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 +51,32 @@ jobs:
         user: __token__
         password: ${{ secrets.PYPI_TOKEN }}
         skip-existing: true
+
+  build-windows:
+    runs-on: windows-latest
+    if: ${{ (github.event_name != 'workflow_dispatch') || (contains(fromJson('["all", "windows"]'), github.event.inputs.build-items)) }}
+
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python
+      uses: actions/setup-python@v5
+      with:
+        python-version: 3.12
+    - name: Install dependencies
+      run: |
+        C:\Miniconda\condabin\conda.bat env update --file conda_windows.yml --name base
+        C:\Miniconda\condabin\conda.bat init powershell
+    - name: Build with pyinstaller
+      run: |
+        pyinstaller windows_folder.spec
+        cd dist\eos
+        Compress-Archive -Path .\* -Destination ..\..\eos.zip
     - name: Archive distribution
       uses: actions/upload-artifact@v4
       with:
-        name: linux-dist
+        name: windows-dist
         path: |
-          dist/*.tar.gz
+          eos.zip
 
   release:
     if: github.event_name != 'workflow_dispatch'
@@ -61,8 +87,11 @@ jobs:
     - uses: actions/download-artifact@v4
       with:
         name: linux-dist
+    - uses: actions/download-artifact@v4
+      with:
+        name: windows-dist
     - uses: ncipollo/release-action@v1
       with:
-        artifacts: "amor*.tar.gz"
+        artifacts: "amor*.tar.gz,*.zip"
         token: ${{ secrets.GITHUB_TOKEN }}
         allowUpdates: true

.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

README.md

@@ -1,12 +0,0 @@
-Software repository for the neutron reflectometer Amor at the Paul Scherrer Institut, Switzerland
-
-reduction of the raw files (.hdf) to reflectivity files in one of the representations of the **ORSO reflectivity file format**:
-
-> `eos.py`  
-> `neos.py` : version for playing and testing
-
-visualisation of the content of a raw file (.hdf):
-
-> `events2histogram.py`
-
-#TODO: real readme for final system needed.

README.rst

@@ -0,0 +1,27 @@
+EOS - The AMOR focusing reflectometry data reduction software
+-------------------------------------------------------------
+
+.. image:: https://img.shields.io/pypi/v/amor-eos.svg
+        :target: https://pypi.python.org/pypi/amor-eos/
+
+
+Software repository for the neutron reflectometer Amor at the Paul Scherrer Institut, Switzerland
+
+Reduction of the raw files (.hdf) to reflectivity files in one of the representations of the **ORSO reflectivity file format**:
+
+  eos.py --help
+
+visualisation of the content of a raw file (.hdf):
+
+  events2histogram.py
+
+:TODO: real readme for final system needed.
+
+Installation
+------------
+Create a virtual python environment (>3.8) and install the PyPI package:
+
+  pip install amor-eos
+
+On Windows you can also use the binary eos.exe that you find in the 
+[GitHub Releases]([https://github.com/jochenstahn/amor/releases/latest) section

