def test_write(self):
print(self.target.to_dict())
fname = 'test.h5'
with HDF5Output(fname, append=True) as out:
self.target.write(out)
os.remove(fname)
def execute(self):
import os
from exorad.tasks import LoadOptions
from exorad.output.hdf5 import HDF5Output
loadOptions = LoadOptions()
buildChannels = BuildChannels()
loadPayload = LoadPayload()
payload_file = self.get_task_param('payload_file')
output = self.get_task_param('output')
ext = os.path.splitext(payload_file)[1]
if ext == '.xml':
payload = loadOptions(filename=payload_file)
if output is not None:
with HDF5Output(output) as out:
channels = buildChannels(payload=payload,
write=True,
output=out)
else:
channels = buildChannels(payload=payload,
write=False,
output=None)
elif ext == 'h5':
payload, channels = loadPayload(input=payload_file)
else:
self.error('Unsupported payload format')
raise IOError('Unsupported payload format')
wl_min, wl_max = payload['common']['wl_min']['value'], payload[
'common']['wl_max']['value']
self.set_output([payload, channels, (wl_min, wl_max)])
def test_write(self):
loadTargetList = LoadTargetList()
targets = loadTargetList(target_list=self.target_list)
fname = 'test.h5'
with HDF5Output(fname) as o:
for target in targets.target:
target.write(o)
os.remove(fname)
def standard_pipeline(options, target_list, output=None, plot=False, full_contrib=False,
n_thread=1, debug=False, log=False):
from exorad.utils.ascii_art import ascii_art
logger.info(ascii_art)
logger.info('code version {}'.format(version))
gc = GlobalCache()
gc['n_thread'] = n_thread
gc['debug'] = debug
if debug: setLogLevel(logging.DEBUG)
if isinstance(log, str): addLogFile(fname=log)
elif log: addLogFile()
if output is not None:
out_dir = pathlib.Path(output).parent.absolute()
if not os.path.exists(out_dir):
os.makedirs(out_dir)
logger.info('output directory created')
logger.info('output directory set as {}'.format(out_dir))
try:
shutil.copy(options, out_dir)
except shutil.SameFileError:
pass
try:
shutil.copy(target_list, out_dir)
except shutil.SameFileError:
pass
else:
out_dir = None
# step 1 load payload
payload, channels, (wl_min, wl_max) = preparePayload(payload_file=options,
output=output)
if full_contrib:
from astropy.table import hstack
for ch in channels:
channels[ch].table = hstack([channels[ch].table, channels[ch].built_instr['optical_path']['signal_table']])
channels[ch].table.remove_column('instrument_signal')
# step 1b plot payload efficiency
if plot:
efficiency_plot(channels=channels, output_dir=out_dir)
# step 2 load targetlist
targets = loadTargetList(target_list=target_list)
# step 3 observe targetlist
targets = observeTargetList(targets=targets.target, payload=payload, channels=channels, wl_range=(wl_min, wl_max),
plot=plot, out_dir=out_dir)
# step 4 save to output
if output is not None:
for target in targets:
with HDF5Output(output, append=True) as out:
targets[target].write(out)
class IOTest(unittest.TestCase):
setLogLevel(logging.INFO)
buildChannels = BuildChannels()
fname = 'test.h5'
with HDF5Output(fname) as o:
channels_built = buildChannels(payload=options, write=True, output=o)
file = h5py.File(fname)
loadPayload = LoadPayload()
payload_loaded, channels_loaded = loadPayload(input=file)
def test_instrument_list(self):
self.assertListEqual(list(self.channels_built.keys()),
list(self.channels_loaded.keys()))
def test_instrument_build_from_file(self):
with self.assertRaises(ValueError):
self.channels_loaded['Phot'].build()
with self.assertRaises(ValueError):
self.channels_loaded['Spec'].build()
os.remove(self.fname)