Retire TreeAnalyzer in favor of TreeStatistics (breaking change)

notebooks/2_convex_hull.ipynb

@@ -23,7 +23,7 @@
    "metadata": {},
    "source": [
     "## Imports\n",
-    "We'll need to 1) import Python modules; 2) initalize ij from local Fiji installation, and 3) import all relevant SNT (Java) classes: [AllenCompartment](https://javadoc.scijava.org/SNT/index.html?sc/fiji/snt/annotation/AllenCompartment.html), [AllenUtils](https://javadoc.scijava.org/SNT/index.html?sc/fiji/snt/annotation/AllenUtils.html), [Annotation3D](https://javadoc.scijava.org/SNT/sc/fiji/snt/viewer/Annotation3D.html), [ConvexHull2D](https://javadoc.scijava.org/SNT/index.html?sc/fiji/snt/analysis/ConvexHull2D.html), [ConvexHull3D](https://javadoc.scijava.org/SNT/index.html?sc/fiji/snt/analysis/ConvexHull3D.html), [MouseLightLoader](https://javadoc.scijava.org/SNT/index.html?sc/fiji/snt/io/MouseLightLoader.html), [PointInImage](https://javadoc.scijava.org/SNT/index.html?sc/fiji/snt/util/PointInImage.html), [Tree](https://javadoc.scijava.org/SNT/index.html?sc/fiji/snt/Tree.html), [TreeAnalyzer](https://javadoc.scijava.org/SNT/index.html?sc/fiji/snt/analysis/TreeAnalyzer.html), [Viewer3D](https://javadoc.scijava.org/SNT/index.html?sc/fiji/snt/viewer/Viewer3D.html):"
+    "We'll need to 1) import Python modules; 2) initalize ij from local Fiji installation, and 3) import all relevant SNT (Java) classes: [AllenCompartment](https://javadoc.scijava.org/SNT/index.html?sc/fiji/snt/annotation/AllenCompartment.html), [AllenUtils](https://javadoc.scijava.org/SNT/index.html?sc/fiji/snt/annotation/AllenUtils.html), [Annotation3D](https://javadoc.scijava.org/SNT/sc/fiji/snt/viewer/Annotation3D.html), [ConvexHull2D](https://javadoc.scijava.org/SNT/index.html?sc/fiji/snt/analysis/ConvexHull2D.html), [ConvexHull3D](https://javadoc.scijava.org/SNT/index.html?sc/fiji/snt/analysis/ConvexHull3D.html), [MouseLightLoader](https://javadoc.scijava.org/SNT/index.html?sc/fiji/snt/io/MouseLightLoader.html), [PointInImage](https://javadoc.scijava.org/SNT/index.html?sc/fiji/snt/util/PointInImage.html), [Tree](https://javadoc.scijava.org/SNT/index.html?sc/fiji/snt/Tree.html), [TreeStatistics](https://javadoc.scijava.org/SNT/index.html?sc/fiji/snt/analysis/TreeStatistics.html), [Viewer3D](https://javadoc.scijava.org/SNT/index.html?sc/fiji/snt/viewer/Viewer3D.html):"
    ]
   },
   {
@@ -57,7 +57,7 @@
     "NodeStatistics = jimport('sc.fiji.snt.analysis.NodeStatistics')\n",
     "PointInImage = jimport('sc.fiji.snt.util.PointInImage')\n",
     "Tree = jimport('sc.fiji.snt.Tree')\n",
-    "TreeAnalyzer = jimport('sc.fiji.snt.analysis.TreeAnalyzer')\n",
+    "TreeStatistics = jimport('sc.fiji.snt.analysis.TreeStatistics')\n",
     "Viewer2D = jimport('sc.fiji.snt.viewer.Viewer2D')\n",
     "Viewer3D = jimport('sc.fiji.snt.viewer.Viewer3D')"
    ]
@@ -93,13 +93,13 @@
     "    of axon terminal nodes and returns a collection containing \n",
     "    these nodes as well as the id of the relevant AllenCompartment\"\"\"\n",
     "    \n",
-    "    # Use TreeAnalyzer to extract the terminal nodes from the Tree.\n",
+    "    # Use TreeStatistics to extract the terminal nodes from the Tree.\n",
     "    # Instantiate a NodeStatistics instance and retrieve a list of the endpoints for\n",
     "    # each target brain region (a BrainAnnotation) in a dictionary, where the keys are\n",
     "    # the brain annotations. Since this neuron was fetched from the MouseLight database,\n",
     "    # the annotations are instances of the AllenCompartment Class\n",
     "    # https://morphonets.github.io/SNT/sc/fiji/snt/annotation/BrainAnnotation.html\n",
-    "    tips = TreeAnalyzer(tree).getTips()\n",
+    "    tips = TreeStatistics(tree).getTips()\n",
     "    node_stats = NodeStatistics(tips)\n",
     "    compartment_dict = node_stats.getAnnotatedNodes()\n",
     "\n",
@@ -127,7 +127,7 @@
    "source": [
     "# Load the reconstruction from the MouseLight database, fetching just the axon\n",
     "tree_axon = get_axon('AA1044')\n",
-    "print(tree_axon.getLabel(), \":\", len(TreeAnalyzer(tree_axon).getTips()), \"terminals\")"
+    "print(tree_axon.getLabel(), \":\", len(TreeStatistics(tree_axon).getTips()), \"terminals\")"
    ]
   },
   {

