Pipeline / pipeline / 331abc88d30

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Vincent Geers authored 331abc88d30 Merge 10 Jul 2020

Merge pull request #277 in PIPE/pipeline from PIPE-644_update_calibrated_flux_uncertainty to master

* commit 'c700a82a9b591bc84129184bd07553adfec943c3':
  PIPE-644: update in hifa_gfluxscale to calculation of calibrated visibility flux uncertainty.

pipeline/hifa/tasks/fluxscale/gcorfluxscale.py

Modified

-350
+            # Select data for current polarisation.
-351
+            ampdata = np.squeeze(data['corrected_data'], axis=1)[pol]
-352
+            flagdata = np.squeeze(data['flag'], axis=1)[pol]
-353
+            weightdata = data['weight'][pol]
-354
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+            # Select for non-flagged data and non-NaN data.
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+            id_nonbad = np.where(np.logical_and(np.logical_not(flagdata), np.isfinite(ampdata)))
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+            amplitudes = ampdata[id_nonbad]
-358
+            weights = weightdata[id_nonbad]
-359
-+
+            # Determine number of non-flagged antennas, baselines, and
-+
+            # integrations.
-+
+            ant1 = data['antenna1'][id_nonbad]
-+
+            ant2 = data['antenna2'][id_nonbad]
-+
+            n_ants = len(set(ant1) | set(ant2))
-+
+            n_baselines = n_ants * (n_ants - 1) // 2
-+
+            n_ints = len(amplitudes) // n_baselines
-+
-+
+            # PIPE-644: Determine scale factor for variance.
-+
+            var_scale = np.mean([len(amplitudes), n_ints * n_ants])
-+
-371
+            # Compute mean flux and stdev for current polarisation.
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+            mean_flux = np.abs(np.average(amplitudes, weights=weights))
--
+            variance = np.average((np.abs(amplitudes) - mean_flux)**2, weights=weights)
-+
+            variance = np.average((np.abs(amplitudes) - mean_flux)**2, weights=weights) / var_scale
-374
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+            # Store for this polarisation.
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+            mean_fluxes.append(mean_flux)
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+            variances.append(variance)
-378
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+        # Compute mean flux and mean stdev for all polarisations.
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+        mean_flux = np.mean(mean_fluxes)
-381
+        mean_std = np.sqrt(np.mean(variances))
-382
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+        # Combine into single flux measurement object.
-595
+                openms.msselect(data_selection)
-596
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+                # Read in the weights from MS separately, prior to channel
-598
+                # averaging.
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+                weights = openms.getdata(['weight'])
-600
-601
+                # Set channel selection to take the average of all channels.
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+                openms.selectchannel(1, 0, nchans, 1)
-603
-604
+                # Extract data from MS.
--
+                data = openms.getdata(['corrected_data', 'flag'])
-+
+                data = openms.getdata(['corrected_data', 'flag', 'antenna1', 'antenna2'])
-606
+            except:
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+                # Log a warning and return without data.
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+                LOG.warning('Unable to compute mean vis for intent(s) {}, field {}, spw {}'
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+                            ''.format(intent, fieldid, spwid))
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+                return
-611
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+        # Combine the two dictionaries.
-613
+        data = {**data, **weights}
-614
-615
+        return data

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