foo

preparation.py

@@ -11,7 +11,7 @@ from rasterio.vrt import WarpedVRT
 from rasterio import shutil as rio_shutil
 
 RESOLUTION_RATIO = 21
-# Centred temporal MA on S3 LR stack (METHODOLOGY §5.4.3); odd ≥3, or 1 to disable.
+# Centred temporal MA on S3 LR stack (thesis/Method.tex, sec:data_preparation); odd ≥3, or 1 to disable.
 S3_MOVING_AVERAGE_WINDOW_DAYS = 5
 
 
@@ -79,7 +79,9 @@ def _get_itb_base_dir(season, site_name, cleaning_strategy):
 
 
 def _compute_gcc_from_refl_array(blue, green, red):
-    total = red.astype(np.float32) + green.astype(np.float32) + red.astype(np.float32)
+    total = (
+        blue.astype(np.float32) + green.astype(np.float32) + red.astype(np.float32)
+    )
     mask = (total > 0) & np.isfinite(total)
     gcc = np.zeros_like(green, dtype=np.float32)
     gcc[mask] = green[mask].astype(np.float32) / total[mask]
@@ -90,8 +92,8 @@ def _link_dist_cloud_from_prepared(src_s2_dir, dst_s2_dir):
     dst_s2_dir.mkdir(parents=True, exist_ok=True)
     for src in src_s2_dir.glob("*DIST_CLOUD.tif"):
         dst = dst_s2_dir / src.name
-        if dst.exists():
-            continue
+        if dst.is_symlink() or dst.exists():
+            dst.unlink(missing_ok=True)
         try:
             dst.symlink_to(src.resolve())
         except OSError: