--- a/imagej2_analyze_skeleton_jython_script.py	Mon Sep 28 16:40:20 2020 +0000
+++ b/imagej2_analyze_skeleton_jython_script.py	Sun Nov 05 10:51:33 2023 +0000
@@ -4,18 +4,37 @@
 from ij import IJ
 from sc.fiji.analyzeSkeleton import AnalyzeSkeleton_
 
-BASIC_NAMES = ['Branches', 'Junctions', 'End-point Voxels',
-               'Junction Voxels', 'Slab Voxels', 'Average branch length',
-               'Triple Points', 'Quadruple Points', 'Maximum Branch Length']
-DETAIL_NAMES = ['Skeleton ID', 'Branch length', 'V1 x', 'V1 y', 'V1 z', 'V2 x',
-                'V2 y', 'V2 z', 'Euclidean distance']
-OPTIONS = ['edm=Overwrite', 'iterations=1', 'count=1']
+BASIC_NAMES = [
+    "Branches",
+    "Junctions",
+    "End-point Voxels",
+    "Junction Voxels",
+    "Slab Voxels",
+    "Average branch length",
+    "Triple Points",
+    "Quadruple Points",
+    "Maximum Branch Length",
+]
+DETAIL_NAMES = [
+    "Skeleton ID",
+    "Branch length",
+    "V1 x",
+    "V1 y",
+    "V1 z",
+    "V2 x",
+    "V2 y",
+    "V2 z",
+    "Euclidean distance",
+]
+OPTIONS = ["edm=Overwrite", "iterations=1", "count=1"]
 
 
 def get_euclidean_distance(vertex1, vertex2):
     x1, y1, z1 = get_points(vertex1)
     x2, y2, z2 = get_points(vertex2)
-    return math.sqrt(math.pow((x2 - x1), 2) + math.pow((y2 - y1), 2) + math.pow((z2 - z1), 2))
+    return math.sqrt(
+        math.pow((x2 - x1), 2) + math.pow((y2 - y1), 2) + math.pow((z2 - z1), 2)
+    )
 
