Label detector: Keep track of contacted label

Author: tferr

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

@@ -282,7 +282,7 @@ private void expandCapacityTo(final int n) {
     private void addToCapacity(final int n) {
         final int currentN = delineations.size();
         final Color[] colors = defaultDelineationColors(Math.min(256, currentN + n));
-        final long lastLabel = delineations.isEmpty() ? 0 : delineations.getLast().label;
+        final long lastLabel = delineations.stream().mapToLong(d -> d.label).max().orElse(0);
         int colorIdx = 0;
         for (int i = 0; i < n; i++) {
             final Delineation del = new Delineation(lastLabel + i + 1, colors[colorIdx++]);
@@ -1243,6 +1243,9 @@ private class Delineation {
                 // labels are applied as negative numbers, so we'll impose positive labels
                 throw new IllegalArgumentException("Label must be greater than 0 and not " + UNDEFINED_LABEL);
             }
+            if (delineations.stream().anyMatch(d -> d.label == label)) {
+                throw new IllegalArgumentException("Duplicate delineation label: " + label);
+            }
             this.color = color;
             this.label = label;
             name = "Delineation " + label;
@@ -1336,7 +1339,10 @@ private JButton assignFromRoiButton() {
                             "No Paths in ROI")) {
                         return;
                     }
-                    if (this.roi != null) untagNodes(paths);
+                    if (this.roi != null) {
+                        // Clear stale labels from the OLD roi's paths, not the new one
+                        untagNodes((this.roi == DUMMY_ROI) ? pafm.getPaths() : pafm.getPathsInROI(this.roi));
+                    }
                     assignRoi(roi, paths);
                     sntui.plugin.updateAllViewers();
                 }
@@ -1417,16 +1423,12 @@ private void updateWidget() {
         public boolean equals(Object o) {
             if (this == o) return true;
             if (o == null || getClass() != o.getClass()) return false;
-            Delineation that = (Delineation) o;
-            return label == that.label &&
-                    Objects.equals(name, that.name) &&
-                    Objects.equals(color, that.color) &&
-                    Objects.equals(roi, that.roi);
+            return label == ((Delineation) o).label;
         }
 
         @Override
         public int hashCode() {
-            return Objects.hash(label, name, color, roi);
+            return Long.hashCode(label);
         }
     }
 

src/main/java/sc/fiji/snt/analysis/detection/Detection.java

@@ -50,6 +50,13 @@ public class Detection {
     public final int nodeIndex;
     /** Distance from the path skeleton at the detection point (physical units) */
     public final double distanceFromSkeleton;
+    /**
+     * Label value from a segmentation/label image associated with this
+     * detection, or {@code -1} if not applicable. Set by
+     * {@link LabelProximityDetector} to identify which label surface
+     * produced the contact.
+     */
+    public final int labelValue;
 
     /**
      * Creates a new detection.
@@ -65,13 +72,33 @@ public class Detection {
     public Detection(final double x, final double y, final double z,
                      final double intensity, final Path path, final int nodeIndex,
                      final double distanceFromSkeleton) {
+        this(x, y, z, intensity, path, nodeIndex, distanceFromSkeleton, -1);
+    }
+
+    /**
+     * Creates a new detection with an associated label value.
+     *
+     * @param x                    X-coordinate in real-world units
+     * @param y                    Y-coordinate in real-world units
+     * @param z                    Z-coordinate in real-world units
+     * @param intensity            intensity at the detection site
+     * @param path                 associated path
+     * @param nodeIndex            index of the nearest node on the path
+     * @param distanceFromSkeleton distance from the skeleton (physical units)
+     * @param labelValue           label-image value associated with this
+     *                             detection, or {@code -1} if not applicable
+     */
+    public Detection(final double x, final double y, final double z,
+                     final double intensity, final Path path, final int nodeIndex,
+                     final double distanceFromSkeleton, final int labelValue) {
         this.x = x;
         this.y = y;
         this.z = z;
         this.intensity = intensity;
         this.path = path;
         this.nodeIndex = nodeIndex;
         this.distanceFromSkeleton = distanceFromSkeleton;
+        this.labelValue = labelValue;
     }
 
     /**
@@ -105,9 +132,12 @@ public double[] xyzct() {
 
     @Override
     public String toString() {
-        return String.format(
-                "Detection[x=%.3f,y=%.3f,z=%.3f; I=%.1f; dist=%.3f; path=%s; node=%d]",
+        final String base = String.format(
+                "Detection[x=%.3f,y=%.3f,z=%.3f; I=%.1f; dist=%.3f; path=%s; node=%d",
                 x, y, z, intensity, distanceFromSkeleton,
                 path != null ? path.getName() : "null", nodeIndex);
+        return (labelValue >= 0)
+                ? base + "; label=" + labelValue + "]"
+                : base + "]";
     }
 }

src/main/java/sc/fiji/snt/analysis/detection/DetectorUtils.java

@@ -181,7 +181,7 @@ public static List<Detection> assignToNearestPaths(final List<Detection> detecti
 
