def test_two_files_one_dbtype(capfd):
pb.run('configs/tli_hitran_two_files_one_dbtype.cfg')
captured = capfd.readouterr()
caps = [
"Read command-line arguments from configuration file:",
"'configs/tli_hitran_two_files_one_dbtype.cfg'",
"Reading input database files:",
"tests/inputs/01_hit12.par",
"tests/inputs/02_4000-4500_HITEMP2010.par",
"There are 2 input database file(s).",
"Initial TLI wavelength (um): 2.300 ( 4347.826 cm-1)",
"Final TLI wavelength (um): 2.400 ( 4166.667 cm-1)",
"Database (1/2): 'HITRAN H2O' (H2O molecule)",
"Number of temperatures: 503",
"Number of isotopes: 9",
"Database (2/2): 'HITRAN CO2' (CO2 molecule)",
"Number of isotopes: 13",
"Cumulative number of isotopes per database: [0, 9, 22]",
"Process HITRAN H2O database between records 60,574 and 61,991.",
"Process HITRAN CO2 database between records 20,424 and 41,477.",
"[ 610 233 163 411 20937 17 27 73]",
"Writing 22,471 transition lines.",
"/HITRAN_H2O_CO2_2.3-2.4um_test.tli'.",
]
for cap in caps:
assert cap in captured.out
def test_two_files_two_databases(capfd):
pb.run('configs/tli_hitran_two_files_two_db_test.cfg')
captured = capfd.readouterr()
caps = [
"Read command-line arguments from configuration file:",
"'configs/tli_hitran_two_files_two_db_test.cfg'",
"Reading input database files:",
"tests/inputs/01_hit12.par",
"tests/inputs/02_4000-4500_HITEMP2010.par",
"There are 2 input database file(s).",
"Initial TLI wavelength (um): 2.000 ( 5000.000 cm-1)",
"Final TLI wavelength (um): 3.000 ( 3333.333 cm-1)",
"Database (1/2): 'HITRAN H2O' (H2O molecule)",
"Number of temperatures: 503",
"Number of isotopes: 9",
"Database (2/2): 'HITRAN CO2' (CO2 molecule)",
"Number of isotopes: 13",
"Cumulative number of isotopes per database: [0, 9, 22]",
"Process HITRAN H2O database between records 42,645 and 66,776.",
"Process HITRAN CO2 database between records 0 and 138,257.",
"[12296 5132 3973 2568 147 99541 9119 22521 220 6854 2]",
"Writing 162,373 transition lines.",
"/HITRAN_H2O_CO2_2.0-3.0um_test.tli'.",
]
for cap in caps:
assert cap in captured.out
def test_pyrat_emission_str(tmp_path):
cfg = make_config(tmp_path,
ROOT + 'tests/configs/spectrum_transmission_test.cfg',
reset={'rt_path': 'emission'})
pyrat = pb.run(cfg)
assert pyrat is not None
assert str(pyrat.spec) == """\
Spectral information:
Wavenumber internal units: cm-1
Wavelength internal units: cm
Wavelength display units (wlunits): um
Low wavenumber boundary (wnlow): 5882.353 cm-1 (wlhigh = 1.70 um)
High wavenumber boundary (wnhigh): 9090.909 cm-1 (wllow = 1.10 um)
Number of samples (nwave): 3209
Sampling interval (wnstep): 1.000 cm-1
Wavenumber array (wn, cm-1):
[ 5882.353 5883.353 5884.353 ... 9088.353 9089.353 9090.353]
Oversampling factor (wnosamp): 2160
Intensity zenithal angles (raygrid, degree): [ 0. 20. 40. 60. 80.]
raygrid internal units: radian
Intensity spectra (intensity, erg s-1 cm-2 sr-1 cm):
[ 7.741e+02 7.734e+02 7.727e+02 ... 3.549e+01 3.545e+01 3.542e+01]
[ 7.741e+02 7.734e+02 7.727e+02 ... 3.549e+01 3.545e+01 3.542e+01]
[ 7.741e+02 7.734e+02 7.727e+02 ... 3.549e+01 3.545e+01 3.542e+01]
[ 7.741e+02 7.734e+02 7.727e+02 ... 3.549e+01 3.545e+01 3.542e+01]
[ 7.741e+02 7.734e+02 7.727e+02 ... 3.549e+01 3.545e+01 3.542e+01]
Emission spectrum (spectrum, erg s-1 cm-2 cm):
[ 2.432e+03 2.430e+03 2.428e+03 ... 1.115e+02 1.114e+02 1.113e+02]
"""
assert str(pyrat.od) == """\
def spectrum_exomol():
pyrat = pb.run(ROOT + 'tests/configs/spectrum_transmission_exomol.cfg')
plt.figure(1)
plt.clf()
plt.plot(1e4 / hcn[0], hcn[1], 'b')
plt.plot(1e4 / pyrat.spec.wn, pyrat.spec.spectrum, 'orange', alpha=0.5)
def test_missing_mass_units(tmp_path, capfd):
cfg = make_config(tmp_path, ROOT+'tests/configs/pt_tcea.cfg',
reset={'mplanet':'1.0'})
pyrat = pb.run(cfg)
assert pyrat is None
captured = capfd.readouterr()
assert "Invalid units 'None' for parameter mplanet." in captured.out
def test_transmission_patchy(tmp_path):
cfg = make_config(tmp_path,
ROOT + 'tests/configs/spectrum_transmission_test.cfg',
reset={
'fpatchy': '0.5',
'rpars': '10.0 -15.0'
})
pyrat = pb.run(cfg)
np.testing.assert_allclose(pyrat.spec.spectrum,
expected['patchy'],
rtol=rtol)
