Minor GUI adjustments

- fix XZ/ZY plane angles reporting values > 0 - simplify Path Analyzer command - sort columns before sorting - polar plot options - misc
morphonets · Aug 19, 2024 · 0282b36 · 0282b36
1 parent 85a8500
commit 0282b36
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Showing 6 changed files with 55 additions and 74 deletions.
diff --git a/src/main/java/sc/fiji/snt/Path.java b/src/main/java/sc/fiji/snt/Path.java
@@ -490,7 +490,7 @@ public double getExtensionAngleXY() {
 	 * @return the overall 'extension' angle in degrees [0-360[ in the XZ plane or zero if path is 2D.
 	 */
 	public double getExtensionAngleXZ() {
-		return getExtensionAngle(MultiDThreePanes.XZ_PLANE);
+		return (is3D()) ? getExtensionAngle(MultiDThreePanes.XZ_PLANE) : 0;
 	}
 
 	/**
@@ -500,7 +500,15 @@ public double getExtensionAngleXZ() {
 	 * @return the overall 'extension' angle in degrees [0-360[ in the ZY plane or zero if path is 2D.
 	 */
 	public double getExtensionAngleZY() {
-		return getExtensionAngle(MultiDThreePanes.ZY_PLANE);
+		return (is3D()) ? getExtensionAngle(MultiDThreePanes.ZY_PLANE) : 0;
+	}
+
+	private boolean is3D() throws IllegalArgumentException {
+		final double zRef = getNodeWithoutChecks(0).getZ();
+		for (int i=0; i< size(); i++) {
+			if (getNodeWithoutChecks(i).getZ() != zRef) return true;
+		}
+		return false;
 	}
 
 	private double getExtensionAngle(final int view) {

diff --git a/src/main/java/sc/fiji/snt/analysis/SNTChart.java b/src/main/java/sc/fiji/snt/analysis/SNTChart.java
@@ -45,47 +45,19 @@
 
 import net.imglib2.roi.geom.real.Polygon2D;
 import org.apache.commons.math3.stat.descriptive.DescriptiveStatistics;
-import org.jfree.chart.ChartMouseEvent;
-import org.jfree.chart.ChartMouseListener;
-import org.jfree.chart.ChartPanel;
-import org.jfree.chart.ChartUtils;
-import org.jfree.chart.JFreeChart;
-import org.jfree.chart.LegendItem;
-import org.jfree.chart.LegendItemSource;
+import org.jfree.chart.*;
 import org.jfree.chart.annotations.*;
 import org.jfree.chart.axis.Axis;
 import org.jfree.chart.axis.CategoryAnchor;
-import org.jfree.chart.entity.AxisEntity;
-import org.jfree.chart.entity.ChartEntity;
-import org.jfree.chart.entity.JFreeChartEntity;
-import org.jfree.chart.entity.PlotEntity;
-import org.jfree.chart.entity.TitleEntity;
-import org.jfree.chart.entity.XYAnnotationEntity;
-import org.jfree.chart.entity.XYItemEntity;
-import org.jfree.chart.plot.CategoryMarker;
-import org.jfree.chart.plot.CategoryPlot;
-import org.jfree.chart.plot.CombinedRangeXYPlot;
-import org.jfree.chart.plot.Marker;
-import org.jfree.chart.plot.Plot;
-import org.jfree.chart.plot.PolarPlot;
-import org.jfree.chart.plot.ValueMarker;
-import org.jfree.chart.plot.XYPlot;
+import org.jfree.chart.entity.*;
+import org.jfree.chart.plot.*;
 import org.jfree.chart.plot.flow.FlowPlot;
 import org.jfree.chart.renderer.AbstractRenderer;
 import org.jfree.chart.renderer.DefaultPolarItemRenderer;
-import org.jfree.chart.renderer.category.AbstractCategoryItemRenderer;
-import org.jfree.chart.renderer.category.BoxAndWhiskerRenderer;
-import org.jfree.chart.renderer.category.CategoryItemRenderer;
+import org.jfree.chart.renderer.category.*;
 import org.jfree.chart.renderer.xy.XYItemRenderer;
-import org.jfree.chart.title.LegendTitle;
-import org.jfree.chart.title.PaintScaleLegend;
-import org.jfree.chart.title.TextTitle;
-import org.jfree.chart.title.Title;
-import org.jfree.chart.ui.HorizontalAlignment;
-import org.jfree.chart.ui.Layer;
-import org.jfree.chart.ui.RectangleAnchor;
-import org.jfree.chart.ui.RectangleEdge;
-import org.jfree.chart.ui.TextAnchor;
+import org.jfree.chart.title.*;
+import org.jfree.chart.ui.*;
 import org.jfree.data.Range;
 import org.jfree.data.category.CategoryDataset;
 import org.jfree.data.statistics.HistogramDataset;
@@ -94,8 +66,7 @@
 import org.scijava.plot.CategoryChart;
 import org.scijava.table.Column;
 import org.scijava.ui.awt.AWTWindows;
-import org.scijava.ui.swing.viewer.plot.jfreechart.CategoryChartConverter;
-import org.scijava.ui.swing.viewer.plot.jfreechart.XYPlotConverter;
+import org.scijava.ui.swing.viewer.plot.jfreechart.*;
 import org.scijava.util.ColorRGB;
 import org.scijava.util.Colors;
 
