ssins write out mask in spectrum

demo/04_ssins.py

@@ -478,9 +478,18 @@ def plot_spectrum(ss, args, obsname, suffix, cmap):
 
     mf = get_match_filter(ss, args)
     apply_match_test(mf, ins, args)
-    ins.sig_array[~np.isfinite(ins.sig_array)] = 0
-
+    ins.sig_array[~np.isfinite(ins.sig_array)] = np.nan
+    ins.metric_array[~np.isfinite(ins.sig_array)] = np.nan
     pols = ss.get_pols()
+
+    # occupancy = np.sum(
+    #     ss.flag_array.reshape(ss.Ntimes, ss.Nbls, ss.Nspws, ss.Nfreqs, len(pols)),
+    #     axis=(1, 2),
+    # ).astype(np.float64)
+    # full_occupancy_value = np.max(occupancy)
+    # ins.sig_array[occupancy > full_occupancy_value / 2] = np.nan
+    # ins.metric_array[occupancy > full_occupancy_value / 2] = np.nan
+
     gps_times = get_gps_times(ss)
     freqs_mhz = (ss.freq_array) / 1e6
     channames = [f"{ch: 8.4f}" for ch in freqs_mhz]
@@ -533,6 +542,8 @@ def plot_spectrum(ss, args, obsname, suffix, cmap):
 
     plt.gcf().set_size_inches(8 * len(pols), 16)
 
+    return ins
+
 
 def plot_flags(ss: UVData, args, obsname, suffix, cmap):
     pols = ss.get_pols()
@@ -786,7 +797,11 @@ def main():
     if args.plot_type == "sigchain":
         plot_sigchain(ss, args, obsname, suffix, cmap)
     elif args.plot_type == "spectrum":
-        plot_spectrum(ss, args, obsname, suffix, cmap)
+        ins = plot_spectrum(ss, args, obsname, suffix, cmap)
+        maskname = f"{base}{suffix}"
+        ins.write(f"{base}{suffix}", output_type="mask", clobber=True)
+        print(f"wrote {maskname}_SSINS_mask.h5")
+
     elif args.plot_type == "flags":
         plot_flags(ss, args, obsname, suffix, cmap)