             if (nearest != v.path || nearestIdx != v.nodeIndex) {
                 reassigned.add(new Detection(v.x, v.y, v.z, v.intensity,
-                        nearest, nearestIdx, Math.sqrt(minDist2)));
+                        nearest, nearestIdx, Math.sqrt(minDist2), v.labelValue));
             } else {
                 reassigned.add(v);
             }

src/main/java/sc/fiji/snt/analysis/detection/LabelProximityDetector.java

@@ -102,7 +102,7 @@ public static List<Detection> detect(final Collection<Path> paths,
                         final int nodeIdx = (int) entry[0];
                         final double dist = entry[1];
                         if (dist <= config.distanceThreshold) {
-                            allDetections.add(createDetection(path, nodeIdx, dist));
+                            allDetections.add(createDetection(path, nodeIdx, dist, labelVal));
                         }
                     }
                 } else {
@@ -116,7 +116,7 @@ public static List<Detection> detect(final Collection<Path> paths,
                         }
                     }
                     if (minIdx >= 0) {
-                        allDetections.add(createDetection(path, minIdx, minDist));
+                        allDetections.add(createDetection(path, minIdx, minDist, labelVal));
                     }
                 }
             }
@@ -138,15 +138,22 @@ public static List<Detection> detect(final Collection<Path> paths,
     }
 
     private static Detection createDetection(final Path path, final int nodeIdx,
-                                             final double distance) {
+                                             final double distance,
+                                             final int labelVal) {
         final PointInImage node = path.getNode(nodeIdx);
         // NMS keeps the highest score, so negate distance so that the closest
         // contact point (smallest distance) survives deduplication
         return new Detection(node.x, node.y, node.z,
                 -distance,
-                path, nodeIdx, 0); // distanceFromSkeleton = 0 (detection is on-skeleton)
+                path, nodeIdx, 0, // distanceFromSkeleton = 0 (detection is on-skeleton)
+                labelVal);
     }
 
+    /**
+     * Collects unique non-zero, positive integer label values from the image.
+     * Negative values and non-integer values are excluded, consistent with
+     * the convention that 0 = background and positive integers = labels.
+     */
     private static Set<Integer> collectLabels(final RandomAccessibleInterval<? extends RealType<?>> img) {
         final Set<Integer> labels = new LinkedHashSet<>();
         final Cursor<? extends RealType<?>> cursor = img.cursor();

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

@@ -179,20 +179,22 @@ public void run() {
 
         SNTUtils.log("Detected " + results.size() + " proximity contacts");
 
-        // Group results by path, resolving fitted paths back to unfitted originals
-        final Map<Path, List<Detection>> resultsByPath = results.stream()
-                .collect(Collectors.groupingBy(d ->
-                        d.path.isFittedVersionOfAnotherPath()
-                                ? d.path.getUnfitted() : d.path
-                ));
+        // Group results by path+label, resolving fitted paths back to unfitted originals
+        final Map<String, List<Detection>> resultsByPathAndLabel = results.stream()
+                .collect(Collectors.groupingBy(d -> {
+                    final Path p = d.path.isFittedVersionOfAnotherPath()
+                            ? d.path.getUnfitted() : d.path;
+                    return p.getName() + (d.labelValue >= 0 ? " [Label " + d.labelValue + "]" : "");
+                }, LinkedHashMap::new, Collectors.toList()));
 
         if (ui != null && outputChoice.toLowerCase().contains("bookmark")) {
 
-            resultsByPath.forEach((path, detections) -> {
+            resultsByPathAndLabel.forEach((groupName, detections) -> {
                 final List<double[]> locs = detections.stream()
                         .map(Detection::xyzct)
                         .collect(Collectors.toList());
-                ui.getBookmarkManager().add(path.getName() + " Proximity ", locs, path.getColor());
+                final Path refPath = detections.getFirst().path;
+                ui.getBookmarkManager().add(groupName, locs, refPath.getColor());
             });
             resetUI();
             ui.selectTab("Bookmarks");
@@ -206,10 +208,10 @@ public void run() {
             }
             RoiManager rm = RoiManager.getInstance2();
             if (rm == null) rm = new RoiManager();
-            for (final Map.Entry<Path, List<Detection>> entry : resultsByPath.entrySet()) {
-                final Path path = entry.getKey();
-                final String name = path.getName() + " (" + entry.getValue().size() + " contacts)";
-                rm.addRoi(RoiConverter.toPointRoi(entry.getValue(), imp, name, path.getColor()));
+            for (final Map.Entry<String, List<Detection>> entry : resultsByPathAndLabel.entrySet()) {
+                final String name = entry.getKey() + " (" + entry.getValue().size() + " contacts)";
+                final Path refPath = entry.getValue().getFirst().path;
+                rm.addRoi(RoiConverter.toPointRoi(entry.getValue(), imp, name, refPath.getColor()));
             }
             resetUI();
             rm.runCommand("sort");