Change variable name to match workflow

Author: anwai98

scripts/datasets/histopathology/check_puma.py

@@ -9,7 +9,8 @@
 
 
 def check_puma():
-    from util import ROOT
+    # from util import ROOT
+    ROOT = "/media/anwai/ANWAI/data"
 
     loader = get_puma_loader(
         path=os.path.join(ROOT, "puma"),

torch_em/data/datasets/histopathology/puma.py

@@ -123,10 +123,11 @@ def _preprocess_inputs(path, annotations, split):
         width, height = 1024, 1024  # roi shape
         transform = from_bounds(minx, miny, maxx, maxy, width, height)
 
-        class_names = [
+        # Extract class ids mapped to each class name.
+        class_ids = [
             CLASS_DICT[nuc_class["name"]] for nuc_class in gdf["classification"].apply(lambda x: ast.literal_eval(x))
         ]
-        semantic_shapes = ((geom, unique_id) for geom, unique_id in zip(gdf.geometry, class_names))
+        semantic_shapes = ((geom, unique_id) for geom, unique_id in zip(gdf.geometry, class_ids))
         semantic_mask = rasterize(
             semantic_shapes, out_shape=(height, width), transform=transform, fill=0, dtype=np.uint8
         )