if (cmesh.getClass() == CustomQuadMesh.class) writeQuadFaces(index,
+			if (cmesh instanceof CustomTriangleMesh) 
+				writeTriangleFaces(index, objWriter, name);
+			else if (cmesh instanceof CustomQuadMesh) writeQuadFaces(index,
 				objWriter, name);
-			else if (cmesh.getClass() == CustomPointMesh.class) writePointFaces(
+			else if (cmesh instanceof CustomPointMesh) writePointFaces(
 				index, objWriter, name);
-			else if (cmesh.getClass() == CustomLineMesh.class) {
+			else if (cmesh instanceof CustomLineMesh) {
 				final CustomLineMesh clm = (CustomLineMesh) cmesh;
 				switch (clm.getMode()) {
 					case CustomLineMesh.PAIRWISE:

src/main/java/ij3d/Content.java

@@ -122,7 +122,7 @@ public Content(final String name,
 	public void addInstant(final ContentInstant ci) {
 		final int timepoint = ci.timepoint;
 		contents.put(timepoint, ci);
-		if (!contents.containsKey(timepoint)) {
+		if (!timepointToSwitchIndex.containsKey(timepoint)) {
 			timepointToSwitchIndex.put(timepoint, contentSwitch.numChildren());
 			contentSwitch.addChild(ci);
 		}

src/main/java/ij3d/Executer.java

@@ -359,7 +359,7 @@ public void saveAsU3D() {
 	}
 
 	public void loadView() {
-		final OpenDialog sd = new OpenDialog("Open view...", "", ".view");
+		final OpenDialog sd = new OpenDialog("Open view...", OpenDialog.getDefaultDirectory(), ".view");
 		final String dir = sd.getDirectory();
 		final String name = sd.getFileName();
 		if (dir == null || name == null) return;
@@ -386,7 +386,7 @@ public void saveView() {
 
 	public void loadSession() {
 		final OpenDialog sd =
-			new OpenDialog("Open session...", "session", ".scene");
+			new OpenDialog("Open session...", OpenDialog.getDefaultDirectory(), ".scene");
 		final String dir = sd.getDirectory();
 		final String name = sd.getFileName();
 		if (dir == null || name == null) return;

src/main/java/ij3d/Image3DUniverse.java

@@ -129,6 +129,7 @@ public class Image3DUniverse extends DefaultAnimatableUniverse {
 	/** A reference to the universe's shortcuts */
 	private ShortCuts shortcuts;
 
+	/** A reference to the universe's context menu */
 	private ContextMenu contextmenu;
 
 	/**
@@ -210,11 +211,16 @@ public void mouseClicked(final MouseEvent e) {
 
 			@Override
 			public void mousePressed(final MouseEvent e) {
-				contextmenu.showPopup(e);
+				// Remove redundant call to show pop-up.
+				// Pop-up is shown on mouse release allowing the mouse 
+				// to be moved over content and the menu will be 
+				// for the correct selected content
+				//contextmenu.showPopup(e);
 			}
 
 			@Override
 			public void mouseReleased(final MouseEvent e) {
+				if (e.isConsumed()) return;
 				contextmenu.showPopup(e);
 			}
 		});
@@ -333,6 +339,7 @@ public boolean isFullScreen() {
 	 */
 	@Override
 	public void cleanup() {
+		sync(false);
 		timeline.pause();
 		removeAllContents();
 		contents.clear();
@@ -443,7 +450,24 @@ public Executer getExecuter() {
 	public ShortCuts getShortcuts() {
 		return shortcuts;
 	}
+
+	/**
+	 * Refresh the shortcuts using the menubar. This should be called if the standard 
+	 * menubar for the ImageJ3DWindow has been modified.
+	 * 
+	 * @see #getMenuBar() 
+	 */
+	public void refreshShortcuts() {
+		shortcuts = new ShortCuts(menubar);
+	}
 
+	/**
+	 * Returns a reference to the universe's context menu.
+	 */
+	public ContextMenu getContextmenu()	{
+		return contextmenu;
+	}
+
 	/**
 	 * Returns a reference to the PointListDialog used by this universe
 	 */
@@ -647,8 +671,8 @@ public void recalculateGlobalMinMax() {
 		final Point3d min = new Point3d();
 		final Point3d max = new Point3d();
 
