update revision info

Handle timezone correctly

.github/workflows/release.yml

@@ -38,6 +38,12 @@ jobs:
     - name: Build PyPI package
       run: |
         python3 -m build
+    - name: Archive distribution
+      uses: actions/upload-artifact@v4
+      with:
+        name: linux-dist
+        path: |
+          dist/*.tar.gz
     - name: Upload to PyPI
       if: github.event_name != 'workflow_dispatch'
       uses: pypa/gh-action-pypi-publish@release/v1
@@ -45,12 +51,6 @@ jobs:
         user: __token__
         password: ${{ secrets.PYPI_TOKEN }}
         skip-existing: true
-    - name: Archive distribution
-      uses: actions/upload-artifact@v4
-      with:
-        name: linux-dist
-        path: |
-          dist/*.tar.gz
 
   build-windows:
     runs-on: windows-latest

.github/workflows/unit_tests.yml

@@ -15,7 +15,7 @@ jobs:
     runs-on: ubuntu-22.04
     strategy:
       matrix:
-        python-version: [3.8, 3.9, '3.10', '3.11', '3.12']
+        python-version: ['3.8', '3.9', '3.10', '3.11', '3.12']
       fail-fast: false
 
     steps:
@@ -31,6 +31,11 @@ jobs:
           pip install pytest
           pip install -r requirements.txt
 
+      - name: Backport to 3.8
+        if: matrix.python-version == '3.8'
+        run: |
+          pip install backports.zoneinfo
+
       - name: Test with pytest
         run: |
           cd tests

libeos/__init__.py

@@ -2,5 +2,5 @@
 Package to handle data redction at AMOR instrument to be used by eos.py script.
 """
 
-__version__ = '2.1.2'
-__date__    = '2024-12-03'
+__version__ = '2.1.3'
+__date__    = '2024-12-13'

libeos/file_reader.py

@@ -3,6 +3,11 @@ import os
 import subprocess
 import sys
 from datetime import datetime, timezone
+try:
+    import zoneinfo
+except ImportError:
+    # for python versions < 3.9 try to use the backports version
+    from backports import zoneinfo
 from typing import List
 
 import h5py
@@ -20,6 +25,9 @@ try:
 except Exception:
     nb_helpers = None
 
+# Time zone used to interpret time strings
+AMOR_LOCAL_TIMEZONE = zoneinfo.ZoneInfo(key='Europe/Zurich')
+
 class AmorData:
     """read meta-data and event streams from .hdf file(s), apply filters and conversions"""
     chopperDetectorDistance: float
@@ -228,13 +236,17 @@ 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
             #nextPulseTime = startTime % np.int64(self.tau*2e9)
-            nextPulseTime = self.pulseTimeS[-1] + chopperPeriod
+            #nextPulseTime = self.pulseTimeS[-1] + chopperPeriod
+            nextPulseTime = pulseTime[0]
         except AttributeError:
+            # first file
             nextPulseTime = pulseTime[0] % np.int64(self.tau*2e9)
-            self.pulseTimeS = np.array([], dtype=np.int64)
+
         for tt in pulseTime:
             while tt - nextPulseTime > self.tau*1e9:
                 self.pulseTimeS = np.append(self.pulseTimeS, nextPulseTime)
@@ -369,7 +381,7 @@ class AmorData:
         self.pixelID_e = self.pixelID_e[filter_e]
         self.wallTime_e = self.wallTime_e[filter_e]
         if np.shape(filter_e)[0]-np.shape(self.tof_e)[0]>0.5:
-            logging.warning(f'#    strange times: {np.shape(filter_e)[0]-np.shape(self.tof_e)[0]}')
+            logging.warning(f'        strange times: {np.shape(filter_e)[0]-np.shape(self.tof_e)[0]}')
 
     def read_event_stream(self):
         self.tof_e = np.array(self.hdf['/entry1/Amor/detector/data/event_time_offset'][:])/1.e9
@@ -433,7 +445,8 @@ class AmorData:
             self.nu = self.config.nu
 
         # extract start time as unix time, adding UTC offset of 1h to time string
-        self.fileDate = datetime.fromisoformat( self.hdf['/entry1/start_time'][0].decode('utf-8')+"+01:00" )
+        dz = datetime.fromisoformat(self.hdf['/entry1/start_time'][0].decode('utf-8'))
+        self.fileDate=dz.replace(tzinfo=AMOR_LOCAL_TIMEZONE)
         self.startTime = np.int64( (self.fileDate.timestamp() ) * 1e9 )
         if self.seriesStartTime is None:
             self.seriesStartTime = self.startTime 

libeos/reduction.py

@@ -372,11 +372,15 @@ class AmorReduction:
         # projection on lambda-z-grid
         lamda_l  = self.grid.lamda()
         alphaF_z  = fromHDF.nu - fromHDF.mu + fromHDF.delta_z
+        # TODO: implement various methods to obtain alpha_i.
         #if self.experiment_config.incidentAngle == 'alphaF':
+        #  # for specular reflectometry with a highly divergent beam
         #  alphaF_z  = fromHDF.nu - fromHDF.mu + fromHDF.delta_z
         #elif self.experiment_config.incidentAngle == 'nu':
+        #  # for specular reflectometry, using kappa nad nu but ignoring mu
         #  alphaF_z  = (fromHDF.nu + fromHDF.delta_z + fromHDF.kap + fromHDF.kad) / 2.
         #else:
+        #  # using kappa, for a collimated incoming beam
         #  pass
         lamda_lz  = (self.grid.lz().T*lamda_l[:-1]).T
         alphaF_lz = self.grid.lz()*alphaF_z
@@ -438,7 +442,7 @@ class AmorReduction:
         if self.monitor > 1e-6 :
             ref_lz   *= self.normMonitor / self.monitor
         else:
-            logging.warning('   too small monitor value for normalisation -> ignoring monitors')
+            logging.info('       too small monitor value for normalisation -> ignoring monitors')
         err_lz    = ref_lz * np.sqrt( 1/(int_lz+.1) + 1/norm_lz ) 
 
         # TODO: allow for non-ideal Delta lambda / lambda (rather than 2.2%)