fix #333

Author: tferr

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

@@ -1111,9 +1111,8 @@ private void redrawEditingPath(final Graphics2D g) {
         // what the user sees. The editableNodeIndex lives on editingPath
         // (always the main/unfitted path), so we temporarily propagate
         // it to the fitted copy for rendering, then clear it afterwards.
-        Path drawPath = editingPath;
-        if (editingPath.getUseFitted() && editingPath.getFitted() != null) {
-            drawPath = editingPath.getFitted();
+        final Path drawPath = editingPath.getVersionInUse();
+        if (drawPath != editingPath) {
             drawPath.setEditableNode(editingPath.getEditableNodeIndex());
             drawPath.setEditableNodeLocked(editingPath.isEditableNodeLocked());
         }
@@ -1745,8 +1744,7 @@ protected void togglePaintMode() {
         // Auto-select nearest node if none is active yet (e.g., user pressed P
         // right after Shift+E without moving the mouse over the path)
         if (editingPath.getEditableNodeIndex() == -1) {
-            final Path matchPath = editingPath.getUseFitted()
-                    ? editingPath.getFitted() : editingPath;
+            final Path matchPath = editingPath.getVersionInUse();
             int nearest = matchPath.indexNearestToCanvasPosition2D(
                     last_x_in_pane_precise, last_y_in_pane_precise, nodeDiameter());
             if (nearest == -1) nearest = 0; // fallback to first node
@@ -1890,8 +1888,7 @@ protected void assignRadiusToEditingNode(final boolean warnOnFailure) {
     private void brushMoveNodes(final Path editingPath) {
         // Resolve fitted path for nearest-node lookup (no distance threshold
         // so fast drags don't outrun the nodes and stall painting)
-        final Path matchPath = editingPath.getUseFitted()
-                ? editingPath.getFitted() : editingPath;
+        final Path matchPath = editingPath.getVersionInUse();
         final int centerNode = matchPath.indexNearestToCanvasPosition2D(
                 last_x_in_pane_precise, last_y_in_pane_precise, Double.MAX_VALUE);
         if (centerNode == -1 || centerNode >= editingPath.size()) return;
@@ -1916,7 +1913,7 @@ private void brushMoveNodes(final Path editingPath) {
     }
 
     private void brushBlendRadii(final Path editingPath) {
-        final Path matchPath = editingPath.getUseFitted() ? editingPath.getFitted() : editingPath;
+        final Path matchPath = editingPath.getVersionInUse();
         final int centerNode = matchPath.indexNearestToCanvasPosition2D(
                 last_x_in_pane_precise, last_y_in_pane_precise, Double.MAX_VALUE);
         if (centerNode == -1 || centerNode >= editingPath.size()) return;

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

@@ -2540,6 +2540,17 @@ public Path getUnfitted() {
 		return fittedVersionOf;
 	}
 
+	/**
+	 * Returns the version of this path that is in use, i.e., the one that is displayed and analyzed: its fitted
+	 * flavor if {@link #getUseFitted()}, otherwise this path. This is the registry-free rule: for the
+	 * registry-aware one see {@link PathAndFillManager#getVersionInUse(Path)}
+	 *
+	 * @return the version in use. Never null
+	 */
+	public Path getVersionInUse() {
+		return getUseFitted() ? fitted : this;
+	}
+
 	/**
 	 * Single source of truth for the "should this fitted-version path be treated as redundant/standalone" decision
 	 * used throughout listings, filters, and measurements.

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

@@ -676,7 +676,7 @@ public synchronized Path[] getPathsStructured() {
     public Collection<Tree> getTrees() {
         final HashMap<String, Tree> map = new HashMap<>();
         allPaths.forEach(p->{
-            final Path pathToUse = (p.getUseFitted()) ? p.getFitted() : p;
+            final Path pathToUse = getVersionInUse(p);
             String treeID = pathToUse.getTreeLabel();
             if (map.get(treeID) == null) {
                 final Tree tree = new Tree();
@@ -704,7 +704,7 @@ public Collection<Tree> getTrees() {
     public Tree getTree(final String treeLabel) {
         final Tree tree = new Tree();
         allPaths.forEach(p->{
-            final Path pathToUse = (p.getUseFitted()) ? p.getFitted() : p;
+            final Path pathToUse = getVersionInUse(p);
             if (treeLabel.equals(pathToUse.getTreeLabel()))
                 tree.add(pathToUse);
         });
@@ -724,7 +724,7 @@ public Tree getTree(final String treeLabel) {
     public Tree getTree(final int treeId) {
         final Tree tree = new Tree();
         allPaths.forEach(p->{
-            final Path pathToUse = (p.getUseFitted()) ? p.getFitted() : p;
+            final Path pathToUse = getVersionInUse(p);
             if (treeId == pathToUse.getTreeID())
                 tree.add(pathToUse);
         });
@@ -1971,9 +1971,7 @@ private void addImportedPathsTo3DViewer() {
                 // never registered) is itself the de facto path and must still be added
                 if (!isDeFactoPath(p) || p.size() < 2)
                     continue;
-                Path pathToAdd;
-                if (p.getUseFitted()) pathToAdd = p.getFitted();
-                else pathToAdd = p;
+                final Path pathToAdd = p.getVersionInUse();
                 pathToAdd.addTo3DViewer(plugin.univ, SNTPrefs.deselectedPathColor(), plugin.colorImage);
             }
         }
@@ -2015,6 +2013,7 @@ public void endElement(final String uri, final String localName,
                     final Integer fittedID = fittedFields.get(p.getID());
                     final Integer fittedVersionOfID = fittedVersionOfFields.get(p.getID());
                     final Boolean useFitted = useFittedFields.get(p.getID());
+                    boolean fitDiscarded = false;
 
                     if (startID != null) {
                         final Path startPath = getPathFromID(startID);
@@ -2056,6 +2055,20 @@ public void endElement(final String uri, final String localName,
 
                             pReversed.setBranchFrom(endPath, endJoinPoint);
 
+                            // reversed() does not carry over the fit: discard it (and its
+                            // registration) so that no dangling fitted links remain
+                            if (fittedID != null) {
+                                final Path fit = getPathFromID(fittedID);
+                                if (fit != null) {
+                                    allPaths.remove(fit);
+                                    pathIdMap.remove(fit.getID(), fit);
+                                    pathNameMap.remove(fit.getName(), fit);
+                                }
+                                fitDiscarded = true;
+                                SNTUtils.log("End-joined path " + p.getID() + " ('" + p.getName()
+                                        + "') was fitted: fit discarded");
+                            }
+
                             for (final Path join : new ArrayList<>(p.connectedPaths)) {
                                 if (join.getParentPath() == p) {
                                     final PointInImage joinPoint = join.getBranchPoint();
@@ -2065,9 +2078,16 @@ public void endElement(final String uri, final String localName,
                             }
                         } // end null-check else
                     }
-                    if (fittedID != null) {
-                        p.fitted = getPathFromID(fittedID);
-                        p.setUseFitted(useFitted);
+                    if (fittedID != null && !fitDiscarded) {
+                        final Path fit = getPathFromID(fittedID);
+                        if (fit == null) {
+                            SNTUtils.log("Malformed traces file: fitted=" + fittedID
+                                    + " referenced by path " + p.getID() + " ('" + p.getName()
+                                    + "') does not exist. Fit skipped.");
+                        } else {
+                            p.fitted = fit;
+                            p.setUseFitted(useFitted);
+                        }
                     }
                     if (fittedVersionOfID != null) {
                         p.fittedVersionOf = getPathFromID(fittedVersionOfID);
@@ -2092,10 +2112,6 @@ else if (p != p.fittedVersionOf.getFitted())
                             throw new TracesFileFormatException(
                                     "Malformed traces file: p didn't match p.fittedVersionOf.fitted");
                     }
-                    else if (p.getUseFitted()) {
-                        throw new TracesFileFormatException(
-                                "Malformed traces file: p.useFitted was true but p.fitted was null");
-                    }
                 }
 
                 // allPaths have been used to store all imported paths, including fitted ones.
@@ -3156,10 +3172,7 @@ synchronized void setPathPointsInVolume(final Collection<Path> paths,
         for (final Path topologyPath : paths) {
             if (pixelIntensity == -1)
                 actualPixelIntensity = (short) ++label;
-            Path p = topologyPath;
-            if (topologyPath.getUseFitted()) {
-                p = topologyPath.getFitted();
-            }
+            final Path p = topologyPath.getVersionInUse();
             final int n = p.size();
 
             final ArrayList<Bresenham3D.IntegerPoint> pointsToJoin =
@@ -3266,7 +3279,8 @@ public synchronized NodeRef nearestNodeOnPaths(final Collection<Path> paths, fin
 
     /**
      * Returns the version of a path that is in use, i.e., the one that is displayed and analyzed: its fitted
-     * flavor if {@link Path#getUseFitted()}, otherwise the path itself. Same rule as {@link Tree#Tree(Collection)}.
+     * flavor if {@link Path#getUseFitted()}, otherwise the path itself. Same rule as
+     * {@link Tree#Tree(Collection)}, which uses the collection itself as registry.
      * A fitted copy whose original is registered with this manager is first resolved to that original (see
      * {@link #isDeFactoPath(Path)}), so that both flavors of a path always resolve to the same version.
      *
@@ -3276,7 +3290,7 @@ public synchronized NodeRef nearestNodeOnPaths(final Collection<Path> paths, fin
     public synchronized Path getVersionInUse(final Path p) {
         if (p == null) return null;
         final Path base = (p.isFittedVersionOfAnotherPath() && !isDeFactoPath(p)) ? p.getUnfitted() : p;
-        return base.getUseFitted() ? base.getFitted() : base;
+        return base.getVersionInUse();
     }
 
     /**
@@ -3680,10 +3694,7 @@ public void exportToCSV(final File outputFile) throws IOException {
         }
         pw.print("\r\n");
         for (final Path p : allPaths) {
-            Path pForLengthAndName = p;
-            if (p.getUseFitted()) {
-                pForLengthAndName = p.getFitted();
-            }
+            final Path pForLengthAndName = p.getVersionInUse();
             if (p.fittedVersionOf != null) continue;
             SNTUtils.csvQuoteAndPrint(pw, p.getID()); //col1: PathID
             pw.print(",");
@@ -3766,7 +3777,7 @@ protected void update3DViewerContents() {
 
             // If path is being rendered with its own custom color, highlight it
             // somehow if is being selected
-            if (p.getUseFitted()) p = p.getFitted();
+            p = p.getVersionInUse();
             if (p.content3D != null) p.content3D.setShaded(!(customColor &&
                     selected));
 

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

@@ -5407,7 +5407,7 @@ private void applyZCorrection(final List<Path> selectedPaths) {
             if (plugin.accessToValidImageData()) {
                 final double maxZ = plugin.depth - 1;
                 for (final Path p : selectedPaths) {
-                    final Path pathToUse = p.getUseFitted() ? p.getFitted() : p;
+                    final Path pathToUse = p.getVersionInUse();
                     for (int node = 0; node < pathToUse.size(); node++) {
                         final double newZ = pathToUse.getNodeWithoutChecks(node).z * factor;
                         if (newZ < 0 || newZ > maxZ) oobNodes++;
@@ -5420,7 +5420,7 @@ private void applyZCorrection(final List<Path> selectedPaths) {
                 }
             }
             for (final Path p : selectedPaths) {
-                final Path pathToUse = p.getUseFitted() ? p.getFitted() : p;
+                final Path pathToUse = p.getVersionInUse();
                 for (int node = 0; node < pathToUse.size(); node++) {
                     final PointInImage current = pathToUse.getNodeWithoutChecks(node);
                     pathToUse.moveNode(node, current.x, current.y, current.z * factor);
@@ -5678,11 +5678,7 @@ private void dowsamplePaths(final List<Path> selectedPaths) {
                 return;
             }
             for (final Path p : selectedPaths) {
-                Path pathToUse = p;
-                if (p.getUseFitted()) {
-                    pathToUse = p.getFitted();
-                }
-                pathToUse.downsample(maxDeviation);
+                p.getVersionInUse().downsample(maxDeviation);
             }
             // Make sure that the 3D viewer and the stacks are redrawn:
             if (plugin.univ != null) {

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

@@ -2592,7 +2592,7 @@ else if (editing && !editingPath.isEditableNodeLocked()) {
 			// then activate the Z-slice of the retrieved node.
 			// When the fitted version is displayed, match against fitted nodes
 			// so the user clicks on what they see
-			final Path matchPath = editingPath.getUseFitted() ? editingPath.getFitted() : editingPath;
+			final Path matchPath = editingPath.getVersionInUse();
 			final int eNode = matchPath.indexNearestToCanvasPosition2D(x, y,
 					getXYCanvas().nodeDiameter());
 			if (eNode != -1) {
@@ -6368,7 +6368,7 @@ private ImagePlus captureView(final ImagePlus holdingImp, final String viewDescr
 			// See PathAndFillManager#isDeFactoPath(Path): only skip a fitted-version path when
 			// its un-fitted counterpart is also registered here to be drawn in its place
 			if (p == null || !pathAndFillManager.isDeFactoPath(p)) continue;
-			final Path drawPath = (p.getUseFitted() && p.getFitted() != null) ? p.getFitted() : p;
+			final Path drawPath = p.getVersionInUse();
 			drawPath.drawPathAsPoints(g, canvas, this);
 		}
 		// this is taken from ImagePlus.flatten()

