Fix UX inconsistencies

Author: tferr

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

@@ -888,7 +888,7 @@ private void updateCmdsOneSelected(final Path p) {
                     ? "<html>Path has never been fitted:<br>Fit will be computed for the first time"
                     : "<html>Path has already been fitted:\nCached properties will be applied");
         }
-        colorMenu.selectSWCColor(new SNTColor(p.getColor(), p.getSWCType()));
+        colorMenu.selectSWCColor(new SNTColor(p.getColor()));
         selectSWCTypeMenuEntry(p.getSWCType());
     }
 
@@ -1714,11 +1714,11 @@ private static class NodeRender extends DefaultTreeCellRenderer {
             final int arc = UIManager.getInt("Component.arc");
             CHIP_ARC = (arc > 0) ? Math.min(arc, 8) : 4;
             final Color fg = UIManager.getColor("Tree.textForeground"); // Tree.foreground is unused. See formdev.com/flatlaf/components/tree/
-            final Color base = (fg != null) ? fg : Color.GRAY;
+            final Color base = (fg != null) ? fg : Color.DARK_GRAY;
             final int r = base.getRed(), gn = base.getGreen(), b = base.getBlue();
             CHIP_BORDER = new Color(r, gn, b, 50);
             CHIP_TEXT = base;
-            CHIP_FILL = new Color(r, gn, b, 10);
+            CHIP_FILL = new Color(r, gn, b, 8);
         }
 
         // Per-cell state populated in getTreeCellRendererComponent
@@ -2858,6 +2858,7 @@ public void actionPerformed(final ActionEvent e) {
             final List<Path> selectedPaths = getSelectedPaths(true);
             if (selectedPaths.isEmpty()) {
                 guiUtils.error("There are no traced paths.");
+                setSelected(false);
                 return;
             }
             removeOrReapplyDefaultTag(selectedPaths, getActionCommand(), isSelected(), true);
@@ -3921,7 +3922,7 @@ public void execute(List<Path> selectedPaths, String cmd) {
                 if (tags.isEmpty() && existingTags.isEmpty()) {
                     return;
                 } else if (tags.isEmpty()) {
-                    deleteCustomTags(selectedPaths);
+                    deleteCustomTags(selectedPaths, false);
                     return;
                 }
 
@@ -5183,7 +5184,7 @@ private void removeTagsThroughPrompt(final List<Path> selectedPaths) {
                 return;
             }
             if (choices[1].equals(choice)) {
-                deleteCustomTags(selectedPaths); // will call refreshManager
+                deleteCustomTags(selectedPaths, true); // will call refreshManager
                 return;
             }
             if (choices[2].equals(choice)) {
@@ -5214,8 +5215,8 @@ private void replaceTags(final List<Path> selectedPaths) {
             guiUtils.centeredMsg(counter + " occurrence(s) replaced.", "Operation Completed");
         }
 
-        private void deleteCustomTags(final List<Path> paths) {
-            if (!plugin.getUI().askUserConfirmation || guiUtils.getConfirmation("Remove custom tags from "
+        private void deleteCustomTags(final List<Path> paths, final boolean deleteWithoutConfirmation) {
+            if (deleteWithoutConfirmation || !plugin.getUI().askUserConfirmation || guiUtils.getConfirmation("Remove custom tags from "
                     + ((paths.size() == pathAndFillManager.size()) ? "all " : "the selected ")
                     + paths.size() + " paths?", "Confirm Tag Removal?")) {
                 paths.forEach(p -> p.setName(TAG_CUSTOM_PATTERN.matcher(p.getName()).replaceAll("")));
@@ -5726,7 +5727,7 @@ void sortArbors() {
             }
             final String[] choices = { "Arbor ID", "Cell label", "Primary path name", "Primary path length",
                     "Primary path mean radius", "Traced channel", "Traced frame" };
-            final String choice = guiUtils.getChoice("Sorting criterion:", "Sort Root-level Paths", choices, choices[0]);
+            final String choice = guiUtils.getChoice("Sort by:", "Sort Root-level Paths", choices, choices[0]);
             if (choice == null)
                 return;
             switch (choice) {
@@ -6061,19 +6062,27 @@ void addExtras() {
         private void showColorCustomizationDialog() {
             // Create the panel with color chooser buttons
             final JPanel panel = new JPanel(new GridBagLayout());
+            panel.setBackground(ProofReadingTagsToolBar.this.getBackground());
             final GridBagConstraints c = GuiUtils.defaultGbc();
+            // Align the component to the left edge of its cell
+            c.anchor = GridBagConstraints.WEST;
+            // Prevent the component from stretching horizontally
+            c.fill = GridBagConstraints.NONE;
             // Create color selection components for each tag
             c.insets = new Insets(0, 0, 5, 0);
             final Map<String, ColorChooserButton> colorButtons = new HashMap<>();
             tagsMap.forEach( (tagName, color) -> {
-                final ColorChooserButton colorButton = new ColorChooserButton(color, capitalized(tagName));
+                final ColorChooserButton colorButton = new ColorChooserButton(color, capitalized(tagName)
+                , 1f, ColorChooserButton.RIGHT);
+                GuiUtils.Buttons.makeBorderless(colorButton);
                 panel.add(colorButton, c);
                 colorButtons.put(tagName, colorButton);
                 c.gridy++;
             });
             // Add reset button
             c.insets.top += 10;
-            final JButton resetButton = new JButton("Reset to Defaults");
+            final JButton resetButton = new JButton("Reset to Defaults", IconFactory.buttonIcon(IconFactory.GLYPH.UNDO, .9f));
+            GuiUtils.Buttons.makeBorderless(resetButton);
             resetButton.addActionListener(e -> {
                 tagsMap.keySet().forEach( tagName -> saveTagColor(tagName, null));
                 tagsMap.clear();
@@ -6084,7 +6093,7 @@ private void showColorCustomizationDialog() {
 
