Tim

The functions to extract the relevant pulses from XGM and TIM data are now relying on the bunch pattern, instead of processing each pattern situation individually. Mostly cleanXGMdata(), selectSASEfromXGM() and getTIMapd() were rewritten.

Notebook for test:

2019-10-28_TIM_XGM_using_bunch_pattern.ipynb

2019-10-28_TIM_XGM_using_bunch_pattern.pdf

Sometimes the bunch pattern is not correct, in this case it is better to load the sase-resolved data of XGM.

xgm.py

@@ -518,7 +518,7 @@ def mcpPeaks(data, intstart, intstop, bkgstart, bkgstop, mcp=1, t_offset=None, n
                 pattern and determine the t_offset assuming mininum pulse 
                 separation of 220 ns and digitizer resolution of 2 GHz.
             npulses: number of pulses. If None, takes the maximum number of
-                pulses according to the bunch patter (field 'npulses_sase3')
+                pulses according to the bunch pattern (field 'npulses_sase3')
             
         Output:
             results: DataArray with dims trainId x max(sase3 pulses) 
@@ -592,7 +592,32 @@ def getTIMapd(data, mcp=1, use_apd=True, intstart=None, intstop=None,
                        t_offset=t_offset, npulses=npulses)
         return tim
     
+    #1. case where number of SASE 3 pulses were not changed during the run:
     sa3 = data['sase3'].where(data['sase3']>1, drop=True)
+    sa3 -= sa3[0,0]
+    idx = np.unique(sa3, axis=0)
+    npulses_sa3 = data['npulses_sase3']
+    maxpulses = int(npulses_sa3.max().values)
+    if npulses is not None:
+        maxpulses = np.min([npulses, maxpulses])
+    if len(idx)==1:
+        if use_apd:
+            apd = data['MCP{}apd'.format(mcp)]
+            initialDelay = data.attrs['run'].get_array(
+                            'SCS_UTC1_ADQ/ADC/1', 'board1.apd.channel_0.initialDelay.value')[0].values
+            upperLimit = data.attrs['run'].get_array(
+                            'SCS_UTC1_ADQ/ADC/1', 'board1.apd.channel_0.upperLimit.value')[0].values
+            period = upperLimit - initialDelay #period of the apd in number of digitizer samples
+            idx /= int(period/440) #440 samples correspond to the separation between two pulses at 4.5 MHz
+            if len(idx)==1:
+                idx = idx[0].astype(int)
+                tim = apd.isel(apdId=idx)
+                return tim
+        else:
+            apd = mcpPeaks(data, intstart, intstop, bkgstart, bkgstop, mcp=mcp, 
+                           t_offset=t_offset, npulses=maxpulses)
+    
+    #2. case where the number of SASE 3 pulses varied during the run:
     npulses_sa3 = data['npulses_sase3']
     maxpulses = int(npulses_sa3.max().values)
     if npulses is not None: