Add unittest for frame splitting action

Reviewed-on: #3

.github/workflows/merge_PR.yml

@@ -0,0 +1,17 @@
+name: Pull Request Merged
+on:
+  pull_request:
+    types: [closed]
+
+jobs:
+  autoupdate_minor:
+    if: github.event.pull_request.merged == true
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+    - uses: actions/setup-python@v5
+      with:
+        python-version: '3.13'
+    - name: Perform PR auto-action
+      run: |
+          python PR_merged.py

.github/workflows/release.yml

@@ -22,7 +22,59 @@ on:
           - all_incl_release
 
 jobs:
+  test:
+
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ['3.8', '3.9', '3.10', '3.11', '3.12']
+      fail-fast: true
+
+    steps:
+      - name: Checkout LFS objects
+        run: git clone https://${{secrets.GITHUB_TOKEN}}@gitea.psi.ch/${{ github.repository }}.git .
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install pytest
+          pip install -r requirements.txt
+
+      - name: Test with pytest
+        run: |
+          export PYTEST_DISABLE_PLUGIN_AUTOLOAD=1
+          python -m pytest tests
+  
+  release:
+    if:  ${{ (github.event_name != 'workflow_dispatch') || (contains(fromJson('["all_incl_release"]'), github.event.inputs.build-items)) }}
+    runs-on: ubuntu-latest
+    needs: [test]
+    steps:
+    - uses: actions/checkout@v4
+    - name: get latest version tag and release note
+      run: |
+        git fetch --depth=500
+        this_tag=$(python -c "import eos;print('v'+eos.__version__)")
+        prev_tag=$(git describe --abbrev=0 --tags `git rev-list --tags --skip=1  --max-count=1`)
+        echo "Relese tag $this_tag with changes since $prev_tag"
+        echo "Changes:
+        " > git_changes.log
+        git log $prev_tag..HEAD --pretty=format:"* %s" >> git_changes.log
+        cat git_changes.log
+        echo "RELEASE_TAG=$this_tag" >> $GITHUB_ENV
+    - name: Create Release
+      uses: actions/gitea-release-action@v1
+      with:
+        name: "Amor-Eos ${{ env.RELEASE_TAG }}"
+        tag_name: "${{ env.RELEASE_TAG }}"
+        body_path: git_changes.log
+
   build-ubuntu-latest:
+    needs: [test]
     runs-on: ubuntu-latest
     if: ${{ (github.event_name != 'workflow_dispatch') || (contains(fromJson('["all", "linux", "all_incl_release"]'), github.event.inputs.build-items)) }}
     permissions:
@@ -31,75 +83,55 @@ jobs:
     - uses: actions/checkout@v4
     - uses: actions/setup-python@v5
       with:
-        python-version: '3.11'
+        python-version: '3.12'
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
         pip install build
         pip install -r requirements.txt
+        pip install wheel build twine
     - 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
-      with:
-      #  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", "all_incl_release"]'), 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
+        twine upload dist/* -u __token__ -p ${{ secrets.PYPI_TOKEN }} --skip-existing
-        C:\Miniconda\condabin\conda.bat init powershell
+        this_tag=$(python -c "import eos;print('v'+eos.__version__)")
-    - name: Build with pyinstaller
+        echo "RELEASE_TAG=$this_tag" >> $GITHUB_ENV
-      run: |
+    - name: Update Release
-        pyinstaller windows_build.spec
+      if:  ${{ (github.event_name != 'workflow_dispatch') || (contains(fromJson('["all_incl_release"]'), github.event.inputs.build-items)) }}
-        cd dist\eos
+      uses: actions/gitea-release-action@v1
-        Compress-Archive -Path .\* -Destination ..\..\eos.zip
-    - name: Archive distribution
-      uses: actions/upload-artifact@v4
       with:
-        name: windows-dist
+        name: "Amor-Eos ${{ env.RELEASE_TAG }}"
-        path: |
+        tag_name: "${{ env.RELEASE_TAG }}"
-          eos.zip
+        files: |-
+          dist/amor*.tar.gz
 
-  release:
+#  build-windows:
-    if:  ${{ (github.event_name != 'workflow_dispatch') || (contains(fromJson('["all_incl_release"]'), github.event.inputs.build-items)) }}
+#    needs: [test]
-    runs-on: ubuntu-latest
+#    runs-on: windows-latest
-    needs: [build-ubuntu-latest, build-windows]
+#    if: ${{ (github.event_name != 'workflow_dispatch') || (contains(fromJson('["all", "windows", "all_incl_release"]'), github.event.inputs.build-items)) }}
-    steps:
+#
-    - uses: actions/checkout@v4
+#    steps:
-      with:
+#    - uses: actions/checkout@v4
-        fetch-depth: 0
+#    - name: Set up Python
-        fetch-tags: true
+#      uses: actions/setup-python@v5
-    - uses: actions/download-artifact@v4
+#      with:
-      with:
+#        python-version: 3.12
-        name: linux-dist
+#    - name: Install dependencies
-    - uses: actions/download-artifact@v4
+#      run: |
-      with:
+#        C:\Miniconda\condabin\conda.bat env update --file conda_windows.yml --name base
-        name: windows-dist
+#        C:\Miniconda\condabin\conda.bat init powershell
-    - name: get latest version tag
+#    - name: Build with pyinstaller
-      run: echo "RELEASE_TAG=$(git describe --abbrev=0 --tags)" >> $GITHUB_ENV
+#      run: |
-    - uses: ncipollo/release-action@v1
+#        pyinstaller windows_build.spec
-      with:
+#        cd dist\eos
-        artifacts: "amor*.tar.gz,*.zip"
+#        Compress-Archive -Path .\* -Destination ..\..\eos.zip
-        token: ${{ secrets.GITHUB_TOKEN }}
+#    - name: Update Release
-        allowUpdates: true
+#      if:  ${{ (github.event_name != 'workflow_dispatch') || (contains(fromJson('["all_incl_release"]'), github.event.inputs.build-items)) }}
-        tag: ${{ env.RELEASE_TAG }}
+#      uses: actions/gitea-release-action@v1
+#      with:
+#        name: "Amor-Eos ${{ env.RELEASE_TAG }}"
+#        tag_name: "${{ env.RELEASE_TAG }}"
+#        files: |-
+#          eos.zip

.github/workflows/unit_tests.yml

@@ -10,18 +10,18 @@ on:
   workflow_dispatch:
 
 jobs:
-  build:
+  test:
 
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-latest
     strategy:
       matrix:
         python-version: ['3.8', '3.9', '3.10', '3.11', '3.12']
       fail-fast: false
 
     steps:
-      - uses: actions/checkout@v4
+      - name: Checkout LFS objects
-        with:
+        run: git clone https://${{secrets.GITHUB_TOKEN}}@gitea.psi.ch/${{ github.repository }}.git .
-            lfs: 'true'
+
       - name: Set up Python ${{ matrix.python-version }}
         uses: actions/setup-python@v5
         with:
@@ -35,4 +35,5 @@ jobs:
 
       - name: Test with pytest
         run: |
+          export PYTEST_DISABLE_PLUGIN_AUTOLOAD=1
           python -m pytest tests

PR_merged.py

@@ -0,0 +1,30 @@
+"""
+Actions performed automatically on pull request merged. Update changed date and minor revision number.
+"""
+
+import os
+from eos import __version__
+from datetime import datetime
+
+INIT_HEADER = '''"""
+Package to handle data redction at AMOR instrument to be used by __main__.py script.
+"""
+
+'''
+
+def main():
+    print("Running PR_merged.py")
+    print(f"  Previous version: {__version__}")
+    version = __version__.split('.')
+    version[2] = str(int(version[2])+1)
+    version = '.'.join(version)
+    print(f"  New version: {version}")
+    now=datetime.now()
+    with open(os.path.join('eos','__init__.py'), 'w') as f:
+        f.write(INIT_HEADER)
+        f.write(f"__version__ = '{version}'\n")
+        f.write(f"__date__    = '{now.strftime('%Y-%m-%d')}'\n")
+
+
+if __name__ == '__main__':
+    main()

eos/__init__.py

@@ -2,5 +2,5 @@
 Package to handle data redction at AMOR instrument to be used by __main__.py script.
 """
 
-__version__ = '3.1.0'
+__version__ = '3.2.4'
-__date__    = '2026-02-20'
+__date__    = '2026-03-02'

eos/command_line.py

@@ -4,7 +4,7 @@ from typing import List, Type
 from .options import ArgParsable
 
 
-def commandLineArgs(config_items: List[Type[ArgParsable]], program_name=None):
+def commandLineArgs(config_items: List[Type[ArgParsable]], program_name=None, extra_args=[]):
     """
     Process command line argument.
     The type of the default values is used for conversion and validation.
@@ -36,4 +36,7 @@ def commandLineArgs(config_items: List[Type[ArgParsable]], program_name=None):
                     f'--{cpc.argument}', **cpc.add_argument_args
                     )
 
+    for ma in extra_args:
+        clas.add_argument(**ma)
+
     return clas.parse_args()

eos/const.py

@@ -5,3 +5,7 @@ Constants used in data reduction.
 hdm = 6.626176e-34/1.674928e-27  # h / m
 lamdaCut = 2.5  # Aa
 lamdaMax = 15.0 # Aa
+
+polarizationConfigs = ['unpolarized', 'unpolarized', 'po', 'mo', 'op', 'pp', 'mp', 'om', 'pm', 'mm']
+polarizationLabels = ['undetermined', 'unpolarized', 'spin-up', 'spin-down', 'op',
+                      'up-up', 'down-up', 'om', 'up-down', 'down-down']

eos/event_analysis.py

@@ -9,7 +9,7 @@ from typing import Tuple
 
 from . import const
 from .event_data_types import EventDataAction, EventDatasetProtocol, append_fields, EVENT_BITMASKS
-from .helpers import filter_project_x, merge_frames, extract_walltime
+from .helpers import filter_project_x, merge_frames, extract_walltime, add_log_to_pulses, merge_frames_w_index
 from .instrument import Detector
 from .options import IncidentAngle
 from .header import Header
@@ -25,8 +25,9 @@ class ExtractWalltime(EventDataAction):
         dataset.data.events = new_events
 
 class MergeFrames(EventDataAction):
-    def __init__(self, lamdaCut=None):
+    def __init__(self, lamdaCut=None, preciseTime=False):
         self.lamdaCut=lamdaCut
+        self.preciseTime=preciseTime
 
     def perform_action(self, dataset: EventDatasetProtocol)->None:
         if self.lamdaCut is None:
@@ -36,7 +37,34 @@ class MergeFrames(EventDataAction):
         tofCut = lamdaCut*dataset.geometry.chopperDetectorDistance/const.hdm*1e-13
         total_offset = (tofCut +
                         dataset.timing.tau * (dataset.timing.ch1TriggerPhase + dataset.timing.chopperPhase/2)/180)
-        dataset.data.events.tof = merge_frames(dataset.data.events.tof, tofCut, dataset.timing.tau, total_offset)
+        if self.preciseTime and 'wallTime' in dataset.data.events.dtype.names:
+            d = dataset.data
+            # put events into precise sub-frame
+            d.events.tof, subframes = merge_frames_w_index(d.events.tof, tofCut, dataset.timing.tau, total_offset)
+            subframes = subframes.astype(int)
+            # add a sub-pulse time 1-tau before and after each existing time
+            utimes, uidxs = np.unique(d.events.wallTime, return_inverse=True)
+            inter_times = np.empty(2*utimes.shape[0]+1, dtype=d.events.wallTime.dtype)
+            tauns = dataset.timing.tau*1e9
+            inter_times[0] = utimes[0]-tauns
+            inter_times[1::2] = utimes
+            inter_times[2::2] = utimes+tauns
+            # use subframe indices to sort existing events into new times
+            d.events.wallTime = inter_times[2*uidxs+subframes+1]
+            # expand pulses array with additional sub-frames
+            new_pulses = np.recarray(2*d.pulses.shape[0]+1, dtype=d.pulses.dtype)
+            new_pulses[0] = d.pulses[0]
+            new_pulses[1::2] = d.pulses
+            new_pulses[2::2] = d.pulses
+            new_pulses.time[0] = d.pulses.time[0]-tauns
+            new_pulses.time[2::2] = d.pulses.time+tauns
+            new_pulses.monitor /= 2.0 # ~preserve total monitor counts
+            d.pulses = new_pulses
+        else:
+            if self.preciseTime:
+                logging.error("    Trying to use precise time frame separation while wallTime is not extracted, yet!")
+            dataset.data.events.tof = merge_frames(dataset.data.events.tof, tofCut, dataset.timing.tau, total_offset)
+
 
 
 class AnalyzePixelIDs(EventDataAction):
@@ -124,5 +152,40 @@ class FilterQzRange(EventDataAction):
         if not 'qz' in dataset.data.events.dtype.names:
             raise ValueError("FilterQzRange requires dataset with qz values per events, perform WavelengthAndQ first")
 