@@ -123,7 +94,6 @@ public class SNTChart extends ChartPanel {
 	private static final Color BACKGROUND_COLOR = Color.WHITE;
 	private static final List<SNTChart> openInstances = new ArrayList<>();
 	private List<SNTChart> otherCombinedCharts;
-	private LegendTitle stashedLegend;
 	private JFrame frame;
 	private String title;
 
@@ -153,8 +123,7 @@ protected SNTChart(final String title, final JFreeChart chart, final Dimension p
 			}
 			setFontSize(GuiUtils.uiFontSize());
 		}
-		// Tweak: Ensure chart is always drawn and not scaled to avoid rendering
-		// artifacts
+		// Tweak: Ensure chart is always drawn and not scaled to avoid rendering artifacts
 		setMinimumDrawWidth(0);
 		setMaximumDrawWidth(Integer.MAX_VALUE);
 		setMinimumDrawHeight(0);
@@ -350,12 +319,8 @@ public void setOutlineVisible(final boolean visible) {
 	}
 
 	public void setLegendVisible(final boolean visible) {
-		if (visible && stashedLegend != null) {
-			getChart().addLegend(stashedLegend);
-		} else if (!visible) {
-			stashedLegend = getChart().getLegend();
-			getChart().removeLegend();
-		}
+		if (getChart().getLegend() != null)
+			getChart().getLegend().setVisible(!getChart().getLegend().isVisible());
 	}
 
 	/**
@@ -1246,6 +1211,7 @@ private void addCustomizationPanel(final JPopupMenu popup) {
 		grids.add(jmi);
 		jmi = new JMenuItem("Legend");
 		jmi.addActionListener( e -> setLegendVisible(!isLegendVisible()));
+		jmi.setEnabled(getChart().getLegend() != null);
 		grids.add(jmi);
 		jmi = new JMenuItem("Outline");
 		jmi.addActionListener( e -> setOutlineVisible(!isOutlineVisible()));
@@ -1271,6 +1237,17 @@ private void addCustomizationPanel(final JPopupMenu popup) {
 			}
 		});
 		grids.add(jmi);
+		GuiUtils.addSeparator(grids, "Polar Plots:");
+		jmi = new JMenuItem("Clockwise/Counterclockwise");
+		jmi.addActionListener( e -> {
+			if (getChart().getPlot() instanceof PolarPlot) {
+				((PolarPlot) getChart().getPlot()).setCounterClockwise(!((PolarPlot) getChart().getPlot()).isCounterClockwise());
+				getChart().fireChartChanged();
+			} else {
+				new GuiUtils(frame).error("This option requires a polar plot.", "Option Not Available");
+			}
+		});
+		grids.add(jmi);
 		popup.add(grids);
 
 		final JMenu utils = new JMenu("Utilities");

diff --git a/src/main/java/sc/fiji/snt/gui/GuiUtils.java b/src/main/java/sc/fiji/snt/gui/GuiUtils.java
@@ -1678,8 +1678,8 @@ public static JMenu helpMenu() {
 		helpMenu.add(MenuItems.devResourceAPI());
 		helpMenu.addSeparator();
 
