Add template script

Author: tferr

src/main/resources/script_templates/Neuroanatomy/Skeletons_and_ROIs/Tip_Montage.groovy

@@ -0,0 +1,85 @@
+#@String(value = "<HTML>This script assembles a montage of small image neighborhoods centered on each<br>tip of a reconstruction. Works on both regular (e.g., TIFF) and pyramidal images<br>(e.g., OME-Zarr, N5).", visibility = "MESSAGE") msg
+#@File(required = false, label = "Reconstruction file (leave empty for demo)") treeFile
+#@File(required = false, label = "Image file (leave empty for demo)") imgFile
+# @int(label = "Window XY size (in pixels)", min = 4) windowXY
+# @int(label = "Window Z thickness (in pixels, 1=2D)", min = 1) windowZ
+#@SNTService sntService
+#@UIService uiService
+
+
+/**
+ *  Builds a montage of all the end-points (tips) of a reconstruction (Tree).
+ *
+ *  Uses sc.fiji.snt.analysis.NodeCollector, which:
+ *   - operates on an ImgPlus, working directly with lazy, pyramid sources (OME-Zarr, N5) w/o loading the whole volume
+ *   - pads out-of-bounds crops with zeros, so the resulting montage forms a uniform grid
+ *   - defaults the channel/frame to the tip's owning Path (overridable)
+ *
+ *  TF 20260609
+ */
+
+import sc.fiji.snt.Tree
+import sc.fiji.snt.analysis.NodeCollector
+import sc.fiji.snt.util.ImgUtils
+
+
+// Abort if running an old version
+sntService.requireVersion("5.0.11")
+
+def tree, imgPlus
+
+// Load data
+if (treeFile && imgFile) {
+    // Use SCIFIO to load ImgPlus (both regular and pyramid file formats supported)
+    imgPlus = ImgUtils.open(imgFile.getAbsolutePath())
+    tree = Tree.fromFile(treeFile.getAbsolutePath())
+} else {
+    // No data specified: Run on demo dataset
+    imgPlus = sntService.demoImgPlus("OP_1")
+    tree = sntService.demoTree("OP_1")
+    windowXY = 40
+    windowZ = 1
+}
+if (!tree || !imgPlus) {
+    uiService.showDialog("Invalid file paths or demo data not available.")
+    return
+}
+
+// Tree must know its source image so that tip coordinates can be unscaled against the right calibration
+tree.assignImage(imgPlus)
+
+// If the window depth is a slab of multiple planes, we will project it (maximum intensity projection)
+def doMIP = (windowZ > 1) ? NodeCollector.Projection.MIP_Z : NodeCollector.Projection.NONE
+
+// Now we can assemble the NodeCollector...
+def collector = NodeCollector.fromTips(imgPlus, tree)
+collector.setWindow(windowXY, windowZ)
+collector.setProjection(doMIP)
+
+//... and retrieve the montage:
+def montage = collector.getMontage(
+        -1, // no. of columns (-1=auto)
+        -1, // no. of columns (-1=auto)
+        1, // scaling factor for each tile in the montage
+        2, // width of the border around each tile
+        false) // label each tile?
+montage.show()
+
+// Other things you can do with the same builder:
+//
+//   // Branch-point montage
+//   NodeCollector.fromBranchPoints(imgPlus, tree).setWindow(20, 1).getMontage().show()
+//
+//   // Every 10th node along all paths
+//   NodeCollector.fromNodes(imgPlus, tree, 10).setWindow(20, 1).getMontage().show()
+//
+//   // Roots of a population of Trees
+//   NodeCollector.fromRoots(imgPlus, listOfTrees).setWindow(20, 1).getMontage().show()
+//
+//   // Arbitrary points (bookmarks, seeds, ...)
+//   NodeCollector collector = new NodeCollector(imgPlus, myPointsCollection)
+//   collector.setWindow(20, 5).setProjection(NodeCollector.Projection.MIP_Z)
+//   collector.getStack().show()  // just the stack, no montage
+//
+//   // Lazy crops as RAIs (without actual materialization of the volume), e.g. for further imglib2 work:
+//   def crops = NodeCollector.fromTips(imgPlus, tree).setWindow(20, 1).getCrops()