Modernize scripts

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

@@ -329,15 +329,18 @@ public static List<String> getAllMetrics() {
 	 * Gets a subset of supported metrics.
 	 *
 	 * @param type the type. Either 'legacy' (metrics supported up to SNTv4.0.5),
-	 *             "safe" (metrics that can be computed from invalid graphs) or
-	 *             'common' (commonly used metrics) or 'quick' (used by the 'quick
-	 *             measure' GUI commands).
+	 *             "safe" (metrics that can be computed from invalid graphs),
+	 *             'common' (commonly used metrics), 'quick' (used by the 'quick
+	 *             measure' GUI commands), or 'all' (shortcut to {@link #getAllMetrics()})
 	 * @return the list metrics
 	 */
 	public static List<String> getMetrics(final String type) {
 		// We could use Arrays.asList() here but that would make list immutable
 		String[] metrics;
 		switch (type) {
+		case "all":
+			measure(getAllMetrics(), true);
+			return getAllMetrics();
 		case "legacy":
 			// Historical metrics up to SNTv4.0.10
 			metrics = new String[] { BRANCH_LENGTH, CONTRACTION, REMOTE_BIF_ANGLES, PARTITION_ASYMMETRY,

src/main/java/sc/fiji/snt/analysis/sholl/parsers/ImageParser.java

@@ -30,7 +30,6 @@
 import org.scijava.command.ContextCommand;
 import org.scijava.plugin.Parameter;
 
-import ij.IJ;
 import ij.ImagePlus;
 import ij.gui.Line;
 import ij.gui.Roi;
@@ -42,6 +41,7 @@
 import sc.fiji.snt.SNTUtils;
 import sc.fiji.snt.analysis.sholl.Profile;
 import sc.fiji.snt.analysis.sholl.ShollUtils;
+import sc.fiji.snt.util.ColorMaps;
 import sc.fiji.snt.util.ShollPoint;
 
 /**
@@ -378,7 +378,7 @@ public ImagePlus getMask() {
 				getMaskProcessor(false, profile.countsAsArray()));
 		img.setCalibration(cal);
 		try {
-			IJ.run(img, "mpl-inferno", "");
+			ColorMaps.applyPlasma(img, 100, false);
 		} catch (final Exception ignored) {
 			// do nothing ...
 		}

src/main/resources/script_templates/Neuroanatomy/Analysis/Draw_Disks_Demo.groovy

@@ -8,10 +8,10 @@
  *       disks in 3D along an axon.
  */
 
-import net.imglib2.Point;
-import net.imglib2.util.LinAlgHelpers;
-import net.imglib2.algorithm.region.hypersphere.HyperSphere;
-import net.imglib2.img.display.imagej.ImageJFunctions;
+import net.imglib2.Point
+import net.imglib2.util.LinAlgHelpers
+import net.imglib2.algorithm.region.hypersphere.HyperSphere
+import net.imglib2.img.display.imagej.ImageJFunctions
 import sc.fiji.snt.*
 import sc.fiji.snt.analysis.*
 import sc.fiji.snt.analysis.graph.*
@@ -21,8 +21,8 @@ import sc.fiji.snt.io.*
 import sc.fiji.snt.plugin.*
 import sc.fiji.snt.util.*
 import sc.fiji.snt.viewer.*
-import ij3d.Image3DUniverse;
-import org.scijava.vecmath.Color3f;
+import ij3d.Image3DUniverse
+import org.jogamp.vecmath.Color3f
 
 // Documentation Resources: https://imagej.net/plugins/snt/scripting
 // Latest SNT API: https://javadoc.scijava.org/SNT/
@@ -76,4 +76,5 @@ def main()
 	univ.addVoltex(imp, new Color3f(0,255,0), "OP_1", 25, new boolean[] {true, true, true}, 1);
 }
 
-main();
+main()
+return null // suppress unsupported output `ij3d.Content` warning

src/main/resources/script_templates/Neuroanatomy/Analysis/Sholl_Rasterize_Shells.py

@@ -20,11 +20,11 @@ def error():
 
 
 shell_width = 10
-imp = IJ.getImage()
-overlay = imp.getOverlay()
 raster_shells = []
+imp = IJ.getImage()
 
-if imp and overlay:
+if imp and imp.getOverlay():
+  overlay = imp.getOverlay()
   for i in range(overlay.size()):
     roi = overlay.get(i)
     if roi.getName() and "Shell" in roi.getName():

src/main/resources/script_templates/Neuroanatomy/Analysis/Strahler_Analysis.py

@@ -1,27 +1,40 @@
-#@File(label="Input file:", description="Reconstruction file (.traces, .swc, json) to be analyzed") input_file
-#@String(label="Restrict to :", choices={"Axon", "Dendrites", "All processes"}) subtree_choice
+#@File(label="Input file (leave empty for demo):", required="false", description="Reconstruction file (.traces, .swc, json) to be analyzed. A folder of files is also supported.") input_file
+#@String(label="Restrict to :", choices={"All processes", "Axon", "Dendrites"}) subtree_choice
 #@ImageJ ij
+#@SNTService snt
 
 
 """
 file:       Strahler_Analysis.py
 author:     Tiago Ferreira
 version:    20220110
-info:       Performs Strahler Analysis on a single reconstruction file.
+info:       Performs Strahler Analysis on a single reconstruction file(s).
             See Batch>Strahler_Bulk_Analysis for a batch processing alternative.
 """
 
 from sc.fiji.snt import Tree
 from sc.fiji.snt.plugin import StrahlerCmd
+import os.path
 
 
-def main():
+def getTrees():
+    global subtree_choice, input_file
 
-    # A single file may contain more than one cell, so by default,
-    # we'll assume it contains a collection of Trees
+    # return a demo reconstruction if input_file is empty:
+    if not str(input_file) or not os.path.isfile(str(input_file)):
+        subtree_choice = "All"
+        return [snt.demoTree("pyramidal")]
+    # A single file may contain more than one cell, so we'll
+    # assume input_file may contain a collection of Trees
     trees = Tree.listFromFile(input_file.getAbsolutePath())
-    if not trees or trees.isEmpty():
-        ij.ui().showDialog("File did not contain a valid reconstruction.", "Error")
+    return trees
+
+
+def main():
+
+    trees = getTrees()
+    if not trees:
+        ij.ui().showDialog("File did not contain valid reconstruction(s).", "Error")
         return
     else:
         msg = []

src/main/resources/script_templates/Neuroanatomy/Batch/Filter_Multiple_Images.py

@@ -12,10 +12,10 @@
 # @Context context
 
 """
-file:	   Filter_Multiple_Images.py
-author:	 Tiago Ferreira, Cameron Arshadi
+file:		Filter_Multiple_Images.py
+author:		Tiago Ferreira, Cameron Arshadi
 version:	20190525
-info:	   Bulk filtering of image files using Frangi Vesselness
+info:		Bulk filtering of image files using Frangi Vesselness
 """
 
 import os

src/main/resources/script_templates/Neuroanatomy/Misc/Monitor_Memory.groovy

@@ -2,4 +2,5 @@
 file:       Monitor_Memory.groovy
 info:       Runs IJ's built in Memory Monitor. Double click for gc
 """
-new ij.plugin.frame.MemoryMonitor()
+new ij.plugin.frame.MemoryMonitor()
+return null // suppress 'ignoring unsupported output' warning