notebooks/5_performance_testing.ipynb

@@ -42,7 +42,7 @@
     "PointInImage = jimport('sc.fiji.snt.util.PointInImage')\n",
     "MouseLightLoader = jimport('sc.fiji.snt.io.MouseLightLoader')\n",
     "Tree = jimport('sc.fiji.snt.Tree')\n",
-    "TreeAnalyzer = jimport('sc.fiji.snt.analysis.TreeAnalyzer')\n",
+    "TreeStatistics = jimport('sc.fiji.snt.analysis.TreeStatistics')\n",
     "Color = jimport('org.scijava.util.Colors')\n",
     "Viewer = jimport('sc.fiji.snt.viewer.Viewer3D')"
    ]

notebooks/7_timelapse_segmentation.ipynb

@@ -342,7 +342,7 @@
    "id": "52cc4ec2",
    "metadata": {},
    "source": [
-    "We can also measure [Trees](https://javadoc.scijava.org/SNT/sc/fiji/snt/Tree.html) with the [TreeAnalyzer](https://javadoc.scijava.org/SNT/sc/fiji/snt/analysis/TreeAnalyzer.html) and [MultiTreeStatistics](https://javadoc.scijava.org/SNT/sc/fiji/snt/analysis/MultiTreeStatistics.html) classes, and plot measurements as a function of time."
+    "We can also measure [Trees](https://javadoc.scijava.org/SNT/sc/fiji/snt/Tree.html) with [TreeStatistics](https://javadoc.scijava.org/SNT/sc/fiji/snt/analysis/TreeStatistics.html) and [MultiTreeStatistics](https://javadoc.scijava.org/SNT/sc/fiji/snt/analysis/MultiTreeStatistics.html) classes, and plot measurements as a function of time."
    ]
   },
   {
@@ -365,15 +365,15 @@
     }
    ],
    "source": [
-    "TreeAnalyzer = jimport(\"sc.fiji.snt.analysis.TreeAnalyzer\")\n",
+    "TreeStatistics = jimport(\"sc.fiji.snt.analysis.TreeStatistics\")\n",
     "MultiTreeStatistics = jimport(\"sc.fiji.snt.analysis.MultiTreeStatistics\")\n",
     "\n",
     "def plot_metric(root_nodes, metric, ax):\n",
     "    # Plot the measurements for each lineage\n",
     "    for i, r in enumerate(roots):\n",
     "        lineage_trees = lineage_to_trees(get_descendants(r))\n",
     "        xs = np.arange(r.frame, r.frame + len(lineage_trees))\n",
-    "        ys = [TreeAnalyzer(tree).getMetric(metric) for tree in lineage_trees]\n",
+    "        ys = [TreeStatistics(tree).getMetric(metric) for tree in lineage_trees]\n",
     "        ax.set_title(f\"{metric} vs Time\")\n",
     "        ax.set_ylabel(f\"{metric}\")\n",
     "        ax.set_xlabel(\"Frame\")\n",

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

@@ -3087,7 +3087,7 @@ protected boolean removeChangeListener(PathChangeListener listener) {
 		return changeListeners.remove(listener);
 	}
 
-// FIXME: Implementing hasCode() and equals() breaks current TreeAnalyzer tests
+// FIXME: Implementing hasCode() and equals() breaks current TreeStatistics tests
 //	@Override
 //	public int hashCode() {
 //		return Objects.hash(id, points, name, order, swcType, treeLabel);

