Merge pull request #151 from DUNE/revert-150-develop-w-noise-filter

Revert "add noise filter features to develop. Code from feature-noise-filter …"

src/proto_nd_flow/reco/charge/calib_prompt_hits.py

@@ -56,12 +56,10 @@ class CalibHitBuilder(H5FlowStage):
             x              f8, pixel x location [cm]
             y              f8, pixel y location [cm]
             z              f8, pixel z location [cm]
-            t_drift        u8, drift time [ticks???]
-            ts_pps         f8, PPS packet timestamp [ns]
+            t_drift        u8, drift time [tick = 100ns]
+            ts_pps         f8, PPS packet timestamp [tick = 100ns]
             io_group       u8, io group ID (PACMAN number)
             io_channel     u8, io channel ID (related to PACMAN number & PACMAN UART Number)
-            chip_id        u8, chip_id on tile 
-            channel_id     u8, channel_id on single chip (0-63)
             Q              f8, hit charge [ke-]
             E              f8, hit energy [MeV]
 
@@ -88,8 +86,6 @@ class CalibHitBuilder(H5FlowStage):
         ('ts_pps', 'u8'),
         ('io_group', 'u8'),
         ('io_channel', 'u8'),
-        ('chip_id', 'u8'),
-        ('channel_id', 'u8'),
         ('Q', 'f8'),
         ('E', 'f8')
     ])
@@ -106,6 +102,11 @@ def __init__(self, **params):
         self.t0_dset_name = params.get('t0_dset_name')
         self.pedestal_file = params.get('pedestal_file', '')
         self.configuration_file = params.get('configuration_file', '')
+        self.pedestal_mv = params.get('pedestal_mv', 580.0)
+        self.vref_mv = params.get('vref_mv', 1568.0)
+        self.vcm_mv = params.get('vcm_mv', 478.1)
+        self.adc_counts = params.get('adc_counts', 256)
+        self.gain = params.get('gain', 4.522)
 
     def init(self, source_name):
         super(CalibHitBuilder, self).init(source_name)
@@ -120,6 +121,7 @@ def run(self, source_name, source_slice, cache):
         if resources['RunData'].is_mc:
             packet_frac_bt = cache['packet_frac_backtrack']
             packet_seg_bt = cache['packet_seg_backtrack']
+
         t0_data = cache[self.t0_dset_name]
         raw_hits = cache[self.raw_hits_dset_name]
 
@@ -215,12 +217,19 @@ def run(self, source_name, source_slice, cache):
                             + packets_arr['chip_id'].astype(int)*100
                             + packets_arr['channel_id'].astype(int))
             hit_uniqueid_str = hit_uniqueid.astype(str)
-            vref = np.array(
-                [self.configuration[unique_id]['vref_mv'] for unique_id in hit_uniqueid_str])
-            vcm = np.array([self.configuration[unique_id]['vcm_mv']
-                            for unique_id in hit_uniqueid_str])
-            ped = np.array([self.pedestal[unique_id]['pedestal_mv']
-                            for unique_id in hit_uniqueid_str])
+            if self.configuration_file != '':
+                vref = np.array(
+                    [self.configuration[unique_id]['vref_mv'] for unique_id in hit_uniqueid_str])
+                vcm = np.array([self.configuration[unique_id]['vcm_mv']
+                                for unique_id in hit_uniqueid_str])
+            else:
+                vref = np.full(len(hit_uniqueid_str), self.vref_mv)
+                vcm = np.full(len(hit_uniqueid_str), self.vcm_mv)
+            if self.pedestal_file != '':
+                ped = np.array([self.pedestal[unique_id]['pedestal_mv']
+                                for unique_id in hit_uniqueid_str])
+            else:
+                ped = np.full(len(hit_uniqueid_str), self.pedestal_mv)
             calib_hits_arr['id'] = calib_hits_slice.start + np.arange(n, dtype=int)
             calib_hits_arr['x'] = x
             if has_mc_truth:
@@ -231,14 +240,12 @@ def run(self, source_name, source_slice, cache):
             calib_hits_arr['t_drift'] = drift_t
             calib_hits_arr['io_group'] = packets_arr['io_group']
             calib_hits_arr['io_channel'] = packets_arr['io_channel']
-            calib_hits_arr['chip_id'] = packets_arr['chip_id']
-            calib_hits_arr['channel_id'] = packets_arr['channel_id']
-            hits_charge = self.charge_from_dataword(packets_arr['dataword'],vref,vcm,ped) # ke-
+            hits_charge = self.charge_from_dataword(packets_arr['dataword'], vref, vcm, ped, self.adc_counts, self.gain) # ke-
             calib_hits_arr['Q'] = hits_charge # ke-
             #FIXME supply more realistic dEdx in the recombination; also apply measured electron lifetime
             calib_hits_arr['E'] = hits_charge * (1000 * units.e) / resources['LArData'].ionization_recombination(mode=2,dEdx=2) * (resources['LArData'].ionization_w / units.MeV) # MeV
             if has_mc_truth:
-                true_recomb = resources['LArData'].ionization_recombination(mode=1,dEdx=packet_seg_bt_arr['dEdx'])
+                true_recomb = resources['LArData'].ionization_recombination(mode=2,dEdx=packet_seg_bt_arr['dEdx'])
                 calib_hits_arr['E_true_recomb_elife'] = np.divide(hits_charge.reshape((hits_charge.shape[0],1)) * (1000 * units.e), true_recomb, out=np.zeros_like(true_recomb), where=true_recomb!=0) / resources['LArData'].charge_reduction_lifetime(t_drift=drift_t_true) * (resources['LArData'].ionization_w / units.MeV) # MeV
 
         # if back tracking information was available, write the merged back tracking
@@ -272,8 +279,8 @@ def run(self, source_name, source_slice, cache):
 
 
     @staticmethod
-    def charge_from_dataword(dw, vref, vcm, ped):
-        return (dw / 256. * (vref - vcm) + vcm - ped) / 4. # hardcoding 4 mV/ke- conv.
+    def charge_from_dataword(dw, vref, vcm, ped, adc_counts, gain):
+        return (dw / adc_counts * (vref - vcm) + vcm - ped) / gain
 
     def load_pedestals(self):
         if self.pedestal_file != '' and not resources['RunData'].is_mc: