Bug fixes for v3.1.5

pom.xml

@@ -11,7 +11,7 @@
 
 	<groupId>sc.fiji</groupId>
 	<artifactId>Simple_Neurite_Tracer</artifactId>
-	<version>3.1.5-SNAPSHOT</version>
+	<version>3.1.5</version>
 
 	<name>Simple Neurite Tracer</name>
 	<description>The ImageJ framework for semi-automated tracing of neurons and other tube-like structures.</description>

src/main/java/tracing/NeuriteTracerResultsDialog.java

@@ -38,6 +38,7 @@
 import java.awt.GridBagConstraints;
 import java.awt.GridBagLayout;
 import java.awt.Insets;
+import java.awt.Point;
 import java.awt.Rectangle;
 import java.awt.TextField;
 import java.awt.event.ActionEvent;
@@ -101,8 +102,9 @@ public class NeuriteTracerResultsDialog extends JDialog implements ActionListene
 
 	public static final boolean verbose = SimpleNeuriteTracer.verbose;
 
-	public PathWindow pw;
-	public FillWindow fw;
+	private PathWindow pw;
+	private FillWindow fw;
+	private SNTPrefs prefs;
 
 	protected JMenuBar menuBar;
 	protected JMenu fileMenu;
@@ -478,7 +480,7 @@ protected void exitRequested() {
 
 		plugin.cancelSearch(true);
 		plugin.notifyListeners(new SNTEvent(SNTEvent.QUIT));
-		new SNTPrefs(plugin).savePluginPrefs();
+		prefs.savePluginPrefs();
 		pw.dispose();
 		fw.dispose();
 		dispose();
@@ -762,6 +764,7 @@ public NeuriteTracerResultsDialog(final String title, final SimpleNeuriteTracer
 		new ClarifyingKeyListener().addKeyAndContainerListenerRecursively(this);
 
 		this.plugin = plugin;
+		prefs = plugin.prefs;
 		final SimpleNeuriteTracer thisPlugin = plugin;
 		this.launchedByArchive = launchedByArchive;
 
@@ -1175,7 +1178,8 @@ protected void displayOnStarting() {
 		SwingUtilities.invokeLater(new Runnable() {
 			@Override
 			public void run() {
-				arrangeDialogs();
+				if (plugin.prefs.isSaveWinLocations())
+					arrangeDialogs();
 				arrangeCanvases();
 				setVisible(true);
 				setPathListVisible(true, false);
@@ -1600,14 +1604,20 @@ else if (reset)
 	}
 
 	private void arrangeDialogs() {
-		final GraphicsDevice activeScreen = getGraphicsConfiguration().getDevice();
-		final int screenWidth = activeScreen.getDisplayMode().getWidth();
-		final int screenHeight = activeScreen.getDisplayMode().getHeight();
-		final Rectangle bounds = activeScreen.getDefaultConfiguration().getBounds();
-
-		setLocation(bounds.x, bounds.y);
-		pw.setLocation(screenWidth - pw.getWidth(), bounds.y);
-		fw.setLocation(bounds.x + getWidth(), screenHeight - fw.getHeight());
+		Point loc = prefs.getPathWindowLocation();
+		if (loc != null)
+			pw.setLocation(loc);
+		loc = prefs.getFillWindowLocation();
+		if (loc != null)
+			fw.setLocation(loc);
+//		final GraphicsDevice activeScreen = getGraphicsConfiguration().getDevice();
+//		final int screenWidth = activeScreen.getDisplayMode().getWidth();
+//		final int screenHeight = activeScreen.getDisplayMode().getHeight();
+//		final Rectangle bounds = activeScreen.getDefaultConfiguration().getBounds();
+//
+//		setLocation(bounds.x, bounds.y);
+//		pw.setLocation(screenWidth - pw.getWidth(), bounds.y);
+//		fw.setLocation(bounds.x + getWidth(), screenHeight - fw.getHeight());
 	}
 
 	private void arrangeCanvases() {
@@ -1885,7 +1895,7 @@ private JMenu tracingMenu() {
 		optionsMenuItem.addActionListener(new ActionListener() {
 			@Override
 			public void actionPerformed(final ActionEvent e) {
-				new SNTPrefs(plugin).promptForOptions();
+				prefs.promptForOptions();
 			}
 		});
 		tracingMenu.add(optionsMenuItem);
@@ -1976,4 +1986,12 @@ public void actionPerformed(final ActionEvent e) {
 		return mi;
 	}
 
