API improvements/fixes

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

@@ -1605,6 +1605,11 @@ public String toString() {
 
 	}
 
+	/**
+	 * Assigns distinct colors to a collection of Trees.
+	 *
+	 * @see SNTColor#getDistinctColors(int)
+	 */
 	public static void assignUniqueColors(final Collection<Tree> trees) {
 		final ColorRGB[] colors = SNTColor.getDistinctColors(trees.size());
 		int i = 0;
@@ -1613,6 +1618,19 @@ public static void assignUniqueColors(final Collection<Tree> trees) {
 		}
 	}
 
+	/**
+	 * Assigns distinct colors to a collection of Trees.
+	 *
+	 * @param excludedHue an optional string defining a hue to be excluded. Either 'red', 'green', or 'blue'.
+	 * @see SNTColor#getDistinctColors(int, String)
+	 */
+	public static void assignUniqueColors(final Collection<Tree> trees, final String excludedHue) {
+		final ColorRGB[] colors = SNTColor.getDistinctColors(trees.size(), excludedHue);
+		int i = 0;
+		for (Iterator<Tree> it = trees.iterator(); it.hasNext(); i++) {
+			it.next().setColor(colors[i]);
+		}
+	}
 	/**
 	 * Assigns the spatial calibration of an image to this Tree.
 	 *

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

@@ -0,0 +1,63 @@
+/*-
+ * #%L
+ * Fiji distribution of ImageJ for the life sciences.
+ * %%
+ * Copyright (C) 2010 - 2024 Fiji developers.
+ * %%
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as
+ * published by the Free Software Foundation, either version 3 of the
+ * License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public
+ * License along with this program.  If not, see
+ * <http://www.gnu.org/licenses/gpl-3.0.html>.
+ * #L%
+ */
+
+package sc.fiji.snt.analysis;
+
+import net.imglib2.display.ColorTable;
+import sc.fiji.snt.viewer.Annotation3D;
+
+
+import java.util.*;
+
+public class AnnotationMapper extends ColorMapper {
+
+    private final Collection<Annotation3D> annotations;
+    private double transparency;
+
+    public AnnotationMapper(final Collection<Annotation3D> annotations) {
+        this.annotations = annotations;
+    }
+
+    /**
+     * @param transparencyPercent the color transparency (in percentage) of mapped annotations
+     */
+    public void setTransparency(final double transparencyPercent) {
+        this.transparency = transparencyPercent;
+    }
+
+    @Override
+    public void map(final String measurement, final ColorTable colorTable) {
+        super.map(measurement, colorTable);
+        for (final Annotation3D annotation : annotations) {
+            final double v = getValue(annotation);
+            if (v < min) min = v;
+            if (v > max) max = v;
+        }
+        for (final Annotation3D annotation : annotations) {
+            annotation.setColor(getColorRGB(getValue(annotation)), transparency);
+        }
+    }
+
+    private double getValue(final Annotation3D annotation) {
+        return annotation.getVolume(); // currently only volume is supported
+    }
+}

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

@@ -453,18 +453,19 @@ public SNTChart getFlowPlot(final String feature, final int depth) {
 	 * Assembles a Flow plot (aka Sankey diagram) for the specified feature using
 	 * "mean" as integration statistic, no cutoff value, and all of the brain
 	 * regions of the specified ontology depth. *
-	 * 
-	 * @param feature the feature ({@value MultiTreeStatistics#LENGTH},
-	 *                {@value MultiTreeStatistics#N_BRANCH_POINTS},
-	 *                {@value MultiTreeStatistics#N_TIPS}, etc.)
-	 * @param depth   the ontological depth of the compartments to be considered
-	 * @param cutoff  a filtering option. If the computed {@code feature} for an
-	 *                annotation is below this value, that annotation is excluded
-	 *                from the plot * @param normalize If true, values are retrieved
-	 *                as ratios. E.g., If {@code feature} is
-	 *                {@value MultiTreeStatistics#LENGTH}, and {@code cutoff} 0.1,
-	 *                BrainAnnotations in {@code annotations} associated with less
-	 *                than 10% of cable length are ignored.
+	 *
+	 * @param feature   the feature ({@value MultiTreeStatistics#LENGTH},
+	 *                  {@value MultiTreeStatistics#N_BRANCH_POINTS},
+	 *                  {@value MultiTreeStatistics#N_TIPS}, etc.)
+	 * @param depth     the ontological depth of the compartments to be considered
+	 * @param cutoff    a filtering option. If the computed {@code feature} for an
+	 *                  annotation is below this value, that annotation is excluded
+	 *                  from the plot
+	 * @param normalize If true, values are retrieved as ratios. E.g., If
+	 *                  {@code feature} is {@value MultiTreeStatistics#LENGTH},
+	 *                  and {@code cutoff} 0.1, BrainAnnotations in
+	 *                  {@code annotations} associated with less than 10% of cable
+	 *                  length are ignored.
 	 * @return the flow plot
 	 */
 	public SNTChart getFlowPlot(final String feature, final int depth, final double cutoff, final boolean normalize) {

