Background subtraction for IPM data

data.py

@@ -150,8 +150,8 @@ class IPMData(Trace):
     hf: np.ndarray = None
     
     
-    def apply_calibration(self, time_range):
-        """Calibrates the profile data by subtracting the average profile measured in the given timespan
+    def subtract_background(self, time_range):
+        """Subtract the average profile measured in the given timespan
         
         Note that this does not affect rms beam sizes
         
@@ -162,13 +162,16 @@ class IPMData(Trace):
         self.y -= np.mean(self.y[window], axis=0)
     
     
+    
+    
     @classmethod
-    def from_file(cls, fname, clean=False, from_event=None, time_offset=0, verbose=0):
+    def from_file(cls, fname, *, clean=False, subtract_background=True, from_event=None, time_offset=0, verbose=0):
         """Read in profile data from a *.tgz file saved with IPM application
            
         :param fname: path to filename
-        :param clean: use adc_clean.dat instead of adc.dat
-        :param from_event: return data from this event, time will also be relative to this event
+        :param clean: if True, use calibrated data from adc_clean.dat instead of raw data from adc.dat
+        :param from_event: return data from this event on, time will also be relative to this event
+        :param subtract_background: if True, subtract background level prior to injection
         
         References: 
             Giacomini, Tino <T.Giacomini@gsi.de>
@@ -209,6 +212,15 @@ class IPMData(Trace):
         scl = np.loadtxt(tar.extractfile('scl.dat'), skiprows=1)
         index, beam_current, dipole, hf, event_40, event_45, event_51, event_user = scl.T
         
+        # background subtraction
+        if subtract_background:
+            assert np.max(event_40) == 1, f'Requested background subtraction prior to injection (event 40), but event 40 not found in data'
+            nbg = np.argmax(event_40) - 3  # before injection
+            x -= np.mean(x[:nbg, :], axis=0)
+            y -= np.mean(y[:nbg, :], axis=0)
+            if verbose: print(f'Background subtracted (first {nbg} profiles or {t[nbg]} s)')
+        
+        # offset relative to from_event
         offset = 0
         if from_event is None:
             offset = 0