flag whole file if one pol is totally flagged

notebooks/delay_filtered_average_zscore.ipynb

@@ -7,7 +7,7 @@
    "source": [
     "# Single File Delay Filtered Average Z-Score\n",
     "\n",
-    "**by Josh Dillon**, last updated July 27, 2023\n",
+    "**by Josh Dillon**, last updated May 10, 2024\n",
     "\n",
     "This notebook is designed to calculate a metric used for finding low-level RFI in redundantly-averaged cross-correlations, which are then incoherently averaged across well-sampled baselines.\n",
     "\n",
@@ -132,11 +132,16 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "# handle the the case where the smooth_cal flags are all True, trying to maintain consistent data shapes\n",
+    "# handle the the case where the visibility flags are all True for at least one pol, trying to maintain consistent data shapes\n",
     "ALL_FLAGGED = False\n",
     "if np.all([flag for flag in cal_flags.values()]):\n",
     "    print('This file is entirely flagged.')\n",
-    "    ALL_FLAGGED = True"
+    "    ALL_FLAGGED = True\n",
+    "else:\n",
+    "    for pol in ('Jee', 'Jnn'):\n",
+    "        if len([ant for ant, flag in cal_flags.items() if ant[1] == pol and not np.all(flag)]) <= 1:\n",
+    "            print(f'Effectively all {pol}-polarized antennas are flagged, so flagging the entire file.')\n",
+    "            ALL_FLAGGED = True"
    ]
   },
   {