conda_windows.yml

@@ -0,0 +1,43 @@
+name: eos_build
+channels:
+  - defaults
+dependencies:
+  - altgraph=0.17.3=py312haa95532_0
+  - blas=1.0=mkl
+  - bzip2=1.0.8=h2bbff1b_6
+  - ca-certificates=2024.11.26=haa95532_0
+  - expat=2.6.3=h5da7b33_0
+  - h5py=3.12.1=py312h3b2c811_0
+  - hdf5=1.12.1=h51c971a_3
+  - icc_rt=2022.1.0=h6049295_2
+  - intel-openmp=2023.1.0=h59b6b97_46320
+  - libffi=3.4.4=hd77b12b_1
+  - llvmlite=0.43.0=py312hf2fb9eb_0
+  - mkl=2023.1.0=h6b88ed4_46358
+  - mkl-service=2.4.0=py312h2bbff1b_1
+  - mkl_fft=1.3.11=py312h827c3e9_0
+  - mkl_random=1.2.8=py312h0158946_0
+  - numba=0.60.0=py312h0158946_0
+  - numpy=1.26.4=py312hfd52020_0
+  - numpy-base=1.26.4=py312h4dde369_0
+  - openssl=3.0.15=h827c3e9_0
+  - packaging=24.1=py312haa95532_0
+  - pefile=2023.2.7=py312haa95532_0
+  - pip=24.2=py312haa95532_0
+  - pyinstaller=6.9.0=py312h0416ee5_0
+  - pyinstaller-hooks-contrib=2024.7=py312haa95532_0
+  - python=3.12.7=h14ffc60_0
+  - pywin32-ctypes=0.2.2=py312haa95532_0
+  - setuptools=75.1.0=py312haa95532_0
+  - sqlite=3.45.3=h2bbff1b_0
+  - tbb=2021.8.0=h59b6b97_0
+  - tk=8.6.14=h0416ee5_0
+  - tzdata=2024b=h04d1e81_0
+  - vc=14.40=h2eaa2aa_1
+  - vs2015_runtime=14.40.33807=h98bb1dd_1
+  - wheel=0.44.0=py312haa95532_0
+  - xz=5.4.6=h8cc25b3_1
+  - zlib=1.2.13=h8cc25b3_1
+  - pip:
+      - orsopy==1.2.1
+      - pyyaml==6.0.2

libeos/__init__.py

@@ -2,5 +2,5 @@
 Package to handle data redction at AMOR instrument to be used by eos.py script.
 """
 
-__version__ = '2.1.1'
-__date__    = '2024-10-30'
+__version__ = '2.1.3'
+__date__    = '2024-12-13'

libeos/file_reader.py

@@ -2,7 +2,12 @@ import logging
 import os
 import subprocess
 import sys
-from datetime import datetime
+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
@@ -20,18 +25,8 @@ try:
 except Exception:
     nb_helpers = None
 
-def get_current_per_pulse(pulseTimeS, currentTimeS, currents):
-    # add currents for early pulses and current time value after last pulse (j+1)
-    currentTimeS = np.hstack([[0], currentTimeS, [pulseTimeS[-1]+1]])
-    currents = np.hstack([[0], currents])
-    pulseCurrentS = np.zeros(pulseTimeS.shape[0], dtype=float)
-    j = 0
-    for i, ti in enumerate(pulseTimeS):
-        if ti >= currentTimeS[j+1]: 
-            j += 1
-        pulseCurrentS[i] = currents[j]
-        #print(f' {i}  {pulseTimeS[i]}  {pulseCurrentS[i]}') 
-    return pulseCurrentS
+# 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"""
@@ -196,6 +191,10 @@ class AmorData:
 
         self.read_event_stream()
         totalNumber = np.shape(self.tof_e)[0]
+        # check for empty event stream
+        if totalNumber == 0:
+             logging.error('empty event stream: can not determine end time')
+             sys.exit()
 
         self.sort_pulses()
 
@@ -204,11 +203,11 @@ class AmorData:
         self.extract_walltime(norm)
 
         # following lines: debugging output to trace the time-offset of proton current and neutron pulses
-        if self.config.monitorType == 'p':
+        if self.config.monitorType == 'x':
             cpp, t_bins = np.histogram(self.wallTime_e, self.pulseTimeS)
             np.savetxt('tme.hst', np.vstack((self.pulseTimeS[:-1], cpp, self.monitorPerPulse[:-1])).T)
 
-        self.average_events_per_pulse()
+        #self.average_events_per_pulse() # for debugging only. VERY time consuming!!!
 
         self.monitor_threshold()
 
@@ -233,25 +232,46 @@ class AmorData:
 
         pulseTime -= np.int64(self.seriesStartTime)
         self.stopTime = pulseTime[-1]
+        pulseTime = pulseTime[pulseTime>=0]
 
         # fill in missing pulse times 
         # TODO: check for real end time
-        pulseTime = pulseTime[pulseTime>=0]
-        firstPulse = pulseTime[0] % np.int64(self.tau*2e9)
         self.pulseTimeS = np.array([], dtype=np.int64)
-        nxt = firstPulse
+        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 = pulseTime[0]
+        except AttributeError:
+            # first file
+            nextPulseTime = pulseTime[0] % np.int64(self.tau*2e9)
+
         for tt in pulseTime:
-            while tt - nxt > self.tau*1e9:
-                self.pulseTimeS = np.append(self.pulseTimeS, nxt)
-                nxt += chopperPeriod
+            while tt - nextPulseTime > self.tau*1e9:
+                self.pulseTimeS = np.append(self.pulseTimeS, nextPulseTime)
+                nextPulseTime += chopperPeriod
             self.pulseTimeS = np.append(self.pulseTimeS, tt)
-            nxt = self.pulseTimeS[-1] + chopperPeriod
+            nextPulseTime = self.pulseTimeS[-1] + chopperPeriod
+
+    def get_current_per_pulse(self, pulseTimeS, currentTimeS, currents):
+        # add currents for early pulses and current time value after last pulse (j+1)
+        currentTimeS = np.hstack([[0], currentTimeS, [pulseTimeS[-1]+1]])
+        currents = np.hstack([[0], currents])
+        pulseCurrentS = np.zeros(pulseTimeS.shape[0], dtype=float)
+        j = 0
+        for i, ti in enumerate(pulseTimeS):
+            if ti >= currentTimeS[j+1]: 
+                j += 1
+            pulseCurrentS[i] = currents[j]
+            #print(f' {i}  {pulseTimeS[i]}  {pulseCurrentS[i]}') 
+        return pulseCurrentS
 
     def associate_pulse_with_monitor(self):
         if self.config.monitorType == 'p': # protonCharge
             self.currentTime -= np.int64(self.seriesStartTime)
             self.currentTime -= np.int64(16e9) # time offset of proton current signal
-            self.monitorPerPulse = get_current_per_pulse(self.pulseTimeS, self.currentTime, self.current) * 2*self.tau * 1e-3
+            self.monitorPerPulse = self.get_current_per_pulse(self.pulseTimeS, self.currentTime, self.current) * 2*self.tau * 1e-3
             # filter low-current pulses
             self.monitorPerPulse = np.where(self.monitorPerPulse > 2*self.tau * self.config.lowCurrentThreshold * 1e-3, self.monitorPerPulse, 0)
         elif self.config.monitorType == 't': # countingTime
@@ -274,7 +294,7 @@ class AmorData:
         if self.config.monitorType == 'p':
             for i, time in enumerate(self.pulseTimeS):
                 events = np.shape(self.wallTime_e[self.wallTime_e == time])[0]
-                #print(f' {i:6.0f} {events:6.0f} {self.monitorPerPulse[i]:6.2f}')
+                logging.info(f'pulse: {i:6.0f}, events: {events:6.0f}, monitor: {self.monitorPerPulse[i]:6.2f}')
 
     def monitor_threshold(self):
         if self.config.monitorType == 'p': # fix to check for file compatibility
@@ -361,7 +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
@@ -424,8 +444,10 @@ class AmorData:
         if self.config.nu:
             self.nu = self.config.nu
 