+	public PathWindow getPathWindow() {
+		return pw;
+	}
+
+	public FillWindow getFillWindow() {
+		return fw;
+	}
+
 }

src/main/java/tracing/PathAndFillManager.java

@@ -2024,7 +2024,17 @@ synchronized void setPathPointsInVolume(final ArrayList<Path> paths, final byte[
 					 */
 					final List<Bresenham3D.IntegerPoint> pointsToDraw = Bresenham3D.bresenham3D(previous, current);
 					for (final Bresenham3D.IntegerPoint ip : pointsToDraw) {
-						slices[ip.z][ip.y * width + ip.x] = (byte) 255;
+						try {
+							slices[ip.z][ip.y * width + ip.x] = (byte) 255;
+						} catch (final ArrayIndexOutOfBoundsException ignored) {
+							final int x = Math.min(width - 1, Math.max(0, ip.x));
+							final int y = Math.min(height - 1, Math.max(0, ip.y));
+							final int z = Math.min(depth - 1, Math.max(0, ip.z));
+							slices[z][y * width + x] = (byte) 255;
+							if (SimpleNeuriteTracer.verbose)
+								SNT.log(String.format("Bresenham3D: Forced out-of-bounds point to [%d][%d * %d + %d]",
+										z, y, width, x));
+						}
 					}
 				}
 

src/main/java/tracing/SNTPrefs.java

@@ -1,6 +1,7 @@
 package tracing;
 
 import java.awt.Font;
+import java.awt.Point;
 
 import ij.Prefs;
 import ij.gui.GenericDialog;
@@ -22,6 +23,7 @@ public class SNTPrefs {
 	private static final int LOOK_FOR_TUBES = 128;
 	private static final int LOOK_FOR_OOF = 256;
 	private static final int SHOW_ONLY_SELECTED = 512;
+	private static final int STORE_WIN_LOCATIONS = 1024;
 	// private static final int JUST_NEAR_SLICES = 1024;
 	private static final int ENFORCE_DEFAULT_PATH_COLORS = 2048;
 	private static final int DEBUG = 4096;
@@ -31,6 +33,11 @@ public class SNTPrefs {
 	private static final String BOOLEANS = "tracing.snt.booleans";
 	private static final String SNAP_XY = "tracing.snt.xysnap";
 	private static final String SNAP_Z = "tracing.snt.zsnap";
+	private static final String PATHWIN_LOC = "tracing.snt.pwloc";
+	private static final String FILLWIN_LOC = "tracing.snt.fwloc";
+
+	//private static final String SNAP_Z = "tracing.snt.zsnap";
+
 	// private final static String NEARBY_VIEW = "tracing.snt.nearbyview";
 
 	private final int UNSET_PREFS = -1;
@@ -60,6 +67,7 @@ private void getBooleans() {
 	}
 
 	protected void loadPluginPrefs() {
+		getBooleans();
 		snt.useCompressedXML = getPref(COMPRESSED_XML);
 		snt.autoCanvasActivation = getPref(AUTO_CANVAS_ACTIVATION);
 		snt.snapCursor = getPref(SNAP_CURSOR);
@@ -121,6 +129,21 @@ protected void savePluginPrefs() {
 		setPref(DEBUG, SimpleNeuriteTracer.verbose);
 		Prefs.set(BOOLEANS, currentBooleans);
 		clearLegacyPrefs();
+		if (isSaveWinLocations()) {
+			final NeuriteTracerResultsDialog rd = snt.resultsDialog;
+			if (rd == null)
+				return;
+			final PathWindow pw = rd.getPathWindow();
+			if (pw != null)
+				Prefs.saveLocation(PATHWIN_LOC, pw.getLocation());
+			final FillWindow fw = rd.getFillWindow();
+			if (fw != null)
+				Prefs.saveLocation(FILLWIN_LOC, fw.getLocation());
+		}
+	}
+
+	protected boolean isSaveWinLocations() {
+		return getPref(STORE_WIN_LOCATIONS);
 	}
 