-        if self.qzRange[1]<0.5:
+        d.events.mask += EVENT_BITMASKS["qRange"]*((self.qzRange[0]>d.events.qz) | (d.events.qz>self.qzRange[1]))
-            d.events.mask += EVENT_BITMASKS["qRange"]*((self.qzRange[0]>d.events.qz) | (d.events.qz>self.qzRange[1]))
+
+class FilterByLog(EventDataAction):
+
+    def __init__(self, filter_string, remove_switchpulse=False):
+        if filter_string.startswith('!'):
+            filter_string = filter_string[1:]
+            remove_switchpulse = True
+        self.filter_string = filter_string
+        self.remove_switchpulse = remove_switchpulse
+
+    def perform_action(self, dataset: EventDatasetProtocol) -> None:
+        filter_variable = None
+        # go through existing keys in reverse order of their length to insure a name containing another is used
+        existing_keys = list(dataset.data.device_logs.keys())
+        existing_keys.sort(key=lambda x: -len(x))
+        for key in existing_keys:
+            if key in self.filter_string:
+                filter_variable = key
+                break
+        if filter_variable is None:
+            logging.warning(f'          could not find suitable parameter to filter on in {self.filter_string}, '
+                            f'available parameters are: {list(sorted(existing_keys))}')
+            return
+        logging.debug(f'          using parameter {filter_variable} to apply filter {self.filter_string}')
+        if not filter_variable in EVENT_BITMASKS:
+            EVENT_BITMASKS[filter_variable] = max(EVENT_BITMASKS.values())*2
+        if not filter_variable in dataset.data.pulses.dtype.names:
+            # interpolate the parameter values for all existing pulses
+            add_log_to_pulses(filter_variable, dataset)
+        fltr_pulses = eval(self.filter_string, {filter_variable: dataset.data.pulses[filter_variable]})
+        if self.remove_switchpulse:
+            switched = fltr_pulses[:-1] & ~fltr_pulses[1:]
+            fltr_pulses[:-1] &= ~switched
+        goodTimeS = dataset.data.pulses.time[fltr_pulses]
+        filter_e = np.logical_not(np.isin(dataset.data.events.wallTime, goodTimeS))
+        dataset.data.events.mask += EVENT_BITMASKS[filter_variable]*filter_e

eos/event_data_types.py

@@ -1,8 +1,8 @@
 """
 Specify the data type and protocol used for event datasets.
 """
-from typing import List, Optional, Protocol, Tuple
+from typing import Dict, List, Optional, Protocol, Tuple
-from dataclasses import dataclass
+from dataclasses import dataclass, field
 from .header import Header
 from abc import ABC, abstractmethod
 from hashlib import sha256
@@ -34,6 +34,7 @@ EVENT_TYPE = np.dtype([('tof', np.float64), ('pixelID', np.uint32), ('mask', np.
 PACKET_TYPE = np.dtype([('start_index', np.uint32), ('time', np.int64)])
 PULSE_TYPE = np.dtype([('time', np.int64), ('monitor', np.float32)])
 PC_TYPE = np.dtype([('current', np.float32), ('time', np.int64)])
+LOG_TYPE = np.dtype([('value', np.float32), ('time', np.int64)])
 
 # define the bitmask for individual event filters
 EVENT_BITMASKS = {
@@ -45,6 +46,8 @@ EVENT_BITMASKS = {
     }
 
 def append_fields(input: np.recarray, new_fields: List[Tuple[str, np.dtype]]):
+    # TODO: This action is used often and time consuming as it runs len(flds) times over all indices.
+    #       Could only be faster if array is allocated in the beginning with all fields, less flexible.
     # add one ore more fields to a recarray, numpy functions seems to fail
     flds = [(name, dtypei[0]) for name, dtypei in input.dtype.fields.items()]
     flds += new_fields
@@ -60,6 +63,7 @@ class AmorEventStream:
     packets: np.recarray # PACKET_TYPE
     pulses: np.recarray  # PULSE_TYPE
     proton_current: np.recarray # PC_TYPE
+    device_logs: Dict[str, np.recarray] = field(default_factory=dict) # LOG_TYPE
 
 class EventDatasetProtocol(Protocol):
     """

eos/event_handling.py

@@ -48,7 +48,7 @@ class ApplyParameterOverwrites(EventDataAction):
                     with open(self.config.sampleModel, 'r') as model_yml:
                         model = yaml.safe_load(model_yml)
                 else:
-                    logging.warning(f'  ! the file {self.config.sampleModel}.yml does not exist. Ignored!')
+                    logging.warning(f'  ! the file {self.config.sampleModel} does not exist. Ignored!')
                     return
             else:
                 model = dict(stack=self.config.sampleModel)
@@ -71,6 +71,8 @@ class CorrectSeriesTime(EventDataAction):
         dataset.data.pulses.time -= self.seriesStartTime
         dataset.data.events.wallTime -= self.seriesStartTime
         dataset.data.proton_current.time -= self.seriesStartTime
+        for value in dataset.data.device_logs.values():
+            value.time -= self.seriesStartTime
         start, stop = dataset.data.events.wallTime[0], dataset.data.events.wallTime[-1]
         logging.debug(f'      wall time from {start/1e9:6.1f} s to {stop/1e9:6.1f} s, '
                       f'series time = {self.seriesStartTime/1e9:6.1f}')
@@ -163,10 +165,12 @@ class ApplyMask(EventDataAction):
         self.bitmask_filter = bitmask_filter
 
     def perform_action(self, dataset: EventDatasetProtocol) ->None:
-        # TODO: why is this action time consuming?
+        # TODO: Most time in test examples is spend here.
+        #       While the actions here are very simple, they act on a large array,
+        #       so even just comparison and indexing become time consuming.
         d = dataset.data
         pre_filter = d.events.shape[0]
-        if logging.getLogger().level == logging.DEBUG:
+        if logging.getLogger().level <= logging.DEBUG:
             # only run this calculation if debug level is actually active
             filtered_by_mask = {}
             for key, value in EVENT_BITMASKS.items():
@@ -181,3 +185,20 @@ class ApplyMask(EventDataAction):
             d.events = d.events[fltr]
         post_filter = d.events.shape[0]
         logging.info(f'      number of events: total = {pre_filter:7d}, filtered = {post_filter:7d}')
+        if d.device_logs == {} or not hasattr(dataset, 'update_info_from_logs'):
+            return
+        # filter pulses and logs to allow update of header information
+        from .helpers import add_log_to_pulses
+        times = np.unique(d.events.wallTime)
+        # make sure all log variables are associated with pulses
+        for key, log in d.device_logs.items():
+            if not key in d.pulses.dtype.names:
+                # interpolate the parameter values for all existing pulses
+                add_log_to_pulses(key, dataset)
+        # remove all pulses that have no more events
+        d.pulses = d.pulses[np.isin(d.pulses.time, times)]
+        for key, log in d.device_logs.items():
+            d.device_logs[key] = np.recarray(d.pulses.shape, dtype = log.dtype)
+            d.device_logs[key].time = d.pulses.time
+            d.device_logs[key].value = d.pulses[key]
+        dataset.update_info_from_logs()

eos/file_reader.py

@@ -3,9 +3,9 @@ Reading of Amor NeXus data files to extract metadata and event stream.
 """
 from typing import BinaryIO, List, Union
 
+import sys
 import h5py
 import numpy as np
-import platform
 import logging
 import subprocess
 
@@ -16,7 +16,8 @@ from orsopy.fileio.model_language import SampleModel
 
 from . import const
 from .header import Header
-from .event_data_types import AmorGeometry, AmorTiming, AmorEventStream, PACKET_TYPE, EVENT_TYPE, PULSE_TYPE, PC_TYPE
+from .event_data_types import AmorGeometry, AmorTiming, AmorEventStream, LOG_TYPE, PACKET_TYPE, EVENT_TYPE, PULSE_TYPE, \
+    PC_TYPE
 
 try:
     import zoneinfo
@@ -27,17 +28,41 @@ except ImportError:
 
 # Time zone used to interpret time strings
 AMOR_LOCAL_TIMEZONE = zoneinfo.ZoneInfo(key='Europe/Zurich')
-
+UTC = zoneinfo.ZoneInfo(key='UTC')
-if  platform.node().startswith('amor'):
-    NICOS_CACHE_DIR = '/home/data/nicosdata/cache/'
-    GREP = '/usr/bin/grep "value"'
-else:
-    NICOS_CACHE_DIR = None
 
 class AmorHeader:
     """
     Collects header information from Amor NeXus fiel without reading event data.
     """
+    # mapping of names to (hdf_path, dtype, nicos_key[, suffix])
+    hdf_paths = dict(
+            title=('entry1/title', str),
+            proposal_id=('entry1/proposal_id', str),
+            user_name=('entry1/user/name', str),
+            user_email=('entry1/user/email', str),
+            sample_name=('entry1/sample/name', str),
+            source_name=('entry1/Amor/source/name', str),
+            sample_model=('entry1/sample/model', str),
+            start_time=('entry1/start_time', str),
+            start_time_fallback=('entry1/Amor/instrument_control_parameters/start_time', str),
+
+            chopper_separation=('entry1/Amor/chopper/pair_separation', float),
+            detector_distance=('entry1/Amor/detector/transformation/distance', float),
+            chopper_distance=('entry1/Amor/chopper/distance', float),
+            sample_temperature=('entry1/sample/temperature', float),
+            sample_magnetic_field=('entry1/sample/magnetic_field', float),
+
+            mu=('entry1/Amor/instrument_control_parameters/mu', float, 'mu'),
+            nu=('entry1/Amor/instrument_control_parameters/nu', float, 'nu'),
+            kap=('entry1/Amor/instrument_control_parameters/kappa', float, 'kappa'),
+            kad=('entry1/Amor/instrument_control_parameters/kappa_offset', float, 'kappa_offset'),
+            div=('entry1/Amor/instrument_control_parameters/div', float, 'div'),
+            ch1_trigger_phase=('entry1/Amor/chopper/ch1_trigger_phase', float, 'ch1_trigger_phase'),
+            ch2_trigger_phase=('entry1/Amor/chopper/ch2_trigger_phase', float, 'ch2_trigger_phase'),
+            chopper_speed=('entry1/Amor/chopper/rotation_speed', float, 'chopper_phase'),
+            chopper_phase=('entry1/Amor/chopper/phase', float, 'chopper_phase'),
+            polarization_config_label=('entry1/Amor/polarization/configuration', int, 'polarization_config_label', '/*'),
+            )
 
     def __init__(self, fileName:Union[str, h5py.File, BinaryIO]):
         if type(fileName) is str:
@@ -48,6 +73,8 @@ class AmorHeader:
         else:
             self.hdf = h5py.File(fileName, 'r')
 
