From 435ebb9741c39e8da39910d658186d835728e9ce Mon Sep 17 00:00:00 2001
From: Claude <noreply@anthropic.com>
Date: Wed, 7 Oct 2026 20:17:57 +0000
Subject: [PATCH] ShapesOut: outlines as annotations (holes and parts kept,
 numeric properties as measurements, Replace); GUI test body

Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01Y2SN8SuEakTdiWy3F2WUqN
---
 .../qupath/LabConstrictorTools.groovy         | 54 ++++++++++++++
 tests/gui_test_shapes_body.groovy             | 71 +++++++++++++++++++
 2 files changed, 125 insertions(+)
 create mode 100644 tests/gui_test_shapes_body.groovy

diff --git a/src/main/resources/org/cellmigrationlab/labconstrictor/qupath/LabConstrictorTools.groovy b/src/main/resources/org/cellmigrationlab/labconstrictor/qupath/LabConstrictorTools.groovy
index 56e48d8..6a24a3c 100644
--- a/src/main/resources/org/cellmigrationlab/labconstrictor/qupath/LabConstrictorTools.groovy
+++ b/src/main/resources/org/cellmigrationlab/labconstrictor/qupath/LabConstrictorTools.groovy
@@ -972,6 +972,9 @@ class LcDialog {
                 case "points":
                     box.children.addAll(boldLabel((r.name ?: "points") + " (points)"), new Label(placePoints(appName, r)), tableView(r.path as String))
                     break
+                case "shapes":
+                    box.children.addAll(boldLabel((r.name ?: "shapes") + " (outlines)"), wrapped(placeShapes(appName, r)))
+                    break
                 case ["image", "labels"]:
                     def open = new Button("Open in QuPath")
                     def path = r.path as String
@@ -1031,6 +1034,57 @@ class LcDialog {
         return xs.size() + " point(s) added to the open image as the annotation '" + name + "'."
     }
 
