Add Choose Tracing Image > From System Clipboard command...

While at it:
- Fix outdated URLs
- Simplify menu entry for TrakeEM2 listener
- Code cleanup

src/main/java/sc/fiji/snt/BookmarkManager.java

@@ -595,7 +595,7 @@ void populateFromFile(final File file) throws IOException {
         final int tIdx = table.getColumnIndex(getHeader()[5]);
 
         if (lIdx == -1 || xIdx == -1 || yIdx == -1 || zIdx == -1)
-            throw new IOException("Unexpected column header(s) in CSV file");
+            throw new IOException("Unexpected column header(s) in CSV file.");
         final List<Bookmark> dataList = new ArrayList<>();
         for (int i = 0; i < table.getRowCount(); i++) {
             dataList.add(new Bookmark((String) table.get(lIdx, i), // label

src/main/java/sc/fiji/snt/FillManagerUI.java

@@ -61,7 +61,7 @@ public class FillManagerUI extends JDialog implements PathAndFillListener,
 	static { net.imagej.patcher.LegacyInjector.preinit(); } // required for _every_ class that imports ij. classes
 
 	private static final long serialVersionUID = 1L;
-	protected static final String FILLING_URI = "https://imagej.net/plugins/snt/step-by-step-instructions#filling";
+	protected static final String FILLING_URI = "https://imagej.net/plugins/snt/walkthroughs#filling";
 	private static final int STATUS_MARGIN = 2;
 	private static final int MARGIN = 10;
 

src/main/java/sc/fiji/snt/PathManagerUI.java

@@ -477,7 +477,7 @@ private JMenu getSpineUtilsMenu(final MultiPathActionListener multiPathListener)
 		menu.add(jmi);
 		menu.addSeparator();
 		jmi = GuiUtils.menuItemTriggeringHelpURL("Spine/Varicosity Utilities Help",
-				"https://imagej.net/plugins/snt/step-by-step-instructions#spinevaricosity-analysis");
+				"https://imagej.net/plugins/snt/walkthroughs#spinevaricosity-analysis");
 		menu.add(jmi);
 		return menu;
 	}
@@ -501,7 +501,7 @@ private JMenu getTimeSequenceMenu(final MultiPathActionListener multiPathListene
 		menu.add(jmi);
 		menu.addSeparator();
 		jmi = GuiUtils.menuItemTriggeringHelpURL("Time-lapse Utilities Help",
-				"https://imagej.net/plugins/snt/step-by-step-instructions#time-lapse-analysis");
+				"https://imagej.net/plugins/snt/walkthroughs#time-lapse-analysis");
 		menu.add(jmi);
 		return menu;
 	}

src/main/java/sc/fiji/snt/SNTUI.java

@@ -94,7 +94,6 @@ public class SNTUI extends JDialog {
 	private JButton showOrHideFillList = new JButton(); // must be initialized
 	private JMenuItem saveMenuItem;
 	private JMenuItem quitMenuItem;
-	private JMenuItem sendToTrakEM2;
 	private JLabel statusText;
 	private JLabel statusBarText;
 	private JButton keepSegment;
@@ -859,7 +858,6 @@ protected void disableImageDependentComponents() {
 	private void disableEverything() {
 		assert SwingUtilities.isEventDispatchThread();
 		disableImageDependentComponents();
-		sendToTrakEM2.setEnabled(false);
 		saveMenuItem.setEnabled(false);
 		quitMenuItem.setEnabled(false);
 	}
@@ -896,7 +894,6 @@ public void changeState(final int newState) {
 				fmUI.setEnabledWhileNotFilling();
 				saveMenuItem.setEnabled(true);
 
-				sendToTrakEM2.setEnabled(plugin.anyListeners());
 				quitMenuItem.setEnabled(true);
 				showPathsSelected.setEnabled(true);
 				updateStatusText("Click somewhere to start a new path...");
@@ -917,7 +914,6 @@ public void changeState(final int newState) {
 				// setFillListVisible(false);
 				saveMenuItem.setEnabled(true);
 
