added scaling parameter to choose from dB and linear; few small label/axes...

added scaling parameter to choose from dB and linear; few small label/axes changes; also added the option --now to not open the GUI window, only saving to file

l2com/plot-bf-hdf5-spectrum.py

@@ -47,7 +47,13 @@ def read_hdf5_file(fname, tscrunch, fscrunch, memory_usage_limit):
             freq = h5[group_name + "/COORDINATES/COORDINATE_1"].attrs["AXIS_VALUES_WORLD"]
             tsamp = h5[group_name + "/COORDINATES/COORDINATE_0"].attrs["INCREMENT"]
             station_list = h5[group_name].attrs["STATIONS_LIST"]
+            # coherent or incoherent addition of stations
+            signal_sum = h5[group_name].attrs["SIGNAL_SUM"]
+            if "IN" in signal_sum: signal_sum = "Incoh sum"
+            else: signal_sum = "Coh sum"
 
+            # number of Stokes components in the whole observation
+            obsnof = h5[group_name].attrs["OBSERVATION_NOF_STOKES"]
             # number of Stokes components in the file
             nof = h5[group_name].attrs["NOF_STOKES"]
             if nof>1:
@@ -122,7 +128,7 @@ def read_hdf5_file(fname, tscrunch, fscrunch, memory_usage_limit):
     # f-scrunching the freq values as well
     freq = np.mean(np.reshape(freq, (int(nchan/fscrunch), fscrunch)), axis=1)
     
-    return (tsamp, freq, chanbw, chanpersub, nsubs, data, stations, nstations, band, antenna_set, stokes_comp, obsid, targets)
+    return (tsamp, freq, chanbw, chanpersub, nsubs, data, stations, signal_sum, nstations, band, antenna_set, stokes_comp, obsnof, obsid, targets)
 
 ###
 ###--- m a i n ---
@@ -135,18 +141,22 @@ if __name__ == "__main__":
                         default=1, type=int)
     parser.add_argument("-f", "--fscrunch", help="scrunch factor in frequency (default: 1)",
                         default=1, type=int)
+    parser.add_argument("-s", "--scale", help="Scaling of the plot: 'linear' or 'dB' (default: dB)",
+                        default="dB", type=str)        
     parser.add_argument("--flagger", help="Flagging routine/package/method to use (default: aoflagger)",
                         default="aoflagger", type=str)        
     parser.add_argument("--noflag", help="Skip flagging of the data to calculate the RFI fraction",
                         action="store_true")
     parser.add_argument("--memory_usage_limit", help="fraction of RAM aimed to be used (in percent, default: 5) [float]",
                         default=5., type=float)    
+    parser.add_argument("--noshow", help="Only save dynamic spectrum to file without opening GUI",
+                        action="store_true")
     parser.add_argument("-v", "--verbose", help="more verbose output",
                         action="store_true")
     args = parser.parse_args()
 
     # Read data
-    (tsamp, freq, chanbw, chanpersub, nsubs, data, stations, nstations, band, antenna_set, stokes, obsid, targets) = \
+    (tsamp, freq, chanbw, chanpersub, nsubs, data, stations, signal_sum, nstations, band, antenna_set, stokes, obsnof, obsid, targets) = \
         read_hdf5_file(args.h5file, args.tscrunch, args.fscrunch, args.memory_usage_limit)
     nsamp, nchan = data.shape # here nsamp is already t-scrunched
     freq *= 1e-6 # in MHz
@@ -154,10 +164,14 @@ if __name__ == "__main__":
 
     # Extract data
     dB = lambda x: 10 * np.log10(x)
-    v = dB(data)
     zm = np.mean(data, axis=0)
     zs = np.std(data, axis=0)
+    if args.scale == "dB":
+        v = dB(data)
         z = dB(zm)
+    else:
+        v = data
+        z = zm
 
     if not args.noflag:
         # Flag data
@@ -207,8 +221,11 @@ if __name__ == "__main__":
     
     fig, (ax1, ax2, ax3) = plt.subplots(3, 1, figsize=(18, 8), sharex=True, gridspec_kw={"height_ratios": [0.1, 0.2, 0.7], "hspace": 0.02})
     
+    ylabel = "Power"
+    if args.scale == "dB": ylabel += " (dB)"
+    else: ylabel += " (arb. units)"
     # Top RFI fraction subplot
-    ax1.set_title(f"L{obsid} | {antenna_set} | {band} | Nsub: {nsubs} | Nchan/sub = {chanpersub} | Nstations = {nstations} | {stations}", loc='left')
+    ax1.set_title(f"L{obsid} | {antenna_set} | {band} | Nsub: {nsubs} | Nchan/sub = {chanpersub} | Nstations = {nstations} ({signal_sum}) | {stations}", loc='left')
     ax1.set_title(f"{targets} | Stokes: {stokes}", loc='right')
     ax1.set_ylabel("RFI (%)")
     ax1.set_ylim(-10, 110)
@@ -218,7 +235,7 @@ if __name__ == "__main__":
     
     # Average spectrum
     ax2.plot(freq, z, color="k", linewidth=0.5)
-    ax2.set_ylabel("Power (dB)")
+    ax2.set_ylabel(ylabel)
     ax2.set_ylim(vmin, vmax)
     ax2.set_xlim(fmin, fmax)
     
@@ -237,8 +254,9 @@ if __name__ == "__main__":
     ax3label=f"Tscrunch: {args.tscrunch}  Fscrunch: {args.fscrunch}"
     props = dict(boxstyle='round', facecolor='white', alpha=0.7)
     ax3.text(0.01, 0.95, ax3label, transform=ax3.transAxes, fontsize=10, verticalalignment='center', bbox=props)
-    fig.colorbar(img, ax=ax3, location="bottom", orientation="horizontal", label="Power (dB)", shrink=1, pad=0.12, fraction=0.05)
+    fig.colorbar(img, ax=ax3, location="bottom", orientation="horizontal", label=ylabel, shrink=1, pad=0.12, fraction=0.05)
     
     plt.savefig(f"L{obsid}_bf_spectrum_stokes{stokes}_tscr{args.tscrunch}_fscr{args.fscrunch}.png", bbox_inches="tight")
+    if not args.noshow:
         plt.show()
     plt.close()