amor-eos 3.2.7__tar.gz → 3.3.0__tar.gz

{amor_eos-3.2.7 → amor_eos-3.3.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: amor_eos
-Version: 3.2.7
+Version: 3.3.0
 Summary: EOS reflectometry reduction for AMOR instrument
 Author: Jochen Stahn - Paul Scherrer Institut
 Author-email: jochen.stahn@psi.ch
@@ -16,6 +16,10 @@ Requires-Dist: numpy
 Requires-Dist: h5py
 Requires-Dist: orsopy
 Requires-Dist: numba
+Requires-Dist: matplotlib
+Requires-Dist: tabulate
+Requires-Dist: ess-streaming-data-types
+Requires-Dist: confluent-kafka
 Requires-Dist: backports.strenum; python_version < "3.11"
 Requires-Dist: backports.zoneinfo; python_version < "3.9"
 Dynamic: license-file

amor_eos-3.3.0/README.rst

@@ -0,0 +1,38 @@
+*************************************************************
+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 --help
+
+visualisation of the content of a raw file (.hdf):
+
+  events2histogram.py
+
+:TODO: real readme for final system needed.
+
+Installation
+============
+
+Python Environment
+------------------
+
+Create a [virtual python environment](https://docs.python.org/3/library/venv.html) (>3.8) and install the PyPI package:
+
+  pip install amor-eos
+
+Windows Binary
+--------------
+
+On Windows you can use the binary eos.exe that you find in the
+[Gitea Releases](https://gitea.psi.ch/sinq-reflectometry/eos/releases/latest) section.
+
+Either extract it to the folder where you analyze your data or choose a common location and make sure
+that is in the system PATH to be able to run the program from command line.

{amor_eos-3.2.7 → amor_eos-3.3.0}/amor_eos.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: amor_eos
-Version: 3.2.7
+Version: 3.3.0
 Summary: EOS reflectometry reduction for AMOR instrument
 Author: Jochen Stahn - Paul Scherrer Institut
 Author-email: jochen.stahn@psi.ch
@@ -16,6 +16,10 @@ Requires-Dist: numpy
 Requires-Dist: h5py
 Requires-Dist: orsopy
 Requires-Dist: numba
+Requires-Dist: matplotlib
+Requires-Dist: tabulate
+Requires-Dist: ess-streaming-data-types
+Requires-Dist: confluent-kafka
 Requires-Dist: backports.strenum; python_version < "3.11"
 Requires-Dist: backports.zoneinfo; python_version < "3.9"
 Dynamic: license-file

{amor_eos-3.2.7 → amor_eos-3.3.0}/amor_eos.egg-info/SOURCES.txt

@@ -11,6 +11,7 @@ amor_eos.egg-info/top_level.txt
 eos/__init__.py
 eos/__main__.py
 eos/command_line.py
+eos/compat.py
 eos/const.py
 eos/e2h.py
 eos/event_analysis.py

{amor_eos-3.2.7 → amor_eos-3.3.0}/amor_eos.egg-info/requires.txt

@@ -2,6 +2,10 @@ numpy
 h5py
 orsopy
 numba
+matplotlib
+tabulate
+ess-streaming-data-types
+confluent-kafka
 
 [:python_version < "3.11"]
 backports.strenum

{amor_eos-3.2.7 → amor_eos-3.3.0}/eos/__init__.py

@@ -2,5 +2,5 @@
 Package to handle data redction at AMOR instrument to be used by __main__.py script.
 """
 
-__version__ = '3.2.7'
-__date__    = '2026-03-13'
+__version__ = '3.3.0'
+__date__    = '2026-07-09'

amor_eos-3.3.0/eos/compat.py

@@ -0,0 +1,44 @@
+"""
+Presever compatibility with previous versions of AMOR datafiles.
+"""
+
+from datetime import datetime
+
+# old hdf parameter mappings, key is last date of validity
+legacy_hdf_paths = {
+        datetime(2026, 3, 18).timestamp():
+        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', '/*'),
+
+        data=('entry1/Amor/detector/data', None),  # data group used to load events from
+        trigger=('entry1/Amor/chopper/ch2_trigger', float),
+        proton_current=('entry1/Amor/detector/proton_current', None),
+        ),
+    }
+# create a sorted list of validity timestamps for quick comparison
+legacy_cutoffs = list(sorted(legacy_hdf_paths.keys()))

{amor_eos-3.2.7 → amor_eos-3.3.0}/eos/event_data_types.py

@@ -29,11 +29,17 @@ class AmorTiming:
     chopperPhase: float
     tau: float
 
+@dataclass
+class DA00EventBuffer:
+    signal: np.ndarray
+    time: np.ndarray
+
 # Structured datatypes used for event streams
 EVENT_TYPE = np.dtype([('tof', np.float64), ('pixelID', np.uint32), ('mask', np.int32)])
 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)])
+BM_TYPE = np.dtype([('value', np.int32), ('time', np.int64)])
 LOG_TYPE = np.dtype([('value', np.float32), ('time', np.int64)])
 
 # define the bitmask for individual event filters
@@ -63,6 +69,7 @@ class AmorEventStream:
     packets: np.recarray # PACKET_TYPE
     pulses: np.recarray  # PULSE_TYPE
     proton_current: np.recarray # PC_TYPE
+    beam_monitor: Optional[np.recarray] = None # BM_TYPE
     device_logs: Dict[str, np.recarray] = field(default_factory=dict) # LOG_TYPE
 
 class EventDatasetProtocol(Protocol):

{amor_eos-3.2.7 → amor_eos-3.3.0}/eos/event_handling.py

@@ -91,6 +91,16 @@ class AssociatePulseWithMonitor(EventDataAction):
                                                               * 2*dataset.timing.tau * 1e-3
         elif self.monitorType==MonitorType.time:
             dataset.data.pulses.monitor  = 2*dataset.timing.tau
+        elif self.monitorType==MonitorType.neutron_monitor:
+            if dataset.data.pulses.monitor is None:
+                logging.warning("    Neutron monitor was selected for normalization but not presend, "
+                                "falling back to proton current")
+                dataset.data.pulses.monitor = self.get_current_per_pulse(dataset.data.pulses.time,
+                                                                         dataset.data.proton_current.time,
+                                                                         dataset.data.proton_current.current) \
+                                              *2*dataset.timing.tau*1e-3
+            else:
+                dataset.data.pulses.monitor = dataset.data.beam_monitor.value / 1e4
         else:  # pulses
             dataset.data.pulses.monitor  = 1
 
@@ -184,7 +194,7 @@ class ApplyMask(EventDataAction):
             fltr = (d.events.mask & (~self.bitmask_filter)) == 0
             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}')
+        logging.info(f'      number of events: total = {pre_filter:7d}, after filtering = {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
@@ -201,4 +211,4 @@ class ApplyMask(EventDataAction):
             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()
+        dataset.update_info_from_logs()