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

@@ -1915,12 +1915,12 @@ private void removeOrReapplyDefaultTag(final Collection<Path> paths, final Strin
 			}
 			break;
 		case "Extension Angle...":
-		case PathAnalyzer.PATH_EXT_ANGLE_XY:
-		case PathAnalyzer.PATH_EXT_ANGLE_XZ:
-		case PathAnalyzer.PATH_EXT_ANGLE_ZY:
-		case PathAnalyzer.PATH_EXT_ANGLE_REL_XY:
-		case PathAnalyzer.PATH_EXT_ANGLE_REL_XZ:
-		case PathAnalyzer.PATH_EXT_ANGLE_REL_ZY:
+		case PathStatistics.PATH_EXT_ANGLE_XY:
+		case PathStatistics.PATH_EXT_ANGLE_XZ:
+		case PathStatistics.PATH_EXT_ANGLE_ZY:
+		case PathStatistics.PATH_EXT_ANGLE_REL_XY:
+		case PathStatistics.PATH_EXT_ANGLE_REL_XZ:
+		case PathStatistics.PATH_EXT_ANGLE_REL_ZY:
 			paths.forEach(p -> p.setName(p.getName().replaceAll(" ?\\[" + SYM_ANGLE + "\\d+.\\d+]|\\[" + SYM_ANGLE + "NaN]", "")));
 			if (reapply) {
 				final boolean relative = cmd.toLowerCase().contains("rel");

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

@@ -49,7 +49,6 @@
 import ij.ImagePlus;
 import sc.fiji.snt.analysis.PathProfiler;
 import sc.fiji.snt.analysis.SNTTable;
-import sc.fiji.snt.analysis.TreeAnalyzer;
 import sc.fiji.snt.analysis.TreeStatistics;
 import sc.fiji.snt.analysis.graph.DirectedWeightedGraph;
 import sc.fiji.snt.gui.GuiUtils;
@@ -340,15 +339,15 @@ public Tree getTree() {
 	}
 
 	/**
-	 * Returns a {@link TreeAnalyzer} instance constructed from current Paths.
+	 * Returns a {@link TreeStatistics} instance constructed from current Paths.
 	 *
 	 * @param selectedPathsOnly If true only selected paths will be considered
-	 * @return the TreeAnalyzer instance
+	 * @return the TreeStatistics instance
 	 * @throws UnsupportedOperationException if SNT is not running
 	 */
-	public TreeAnalyzer getAnalyzer(final boolean selectedPathsOnly) {
+	public TreeStatistics getAnalyzer(final boolean selectedPathsOnly) {
 		accessActiveInstance(false);
-		final TreeAnalyzer tAnalyzer = new TreeAnalyzer(getTree(selectedPathsOnly));
+		final TreeStatistics tAnalyzer = new TreeStatistics(getTree(selectedPathsOnly));
 		tAnalyzer.setContext(getContext());
 		tAnalyzer.setTable(getTable(), PathManagerUI.TABLE_TITLE);
 		return tAnalyzer;

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

@@ -42,7 +42,7 @@
 import org.scijava.util.ColorRGB;
 import org.scijava.util.Types;
 import sc.fiji.snt.analysis.SNTTable;
-import sc.fiji.snt.analysis.TreeAnalyzer;
+import sc.fiji.snt.analysis.TreeStatistics;
 import sc.fiji.snt.analysis.sholl.ShollUtils;
 import sc.fiji.snt.event.SNTEvent;
 import sc.fiji.snt.gui.*;
@@ -2669,7 +2669,7 @@ private JMenuBar createMenuBar() {
 			final Tree tree = getPathManager().getSingleTree();
 			if (tree == null) return;
 			try {
-				final TreeAnalyzer ta = new TreeAnalyzer(tree);
+				final TreeStatistics ta = new TreeStatistics(tree);
 				ta.setContext(plugin.getContext());
 				if (ta.getParsedTree().isEmpty()) {
 					guiUtils.error("None of the selected paths could be measured.");

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

@@ -37,7 +37,7 @@
 import ij.ImagePlus;
 import ij.ImageStack;
 import ij.measure.Calibration;
-import sc.fiji.snt.analysis.TreeAnalyzer;
+import sc.fiji.snt.analysis.TreeStatistics;
 import sc.fiji.snt.analysis.graph.DirectedWeightedGraph;
 import sc.fiji.snt.hyperpanes.MultiDThreePanes;
 import sc.fiji.snt.io.MouseLightLoader;
@@ -1773,7 +1773,7 @@ else if (isZY)
 					if (centroid) {
 						refPath = tree.get(0).createPath();
 						refPath.addNode(tree.getRoot());
-						final Set<PointInImage> tips = new TreeAnalyzer(tree).getTips();
+						final Set<PointInImage> tips = new TreeStatistics(tree).getTips();
 						tips.remove(tree.getRoot());
 						if (!tips.isEmpty()) refPath.addNode(SNTPoint.average(tips));
 					} else {
@@ -1814,7 +1814,7 @@ public static void main(final String[] args) {
 		//final Tree tree = new Tree("/home/tferr/Downloads/test_swc.swc");
 		final Tree tree = new SNTService().demoTree("fractal");
 		tree.swapAxes(Z_AXIS, Y_AXIS);
-		TreeAnalyzer analyzer = new TreeAnalyzer(tree);
+		TreeStatistics analyzer = new TreeStatistics(tree);
 		System.out.println("Creating graph...");
 
 		DirectedWeightedGraph graph = tree.getGraph();
@@ -1831,7 +1831,7 @@ public static void main(final String[] args) {
 		MouseLightLoader loader = new MouseLightLoader("AA0174");
 		Tree refSubTree = loader.getTree("axon");
 		DirectedWeightedGraph refGraph = refSubTree.getGraph();
-		TreeAnalyzer refAnalyzer = new TreeAnalyzer(refSubTree);
+		TreeStatistics refAnalyzer = new TreeStatistics(refSubTree);
 
 		System.out.println("Creating Subtree...");
 		Tree aTree = tree.subTree("axon");
@@ -1846,7 +1846,7 @@ public static void main(final String[] args) {
 		System.out.println("Avg time (all runs): " + SNTUtils.formatDouble(total % 1000 /nTimes, 4));
 
 		graph = aTree.getGraph();
-		analyzer = new TreeAnalyzer(aTree);
+		analyzer = new TreeStatistics(aTree);
 		System.out.println("Subtree properties:");
 		System.out.println("Label:     \t\t" + aTree.getLabel());
 		System.out.println("nPaths:    \t\t" + analyzer.getNPaths() + "/" + refAnalyzer.getNPaths());
@@ -1858,7 +1858,7 @@ public static void main(final String[] args) {
 		System.out.println("Branches:  \t\t" + analyzer.getBranches().size() + "/" + refAnalyzer.getBranches().size());
 
 		// Did the filtering affect original tree?
-		analyzer = new TreeAnalyzer(tree);
+		analyzer = new TreeStatistics(tree);
 		graph = tree.getGraph();
 		System.out.println("\nOriginal Tree Before/After Filtering:");
 		System.out.println("Label:      \t\t" + tree.getLabel());

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

@@ -33,6 +33,7 @@
 import java.util.Collection;
 
 /**
+ * Parent class for convex hull analysis
  * @author Cameron Arshadi
  */
 public abstract class AbstractConvexHull {

src/main/java/sc/fiji/snt/analysis/ConvexHull3D.java

@@ -33,6 +33,7 @@
 import java.util.Collection;
 
 /**
+ * Convex hull analysis in 3D.
  * @author Cameron Arshadi
  */
 public class ConvexHull3D extends AbstractConvexHull {

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

@@ -832,7 +832,7 @@ void compute(final Collection<BrainAnnotation> annotations, final Collection<Tre
 				for (final Tree tree : trees) {
 					if (tree == null)
 						continue;
-					final TreeAnalyzer analyzer = new TreeAnalyzer(tree);
+					final TreeStatistics analyzer = new TreeStatistics(tree);
 					final boolean includeChildren = annotation.getOntologyDepth() > 0;
 					double value;
 					switch (normFeature) {
@@ -841,12 +841,12 @@ void compute(final Collection<BrainAnnotation> annotations, final Collection<Tre
 								: analyzer.getCableLength(annotation, includeChildren);
 						break;
 					case N_BRANCH_POINTS:
-						value = (normalize) ? analyzer.getNbranchPointsNorm(annotation, includeChildren)
-								: analyzer.getNbranchPoints(annotation, includeChildren);
+						value = (normalize) ? analyzer.getNBranchPointsNorm(annotation, includeChildren)
+								: analyzer.getNBranchPoints(annotation, includeChildren);
 						break;
 					case N_TIPS:
-						value = (normalize) ? analyzer.getNtipsNorm(annotation, includeChildren)
-								: analyzer.getNtips(annotation, includeChildren);
+						value = (normalize) ? analyzer.getNTipsNorm(annotation, includeChildren)
+								: analyzer.getNTips(annotation, includeChildren);
 						break;
 					default:
 						throw new IllegalArgumentException("Unrecognized feature");

