Metrics: Add ACI, organize names...

... While at it add missing metrics and cleanup imports/unused code

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

@@ -32,7 +32,6 @@
 import org.apache.commons.math3.analysis.polynomials.PolynomialFunction;
 import org.apache.commons.math3.analysis.polynomials.PolynomialSplineFunction;
 import org.apache.commons.math3.stat.StatUtils;
-import org.apache.commons.math3.stat.descriptive.SummaryStatistics;
 import org.apache.commons.math3.stat.regression.SimpleRegression;
 import org.apache.commons.math3.util.MathUtils;
 import org.scijava.util.ColorRGB;
@@ -399,6 +398,39 @@ public double getContraction() {
 		return eDistance / length;
 	}
 
+	/**
+	 * Gets the fractal dimension of this path.
+	 *
+	 * @return the fractal dimension of this path or Double.NaN if this path has less than 5 nodes
+	 */
+	public double getFractalDimension() {
+		if (size() < 5) { // Must have at least 4 points after the start-node
+			return Double.NaN;
+		}
+		final List<Double> pathDists = new ArrayList<>();
+		final List<Double> eucDists = new ArrayList<>();
+		for (int i = 1; i < size(); i++) { //Start at the second node
+			double pDist = getNodeWithoutChecks(i).distanceTo(getNodeWithoutChecks(i - 1));
+			if (!pathDists.isEmpty()) {
+				double cumDist = pathDists.get(i - 2) + pDist;
+				pathDists.add(cumDist);
+			} else {
+				pathDists.add(pDist);
+			}
+			double eDist = getNodeWithoutChecks(i).distanceTo(getNodeWithoutChecks(0));
+			eucDists.add(eDist);
+		}
+		double numerator = 0.0;
+		for (int i = 0; i < eucDists.size(); i++) {
+			numerator += Math.log(1 + eucDists.get(i)) * Math.log(1 + pathDists.get(i));
+		}
+		double denominator = 0.0;
+		for (final double eucDist : eucDists) {
+			denominator += Math.log(1 + eucDist) * Math.log(1 + eucDist);
+		}
+		return (double) numerator / denominator;
+	}
+
 	/**
 	 * Gets the length of this Path
 	 *
@@ -419,8 +451,8 @@ public double getLength() {
 	/*
 	 * Computes the angle between the specified node and its two flanking neighbors.
 	 * <p>
-	 * If A being the specified node, B its previous neighbor, and C is subsequent neighbor, computes the angle
-	 * between the vectors BA, and BC.
+	 * With B being the specified node, A its previous neighbor, and C is subsequent neighbor, computes the angle
+	 * between the vectors AB, and BC.
 	 * </p>
 	 * @return the angle in degrees (0-360 range) or Double.NaN if specified node does not have sufficient neighbors
 	 */

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

@@ -30,7 +30,6 @@
 import net.imagej.display.ColorTables;
 import net.imglib2.display.ColorTable;
 
-import org.checkerframework.checker.units.qual.A;
 import sc.fiji.snt.SNTUtils;
 import sc.fiji.snt.Tree;
 import sc.fiji.snt.annotation.AllenCompartment;