+    static Label wrapped(String text) {
+        def l = new Label(text)
+        l.wrapText = true
+        return l
+    }
+
+    static final int MAX_SHAPES = 50000      // outlines added to the image; the rest are counted in the message
+
+    /** Outlines (GeoJSON Polygon / MultiPolygon, [x, y] with pixel centres at integers) become annotations named "<app>:<output> <label>"
+     *  on the image they were found in (when that was the image open in QuPath); holes and parts are kept; numeric properties become
+     *  measurements. Replace() removes the previous annotations of this output. */
+    String placeShapes(String appName, Map r) {
+        def data = qupath?.imageData
+        def target = r.apply_to ?: currentTool?.inputs?.find { it.type in ["image", "labels"] }?.name
+        def chosen = target ? imageChoiceAtRun[target] : null
+        if (data == null || chosen == null || !chosen.startsWith("Current image"))
+            return "Not placed on an image (the outlines were not found in the image open in QuPath)."
+        def collection = new Gson().fromJson(new File(r.path as String).getText("UTF-8"), Map)
+        def factory = new org.locationtech.jts.geom.GeometryFactory()
+        def ring = { List points -> factory.createLinearRing(points.collect { new org.locationtech.jts.geom.Coordinate((it[0] as double) + 0.5d, (it[1] as double) + 0.5d) } as org.locationtech.jts.geom.Coordinate[]) }   // pixel centres
+        def prefix = appName + ":" + r.name
+        def objects = [], holes = 0, total = collection.features.size()
+        for (feature in collection.features) {
+            if (objects.size() >= MAX_SHAPES) break
+            def geometry = feature.geometry
+            def parts = geometry.type == "Polygon" ? [geometry.coordinates] : geometry.coordinates
+            def polygons = parts.collect { part ->
+                if (part.size() > 1) holes++
+                factory.createPolygon(ring(part[0] as List), part.drop(1).collect { ring(it as List) } as org.locationtech.jts.geom.LinearRing[])
+            }
+            def shape = polygons.size() == 1 ? polygons[0] : factory.createMultiPolygon(polygons as org.locationtech.jts.geom.Polygon[])
+            def obj = PathObjects.createAnnotationObject(qupath.lib.roi.GeometryTools.geometryToROI(shape, ImagePlane.getDefaultPlane()))
+            def label = feature.get("properties")?.get("label")   // .get(): on a map, Groovy's feature.properties and feature["properties"] give the bean properties, not the JSON key
+            if (label instanceof Number && (label as double) == Math.floor(label as double)) label = (label as double).longValue()      // Gson reads every number as a double: 1.0 -> 1
+            obj.name = prefix + " " + (label != null ? label : objects.size() + 1)
+            feature.get("properties")?.each { k, v -> if (v instanceof Number) obj.measurementList.put(k.toString(), v as double) }   // numeric properties become measurements
+            objects << obj
+        }
+        def hierarchy = data.hierarchy
+        def replacing = currentTool.outputs.any { it.name == r.name && it.replace }
+        if (replacing) {
+            def previous = hierarchy.annotationObjects.findAll { it.name?.startsWith(prefix + " ") }
+            if (previous) hierarchy.removeObjects(previous, true)       // Replace()
+        }
+        hierarchy.addObjects(objects)
+        def text = objects.size() + " outline(s) added to the open image as annotations named '" + prefix + " <label>'."
+        if (total > MAX_SHAPES) text += " Showing the first " + MAX_SHAPES + " of " + total + "."
+        if (holes) text += " " + holes + " outline(s) have holes (kept)."
+        return text
+    }
+
     /** A small preview of a result image (first plane, first channel, scaled to the window); labels get a colour per label. */
     static Node previewNode(String path, boolean labels) {
         def server = ImageServers.buildServer(path)
diff --git a/tests/gui_test_shapes_body.groovy b/tests/gui_test_shapes_body.groovy
new file mode 100644
index 0000000..bac3d2b
--- /dev/null
+++ b/tests/gui_test_shapes_body.groovy
@@ -0,0 +1,71 @@
+
+// ================================================================== GUI test body (appended to the tool script by tests/run_gui_test.sh)
+import javafx.embed.swing.SwingFXUtils
+import javax.imageio.ImageIO
+import java.util.concurrent.CountDownLatch
+import java.awt.image.BufferedImage
+import javafx.stage.Window
+
+def OUT = new File(System.getProperty("lc.test.out", "/tmp/qp_shots")); OUT.mkdirs()
+def FX = "/home/tester/q/fx"
+def results = [:]
+def fx = { Closure c ->
+    if (Platform.isFxApplicationThread()) return c()
+    def latch = new CountDownLatch(1); def box = [null, null]
+    Platform.runLater { try { box[0] = c() } catch (Throwable t) { box[1] = t } finally { latch.countDown() } }
+    latch.await()
+    if (box[1] != null) throw box[1]
+    return box[0]
+}
+def expect = { String name, boolean ok, Object detail = "" ->
+    results[name] = ok
+    println((ok ? "PASS " : "FAIL ") + name + (ok ? "" : " -> " + detail))
+}
+def shot = { String name, Stage st ->
+    Thread.sleep(600)
+    fx {
+        def img = st.scene.snapshot(null)
+        ImageIO.write(SwingFXUtils.fromFXImage(img, null), "png", new File(OUT, name + ".png"))
+    }
+    println "SHOT " + name
+}
+def waitIdle = { dlg, int seconds = 300 ->
+    def end = System.currentTimeMillis() + seconds * 1000
+    while (System.currentTimeMillis() < end) { Thread.sleep(200); if (!dlg.running && fx { !dlg.runButton.disable }) return true }
+    return false
+}
+def status = { dlg -> fx { dlg.status.text } }
+def pick = { dlg, app, tool -> fx { dlg.appBox.value = app }; fx { dlg.toolBox.value = tool } }
+def resultStages = { Window.getWindows().findAll { it instanceof Stage && it.showing && it.title?.contains(": ") && it.title != "LabConstrictor: last run" } }
+
+
+Thread.start("lc-gui-test") {
+    try {
+        fx {
+            def dir = new File("/tmp/qp_project_shapes"); dir.deleteDir()
+            qupath.lib.gui.prefs.PathPrefs.imageTypeSettingProperty().set(qupath.lib.gui.prefs.PathPrefs.ImageTypeSetting.AUTO_ESTIMATE)
+            def project = qupath.lib.projects.Projects.createProject(dir, BufferedImage)
+            def server = qupath.lib.images.servers.ImageServers.buildServer("/home/user/LabConstrictor-Fiji/tests/fixtures/blobs.tif")
+            def entry = project.addImage(server.getBuilder()); entry.setImageName("blobs.tif")
+            project.syncChanges(); qupath.setProject(project); qupath.openImageEntry(entry); entry
+        }
+        Thread.sleep(2500)
+        def dlg = fx { lcShow() }
+        Thread.sleep(800)
+        pick(dlg, "interactions", "Outline the blobs"); Thread.sleep(1500)
+        def annotations = { fx { qupath.imageData.hierarchy.annotationObjects.findAll { it.name?.startsWith("interactions:outlines ") } } }
+        fx { dlg.run() }; Thread.sleep(1500); waitIdle(dlg, 120)
+        println "STATUS " + status(dlg)
+        def found = annotations()
+        expect("one_annotation_per_blob", found.size() == 4, found*.name)
+        expect("names_carry_the_label", found.any { it.name == "interactions:outlines 1" }, found*.name)
+        expect("measurements_from_properties", found.every { it.getMeasurementList().getMeasurementNames().containsAll(["area", "label"]) }, found.collect { it.getMeasurementList().getMeasurementNames() })
+        def ring = found.find { it.getMeasurementList().get("area") > 300 }
+        expect("hole_is_kept", ring != null && ring.getROI().getArea() < 20 * 20 - 40, ring?.getROI()?.getArea())
+        expect("annotations_are_on_the_blob", found.every { it.ROI.boundsX >= 0 && it.ROI.boundsX < 80 && it.ROI.boundsY >= 0 && it.ROI.boundsY < 60 }, found.collect { [it.ROI.boundsX, it.ROI.boundsY] })
+        shot("qp_shapes_1_after", dlg.stage)
+        fx { dlg.run() }; Thread.sleep(1500); waitIdle(dlg, 120)
+        expect("replace_leaves_one_set", annotations().size() == 4, annotations()*.name)
+    } catch (Throwable t) { t.printStackTrace() }
+    finally { println "RESULTS " + results; Thread.sleep(500); System.exit(0) }
+}