SNTUI: Corrections/improvements to accommodate online docs

Also: saveMenuItem was being enabled/disabled across states. That made
sense when it was the only entry point for saving, but now that there many
other (and those are not being tracked), we no longer use saveMenuItem
as a class field

Author: tferr

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

@@ -96,7 +96,6 @@ public class SNTUI extends JDialog {
     protected JSpinner snapWindowZsizeSpinner;
     private JButton showOrHidePathList;
     private JButton showOrHideFillList = new JButton(); // must be initialized
-    private JMenuItem saveMenuItem;
     private JMenuItem quitMenuItem;
     private JLabel statusText;
     private JLabel statusBarText;
@@ -109,7 +108,6 @@ public class SNTUI extends JDialog {
     private JSpinner assignDiameterSpinner;
     private JCheckBox confirmTemporarySegmentsCheckbox;
     private JRadioButtonMenuItem standardTracingRbmi;
-    private JRadioButtonMenuItem rubberBandTracingRbmi;
 
     // UI controls for auto-tracing
     private JComboBox<String> searchAlgoChoice;
@@ -914,7 +912,6 @@ protected void disableImageDependentComponents() {
     private void disableEverything() {
         assert SwingUtilities.isEventDispatchThread();
         disableImageDependentComponents();
-        saveMenuItem.setEnabled(false);
         quitMenuItem.setEnabled(false);
     }
 
@@ -1024,7 +1021,6 @@ public void enter() {
             partsNearbyCSpinner.setEnabled(isStackAvailable());
             setEnableAutoTracingComponents(plugin.isAstarEnabled(), true);
             fmUI.setEnabledWhileNotFilling();
-            saveMenuItem.setEnabled(true);
             quitMenuItem.setEnabled(true);
             showPathsSelected.setEnabled(true);
             updateStatusText("Click somewhere to start a new path...");
@@ -1049,7 +1045,6 @@ public void enter() {
             setEnableAutoTracingComponents(false, false);
             plugin.discardFill();
             fmUI.setEnabledWhileNotFilling();
-            saveMenuItem.setEnabled(true);
             quitMenuItem.setEnabled(true);
             showPathsSelected.setEnabled(true);
             updateRebuildCanvasButton();
@@ -2914,7 +2909,7 @@ private JMenu fileMenu(final ScriptInstaller installer) {
 
         // Save
         fileMenu.addSeparator();
-        saveMenuItem = new JMenuItem("Save Tracings", IconFactory.menuIcon(IconFactory.GLYPH.SAVE));
+        final JMenuItem saveMenuItem = new JMenuItem("Save Tracings", IconFactory.menuIcon(IconFactory.GLYPH.SAVE));
         saveMenuItem.setToolTipText("Saves tracings to a TRACES (XML) file. "
                 + "This file may be gzip compressed as per options in the Preferences dialog.");
         saveMenuItem.setAccelerator(
@@ -3293,7 +3288,7 @@ private JMenu viewMenu() {
             // Calculate usable area (excluding taskbar, dock, etc.)
             final int usableX = screenBounds.x + insets.left;
             final int usableY = screenBounds.y + insets.top;
-            final int usableWidth = screenBounds.width - insets.left - insets.right;
+            //final int usableWidth = screenBounds.width - insets.left - insets.right;
             final int usableHeight = screenBounds.height - insets.top - insets.bottom;
 
             // Position dialogs on the same screen
@@ -3863,7 +3858,7 @@ public void itemStateChanged(final ItemEvent e) {
         optionsMenu.add(GuiUtils.leftAlignedLabel("Tracing Mode:", false));
         final ButtonGroup tracingModeButtonGroup = new ButtonGroup();
         standardTracingRbmi = new JRadioButtonMenuItem("Standard", !plugin.rubberBandTracing);
-        rubberBandTracingRbmi = new JRadioButtonMenuItem("Live Preview", plugin.rubberBandTracing);
+        final JRadioButtonMenuItem rubberBandTracingRbmi = new JRadioButtonMenuItem("Live Preview", plugin.rubberBandTracing);
         GuiUtils.addTooltip(rubberBandTracingRbmi, "<html>Continuously previews the path to the cursor position as you move the mouse.<br>"
                 + "Click to confirm each segment. Only recommended for 2D images.");
         tracingModeButtonGroup.add(standardTracingRbmi);
@@ -3898,7 +3893,7 @@ public void itemStateChanged(final ItemEvent e) {
         });
         optionsMenu.addSeparator();
         optionsMenu.add(GuiUtils.MenuItems.openHelpURL("Help on Algorithm Settings",
-                "https://imagej.net/plugins/snt/manual#auto-tracing"));
+                "https://imagej.net/plugins/snt/manual#algorithm-settings"));
         aStarPanel = new JPanel(new BorderLayout());
         aStarPanel.add(checkboxPanel, BorderLayout.CENTER);
         aStarPanel.add(optionsButton, BorderLayout.EAST);

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

@@ -71,10 +71,10 @@ public class PrefsCmd extends OptionsPlugin {
 	@Parameter(required = false)
 	private SwingLookAndFeelService lafService;
 
-    @Parameter(required = false, visibility = ItemVisibility.MESSAGE, label = HEADER_HTML + "I. IO and Performance:")
+    @Parameter(required = false, visibility = ItemVisibility.MESSAGE, label = HEADER_HTML + "I. I/O and Performance:")
     private String HEADER1;
 
-    @Parameter(label="No. parallel threads",
+    @Parameter(label="No. of parallel threads",
             description="<HTML><div WIDTH=500>The max. no. of parallel threads to be used by SNT, as specified in IJ's"
                     + "Edit>Options>Memory &amp; Threads... Set it to 0 to use the available processors on your computer")
     private int nThreads;
@@ -240,7 +240,7 @@ public void reset() {
 
 	@SuppressWarnings("unused")
 	private void lafHelp() {
-		new GuiUtils().showHTMLDialog("<HTML>"
+		new GuiUtils().showHTMLDialog("<HTML><div WIDTH=500>"
 				+ "SNT's <i>Look and Feel</i> (L&F) preference has been integrated into Fiji. "
 				+ "It is advised to use Fiji's <i>Edit>Look and Feel...</i> prompt instead.<br><br>"
 				+ "Note that setting a L&F does not affect AWT widgets. Thus, while a dark theme can be applied "

src/main/java/sc/fiji/snt/plugin/SpineExtractorCmd.java

@@ -63,7 +63,7 @@
 @Plugin(type = Command.class, label = "Extract Spine/Varicosity Counts from ROI(s)...", initializer = "init")
 public class SpineExtractorCmd extends CommonDynamicCmd {
 
-	private static final String MSG = "<br>To initiate counts, right-click on image and run \"Count Spine/Varicosities...\"";
+	private static final String MSG = "<br>Run \"Spine/Varicosity Utilities Help...\" for details on how to annotate locations.";
 
 	@Parameter(required = false, label = "Source of Multipoint ROI(s):") // choices set by #init()
 	private String roiSource;