-				sendToTrakEM2.setEnabled(plugin.anyListeners());
 				quitMenuItem.setEnabled(true);
 				showPathsSelected.setEnabled(true);
 				updateRebuildCanvasButton();
@@ -2521,6 +2517,9 @@ private JMenuBar createMenuBar() {
 		});
 		changeImpMenu.add(getImportActionMenuItem(ImportAction.IMAGE));
 		changeImpMenu.add(fromList);
+		final JMenuItem fromClipboard = getImportActionMenuItem(ImportAction.IMAGE_CLIPBOARD);
+		fromClipboard.setIcon(IconFactory.getMenuIcon(GLYPH.CLIPBOARD));
+		changeImpMenu.add(fromClipboard);
 		fileMenu.add(changeImpMenu);
 		fileMenu.addSeparator();
 		final JMenuItem autoTrace = getImportActionMenuItem(ImportAction.AUTO_TRACE_IMAGE);
@@ -2561,8 +2560,13 @@ private JMenuBar createMenuBar() {
 		fileMenu.add(restoreMenuItem);
 
 		fileMenu.addSeparator();
-		sendToTrakEM2 = new JMenuItem("Send to TrakEM2");
-		sendToTrakEM2.addActionListener(e -> plugin.notifyListeners(new SNTEvent(SNTEvent.SEND_TO_TRAKEM2)));
+		final JMenuItem sendToTrakEM2 = new JMenuItem("Send to TrakEM2", IconFactory.getMenuIcon('T', false));
+		sendToTrakEM2.addActionListener(e -> {
+			if (!plugin.anyListeners())
+				error("TrakEM2 is either not running or not listening to SNT events.");
+			else
+				plugin.notifyListeners(new SNTEvent(SNTEvent.SEND_TO_TRAKEM2));
+		});
 		fileMenu.add(sendToTrakEM2);
 		fileMenu.add(showFolderMenu(installer));
 
@@ -4343,6 +4347,8 @@ static String getImportActionName(final int type) {
 				return "NDF...";
 			case ImportAction.TRACES:
 				return "TRACES...";
+			case ImportAction.IMAGE_CLIPBOARD:
+				return "From System Clipboard";
 			default:
 				throw new IllegalArgumentException("Unknown type '" + type + "'");
 			}
@@ -4619,6 +4625,7 @@ private class ImportAction {
 		private static final int DEMO = 6;
 		private static final int AUTO_TRACE_IMAGE = 7;
 		private static final int NDF = 8;
+		private static final int IMAGE_CLIPBOARD = 9;
 
 		private final int type;
 		private File file;
@@ -4669,10 +4676,12 @@ private void run() {
 				choice.load(); // will reset UI
 				break;
 			case IMAGE:
+			case IMAGE_CLIPBOARD:
 				if (plugin.isSecondaryDataAvailable()) {
 					flushSecondaryDataPrompt();
 				}
-				inputs.put("file", file);
+				inputs.put("file", (IMAGE==type) ? file : null);
+				inputs.put("clipboard", IMAGE_CLIPBOARD==type);
 				(new DynamicCmdRunner(OpenDatasetCmd.class, inputs, LOADING)).run();
 				break;
 			case JSON:

src/main/java/sc/fiji/snt/gui/DemoRunner.java

@@ -346,8 +346,7 @@ public void load() {
 
 		entry.summary = "Downloads the test dataset of the Spot Spine software (image stack and traced dendrite).";
 		entry.data = "Image (3D; 0.7MB) and tracings (160KB)";
-		entry.source = "Spot Spine (https://imagej.net/plugins/spot-spine) manuscript, doi:10.12688/f1000research.146327.2" +
-				".146327.1";
+		entry.source = "Spot Spine (https://imagej.net/plugins/spot-spine) manuscript, doi:10.12688/f1000research.146327.2";
 		entry.online = true;
 		entry.tracingsURL = "https://raw.githubusercontent.com/morphonets/misc/master/dataset-demos/SpotSpine/SpotSpine_ImageStack_Test.swc";
 		return entry;

