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adapted parameter pathes for hdf file, introduced chopper phases from file

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stahn
2025-05-29 18:11:51 +02:00
parent a947a70d2d
commit 5f94cc7b92
1 changed files with 20 additions and 69 deletions
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89
libeos/file_reader.py
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@@ -203,6 +203,8 @@ class AmorData:
self.filter_project_x()
self.correct_for_chopper_phases()
self.correct_for_chopper_opening()
self.calculate_derived_properties()
@@ -216,7 +218,7 @@ class AmorData:
#self.chopper2TriggerTime = self.chopper1TriggerTime
# + np.array(self.hdf['entry1/Amor/chopper/ch2_trigger/event_time_offset'][:], dtype=np.int64)
self.startTime = self.chopper1TriggerTime[0]
self.stopTime = self.chopper1TriggerTime[-2]
self.stopTime = self.chopper1TriggerTime[-3]
if self.seriesStartTime is None:
self.seriesStartTime = self.startTime
logging.debug(f' series start time (epoch): {self.seriesStartTime/1e9:13.2f} s')
@@ -233,65 +235,6 @@ class AmorData:
self.pixelID_e = np.array(self.hdf['/entry1/Amor/detector/data/event_id'][:], dtype=np.int64)
self.dataPacket_p = np.array(self.hdf['/entry1/Amor/detector/data/event_index'][:], dtype=np.uint64)
self.dataPacketTime_p = np.array(self.hdf['/entry1/Amor/detector/data/event_time_zero'][:], dtype=np.int64)
#if self.config.monitorType in ['auto', 'p']:
# try:
# self.currentTime = np.array(self.hdf['entry1/Amor/detector/proton_current/time'][:], dtype=np.int64)
# self.current = np.array(self.hdf['entry1/Amor/detector/proton_current/value'][:,0], dtype=float)
# if len(self.current)>4:
# self.config.monitorType = 'p'
# else:
# self.config.monitorType = 't'
# except(KeyError, IndexError):
# self.config.monitorType = 't'
#else:
# self.config.monitorType = 't'
#TODO: protonMonitor
# def sort_pulses(self):
# pulseTime = np.sort(self.dataPacketTime_p)
# print(np.shape(pulseTime))
# pulseTime = pulseTime[np.abs(pulseTime[:]-np.roll(pulseTime, 1)[:])>5]
# print(np.shape(pulseTime))
# pulseTime -= np.int64(self.seriesStartTime)
# pulseTime = pulseTime[pulseTime>=0]
# print(np.shape(pulseTime))
# pulseTime = pulseTime[pulseTime<=(self.stopTime-self.seriesStartTime)]
# print(np.shape(pulseTime))
#
# chopperPeriod = np.int64(2*self.tau*1e9)
#
# # fill in missing pulse times
# # TODO: check for real end time
# try:
# # further files
# # TODO: use the first pulse of the respective measurement
# #nextPulseTime = startTime % np.int64(self.tau*2e9)
# #nextPulseTime = self.pulseTimeS[-1] + chopperPeriod
# nextPulseTime = pulseTime[0]
# except AttributeError:
# # first file
# nextPulseTime = pulseTime[0] % np.int64(self.tau*2e9)
#
# # calculate where time tiefference between pulses exceeds its time by more than 1/2
# # this yields the number of missing pulses
# pulseLengths = pulseTime[1:]-pulseTime[:-1]
# pulseExtra = (pulseLengths-np.int64(self.tau*1e9))//np.int64(self.tau*2e9)
# gap_indices = np.where(pulseExtra>0)[0]
#
# if len(gap_indices)==0:
# # no missing pulses, just use given array
# self.pulseTimeS = np.array(pulseTime, dtype=np.int64)
# return
# self.pulseTimeS = np.array(pulseTime[:gap_indices[0]+1], dtype=np.int64)
# last_index = gap_indices[0]
# for gapi in gap_indices[1:]:
# # insert missing pulses into each gap
# gap_pulses = pulseTime[last_index]+np.arange(1, pulseExtra[last_index]+1)*chopperPeriod
# self.pulseTimeS = np.append(self.pulseTimeS, gap_pulses)
# self.pulseTimeS = np.append(self.pulseTimeS, pulseTime[last_index+1:gapi+1])
# last_index = gapi
# if last_index<len(pulseTime):
# self.pulseTimeS = np.append(self.pulseTimeS, pulseTime[last_index:-1])
def get_current_per_pulse(self, pulseTimeS, currentTimeS, currents):
# add currents for early pulses and current time value after last pulse (j+1)
@@ -356,7 +299,8 @@ class AmorData:
def calculate_derived_properties(self):
self.lamdaMax = const.lamdaCut+1.e13*self.tau*const.hdm/(self.chopperDetectorDistance+124.)
