From 3327d7d890e4db397452acfcbca717abea382a89 Mon Sep 17 00:00:00 2001
From: Artur Glavic <artur.glavic@psi.ch>
Date: Mon, 24 Aug 2026 11:26:27 +0200
Subject: [PATCH] Add correction of pulse times from packet times if no chopper
 or monitor triggers exist

---
 eos/__main__.py               |  3 ++-
 eos/event_handling.py         |  2 +-
 eos/file_reader.py            | 18 +++++++++++++++++-
 eos/options.py                |  8 ++++++++
 eos/reduction_reflectivity.py |  3 +++
 5 files changed, 31 insertions(+), 3 deletions(-)

diff --git a/eos/__main__.py b/eos/__main__.py
index c3fff27..5eefbfe 100644
--- a/eos/__main__.py
+++ b/eos/__main__.py
@@ -8,6 +8,7 @@ Author: Jochen Stahn (algorithms, python draft),
 import logging
 
 # need to do absolute import here as pyinstaller requires it
+from eos import __version__
 from eos.options import ReflectivityConfig, ReaderConfig, ExperimentConfig, ReflectivityReductionConfig, ReflectivityOutputConfig
 from eos.command_line import commandLineArgs
 from eos.logconfig import setup_logging, update_loglevel, setup_logfile
@@ -29,7 +30,7 @@ def main():
 
     if output_config.logFile:
         setup_logfile()
-    logging.warning('######## eos - data reduction for Amor ########')
+    logging.warning(f'######## eos ({__version__}) - data reduction for Amor ########')
 
     # only import heavy module if sufficient command line parameters were provided
     from eos.reduction_reflectivity import ReflectivityReduction
diff --git a/eos/event_handling.py b/eos/event_handling.py
index bcd42c8..76169f4 100644
--- a/eos/event_handling.py
+++ b/eos/event_handling.py
@@ -184,7 +184,7 @@ class ApplyMask(EventDataAction):
             # only run this calculation if debug level is actually active
             filtered_by_mask = {}
             for key, value in EVENT_BITMASKS.items():
-                filtered_by_mask[key] = ((d.events.mask & value)!=0).sum()
+                filtered_by_mask[key] = int(((d.events.mask & value)!=0).sum())
             logging.debug(f"        Removed by filters: {filtered_by_mask}")
         if self.bitmask_filter is None:
             d.events = d.events[d.events.mask==0]
diff --git a/eos/file_reader.py b/eos/file_reader.py
index 5871d6a..1678d75 100644
--- a/eos/file_reader.py
+++ b/eos/file_reader.py
@@ -379,6 +379,7 @@ class AmorEventData(AmorHeader):
     data: AmorEventStream
 
     eventStartTime: np.int64
+    correctTimeFallback:bool = True
 
     def __init__(self, fileName:Union[str, h5py.File, BinaryIO], first_index:int=0, max_events:int=100_000_000):
         if type(fileName) is str:
@@ -523,8 +524,23 @@ class AmorEventData(AmorHeader):
             logging.critical('      No chopper trigger data available, using first monitor time!')
             startTime = np.array(self._beam_monitor.time[0], dtype=np.int64)
             pulseTimeS = self._beam_monitor.time
+        elif self.correctTimeFallback:
+            logging.critical(
+                '      No chopper trigger data or monitor time available, using event stearm and packet times instead!')
+            data_group = self.hdf[self.hdf_paths['data'][0]]
+            startTime = np.array(data_group['event_time_zero'][0], dtype=np.int64)
+            stopTime = np.array(data_group['event_time_zero'][-1], dtype=np.int64)
+            pulseTimeS = np.arange(startTime, stopTime, self.timing.tau*1e9, dtype=np.int64)
+            # find times that are closest to the next packet time and correct them to fit exactly
+            all_times = np.unique(packets.time)
+            all_times.sort()
+            tauhalf = self.timing.tau*5e8
+            for ti in all_times:
+                idx = np.where((pulseTimeS+tauhalf)>=ti)[0][0]
+                # to keep approximate tau spacing, correct all times after the current packet
+                pulseTimeS[idx:] -= (pulseTimeS[idx]-ti)
         else:
-            logging.critical('      No chopper trigger data available, using event steram instead, pulse filtering will fail!')
+            logging.critical('      No chopper trigger data or monitor time available, using event steram instead, pulse filtering will fail!')
             data_group = self.hdf[self.hdf_paths['data'][0]]
             startTime = np.array(data_group['event_time_zero'][0], dtype=np.int64)
             stopTime = np.array(data_group['event_time_zero'][-2], dtype=np.int64)
diff --git a/eos/options.py b/eos/options.py
index 7e9bd46..5a9aebd 100644
--- a/eos/options.py
+++ b/eos/options.py
@@ -490,6 +490,14 @@ class ReflectivityReductionConfig(ArgParsable):
                 },
             )
 
+    correctTimeFallback: bool = field(
+            default=True,
+            metadata={
+                'group': 'data manicure',
+                'help':  'if falleng back to event stream for pulse time estimation, correct exact values '
+                         'to recover filtering options (slower)',
+                },
+            )
 
 class OutputFomatOption(StrEnum):
     Rqz_ort = "Rqz.ort"
diff --git a/eos/reduction_reflectivity.py b/eos/reduction_reflectivity.py
index 72c9a2f..484fff8 100644
--- a/eos/reduction_reflectivity.py
+++ b/eos/reduction_reflectivity.py
@@ -82,6 +82,9 @@ class ReflectivityReduction:
 
         self.grid = LZGrid(self.config.reduction.qResolution, self.config.reduction.qzRange)
 
+        # transfer option to data reader
+        AmorEventData.correctTimeFallback = self.config.reduction.correctTimeFallback
+
     def reduce(self):
         if not os.path.exists(f'{self.config.output.outputPath}'):
             logging.debug(f'Creating destination path {self.config.output.outputPath}')