def create_chemistry(config):
try:
chemistry = config.pop('chemistry_type').lower()
except KeyError:
log.error('No chemistry defined in input')
raise KeyError
if chemistry in ('ace','equilibrium'):
return create_ace(config)
elif chemistry in ('file', ):
from taurex.chemistry import ChemistryFile
return create_klass(config, ChemistryFile)
elif chemistry in ('custom',):
from taurex.chemistry import Chemistry
config['chemistry_type'] = 'custom'
config, klass = determine_klass(config, 'chemistry_type', None,
Chemistry)
obj = klass(**config)
return obj
elif chemistry in ('taurex', 'complex', 'defined', 'free'):
from taurex.data.profiles.chemistry import TaurexChemistry
gases = []
config_key=[]
for key, value in config.items():
if isinstance(value, dict):
log.debug('FOUND GAS {} {}'.format(key, value))
config_key.append(key)
gas_type = value.pop('gas_type').lower()
klass = gas_factory(gas_type)
gases.append(klass(molecule_name=key, **value))
for k in config_key: del config[k]
log.debug('leftover keys {}'.format(config))
obj = TaurexChemistry(**config)
for g in gases:
obj.addGas(g)
return obj
else:
raise ValueError('Unknown chemistry type {}'.format(chemistry))
def test_taurex_chemistry(self):
from taurex.data.profiles.chemistry import TaurexChemistry, ConstantGas
from taurex.cache import OpacityCache
molecules = ['H2O', 'CH4']
mix_ratios = [1e-2, 1e-8]
molecule_classes = [ConstantGas, ConstantGas]
with patch.object(OpacityCache,
"find_list_of_molecules") as mock_my_method:
mock_my_method.return_value = molecules
chemistry = TaurexChemistry(fill_gases=['H2', 'N2'], ratio=0.145)
for mol, mix, klass in zip(molecules, mix_ratios,
molecule_classes):
chemistry.addGas(klass(mol, mix))
chemistry.initialize_chemistry(100, None, None, None)
file_path = self.gen_valid_hdf5_output(chemistry, 'Test')
with patch.object(OpacityCache,
"find_list_of_molecules") as mock_my_method:
mock_my_method.return_value = molecules
with h5py.File(file_path, 'r') as f:
loaded = load_chemistry_from_hdf5(f['Test'])
loaded.initialize_chemistry(100, None, None, None)
self.assertTrue(set(chemistry._fill_gases) == set(loaded._fill_gases))
self.assertTrue(set(chemistry._fill_ratio) == set(loaded._fill_ratio))
np.testing.assert_equal(chemistry.activeGasMixProfile,
loaded.activeGasMixProfile)
def test_directimage(self):
from taurex.util.hdf5 import load_model_from_hdf5
from taurex.model import DirectImageModel
from taurex.data.profiles.chemistry import TaurexChemistry, ConstantGas
from taurex.contributions import AbsorptionContribution, RayleighContribution
from taurex.cache import OpacityCache
with patch.object(OpacityCache,
"find_list_of_molecules") as mock_my_method:
mock_my_method.return_value = ['H2O']
chem = TaurexChemistry()
chem.addGas(ConstantGas())
tm = DirectImageModel(chemistry=chem, ngauss=10)
tm.add_contribution(AbsorptionContribution())
tm.add_contribution(RayleighContribution())
tm.build()
tm.initialize_profiles()
wngrid = np.linspace(100, 400)
tm.star.initialize(wngrid)
with patch.object(DirectImageModel, "model") as mock_my_method:
mock_my_method = None
file_path = self.gen_valid_hdf5_output(tm, 'Test')
with h5py.File(file_path, 'r') as f:
loaded = load_model_from_hdf5(f['Test']['ModelParameters'])
loaded.build()
loaded.initialize_profiles()
wngrid = np.linspace(100, 400)
self.assertTrue(isinstance(loaded, DirectImageModel))
np.testing.assert_array_equal(loaded.densityProfile, tm.densityProfile)
truth_contrib = [type(c) for c in tm.contribution_list]
loaded_contrib = [type(c) for c in loaded.contribution_list]
self.assertTrue(set(truth_contrib) == set(loaded_contrib))
self.assertEqual(tm._ngauss, loaded._ngauss)
def _setup_defaults(self, nlayers, atm_min_pressure, atm_max_pressure):
if self._pressure_profile is None:
from taurex.data.profiles.pressure import SimplePressureProfile
self.info('No pressure profile defined, using simple pressure '
'profile with')
self.info('parameters nlayers: %s, atm_pressure_range=(%s,%s)',
nlayers, atm_min_pressure, atm_max_pressure)
self._pressure_profile = \
SimplePressureProfile(nlayers, atm_min_pressure,
atm_max_pressure)
if self._planet is None:
from taurex.data import Planet
self.warning('No planet defined, using Jupiter as planet')
self._planet = Planet()
if self._temperature_profile is None:
from taurex.data.profiles.temperature import Isothermal
self.warning('No temeprature profile defined using default '
'Isothermal profile with T=1500 K')
self._temperature_profile = Isothermal()
if self._chemistry is None:
from taurex.data.profiles.chemistry import TaurexChemistry, \
ConstantGas
tc = TaurexChemistry()
self.warning('No gas profile set, using constant profile with H2O '
'and CH4')
tc.addGas(ConstantGas('H2O', mix_ratio=1e-5))
tc.addGas(ConstantGas('CH4', mix_ratio=1e-6))
self._chemistry = tc
if self._star is None:
from taurex.data.stellar import BlackbodyStar
self.warning('No star, using the Sun')
self._star = BlackbodyStar()
def _compute_inital_mu(self):
from taurex.data.profiles.chemistry import TaurexChemistry, ConstantGas
tc = TaurexChemistry()
tc.addGas(ConstantGas('H2O'))
self._inital_mu = tc