-		final Iterator it = contents();
-		Content c = (Content) it.next();
+		final Iterator<Content> it = contents();
+		Content c = it.next();
 		c.getMin(min);
 		c.getMax(max);
 		globalMin.set(min);
@@ -1424,7 +1448,7 @@ public void removeContent(final String name) {
 	 * universe.
 	 */
 	@Override
-	public Iterator contents() {
+	public Iterator<Content> contents() {
 		return contents.values().iterator();
 	}
 
@@ -1434,7 +1458,7 @@ public Iterator contents() {
 	 * 
 	 * @return
 	 */
-	public Collection getContents() {
+	public Collection<Content> getContents() {
 		if (contents == null) return null;
 		return contents.values();
 	}
@@ -1495,7 +1519,7 @@ public void loadView(final String file) throws IOException {
 	public void resetView() {
 		fireTransformationStarted();
 
-		// rotate so that y shows downwards
+		// rotate so that y shows downwards, z-axis away from the viewer
 		final Transform3D t = new Transform3D();
 		final AxisAngle4d aa = new AxisAngle4d(1, 0, 0, Math.PI);
 		t.set(aa);
@@ -1521,72 +1545,84 @@ public void resetView() {
 	 * @param angle The angle in radians.
 	 */
 	public void rotateUniverse(final Vector3d axis, final double angle) {
+		fireTransformationStarted();
 		viewTransformer.rotate(axis, angle);
+		fireTransformationUpdated();
+		fireTransformationFinished();
 	}
 
 	/**
-	 * Rotate the univere so that the user looks in the negative direction of the
-	 * z-axis.
+	 * Resets the rotation transform. This is used to provide specific view orientations.
+	 *
+	 * @param aa2 the new rotation transform (applied to the reset rotation)
 	 */
-	public void rotateToNegativeXY() {
+	private void resetRotationTransform(AxisAngle4d aa2) {
 		fireTransformationStarted();
-		getRotationTG().setTransform(new Transform3D());
+		// rotate so that y shows downwards, z-axis away from the viewer
+		// (i.e. reset the rotation). This is equivalent to rotateToPositiveXY.
+		final Transform3D t = new Transform3D();
+		final AxisAngle4d aa = new AxisAngle4d(1, 0, 0, Math.PI);
+		t.set(aa);
+		if (aa2 != null)
+		{
+			final Transform3D t2 = new Transform3D();
+			t2.set(aa2);
+			t.mul(t2);
+		}
+		getRotationTG().setTransform(t);
+		// TODO - The bounding box and coordinate system are not refreshed.
+		fireTransformationUpdated();
 		fireTransformationFinished();
 	}
-
+
+	// The methods below rotate the default view to look along a given axis
+
 	/**
-	 * Rotate the univere so that the user looks in the positive direction of the
+	 * Rotate the universe so that the user looks in the negative direction of the
 	 * z-axis.
 	 */
+	public void rotateToNegativeXY() {
+		resetRotationTransform(new AxisAngle4d(0, 1, 0, Math.PI));
+	}
+
+	/**
+	 * Rotate the universe so that the user looks in the positive direction of the
+	 * z-axis. This is the default view.
+	 */
 	public void rotateToPositiveXY() {
-		fireTransformationStarted();
-		getRotationTG().setTransform(new Transform3D());
-		waitForNextFrame();
-		rotateUniverse(new Vector3d(0, 1, 0), Math.PI);
+		resetRotationTransform(null);
 	}
 
 	/**
-	 * Rotate the univere so that the user looks in the negative direction of the
+	 * Rotate the universe so that the user looks in the negative direction of the
 	 * y-axis.
 	 */
 	public void rotateToNegativeXZ() {
-		fireTransformationStarted();
-		getRotationTG().setTransform(new Transform3D());
-		waitForNextFrame();
-		rotateUniverse(new Vector3d(1, 0, 0), Math.PI / 2);
+		resetRotationTransform(new AxisAngle4d(1, 0, 0, Math.PI / 2));
 	}
 
 	/**
-	 * Rotate the univere so that the user looks in the positive direction of the
+	 * Rotate the universe so that the user looks in the positive direction of the
 	 * y-axis.
 	 */
 	public void rotateToPositiveXZ() {
-		fireTransformationStarted();
-		getRotationTG().setTransform(new Transform3D());
-		waitForNextFrame();
-		rotateUniverse(new Vector3d(0, 1, 0), -Math.PI / 2);
+		resetRotationTransform(new AxisAngle4d(1, 0, 0, -Math.PI / 2));
 	}
 
