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changed path variable names + new option lowCurrentThreshold

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This commit is contained in:
stahn
2024-10-04 15:10:11 +02:00
parent 1f394b0e86
commit b848d66290
4 changed files with 44 additions and 35 deletions
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24
libeos/command_line.py
View File

@@ -26,14 +26,14 @@ def commandLineArgs():
input_data.add_argument("-nm", "--normalisationMethod",
default = Defaults.normalisationMethod,
help = "normalisation method: [o]verillumination, [u]nderillumination, [d]irect_beam")
input_data.add_argument("--raw",
input_data.add_argument("-rp", "--rawPath",
type = str,
default = Defaults.raw,
help = "relative path to directory with .hdf files")
input_data.add_argument("-d", "--dataPath",
default = Defaults.rawPath,
help = "ath to directory with .hdf files")
input_data.add_argument("-op", "--outputPath",
type = str,
default = Defaults.dataPath,
help = "relative path for output")
default = Defaults.outputPath,
help = "path for output")
input_data.add_argument("-Y", "--year",
default = Defaults.year,
type = int,
@@ -98,6 +98,11 @@ def commandLineArgs():
nargs = 2,
type = float,
help = "q_z range")
masks.add_argument("-ct", "--lowCurrentThreshold",
default = Defaults.lowCurrentThreshold,
type = float,
help = "proton current threshold for discarding neutron pulses")
overwrite = clas.add_argument_group('overwrite')
overwrite.add_argument("-cs", "--chopperSpeed",
@@ -172,8 +177,7 @@ def command_line_options():
reader_config = ReaderConfig(
year = clas.year,
raw = clas.raw,
dataPath = clas.dataPath
rawPath = clas.rawPath,
)
experiment_config = ExperimentConfig(
sampleModel = clas.sampleModel,
@@ -182,6 +186,7 @@ def command_line_options():
yRange = clas.yRange,
lambdaRange = clas.lambdaRange,
qzRange = clas.qzRange,
lowCurrentThreshold = clas.lowCurrentThreshold,
incidentAngle = clas.incidentAngle,
mu = clas.mu,
nu = clas.nu,
@@ -202,7 +207,8 @@ def command_line_options():
)
output_config = OutputConfig(
outputFormats = output_format_list(clas.outputFormat),
outputName = clas.outputName
outputName = clas.outputName,
outputPath = clas.outputPath,
)
return EOSConfig(reader_config, experiment_config, reduction_config, output_config)