 
 def get_graph_length(graph):
@@ -46,29 +65,29 @@
     return graphs
 
 
-def save(result, output, show_detailed_info, calculate_largest_shortest_path, sep='\t'):
+def save(result, output, show_detailed_info, calculate_largest_shortest_path, sep="\t"):
     num_trees = int(result.getNumOfTrees())
-    outf = open(output, 'wb')
-    outf.write('# %s\n' % sep.join(BASIC_NAMES))
+    outf = open(output, "wb")
+    outf.write("# %s\n" % sep.join(BASIC_NAMES))
     for index in range(num_trees):
-        outf.write('%d%s' % (result.getBranches()[index], sep))
-        outf.write('%d%s' % (result.getJunctions()[index], sep))
-        outf.write('%d%s' % (result.getEndPoints()[index], sep))
-        outf.write('%d%s' % (result.getJunctionVoxels()[index], sep))
-        outf.write('%d%s' % (result.getSlabs()[index], sep))
-        outf.write('%.3f%s' % (result.getAverageBranchLength()[index], sep))
-        outf.write('%d%s' % (result.getTriples()[index], sep))
-        outf.write('%d%s' % (result.getQuadruples()[index], sep))
-        outf.write('%.3f' % result.getMaximumBranchLength()[index])
+        outf.write("%d%s" % (result.getBranches()[index], sep))
+        outf.write("%d%s" % (result.getJunctions()[index], sep))
+        outf.write("%d%s" % (result.getEndPoints()[index], sep))
+        outf.write("%d%s" % (result.getJunctionVoxels()[index], sep))
+        outf.write("%d%s" % (result.getSlabs()[index], sep))
+        outf.write("%.3f%s" % (result.getAverageBranchLength()[index], sep))
+        outf.write("%d%s" % (result.getTriples()[index], sep))
+        outf.write("%d%s" % (result.getQuadruples()[index], sep))
+        outf.write("%.3f" % result.getMaximumBranchLength()[index])
         if calculate_largest_shortest_path:
-            outf.write('%s%.3f%s' % (sep, result.shortestPathList.get(index), sep))
-            outf.write('%d%s' % (result.spStartPosition[index][0], sep))
-            outf.write('%d%s' % (result.spStartPosition[index][1], sep))
-            outf.write('%d\n' % result.spStartPosition[index][2])
+            outf.write("%s%.3f%s" % (sep, result.shortestPathList.get(index), sep))
+            outf.write("%d%s" % (result.spStartPosition[index][0], sep))
+            outf.write("%d%s" % (result.spStartPosition[index][1], sep))
+            outf.write("%d\n" % result.spStartPosition[index][2])
         else:
-            outf.write('\n')
+            outf.write("\n")
     if show_detailed_info:
-        outf.write('# %s\n' % sep.join(DETAIL_NAMES))
+        outf.write("# %s\n" % sep.join(DETAIL_NAMES))
         # The following index is a placeholder for the skeleton ID.
         # The terms "graph" and "skeleton" refer to the same thing.
         # Also, the SkeletonResult.java code states that the
@@ -80,23 +99,23 @@
                 x1, y1, z1 = get_points(vertex1)
                 vertex2 = edge.getV2()
                 x2, y2, z2 = get_points(vertex2)
-                outf.write('%d%s' % (index + 1, sep))
-                outf.write('%.3f%s' % (edge.getLength(), sep))
-                outf.write('%d%s' % (x1, sep))
-                outf.write('%d%s' % (y1, sep))
-                outf.write('%d%s' % (z1, sep))
-                outf.write('%d%s' % (x2, sep))
-                outf.write('%d%s' % (y2, sep))
-                outf.write('%d%s' % (z2, sep))
-                outf.write('%.3f' % get_euclidean_distance(vertex1, vertex2))
+                outf.write("%d%s" % (index + 1, sep))
+                outf.write("%.3f%s" % (edge.getLength(), sep))
+                outf.write("%d%s" % (x1, sep))
+                outf.write("%d%s" % (y1, sep))
+                outf.write("%d%s" % (z1, sep))
+                outf.write("%d%s" % (x2, sep))
+                outf.write("%d%s" % (y2, sep))
+                outf.write("%d%s" % (z2, sep))
+                outf.write("%.3f" % get_euclidean_distance(vertex1, vertex2))
                 if calculate_largest_shortest_path:
                     # Keep number of separated items the same for each line.
-                    outf.write('%s %s' % (sep, sep))
-                    outf.write(' %s' % sep)
-                    outf.write(' %s' % sep)
-                    outf.write(' \n')
+                    outf.write("%s %s" % (sep, sep))
+                    outf.write(" %s" % sep)
+                    outf.write(" %s" % sep)
+                    outf.write(" \n")
                 else:
-                    outf.write('\n')
+                    outf.write("\n")
     outf.close()
 
 
@@ -109,8 +128,8 @@
 prune_ends = sys.argv[-4] == "yes"
 calculate_largest_shortest_path = sys.argv[-3] == "yes"
 if calculate_largest_shortest_path:
-    BASIC_NAMES.extend(['Longest Shortest Path', 'spx', 'spy', 'spz'])
-    DETAIL_NAMES.extend([' ', ' ', ' ', ' '])
+    BASIC_NAMES.extend(["Longest Shortest Path", "spx", "spy", "spz"])
+    DETAIL_NAMES.extend([" ", " ", " ", " "])
 show_detailed_info = sys.argv[-2] == "yes"
 output = sys.argv[-1]
 
@@ -135,14 +154,21 @@
 # Run AnalyzeSkeleton
 analyze_skeleton = AnalyzeSkeleton_()
 analyze_skeleton.setup("", input_image_plus_copy)
-if prune_cycle_method == 'none':
+if prune_cycle_method == "none":
     prune_index = analyze_skeleton.NONE
-elif prune_cycle_method == 'shortest_branch':
+elif prune_cycle_method == "shortest_branch":
     prune_index = analyze_skeleton.SHORTEST_BRANCH
-elif prune_cycle_method == 'lowest_intensity_voxel':
+elif prune_cycle_method == "lowest_intensity_voxel":
     prune_index = analyze_skeleton.LOWEST_INTENSITY_VOXEL
-elif prune_cycle_method == 'lowest_intensity_branch':
+elif prune_cycle_method == "lowest_intensity_branch":
     prune_index = analyze_skeleton.LOWEST_INTENSITY_BRANCH
-result = analyze_skeleton.run(prune_index, prune_ends, calculate_largest_shortest_path, input_image_plus_copy, True, True)
+result = analyze_skeleton.run(
+    prune_index,
+    prune_ends,
+    calculate_largest_shortest_path,
+    input_image_plus_copy,
+    True,
+    True,
+)
 # Save the results.
 save(result, output, show_detailed_info, calculate_largest_shortest_path)