sinq-reflectometry/eos
0
1
Fork 0
Code Issues Pull Requests 1 Actions Packages Projects Releases 1 Wiki Activity

adaption to next orsopy version

Browse Source
This commit is contained in:
stahn
2024-02-23 08:22:08 +01:00
parent bac3c1dfa3
commit 127cbf6e22
1 changed files with 28 additions and 28 deletions
Download Patch File Download Diff File Expand all files Collapse all files

56
neos.py
View File

@@ -154,7 +154,7 @@ class Defs:
hdm = 6.626176e-34/1.674928e-27 # h / m
lamdaCut = 2.5 # Aa
#=====================================================================================================
class Orso:
class Header:
'''orso compatible output file header content'''
def __init__(self):
@@ -193,8 +193,8 @@ class Orso:
columns = [
fileio.Column('Qz', '1/angstrom', 'normal momentum transfer'),
fileio.Column('R', '', 'specular reflectivity'),
fileio.ErrorColumn(error_of='R', error_type='uncertainty', value_is='sigma'),
fileio.ErrorColumn(error_of='Qz', error_type='resolution', value_is='sigma'),
fileio.ErrorColumn(error_of='R', error_type='uncertainty', distribution='gaussian', value_is='sigma'),
fileio.ErrorColumn(error_of='Qz', error_type='resolution', distribution='gaussian', value_is='sigma'),
]
return columns
@@ -296,7 +296,7 @@ class AmorData:
user_name = self.hdf['entry1/user/name'][0].decode('utf-8')
user_affiliation = 'unknown'
user_email = self.hdf['entry1/user/email'][0].decode('utf-8')
user_orcid = 'unknown'
user_orcid = None
sampleName = self.hdf['entry1/sample/name'][0].decode('utf-8')
model = self.hdf['entry1/sample/model'][0].decode('utf-8')
instrumentName = 'Amor'
@@ -312,13 +312,14 @@ class AmorData:
model = None
# assembling orso header information
orso.owner = fileio.Person(
header.owner = fileio.Person(
name = user_name,
affiliation = user_affiliation,
contact = user_email,
orcid = user_orcid,
)
orso.experiment = fileio.Experiment(
if user_orcid:
header.owner.orcid = user_orcid
header.experiment = fileio.Experiment(
title = title,
instrument = instrumentName,
start_date = start_date,
@@ -326,12 +327,12 @@ class AmorData:
facility = source,
proposalID = proposal_id
)
orso.sample = fileio.Sample(
header.sample = fileio.Sample(
name = sampleName,
model = model,
sample_parameters = None,
)
orso.measurement_scheme = 'angle- and energy-dispersive'
header.measurement_scheme = 'angle- and energy-dispersive'
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))
@@ -381,19 +382,19 @@ class AmorData:
# add header content
if self.readHeaderInfo:
self.readHeaderInfo = False
orso.measurement_instrument_settings = fileio.InstrumentSettings(
header.measurement_instrument_settings = fileio.InstrumentSettings(
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'),
wavelength = fileio.ValueRange(defs.lamdaCut, clas.lambdaRange[1], 'angstrom'),
polarization = 'unpolarized',
mu = fileio.Value(self.mu, 'deg', comment='sample angle to horizon'),
nu = fileio.Value(self.nu, 'deg', comment='detector angle to horizon'),
)
header.measurement_instrument_settings.mu = fileio.Value(self.mu, 'deg', comment='sample angle to horizon')
header.measurement_instrument_settings.nu = fileio.Value(self.nu, 'deg', comment='detector angle to horizon')
if norm:
orso.measurement_additional_files.append(fileio.File(file=fileName.split('/')[-1], timestamp=fileDate))
header.measurement_additional_files.append(fileio.File(file=fileName.split('/')[-1], timestamp=fileDate))
else:
orso.measurement_data_files.append(fileio.File(file=fileName.split('/')[-1], timestamp=fileDate))
header.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
@@ -453,11 +454,11 @@ class AmorData:
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 = 2 * np.pi * ( np.cos( np.deg2rad(alphaF_e) ) - np.cos( np.deg2rad( alphaI ) ) ) / lamda_e
orso.measurement_scheme = 'energy-dispersive',
header.measurement_scheme = 'energy-dispersive',
else:
qz_e = 4 * np.pi * np.sin( np.deg2rad(alphaF_e) ) / lamda_e
# qx_e = 0.
orso.measurement_scheme = 'angle- and energy-dispersive'
header.measurement_scheme = 'angle- and energy-dispersive'
# filter q_z range
if clas.qzRange[1] < 0.3 and not norm:
@@ -514,7 +515,7 @@ def normalisation_map(short_notation):
fh.close()
for i, entry in enumerate(normFileList):
normFileList[i] = entry.split('/')[-1]
orso.measurement_additional_files = normFileList
header.measurement_additional_files = normFileList
else:
print(f'# normalisation matrix: using the files {normalisation_list}')
fromHDF.read_data(short_notation, norm=True)
@@ -535,7 +536,6 @@ def normalisation_map(short_notation):
head = head.replace('raw/', '')
np.savetxt(f'{clas.dataPath}/{name}.norm', norm_lz, header = head)
normFileList = fromHDF.file_list
#orso.measurement_additional_files = normFileList
return norm_lz, normAngle, normFileList
#=====================================================================================================
def output_format_list(outputFormat):
@@ -713,10 +713,10 @@ class Grid:
#=====================================================================================================
def main():
global startTime, grid, clas, orso
clas = commandLineArgs()
grid = Grid()
orso = Orso()
global startTime, grid, clas, header
clas = commandLineArgs()
grid = Grid()
header = Header()
startTime = 0
if not os.path.exists(f'{clas.dataPath}'):
os.system(f'mkdir {clas.dataPath}')
@@ -738,7 +738,7 @@ def main():
if clas.normalisationFileIdentifier:
normalise = True
norm_lz, normAngle, normFileList = normalisation_map(clas.normalisationFileIdentifier[0])
orso.reduction.corrections.append('normalisation with \'additional files\'')
header.reduction.corrections.append('normalisation with \'additional files\'')
else:
normalise = False
norm_lz = grid.lz()
@@ -751,7 +751,7 @@ def main():
sq_q, sR_q, sdR_q, sFileName = loadRqz(clas.subtract)
subtract = True
print(f'# loaded background file: {sFileName}')
orso.reduction.corrections.append(f'background from \'{sFileName}\' subtracted')
header.reduction.corrections.append(f'background from \'{sFileName}\' subtracted')
else:
subtract = False
@@ -760,7 +760,7 @@ def main():
datasetsRlt = []
for i, short_notation in enumerate(clas.fileIdentifier):
print('# reading input:')
orso.measurement_data_files = []
header.measurement_data_files = []
fromHDF.read_data(short_notation)
if clas.timeSlize:
@@ -784,7 +784,7 @@ 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(orso.data_source(), orso.reduction, columns)
headerRqz = fileio.Orso(header.data_source(), header.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())
@@ -831,7 +831,7 @@ def main():
err_lz *= clas.scale[-1]
if 'Rqz.ort' in output_format_list(clas.outputFormat):
headerRqz = fileio.Orso(orso.data_source(), orso.reduction, orso.columns())
headerRqz = fileio.Orso(header.data_source(), header.reduction, header.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')
@@ -882,7 +882,7 @@ def main():
fileio.Column('mask', '', 'pixels used for calculating R(q_z)'),
]
#data_source = fromHDF.data_source
headerRlt = fileio.Orso(orso.data_source, orso.reduction, columns)
headerRlt = fileio.Orso(header.data_source, header.reduction, columns)
ts, zs=ref_lz.shape
lindex_lz=np.tile(np.arange(1, ts+1), (zs, 1)).T