src/main/java/sc/fiji/snt/gui/GuiUtils.java

@@ -1601,7 +1601,7 @@ public static JMenu helpMenu() {
 		mi = menuItemTriggeringURL("Screencasts", URL + "screencasts");
 		mi.setIcon(IconFactory.getMenuIcon(GLYPH.VIDEO));
 		helpMenu.add(mi);
-		mi = menuItemTriggeringURL("Step-by-step Instructions", URL + "step-by-step-instructions");
+		mi = menuItemTriggeringURL("Walkthroughs", URL + "walkthroughs");
 		mi.setIcon(IconFactory.getMenuIcon(GLYPH.FOOTPRINTS));
 		helpMenu.add(mi);
 

src/main/java/sc/fiji/snt/gui/SNTCommandFinder.java

@@ -28,6 +28,7 @@
 import org.scijava.ui.awt.AWTWindows;
 import org.scijava.util.PlatformUtils;
 import sc.fiji.snt.SNTUI;
+import sc.fiji.snt.SNTUtils;
 import sc.fiji.snt.viewer.Viewer3D;
 
 import javax.swing.*;
@@ -258,7 +259,7 @@ private void recordCmdSNTUI(final CmdAction cmdAction) {
 		}
 		if (promptCmd) {
 			switch (cmdAction.id) {
-			// FIXME: This should be move to the executing command
+			// FIXME: This should be moved to the executing command
 			case "Path-based Distributions...":
 			case "Branch-based Distributions...":
 				sb.append("\", \"metric 1 chosen in prompt\", \"[true or false (default) for polar histogram]\", \"[metric 2]\", \"[...]\")");
@@ -332,6 +333,7 @@ private void recordComment(final String string) {
 	public void toggleVisibility() {
 		if (frame == null || table == null) {
 			assemblePalette();
+			SNTUtils.log(String.format("Command Finder: %d commands indexed", (cmdScrapper.cmdMap.size()+cmdScrapper.otherMap.size())));
 		}
 		if (frame.isVisible()) {
 			hideWindow();

src/main/java/sc/fiji/snt/gui/ScriptInstaller.java

@@ -69,6 +69,7 @@ public class ScriptInstaller implements MenuKeyListener {
 	private static TextEditor editor;
 
 	private boolean openInsteadOfRun;
+	private Icon icon;
 
 	public ScriptInstaller(final Context context, final Component parent){
 		context.inject(this);
@@ -78,6 +79,7 @@ public ScriptInstaller(final Context context, final Component parent){
 			ui = null;
 		guiUtils = new GuiUtils(parent);
 		init();
+		icon = UIManager.getIcon("Tree.openIcon");
 	}
 
 	private void init() {
@@ -242,7 +244,7 @@ private JMenuItem menuItem(final ScriptInfo si, final boolean trimExtension) {
 
 	private void updateMenuItemIcon(final JMenuItem item) {
 		if (openInsteadOfRun && (item.isSelected() || item.isArmed())) {
-			item.setIcon(IconFactory.getMenuIcon(GLYPH.EYE));
+			item.setIcon(icon);
 		} else {
 			item.setIcon(null);
 		}

src/main/java/sc/fiji/snt/gui/cmds/OpenDatasetCmd.java

@@ -49,10 +49,15 @@ public class OpenDatasetCmd extends CommonDynamicCmd {
 	@Parameter(required=false, persist = false)
 	private File file;
 
