new commissioning scripts added together with some updates

l2com/create-input-json-pulp2.sh

@@ -48,7 +48,7 @@ echo "    \"use_pdmp\": false,"
 echo "    \"use_paz\": true,"
 echo "    \"use_clfd\": true,"
 echo "    \"nozap\": false,"
-echo "    \"tsubint\": 5,"
+echo "    \"tsubint\": 10,"
 echo "    \"sp_subint\": false,"
 echo "    \"remove_dm_delays\": false,"
 echo "    \"nbins\": 256,"

l2com/get_rfi_fraction.py

@@ -17,7 +17,8 @@ if __name__=="__main__":
         #
         usage = "Usage: %prog [options] <ar-file>"
         cmdline = opt.OptionParser(usage)
-        cmdline.add_option('-v', '--verbose', dest='is_verbose', action="store_true", help="Verbose output, print extra info", default=False)
+        cmdline.add_option('--percent', dest='is_percent', action="store_true", help="print RFI fraction in %", default=False)
+        cmdline.add_option('-v', '--verbose', dest='is_verbose', action="store_true", help="verbose output, print extra info", default=False)
 
         # reading cmd options
         (opts,args) = cmdline.parse_args()
@@ -69,5 +70,6 @@ if __name__=="__main__":
         # re-reading weights again and calculate the RFI fraction
         weights=raw.get_weights()
         rfi_fraction=1.-np.sum(weights)/(orig_nsubint*orig_nchan)
-        if opts.is_verbose: print ("RFI fraction = %f   Bad subints/chans = %d (%d)" % (rfi_fraction, badpoints, orig_nsubint * orig_nchan))
-        else: print (rfi_fraction)
+        if opts.is_percent: rfi_fraction *= 100.
+        if opts.is_verbose: print ("RFI fraction = %g %s   Bad subints/chans = %d (%d)" % (rfi_fraction, opts.is_percent and "%" or "", badpoints, orig_nsubint * orig_nchan))
+        else: print ("%g %s" % (rfi_fraction, opts.is_percent and "%" or ""))

l2com/pol-xxyy-stokes-uncal.py

@@ -42,19 +42,20 @@ if __name__ == "__main__":
     args = parser.parse_args()
 
     note="Frequency vs. Phase"
-    binshift=20
     stokes=["I", "Q", "U", "V"]
 
+    binshift=50
+
     # Read data
     raw = pc.Archive_load(args.arfile)
     if not(raw.get_dedispersed()):
         raw.dedisperse()
     raw.remove_baseline()
     raw.centre_max_bin()
-    nchan = raw.get_nchan()
-    nsubint = raw.get_nsubint()
     if args.fscrunch > 1: raw.fscrunch(args.fscrunch)
+    nsubint = raw.get_nsubint()
     if nsubint > 1: raw.tscrunch()
+    nchan = raw.get_nchan()
     nbins = raw.get_nbin()
     r = raw.get_data()
     #time stokes f phase
@@ -66,9 +67,11 @@ if __name__ == "__main__":
         ax = fig.add_subplot(2,2,pol+1)
         lbin=nbins//2-binshift
         rbin=nbins//2+binshift
-        sp=normalize(data[pol,:,lbin:rbin], nchan)
-        gmax = np.max([np.abs(np.min(sp)), np.abs(np.max(sp))])
-        ax.imshow(sp, interpolation='none', aspect='auto', origin='lower', cmap="bwr", vmax=gmax, vmin=-gmax)
+        sp=normalize(data[pol,:,:], nchan)
+        v=sp[:,lbin:rbin]
+        gmin, gmax = np.nanpercentile(v[(v!=-np.inf) & (v!=np.nan)], (0.05, 99.95))
+        gmax = np.max([np.abs(gmin), np.abs(gmax)])
+        ax.imshow(sp[:,lbin:rbin], interpolation='none', aspect='auto', origin='lower', cmap="bwr", vmax=gmax, vmin=-gmax)
         ax.set_xticklabels([])
         ax.set_yticklabels([])
         #plt.xlabel("Phase")