Code cleanup and minor fixes

- Cleanup pom - DemoRunner: Remove unimplemented code - SigmaPalette: Workaround startup NPE on MacOS - PathManagerUI: Remove legacy option - Jython Template: Ensure imported classes appear in Ctrl+Space auto-completion - Script: Remove outdated LUT option
morphonets · Oct 25, 2023 · aaf65ed · aaf65ed
1 parent 372bfc4
commit aaf65ed
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Showing 6 changed files with 39 additions and 43 deletions.
diff --git a/pom.xml b/pom.xml
@@ -143,22 +143,18 @@
 		<sciview.version>906892d</sciview.version>
 		<scenery.version>db26f01</scenery.version>
 		<font-awesome.version>6.4.2</font-awesome.version>
-		<flatlaf.version>3.2.1</flatlaf.version>
-		<flatlaf-jide-oss.version>3.2.2</flatlaf-jide-oss.version>
-		<log4j.version>2.20.0</log4j.version>
-		<smile-core.version>3.0.2</smile-core.version>
+		<flatlaf.version>3.2.5</flatlaf.version>
+		<flatlaf-jide-oss.version>${flatlaf.version}</flatlaf-jide-oss.version>
+		<log4j.version>2.21.0</log4j.version>
 		<jide-oss.version>3.7.14</jide-oss.version>
-		<annotations.version>13.0</annotations.version>
+		<annotations.version>24.0.1</annotations.version>
 		<fastutil-core.version>8.5.12</fastutil-core.version>
-		<jheaps.version>0.14</jheaps.version>
-		<jide-oss.version>3.7.12</jide-oss.version>
-		<log4j.version>2.19.0</log4j.version>
 		<log4j-api.version>${log4j.version}</log4j-api.version>
 		<log4j-core.version>${log4j.version}</log4j-core.version>
 		<scenery.version>0.8.0</scenery.version>
 		<sciview.version>ba959ae644</sciview.version>
-		<smile.version>3.0.0</smile.version>
-		<smile-base.version>3.0.2</smile-base.version>
+		<smile.version>3.0.2</smile.version>
+		<smile-base.version>${smile.version}</smile-base.version>
 		<smile-core.version>${smile.version}</smile-core.version>
 
 		<!-- NB: Deploy releases to the SciJava Maven repository. -->
@@ -453,7 +449,6 @@
 		<dependency>
 			<groupId>org.jheaps</groupId>
 			<artifactId>jheaps</artifactId>
-			<version>${jheaps.version}</version>
 		</dependency>
 		<dependency>
 			<groupId>sc.iview</groupId>

diff --git a/src/main/java/sc/fiji/snt/PathManagerUI.java b/src/main/java/sc/fiji/snt/PathManagerUI.java
@@ -2114,9 +2114,6 @@ private void runDistributionAnalysisCmd(final Collection<Tree> trees, final Stri
 		input.put("calledFromPathManagerUI", true);
 		if (metric != null) input.put("measurementChoice", metric);
 		if (polar != null) input.put("polar", polar);
-		if (trees.size() == 1) {
-	 		input.put("onlyConnectivitySafeMetrics", false);
-		}
 		cmdService.run(DistributionCPCmd.class, true, input);
 	}
 

diff --git a/src/main/java/sc/fiji/snt/gui/DemoRunner.java b/src/main/java/sc/fiji/snt/gui/DemoRunner.java
@@ -65,15 +65,16 @@ public DemoRunner(final SNTUI ui, final SNT snt) {
 		entries.add(demo7());
 		entries.add(demo8());
 		entries.add(demo9());
-		entries.add(demo10());
+		//entries.add(demo10());
 	}
 
 	private Demo demo1() {
 		final Demo entry = new Demo(1, "Drosophila ddaC neuron (Autotrace demo)") {
 			@Override
 			public ImagePlus getImage() {
 				final ImagePlus imp = sntService.demoImage("ddaC");
-				imp.setRoi(320, 380, 20, 20); // mark soma
+				if (imp != null)
+					imp.setRoi(320, 380, 20, 20); // mark soma
 				return imp;
 			}
 
@@ -254,30 +255,30 @@ public void load() {
 		return entry;
 	}
 
-	private Demo demo10() {
-		final Demo entry = new Demo(10, "Segmented astrocyte (2D image)") {
-			@Override
-			public ImagePlus getImage() {
-				final ImagePlus imp = ij.IJ.openImage("http://wsr.imagej.net/images/mitosis.tif");
-				imp.setPosition(2, 4, 31); // k-fibers channel, mid Z-range, traced time point
-				return imp;
-			}
-
-			@Override
-			public void load() {
-				super.load();
-				// apply tags
-				ui.getPathManager().applyDefaultTags("Traced Channel");
-				ui.getPathManager().applyDefaultTags("Traced Frame");
-			}
-		};
-		entry.summary = "Downloads a Drosophila S2 cell undergoing mitosis in which K-fibers were traced during anaphase.";
-		entry.data = "Image (5D; 2-channel, 3D timelapse, 33MB)";
-		entry.source = "ImageJ sample image, PMID 19720876";
-		entry.online = true;
-		entry.tracingsURL = "https://raw.githubusercontent.com/morphonets/SNTmanuscript/718e4b90fb4bb61f382edcf467173b53045b25e0/FigS3_5D-Tracing/traces/mitosis.traces";
-		return entry;
-	}
+//	private Demo demo10() {
+//		final Demo entry = new Demo(10, "Segmented astrocyte (2D image)") {
+//			@Override
+//			public ImagePlus getImage() {
+//				final ImagePlus imp = ij.IJ.openImage("http://wsr.imagej.net/images/mitosis.tif");
+//				imp.setPosition(2, 4, 31); // k-fibers channel, mid Z-range, traced time point
+//				return imp;
+//			}
+//
+//			@Override
+//			public void load() {
+//				super.load();
+//				// apply tags
+//				ui.getPathManager().applyDefaultTags("Traced Channel");
+//				ui.getPathManager().applyDefaultTags("Traced Frame");
+//			}
+//		};
+//		entry.summary = "Downloads a Drosophila S2 cell undergoing mitosis in which K-fibers were traced during anaphase.";
+//		entry.data = "Image (5D; 2-channel, 3D timelapse, 33MB)";
+//		entry.source = "ImageJ sample image, PMID 19720876";
+//		entry.online = true;
+//		entry.tracingsURL = "https://raw.githubusercontent.com/morphonets/SNTmanuscript/718e4b90fb4bb61f382edcf467173b53045b25e0/FigS3_5D-Tracing/traces/mitosis.traces";
+//		return entry;
+//	}
 
 	private void error(final Throwable ex) {
 		ui.error("Loading of data failed (" + ex.getMessage() + " error). See Console for details.");

diff --git a/src/main/java/sc/fiji/snt/gui/SigmaPalette.java b/src/main/java/sc/fiji/snt/gui/SigmaPalette.java
@@ -568,7 +568,8 @@ private void updateSigmaFromMouseEvent(final MouseEvent e) {
 					}
 				}
 				updateOverlayLabels();
-				paletteWindow.repaint(); // call createSubtitle()
+				if (paletteWindow != null)
+					paletteWindow.repaint(); // call createSubtitle()
 				mouseMovedAcceptedSigmaIndex = -1;
 			}
 		}

diff --git a/src/main/resources/script_templates/Neuroanatomy/Boilerplate/PY.py b/src/main/resources/script_templates/Neuroanatomy/Boilerplate/PY.py
@@ -15,7 +15,9 @@
 """
 
 from sc.fiji.snt import Path, PathAndFillManager, SNT, SNTUI, Tree
-from sc.fiji.snt.analysis import *
+from sc.fiji.snt.analysis import GroupedTreeStatistics, MultiTreeStatistics, NodeStatistics, TreeStatistics,\
+            ConvexHullAnalyzer, PersistenceAnalyzer, ShollAnalyzer, StrahlerAnalyzer, NodeColorMapper,\
+            TreeColorMapper, PathProfiler, PathStraightener, RoiConverter, SkeletonConverter, SNTChart, SNTTable
 from sc.fiji.snt.analysis.graph import DirectedWeightedGraph
 from sc.fiji.snt.analysis.sholl.parsers import TreeParser
 from sc.fiji.snt.annotation import AllenCompartment, AllenUtils, VFBUtils, ZBAtlasUtils

diff --git a/...ipt_templates/Neuroanatomy/Render/Render_Cell_Collection_2D_(Skeletonized_Montage).groovy b/...ipt_templates/Neuroanatomy/Render/Render_Cell_Collection_2D_(Skeletonized_Montage).groovy
@@ -3,7 +3,7 @@
 #@ int (label="Number of columns", value=0) columns
 #@ int (label="Number of rows", value=0) rows
 #@ Float (label="Scale factor for reconstructions", value=1.0) scale
-#@ String (label="Color mapping:", choices={"Ice.lut", "mpl-viridis.lut", "glasbey_on_dark.lut"}, value="glasbey_on_dark.lut") lutName
+#@ String (label="Color mapping:", choices={"mpl-viridis.lut", "glasbey_on_dark.lut"}, value="glasbey_on_dark.lut") lutName
 #@ SNTService snt
 
 /**