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

@@ -149,7 +149,7 @@ private void mapInternal(final String measurement, final ColorTable colorTable)
 		super.map(measurement, colorTable);
 		if (Arrays.asList(MULTI_TREE_FLAGS).contains(measurement)) {
 			for (final MappedTree mt : mappedTrees) {
-				final TreeAnalyzer analyzer = new TreeAnalyzer(mt.tree);
+				final TreeStatistics analyzer = new TreeStatistics(mt.tree);
 				switch (measurement) {
 					case ASSIGNED_VALUE:
 						integerScale = false;

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

@@ -48,10 +48,10 @@
 import sc.fiji.snt.util.PointInImage;
 
 /**
- * Computes summary and descriptive statistics from a Collection of nodes.
+ * Computes summary and descriptive statistics from a Collection of nodes, including convenience methods to plot
+ * distributions of such data.
  * 
  * @author Tiago Ferreira
- * @param <T>
  */
 public class NodeStatistics <T extends PointInImage> {
 
@@ -614,7 +614,7 @@ public static void main(final String[] args) {
 		hist.annotate("Free text");
 		hist.show();
 		final MouseLightLoader loader = new MouseLightLoader("AA0001");
-		final TreeAnalyzer analyzer = new TreeAnalyzer(loader.getTree("axon"));
+		final TreeStatistics analyzer = new TreeStatistics(loader.getTree("axon"));
 		final NodeStatistics<?> nStats = new NodeStatistics<>(analyzer.getTips());
 		final SNTChart plot = nStats.getAnnotatedFrequencyHistogram(6, "ratio", analyzer.tree);
 		plot.annotateCategory("CA1", "Not showing");

src/main/java/sc/fiji/snt/analysis/PathAnalyzer.java → src/main/java/sc/fiji/snt/analysis/PathStatistics.java

@@ -33,23 +33,23 @@
 import sc.fiji.snt.TreeProperties;
 
 /*
- * A flavor of TreeStatistics that does not do graph conversions, ensuring paths
- * can be measured independently of their connectivity.
+ * A flavor of TreeStatistics that does not do graph conversions, ensuring paths can be measured independently of
+ * their connectivity.
  */
-public class PathAnalyzer extends TreeStatistics {
+public class PathStatistics extends TreeStatistics {
 
 	/** Flag for {@value #N_CHILDREN} analysis. */
 	public static final String N_CHILDREN = "No. of children";
 
-	public PathAnalyzer(Collection<Path> paths, String label) {
+	public PathStatistics(Collection<Path> paths, String label) {
 		super(new Tree(paths));
 		tree.setLabel(label);
 		final String unit = paths.iterator().next().getCalibration().getUnit();
 		if (paths.stream().allMatch(p -> p.getCalibration().getUnit().equals(unit)))
 			tree.getProperties().setProperty(TreeProperties.KEY_SPATIAL_UNIT, unit);
 	}
 
-	public PathAnalyzer(final Path path) {
+	public PathStatistics(final Path path) {
 		this(Collections.singleton(path), path.getName());
 	}
 
@@ -64,10 +64,10 @@ public int getNBranches() {
 	}
 
 	@Override
-	public Number getMetric(final String metric) throws IllegalArgumentException {
+	public Number getMetric(final String metric) throws UnknownMetricException {
 		if ("Path ID".equalsIgnoreCase(metric))
 			return (tree.size() == 1) ? tree.list().get(0).getID() : Double.NaN;
-		return getMetricInternal(getNormalizedMeasurement(metric));
+		return super.getMetric(metric);
 	}
 
 	@Override
@@ -185,7 +185,7 @@ public Number getMetric(final String metric, final Path path) throws UnknownMetr
 				// we can recycle the logic behind #assembleStats(). Since, all
 				// getBranches() related code has been (hopefully) overridden, this will
 				// effectively retrieve the single-value metric for this path.
-				final PathAnalyzer analyzer = new PathAnalyzer(path);
+				final PathStatistics analyzer = new PathStatistics(path);
 				final SummaryStatistics dummy = new SummaryStatistics();
 				analyzer.assembleStats(new StatisticsInstance(dummy), metric);
 				return dummy.getMax(); // since N=1, same as the value itself
@@ -199,7 +199,7 @@ public void measureIndividualPaths(final Collection<String> metrics, final boole
 			final int row = getNextRow(path.getName());
 			table.set(getCol("SWC Type(s)"), row, Path.getSWCtypeName(path.getSWCType(), true)); // plural heading for consistency with other commands
 			measuringMetrics.forEach(metric -> {
-				table.set(getCol(metric), row, new PathAnalyzer(path).getMetric(metric, path));
+				table.set(getCol(metric), row, new PathStatistics(path).getMetric(metric, path));
 			});
 		});
 		if (summarize && table instanceof SNTTable) {