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

@@ -115,13 +115,8 @@ protected void drawOverlay(final Graphics2D g) {
 
 				if (p.fittedVersionOf != null) continue;
 
-				Path drawPath = p;
-
-				// If the path suggests using the fitted version, draw that
-				// instead:
-				if (p.getUseFitted()) {
-					drawPath = p.getFitted();
-				}
+				// Draw the version in use (fitted if flagged)
+				final Path drawPath = p.getVersionInUse();
 
 				// Selection state is always tracked on the main (unfitted) path,
 				// not the fitted copy, so test against p rather than drawPath

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

@@ -93,22 +93,20 @@ public Tree() {
 	 *
 	 * @param paths the Collection of paths forming this tree. Null not allowed.
 	 *          Note that when a Path has been fitted and
-	 *          {@link Path#getUseFitted()} is true, its fitted 'flavor' is used.
+	 *          {@link Path#getUseFitted()} is true, its fitted 'flavor' is used
+	 *          (see {@link Path#getVersionInUse()}). A fitted copy whose original is
+	 *          also in the collection is not added twice.
 	 */
 	public Tree(final Collection<Path> paths) {
 		if (paths == null) throw new IllegalArgumentException(
 			"Cannot instantiate a new tree from a null collection");
 		tree = new ArrayList<>(paths.size());
+		final Set<Path> lookup = new HashSet<>(paths);
 		for (final Path p : paths) {
-			if (p == null) continue;
-			Path pathToAdd;
-			// If fitted flavor of path exists use it instead
-			if (p.getUseFitted() && p.getFitted() != null) {
-				pathToAdd = p.getFitted();
-			} else {
-				pathToAdd = p;
-			}
-			tree.add(pathToAdd);
+			// A fitted copy whose original is also in paths is skipped: the
+			// original resolves to the same version (see isDeFactoPath(Collection))
+			if (p == null || !p.isDeFactoPath(lookup)) continue;
+			tree.add(p.getVersionInUse());
 		}
 		final String unit = getCommonUnit(paths);
 		if (unit != null)

src/main/java/sc/fiji/snt/analysis/ProfileProcessor.java

@@ -87,7 +87,7 @@ public String toString() {
 	}
 
 	public ProfileProcessor(final RandomAccessibleInterval<T> rai, final Path path) {
-		this.path = (path.getUseFitted()) ? path.getFitted() : path;
+		this.path = path.getVersionInUse();
 		this.rai = rai;
 		this.intervalMin = Intervals.minAsLongArray(rai);
 		this.intervalMax = Intervals.maxAsLongArray(rai);

src/main/java/sc/fiji/snt/analysis/TreeStatistics.java

@@ -381,8 +381,8 @@ public TreeStatistics(final Collection<Path> paths, String label) {
         tree = new Tree(paths);
         tree.setLabel(label);
         for (final Path p : tree.list()) {
-            // If fitted flavor of path exists use it instead
-            if (p.getUseFitted()) {
+            // tree.list() holds the versions in use: fitted flavors are fitted copies
+            if (p.isFittedVersionOfAnotherPath()) {
                 fittedPathsCounter++;
             }
         }

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

@@ -718,7 +718,7 @@ private <V extends RealType<V>> Img<U> computeSpectralSimilarity(final U type, f
 			// represent the actual structure the user is tracing
 			final List<Path> resolvedPaths = new ArrayList<>(selectedPaths.size());
 			for (final Path p : selectedPaths) {
-				resolvedPaths.add(p.getUseFitted() && p.getFitted() != null ? p.getFitted() : p);
+				resolvedPaths.add(p.getVersionInUse());
 			}
 			// See computeAndDisplayAverageColor() for why getActiveCanvasPixelOffset() is needed here
 			final sc.fiji.snt.util.PointInCanvas offset = snt.getActiveCanvasPixelOffset();