-        self.fileDate = datetime.fromisoformat( self.hdf['/entry1/start_time'][0].decode('utf-8') )
-        self.startTime = np.int64( self.fileDate.timestamp() * 1e9 )
+        # extract start time as unix time, adding UTC offset of 1h to time string
+        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
@@ -388,7 +392,11 @@ class AmorReduction:
         mask_lz   = np.where(np.isnan(norm_lz), False, True)
         mask_lz   = np.logical_and(mask_lz, np.where(np.absolute(thetaN_lz)>5e-3, True, False))
         mask_lz   = np.logical_and(mask_lz, np.where(np.absolute(alphaF_lz)>5e-3, True, False))
-        if self.reduction_config.thetaRange[1]<12:
+        if self.reduction_config.thetaRangeR[1]<12:
+          t0 = fromHDF.nu - fromHDF.mu
+          mask_lz   = np.logical_and(mask_lz, np.where(alphaF_lz-t0 >= self.reduction_config.thetaRangeR[0], True, False))
+          mask_lz   = np.logical_and(mask_lz, np.where(alphaF_lz-t0 <= self.reduction_config.thetaRangeR[1], True, False))
+        elif self.reduction_config.thetaRange[1]<12:
           mask_lz   = np.logical_and(mask_lz, np.where(alphaF_lz >= self.reduction_config.thetaRange[0], True, False))
           mask_lz   = np.logical_and(mask_lz, np.where(alphaF_lz <= self.reduction_config.thetaRange[1], True, False))
         else:
@@ -396,10 +404,6 @@ class AmorReduction:
                                               fromHDF.nu - fromHDF.mu + fromHDF.div/2]
           mask_lz   = np.logical_and(mask_lz, np.where(alphaF_lz >= self.reduction_config.thetaRange[0], True, False))
           mask_lz   = np.logical_and(mask_lz, np.where(alphaF_lz <= self.reduction_config.thetaRange[1], True, False))
-        if self.reduction_config.thetaRangeR[1]<12:
-          t0 = fromHDF.nu - fromHDF.mu
-          mask_lz   = np.logical_and(mask_lz, np.where(alphaF_lz-t0 >= self.reduction_config.thetaRangeR[0], True, False))
-          mask_lz   = np.logical_and(mask_lz, np.where(alphaF_lz-t0 <= self.reduction_config.thetaRangeR[1], True, False))
         if self.experiment_config.lambdaRange[1]<15:
           mask_lz   = np.logical_and(mask_lz, np.where(lamda_lz >= self.experiment_config.lambdaRange[0], True, False))
           mask_lz   = np.logical_and(mask_lz, np.where(lamda_lz <= self.experiment_config.lambdaRange[1], True, False))
@@ -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%)

setup.cfg

@@ -7,6 +7,7 @@ version = attr: libeos.__version__
 author = Jochen Stahn - Paul Scherrer Institut
 author_email = jochen.stahn@psi.ch
 description = EOS reflectometry reduction for AMOR instrument
+long_description = Reduces data obtained by focusing time of flight neutron reflectivity to full reflectivity curve.
 license = MIT
 classifiers =
     Programming Language :: Python :: 3

windows_build.spec

@@ -12,7 +12,7 @@ a = Analysis(
     runtime_hooks=[],
     excludes=[],
     noarchive=False,
-    optimize=0,
+    optimize=1,
 )
 pyz = PYZ(a.pure)
 

windows_folder.spec

@@ -0,0 +1,44 @@
+# -*- mode: python ; coding: utf-8 -*-
+
+
+a = Analysis(
+    ['eos.py'],
+    pathex=[],
+    binaries=[],
+    datas=[],
+    hiddenimports=[],
+    hookspath=[],
+    hooksconfig={},
+    runtime_hooks=[],
+    excludes=[],
+    noarchive=False,
+    optimize=1,
+)
+pyz = PYZ(a.pure)
+
+exe = EXE(
+    pyz,
+    a.scripts,
+    [],
+    exclude_binaries=True,
+    name='eos',
+    debug=False,
+    bootloader_ignore_signals=False,
+    strip=False,
+    upx=True,
+    console=True,
+    disable_windowed_traceback=False,
+    argv_emulation=False,
+    target_arch=None,
+    codesign_identity=None,
+    entitlements_file=None,
+)
+coll = COLLECT(
+    exe,
+    a.binaries,
+    a.datas,
+    strip=False,
+    upx=True,
+    upx_exclude=[],
+    name='eos',
+)