if nb_helpers:
#if nb_helpers:
if False:
self.lamda_e, self.qz_e, self.mask_e = nb_helpers.calculate_derived_properties_focussing(
self.tof_e, self.detXdist_e, self.delta_e, self.mask_e,
self.config.lambdaRange[0], self.config.lambdaRange[1], self.nu, self.mu,
@@ -364,6 +308,7 @@ class AmorData:
)
return
# lambda
print(self.chopperDetectorDistance)
self.lamda_e = (1.e13*const.hdm)*self.tof_e/(self.chopperDetectorDistance+self.detXdist_e)
self.mask_e = np.logical_and(self.mask_e, (self.config.lambdaRange[0]<=self.lamda_e) & (
self.lamda_e<=self.config.lambdaRange[1]))
@@ -386,6 +331,9 @@ class AmorData:
self.qx_e = 2*np.pi * ((np.cos(np.deg2rad(alphaF_e)) - np.cos(np.deg2rad(alphaI)))/self.lamda_e)
self.header.measurement_scheme = 'energy-dispersive'
def correct_for_chopper_phases(self):
self.tof_e += self.tau * (self.ch1TriggerPhase + self.chopperPhase/2)/180
def correct_for_chopper_opening(self):
# correct tof for beam size effect at chopper: t_cor = (delta / 180 deg) * tau
if self.config.incidentAngle == 'alphaF':
@@ -407,7 +355,7 @@ class AmorData:
self.mask_e = (self.config.yRange[0]<=detY_e) & (detY_e<=self.config.yRange[1])
def merge_frames(self):
total_offset = self.tofCut+self.tau*self.config.chopperPhaseOffset/180.
total_offset = self.tofCut + self.tau * (self.ch1TriggerPhase + self.chopperPhase/2)/180
if nb_helpers:
self.tof_e = nb_helpers.merge_frames(self.tof_e, self.tofCut, self.tau, total_offset)
else:
@@ -425,7 +373,8 @@ class AmorData:
def read_individual_header(self):
self.chopperDistance = float(np.take(self.hdf['entry1/Amor/chopper/pair_separation'], 0))
self.detectorDistance = float(np.take(self.hdf['entry1/Amor/detector/transformation/distance'], 0))
self.chopperDetectorDistance = self.detectorDistance-float(np.take(self.hdf['entry1/Amor/chopper/distance'], 0))
#self.chopperDetectorDistance = self.detectorDistance-float(np.take(self.hdf['entry1/Amor/chopper/distance'], 0))
self.chopperDetectorDistance = 19000
self.tofCut = const.lamdaCut*self.chopperDetectorDistance/const.hdm*1.e-13
polarizationStates = [
@@ -441,12 +390,12 @@ class AmorData:
'mm',
]
try:
self.mu = float(np.take(self.hdf['/entry1/Amor/master_parameters/mu/value'], 0))
self.nu = float(np.take(self.hdf['/entry1/Amor/master_parameters/nu/value'], 0))
self.mu = float(np.take(self.hdf['/entry1/Amor/instrument_control_parameters/mu'], 0))
self.nu = float(np.take(self.hdf['/entry1/Amor/instrument_control_parameters/nu'], 0))
self.kap = 0.245
#self.kap = float(np.take(self.hdf['/entry1/Amor/master_parameters/kap/value'], 0))
self.kad = float(np.take(self.hdf['/entry1/Amor/master_parameters/kad/value'], 0))
self.div = float(np.take(self.hdf['/entry1/Amor/master_parameters/div/value'], 0))
#self.kap = float(np.take(self.hdf['/entry1/Amor/instrument_control_parameters/kap/value'], 0))
self.kad = float(np.take(self.hdf['/entry1/Amor/instrument_control_parameters/kad'], 0))
self.div = float(np.take(self.hdf['/entry1/Amor/instrument_control_parameters/div'], 0))
self.chopperSpeed = float(np.take(self.hdf['/entry1/Amor/chopper/rotation_speed'], 0))
#self.chopperSpeed = float(np.take(self.hdf['/entry1/Amor/chopper/rotation_speed/value'], 0))
self.chopperPhase = float(np.take(self.hdf['/entry1/Amor/chopper/phase'], 0))
@@ -459,6 +408,7 @@ class AmorData:
except(KeyError, IndexError):
logging.warning(" using parameters from nicos cache")
year_date = str(self.start_date).replace('-', '/', 1)
# TODO: check new cache pathes
#cachePath = '/home/amor/nicosdata/amor/cache/'
#cachePath = '/home/nicos/amorcache/'
cachePath = '/home/amor/cache/'
@@ -474,7 +424,8 @@ class AmorData:
self.div = float(value)
value = str(subprocess.getoutput(f'/usr/bin/grep "value" {cachePath}nicos-ch1_speed/{year_date}')).split('\t')[-1]
self.chopperSpeed = float(value)
self.chopperPhase = self.config.chopperPhase
value = str(subprocess.getoutput(f'/usr/bin/grep "value" {cachePath}nicos-chopper_phase/{year_date}')).split('\t')[-1]
self.chopperPhase = float(value)
self.tau = 30. / self.chopperSpeed
if self.config.muOffset: