RootScope v4: manuscript model (LightGBM per round, 3 seeds, layer + soft-neighbor context, radial prior)

rootscope/classify_v4.py

@@ -67,6 +67,13 @@ def classify(df_base, masks, source_file="image.tif", model_dir=None, seeds=None
     ctx.MASK = "<in-memory>"
     ctx.CL = CLASSES
 
+    # The 4 nearest-neighbour cell-type columns are model inputs that exist only
+    # as placeholders before round 1 (-1 = unknown); stage_features does not
+    # produce them, so create them here. fill_neighbors overwrites them from round 2.
+    for c in _eh.NEIGHBOR_CT_COLS:
+        if c not in geom.columns:
+            geom[c] = -1.0
+
     missing = [c for c in fcols if c not in geom.columns
                and c not in ctx.RINGCOLS and not c.startswith(("nbp_", "agree_"))]
     if missing: