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 1/3] 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"

From 87a246196f007b1d93a1f0057ffc71e0eba17dee Mon Sep 17 00:00:00 2001
From: Artur Glavic <artur.glavic@psi.ch>
Date: Tue, 28 Jan 2025 16:02:54 +0100
Subject: [PATCH 2/3] apply scaling factor when time slicing

---
 libeos/reduction.py | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/libeos/reduction.py b/libeos/reduction.py
index 6456a1c..717d86e 100644
--- a/libeos/reduction.py
+++ b/libeos/reduction.py
@@ -199,6 +199,12 @@ class AmorReduction:
 
             qz_lz, qx_lz, ref_lz, err_lz, res_lz, lamda_lz, theta_lz, int_lz, mask_lz = self.project_on_lz(
                     self.file_reader, self.norm_lz, self.normAngle, lamda_e, detZ_e)
+            try:
+                ref_lz *= self.reduction_config.scale[i]
+                err_lz *= self.reduction_config.scale[i]
+            except IndexError:
+                ref_lz *= self.reduction_config.scale[-1]
+                err_lz *= self.reduction_config.scale[-1]
             q_q, R_q, dR_q, dq_q = self.project_on_qz(qz_lz, ref_lz, err_lz, res_lz, self.norm_lz, mask_lz)
 
             filter_q = np.where((self.experiment_config.qzRange[0]<q_q) & (q_q<self.experiment_config.qzRange[1]),

From 96681c8f815161fae79095ba0596e5a0bfcd76e6 Mon Sep 17 00:00:00 2001
From: Artur Glavic <artur.glavic@psi.ch>
Date: Tue, 28 Jan 2025 16:17:48 +0100
Subject: [PATCH 3/3] fix case where there is no pulse missing

---
 libeos/file_reader.py | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/libeos/file_reader.py b/libeos/file_reader.py
index d336b41..351678d 100644
--- a/libeos/file_reader.py
+++ b/libeos/file_reader.py
@@ -252,6 +252,10 @@ class AmorData:
         pulseExtra = (pulseLengths-np.int64(self.tau*1e9))//np.int64(self.tau*2e9)
         gap_indices = np.where(pulseExtra>0)[0]
 
+        if len(gap_indices)==0:
+            # no missing pulses, just use given array
+            self.pulseTimeS = np.array(pulseTime, dtype=np.int64)
+            return
         self.pulseTimeS = np.array(pulseTime[:gap_indices[0]+1], dtype=np.int64)
         last_index = gap_indices[0]
         for gapi in gap_indices[1:]: