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='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:
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:
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 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)
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)
if __name__ == '__main__':
from sys import argv
# turn on printing of errors
level = nudie.logging.INFO
nudie.show_errors(level)
if len(argv) < 2:
s = 'need a configuration file name as a parameter'
nudie.log.error(s)
sys.exit(-1)
main(argv[1], level)
import nudie
from nudie.dataset import *
from dask.delayed import delayed
nudie.show_errors(nudie.logging.INFO)
'''
d = Dataset('test.h5', 'w')
print('readonly? {!s}'.format(d.readonly))
try:
d = Dataset('test2.h5', 'r')
print('readonly? {!s}'.format(d.readonly))
except Exception:
pass
PP('pp-phasing-batch00.h5')
DD('2d-phasing-batch00.h5')
DDESS('2dess-batch00.h5')
TG('tg-batch00.h5')
TGStark('tg-stark-batch00.h5')
'''
c = Config({
'FastDazzlerSetupLoader': {
'batch_path': 'test-data/clh-linear-stark-s3-batch00',
'batch_name': 'clh-linear-stark-s3',
'data_type': LinearStark,
'allow_parallel': True,
}
})
loader = FastDazzlerSetupLoader(config=c)
a = loader.load()
from __future__ import division
import pytest
import numpy as np
import itertools as it
import nudie
nudie.show_errors(nudie.logging.DEBUG)
def test_BoolStr():
for s in ['True', '1', 'tRue', 'YES', 'ON', 'yEs']:
assert nudie.schema.BoolStr(s) == True
for s in ['false', '0', 'FaLSE', 'OFF', 'ofF', 'NO', 'no']:
assert nudie.schema.BoolStr(s) == False
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
''')