def test_parse_config_apply_phase(tmpdir):
p = tmpdir.join('test_cfg.ini')
p.write(\
'''
[phasing]
path = 15-05-12
reference name = d1d2-2d
reference batch = 0
2d name = d1d2-2d
''')
with pytest.raises(ValueError):
nudie.parse_config(p.strpath, which='phasing')
def main(config, verbosity=nudie.logging.INFO):
nudie.show_errors(verbosity)
try:
try:
val = nudie.parse_config(config, which='tg')['tg']
except ValueError as e:
nudie.log.error('could not validate file. Please check ' +\
'configuration options.')
return
if val['stark']:
s = 'the stark flag is set in the configuration. You should be ' +\
'running the stark-tg.py script.'
nudie.log.error(s)
return
run(tg_name=val['jobname'],
tg_batch=val['batch'],
when=val['when'],
wavelengths=val['wavelengths'],
plot=val['plot'],
pad_to=val['detection axis zero pad to'],
prd_est=val['probe ref delay'],
lo_width=val['lo width'],
dc_width=val['dc width'],
gaussian_power=val['gaussian power'],
analysis_path=val['analysis path'],
datapath=val['data path'])
except Exception as e:
nudie.log.exception(e)
def main(config, verbosity=nudie.logging.INFO):
nudie.show_errors(verbosity)
try:
try:
val = nudie.parse_config(config, which='linear')['linear']
except ValueError as e:
nudie.log.error('could not validate file. Please check ' +\
'configuration options.')
return
if val['stark'] != True:
s = 'the stark flag is not set in the configuration. ' +\
'Are you sure you are using the right configuration file?'
nudie.log.error(s)
return
run(stark_name=val['jobname'],
stark_batch=val['batch'],
when=val['when'],
wavelengths=val['wavelengths'],
plot=val['plot'],
analysis_path=val['analysis path'],
datapath=val['data path'])
except Exception as e:
nudie.log.exception(e)
def main(config, verbosity=nudie.logging.INFO):
nudie.show_errors(verbosity)
try:
try:
val = nudie.parse_config(config, which='phasing')['phasing']
except ValueError as e:
nudie.log.error('could not validate file. Please check ' +\
'configuration options.')
return
if val['copy']:
s = '`copy` flag is set. You should be using the apply-phase.py ' +\
'script instead'
nudie.log.error(s)
return
run(val['path'],
val['reference name'],
val['reference batch'],
val['experiment name'],
val['experiment batch'],
plot=val['plot'],
force=val['force'],
limits=val['pixel range to fit'],
phaselock_wl=val['phaselock wl'],
central_wl=val['central wl'],
nsteps=val['nsteps'],
niter_success=val['nstep success'],
phasing_guess=val['phasing guess'],
phase_time=val['phasing t2'],
excitation_axis_zero_pad_to=val['excitation axis zero pad to'],
smooth_t1=val['smooth t1'])
except Exception as e:
nudie.log.exception(e)
def main(config, verbosity=nudie.logging.INFO):
nudie.show_errors(verbosity)
try:
val = nudie.parse_config(config, which='2d')['2d']
if val['stark'] != True:
s = 'this is not a stark dataset according to the config file. ' +\
'Are you sure you shouldn\'t be running the 2d script?'
nudie.log.error(s)
return
run(dd_name=val['jobname'],
dd_batch=val['batch'],
when=val['when'],
wavelengths=val['wavelengths'],
plot=val['plot'],
central_wl=val['central wl'],
phaselock_wl=val['phaselock wl'],
pad_to=val['detection axis zero pad to'],
waveforms_per_table=val['waveforms per table'],
prd_est=val['probe ref delay'],
lo_width=val['lo width'],
dc_width=val['dc width'],
gaussian_power=val['gaussian power'],
analysis_path=val['analysis path'],
min_field=val['field on threshold'],
detrend_t1=val['detrend t1'],
datapath=val['data path'])
except Exception as e:
nudie.log.exception(e)
def main(config, verbosity=nudie.logging.INFO):
nudie.show_errors(verbosity)
try:
try:
val = nudie.parse_config(config, which='phasing')['phasing']
except ValueError as e:
nudie.log.error('could not validate file. Please check ' +\
'configuration options.')
return
if val['copy'] == False:
s = '`copy` flag is not set. You should be using the phasing.py ' +\
'script instead'
nudie.log.error(s)
return
run(val['path'],
val['reference name'],
val['reference batch'],
val['experiment name'],
val['experiment batch'],
plot=val['plot'],
force=val['force'],
phase_correct=val['phase correct'],
smooth_t1=val['smooth t1'])
except Exception as e:
nudie.log.exception(e)
def main(config, verbosity=nudie.logging.INFO):
nudie.show_errors(verbosity)
try:
try:
val = nudie.parse_config(config, which='pump probe')['pump probe']
except ValueError as e:
nudie.log.error('could not validate file. Please check ' +\
'configuration options.')
return
run(pp_name=val['jobname'],
pp_batch=val['batch'],
when=val['when'],
plot=val['plot'],
wavelengths=val['wavelengths'],
exclude=val['exclude'],
analysis_path=val['analysis path'],
datapath=val['data path'])
except Exception as e:
nudie.log.exception(e)
def test_parse_config_basic(tmpdir):
p = tmpdir.join('test_cfg.ini')
p.write(\
'''
[pump probe]
jobname = asldkfja
batch = 10
when = 09123
wavelengths = alkdfja
analysis path = alksdjfalskdjf
''')
with pytest.raises(ValueError):
nudie.parse_config(p.strpath, which='asldkajslkdj')
with pytest.raises(ValueError):
nudie.parse_config(p.strpath, which='2d')
with pytest.raises(ValueError):
nudie.parse_config(p.strpath, which='phasing')
nudie.parse_config(p.strpath, which='pump probe')
def main(config, verbosity=nudie.logging.INFO):
nudie.show_errors(verbosity)
try:
try:
val = nudie.parse_config(config, which='2d')['2d']
except ValueError as e:
nudie.log.error('could not validate file. Please check ' +\
'configuration options.')
return
if val['stark']:
s = 'the stark flag is set in the configuration. You should be ' +\
'running the stark-2d.py script.'
nudie.log.error(s)
return
run(dd_name=val['jobname'],
dd_batch=val['batch'],
when=val['when'],
wavelengths=val['wavelengths'],
plot=val['plot'],
pump_chop=val['pump chop'],
central_wl=val['central wl'],
phaselock_wl=val['phaselock wl'],
pad_to=val['detection axis zero pad to'],
waveforms_per_table=val['waveforms per table'],
prd_est=val['probe ref delay'],
lo_width=val['lo width'],
dc_width=val['dc width'],
gaussian_power=val['gaussian power'],
analysis_path=val['analysis path'],
detrend_t1=val['detrend t1'],
datapath=val['data path'])
except Exception as e:
nudie.log.exception(e)