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

fixed second line, added TODO for normalisation

Browse Source
This commit is contained in:
stahn
2024-02-23 15:06:42 +01:00
parent 2be5eea18c
commit 6fc82047f0
1 changed files with 13 additions and 27 deletions
Download Patch File Download Diff File Expand all files Collapse all files

40
neos.py
View File

@@ -38,7 +38,7 @@ def commandLineArgs():
Process command line argument.
The type of the default values is used for conversion and validation.
'''
msg = "EOS reads data from (one or several) raw file(s) of the .hdf format, \
msg = "eos reads data from (one or several) raw file(s) of the .hdf format, \
performs various corrections, conversations and projections and exports\
the resulting reflectivity in an orso-compatible format."
clas = argparse.ArgumentParser(description = msg)
@@ -383,9 +383,9 @@ class AmorData:
if self.readHeaderInfo:
self.readHeaderInfo = False
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'),
incident_angle = fileio.ValueRange(round(self.mu+self.kap+self.kad-0.5*self.div, 3),
round(self.mu+self.kap+self.kad+0.5*self.div, 3),
'deg'),
wavelength = fileio.ValueRange(defs.lamdaCut, clas.lambdaRange[1], 'angstrom'),
polarization = fileio.Polarization.unpolarized,
)
@@ -524,6 +524,9 @@ def normalisation_map(short_notation):
detZ_e = fromHDF.detZ_e
norm_lz, bins_l, bins_z = np.histogram2d(lamda_e, detZ_e, bins = (grid.lamda(), grid.z()))
norm_lz = np.where(norm_lz>0, norm_lz, np.nan)
# TODO: correct for the SM reflectivity
# q_lz
# -> Rsm_lz
if len(lamda_e) > 1e6:
head = f'normalisation matrix based on the measurements \n\
{fromHDF.file_list} \n\
@@ -724,16 +727,6 @@ 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),
# )
# load or create normalisation matrix
if clas.normalisationFileIdentifier:
normalise = True
@@ -765,13 +758,8 @@ def main():
if clas.timeSlize:
wallTime_e = fromHDF.wallTime_e
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.Column('time', 's', 'time relative to start of measurement series'),
]
headerRqz = fileio.Orso(header.data_source(), header.reduction, header.columns())
columns = np.append(header.columns(), fileio.Column('time', 's', 'time relative to start of measurement series'))
interval = clas.timeSlize[0]
try:
@@ -833,11 +821,7 @@ def main():
if 'Rqz.ort' in output_format_list(clas.outputFormat):
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')
# headerRqz.data_source.measurement.instrument_settings.nu = fileio.Value(fromHDF.nu, 'deg', comment='detector angle to horizon')
headerRqz = fileio.Orso(**headerRqz.to_dict())
#print(headerRqz)
# projection on q-grid
q_q, R_q, dR_q, dq_q = project_on_qz(qz_lz, ref_lz, err_lz, res_lz, norm_lz, mask_lz)
@@ -914,11 +898,13 @@ def main():
if 'Rqz.ort' in output_format_list(clas.outputFormat):
print(f'# {clas.dataPath}/{clas.outputName}.Rqz.ort')
fileio.save_orso(datasetsRqz, f'{clas.dataPath}/{clas.outputName}.Rqz.ort', data_separator='\n')
theSecondLine = f' {header.experiment.title} | {header.experiment.start_date} | sample {header.sample.name} | R(q_z)'
fileio.save_orso(datasetsRqz, f'{clas.dataPath}/{clas.outputName}.Rqz.ort', data_separator='\n', comment=theSecondLine)
if 'Rlt.ort' in output_format_list(clas.outputFormat):
print(f'# {clas.dataPath}/{clas.outputName}.Rlt.ort')
fileio.save_orso(datasetsRlt, f'{clas.dataPath}/{clas.outputName}.Rlt.ort', data_separator='\n')
theSecondLine = f' {header.experiment.title} | {header.experiment.start_date} | sample {header.sample.name} | R(lambda, theta)'
fileio.save_orso(datasetsRlt, f'{clas.dataPath}/{clas.outputName}.Rlt.ort', data_separator='\n', comment=theSecondLine)
print('')
#=====================================================================================================