+        self._log_keys = []
+
         self.read_header_info()
         self.read_instrument_configuration()
 
@@ -57,52 +84,89 @@ class AmorHeader:
         del(self.hdf)
 
     def _replace_if_missing(self, key, nicos_key, dtype=float, suffix=''):
-        try:
+        from .nicos_interface import lookup_nicos_value
-            return dtype(self.hdf[f'/entry1/Amor/{key}'][0])
+        year = self.fileDate.strftime('%Y')
-        except(KeyError, IndexError):
+        return lookup_nicos_value(key, nicos_key, dtype, suffix, year)
-            if NICOS_CACHE_DIR:
-                try:
-                    logging.info(f"     using parameter {nicos_key} from nicos cache")
-                    year_date = self.fileDate.strftime('%Y')
-                    call = f'{GREP} {NICOS_CACHE_DIR}nicos-{nicos_key}/{year_date}{suffix}'
-                    value = str(subprocess.getoutput(call)).split('\t')[-1]
-                    return dtype(value)
-                except Exception:
-                    logging.error(f"Couldn't get value from nicos cache {nicos_key}, {call}")
-                    return dtype(0)
-            else:
-                logging.warning(f"     parameter {key} not found, relpace by zero")
-                return dtype(0)
 
-     def get_hdf_single_entry(self, path):
+    def rv(self, key):
-         if not np.shape(self.hdf['entry1/title']):
+        """
+        Generic read value methos based on key in hdf_paths dictionary.
+        """
+        hdf_path, dtype, *nicos = self.hdf_paths[key]
+        try:
+            hdfgrp = self.hdf[hdf_path]
+            if hdfgrp.attrs.get('NX_class', None) == 'NXlog':
+                # use the last value that was recoreded before the count started
+                time_column = hdfgrp['time'][:]
+                try:
+                    start_index = np.where(time_column<=self._start_time_ns)[0][0]
+                except IndexError:
+                    start_index = 0
+                if hdfgrp['value'].ndim==1:
+                    output = dtype(hdfgrp['value'][start_index])
+                else:
+                    output = dtype(hdfgrp['value'][start_index, 0])
+                # make sure key is only appended if no exception was raised
+                self._log_keys.append(key)
+                return output
+            elif dtype is str:
+                return self.read_string(hdf_path)
+            else:
+                if len(hdfgrp.shape)==1:
+                    return dtype(hdfgrp[0])
+                else:
+                    return dtype(hdfgrp[()])
+        except (KeyError, IndexError):
+            if nicos:
+                nicos_key = nicos[0]
+                suffix = nicos[1] if len(nicos)>1 else ''
+                return self._replace_if_missing(key, nicos_key, dtype, suffix)
+            else:
+                raise
+
+
+    def read_string(self, path):
+        if not np.shape(self.hdf[path]):
             return self.hdf[path][()].decode('utf-8')
         else:
             # format until 2025
             return self.hdf[path][0].decode('utf-8')
 
     def read_header_info(self):
+        self._start_time_ns = np.uint64(0)
+        try:
+            start_time = self.rv('start_time')
+        except KeyError:
+            start_time = self.rv('start_time_fallback')
+
+        # extract start time as unix time, adding UTC offset of 1h to time string
+        if start_time.endswith('Z') and sys.version_info.minor<11:
+            # older python versions did not support Z format
+            start_time = start_time[:-1]
+            TZ = UTC
+        else:
+            TZ = AMOR_LOCAL_TIMEZONE
+        start_date = datetime.fromisoformat(start_time)
+        self.fileDate = start_date.replace(tzinfo=TZ)
+        self._start_time_ns = np.uint64(self.fileDate.timestamp()*1e9)
+
         # read general information and first data set
-        title = self.get_hdf_single_entry('entry1/title')
+        title = self.rv('title')
-        proposal_id = self.get_hdf_single_entry('entry1/proposal_id')
+        proposal_id = self.rv('proposal_id')
-        user_name = self.get_hdf_single_entry('entry1/user/name')
+        user_name = self.rv('user_name')
         user_affiliation = 'unknown'
-        user_email = self.get_hdf_single_entry('entry1/user/email')
+        user_email = self.rv('user_email')
         user_orcid = None
-        sampleName = self.get_hdf_single_entry('entry1/sample/name')
+        sampleName = self.rv('sample_name')
         instrumentName = 'Amor'
-        source = self.get_hdf_single_entry('entry1/Amor/source/name')
+        source = self.rv('source_name')
         sourceProbe = 'neutron'
-        model = self.get_hdf_single_entry('entry1/sample/model')
+        model = self.rv('sample_model')
         if 'stack' in model:
             import yaml
             model = yaml.safe_load(model)
         else:
             model = dict(stack=model)
-        start_time = self.get_hdf_single_entry('entry1/start_time')
-        # extract start time as unix time, adding UTC offset of 1h to time string
-        start_date = datetime.fromisoformat(start_time)
-        self.fileDate = start_date.replace(tzinfo=AMOR_LOCAL_TIMEZONE)
 
         self.owner = fileio.Person(
                 name=user_name,
@@ -130,28 +194,32 @@ class AmorHeader:
                 sample_parameters={},
                 )
         # while event times are not evaluated, use average_value reported in file for SEE
-        if self.hdf['entry1/sample'].get('temperature', None) is not None \
+        if self.hdf['entry1/sample'].get('temperature', None) is not None:
-            and float(self.hdf['entry1/sample/temperature/average_value'][0])>0:
+            try:
-            self.sample.sample_parameters['temperature'] = fileio.Value(
+                sample_temperature = self.rv('sample_temperature')
-                    float(self.hdf['entry1/sample/temperature/average_value'][0]), unit='K')
+            except IndexError: pass
+            else:
+                self.sample.sample_parameters['temperature'] = fileio.Value(sample_temperature, unit='K')
         if self.hdf['entry1/sample'].get('magnetic_field', None) is not None:
-            self.sample.sample_parameters['magnetic_field'] = fileio.Value(
+            try:
-                    float(self.hdf['entry1/sample/magnetic_field/average_value'][0]), unit='T')
+                sample_magnetic_field = self.rv('sample_magnetic_field')
+            except IndexError: pass
+            else:
+                self.sample.sample_parameters['magnetic_field'] = fileio.Value(sample_magnetic_field, unit='T')
 
     def read_instrument_configuration(self):
-        chopperSeparation = float(np.take(self.hdf['entry1/Amor/chopper/pair_separation'], 0))
+        chopperSeparation = self.rv('chopper_separation')
-        detectorDistance = float(np.take(self.hdf['entry1/Amor/detector/transformation/distance'], 0))
+        detectorDistance = self.rv('detector_distance')
-        chopperDetectorDistance = detectorDistance-float(np.take(self.hdf['entry1/Amor/chopper/distance'], 0))
+        chopperDistance = self.rv('chopper_distance')
+        chopperDetectorDistance = detectorDistance - chopperDistance
 
-        polarizationConfigs = ['unpolarized', 'unpolarized', 'po', 'mo', 'op', 'pp', 'mp', 'om', 'pm', 'mm']
+        mu = self.rv('mu')
-
+        nu = self.rv('nu')
-        mu = self._replace_if_missing('instrument_control_parameters/mu', 'mu', float)
+        kap = self.rv('kap')
-        nu = self._replace_if_missing('instrument_control_parameters/nu', 'nu', float)
+        kad = self.rv('kad')
-        kap = self._replace_if_missing('instrument_control_parameters/kappa', 'kappa', float)
+        div = self.rv('div')
-        kad = self._replace_if_missing('instrument_control_parameters/kappa_offset', 'kappa_offset', float)
+        ch1TriggerPhase = self.rv('ch1_trigger_phase')
-        div = self._replace_if_missing('instrument_control_parameters/div', 'div', float)
+        ch2TriggerPhase = self.rv('ch2_trigger_phase')
-        ch1TriggerPhase = self._replace_if_missing('chopper/ch1_trigger_phase', 'ch1_trigger_phase', float)
-        ch2TriggerPhase = self._replace_if_missing('chopper/ch2_trigger_phase', 'ch2_trigger_phase', float)
         try:
             chopperTriggerTime = (float(self.hdf['entry1/Amor/chopper/ch2_trigger/event_time_zero'][7]) \
                                   -float(self.hdf['entry1/Amor/chopper/ch2_trigger/event_time_zero'][0])) \
@@ -159,8 +227,8 @@ class AmorHeader:
             chopperTriggerTimeDiff = float(self.hdf['entry1/Amor/chopper/ch2_trigger/event_time_offset'][2])
         except (KeyError, IndexError):
             logging.debug('      chopper speed and phase taken from .hdf file')
-            chopperSpeed = self._replace_if_missing('chopper/rotation_speed', 'chopper_phase', float)
+            chopperSpeed = self.rv('chopper_speed')
-            chopperPhase = self._replace_if_missing('chopper/phase', 'chopper_phase', float)
+            chopperPhase = self.rv('chopper_phase')
             tau = 30/chopperSpeed
         else:
             tau = int(1e-6*chopperTriggerTime/2+0.5)*(1e-3)
@@ -172,8 +240,8 @@ class AmorHeader:
                                      chopperSeparation, detectorDistance, chopperDetectorDistance)
         self.timing = AmorTiming(ch1TriggerPhase, ch2TriggerPhase, chopperSpeed, chopperPhase, tau)
 
-        polarizationConfigLabel = self._replace_if_missing('polarization/configuration/average_value', 'polarization_config_label', int, suffix='/*')
+        polarizationConfigLabel = self.rv('polarization_config_label')
-        polarizationConfig = fileio.Polarization(polarizationConfigs[polarizationConfigLabel])
+        polarizationConfig = fileio.Polarization(const.polarizationConfigs[polarizationConfigLabel])
         logging.debug(f'      polarization configuration: {polarizationConfig} (index {polarizationConfigLabel})')
 
 
@@ -258,7 +326,13 @@ class AmorEventData(AmorHeader):
 
         super().__init__(hdf)
         self.hdf = hdf
-        self.read_event_stream()
+        try:
+            self.read_event_stream()
+        except EOFError:
+            self.hdf.close()
+            del(self.hdf)
+            raise
+        self.read_log_streams()
 
         if type(fileName) is str:
             # close the input file to free memory, only if the file was opened in this object
@@ -281,15 +355,26 @@ class AmorEventData(AmorHeader):
             raise EOFError(f'No event packet found starting at event #{self.first_index}, '
                            f'number of events is {self.hdf["/entry1/Amor/detector/data/event_time_offset"].shape[0]}')
         packets = packets[start_packet:]
+        if packets.shape[0]==0:
+            raise EOFError(f'No more packets left after start_packet filter')
 
         nevts = self.hdf['/entry1/Amor/detector/data/event_time_offset'].shape[0]
         if (nevts-self.first_index)>self.max_events:
             end_packet = np.where(packets.start_index<=(self.first_index+self.max_events))[0][-1]
-            self.last_index = packets.start_index[end_packet]-1
+            end_packet = max(1, end_packet)
+            if len(packets)==1:
+                self.last_index = nevts-1
+            else:
+                self.last_index = packets.start_index[end_packet]-1
             packets = packets[:end_packet]
         else:
             self.last_index = nevts-1
             self.EOF = True
+
+        if packets.shape[0]==0:
+            raise EOFError(f'No more packets left after end_packet filter, first_index={self.first_index}, '
+                           f'max_events={self.max_events}, nevts={nevts}')
+
         nevts = self.last_index+1-self.first_index
 
         # adapte packet to event index relation
@@ -308,6 +393,45 @@ class AmorEventData(AmorHeader):
             # label the file name if not all events were used
             self.file_list[0] += f'[{self.first_index}:{self.last_index}]'
 
+    def read_log_streams(self):
+        """
+        Read the individual NXlog datasets that can later be used for filtering etc.
+        """
+        for key in self._log_keys:
+            hdf_path, dtype, *_ = self.hdf_paths[key]
+            hdfgroup = self.hdf[hdf_path]
+            shape = hdfgroup['time'].shape
+            data = np.recarray(shape, dtype=np.dtype([('value', self.hdf_paths[key][1]), ('time', np.int64)]))
+            data.time = hdfgroup['time'][:]
+            if len(hdfgroup['value'].shape)==1:
+                data.value = hdfgroup['value'][:]
+            else:
+                data.value = hdfgroup['value'][:, 0]
+            self.data.device_logs[key] = data
+
+    def update_info_from_logs(self):
+        RELEVANT_ITEMS = ['sample_temperature', 'sample_magnetic_field', 'polarization_config_label']
+        for key, log in self.data.device_logs.items():
+            if key not in RELEVANT_ITEMS:
+                continue
+            if log.value.dtype in [np.int8, np.int16, np.int32, np.int64]:
+                # for integer items (flags) report the most common one
+                value = np.bincount(log.value).argmax()
+                if logging.getLogger().getEffectiveLevel() <= logging.DEBUG \
+                        and np.unique(log.value).shape[0]>1:
+                    logging.debug(f'        filtered values for {key} not unique, '
+                                  f'has {np.unique(log.value).shape[0]} values')
+            else:
+                value = log.value.mean()
+            if key == 'polarization_config_label':
+                self.instrument_settings.polarization = fileio.Polarization(const.polarizationConfigs[value])
+            elif key == 'sample_temperature':
+                self.sample.sample_parameters['temperature'].magnitue = value
+            elif key == 'sample_magnetic_field':
+                self.sample.sample_parameters['magnetic_field'].magnitue = value
+
+
+
     def read_chopper_trigger_stream(self, packets):
         chopper1TriggerTime = np.array(self.hdf['entry1/Amor/chopper/ch2_trigger/event_time_zero'][:-2], dtype=np.int64)
         #self.chopper2TriggerTime = self.chopper1TriggerTime + np.array(self.hdf['entry1/Amor/chopper/ch2_trigger/event_time'][:-2], dtype=np.int64)
@@ -316,7 +440,7 @@ class AmorEventData(AmorHeader):
             startTime = chopper1TriggerTime[0]
             pulseTimeS = chopper1TriggerTime
         else:
-            logging.warn('     no chopper trigger data available, using event steram instead')
+            logging.critical('     No chopper trigger data available, using event steram instead, pulse filtering will fail!')
             startTime = np.array(self.hdf['/entry1/Amor/detector/data/event_time_zero'][0], dtype=np.int64)
             stopTime = np.array(self.hdf['/entry1/Amor/detector/data/event_time_zero'][-2], dtype=np.int64)
             pulseTimeS = np.arange(startTime, stopTime, self.timing.tau*1e9, dtype=np.int64)
@@ -324,7 +448,7 @@ class AmorEventData(AmorHeader):
         pulses.time = pulseTimeS
         pulses.monitor = 1. # default is monitor pulses as it requires no calculation
         # apply filter in case the events were filtered
-        if self.first_index>0 or not self.EOF:
+        if (self.first_index>0 or not self.EOF):
             pulses = pulses[(pulses.time>=packets.time[0])&(pulses.time<=packets.time[-1])]
         self.eventStartTime = startTime
         return pulses
@@ -332,7 +456,11 @@ class AmorEventData(AmorHeader):
     def read_proton_current_stream(self, packets):
         proton_current = np.recarray(self.hdf['entry1/Amor/detector/proton_current/time'].shape, dtype=PC_TYPE)
         proton_current.time = self.hdf['entry1/Amor/detector/proton_current/time'][:]
-        proton_current.current = self.hdf['entry1/Amor/detector/proton_current/value'][:,0]
+        if self.hdf['entry1/Amor/detector/proton_current/value'].ndim==1:
+            proton_current.current = self.hdf['entry1/Amor/detector/proton_current/value'][:]
+        else:
+            proton_current.current = self.hdf['entry1/Amor/detector/proton_current/value'][:,0]
+
         if self.first_index>0 or not self.EOF:
             proton_current = proton_current[(proton_current.time>=packets.time[0])&
                                             (proton_current.time<=packets.time[-1])]

eos/helpers.py

@@ -2,9 +2,38 @@
 Helper functions used during calculations. Uses numba enhanced functions if available, otherwise numpy based
 fallback is imported.
 """
+import numpy as np
+from .event_data_types import EventDatasetProtocol, append_fields
 
 try:
-    from .helpers_numba import merge_frames, extract_walltime, filter_project_x, calculate_derived_properties_focussing
+    from .helpers_numba import merge_frames, extract_walltime, filter_project_x, \
+        calculate_derived_properties_focussing, merge_frames_w_index
 except ImportError:
-    from .helpers_fallback import merge_frames, extract_walltime, filter_project_x, calculate_derived_properties_focussing
+    import logging
+    logging.warning('Cannot import numba enhanced functions, is it installed?')
+    from .helpers_fallback import merge_frames, extract_walltime, filter_project_x, \
+        calculate_derived_properties_focussing, merge_frames_w_index
+
+def add_log_to_pulses(key, dataset: EventDatasetProtocol):
+    """
+    Add a log value for each pulse to the pulses array.
+    """
+    pulses = dataset.data.pulses
+    log_data = dataset.data.device_logs[key]
+    if log_data.time[0]>0:
+        logTimeS = np.hstack([[0], log_data.time, [pulses.time[-1]+1]])
+        logValues = np.hstack([[log_data.value[0]], log_data.value])
+    else:
+        logTimeS = np.hstack([log_data.time, [pulses.time[-1]+1]])
+        logValues = log_data.value
+    pulseLogS = np.zeros(pulses.time.shape[0], dtype=log_data.value.dtype)
+    j = 0
+    for i, ti in enumerate(pulses.time):
+        # find the last current item that was before this pulse
+        while ti>=logTimeS[j+1]:
+            j += 1
+        pulseLogS[i] = logValues[j]
+    pulses = append_fields(pulses, [(key, pulseLogS.dtype)])
+    pulses[key] = pulseLogS
+    dataset.data.pulses = pulses
 

eos/helpers_fallback.py

@@ -8,6 +8,17 @@ def merge_frames(tof_e, tofCut, tau, total_offset):
     # tof shifted to 1 frame
     return np.remainder(tof_e-(tofCut-tau), tau)+total_offset
 
+def merge_frames_w_index(tof_e, tofCut, tau, total_offset):
+    """
+    Version of merge frames that also returns a frame index for each pulse:
+    0  - belongs to the frame it was measured in
+    -1 - arrived in this frame but belongs to the previous neutron pulse
+    1  - belongs to the second neutron pulse of the original frame
+    """
+    new_tof = merge_frames(tof_e, tofCut, tau, total_offset)
+    frame_idx = np.floor_divide(tof_e-tofCut, tau)
+    return new_tof, frame_idx
+
 def extract_walltime(tof_e, dataPacket_p, dataPacketTime_p):
     output = np.empty(np.shape(tof_e)[0], dtype=np.int64)
     for i in range(len(dataPacket_p)-1):

eos/helpers_numba.py

@@ -11,6 +11,22 @@ def merge_frames(tof_e, tofCut, tau, total_offset):
         tof_e_out[ti] = ((tof_e[ti]-dt)%tau)+total_offset  # tof shifted to 1 frame
     return tof_e_out
 
+@nb.jit(nb.float64[:,:](nb.float64[:], nb.float64, nb.float64, nb.float64),
+        nopython=True, parallel=True, cache=True)
+def merge_frames_w_index(tof_e, tofCut, tau, total_offset):
+    """
+    Version of merge frames that also returns a frame index for each pulse:
+    0  - belongs to the frame it was measured in
+    -1 - arrived in this frame but belongs to the previous neutron pulse
+    1  - belongs to the second neutron pulse of the original frame
+    """
+    tof_idx_out = np.empty((2, tof_e.shape[0]), dtype=np.float64)
+    dt = (tofCut-tau)
+    for ti in nb.prange(tof_e.shape[0]):
+        tof_idx_out[0, ti] = ((tof_e[ti]-dt)%tau)+total_offset  # tof shifted to 1 frame
+        tof_idx_out[1, ti] = ((tof_e[ti]-tofCut) // tau)  # tof shifted to 1 frame
+    return tof_idx_out
+
 @nb.jit(nb.int64[:](nb.float64[:], nb.uint32[:], nb.int64[:]),
         nopython=True, parallel=True, cache=True)
 def extract_walltime(tof_e, dataPacket_p, dataPacketTime_p):

eos/kafka_serializer.py

@@ -160,7 +160,7 @@ class ESSSerializer:
                     )
             self.producer.flush()
             if isinstance(command, Stop):
-                if command.hist_id == self._active_histogram_yz:
+                if command.hist_id in [self._active_histogram_yz, self._active_histogram_tofz]:
                     self.count_stopped.set()
                 else:
                     return

eos/ls.py

@@ -0,0 +1,54 @@
+"""
+eosls executable script to list available datafiles in current folder with some metadata information.
+
+Author: Jochen Stahn (algorithms, python draft),
+        Artur Glavic (structuring and optimisation of code)
+"""
+import os
+import logging
+
+from eos.command_line import commandLineArgs
+
+def main():
+    logging.getLogger().setLevel(logging.CRITICAL)
+    clas = commandLineArgs([], 'eosls', extra_args=[
+        dict(dest='path', nargs='*', default=['.'], help='paths to list file in')])
+
+    from glob import glob
+    import tabulate
+    from eos.file_reader import AmorHeader
+
+    files = []
+    for path in clas.path:
+        files+=glob(os.path.join(path, 'amor*.hdf'))
+    files.sort()
+
+    data = {
+        'File name': [],
+        'Start Time': [],
+        'mu': [],
+        'nu': [],
+        'div': [],
+        'Sample': [],
+        'T [K]': [],
+        'H [T]': [],
+        }
+    for fi in files:
+        data['File name'].append(os.path.basename(fi))
+        ah = AmorHeader(fi)
+        data['Sample'].append(ah.sample.name)
+        data['Start Time'].append(ah.fileDate.strftime('%y %m-%d %H:%M:%S'))
+        data['mu'].append('%.3f' % ah.geometry.mu)
+        data['nu'].append('%.3f' % ah.geometry.nu)
+        data['div'].append('%.3f' % ah.geometry.div)
+
+        T = ah.sample.sample_parameters.get('temperature', None)
+        data['T [K]'].append(T.magnitude if T is not None else '-')
+
+        H = ah.sample.sample_parameters.get('magnetic_field', None)
+        data['H [T]'].append(H.magnitude if H is not None else '-')
+
+    print(tabulate.tabulate(data, headers="keys"))
+
+if __name__ == '__main__':
+    main()

eos/nicos.py

@@ -1,5 +1,5 @@
 """
-events2histogram vizualising data from Amor@SINQ, PSI
+amor-nicos vizualising data from Amor@SINQ, PSI
 