-		mi = menuItemTriggeringURL("SNT's Algorithms", "https://github.com/morphonets/SNT/blob/master/NOTES.md#algorithms");
-		mi.setIcon(IconFactory.getMenuIcon(GLYPH.COGS));
+		mi = menuItemTriggeringURL("Implemented Algorithms", "https://github.com/morphonets/SNT/blob/master/NOTES.md#algorithms");
+		mi.setIcon(IconFactory.getMenuIcon(GLYPH.MATH));
 		helpMenu.add(mi);
 		mi = menuItemTriggeringURL("SNT Manuscript", "http://dx.doi.org/10.1038/s41592-021-01105-7");
 		mi.setIcon(IconFactory.getMenuIcon(GLYPH.FILE));

diff --git a/src/main/java/sc/fiji/snt/gui/cmds/SNTLoaderCmd.java b/src/main/java/sc/fiji/snt/gui/cmds/SNTLoaderCmd.java
@@ -101,7 +101,7 @@ public class SNTLoaderCmd extends DynamicCommand {
 	private String SPACER1;
 
 	@Parameter(required = false, label = "Reconstruction file", //
-			description="The reconstruction file to be loaded (.traces, .(e)swc or .json) (optional)",
+			description="The reconstruction file to be loaded: JSON, NDF, SWC, or TRACES (optional)",
 		style = FileWidget.OPEN_STYLE, callback = "tracesFileChanged")
 	private File tracesFile;
 
@@ -115,7 +115,7 @@ public class SNTLoaderCmd extends DynamicCommand {
 
 	@Parameter(required = false, label = "Tracing channel",
 		description = DEF_DESCRIPTION, min = "1", //
-		max = ""+ ij.CompositeImage.MAX_CHANNELS +"", callback = "channelChanged")
+		max = ""+ ij.CompositeImage.MAX_CHANNELS, callback = "channelChanged")
 	private int channel;
 
 	private Collection<ImagePlus> openImps;

diff --git a/src/main/java/sc/fiji/snt/plugin/PathAnalyzerCmd.java b/src/main/java/sc/fiji/snt/plugin/PathAnalyzerCmd.java
@@ -22,11 +22,7 @@
 
 package sc.fiji.snt.plugin;
 
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
+import java.util.*;
 
 import org.scijava.ItemVisibility;
 import org.scijava.command.Command;
@@ -65,14 +61,8 @@ public class PathAnalyzerCmd extends CommonDynamicCmd {
 	@Parameter(label = "Fractal dimension")
 	private boolean fractalDimension;
 
-	@Parameter(label = "Extension angle (XY plane)")
-	private boolean extensionAngleXY;
-
-	@Parameter(label = "Extension angle (XZ plane)")
-	private boolean extensionAngleXZ;
-
-	@Parameter(label = "Extension angle (ZY plane)")
-	private boolean extensionAngleZY;
+	@Parameter(label = "Extension angles")
+	private boolean extensionAngles;
 
 	@Parameter(label = "Length")
 	private boolean pathLength;
@@ -83,6 +73,9 @@ public class PathAnalyzerCmd extends CommonDynamicCmd {
 	@Parameter(label = "No. of branch points")
 	private boolean nBranchPoints;
 
+	@Parameter(label = "No. of children")
+	private boolean nChildren;
+
 	@Parameter(label = "No. of nodes (fragmentation)")
 	private boolean pathFragmentation;
 