 	private void setPref(final int key, final boolean value) {
@@ -130,11 +153,21 @@ private void setPref(final int key, final boolean value) {
 			currentBooleans &= ~key;
 	}
 
+	protected Point getPathWindowLocation() {
+		return Prefs.getLocation(PATHWIN_LOC);
+	}
+
+	protected Point getFillWindowLocation() {
+		return Prefs.getLocation(FILLWIN_LOC);
+	}
+
 	private void resetOptions() {
 		clearLegacyPrefs();
 		Prefs.set(BOOLEANS, null);
 		Prefs.set(SNAP_XY, null);
 		Prefs.set(SNAP_Z, null);
+		Prefs.set(FILLWIN_LOC, null);
+		Prefs.set(PATHWIN_LOC, null);
 		currentBooleans = UNSET_PREFS;
 	}
 
@@ -144,7 +177,7 @@ private void clearLegacyPrefs() {
 
 	protected void promptForOptions() {
 
-		final int startupOptions = 6;
+		final int startupOptions = 7;
 		final int pluginOptions = 2;
 
 		final String[] startupLabels = new String[startupOptions];
@@ -176,6 +209,10 @@ protected void promptForOptions() {
 		startupLabels[idx] = "Load_default \".traces\" file (if present)";
 		startupStates[idx++] = snt.look4tracesFile;
 
+		startupItems[idx] = STORE_WIN_LOCATIONS;
+		startupLabels[idx] = "Remember window locations across restarts";
+		startupStates[idx++] = isSaveWinLocations();
+
 		final String[] pluginLabels = new String[pluginOptions];
 		final int[] pluginItems = new int[pluginOptions];
 		final boolean[] pluginStates = new boolean[pluginOptions];

src/main/java/tracing/ShollAnalysisPlugin.java

@@ -285,7 +285,7 @@ private boolean showDialog() {
 		if (gd.wasCanceled())
 			return false;
 		else if (gd.wasOKed()) {
-			sholl.gui.Utils.improveRecording();
+			Utils.improveRecording();
 			return dialogItemChanged(gd, null);
 		}
 		return false;
@@ -317,7 +317,7 @@ public void run() {
 		popup.addSeparator();
 		mi = Utils.menuItemTrigerringURL("Online Documentation", Sholl_Analysis.URL + "#Traces");
 		popup.add(mi);
-		mi = sholl.gui.Utils.menuItemTriggeringResources();
+		mi = Utils.menuItemTriggeringResources();
 		popup.add(mi);
 		return popup;
 	}
@@ -356,15 +356,15 @@ public boolean dialogItemChanged(final GenericDialog arg0, final AWTEvent event)
 		for (int i = 2; i < cbxs.size(); i++)
 			((Checkbox) cbxs.get(i)).setEnabled(restrictBySWCType);
 
-		boolean enableOK = true;
+		//boolean enableOK = true;
 		String warning = "";
 
 		if (impRequired && !validImageFile(new File(imgPath))) {
-			enableOK = false;
+			//enableOK = false;
 			warning += "Not a valid image. ";
 		}
 		if (!validTracesFile(new File(tracesPath))) {
-			enableOK = false;
+			//enableOK = false;
 			warning += "Not a valid .traces/.(e)swc file";
 		}
 		if (!warning.isEmpty()) {
@@ -375,7 +375,7 @@ public boolean dialogItemChanged(final GenericDialog arg0, final AWTEvent event)
 			infoMsg.setText(defaultInfoMsg);
 		}
 
-		return enableOK;
+		return true; //enableOK
 	}
 
 	private String getFilePathWithoutExtension(final String filePath) {
@@ -451,10 +451,8 @@ private boolean validTracesFile(final File file) {
 	 * We'll need to remove those to avoid I/O errors.
 	 */
 	private String normalizedPath(final String path) {
-		// This is way to simplistic: See
 		// chase-seibert.github.io/blog/2009/04/10/java-replaceall-fileseparator.html
-		return path.replaceAll(Matcher.quoteReplacement(File.separator) + "+",
-				Matcher.quoteReplacement(File.separator));
+		return path.replaceAll("(?<!^)(\\\\|/){2,}", Matcher.quoteReplacement(File.separator));
 	}
 
 	private String swcTypeCodesToString() {

src/main/java/tracing/SimpleNeuriteTracer.java

@@ -96,6 +96,7 @@ public class SimpleNeuriteTracer extends ThreePanes
 	protected static final int ballRadiusMultiplier = 5;
 
 	protected PathAndFillManager pathAndFillManager;
+	protected SNTPrefs prefs;
 
 	protected boolean use3DViewer;
 	protected Image3DUniverse univ;
@@ -1219,7 +1220,7 @@ public void startFillerThread(final FillerThread filler) {
 		this.filler = filler;
 
 		filler.addProgressListener(this);
-		filler.addProgressListener(resultsDialog.fw);
+		filler.addProgressListener(resultsDialog.getFillWindow());
 
 		addThreadToDraw(filler);
 
@@ -1236,7 +1237,7 @@ public void startFillerThread(final FillerThread filler) {
 	synchronized public void startFillingPaths(final Set<Path> fromPaths) {
 
 		// currentlyFilling = true;
-		resultsDialog.fw.pauseOrRestartFilling.setText("Pause");
+		resultsDialog.getFillWindow().pauseOrRestartFilling.setText("Pause");
 
 		filler = new FillerThread(xy, stackMin, stackMax, false, // startPaused
 				true, // reciprocal
@@ -1246,7 +1247,7 @@ synchronized public void startFillingPaths(final Set<Path> fromPaths) {
 		addThreadToDraw(filler);
 
 		filler.addProgressListener(this);
-		filler.addProgressListener(resultsDialog.fw);
+		filler.addProgressListener(resultsDialog.getFillWindow());
 
 		filler.setSourcePaths(fromPaths);
 
@@ -1565,14 +1566,14 @@ public void selectPath(final Path p, final boolean addToExistingSelection) {
 		else
 			pathsToSelect.add(p);
 		if (addToExistingSelection) {
-			pathsToSelect.addAll(resultsDialog.pw.getSelectedPaths());
+			pathsToSelect.addAll(resultsDialog.getPathWindow().getSelectedPaths());
 		}
-		resultsDialog.pw.setSelectedPaths(pathsToSelect, this);
+		resultsDialog.getPathWindow().setSelectedPaths(pathsToSelect, this);
 	}
 
 	public Set<Path> getSelectedPaths() {
-		if (resultsDialog.pw != null) {
-			return resultsDialog.pw.getSelectedPaths();
+		if (resultsDialog.getPathWindow() != null) {
+			return resultsDialog.getPathWindow().getSelectedPaths();
 		}
 		throw new RuntimeException("getSelectedPaths was called when resultsDialog.pw was null");
 	}

src/main/java/tracing/Simple_Neurite_Tracer.java

@@ -184,7 +184,7 @@ public void run(final String ignoredArguments) {
 					spacing_units = "" + calibration.getUnit();
 			}
 
-			final SNTPrefs prefs = new SNTPrefs(this);
+			prefs = new SNTPrefs(this);
 			prefs.loadStartupPrefs();
 
 			final GenericDialog gd = new GenericDialog("Simple Neurite Tracer (v" + SNT.VERSION + ")");