             // Show the option pane
             final int result = JOptionPane.showConfirmDialog(PathManagerUI.this,
-                    panel, "Proofreading Tag Colors", JOptionPane.OK_CANCEL_OPTION, JOptionPane.PLAIN_MESSAGE);
+                    panel, "Proofreading Tags", JOptionPane.OK_CANCEL_OPTION, JOptionPane.PLAIN_MESSAGE);
 
             // save the new colors if user pressed OK
             if (result == JOptionPane.OK_OPTION) {
@@ -6190,13 +6199,12 @@ void summarizeTags() {
                 else
                     dataset.put("none", dataset.get("none")+1);
             });
-            final SNTChart chart = AnalysisUtils.ringPlot(String.format("Tags (All %d Paths)", paths.size()), dataset, colors);
+            final SNTChart chart = AnalysisUtils.ringPlot(String.format("Proofreading Tags (All %d Paths)", paths.size()), dataset, colors);
             if (ringChart != null && ringChart.isVisible()) {
                 ringChart.replace(chart);
-                ringChart.getFrame().setTitle(String.format("Tags (All %d Paths)", paths.size()));
                 ringChart.show();
             } else {
-                chart.getFrame().setLocationRelativeTo(ProofReadingTagsToolBar.this);
+                chart.getFrame().setLocationRelativeTo(PathManagerUI.this);
                 chart.show();
                 ringChart = chart;
             }

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

@@ -61,7 +61,7 @@ public class PathManagerUISearchableBar extends SNTSearchableBar {
 	 * @param pmui the PathManagerUI instance
 	 */
 	public PathManagerUISearchableBar(final PathManagerUI pmui) {
-		super(pmui.getSearchable(), "Text filtering");
+		super(pmui.getSearchable(), "Type to select");
 		this.pmui = pmui;
 		guiUtils = new GuiUtils(pmui);
 		setGuiUtils(guiUtils);

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

@@ -64,7 +64,7 @@ public class SNTSearchableBar extends SearchableBar {
 	protected boolean subFilteringEnabled;
 
 	public SNTSearchableBar(final Searchable searchable) {
-		this(searchable, "Search");
+		this(searchable, "Type to select");
 	}
 
 	public SNTSearchableBar(final Searchable searchable, final String placeholder) {

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

@@ -26,6 +26,7 @@
 import com.formdev.flatlaf.icons.FlatSearchIcon;
 import com.formdev.flatlaf.icons.FlatSearchWithHistoryIcon;
 import com.formdev.flatlaf.ui.FlatRoundBorder;
+import sc.fiji.snt.util.SNTColor;
 
 import javax.swing.*;
 import java.awt.*;
@@ -154,12 +155,7 @@ public void enlarge(final float enlargeFactor) {
     public static Color iconColor() {
          if (iconColor == null) {
              iconColor = UIManager.getColor("SearchField.searchIconColor");
-             if (iconColor == null) {
-                 iconColor = Color.DARK_GRAY;
-             } else {
-                 // somehow transparency is not being set(!?), so we'll get it here
-                 iconColor = new Color(iconColor.getRed(), iconColor.getGreen(), iconColor.getBlue(), iconColor.getAlpha());
-             }
+             if (iconColor == null) iconColor = IconFactory.defaultColor();
          }
         return iconColor;
     }

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

@@ -381,17 +381,17 @@ protected void runCommand() {
                 return;
             }
 
-            // Retrieve ROI. If not found, look for it in the image overlay or on second image
-            final Roi roi = getRoi(chosenMaskImp, chosenOrigImp, (snt != null) ? snt.getImagePlus() : null);
-
             // Aggregate unexpected settings for validation
             final boolean isSame = !isFileMode() && (maskImgChoice != null && maskImgChoice.equals(originalImgChoice));
             final boolean isSegmented = isSegmented(chosenMaskImp);
             final boolean isCompatible = chosenOrigImp == null || ImpUtils.sameCalibration(chosenMaskImp, chosenOrigImp);
             final boolean isSameDim = chosenOrigImp == null || ImpUtils.sameXYZDimensions(chosenOrigImp, chosenMaskImp);
             final boolean isValidConnectDist = maxConnectDist > 0d;
-            final boolean isValidRoi = roi != null && roi.isArea();
             final boolean autoDetectSoma = ROI_AUTO_DETECT.equals(rootChoice);
+
+            // Retrieve ROI. If not found, look for it in the image overlay or on second image
+            final Roi roi = (autoDetectSoma) ? null : getRoi(chosenMaskImp, chosenOrigImp, (snt != null) ? snt.getImagePlus() : null);
+            final boolean isValidRoi = roi != null && roi.isArea();
             boolean inferRootFromRoi = !ROI_UNSET.equals(rootChoice) && !autoDetectSoma;
 
             if (isSame || !isValidOrigImg || !isSegmented || !isSameDim || !isCompatible || (!isValidRoi && inferRootFromRoi)
@@ -409,7 +409,7 @@ protected void runCommand() {
             SNTUtils.log("Segmented image: " + chosenMaskImp.getTitle());
             SNTUtils.log("Segmented image thresholded/binarized: " + isSegmented);
             SNTUtils.log("Original image: " + ((chosenOrigImp == null) ? null : chosenOrigImp.getTitle()));
-            SNTUtils.log("Root-defining strategy: " + rootChoice);
+            SNTUtils.log("ROI strategy: " + rootChoice);
             SNTUtils.log("ROI: " + roi);
 
             // Skeletonize all images again, just to ensure we are indeed dealing with skeletons
@@ -427,10 +427,14 @@ protected void runCommand() {
                 final SomaUtils.SomaResult somaResult = SomaUtils.detectSoma(
                         ImpUtils.toImgPlus(chosenMaskImp), -1d, -1);
                 if (somaResult != null && somaResult.hasContour()) {
-                    final Roi somaRoi = somaResult.createContourRoi();
-                    if (somaRoi != null && somaResult.zSlice() >= 0) somaRoi.setPosition(somaResult.zSlice() + 1);
-                    converter.setRootRoi(somaRoi, BinaryTracer.ROI_CENTROID);
                     SNTUtils.log("Auto-detected soma: " + somaResult);
+                    final Roi somaRoi = somaResult.createContourRoi();
+                    if (somaRoi != null && somaResult.zSlice() >= 0) {
+                        somaRoi.setPosition(somaResult.zSlice() + 1);
+                        converter.setRootRoi(somaRoi, BinaryTracer.ROI_CENTROID);
+                        chosenMaskImp.setRoi(somaRoi);
+                    }
+                    SNTUtils.log("Auto-detected soma ROI: " + somaRoi);
                 } else {
                     SNTUtils.log("Soma auto-detection did not find a soma. Using arbitrary root.");
                 }
@@ -447,7 +451,6 @@ protected void runCommand() {
                                 converter.getPruneMode() == BinaryTracer.LOWEST_INTENSITY_VOXEL))
                     SNTUtils.log("Intensity-based pruning failed (unsupported image type!?): Defaulting to fallback strategy");
                 converter.setPruneMode(BinaryTracer.PERIPHERAL_SEGMENTS);
-
                 try {
                     trees = converter.getTrees();
                 } catch (final IllegalStateException ex) {
@@ -456,6 +459,10 @@ protected void runCommand() {
                     SNTUtils.error("", ex);
                     return;
                 }
+            } catch (final IllegalArgumentException iae) {
+                error(iae.getMessage() +".");
+                SNTUtils.error("", iae);
+                return;
             }
             if (trees == null) {
                 error("No paths could be extracted. No structures found in image!?");

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

@@ -278,12 +278,9 @@ public void run() {
                                 "You can now run 'Grow Analysis...' on the dataset.", paths.size(), groupCounter,
 						timePointsParsed), "Matching Completed");
 			}
-			if (ui != null) {
-				ui.getPathManager().update();
-				resetUI();
-			}
+			if (ui != null) ui.getPathManager().update();
 		}
-
+		resetUI();
 	}
 
 	/* null: consider all time-points; empty set: assume invalid input */