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

@@ -307,6 +307,16 @@ public SNTChart getPolarHistogram(final String metric) {
 		}
 	}
 
+	public SNTTable getRawValues(final String metric) {
+		final String normMeasurement = getNormalizedMeasurement(metric);
+		final HistogramDatasetPlusMulti datasetPlus = new HistogramDatasetPlusMulti(normMeasurement);
+		try {
+			return datasetPlus.getTable();
+		} catch (final IllegalArgumentException ex) {
+			throw new IllegalArgumentException("TreeStatistics metric is likely not supported by MultiTreeStatistics",
+					ex);
+		}
+	}
 	@Override
 	public Set<PointInImage> getTips() {
 		assignGroupToSuperTree();
@@ -404,6 +414,11 @@ class HistogramDatasetPlusMulti extends HDPlus {
 				values.add(v);
 			}
 		}
+		SNTTable getTable() {
+			final SNTTable table = new SNTTable();
+			table.addColumn(measurement, lastDstats.dStats.getValues());
+			return table;
+		}
 	}
 
 	public static List<String> getMetrics() {

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

@@ -30,10 +30,10 @@
 
 import org.scijava.Context;
 
-import net.imagej.display.ColorTables;
 import net.imglib2.display.ColorTable;
 import sc.fiji.snt.SNTService;
 import sc.fiji.snt.Tree;
+import sc.fiji.snt.util.ColorMaps;
 import sc.fiji.snt.util.PointInImage;
 import sc.fiji.snt.util.SNTPoint;
 import sc.fiji.snt.viewer.Viewer3D;
@@ -222,12 +222,12 @@ public static void main(final String... args) {
 		final List<PointInImage> nodes = tree.getNodes();
 		final NodeStatistics<?> nodeStats = new NodeStatistics<>(nodes);
 		final NodeColorMapper mapper = new NodeColorMapper(nodeStats);
-		mapper.map("x-coord", ColorTables.ICE);
+		mapper.map("x-coord", ColorMaps.ICE);
 		final Viewer3D viewer1 = new Viewer3D();
 		viewer1.annotatePoints(nodes, "dummy annotation");
 		//viewer.annotatePoints(mapper.getNodes(), "dummy annotation");
 		nodeStats.assignBranches(tree);
-		mapper.map("length", ColorTables.ICE);
+		mapper.map("length", ColorMaps.ICE);
 		final Viewer3D viewer2 = new Viewer3D();
 		viewer2.annotatePoints(nodes, "dummy annotation");
 		viewer1.show();

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

@@ -182,6 +182,43 @@ private void assembleStats() throws UnknownMetricException {
 		}
 	}
 
+	/**
+	 * Filters the current pool of nodes matching a measurement-based criterion.
+	 *
+	 * @param metric     the measurement ({@link #X_COORDINATES}, {@link #Y_COORDINATES},
+	 *                    {@link #BRANCH_ORDER}, etc.)
+	 * @param lowerBound the lower metric value (inclusive)
+	 * @param upperBound the upper metric value (inclusive)
+	 * @return the filtered list.
+	 */
+	public List<T> filter(final String metric, final double lowerBound, final double upperBound) throws UnknownMetricException {
+        currentMetric = getNormalizedMeasurement(metric);
+		switch (currentMetric) {
+			case BRANCH_LENGTH:
+				assessIfBranchesHaveBeenAssigned();
+				return points.stream().filter(p ->
+						p.getPath().getLength() >= lowerBound && p.getPath().getLength() <= upperBound).collect(Collectors.toList());
+			case BRANCH_ORDER:
+				assessIfBranchesHaveBeenAssigned();
+				return points.stream().filter(p ->
+						p.getPath().getOrder() >= lowerBound && p.getPath().getOrder() <= upperBound).collect(Collectors.toList());
+			case VALUES:
+				return points.stream().filter(p ->
+						p.v >= lowerBound && p.v <= upperBound).collect(Collectors.toList());
+			case X_COORDINATES:
+				return points.stream().filter(p ->
+						p.getX() >= lowerBound && p.getX() <= upperBound).collect(Collectors.toList());
+			case Y_COORDINATES:
+				return points.stream().filter(p ->
+						p.getY() >= lowerBound && p.getY() <= upperBound).collect(Collectors.toList());
+			case Z_COORDINATES:
+				return points.stream().filter(p ->
+						p.getZ() >= lowerBound && p.getZ() <= upperBound).collect(Collectors.toList());
+			default:
+				throw new UnknownMetricException("Unrecognized metric: " + currentMetric);
+		}
+	}
+
 	/**
 	 * Gets the relative frequencies histogram for a univariate measurement. The
 	 * number of bins is determined using the Freedman-Diaconis rule.

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

@@ -719,7 +719,7 @@ public void saveAsPNG(final File file) throws IOException {
 
 	public void saveAsPNG(final String filePath) throws IOException {
 		final File f = new File((filePath.toLowerCase().endsWith(".png")) ? filePath : filePath + ".png");
-		f.mkdirs();
+		if(!f.getParentFile().exists()) f.getParentFile().mkdirs();
 		saveAsPNG(f);
 	}
 

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

@@ -376,7 +376,7 @@ public static String toString(final GenericTable table, final int firstRow, fina
 
 	public static void save(final Table<?, ?> table, final char columnSep, final boolean saveColHeaders,
 			final boolean saveRowHeaders, final File outputFile) throws IOException {
-		if(!outputFile.exists()) outputFile.mkdirs();
+		if(!outputFile.getParentFile().exists()) outputFile.getParentFile().mkdirs();
 		final FileOutputStream fos = new FileOutputStream(outputFile, false);
 		final OutputStreamWriter osw = new OutputStreamWriter(fos, StandardCharsets.UTF_8);
 		final PrintWriter pw = new PrintWriter(new BufferedWriter(osw), true);

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

@@ -22,7 +22,7 @@
 
 package sc.fiji.snt.analysis;
 
-class UnknownMetricException extends IllegalArgumentException {
+public class UnknownMetricException extends IllegalArgumentException {
 	private static final long serialVersionUID = 1L;
 
 	protected UnknownMetricException(final String msg) {

src/main/java/sc/fiji/snt/annotation/AllenUtils.java

@@ -155,6 +155,8 @@ public static AllenCompartment getCompartment(final int id) {
 	 *         null if no match was found
 	 */
 	public static AllenCompartment getCompartment(final String nameOrAcronym) {
+		if (nameOrAcronym.equalsIgnoreCase("root"))
+			return getCompartment(AllenUtils.BRAIN_ROOT_ID);
 		areaList = getBrainAreasList();
 		for (int n = 0; n < areaList.length(); n++) {
 			final JSONObject area = (JSONObject) areaList.get(n);

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

@@ -1281,7 +1281,7 @@ public void mouseClicked(final MouseEvent me) {
 					SNTUtils.getContext().getService(CommandService.class).run("org.scijava.plugins.commands.debug.SystemInformation", true);
 					timer = new Timer(3000, e -> d.dispose());
 				} else {
-					ijDetails.setText("<HTML>SystemInformation command not found!?");
+					ijDetails.setText("<HTML>System Information command not found!?");
 					timer = new Timer(3000, e -> ijDetails.setText(details));
 				}
 				timer.setRepeats(false);

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

@@ -22,7 +22,6 @@
 package sc.fiji.snt.gui.cmds;
 
 import net.imagej.ImageJ;
-import net.imagej.display.ColorTables;
 
 import org.scijava.ItemVisibility;
 import org.scijava.command.Command;
@@ -36,6 +35,7 @@
 import sc.fiji.snt.analysis.graph.AnnotationWeightedEdge;
 import sc.fiji.snt.analysis.graph.GraphColorMapper;
 import sc.fiji.snt.annotation.BrainAnnotation;
+import sc.fiji.snt.util.ColorMaps;
 import sc.fiji.snt.viewer.GraphViewer;
 import sc.fiji.snt.viewer.geditor.AnnotationGraphAdapter;
 import sc.fiji.snt.viewer.geditor.GraphEditor;
@@ -118,7 +118,7 @@ public void run() {
 			graphViewer.setContext(getContext());
 			final GraphEditor editor = graphViewer.getEditor();
 			final GraphColorMapper<BrainAnnotation, AnnotationWeightedEdge> mapper = new GraphColorMapper<>();
-			mapper.map(annotationGraph, GraphColorMapper.EDGE_WEIGHT, ColorTables.ICE);
+			mapper.map(annotationGraph, GraphColorMapper.EDGE_WEIGHT, ColorMaps.ICE);
 			final AnnotationGraphAdapter graphAdapter = (AnnotationGraphAdapter) (editor.getGraphComponent()
 					.getGraph());
 			graphAdapter.scaleEdgeWidths(1, (large) ? 15 : 10, "linear");

