Merge remote-tracking branch 'AMOR-DR/main'

# Conflicts:
#	eos/file_reader.py

eos/event_data_types.py

@@ -39,6 +39,7 @@ 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)])
+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
@@ -68,6 +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

@@ -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

@@ -7,6 +7,7 @@ import sys
 import h5py
 import numpy as np
 import logging
+import subprocess
 
 from datetime import datetime
 
@@ -16,7 +17,7 @@ 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, DA00EventBuffer
+    PC_TYPE, BM_TYPE, DA00EventBuffer
 
 try:
     import zoneinfo
@@ -74,7 +75,7 @@ class AmorHeader:
 
             data=('entry1/detector/data', None),  # data group used to load events from
             trigger=('entry1/detector/trigger', float),
-            monitor=('entry1/beam_monitor', None), # special data group (da00 flat-buffer scheme)
+            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),
             )
@@ -457,14 +458,15 @@ class AmorEventData(AmorHeader):
         events.pixelID = data_group['event_id'][self.first_index:self.last_index+1]
         events.mask = 0
 
-        self._monitor = self.rv('monitor', default=None)
+        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)
 
         # read parameter logs not present in old files to ensure they are in self._log_keys if they exist
         _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
@@ -521,8 +523,8 @@ class AmorEventData(AmorHeader):
             pulseTimeS = chopper1TriggerTime
         else:
             logging.critical('     No chopper trigger data available, using event steram instead, pulse filtering will fail!')
-            startTime = np.array(self._monitor.time[0], dtype=np.int64)
-            pulseTimeS = self._monitor.time
+            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
@@ -546,6 +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]
+
     def info(self):
         output = ""
         for key in ['owner', 'experiment', 'sample', 'instrument_settings']:
@@ -562,10 +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
 
@@ -593,5 +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

@@ -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',
@@ -434,7 +434,7 @@ class ReflectivityReductionConfig(ArgParsable):
                 'group': 'input data',
                 'help': 'apply convolution on lambda axes to smooth the normalization data, useful for low statistics'})
     scale: List[float] = field(
-            default_factory=lambda: [1.],
+            default_factory=lambda: [],
             metadata={
                 'short': 's',
                 'group': 'data manicure',

eos/projection.py

@@ -248,9 +248,9 @@ class LZProjection(ProjectionInterface):
     def scale(self, factor: float):
         if not self.is_normalized:
             raise ValueError("Dataset needs to be normalized, first")
-        self.data.ref *= factor
-        self.data.err *= factor
-        self.norm_monitor /= factor
+        self.data.ref /= factor
+        self.data.err /= factor
+        self.norm_monitor *= factor
 
     def project_on_qz(self):
         if not self.is_normalized:
@@ -829,4 +829,4 @@ class CombinedProjection(ProjectionInterface):
             pi.update_plot()
 
     # def update_range(self, event):
-    #     ...
+    #     ...

eos/reduction_reflectivity.py

@@ -204,11 +204,12 @@ class ReflectivityReduction:
         logging.info(f'    monitor = {self.monitor:8.2f} {MONITOR_UNITS[self.config.experiment.monitorType]}')
 
         proj:LZProjection = self.project_on_lz()
-        try:
-            scale = self.config.reduction.scale[i]
-        except IndexError:
-            scale = self.config.reduction.scale[-1]
-        proj.scale(scale)
+        if not self.config.reduction.is_default('scale'):
+            try:
+                scale = self.config.reduction.scale[i]
+            except IndexError:
+                scale = self.config.reduction.scale[-1]
+            proj.scale(scale)
 
         if 'Rqz.ort' in self.config.output.outputFormats:
             headerRqz = self.header.orso_header()