14
libeos/file_reader.py
View File

@@ -120,7 +120,7 @@ class AmorData:
def path_generator(self, number):
fileName = f'amor{self.reader_config.year}n{number:06d}.hdf'
path = ''
for rawd in self.reader_config.raw:
for rawd in self.reader_config.rawPath:
if os.path.exists(os.path.join(rawd,fileName)):
path = rawd
break
@@ -128,7 +128,7 @@ class AmorData:
if os.path.exists(f'/afs/psi.ch/project/sinqdata/{self.reader_config.year}/amor/{int(number/1000)}/{fileName}'):
path = f'/afs/psi.ch/project/sinqdata/{self.reader_config.year}/amor/{int(number/1000)}'
else:
sys.exit(f'# ERROR: the file {fileName} can not be found in {self.reader_config.raw}!')
sys.exit(f'# ERROR: the file {fileName} can not be found in {self.reader_config.rawPath}')
return os.path.join(path, fileName)
#-------------------------------------------------------------------------------------------------
def expand_file_list(self, short_notation):
@@ -168,7 +168,7 @@ class AmorData:
if self.readHeaderInfo:
self.read_header_info()
logging.warning(f' data from file: {fileName}')
logging.warning(f' from file: {fileName}')
self.read_individual_header()
# add header content
@@ -244,11 +244,11 @@ class AmorData:
def associate_pulse_with_monitor(self):
if self.monitorType == 'protonCharge':
lowCurrentThreshold = 0.05 # mA
#lowCurrentThreshold = 0.05 # mA
self.currentTime -= self.seriesStartTime
self.monitorPerPulse = get_current_per_pulse(self.pulseTimeS, self.currentTime, self.current) * 2*self.tau * 1e-3
# filter low-current pulses
self.monitorPerPulse = np.where(self.monitorPerPulse > 2*self.tau *lowCurrentThreshold, self.monitorPerPulse, 0)
self.monitorPerPulse = np.where(self.monitorPerPulse > 2*self.tau * self.config.lowCurrentThreshold/1e3, self.monitorPerPulse, 0)
# remove 'partially filled' pulses
self.monitorPerPulse[0] = 0
self.monitorPerPulse[-1] = 0
@@ -275,8 +275,8 @@ class AmorData:
self.tof_e = self.tof_e[filter_e]
self.pixelID_e = self.pixelID_e[filter_e]
self.wallTime_e = self.wallTime_e[filter_e]
logging.warning(f' rejected {np.shape(self.monitorPerPulse)[0]-np.shape(goodTimeS)[0]} pulses due to low beam current')
logging.warning(f' rejected {np.shape(filter_e)[0]-np.shape(self.tof_e)[0]} events due to low beam current')
logging.info(f' rejected {np.shape(self.monitorPerPulse)[0]-np.shape(goodTimeS)[0]} pulses due to low beam current')
logging.info(f' rejected {np.shape(filter_e)[0]-np.shape(self.tof_e)[0]} events due to low beam current')
def filter_qz_range(self, norm):
if self.config.qzRange[1]<0.3 and not norm:

19
libeos/options.py
View File

@@ -5,13 +5,14 @@ from dataclasses import dataclass, field
from typing import Optional, Tuple
from datetime import datetime
from os import path
import numpy as np
import logging
class Defaults:
# fileIdentifier
dataPath = '.'
raw = ['.', path.join('.','raw'), path.join('..','raw'), path.join('..','..','raw')]
outputPath = '.'
rawPath = ['.', path.join('.','raw'), path.join('..','raw'), path.join('..','..','raw')]
year = datetime.now().year
normalisationFileIdentifier = []
normalisationMethod = 'o'
@@ -35,6 +36,7 @@ class Defaults:
mu = 0
nu = 0
sampleModel = None
lowCurrentThreshold = 50
#
@@ -42,8 +44,7 @@ class Defaults:
@dataclass
class ReaderConfig:
year: int
dataPath: str
raw: Tuple[str]
rawPath: Tuple[str]
startTime: Optional[float] = 0
@dataclass
@@ -53,6 +54,7 @@ class ExperimentConfig:
yRange: Tuple[float, float]
lambdaRange: Tuple[float, float]
qzRange: Tuple[float, float]
lowCurrentThreshold: float
sampleModel: Optional[str] = None
chopperPhaseOffset: float = 0
@@ -80,6 +82,7 @@ class ReductionConfig:
class OutputConfig:
outputFormats: list
outputName: str
outputPath: str
@dataclass
class EOSConfig:
@@ -105,10 +108,10 @@ class EOSConfig:
inpt += f' -Y {self.reader.year}'
else:
inpt += f' -Y {datetime.now().year}'
if self.reader.dataPath != '.':
inpt += f' --dataPath {self.reader.dataPath}'
#if self.reader.raw != '.':
# inpt = f' --rawd {self.reader.raw}'
if self.output.outputPath != '.':
inpt += f' --outputdPath {self.output.outputPath}'
if np.shape(self.reader.rawPath)[0] == 1:
inpt += f' --rawPath {self.reader.rawPath}'
if self.reduction.subtract:
inpt += f' -subtract {self.reduction.subtract}'
if self.reduction.normalisationFileIdentifier:

22
libeos/reduction.py
View File

@@ -23,9 +23,9 @@ class AmorReduction:
self.header.reduction.call = config.call_string()
def reduce(self):
if not os.path.exists(f'{self.reader_config.dataPath}'):
logging.debug(f'Creating destination path {self.reader_config.dataPath}')
os.system(f'mkdir {self.reader_config.dataPath}')
if not os.path.exists(f'{self.output_config.outputPath}'):
logging.debug(f'Creating destination path {self.output_config.outputPath}')
os.system(f'mkdir {self.output_config.outputPath}')
# load or create normalisation matrix
if self.reduction_config.normalisationFileIdentifier:
@@ -185,15 +185,15 @@ class AmorReduction:
# make overwriting log lines possible by removing newline at the end
#logging.StreamHandler.terminator = "\r"
logging.warning(f' time slizing')
logging.info(' slize time monitor')
for ti, time in enumerate(np.arange(start, stop, interval)):
logging.info(f' slize {ti:4d} t = {time:5.0f}')
filter_e = np.where((time<wallTime_e) & (wallTime_e<time+interval), True, False)
lamda_e = self.file_reader.lamda_e[filter_e]
detZ_e = self.file_reader.detZ_e[filter_e]
filter_m = np.where((time<pulseTimeS) & (pulseTimeS<time+interval), True, False)
self.monitor = np.sum(self.file_reader.monitorPerPulse[filter_m])
logging.info(f' monitor = {self.monitor:7.2f}')
logging.info(f' {ti:<4d} {time:5.0f} {self.monitor:7.2f}')
qz_lz, qx_lz, ref_lz, err_lz, res_lz, lamda_lz, theta_lz, int_lz, mask_lz = self.project_on_lz(
self.file_reader, self.norm_lz, self.normAngle, lamda_e, detZ_e)
@@ -227,16 +227,16 @@ class AmorReduction:
self.datasetsRqz.append(orso_data)
# reset normal logging behavior
#logging.StreamHandler.terminator = "\n"
logging.info(f' done')
logging.info(f' done {time+interval:5.0f}')
def save_Rqz(self):
fname = os.path.join(self.reader_config.dataPath, f'{self.output_config.outputName}.Rqz.ort')
fname = os.path.join(self.output_config.outputPath, f'{self.output_config.outputName}.Rqz.ort')
logging.warning(f' {fname}')
theSecondLine = f' {self.header.experiment.title} | {self.header.experiment.start_date} | sample {self.header.sample.name} | R(q_z)'
fileio.save_orso(self.datasetsRqz, fname, data_separator='\n', comment=theSecondLine)
def save_Rtl(self):
fname = os.path.join(self.reader_config.dataPath, f'{self.output_config.outputName}.Rlt.ort')
fname = os.path.join(self.output_config.outputPath, f'{self.output_config.outputName}.Rlt.ort')
logging.warning(f' {fname}')
theSecondLine = f' {self.header.experiment.title} | {self.header.experiment.start_date} | sample {self.header.sample.name} | R(lambda, theta)'
fileio.save_orso(self.datasetsRlt, fname, data_separator='\n', comment=theSecondLine)
@@ -304,7 +304,7 @@ class AmorReduction:
return q_q[1:], R_q, dR_q, dq_q
def loadRqz(self, name):
fname = os.path.join(self.reader_config.dataPath, name)
fname = os.path.join(self.output_config.outputPath, name)
if os.path.exists(fname):
fileName = fname
elif os.path.exists(f'{fname}.Rqz.ort'):
@@ -317,12 +317,12 @@ class AmorReduction:
return q_q, Sq_q, dS_q, fileName
def create_normalisation_map(self, short_notation):
dataPath = self.reader_config.dataPath
outputPath = self.output_config.outputPath
normalisation_list = expand_file_list(short_notation)
name = str(normalisation_list[0])
for i in range(1, len(normalisation_list), 1):
name = f'{name}_{normalisation_list[i]}'
n_path = os.path.join(dataPath, f'{name}.norm')
n_path = os.path.join(outputPath, f'{name}.norm')
if os.path.exists(n_path):
logging.warning(f'normalisation matrix: found and using {n_path}')
with open(n_path, 'rb') as fh: