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reorganisation of orso headers. nit tested

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stahn
2024-01-31 15:37:27 +01:00
parent cd237c7fa5
commit 3794970d33
1 changed files with 91 additions and 43 deletions
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134
neos.py
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@@ -7,11 +7,13 @@ Author: Jochen Stahn
conventions (not strictly followed, yet):
- array names end with the suffix '_x[y]' with the meaning
_e = events
_e = events
_tof
_l = lambda
_t = theta
_q = q_z
_l = lambda
_t = theta
_z = detector z
_lz = (lambda, detector z)
_q = q_z
- to come
"""
@@ -152,6 +154,52 @@ class Defs:
hdm = 6.626176e-34/1.674928e-27 # h / m
lamdaCut = 2.5 # Aa
#=====================================================================================================
class Orso:
'''orso compatible output file header content'''
def __init__():
self.data_source = fileio.DataSource(
fileio.Person(
None,
None,
contact = None,
),
fileio.Experiment(
title = None,
instrument = None,
start_date = None,
probe = None,
facility = None,
proposalID = None
),
fileio.Sample(
name = None,
model = None,
sample_parameters = None,
),
fileio.Measurement(
instrument_settings = fileio.InstrumentSettings(
incident_angle = fileio.ValueRange(None, None, 'deg'),
wavelength = fileio.ValueRange(None, None, 'angstrom'),
polarisation = None,
configuration = None,
),
scheme = 'angle- and energy-dispersive',
data_files = [],
additional_files = None,
),
)
self.reduction = fileio.Reduction(
software = fileio.Software('eos', version=__version__),
timestamp = datetime.now(),
creator = None,
corrections = ['histogramming in lambda and alpha_f',
'gravity'],
computer = platform.node(),
call = ' '.join(sys.argv),
)
#=====================================================================================================
class AmorData:
'''read meta-data and event streams from .hdf file(s), apply filters and conversions'''
#-------------------------------------------------------------------------------------------------
@@ -274,13 +322,12 @@ class AmorData:
model = clas.sampleModel
# assembling orso header information
self.data_source = fileio.DataSource(
fileio.Person(
orso.data_source.owner = fileio.Person(
user_name,
None,
contact = user_email,
),
fileio.Experiment(
orso.data_source.experiment = fileio.Experiment(
title = title,
instrument = instrumentName,
start_date = self.start_date,
@@ -288,20 +335,19 @@ class AmorData:
facility = source,
proposalID = proposal_id
),
fileio.Sample(
orso.data_source.sample = fileio.Sample(
name = sampleName,
model = model,
sample_parameters = None,
),
fileio.Measurement(
instrument_settings = fileio.InstrumentSettings(
incident_angle = fileio.ValueRange(None, None, 'deg'),
wavelength = fileio.ValueRange(None, None, 'angstrom'),
polarisation = None,
configuration = None,
),
data_files = [],
scheme = 'angle- and energy-dispersive',
orso.data_source.measurement.instrument_settings = fileio.InstrumentSettings(
incident_angle = fileio.ValueRange(None, None, 'deg'),
wavelength = fileio.ValueRange(None, None, 'angstrom'),
polarisation = None,
configuration = None,
),
orso.data_source.measurement.data_files = [],
orso.data_source.measurement.scheme = 'angle- and energy-dispersive',
),
)
@@ -353,13 +399,13 @@ class AmorData:
# add header content
if self.readHeaderInfo:
self.readHeaderInfo = False
self.data_source.measurement.instrument_settings.incident_angle = fileio.ValueRange(self.mu+self.kap+self.kad-0.5*self.div,
orso.data_source.measurement.instrument_settings.incident_angle = fileio.ValueRange(self.mu+self.kap+self.kad-0.5*self.div,
self.mu+self.kap+self.kad+0.5*self.div,
'deg')
self.data_source.measurement.instrument_settings.wavelength = fileio.ValueRange(defs.lamdaCut, clas.lambdaRange[1], 'angstrom')
self.data_source.measurement.instrument_settings.mu = fileio.Value(self.mu, 'deg', comment='sample angle to horizon')
self.data_source.measurement.instrument_settings.nu = fileio.Value(self.nu, 'deg', comment='detector angle to horizon')
self.data_source.measurement.data_files.append(fileio.File(file=fileName.split('/')[-1], timestamp=fileDate))
orso.data_source.measurement.instrument_settings.wavelength = fileio.ValueRange(defs.lamdaCut, clas.lambdaRange[1], 'angstrom')
orso.data_source.measurement.instrument_settings.mu = fileio.Value(self.mu, 'deg', comment='sample angle to horizon')
orso.data_source.measurement.instrument_settings.nu = fileio.Value(self.nu, 'deg', comment='detector angle to horizon')
orso.data_source.measurement.data_files.append(fileio.File(file=fileName.split('/')[-1], timestamp=fileDate))
print(f'# mu = {self.mu:6.3f}, nu = {self.nu:6.3f}, kap = {self.kap:6.3f}, kad = {self.kap:6.3f}')
# TODO: should extract monitor from counts or beam current times time
@@ -419,10 +465,10 @@ class AmorData:
# q_z
if clas.offSpecular:
alphaI = self.kap + self.kad + self.mu
qz_e = 2*np.pi * ( np.sin( np.deg2rad(alphaF_e) ) + np.sin( np.deg2rad( alphaI ) ) ) / lamda_e
# qx_e = ....
qz_e = 2 * np.pi * ( np.sin( np.deg2rad(alphaF_e) ) + np.sin( np.deg2rad( alphaI ) ) ) / lamda_e
qx_e = 2 * np.pi * ( np.cos( np.deg2rad(alphaF_e) ) - np.cos( np.deg2rad( alphaI ) ) ) / lamda_e
else:
qz_e = 4*np.pi * np.sin( np.deg2rad(alphaF_e) ) / lamda_e
qz_e = 4 * np.pi * np.sin( np.deg2rad(alphaF_e) ) / lamda_e
# qx_e = 0.
# filter q_z range
@@ -494,6 +540,7 @@ def normalisation_map(short_notation):
head = f'normalisation matrix based on the measurements \n {fromHDF.file_list} \n nu - mu = {normAngle}\n shape= {np.shape(norm_lz)} (lambda, z) \n measured at mu = {fromHDF.mu:6.3f} deg \n N(l_lambda, z) = theta(z) / sum_i=-1..1 I(l_lambda+i, z)'
np.savetxt(f'{clas.dataPath}/{name}.norm', norm_lz, header = head)
normFileList = fromHDF.file_list
orso.data_source.measurement.additional_files = normFileList
return norm_lz, normAngle, normFileList
#=====================================================================================================
def output_format_list(outputFormat):
@@ -671,9 +718,10 @@ class Grid:
#=====================================================================================================
def main():
global startTime, grid, clas
global startTime, grid, clas, orso
clas = commandLineArgs()
grid = Grid()
orso = Orso()
startTime = 0
if not os.path.exists(f'{clas.dataPath}'):
os.system(f'mkdir {clas.dataPath}')
@@ -681,21 +729,21 @@ def main():
print('\n######## eos - data reduction for Amor ########')
reduction = fileio.Reduction(
software = fileio.Software('eos', version=__version__),
timestamp = datetime.now(),
creator = None,
corrections = ['histogramming in lambda and alpha_f',
'gravity'],
computer = platform.node(),
call = ' '.join(sys.argv),
)
#reduction = fileio.Reduction(
# software = fileio.Software('eos', version=__version__),
# timestamp = datetime.now(),
# creator = None,
# corrections = ['histogramming in lambda and alpha_f',
# 'gravity'],
# computer = platform.node(),
# call = ' '.join(sys.argv),
# )
# load or create normalisation matrix
if clas.normalisationFileIdentifier:
normalise = True
norm_lz, normAngle, normFileList = normalisation_map(clas.normalisationFileIdentifier[0])
reduction.corrections.append('normalisation with \'additional files\'')
orso.reduction.corrections.append('normalisation with \'additional files\'')
else:
normalise = False
norm_lz = grid.lz()
@@ -708,7 +756,7 @@ def main():
sq_q, sR_q, sdR_q, sFileName = loadRqz(clas.subtract)
subtract = True
print(f'# loaded background file: {sFileName}')
reduction.corrections.append(f'background from \'{sFileName}\' subtracted')
orso.reduction.corrections.append(f'background from \'{sFileName}\' subtracted')
else:
subtract = False
@@ -728,7 +776,7 @@ def main():
fileio.ErrorColumn(error_of='Qz', error_type='resolution', value_is='sigma'),
fileio.Column('time', 's', 'time relative to start of measurement series'),
]
data_source = fromHDF.data_source
#data_source = fromHDF.data_source
interval = clas.timeSlize[0]
try:
@@ -741,7 +789,7 @@ def main():
stop = wallTime_e[-1]
for i, time in enumerate(np.arange(start, stop, interval)):
print(f'# time slize {i:4n}', end='\r')
headerRqz = fileio.Orso(data_source, reduction, columns)
headerRqz = fileio.Orso(orso.data_source, orso.reduction, columns)
headerRqz.data_set = f'Nr {i} : time = {time:8.1f} s to {time+interval:8.1f} s'
headerRqz = fileio.Orso(**headerRqz.to_dict())
@@ -794,8 +842,8 @@ def main():
fileio.ErrorColumn(error_of='R', error_type='uncertainty', value_is='sigma'),
fileio.ErrorColumn(error_of='Qz', error_type='resolution', value_is='sigma'),
]
data_source = fromHDF.data_source
headerRqz = fileio.Orso(data_source, reduction, columns)
#data_source = fromHDF.data_source
headerRqz = fileio.Orso(orso.data_source, orso.reduction, columns)
headerRqz.data_set = f'Nr {i} : mu = {fromHDF.mu:6.3f} deg'
if i>0 :
headerRqz.data_source.measurement.instrument_settings.mu = fileio.Value(fromHDF.mu, 'deg', comment='sample angle to horizon')
@@ -844,8 +892,8 @@ def main():
fileio.Column('norm', '', 'normalisation matrix'),
fileio.Column('mask', '', 'pixels used for calculating R(q_z)'),
]
data_source = fromHDF.data_source
headerRlt = fileio.Orso(data_source, reduction, columns)
#data_source = fromHDF.data_source
headerRlt = fileio.Orso(orso.data_source, orso.reduction, columns)
ts, zs=ref_lz.shape
lindex_lz=np.tile(np.arange(1, ts+1), (zs, 1)).T