+	@Parameter(required=false, persist = false)
+	private boolean clipboard;
+
 	@SuppressWarnings("unused")
 	private void init() {
 		init(true);
-		if (file == null || !file.exists()) {
+		if (clipboard)
+			resolveInput("file");
+		else if (file == null || !file.exists()) {
 			file = new GuiUtils(ui).getImageFile(file);
 			resolveInput("file");
 		}
@@ -66,26 +71,34 @@ public void run() {
 //			final Dataset ds = ioService.open(file.getAbsolutePath());
 //			final ImagePlus imp = convertService.convert(ds, ImagePlus.class);
 //			snt.initialize(imp);
-			if (file != null) {
-				ImagePlus imp = ImpUtils.open(file);
-				imp = ChooseDatasetCmd.convertInPlaceToCompositeAsNeeded(ui, imp);
-				if (imp.getType() != ImagePlus.COLOR_RGB) {
-					snt.initialize(imp);
-				}
+			if (clipboard) {
+				final ImagePlus imp = ImpUtils.getSystemClipboard(true);
+				if (imp == null)
+					error("No (valid) image found on system clipboard.");
+				else
+					initializeSNT(imp);
+			} else if (file != null) {
+				initializeSNT(ImpUtils.open(file));
 			}
 		}
 		catch (final NullPointerException ex) {
 			error("Loading of image failed (see Console for details)... "
 					+ "File may not be valid or may encode a proprietary format "
 					+ "not immediately recognized. Please open the image using "
-					+ "IJ/Bioformats (if not yet open). Then, load it in SNT using "
+					+ "Bioformats (if not yet open). Then, load it in SNT using "
 					+ "'Choose Tracing Image -> From Open Image...'.");
 			ex.printStackTrace();
 		} finally {
 			resetUI();
 		}
 	}
 
+	void initializeSNT(ImagePlus imp) {
+		imp = ChooseDatasetCmd.convertInPlaceToCompositeAsNeeded(ui, imp);
+		if (imp.getType() != ImagePlus.COLOR_RGB)
+			snt.initialize(imp);
+	}
+
 	public static void main(final String... args) {
 		final ImageJ ij = new ImageJ();
 		ij.ui().showUI();

src/main/java/sc/fiji/snt/util/ImpUtils.java

@@ -35,6 +35,11 @@
 import sc.fiji.snt.SNTUtils;
 import sc.fiji.snt.Tree;
 
+import java.awt.*;
+import java.awt.datatransfer.Clipboard;
+import java.awt.datatransfer.DataFlavor;
+import java.awt.datatransfer.Transferable;
+import java.awt.image.BufferedImage;
 import java.awt.image.IndexColorModel;
 import java.io.File;
 import java.io.InputStream;
@@ -275,6 +280,47 @@ public static ImagePlus combineSkeletons(final Collection<Tree> trees, final boo
 		return imp;
 	}
 
+	/**
+	 * Retrieves an ImagePlus from the system clipboard
+	 *
+	 * @param asMultiChannel if true and clipboard contains RGB data image is returned as composite (RGB/8-bit grayscale otherwise)
+	 * @return the image stored in the system clipboard or null if no image found
+	 */
+	public static ImagePlus getSystemClipboard(final boolean asMultiChannel) {
+		try {
+			final Clipboard clipboard = Toolkit.getDefaultToolkit().getSystemClipboard();
+			final Transferable transferable = clipboard.getContents(null);
+			if (transferable != null && transferable.isDataFlavorSupported(DataFlavor.imageFlavor)) {
+				final Image img = (Image) transferable.getTransferData(DataFlavor.imageFlavor);
+				final int width = img.getWidth(null);
+				final int height = img.getHeight(null);
+				final BufferedImage bi = new BufferedImage(width, height, BufferedImage.TYPE_INT_RGB);
+				final Graphics g = bi.createGraphics();
+				g.drawImage(img, 0, 0, null);
+				g.dispose();
+				final ImagePlus result = new ImagePlus("Clipboard", bi);
+				final boolean isGray = isGrayscale(bi, width, height);
+				if (isGray) convertTo8bit(result);
+				return (asMultiChannel && !isGray) ? convertRGBtoComposite(result) : result;
+			}
+		} catch (final Throwable e) {
+			SNTUtils.error("No image in clipboard", e);
+		}
+		return null;
+	}
+
+	private static boolean isGrayscale(final BufferedImage image, final int width, final int height) {
+		for (int i = 0; i < width; i++) { // https://stackoverflow.com/a/36173328
+			for (int j = 0; j < height; j++) {
+				final int pixel = image.getRGB(i, j);
+				final int red = (pixel >> 16) & 0xff;
+				final int green = (pixel >> 8) & 0xff;
+				if (red != green || green != ((pixel) & 0xff)) return false;
+			}
+		}
+		return true;
+	}
+
 	/**
 	 * Returns one of the demo images bundled with SNT image associated with the
 	 * demo (fractal) tree.