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Merge pull request #4 from jochenstahn/input_update

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Small fixes and improvements
This commit is contained in:
Jochen Stahn
2024-09-25 11:02:16 +02:00
committed by GitHub
parent ee077b19f7 26fdfd64d6
commit 55d102f3c0
6 changed files with 84 additions and 72 deletions
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libeos/__init__.py
+2 -2
View File
@@ -2,5 +2,5 @@
Package to handle data redction at AMOR instrument to be used by eos.py script.
"""
__version__ = '2.0'
__date__ = '2024-03-04'
__version__ = '2.1'
__date__ = '2024-08-25'
libeos/command_line.py
-1
View File
@@ -1,5 +1,4 @@
import argparse
from datetime import date
from .logconfig import update_loglevel
from .options import ReaderConfig, EOSConfig, ExperimentConfig, OutputConfig, ReductionConfig, Defaults
libeos/file_reader.py
+16 -12
View File
@@ -9,6 +9,7 @@ import h5py
import numpy as np
import scipy as sp
from orsopy import fileio
from orsopy.fileio.model_language import SampleModel
from . import const
from .header import Header
@@ -44,6 +45,8 @@ class AmorData:
tofCut: float
start_date: str
seriesStartTime = None
#-------------------------------------------------------------------------------------------------
def __init__(self, header: Header, reader_config: ReaderConfig, config: ExperimentConfig,
short_notation:str, norm=False):
@@ -178,15 +181,13 @@ class AmorData:
self.read_event_stream()
totalNumber = np.shape(self.tof_e)[0]
self.sort_pulses()
self.associate_pulse_with_current()
self.sort_events_by_pulse()
self.define_monitor()
self.extract_walltime(norm)
# sort the events into the related pulses
self.monitor_threshold()
self.extract_walltime(norm)
self.filter_strange_times()
@@ -207,12 +208,10 @@ class AmorData:
pulseTime = np.sort(self.dataPacketTime_p)
pulseTime = pulseTime[np.abs(pulseTime[:]-np.roll(pulseTime, 1)[:])>5]
try:
self.seriesStartTime
except:
self.seriesStartTime = pulseTime[0]
if self.seriesStartTime is None:
self.seriesStartTime = float(pulseTime[0])
pulseTime -= self.seriesStartTime
stopTime = pulseTime[-1]
self.stopTime = float(pulseTime[-1])
# fill in missing pulse times
# TODO: check for real end time
@@ -223,6 +222,8 @@ class AmorData:
self.pulseTimeS = np.append(self.pulseTimeS, nxt)
nxt += chopperPeriod
self.pulseTimeS = np.append(self.pulseTimeS, tt)
# remove 'partially filled' pulses
self.pulseTimeS = self.pulseTimeS[1:-1]
def associate_pulse_with_current(self):
if self.monitorType == 'protonCharge':
@@ -350,11 +351,14 @@ class AmorData:
self.pixelID_e = np.array(self.hdf['/entry1/Amor/detector/data/event_id'][:], dtype=int)
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.uint64)/1e9
self.dataPacketTime_p = np.array(self.hdf['/entry1/Amor/detector/data/event_time_zero'][:], dtype=int)
self.dataPacketTime_p = np.array(self.hdf['/entry1/Amor/detector/data/event_time_zero'][:], dtype=float)
try:
self.currentTime = np.array(self.hdf['entry1/Amor/detector/proton_current/time'][:], dtype=int)
self.current = np.array(self.hdf['entry1/Amor/detector/proton_current/value'][:,0], dtype=float)
self.monitorType = 'protonCharge'
if len(self.current)>0:
self.monitorType = 'protonCharge'
else:
self.monitorType = 'countingTime'
except(KeyError, IndexError):
self.monitorType = 'countingTime'
libeos/options.py
+48 -47
View File
@@ -5,6 +5,7 @@ from dataclasses import dataclass, field
from typing import Optional, Tuple
from datetime import datetime
import logging
class Defaults:
# fileIdentifier
@@ -99,64 +100,64 @@ class EOSConfig:
base = 'python eos.py'
inpt = ''
if self.reader_config.year:
inpt += f' -Y {self.reader_config.year}'
if self.reader.year:
inpt += f' -Y {self.reader.year}'
else:
inpt += f' -Y {datetime.now().year}'
if self.reader_config.dataPath != '.':
inpt += f' --dataPath {self.reader_config.dataPath}'
#if self.reader_config.raw != '.':
# inpt = f' --rawd {self.reader_config.raw}'
if self.reduction_config.subtract:
inpt += f' -subtract {self.reduction_config.subtract}'
if self.reduction_config.normalisationFileIdentifier:
inpt += f' -n {" ".join(self.reduction_config.normalisationFileIdentifier)}'
if self.reduction_config.fileIdentifier:
inpt += f' -f {" ".join(self.reduction_config.fileIdentifier)}'
if self.reader.dataPath != '.':
inpt += f' --dataPath {self.reader.dataPath}'
#if self.reader.raw != '.':
# inpt = f' --rawd {self.reader.raw}'
if self.reduction.subtract:
inpt += f' -subtract {self.reduction.subtract}'
if self.reduction.normalisationFileIdentifier:
inpt += f' -n {" ".join(self.reduction.normalisationFileIdentifier)}'
if self.reduction.fileIdentifier:
inpt += f' -f {" ".join(self.reduction.fileIdentifier)}'
otpt = ''
if self.reduction_config.qResolution:
otpt += f' -r {self.reduction_config.qResolution}'
if self.output_config.outputName:
otpt += f' -o {self.output_config.outputName}'
if self.output_config.outputFormats != ['Rqz.ort']:
otpt += f' -of {" ".join(self.output_config.outputFormats)}'
if self.reduction.qResolution:
otpt += f' -r {self.reduction.qResolution}'
if self.output.outputName:
otpt += f' -o {self.output.outputName}'
if self.output.outputFormats != ['Rqz.ort']:
otpt += f' -of {" ".join(self.output.outputFormats)}'
mask = ''
if self.experiment_config.yRange != Defaults.yRange:
mask += f' -y {" ".join(str(ii) for ii in self.experiment_config.yRange)}'
if self.experiment_config.lambdaRange!= Defaults.lambdaRange:
mask += f' -l {" ".join(str(ff) for ff in self.experiment_config.lambdaRange)}'
if self.reduction_config.thetaRange != Defaults.thetaRange:
mask += f' -T {" ".join(str(ff) for ff in self.reduction_config.thetaRange)}'
elif self.reduction_config.thetaRangeR != Defaults.thetaRangeR:
mask += f' -t {" ".join(str(ff) for ff in self.reduction_config.thetaRangeR)}'
if self.experiment_config.qzRange!= Defaults.qzRange:
mask += f' -q {" ".join(str(ff) for ff in self.experiment_config.qzRange)}'
if self.experiment.yRange != Defaults.yRange:
mask += f' -y {" ".join(str(ii) for ii in self.experiment.yRange)}'
if self.experiment.lambdaRange!= Defaults.lambdaRange:
mask += f' -l {" ".join(str(ff) for ff in self.experiment.lambdaRange)}'
if self.reduction.thetaRange != Defaults.thetaRange:
mask += f' -T {" ".join(str(ff) for ff in self.reduction.thetaRange)}'
elif self.reduction.thetaRangeR != Defaults.thetaRangeR:
mask += f' -t {" ".join(str(ff) for ff in self.reduction.thetaRangeR)}'
if self.experiment.qzRange!= Defaults.qzRange:
mask += f' -q {" ".join(str(ff) for ff in self.experiment.qzRange)}'
para = ''
if self.experiment_config.chopperPhase != Defaults.chopperPhase:
para += f' --chopperPhase {self.experiment_config.chopperPhase}'
if self.experiment_config.chopperPhaseOffset != Defaults.chopperPhaseOffset:
para += f' --chopperPhaseOffset {self.experiment_config.chopperPhaseOffset}'
if self.experiment_config.mu:
para += f' --mu {self.experiment_config.mu}'
elif self.experiment_config.muOffset:
para += f' --muOffset {self.experiment_config.muOffset}'
if self.experiment_config.nu:
para += f' --nu {self.experiment_config.nu}'
if self.experiment.chopperPhase != Defaults.chopperPhase:
para += f' --chopperPhase {self.experiment.chopperPhase}'
if self.experiment.chopperPhaseOffset != Defaults.chopperPhaseOffset:
para += f' --chopperPhaseOffset {self.experiment.chopperPhaseOffset}'
if self.experiment.mu:
para += f' --mu {self.experiment.mu}'
elif self.experiment.muOffset:
para += f' --muOffset {self.experiment.muOffset}'
if self.experiment.nu:
para += f' --nu {self.experiment.nu}'
modl = ''
if self.experiment_config.sampleModel:
modl += f" --sampleModel '{self.experiment_config.sampleModel}'"
if self.experiment.sampleModel:
modl += f" --sampleModel '{self.experiment.sampleModel}'"
acts = ''
if self.reduction_config.autoscale:
acts += f' --autoscale {" ".join(str(ff) for ff in self.reduction_config.autoscale)}'
if self.reduction_config.scale != Defaults.scale:
acts += f' --scale {self.reduction_config.scale}'
if self.reduction_config.timeSlize:
acts += f' --timeSlize {" ".join(str(ff) for ff in self.reduction_config.timeSlize)}'
if self.reduction.autoscale:
acts += f' --autoscale {" ".join(str(ff) for ff in self.reduction.autoscale)}'
if self.reduction.scale != Defaults.scale:
acts += f' --scale {self.reduction.scale}'
if self.reduction.timeSlize:
acts += f' --timeSlize {" ".join(str(ff) for ff in self.reduction.timeSlize)}'
mlst = base + inpt + otpt
if mask:
@@ -179,7 +180,7 @@ class EOSConfig:
if modl:
mlst += ' ' + modl
print(mlst)
logging.debug(f'Argument list build in EOSConfig.call_string: {mlst}')
return mlst
libeos/reduction.py
+6 -6
View File
@@ -18,9 +18,9 @@ class AmorReduction:
self.reduction_config = config.reduction
self.output_config = config.output
self.grid = Grid(config.reduction.qResolution, config.experiment.qzRange)
self.header = Header()
self.header.reduction.call = EOSConfig.call_string(self)
self.header = Header()
self.header.reduction.call = config.call_string()
def reduce(self):
if not os.path.exists(f'{self.reader_config.dataPath}'):
@@ -80,8 +80,8 @@ class AmorReduction:
self.file_reader, self.norm_lz, self.normAngle, lamda_e, detZ_e)
monitor = self.file_reader.monitor
if monitor>1 :
ref_lz *= 1/monitor
err_lz *= 1/monitor
ref_lz /= monitor
err_lz /= monitor
try:
ref_lz *= self.reduction_config.scale[i]
err_lz *= self.reduction_config.scale[i]
@@ -93,7 +93,7 @@ class AmorReduction:
headerRqz.data_set = f'Nr {i} : mu = {self.file_reader.mu:6.3f} deg'
if qz_lz[0,int(np.shape(qz_lz)[1]/2)] < 0:
# assuming a 'measurement from below'
# assuming a 'measurement from below' when center of detector at negative qz
qz_lz *= -1
# projection on qz-grid
@@ -221,7 +221,7 @@ class AmorReduction:
self.datasetsRqz.append(orso_data)
# reset normal logging behavior
logging.StreamHandler.terminator = "\n"
logging.warning(f' time slize {ti:4d}, done')
logging.warning(f' time slizing, done')
def save_Rqz(self):
fname = os.path.join(self.reader_config.dataPath, f'{self.output_config.outputName}.Rqz.ort')
tests/test_full_analysis.py
+12 -4
View File
@@ -6,6 +6,8 @@ from libeos import options, reduction, logconfig
logconfig.setup_logging()
logconfig.update_loglevel(True, False)
# TODO: add test for new features like proton charge normalization
class FullAmorTest(TestCase):
@classmethod
def setUpClass(cls):
@@ -19,7 +21,9 @@ class FullAmorTest(TestCase):
self.pr.enable()
self.reader_config = options.ReaderConfig(
year=2023,
dataPath=os.path.join('..', "test_data"))
dataPath=os.path.join('..', "test_data"),
raw=(os.path.join('..', "test_data"),)
)
def tearDown(self):
self.pr.disable()
@@ -37,14 +41,16 @@ class FullAmorTest(TestCase):
yRange=(11., 41.),
lambdaRange=(2., 15.),
qzRange=(0.005, 0.30),
offSpecular=False,
incidentAngle=options.Defaults.incidentAngle,
mu=0,
nu=0,
muOffset=0.0,
sampleModel='air | 10 H2O | D2O'
)
reduction_config = options.ReductionConfig(
normalisationMethod=options.Defaults.normalisationMethod,
qResolution=0.01,
qzRange=options.Defaults.qzRange,
thetaRange=(-12., 12.),
thetaRangeR=(-12., 12.),
fileIdentifier=["610"],
@@ -72,19 +78,21 @@ class FullAmorTest(TestCase):
yRange=(11., 41.),
lambdaRange=(2., 15.),
qzRange=(0.005, 0.30),
offSpecular=False,
incidentAngle=options.Defaults.incidentAngle,
mu=0,
nu=0,
muOffset=0.0
)
reduction_config = options.ReductionConfig(
qResolution=0.01,
qzRange=options.Defaults.qzRange,
normalisationMethod=options.Defaults.normalisationMethod,
thetaRange=(-12., 12.),
thetaRangeR=(-12., 12.),
fileIdentifier=["610", "611", "608,612-613", "609"],
scale=[1],
normalisationFileIdentifier=["614"],
autoscale=(0.005, 0.008)
autoscale=(True, True)
)
output_config = options.OutputConfig(
outputFormats=["Rqz.ort"],