 Author: Jochen Stahn (algorithms, python draft),
         Artur Glavic (structuring and optimisation of code)

eos/nicos_interface.py

@@ -0,0 +1,60 @@
+"""
+Functions used to directly access information from nicos.
+"""
+
+import socket
+import platform
+import logging
+import subprocess
+
+ON_AMOR = platform.node().startswith('amor')
+NICOS_CACHE_DIR = '/home/data/nicosdata/cache/'
+GREP = '/usr/bin/grep "value"'
+
+
+def lookup_nicos_value(key, nicos_key, dtype=float, suffix='', year="2026"):
+    # TODO: Implement direct communication to nicos to read the cache
+    if nicos_key=='ignore':
+        return dtype(0)
+    try:
+        logging.debug(f'     trying socket request for device {nicos_key}')
+        response = nicos_single_request(nicos_key)
+        logging.info(f"     using parameter {nicos_key} from nicos cache via socket")
+        return dtype(response)
+    except Exception as e:
+        logging.debug(f'       socket request failed with {e!r}')
+    if ON_AMOR:
+        logging.debug(f"     trying to extract {nicos_key} from nicos cache files")
+        call = f'{GREP} {NICOS_CACHE_DIR}nicos-{nicos_key}/{year}{suffix}'
+        try:
+            value = str(subprocess.getoutput(call)).split('\t')[-1]
+            logging.info(f"     using parameter {nicos_key} from nicos cache file")
+            return dtype(value)
+        except Exception:
+            logging.error(f"       couldn't get value from nicos cache {nicos_key}, {call}")
+            return dtype(0)
+    else:
+        logging.warning(f"     parameter {key} not found, relpace by zero")
+        return dtype(0)
+
+def nicos_single_request(device):
+    sentinel = b'\n'
+    with socket.socket(socket.AF_INET, socket.SOCK_STREAM) as s:
+        s.settimeout(1.0)
+        s.connect(('amor', 14869))
+
+        tosend = f'@nicos/{device}/value?\n'
+
+        # write request
+        # self.log.debug("get_explicit: sending %r", tosend)
+        s.sendall(tosend.encode())
+
+        # read response
+        data = b''
+        while not data.endswith(sentinel):
+            newdata = s.recv(8192)  # blocking read
+            if not newdata:
+                raise IOError('cache closed connection')
+            data += newdata
+        s.shutdown(socket.SHUT_RDWR)
+    return data.decode('utf-8').split('=')[-1]

eos/options.py

@@ -471,6 +471,25 @@ class ReflectivityReductionConfig(ArgParsable):
                 },
             )
 
+    logfilter: List[str] = field(
+            default_factory=lambda: [],
+            metadata={
+                'short': 'lf',
+                'group': 'region of interest',
+                'help':  'filter using comparison to a log values, multpiple allowd (example "sample_temperature<150")',
+                },
+            )
+
+    preciseTiming: bool = field(
+            default=False,
+            metadata={
+                'short': 'pt',
+                'group': 'data manicure',
+                'help':  're-assign events to actual neutron pulses => '
+                         '2xbetter filter resolution but extra computation (experimental)',
+                },
+            )
+
 
 class OutputFomatOption(StrEnum):
     Rqz_ort = "Rqz.ort"
@@ -534,6 +553,14 @@ class ReflectivityOutputConfig(ArgParsable):
                 },
             )
 
+    append: bool = field(
+            default=False,
+            metadata={
+                'group': 'output',
+                'help': 'if file already exists, append result as additional ORSO dataset (only Rqz.ort)',
+                },
+            )
+
     def _output_format_list(self, outputFormat):
         format_list = []
         if OutputFomatOption.ort in outputFormat\

eos/projection.py

@@ -224,6 +224,7 @@ class LZProjection(ProjectionInterface):
         # do not perform gravity correction for footprint, would require norm detector distance that is unknown here
         fp_corr_lz = np.where(np.absolute(delta_lz+norm.angle)>5e-3,
                               (delta_lz+self.angle)/(delta_lz+norm.angle), np.nan)
+        fp_corr_lz[fp_corr_lz<0] = np.nan
         self.data.mask &=  np.logical_not(np.isnan(fp_corr_lz))
         self.data.norm = norm_lz*fp_corr_lz
         self.norm_monitor = norm.monitor

eos/reduction_e2h.py

@@ -268,7 +268,7 @@ class E2HReduction:
             return
         try:
             # check that events exist in the new file
-            AmorEventData(new_files[-1], 0, max_events=1000)
+            AmorEventData(new_files[-1], 0, max_events=1_000)
         except Exception:
             logging.debug("Problem when trying to load new dataset", exc_info=True)
             return

eos/reduction_reflectivity.py

@@ -5,6 +5,8 @@ import sys
 import numpy as np
 from orsopy import fileio
 
+from .event_analysis import FilterByLog
+from .event_handling import ApplyMask
 from .file_reader import AmorEventData
 from .header import Header
 from .path_handling import PathResolver
@@ -63,12 +65,15 @@ class ReflectivityReduction:
             # the filtering only makes sense if using actual monitor data, not time
             self.dataevent_actions |= eh.FilterMonitorThreshold(self.config.experiment.lowCurrentThreshold)
         self.dataevent_actions |= eh.FilterStrangeTimes()
-        self.dataevent_actions |= ea.MergeFrames()
+        self.dataevent_actions |= ea.MergeFrames(preciseTime=self.config.reduction.preciseTiming)
         self.dataevent_actions |= ea.AnalyzePixelIDs(self.config.experiment.yRange)
         self.dataevent_actions |= eh.TofTimeCorrection(self.config.experiment.incidentAngle==IncidentAngle.alphaF)
         self.dataevent_actions |= ea.CalculateWavelength(self.config.experiment.lambdaRange)
         self.dataevent_actions |= ea.CalculateQ(self.config.experiment.incidentAngle)
-        self.dataevent_actions |= ea.FilterQzRange(self.config.reduction.qzRange)
+        if not self.config.reduction.is_default('qzRange'):
+            self.dataevent_actions |= ea.FilterQzRange(self.config.reduction.qzRange)
+        for lf in self.config.reduction.logfilter:
+            self.dataevent_actions |= ea.FilterByLog(lf)
         self.dataevent_actions |= eh.ApplyMask()
 
         self.grid = LZGrid(self.config.reduction.qResolution, self.config.reduction.qzRange)
@@ -106,7 +111,7 @@ class ReflectivityReduction:
         # output
         if self.config.output.is_default('outputName'):
             import datetime
-            _date = datetime.datetime.now().replace(microsecond=0).isoformat()
+            _date = datetime.datetime.now().replace(microsecond=0).isoformat().replace(':', '-')
             if self.header.sample.name:
                 _sampleName = self.header.sample.name.replace(' ', '_')
             else:
@@ -162,7 +167,31 @@ class ReflectivityReduction:
             self.header.measurement_data_files.append(fileio.File( file=os.path.basename(fileName),
                                                                    timestamp=self.dataset.fileDate))
 
-
+        if 'polarization_config_label' in self.dataset.data.device_logs:
+            pols = np.unique(self.dataset.data.device_logs['polarization_config_label'].value)
+            pols = pols[pols>0]
+            if len(pols)>1:
+                logging.warning(f'    found {len(pols)} polarization configurations, splitting dataset accordingly')
+                from copy import deepcopy
+                from . import const
+                full_ds = deepcopy(self.dataset)
+                for pi in pols:
+                    plabel = const.polarizationLabels[pi]
+                    pol_filter = FilterByLog(f'polarization_config_label=={pi}',
+                                             remove_switchpulse=True) | ApplyMask()
+                    logging.info(f'    filter {plabel} using polarization_config_label=={pi}')
+                    pol_filter(self.dataset)
+                    self.dataset.update_header(self.header)
+                    pol_filter.update_header(self.header)
+                    if self.config.reduction.timeSlize:
+                        if i>0:
+                            logging.warning(
+                                "    time slizing should only be used for one set of datafiles, check parameters")
+                        self.analyze_timeslices(i, polstr=f' : polarization = {plabel}')
+                    else:
+                        self.analyze_unsliced(i, polstr=f' : polarization = {plabel}')
+                    self.dataset = deepcopy(full_ds)
+                return
         if self.config.reduction.timeSlize:
             if i>0:
                 logging.warning("    time slizing should only be used for one set of datafiles, check parameters")
@@ -170,7 +199,7 @@ class ReflectivityReduction:
         else:
             self.analyze_unsliced(i)
 
-    def analyze_unsliced(self, i):
+    def analyze_unsliced(self, i, polstr=''):
         self.monitor = self.dataset.data.pulses.monitor.sum()
         logging.info(f'    monitor = {self.monitor:8.2f} {MONITOR_UNITS[self.config.experiment.monitorType]}')
 
@@ -183,7 +212,7 @@ class ReflectivityReduction:
 
         if 'Rqz.ort' in self.config.output.outputFormats:
             headerRqz = self.header.orso_header()
-            headerRqz.data_set = f'Nr {i} : mu = {self.dataset.geometry.mu:6.3f} deg'
+            headerRqz.data_set = f'Nr {i} : mu = {self.dataset.geometry.mu:6.3f} deg{polstr}'
 
             # projection on qz-grid
             result = proj.project_on_qz()
@@ -258,7 +287,7 @@ class ReflectivityReduction:
                 proj.plot(colorbar=True, cmap=str(self.config.output.plot_colormap))
                 plt.title(f'{self.config.reduction.fileIdentifier[i]}')
 
-    def analyze_timeslices(self, i):
+    def analyze_timeslices(self, i, polstr=''):
         wallTime_e = np.float64(self.dataset.data.events.wallTime)/1e9
         pulseTimeS = np.float64(self.dataset.data.pulses.time)/1e9
         interval = self.config.reduction.timeSlize[0]
@@ -308,7 +337,7 @@ class ReflectivityReduction:
 
             headerRqz = self.header.orso_header(
                     extra_columns=[fileio.Column('time', 's', 'time relative to start of measurement series')])
-            headerRqz.data_set = f'{i}_{ti}: time = {time:8.1f} s  to {time+interval:8.1f} s'
+            headerRqz.data_set = f'{i}_{ti}: time = {time:8.1f} s  to {time+interval:8.1f} s{polstr}'
             orso_data = fileio.OrsoDataset(headerRqz, result.data_for_time(time))
             self.datasetsRqz.append(orso_data)
 