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

@@ -84,10 +84,15 @@ private void init() {
 
 	@Override
 	public void run() {
-		if (trees == null || trees.isEmpty()) {
+		if (trees == null) {
 			error("No reconstructions have been specified.");
 			return;
 		}
+		trees.removeIf(tree -> tree == null || tree.isEmpty());
+		if (trees.isEmpty()) { // may happen with auto-traced structures!?
+			error("No valid reconstructions exist.");
+			return;
+		}
 		String transformationFlags = normalize;
 		if (!type.toLowerCase().contains("3d"))
 			transformationFlags += " " + view;
@@ -106,17 +111,18 @@ public void run() {
 	}
 
 	private static Viewer3D.ViewMode getView(final String flag) {
-		if (flag.toLowerCase().contains("xz"))
+		final String lcFlag = flag.toLowerCase();
+		if (lcFlag.contains("xz") || lcFlag.contains("zx"))
 			return Viewer3D.ViewMode.XZ;
-		if (flag.toLowerCase().contains("zy"))
+		if (lcFlag.contains("yz") || lcFlag.contains("zy"))
 			return Viewer3D.ViewMode.YZ;
-		return Viewer3D.ViewMode.XY;
+		return Viewer3D.ViewMode.DEFAULT;
 	}
 
 	private static Collection<Tree> getTreesForRendering(final Collection<Tree> trees, final String renderOptions) {
 		final String options = renderOptions.toLowerCase();
-		final boolean isZY = options.contains("zy");
-		final boolean isXZ = options.contains("xz");
+		final boolean isZY = options.contains("zy") || options.contains("yz");
+		final boolean isXZ = options.contains("xz") || options.contains("zx");
 		final boolean center = options.contains("norm") || options.contains("relative") || options.contains("center");
 		final Collection<Tree> renderingTrees;
 		if (center || isZY || isXZ) {
@@ -168,7 +174,7 @@ private static Object singleScene(final Collection<Tree> renderingTrees, final S
 			result.add(renderingTrees);
 			result.show();
 			return result;
-		} else if (flags.contains("3d")) {
+		} else if (flags.contains("3d") || flags.contains("interactive")) {
 			final Viewer3D result = new Viewer3D();
 			result.add(renderingTrees);
 			result.setViewMode(getView(renderOptions));
@@ -190,10 +196,10 @@ private static Object singleScene(final Collection<Tree> renderingTrees, final S
 	 *                      <tt>2d raster</tt>: trees are rendered as 2D skeletonized images<br>
 	 *                      <tt>2d vector</tt>: trees are rendered in a static (non-interactive) Viewer2D<br>
 	 *                      <tt>3d</tt>: trees are rendered in interactive Viewer3D canvas(es)<br>
-	 *                      <tt>xz</tt>: whether trees should be rendered in a XZ view (default is XY)<br>
-	 *                      <tt>zy</tt>: whether trees should be rendered in a ZY view (default is XY)<br>
-	 *                      <tt>center</tt>: whether trees should be  translated so that their roots/somas are displayed at a
-	 *                      common origin (0,0,0)
+	 *                      <tt>xz</tt>: whether trees should be displayed in a XZ view (default is XY)<br>
+	 *                      <tt>zy</tt>: whether trees should be displayed in a ZY view (default is XY)<br>
+	 *                      <tt>center</tt>: whether trees should be  translated so that their roots/somas are displayed
+	 *                      at a common origin (0,0,0)<br>
 	 *                     </p>
 	 * @return a reference to the displayed viewer
 	 */

src/main/java/sc/fiji/snt/plugin/ij1/Strahler.java

@@ -406,7 +406,7 @@ public void run(final String arg) {
 			if (outIS)
 				imp2.show();
 			ip3.setMinAndMax(0, order);
-			ColorMaps.applyMagmaColorMap(imp3, 200, false);
+			ColorMaps.applyPlasma(imp3, 200, false);
 			if (validRootRoi)
 				imp3.setRoi(rootRoi);
 			imp3.show();