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J. Stahn

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- added flatbuffer scheme 'da00' for the bema monitor
- reading in beam monitor signal (not yet used: there are changes / bug-fixes in 'da00' planned for the near future)
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Sinq User Console Account
2026-05-29 10:22:39 +02:00
parent 6951b15630
commit 855c23b0ee
5 changed files with 52 additions and 21 deletions
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eos/event_data_types.py
+7
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@@ -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.int64), ('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: np.recarray # BM_TYPE
device_logs: Dict[str, np.recarray] = field(default_factory=dict) # LOG_TYPE
class EventDatasetProtocol(Protocol):
eos/event_handling.py
+3 -1
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@@ -91,6 +91,8 @@ 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:
dataset.data.pulses.monitor = dataset.data.beam_monitor.value / 1e4
else: # pulses
dataset.data.pulses.monitor = 1
@@ -201,4 +203,4 @@ 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()
eos/file_reader.py
+39 -17
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@@ -7,7 +7,6 @@ import sys
import h5py
import numpy as np
import logging
import subprocess
from datetime import datetime
@@ -17,7 +16,7 @@ from orsopy.fileio.model_language import SampleModel
from . import const, compat
from .header import Header
from .event_data_types import AmorGeometry, AmorTiming, AmorEventStream, LOG_TYPE, PACKET_TYPE, EVENT_TYPE, PULSE_TYPE, \
PC_TYPE
PC_TYPE, BM_TYPE, DA00EventBuffer
try:
import zoneinfo
@@ -33,7 +32,7 @@ NO_DEFAULT_VALUE = object() # just for allowing None default value in AmorHeader
class AmorHeader:
"""
Collects header information from Amor NeXus fiel without reading event data.
Collects header information from Amor NeXus file without reading event data.
"""
# mapping of names to (hdf_path, dtype, nicos_key[, suffix])
hdf_paths = dict(
@@ -44,7 +43,7 @@ class AmorHeader:
user_affiliation=('entry1/user/affiliation', str),
sample_name=('entry1/sample/name', str),
sample_model=('entry1/sample/model', str),
sample_geometry=('entry1/sample/geometry', dict),
sample_geometry=('entry1/sample/geometry', str),
source_name=('entry1/Amor/source/name', str),
start_time=('entry1/start_time', str),
start_time_fallback=('entry1/Amor/measurement_configuration/start_time', str),
@@ -52,7 +51,7 @@ class AmorHeader:
chopper_separation=('entry1/Amor/chopper/pair_separation', float),
chopper_distance=('entry1/Amor/chopper/distance', float),
detector_distance=('entry1/Amor/detector/transformation/distance', float),
detector_distance=('entry1/Amor/detector_stage/transformation/distance', float),
sample_temperature=('entry1/sample/environment/temperature', float),
sample_magnetic_field=('entry1/sample/environment/magnetic_field', float),
sample_current=('entry1/sample/environment/current', float),
@@ -68,14 +67,14 @@ class AmorHeader:
virtual_source_vertical=('entry1/Amor/virtual_source/vertical', float),
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_speed=('entry1/Amor/chopper/rotation_speed', float, 'chopper_speed'),
chopper_phase=('entry1/Amor/chopper/phase', float, 'chopper_phase'),
polarization_config_label=('entry1/Amor/polarization/configuration', int, 'polarization_config_label', '/*'),
data=('entry1/detector/data', None), # data group used to load events from
trigger=('entry1/detector/trigger', float),
monitor=('entry1/detector/monitor', float),
beam_monitor=('entry1/beam_monitor', None), # special data group (da00 flat-buffer scheme)
proton_current=('entry1/detector/proton_current', float),
acquisition_filter=('entry1/detector/acquisition_filter', int),
)
@@ -147,6 +146,9 @@ class AmorHeader:
return output, unit
else:
return output
elif hdfgrp.attrs.get('writer_module', None) == 'da00':
# da00 float-buffer stream data
return DA00EventBuffer(signal=hdfgrp['signal'][:], time=hdfgrp['time'][:])
elif dtype is str:
return self.read_string(hdf_path)
else:
@@ -262,7 +264,8 @@ class AmorHeader:
)
sample_geometry = self.rv('sample_geometry', default=None)
if sample_geometry:
self.sample.geometry = sample_geometry
import yaml
self.sample.geometry = yaml.safe_load(sample_geometry)
# while event times are not evaluated, use first value reported in file for SEE
for param in self.SEE_PARAMS:
key = f'sample_{param}'
@@ -454,14 +457,16 @@ class AmorEventData(AmorHeader):
events.pixelID = data_group['event_id'][self.first_index:self.last_index+1]
events.mask = 0
self._beam_monitor = self.rv('beam_monitor', default=None)
pulses = self.read_chopper_trigger_stream(packets)
current = self.read_proton_current_stream(packets)
beam_monitor = self.read_proton_current_stream(packets)
#beam_monitor = self.read_beam_monitor_stream(packets) TODO
# read parameter logs not present in old files to ensure they are in self._log_keys if they exist
_monitor = self.rv('monitor', default=None)
_acquisition_filter = self.rv('acquisition_filter', default=None)
self.data = AmorEventStream(events, packets, pulses, current)
self.data = AmorEventStream(events, packets, pulses, current, beam_monitor)
if self.first_index>0 and not self.EOF:
# label the file name if not all events were used
@@ -488,8 +493,11 @@ class AmorEventData(AmorHeader):
sample_keys = [f'sample_{param}' for param in self.SEE_PARAMS]
relevant_items += sample_keys
for key, log in self.data.device_logs.items():
# if SE is missing there can be a missing key or empty dataset
if key not in relevant_items:
continue
if log.value.size == 0:
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()
@@ -515,10 +523,8 @@ class AmorEventData(AmorHeader):
pulseTimeS = chopper1TriggerTime
else:
logging.critical(' No chopper trigger data available, using event steram instead, pulse filtering will fail!')
data_group = self.hdf[self.hdf_paths['data'][0]]
startTime = np.array(data_group['event_time_zero'][0], dtype=np.int64)
stopTime = np.array(data_group['event_time_zero'][-2], dtype=np.int64)
pulseTimeS = np.arange(startTime, stopTime, self.timing.tau*1e9, dtype=np.int64)
startTime = np.array(self._beam_monitor.time[0], dtype=np.int64)
pulseTimeS = self._beam_monitor.time
pulses = np.recarray(pulseTimeS.shape, dtype=PULSE_TYPE)
pulses.time = pulseTimeS
pulses.monitor = 1. # default is monitor pulses as it requires no calculation
@@ -542,6 +548,20 @@ class AmorEventData(AmorHeader):
(proton_current.time<=packets.time[-1])]
return proton_current
def read_beam_monitor_stream(self, packets):
_signal = self._beam_monitor.signal
_time = self._beam_monitor.time
plse = np.array([0, 5, 6, 11])
base = np.array([2, 3, 8, 9])
i = 0
beam_monitor = np.recarray(shape=np.shape(packets.time)[0], dtype=BM_TYPE)
for tt, tme in enumerate(_time):
if (tme>=packets.time[0])&(tme<=packets.time[-1]):
beam_monitor.value[i] = _signal[tt][plse].sum() - _signal[tt][base].sum()
beam_monitor.time[i] = tme
i += 1
return beam_monitor[:i+1] # TODO: the '+1' is strange. Why needed?
def info(self):
output = ""
for key in ['owner', 'experiment', 'sample', 'instrument_settings']:
@@ -558,10 +578,11 @@ class AmorEventData(AmorHeader):
new_events = np.concatenate([self.data.events, other.data.events]).view(np.recarray)
new_pulses = np.concatenate([self.data.pulses, other.data.pulses]).view(np.recarray)
new_proton_current = np.concatenate([self.data.proton_current, other.data.proton_current]).view(np.recarray)
new_beam_monitor = np.concatenate([self.data.beam_monitor, other.data.beam_monitor]).view(np.recarray)
new_packets = np.concatenate([self.data.packets, other.data.packets]).view(np.recarray)
new_packets.start_index[self.data.packets.shape[0]:] += self.data.events.shape[0]
self.data = AmorEventStream(new_events, new_packets, new_pulses, new_proton_current)
# Indicate that this is amodified dataset, basically counts number of appends as negative indices
self.data = AmorEventStream(new_events, new_packets, new_pulses, new_proton_current, new_beam_monitor)
# Indicate that this is a modified dataset, basically counts number of appends as negative indices
self.last_index = min(self.last_index-1, -1)
self.file_list += other.file_list
@@ -589,5 +610,6 @@ class AmorEventData(AmorHeader):
setattr(output, key, value)
# TODO: this is not strictly correct, as the packet/event relationship is lost
output.data = AmorEventStream(self.data.events[event_filter], self.data.packets,
self.data.pulses[pulse_filter], self.data.proton_current)
self.data.pulses[pulse_filter], self.data.proton_current,
self.data.beam_monitor)
return output
eos/options.py
+2 -2
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@@ -247,7 +247,7 @@ class MonitorType(StrEnum):
debug = 'x'
MONITOR_UNITS = {
MonitorType.neutron_monitor: 'cnts',
MonitorType.neutron_monitor: 'au',
MonitorType.proton_charge: 'mC',
MonitorType.time: 's',
MonitorType.auto: 'various',
@@ -273,7 +273,7 @@ class ExperimentConfig(ArgParsable):
},
)
chopperSpeed: float = field(
default=500,
default=450,
metadata={
'short': 'cs',
'group': 'instrument settings',
eos/projection.py
+1 -1
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@@ -829,4 +829,4 @@ class CombinedProjection(ProjectionInterface):
pi.update_plot()
# def update_range(self, event):
# ...
# ...