@@ -326,8 +355,23 @@ class ReflectivityReduction:
     def save_Rqz(self):
         fname = os.path.join(self.config.output.outputPath, f'{self.config.output.outputName}.Rqz.ort')
         logging.warning(f'    {fname}')
-        theSecondLine = f' {self.header.experiment.title} | {self.header.experiment.start_date} | sample {self.header.sample.name} | R(q_z)'
+        if os.path.exists(fname) and self.config.output.append:
-        fileio.save_orso(self.datasetsRqz, fname, data_separator='\n', comment=theSecondLine)
+            logging.info('        file already exists, append as new dataset')
+            with open(fname, 'r') as f:
+                f.readline()
+                theSecondLine = f.readline()[3:]
+            prev_data = fileio.load_orso(fname)
+            prev_names = [di.info.data_set for di in prev_data]
+            for i, di in enumerate(self.datasetsRqz):
+                while di.info.data_set in prev_names:
+                    if di.info.data_set.startswith('Nr '):
+                        di.info.data_set = f'Nr {i+len(prev_data)} :'+di.info.data_set.split(':', 1)[1]
+                        break
+                    di.info.data_set = di.info.data_set+'_'
+            fileio.save_orso(prev_data+self.datasetsRqz, fname, data_separator='\n', comment=theSecondLine)
+        else:
+            theSecondLine = f' {self.header.experiment.title} | {self.header.experiment.start_date} | sample {self.header.sample.name} | R(q_z)'
+            fileio.save_orso(self.datasetsRqz, fname, data_separator='\n', comment=theSecondLine)
 
     def save_Rtl(self):
         fname = os.path.join(self.config.output.outputPath, f'{self.config.output.outputName}.Rlt.ort')

requirements.txt

@@ -3,5 +3,6 @@ h5py
 orsopy
 numba
 matplotlib
+tabulate
 backports.strenum; python_version<"3.11"
 backports.zoneinfo; python_version<"3.9"

setup.cfg

@@ -34,5 +34,6 @@ Homepage = "https://github.com/jochenstahn/amor"
 [options.entry_points]
 console_scripts =
     eos = eos.__main__:main
+    eosls = eos.ls:main
     events2histogram = eos.e2h:main
     amor-nicos = eos.nicos:main

