Allow computations on cached data when main image closed

Author: tferr

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

@@ -340,7 +340,7 @@ private void connectToEditingPath(final Path source, final Path destination) {
         final Tree newTree = destinationGraph.getTreeWithSamePathStructure();
 //		enableEditMode(false);
         tracerPlugin.setEditingPath(null);
-        final Calibration cal = tracerPlugin.getImagePlus().getCalibration(); // snt the instance of the plugin
+        final Calibration cal = tracerPlugin.getCalibration(); // snt the instance of the plugin
         newTree.list().forEach(p -> p.setSpacing(cal));
         final boolean existingEnableUiUpdates = pathAndFillManager.enableUIupdates;
         pathAndFillManager.enableUIupdates = false;
@@ -1374,7 +1374,7 @@ protected void assignTreeRootToEditingNode(final boolean warnOnFailure) {
         editingGraph.setRoot(newRoot);
         final Tree newTree = editingGraph.getTreeWithSamePathStructure();
         tracerPlugin.setEditingPath(null);
-        final Calibration cal = tracerPlugin.getImagePlus().getCalibration();
+        final Calibration cal = tracerPlugin.getCalibration();
         pathAndFillManager.deletePaths(editingTree.list());
         newTree.list().forEach(p -> {
             p.setSpacing(cal);
@@ -1413,7 +1413,7 @@ protected void splitTreeAtEditingNode(final boolean warnOnFailure) {
         final Tree descendentTree = descendantGraph.getTreeWithSamePathStructure();
 //		enableEditMode(false);
         tracerPlugin.setEditingPath(null);
-        final Calibration cal = tracerPlugin.getImagePlus().getCalibration(); // snt the instance of the plugin
+        final Calibration cal = tracerPlugin.getCalibration(); // snt the instance of the plugin
         ancestorTree.list().forEach(p -> p.setSpacing(cal));
         descendentTree.list().forEach(p -> p.setSpacing(cal));
         final boolean existingEnableUiUpdates = pathAndFillManager.enableUIupdates;

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

@@ -1336,7 +1336,7 @@ protected void reloadFills(int[] selectedIndices) {
         for (int ind : selectedIndices) {
             Fill fill = allFills.get(ind);
             FillerThread filler = FillerThread.fromFill(
-                    scope, plugin.getImagePlus().getCalibration(),
+                    scope, plugin.getCalibration(),
                     plugin.getStats(), fill);
             loadedFills.put(fill, filler);
             plugin.addFillerThread(filler);

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

@@ -3889,7 +3889,7 @@ private static int getView(final String view) {
         };
 	}
 
-    private Calibration getCalibration() {
+    public Calibration getCalibration() {
         final Calibration calibration = new Calibration();
         calibration.pixelWidth = x_spacing;
         calibration.pixelHeight = y_spacing;

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

@@ -1392,7 +1392,7 @@ private boolean imgDimensionsChanged() {
 				|| plugin.getDepth() != imp.getNSlices() || plugin.getChannel() > imp.getNChannels()
 				|| plugin.getFrame() > imp.getNFrames())
 			return true;
-		final Calibration cal = plugin.getImagePlus().getCalibration();
+		final Calibration cal = imp.getCalibration();
 		return (plugin.getPixelWidth() != cal.pixelWidth || plugin.getPixelHeight() != cal.pixelHeight
 				|| plugin.getPixelDepth() != cal.pixelDepth);
 	}

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

@@ -398,20 +398,14 @@ private void runCommand() {
 					"Single-scale Filter Chosen");
 		}
 		final RandomAccessibleInterval<T> in = getInputData();
-		final Calibration cal = sntService.getInstance().getImagePlus().getCalibration();
+		final Calibration cal = sntService.getInstance().getCalibration();
 		final double[] spacing = new double[]{cal.pixelWidth, cal.pixelHeight, cal.pixelDepth};
-		final U type;
-		switch (outputType) {
-			case FLOAT:
-				type = (U) new FloatType();
-				break;
-			case DOUBLE:
-				type = (U) new DoubleType();
-				break;
-			default:
-				throw new IllegalArgumentException("Unknown output type");
-		}
-		final int cellDim = 32; // side length for cell
+		final U type = switch (outputType) {
+            case FLOAT -> (U) new FloatType();
+            case DOUBLE -> (U) new DoubleType();
+            default -> throw new IllegalArgumentException("Unknown output type");
+        };
+        final int cellDim = 32; // side length for cell
 		final Img<U> out;
 		switch (filter) {
 			case FRANGI:

src/main/java/sc/fiji/snt/tracing/TracerThread.java

@@ -57,7 +57,7 @@ public TracerThread(final SNT snt, final int start_x, final int start_y, final i
 	{
 		this(snt, snt.getLoadedData(), start_x, start_y, start_z, goal_x, goal_y, goal_z,
 				new Reciprocal(snt.getStats().min, snt.getStats().max),
-				new Euclidean(snt.getImagePlus().getCalibration()));
+				new Euclidean(snt.getCalibration()));
 	}
 
 	public TracerThread(final SNT snt, final int start_x, final int start_y, final int start_z,