From 3607de986422db592ce7ce9b95fa8c97fe791d94 Mon Sep 17 00:00:00 2001
From: Artur Glavic <artur.glavic@psi.ch>
Date: Tue, 28 Jan 2025 16:00:52 +0100
Subject: [PATCH] replace pulseTimeS generation in for loop by filling of pulse
 gaps

---
 libeos/file_reader.py | 23 ++++++++++++++++-------
 libeos/reduction.py   |  4 ++--
 2 files changed, 18 insertions(+), 9 deletions(-)

diff --git a/libeos/file_reader.py b/libeos/file_reader.py
index 0ff259e..d336b41 100644
--- a/libeos/file_reader.py
+++ b/libeos/file_reader.py
@@ -236,7 +236,6 @@ class AmorData:
 
         # fill in missing pulse times 
         # TODO: check for real end time
-        self.pulseTimeS = np.array([], dtype=np.int64)
         try:
             # further files
             # TODO: use the first pulse of the respective measurement
@@ -247,12 +246,22 @@ class AmorData:
             # first file
             nextPulseTime = pulseTime[0] % np.int64(self.tau*2e9)
 
-        for tt in pulseTime:
-            while tt - nextPulseTime > self.tau*1e9:
-                self.pulseTimeS = np.append(self.pulseTimeS, nextPulseTime)
-                nextPulseTime += chopperPeriod
-            self.pulseTimeS = np.append(self.pulseTimeS, tt)
-            nextPulseTime = self.pulseTimeS[-1] + chopperPeriod
+        # calculate where time tiefference between pulses exceeds its time by more than 1/2
+        # this yields the number of missing pulses
+        pulseLengths = pulseTime[1:]-pulseTime[:-1]
+        pulseExtra = (pulseLengths-np.int64(self.tau*1e9))//np.int64(self.tau*2e9)
+        gap_indices = np.where(pulseExtra>0)[0]
+
+        self.pulseTimeS = np.array(pulseTime[:gap_indices[0]+1], dtype=np.int64)
+        last_index = gap_indices[0]
+        for gapi in gap_indices[1:]:
+            # insert missing pulses into each gap
+            gap_pulses = pulseTime[last_index]+np.arange(1, pulseExtra[last_index]+1)*chopperPeriod
+            self.pulseTimeS = np.append(self.pulseTimeS, gap_pulses)
+            self.pulseTimeS = np.append(self.pulseTimeS, pulseTime[last_index+1:gapi+1])
+            last_index = gapi
+        if last_index<len(pulseTime):
+            self.pulseTimeS = np.append(self.pulseTimeS, pulseTime[last_index:-1])
 
     def get_current_per_pulse(self, pulseTimeS, currentTimeS, currents):
         # add currents for early pulses and current time value after last pulse (j+1)
diff --git a/libeos/reduction.py b/libeos/reduction.py
index bc00d49..6456a1c 100644
--- a/libeos/reduction.py
+++ b/libeos/reduction.py
@@ -178,11 +178,11 @@ class AmorReduction:
         interval = self.reduction_config.timeSlize[0]
         try:
             start = self.reduction_config.timeSlize[1]
-        except:
+        except IndexError:
             start = 0
         try:
             stop = self.reduction_config.timeSlize[2]
-        except:
+        except IndexError:
             stop = wallTime_e[-1]
         # make overwriting log lines possible by removing newline at the end
         #logging.StreamHandler.terminator = "\r"