tests/test_event_handling.py

@@ -0,0 +1,572 @@
+import os
+import numpy as np
+import logging
+
+from unittest import TestCase
+from datetime import datetime
+from copy import deepcopy
+
+from orsopy.fileio import Person, Experiment, Sample, InstrumentSettings, Value, ValueRange, Polarization
+
+from eos import const
+from eos.header import Header
+from eos.event_data_types import EVENT_BITMASKS, AmorGeometry, AmorTiming, AmorEventStream, \
+    EventDataAction, EventDatasetProtocol, PACKET_TYPE, PC_TYPE, PULSE_TYPE, EVENT_TYPE, append_fields
+from eos.event_handling import ApplyPhaseOffset, ApplyParameterOverwrites, CorrectChopperPhase, CorrectSeriesTime, \
+    AssociatePulseWithMonitor, FilterMonitorThreshold, FilterStrangeTimes, TofTimeCorrection, ApplyMask
+from eos.event_analysis import ExtractWalltime, MergeFrames, AnalyzePixelIDs, CalculateWavelength, CalculateQ, \
+    FilterQzRange, FilterByLog
+from eos.options import MonitorType, IncidentAngle, ExperimentConfig
+
+
+class MockEventData:
+    """
+    Simulated dataset to be used with event handling unit tests
+    """
+    geometry: AmorGeometry
+    timing: AmorTiming
+    data: AmorEventStream
+
+    def __init__(self):
+        self.geometry = AmorGeometry(mu=2.0, nu=1.0, kap=0.5, kad=0.0, div=1.5,
+                                     chopperSeparation=1000.0, detectorDistance=4000., chopperDetectorDistance=18842.)
+        self.timing = AmorTiming(
+                ch1TriggerPhase=-9.1, ch2TriggerPhase=6.75,
+                chopperPhase=0.17, chopperSpeed=500., tau=0.06
+                )
+        self.create_data()
+
+    def create_data(self):
+        # list of events, here with random time of fligh and pixel location
+        events = np.recarray((10000, ), dtype=EVENT_TYPE)
+        events.tof = np.random.uniform(low=0., high=0.12, size=events.shape)
+        events.pixelID = np.random.randint(0, 28671, size=events.shape)
+        events.mask = 0
+
+        # list of data packates containing previous events
+        packets = np.recarray((1000,), dtype=PACKET_TYPE)
+        packets.start_index = np.linspace(0, events.shape[0]-1, packets.shape[0], dtype=np.uint32)
+        packets.time = np.linspace(1700000000000000000, 1700000000000000000+3_600_000_000_000,
+                                   packets.shape[0], dtype=np.int64)
+
+        # chopper pulses within the measurement time
+        pulses = np.recarray((packets.shape[0],), dtype=PULSE_TYPE)
+        pulses.monitor = 1.0
+        pulses.time = packets.time
+
+        # proton current information with independent timing
+        proton_current = np.recarray((50,), dtype=PC_TYPE)
+        proton_current.current = 1500.0
+        proton_current[np.random.randint(0, proton_current.shape[0]-1, 10)] = 0. # random time with no current
+        proton_current.time = np.linspace(1700000000000000300, 1700000000000000000+3_600_000_000_000,
+                                   proton_current.shape[0], dtype=np.int64)
+
+        self.data = AmorEventStream(events, packets, pulses, proton_current)
+        self.orig_data = deepcopy(self.data)
+
+
+    def append(self, other):
+        raise NotImplementedError("Just for testing, no append")
+
+    def update_header(self, header:Header):
+        # update a header with the information read from file
+        header.owner = Person(name="test user", affiliation='PSI')
+        header.experiment = Experiment(title='test experiment', instrument='amor',
+                                       start_date=datetime.now(), probe="neutron")
+        header.sample = Sample(name='test sample')
+        header.measurement_instrument_settings = InstrumentSettings(incident_angle=Value(1.5, 'deg'),
+            wavelength = ValueRange(3.0, 12.5, 'angstrom'),
+            polarization = Polarization.unpolarized)
+
+    def update_info_from_logs(self):
+        RELEVANT_ITEMS = ['sample_temperature', 'sample_magnetic_field', 'polarization_config_label']
+        for key, log in self.data.device_logs.items():
+            if key not in RELEVANT_ITEMS:
+                continue
+            if log.value.dtype in [np.int8, np.int16, np.int32, np.int64]:
+                # for integer items (flags) report the most common one
+                value = np.bincount(log.value).argmax()
+                if logging.getLogger().getEffectiveLevel() <= logging.DEBUG \
+                        and np.unique(log.value).shape[0]>1:
+                    logging.debug(f'        filtered values for {key} not unique, '
+                                  f'has {np.unique(log.value).shape[0]} values')
+            else:
+                value = log.value.mean()
+            if key == 'polarization_config_label':
+                self.instrument_settings.polarization = Polarization(const.polarizationConfigs[value])
+            elif key == 'sample_temperature':
+                self.sample.sample_parameters['temperature'].magnitue = value
+            elif key == 'sample_magnetic_field':
+                self.sample.sample_parameters['magnetic_field'].magnitue = value
+
+
+class TestActionClass(TestCase):
+    @classmethod
+    def setUpClass(cls):
+        """
+        Create test classes to be used
+        """
+        class T1(EventDataAction):
+            def perform_action(self, event: EventDatasetProtocol):
+                event.data.events.mask += 1
+        class T2(EventDataAction):
+            def perform_action(self, event: EventDatasetProtocol):
+                event.data.events.mask += 2
+        class T4(EventDataAction):
+            def perform_action(self, event: EventDatasetProtocol):
+                event.data.events.mask += 4
+        cls.T1=T1; cls.T2=T2; cls.T4=T4
+
+        class H1(EventDataAction):
+            def perform_action(self, event: EventDatasetProtocol):
+                ...
+            def update_header(self, header:Header) ->None:
+                header.sample.name = 'h1'
+        class H2(EventDataAction):
+            def perform_action(self, event: EventDatasetProtocol):
+                ...
+            def update_header(self, header: Header) -> None:
+                header.sample.name = 'h2'
+        class HN(EventDataAction):
+            def __init__(self, n):
+                self._n = n
+            def perform_action(self, event: EventDatasetProtocol):
+                ...
+            def update_header(self, header: Header) -> None:
+                header.sample.name = self._n
+        cls.H1=H1; cls.H2=H2; cls.HN = HN
+
+    def setUp(self):
+        self.d = MockEventData()
+        self.header = Header()
+        self.d.update_header(self.header)
+
+    def test_individual(self):
+        t1 = self.T1()
+        t2 = self.T2()
+        t4 = self.T4()
+
+        np.testing.assert_array_equal(self.d.data.events.mask, 0)
+        t1.perform_action(self.d)
+        np.testing.assert_array_equal(self.d.data.events.mask, 1)
+        t2.perform_action(self.d)
+        np.testing.assert_array_equal(self.d.data.events.mask, 3)
+        t4.perform_action(self.d)
+        np.testing.assert_array_equal(self.d.data.events.mask, 7)
+
+    def test_header(self):
+        h1 = self.H1()
+        h2 = self.H2()
+        h3 = self.HN('h3')
+        h4 = self.HN('h4')
+
+        h1.update_header(self.header)
+        self.assertEqual(self.header.sample.name, 'h1')
+        h2.update_header(self.header)
+        self.assertEqual(self.header.sample.name, 'h2')
+        h3.update_header(self.header)
+        self.assertEqual(self.header.sample.name, 'h3')
+        h4.update_header(self.header)
+        self.assertEqual(self.header.sample.name, 'h4')
+
+    def test_combination(self):
+        t1 = self.T1()
+        t2 = self.T2()
+        t4 = self.T4()
+        t12 = t1 | t2
+        t24 = t2 | t4
+        t1224 = t1 | t2 | t2 | t4
+        t1224b = t12 | t24
+
+        np.testing.assert_array_equal(self.d.data.events.mask, 0)
+        t12.perform_action(self.d)
+        np.testing.assert_array_equal(self.d.data.events.mask, 3)
+        t24.perform_action(self.d)
+        np.testing.assert_array_equal(self.d.data.events.mask, 9)
+
+        t1224.perform_action(self.d)
+        np.testing.assert_array_equal(self.d.data.events.mask, 18)
+        t1224b.perform_action(self.d)
+        np.testing.assert_array_equal(self.d.data.events.mask, 27)
+
+
+    def test_combine_header(self):
+        h1 = self.H1()
+        h2 = self.H2()
+        h3 = self.HN('h3')
+        h4 = self.HN('h4')
+
+        (h1|h2).update_header(self.header)
+        self.assertEqual(self.header.sample.name, 'h2')
+        (h2|h1).update_header(self.header)
+        self.assertEqual(self.header.sample.name, 'h1')
+        (h3|h4).update_header(self.header)
+        self.assertEqual(self.header.sample.name, 'h4')
+        (h4|h3).update_header(self.header)
+        self.assertEqual(self.header.sample.name, 'h3')
+
+    def test_abstract_misssing(self):
+        with self.assertRaises(TypeError):
+            class E(EventDataAction):
+                ...
+            _ = E()
+
+    def test_hash(self):
+        """
+        Check that hashes of different actions are different but
+        instances of same action have same hash
+        """
+        t1 = self.T1()
+        t1b = self.T1()
+        t2 = self.T2()
+        t4 = self.T4()
+        h3 = self.HN('h3')
+        h3b = self.HN('h3')
+        h4 = self.HN('h4')
+
+        self.assertNotEqual(t1.action_hash(), t2.action_hash())
+        self.assertNotEqual(t2.action_hash(), t4.action_hash())
+        self.assertNotEqual(t1.action_hash(), t4.action_hash())
+        self.assertNotEqual(h3.action_hash(), h4.action_hash())
+        self.assertEqual(t1.action_hash(), t1b.action_hash())
+        self.assertEqual(h3.action_hash(), h3b.action_hash())
+
+
+class TestSimpleActions(TestCase):
+    def setUp(self):
+        self.d = MockEventData()
+        self.header = Header()
+        self.d.update_header(self.header)
+
+    def test_chopper_phase(self):
+        cp = CorrectChopperPhase()
+        cp.perform_action(self.d)
+        np.testing.assert_array_equal(
+                self.d.data.events.tof,
+                self.d.orig_data.events.tof+
+                self.d.timing.tau*(self.d.timing.ch1TriggerPhase-self.d.timing.chopperPhase/2)/180
+                )
+
+    def _extract_walltime(self):
+        # Extract wall time for events and orig copy
+        wt = ExtractWalltime()
+        d = self.d.data
+        self.d.data = self.d.orig_data
+        wt.perform_action(self.d)
+        self.d.data = d
+        wt.perform_action(self.d)
+
+    def test_extract_walltime(self):
+        self._extract_walltime()
+        # wallTime should be always a time present in the packet times
+        np.testing.assert_array_equal(np.isin(self.d.data.events.wallTime, self.d.data.packets.time), True)
+        # make sure extraction works on both original and copy
+        np.testing.assert_array_equal(self.d.data.events.wallTime, self.d.orig_data.events.wallTime)
+
+    def test_series_time(self):
+        corr = 100
+        ct = CorrectSeriesTime(corr)
+
+        with self.assertRaises(ValueError):
+            ct.perform_action(self.d)
+
+        self._extract_walltime()
+
+
+        ct.perform_action(self.d)
+        np.testing.assert_array_equal(
+                self.d.data.pulses.time,
+                self.d.orig_data.pulses.time-corr
+                )
+        np.testing.assert_array_equal(
+                self.d.data.events.wallTime,
+                self.d.orig_data.events.wallTime-corr
+                )
+        np.testing.assert_array_equal(
+                self.d.data.proton_current.time,
+                self.d.orig_data.proton_current.time-corr
+                )
+
+    def test_associate_monitor(self):
+        amPC = AssociatePulseWithMonitor(MonitorType.proton_charge)
+        amT = AssociatePulseWithMonitor(MonitorType.time)
+        amN = AssociatePulseWithMonitor(MonitorType.neutron_monitor)
+
+        self.d.data.pulses.monitor = 13
+        amN.perform_action(self.d)
+        np.testing.assert_array_equal(self.d.data.pulses.monitor, 1)
+
+        self.d.data.pulses.monitor = 13
+        amT.perform_action(self.d)
+        np.testing.assert_array_equal(self.d.data.pulses.monitor, np.float32(2*self.d.timing.tau))
+
+        self.d.data.pulses.monitor = 13
+        amPC.perform_action(self.d)
+        pcm = self.d.data.proton_current.current *2*self.d.timing.tau*1e-3
+        np.testing.assert_array_equal(np.isin(self.d.data.pulses.monitor, pcm), True)
+
+    def test_filter_monitor_threashold(self):
+        amPC = AssociatePulseWithMonitor(MonitorType.proton_charge)
+        fmt = amPC | FilterMonitorThreshold(1000.)
+        fma = amPC | FilterMonitorThreshold(2000.)
+        fm0 = amPC | FilterMonitorThreshold(-1.0)
+
+        with self.assertRaises(ValueError):
+            fmt.perform_action(self.d)
+
+        self._extract_walltime()
+        fm0.perform_action(self.d)
+        self.assertEqual(self.d.data.events.mask.sum(), 0)
+        fmt.perform_action(self.d)
+        # calculate, which events should have 0 monitor
+        zero_times = self.d.data.pulses.time[self.d.data.pulses.monitor==0]
+        zero_sum = np.isin(self.d.data.events.wallTime, zero_times).sum()
+        self.assertEqual(self.d.data.events.mask.sum(), zero_sum*EVENT_BITMASKS['MonitorThreshold'])
+        # filter all events
+        self.d.data.events.mask = 0
+        fma.perform_action(self.d)
+        self.assertEqual(self.d.data.events.mask.sum(), self.d.data.events.shape[0]*EVENT_BITMASKS['MonitorThreshold'])
+
+    def test_filter_strage_times(self):
+        st = FilterStrangeTimes()
+
+        st.perform_action(self.d)
+        self.assertEqual(self.d.data.events.mask.sum(), 0)
+
+        # half events should be strange times (outside of ToF frame)
+        self.d.data.events.tof += self.d.timing.tau
+        st.perform_action(self.d)
+        self.assertEqual(self.d.data.events.mask.sum(),
+                         (self.d.data.events.tof>2*self.d.timing.tau).sum()*EVENT_BITMASKS['StrangeTimes'])
+
+    def test_apply_phase_offset(self):
+        action = ApplyPhaseOffset(12.5)
+        action.perform_action(self.d)
+        self.assertEqual(self.d.timing.ch1TriggerPhase, 12.5)
+
+    def test_apply_parameter_overwrites(self):
+        action = ApplyParameterOverwrites(ExperimentConfig(muOffset=0.25, mu=3.5, nu=4.5))
+        action.perform_action(self.d)
+        self.assertEqual(self.d.geometry.mu, 3.5)
+        self.assertEqual(self.d.geometry.nu, 4.5)
+
+        action = ApplyParameterOverwrites(ExperimentConfig(muOffset=0.25))
+        action.perform_action(self.d)
+        self.assertEqual(self.d.geometry.mu, 3.75)
+
+        action = ApplyParameterOverwrites(ExperimentConfig(sampleModel='air | Si | Fe'))
+        action.update_header(self.header)
+        self.assertIsNotNone(self.header.sample.model)
+
+    def test_apply_sample_model_file(self):
+        if os.path.isfile('test.yaml'):
+            os.remove('test.yaml')
+        action = ApplyParameterOverwrites(ExperimentConfig(sampleModel='test.yaml'))
+        action.update_header(self.header)
+        self.assertIsNone(self.header.sample.model)
+
+        with open('test.yaml', 'w') as fh:
+            fh.write("""stack: air | Si | Fe""")
+
+        try:
+            action = ApplyParameterOverwrites(ExperimentConfig(sampleModel='test.yaml'))
+            action.update_header(self.header)
+            self.assertEqual(self.header.sample.model.stack, 'air | Si | Fe')
+        finally:
+            os.remove('test.yaml')
+
+    def test_tof_time_correction(self):
+        action = TofTimeCorrection()
+        with self.assertRaises(ValueError):
+            action.perform_action(self.d)
+
+        new_events = append_fields(self.d.data.events, [('delta', np.float64)])
+        new_events.delta = 10.0
+        self.d.data.events = new_events
+        tof_before = self.d.data.events.tof.copy()
+        action.perform_action(self.d)
+        np.testing.assert_allclose(
+            self.d.data.events.tof,
+            tof_before - (10.0 / 180.0) * self.d.timing.tau
+        )
+
+        self.d.create_data()
+        new_events = append_fields(self.d.data.events, [('delta', np.float64)])
+        new_events.delta = 10.0
+        self.d.data.events = new_events
+        tof_before = self.d.data.events.tof.copy()
+        action = TofTimeCorrection(correct_chopper_opening=False)
+        action.perform_action(self.d)
+        np.testing.assert_allclose(
+            self.d.data.events.tof,
+            tof_before - (self.d.geometry.kad / 180.0) * self.d.timing.tau
+        )
+
+    def test_apply_mask(self):
+        self.d.data.events = self.d.data.events[:6].copy()
+        self.d.data.events.mask[:] = [0, 1, 2, 3, 4, 5]
+
+        action = ApplyMask()
+        action.perform_action(self.d)
+        self.assertEqual(self.d.data.events.shape[0], 1)
+        self.assertEqual(self.d.data.events.mask[0], 0)
+
+        self.d.create_data()
+        self.d.data.events = self.d.data.events[:6].copy()
+        self.d.data.events.mask[:] = [0, 1, 2, 3, 4, 5]
+        action = ApplyMask(bitmask_filter=EVENT_BITMASKS['MonitorThreshold'])
+        action.perform_action(self.d)
+        np.testing.assert_array_equal(self.d.data.events.mask, np.array([0, EVENT_BITMASKS['MonitorThreshold']],
+                                                                        dtype=np.int32))
+
+    def test_merge_frames(self):
+        action = MergeFrames(lamdaCut=0.0, preciseTime=False)
+        action.perform_action(self.d)
+        self.assertEqual(self.d.data.events.tof.shape, self.d.orig_data.events.tof.shape)
+        np.testing.assert_array_compare(lambda x,y: x<=y, self.d.data.events.tof, self.d.orig_data.events.tof)
+        self.assertTrue((-self.d.timing.tau<=self.d.data.events.tof).all())
+        np.testing.assert_array_less(self.d.data.events.tof, self.d.timing.tau)
+
+        action = MergeFrames(lamdaCut=2.0, preciseTime=False)
+        self.d.data.events.tof = self.d.orig_data.events.tof[:]
+        action.perform_action(self.d)
+        tofCut = 2.0*self.d.geometry.chopperDetectorDistance/const.hdm*1e-13
+        self.assertTrue((tofCut-self.d.timing.tau<=self.d.data.events.tof).all())
+        self.assertTrue((self.d.data.events.tof<=tofCut+self.d.timing.tau).all())
+
+    def test_merge_frames_splitting(self):
+        action = MergeFrames(lamdaCut=0.0, preciseTime=True)
+        self._extract_walltime()
+        action.perform_action(self.d)
+        self.assertEqual(self.d.data.events.tof.shape, self.d.orig_data.events.tof.shape)
+        np.testing.assert_array_compare(lambda x,y: x<=y, self.d.data.events.tof, self.d.orig_data.events.tof)
+        self.assertEqual(self.d.data.pulses.shape[0], self.d.orig_data.pulses.shape[0]*2+1)
+        np.testing.assert_array_less(self.d.orig_data.pulses.time[:-1], self.d.orig_data.pulses.time[1:])
+        np.testing.assert_array_less(self.d.data.pulses.time[:-1], self.d.data.pulses.time[1:])
+
+    def test_analyze_pixel_ids(self):
+        action = AnalyzePixelIDs((1000, 1001))
+        action.perform_action(self.d)
+        self.assertIn('detZ', self.d.data.events.dtype.names)
+        self.assertIn('detXdist', self.d.data.events.dtype.names)
+        self.assertIn('delta', self.d.data.events.dtype.names)
+        self.assertEqual(
+            np.bitwise_and(self.d.data.events.mask, EVENT_BITMASKS['yRange']).astype(bool).sum(),
+            self.d.data.events.shape[0]
+        )
+        # TODO: maybe add a test actually checking correct detector-id resolution
+
+    def test_calculate_wavelength(self):
+        action = CalculateWavelength((3.0, 5.0))
+        with self.assertRaises(ValueError):
+            action.perform_action(self.d)
+
+        new_events = append_fields(self.d.data.events, [('detXdist', np.float64)])
+        new_events.detXdist = 0.0
+        self.d.data.events = new_events
+        action.perform_action(self.d)
+        self.assertIn('lamda', self.d.data.events.dtype.names)
+        flt = self.d.data.events.mask!=EVENT_BITMASKS['LamdaRange']
+        # check all wavelength in range not filtered
+        np.testing.assert_array_less(self.d.data.events.lamda[flt], 5.0)
+        np.testing.assert_array_less(3.0, self.d.data.events.lamda[flt])
+        # check all wavelength out of range filtered
+        flt = self.d.data.events.mask==EVENT_BITMASKS['LamdaRange']
+        self.assertTrue(((self.d.data.events.lamda[flt]<3.0)|(self.d.data.events.lamda[flt]>5.0)).all())
+
+    def test_calculate_q(self):
+        action = CalculateQ(IncidentAngle.alphaF)
+        with self.assertRaises(ValueError):
+            action.perform_action(self.d)
+
+        # TODO: add checks for actual resulting values
+
+        new_events = append_fields(self.d.data.events, [('lamda', np.float64), ('delta', np.float64)])
+        new_events.lamda = 5.0
+        new_events.delta = 0.0
+        self.d.data.events = new_events
+        action.perform_action(self.d)
+        self.assertIn('qz', self.d.data.events.dtype.names)
+        self.assertNotIn('qx', self.d.data.events.dtype.names)
+        action.update_header(self.header)
+        self.assertEqual(self.header.measurement_scheme, 'angle- and energy-dispersive')
+
+        self.d.create_data()
+        new_events = append_fields(self.d.data.events, [('lamda', np.float64), ('delta', np.float64)])
+        new_events.lamda = 5.0
+        new_events.delta = 0.0
+        self.d.data.events = new_events
+        action = CalculateQ(IncidentAngle.mu)
+        action.perform_action(self.d)
+        self.assertIn('qz', self.d.data.events.dtype.names)
+        self.assertIn('qx', self.d.data.events.dtype.names)
+        action.update_header(self.header)
+        self.assertEqual(self.header.measurement_scheme, 'energy-dispersive')
+
+        self.d.create_data()
+        new_events = append_fields(self.d.data.events, [('lamda', np.float64), ('delta', np.float64)])
+        new_events.lamda = 5.0
+        new_events.delta = 0.0
+        self.d.data.events = new_events
+        action = CalculateQ(IncidentAngle.nu)
+        action.perform_action(self.d)
+        self.assertIn('qz', self.d.data.events.dtype.names)
+        self.assertNotIn('qx', self.d.data.events.dtype.names)
+        action.update_header(self.header)
+        self.assertEqual(self.header.measurement_scheme, 'energy-dispersive')
+
+    def test_filter_qz_range(self):
+        action = FilterQzRange((0.1, 0.2))
+        with self.assertRaises(ValueError):
+            action.perform_action(self.d)
+
+        self.d.data.events = self.d.data.events[:5].copy()
+        new_events = append_fields(self.d.data.events, [('qz', np.float64)])
+        new_events.qz = np.array([0.05, 0.1, 0.15, 0.2, 0.25])
+        self.d.data.events = new_events
+        action.perform_action(self.d)
+        np.testing.assert_array_equal(
+            self.d.data.events.mask,
+            np.array([1, 0, 0, 0, 1], dtype=np.int32) * EVENT_BITMASKS['qRange']
+        )
+
+    def test_filter_by_log(self):
+        action = FilterByLog("test_log==0") | ApplyMask()
+        class LogWarnError(Exception):
+            ...
+        def warn_raise(*args, **kwargs):
+            raise LogWarnError()
+        _orig_warn = logging.warning
+        try:
+            logging.warning = warn_raise
+            with self.assertRaises(LogWarnError):
+                action.perform_action(self.d)
+        finally:
+            logging.warning = _orig_warn
+
+        self._extract_walltime()
+
+        test_log = np.recarray(shape=(2,), dtype=np.dtype([('value', np.int32),
+                                                           ('time', np.int64)]))
+        test_log.time = [-5, self.d.data.pulses.time[100]+123]
+        test_log.value = [0, 1]
+        self.d.data.device_logs['test_log'] = test_log
+        action.perform_action(self.d)
+        self.assertEqual(self.d.data.pulses.shape[0], 101)
+
+    def test_filter_by_log_switchpulse(self):
+        action = FilterByLog("!test_log==0") | ApplyMask()
+        self._extract_walltime()
+
+        test_log = np.recarray(shape=(2,), dtype=np.dtype([('value', np.int32),
+                                                           ('time', np.int64)]))
+        test_log.time = [-5, self.d.data.pulses.time[100]+123]
+        test_log.value = [0, 1]
+        self.d.data.device_logs['test_log'] = test_log
+        self.d.data.device_logs['check_log'] = test_log.copy()
+        action.perform_action(self.d)
+        self.assertEqual(self.d.data.pulses.shape[0], 100)
+        np.testing.assert_array_equal(
+                self.d.data.device_logs['test_log'],
+                self.d.data.device_logs['check_log'],
+                )

tests/test_full_analysis.py

@@ -1,8 +1,10 @@
 import os
 import cProfile
+import numpy as np
 from unittest import TestCase
 from dataclasses import fields, MISSING
 from eos import options, reduction_reflectivity, logconfig
+from orsopy import fileio
 
 logconfig.setup_logging()
 logconfig.update_loglevel(1)
@@ -38,30 +40,25 @@ class FullAmorTest(TestCase):
     def tearDown(self):
         self.pr.disable()
         for fi in ['test_results/test.Rqz.ort', 'test_results/5952.norm']:
-            try:
+           try:
-                os.unlink(fi)
+               os.unlink(fi)
-            except FileNotFoundError:
+           except FileNotFoundError:
-                pass
+               pass
 
     def test_time_slicing(self):
         experiment_config = options.ExperimentConfig(
-                chopperSpeed=self._field_defaults['ExperimentConfig']['chopperSpeed'],
                 chopperPhase=-13.5,
                 chopperPhaseOffset=-5,
-                monitorType=self._field_defaults['ExperimentConfig']['monitorType'],
-                lowCurrentThreshold=self._field_defaults['ExperimentConfig']['lowCurrentThreshold'],
                 yRange=(18, 48),
                 lambdaRange=(3., 11.5),
-                incidentAngle=self._field_defaults['ExperimentConfig']['incidentAngle'],
                 mu=0,
                 nu=0,
                 muOffset=0.0,
                 sampleModel='air | 10 H2O | D2O'
                 )
         reduction_config = options.ReflectivityReductionConfig(
-                normalisationMethod=self._field_defaults['ReflectivityReductionConfig']['normalisationMethod'],
                 qResolution=0.01,
-                qzRange=self._field_defaults['ReflectivityReductionConfig']['qzRange'],
+                qzRange=(0.01, 0.15),
                 thetaRange=(-0.75, 0.75),
                 fileIdentifier=["6003-6005"],
                 scale=[1],
@@ -84,22 +81,16 @@ class FullAmorTest(TestCase):
 
     def test_noslicing(self):
         experiment_config = options.ExperimentConfig(
-                chopperSpeed=self._field_defaults['ExperimentConfig']['chopperSpeed'],
                 chopperPhase=-13.5,
                 chopperPhaseOffset=-5,
-                monitorType=self._field_defaults['ExperimentConfig']['monitorType'],
-                lowCurrentThreshold=self._field_defaults['ExperimentConfig']['lowCurrentThreshold'],
                 yRange=(18, 48),
                 lambdaRange=(3., 11.5),
-                incidentAngle=self._field_defaults['ExperimentConfig']['incidentAngle'],
                 mu=0,
                 nu=0,
                 muOffset=0.0,
                 )
         reduction_config = options.ReflectivityReductionConfig(
-                normalisationMethod=self._field_defaults['ReflectivityReductionConfig']['normalisationMethod'],
                 qResolution=0.01,
-                qzRange=self._field_defaults['ReflectivityReductionConfig']['qzRange'],
                 thetaRange=(-0.75, 0.75),
                 fileIdentifier=["6003", "6004", "6005"],
                 scale=[1],
@@ -117,3 +108,57 @@ class FullAmorTest(TestCase):
         # run second time to reuse norm file
         reducer = reduction_reflectivity.ReflectivityReduction(config)
         reducer.reduce()
+
+    def test_eventfilter(self):
+        self.reader_config.year = 2026
+        experiment_config = options.ExperimentConfig()
+        reduction_config = options.ReflectivityReductionConfig(fileIdentifier=["826"],
+                                                               logfilter=['polarization_config_label==2'])
+        output_config = options.ReflectivityOutputConfig(
+                outputFormats=[options.OutputFomatOption.Rqz_ort],
+                outputName='test',
+                outputPath='test_results',
+                )
+        config=options.ReflectivityConfig(self.reader_config, experiment_config, reduction_config, output_config)
+        reducer = reduction_reflectivity.ReflectivityReduction(config)
+        reducer.reduce()
+        espin_up = reducer.dataset.data.events.shape[0]
+
+        reduction_config.logfilter = ['polarization_config_label==3']
+        output_config.append = True
+        reducer = reduction_reflectivity.ReflectivityReduction(config)
+        reducer.reduce()
+        espin_down = reducer.dataset.data.events.shape[0]
+        # measurement should have about 2x as many counts in spin_down
+        self.assertAlmostEqual(espin_down/espin_up, 2., 2)
+
+        # perform the same filter but remove pulses during which the switch occured
+        reduction_config.logfilter = ['!polarization_config_label==3']
+        output_config.append = True
+        reducer = reduction_reflectivity.ReflectivityReduction(config)
+        reducer.reduce()
+        espin_down2 = reducer.dataset.data.events.shape[0]
+        # measurement should have about 2x as many counts in spin_down
+        self.assertLess(espin_down2, espin_down)
+
+    def test_polsplitting(self):
+        self.reader_config.year = 2026
+        experiment_config = options.ExperimentConfig()
+        reduction_config = options.ReflectivityReductionConfig(fileIdentifier=["826"])
+        output_config = options.ReflectivityOutputConfig(
+                outputFormats=[options.OutputFomatOption.Rqz_ort],
+                outputName='test',
+                outputPath='test_results',
+                )
+        config=options.ReflectivityConfig(self.reader_config, experiment_config, reduction_config, output_config)
+        reducer = reduction_reflectivity.ReflectivityReduction(config)
+        reducer.reduce()
+
+        results = fileio.load_orso(os.path.join(output_config.outputPath, output_config.outputName+'.Rqz.ort'))
+        self.assertEqual(len(results), 2)
+        self.assertEqual(results[0].info.data_source.measurement.instrument_settings.polarization, 'po')
+        self.assertEqual(results[1].info.data_source.measurement.instrument_settings.polarization, 'mo')
+        espin_up = np.nansum(results[0].data[:,1])
+        espin_down = np.nansum(results[1].data[:,1])
+        # the total intensity should be around equal as events are doubled and monitor counts are doubled
+        self.assertAlmostEqual(espin_down/espin_up, 1., 2)

update.md

@@ -3,14 +3,14 @@ Make new release
 
 - Update revision in `eos/__init__.py`
 - Commit changes `git commit -a -m "your message here"`
-- Tag version `git tag v3.x.y`
+- Push changes `git push`
-- Push changes `git push` and `git push --tags`
+- Use the workflow dispatch for [**Release**](https://gitea.psi.ch/sinq-reflectometry/eos/actions?workflow=release.yml&actor=0&status=0) action 
-- This should trigger the **Release** action on GitHub that builds a new version and uploads it to PyPI.
+  on Gitea with option "all_incl_release", that builds a new version, releases it and uploads it to PyPI.
 
 
-Update on AMOR
+Update on AMOR-DR
-==============
+=================
 
-- Login via SSH using the **amor** user.
+- Login via SSH using the **amor-dr** user.
 - Activate eos virtual environment `source /home/software/virtualenv/eosenv/bin/activate`
 - Update eos packge `pip install --upgrade amor-eos`