@@ -146,11 +139,10 @@ private void setAllCheckboxesEnabled(final boolean enable) {
 		convexHull = enable;
 		fractalDimension = enable;
 		nBranchPoints = enable;
+		nChildren = enable;
 		pathContraction = enable;
 		pathFragmentation = enable;
-		extensionAngleXY = enable;
-		extensionAngleXZ = enable;
-		extensionAngleZY = enable;
+		extensionAngles = enable;
 		pathLength = enable;
 		pathMeanRadius = enable;
 		pathNSpines = enable;
@@ -167,11 +159,10 @@ private void toggleCheckboxes() {
 		convexHull = !convexHull;
 		fractalDimension = !fractalDimension;
 		nBranchPoints = !nBranchPoints;
+		nChildren = !nChildren;
 		pathContraction = !pathContraction;
 		pathFragmentation = !pathFragmentation;
-		extensionAngleXY = !extensionAngleXY;
-		extensionAngleXZ = !extensionAngleXZ;
-		extensionAngleZY = !extensionAngleZY;
+		extensionAngles= !extensionAngles;
 		pathLength = !pathLength;
 		pathMeanRadius = !pathMeanRadius;
 		pathNSpines = !pathNSpines;
@@ -198,11 +189,14 @@ public void run() {
 		}
 		if (fractalDimension) metrics.add(PathAnalyzer.PATH_FRACTAL_DIMENSION);
 		if (nBranchPoints) metrics.add(PathAnalyzer.N_BRANCH_POINTS);
+		if (nChildren) metrics.add(PathAnalyzer.N_CHILDREN);
 		if (pathContraction) metrics.add(PathAnalyzer.PATH_CONTRACTION);
 		if (pathFragmentation) metrics.add(PathAnalyzer.N_PATH_NODES);
-		if (extensionAngleXY) metrics.add(PathAnalyzer.PATH_EXT_ANGLE_XY);
-		if (extensionAngleXZ) metrics.add(PathAnalyzer.PATH_EXT_ANGLE_XZ);
-		if (extensionAngleZY) metrics.add(PathAnalyzer.PATH_EXT_ANGLE_ZY);
+		if (extensionAngles) {
+			metrics.add(PathAnalyzer.PATH_EXT_ANGLE_XY);
+			metrics.add(PathAnalyzer.PATH_EXT_ANGLE_XZ);
+			metrics.add(PathAnalyzer.PATH_EXT_ANGLE_ZY);
+		}
 		if (pathLength) metrics.add(PathAnalyzer.PATH_LENGTH);
 		if (pathMeanRadius) metrics.add(PathAnalyzer.PATH_MEAN_RADIUS);
 		if (pathOrder) metrics.add(PathAnalyzer.PATH_ORDER);
@@ -222,6 +216,7 @@ public void run() {
 		final PathAnalyzer analyzer = new PathAnalyzer(paths, "");
 		analyzer.setContext(getContext());
 		analyzer.setTable(table, TABLE_TITLE);
+		Collections.sort(metrics);
 		analyzer.measureIndividualPaths(metrics, summarize); // will display table
 		resetUI();
 	}

diff --git a/src/main/java/sc/fiji/snt/plugin/PathSpineAnalysisCmd.java b/src/main/java/sc/fiji/snt/plugin/PathSpineAnalysisCmd.java
@@ -186,7 +186,8 @@ private void addSeries(final XYPlot plot, final String label, final List<Double>
 			final ColorRGB color) {
 		if (y != null) {
 			final XYSeries series = plot.addXYSeries();
-			series.setStyle(plotService.newSeriesStyle(color, LineStyle.SOLID, MarkerStyle.FILLEDCIRCLE));
+			series.setStyle(plotService.newSeriesStyle(color, (anyMetric)  ? LineStyle.NONE : LineStyle.SOLID,
+					MarkerStyle.FILLEDCIRCLE));
 			series.setValues(x, y);
 			series.setLabel(label);
 		}