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

@@ -1301,41 +1301,14 @@ public double getAvgPartitionAsymmetry() throws IllegalArgumentException {
 	 * 
 	 * @return a list containing the fractal dimension of each branch
 	 * @see StrahlerAnalyzer#getBranches()
+	 * @see Path#getFractalDimension()
 	 * @throws IllegalArgumentException if the tree contains multiple roots or loops
 	 */
 	public List<Double> getFractalDimension() throws IllegalArgumentException {
-		final List<Path> branches = getBranches();
 		final List<Double> fractalDims = new ArrayList<>();
-		for (final Path b : branches) {
-			// Must have at least 4 points after the start-node in a branch
-			if (b.size() < 5) {
-				continue;
-			}
-			final List<Double> pathDists = new ArrayList<>();
-			final List<Double> eucDists  = new ArrayList<>();
-			// Start at the second node in the branch
-			for (int i = 1; i < b.size(); i++) {
-				double pDist = b.getNode(i).distanceTo(b.getNode(i-1));
-				if (!pathDists.isEmpty()) {
-					double cumDist = pathDists.get(i-2) + pDist;
-					pathDists.add(cumDist);
-				}
-				else {
-					pathDists.add(pDist);
-				}
-				double eDist = b.getNode(i).distanceTo(b.getNode(0));
-				eucDists.add(eDist);
-			}
-			double numerator = 0.0;
-			for (int i = 0; i < eucDists.size(); i++) {
-				numerator += Math.log(1 + eucDists.get(i)) * Math.log(1 + pathDists.get(i));
-			}
-			double denominator = 0.0;
-			for (int i = 0; i < eucDists.size(); i++) {
-				denominator += Math.log(1 + eucDists.get(i)) * Math.log(1 + eucDists.get(i));
-			}
-			double fDim = (double) numerator / denominator;
-			fractalDims.add(fDim);	
+		for (final Path b : getBranches()) {
+			final double fDim = b.getFractalDimension();
+			if (!Double.isNaN(fDim)) fractalDims.add(fDim);
 		}
 		return fractalDims;
 	}

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

@@ -210,7 +210,7 @@ public boolean isCellEditable(final int row, final int column) {
 			// Enlarge default width of first column. Another option would be to have all
 			// columns to auto-fit at all times, e.g., https://stackoverflow.com/a/25570812.
 			// Maybe that would be better?
-			final String prototypeMetric = TreeStatistics.TERMINAL_EXTENSION_ANGLE_XY;
+			final String prototypeMetric = TreeStatistics.GRAPH_DIAMETER_ANGLE_XY;
 			for (int i = 0; i < statsTable.getColumnCount(); ++i) {
 				final int width = SwingUtilities.computeStringWidth(statsTable.getFontMetrics(statsTable.getFont()),
 						(i == 0) ? prototypeMetric : MEAN);

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

@@ -179,7 +179,6 @@ public void setCollapsed(final boolean collapse) {
 	private CollapsiblePanel warningPanel() {
 		final JLabel label = GuiUtils.leftAlignedLabel("<HTML>The following data is not stored in SWC files:" //
 				+ "<ul>" //
-				+ "  <li>Image properties</li>"//
 				+ "  <li><i>Fits</i>: Path refinements that do not override original nodes</li>"//
 				+ "  <li><i>Fills</i>: All types</li>"//
 				+ "  <li>Channel and frame position of path(s)</li>"//

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

@@ -24,7 +24,6 @@
 
 import java.io.File;
 import java.util.ArrayList;
-import java.util.Arrays;
 import java.util.Iterator;
 import java.util.List;
 

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

@@ -196,7 +196,7 @@ public void run() {
 			metrics.add(PathAnalyzer.CONVEX_HULL_ELONGATION);
 			metrics.add(PathAnalyzer.CONVEX_HULL_ROUNDNESS);
 		}
-		if (fractalDimension) metrics.add(PathAnalyzer.BRANCH_FRACTAL_DIMENSION); // will be computed for paths
+		if (fractalDimension) metrics.add(PathAnalyzer.PATH_FRACTAL_DIMENSION);
 		if (nBranchPoints) metrics.add(PathAnalyzer.N_BRANCH_POINTS);
 		if (pathContraction) metrics.add(PathAnalyzer.PATH_CONTRACTION);
 		if (pathFragmentation) metrics.add(PathAnalyzer.N_PATH_NODES);

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

@@ -200,15 +200,6 @@ private void removeColorCoding() {
 		statusService.showStatus("Color code removed...");
 	}
 
-	private boolean isLargeData() {
-		 long sum = 0;
-		 for (final Tree tree : trees) {
-			 sum += tree.getNodesCount();
-			 if (sum > 10000) return true;
-		 }
-		 return false;
-	}
-
 	/* IDE debug method **/
 	public static void main(final String[] args) throws IOException {
 		final ImageJ ij = new ImageJ();