 	/**
-	 * Rotate the univere so that the user looks in the negative direction of the
+	 * Rotate the universe so that the user looks in the negative direction of the
 	 * x-axis.
 	 */
 	public void rotateToNegativeYZ() {
-		fireTransformationStarted();
-		getRotationTG().setTransform(new Transform3D());
-		waitForNextFrame();
-		rotateUniverse(new Vector3d(0, 1, 0), Math.PI / 2);
+		resetRotationTransform(new AxisAngle4d(0, 1, 0, Math.PI / 2));
 	}
 
 	/**
-	 * Rotate the univere so that the user looks in the positive direction of the
+	 * Rotate the universe so that the user looks in the positive direction of the
 	 * x-axis.
 	 */
 	public void rotateToPositiveYZ() {
-		fireTransformationStarted();
-		getRotationTG().setTransform(new Transform3D());
-		waitForNextFrame();
-		rotateUniverse(new Vector3d(1, 0, 0), -Math.PI / 2);
+		resetRotationTransform(new AxisAngle4d(0, 1, 0, -Math.PI / 2));
 	}
 
 	/**

src/main/java/ij3d/UniverseSynchronizer.java

@@ -47,7 +47,13 @@ public void transformationUpdated(final View view) {
 
 			@Override
 			public void universeClosed() {
-				removeUniverse(u);
+				//removeUniverse(u);
+				// Do not call removeUniverse(u)
+				// as this will remove this adapter from the list of universe listeners
+				// (i.e. u.removeUniverseListener(l))
+				// so modifying the current list of listeners on which universeClosed()
+				// is currently being invoked by the closing universe.
+				universes.remove(u);
 			}
 		};
 		u.addUniverseListener(l);
@@ -75,6 +81,7 @@ private static final void setGlobalTransform(final Image3DUniverse u,
 		final int num = group.getNumTransforms();
 		for (int i = 0; i < num; i++)
 			group.getTransformGroup(i).setTransform(transform.transforms[i]);
+		u.getViewPlatformTransformer().updateFrontBackClip();
 		u.fireTransformationUpdated();
 	}
 

src/main/java/ij3d/behaviors/InteractiveBehavior.java

@@ -323,7 +323,12 @@ else if (c != null && c.getType() == ContentConstants.ORTHO && axis != -1)
 					case KeyEvent.VK_PAGE_DOWN:
 						viewTransformer.zoom(-1);
 						return;
-
+					case KeyEvent.VK_COMMA:
+						viewTransformer.rotateZ(TWO_RAD);
+						return;
+					case KeyEvent.VK_PERIOD:
+						viewTransformer.rotateZ(-TWO_RAD);
+						return;
 				}
 			}
 			// If we arrive here, the event was not handled.

src/main/java/ij3d/shapes/BoundingBox.java

@@ -89,6 +89,9 @@ public BoundingBox(final Point3f minp, final Point3f maxp, final Color3f color)
 		final float ly = max.y - min.y;
 		final float lz = max.z - min.z;
 		final float max = Math.max(lx, Math.max(ly, lz));
+		if (max <= 0)
+			// No bounding box
+			return;
 		float min = Math.min(lx, Math.min(ly, lz));
 		if (min == 0 || max / min > 100) min = max;
 		double tmp = 0.00001f;
@@ -198,12 +201,17 @@ private Appearance createAppearance(final Color3f color) {
 
 	private Geometry makeLine(final Point3f start, final Point3f end,
 		final Color3f color, final float tickDistance, final float first,
-		final float tickSize, final boolean noTicks)
+		final float tickSize, boolean noTicks)
 	{
 		final float lineLength = start.distance(end);
 		final int nTicks =
 			(int) Math.floor((lineLength - first) / tickDistance) + 1;
 
+		// Avoid negative array size. This occurs when the (lineLength - first)
+		// is negative. 
+		if (nTicks < 1)
+			noTicks = true;
+
 		final int n = noTicks ? 2 : nTicks * 6 + 2;
 
 		final Point3f[] coords = new Point3f[n];

src/main/java/ij3d/shapes/CoordinateSystem.java

@@ -49,6 +49,10 @@ public CoordinateSystem(final float length, final Color3f color) {
 		this.length = length;
 		this.color = color;
 		setCapability(BranchGroup.ALLOW_DETACH);
+
+		// No coordinate system
+		if (length <= 0)
+			return;
 
 		final Shape3D lines = new Shape3D();
 		lines.setGeometry(createGeometry());