np.testing.assert_allclose(pyrat.spec.clear,
expected['patchy_clear'],
rtol=rtol)
np.testing.assert_allclose(pyrat.spec.cloudy,
expected['patchy_cloudy'],
rtol=rtol)
pyrat.cloud.fpatchy = 0.0
pyrat.run()
np.testing.assert_allclose(pyrat.spec.spectrum,
expected['patchy_clear'],
rtol=rtol)
pyrat.cloud.fpatchy = 1.0
pyrat.run()
np.testing.assert_allclose(pyrat.spec.spectrum,
expected['patchy_cloudy'],
rtol=rtol)
def test_units_separate(tmp_path):
cfg = make_config(tmp_path,
ROOT + 'tests/configs/pt_isothermal.cfg',
reset={
'mplanet': '1.0',
'mpunits': 'mjup'
})
pressure, temperature, abundances, species, radius = pb.run(cfg)
def test_invalid_file_path(tmp_path, capfd, param, invalid_path):
cfg = make_config(tmp_path, ROOT+'tests/configs/pt_isothermal.cfg',
reset={param:'nope/file.dat'})
pyrat = pb.run(cfg)
captured = capfd.readouterr()
assert pyrat is None
assert "Error in module: 'parser.py', function: 'parse'" in captured.out
assert invalid_path[param] in captured.out
def test_transmission_deck(tmp_path):
cfg = make_config(tmp_path,
ROOT + 'tests/configs/spectrum_transmission_test.cfg',
remove=['tlifile', 'csfile', 'rayleigh', 'alkali'])
pyrat = pb.run(cfg)
np.testing.assert_allclose(pyrat.spec.spectrum,
expected['deck'],
rtol=rtol)
def test_lower_equal(tmp_path, capfd, param):
cfg = make_config(tmp_path, ROOT+'tests/configs/pt_isothermal.cfg',
reset={param:'1.1'})
pyrat = pb.run(cfg)
assert pyrat is None
captured = capfd.readouterr()
assert "Error in module: 'parser.py', function: 'parse'" in captured.out
assert "({:s}) must be <= ".format(param) in captured.out
def test_greater_than(tmp_path, capfd, param, value):
cfg = make_config(tmp_path, ROOT+'tests/configs/pt_tcea.cfg',
reset={param:value})
pyrat = pb.run(cfg)
assert pyrat is None
captured = capfd.readouterr()
assert "Error in module: 'parser.py', function: 'parse'" in captured.out
assert "({:s}) must be > ".format(param) in captured.out
def main():
cfile = 'run_HATP-41b_tsiaras/mcmc_HATP-41b_tsiaras_w00000-mc.cfg'
folder, cfile = os.path.split(cfile)
_, planet, dset = folder.split('_')
with pt.cd(folder):
pyrat = pb.run(cfile, run_step='init', no_logfile=True)
with np.load(pyrat.ret.mcmcfile) as mcmc:
post, zchain, zmask = mc3.utils.burn(mcmc)
texnames = mcmc['texnames']
bestp = mcmc['bestp']
imol = np.in1d(mcmc['ifree'], pyrat.ret.imol)
posteriors = pyrat.ret.posterior = post
u, uind, uinv = np.unique(posteriors[:, 0],
return_index=True,
return_inverse=True)
nunique = np.size(u)
# Get mean molecular mass:
ZX_ratio = np.zeros(nunique, np.double)
params = pyrat.ret.params
for k in range(nunique):
params[imol] = posteriors[uind[k], imol]
ZX_ratio[k] = ZX(params, pyrat)
iN2 = pyrat.ret.pnames.index('log(N2)')
# Metal mass fraction relative to solar values, i.e., [Z/X]:
posteriors[:, iN2] = ZX_ratio[uinv]
bestp[iN2] = ZX(bestp, pyrat)
texnames[iN2] = r"$[Z/X]$"
posteriors = roll(posteriors, indices=pyrat.ret.imol[:-1])
bestp = roll(bestp, indices=pyrat.ret.imol[:-1])
texnames = roll(texnames, indices=pyrat.ret.imol[:-1])
texnames[4] = texnames[4].replace('f', 'X')
rect = [0.105, 0.11, 0.99, 0.99]
ranges = [(100, 3000), (1.49, 1.68), (-4.5, 2.6), (-5.5, 2.5),
(-7., -0.45)]
plt.figure(316, (6, 6))
plt.clf()
axes, cax = mc3.plots.pairwise(posteriors,
pnames=texnames,
ranges=ranges,
fignum=8,
rect=rect,
nbins=20)
ax = axes[1][2]
plt.text(0.15, 0.125, 'cloudy', rotation=45, transform=ax.transAxes)
plt.text(0.70, 0.25, 'heavy', rotation=45, transform=ax.transAxes)
plt.text(0.75, 0.67, 'deplet', rotation=90, transform=ax.transAxes)
ax = axes[3][3]
plt.text(0.05, 0.30, 'cloudy', rotation=305, transform=ax.transAxes)
plt.text(0.55, 0.75, 'heavy', rotation=0, transform=ax.transAxes)
plt.text(0.65, 0.10, 'deplet', rotation=0, transform=ax.transAxes)
plt.savefig(f'plots/WFC3_{planet}_{dset}_correlation.pdf')
plt.savefig(f'plots/WFC3_{planet}_{dset}_correlation.png', dpi=300)
def test_atmosphere_tea_missing_elements(tmp_path, capfd, undefined):
cfg = make_config(tmp_path,
ROOT+'tests/configs/atmosphere_tea_test.cfg',
remove=['elements'])
pyrat = pb.run(cfg)
assert pyrat is None
captured = capfd.readouterr()
assert "Error in module: 'driver.py', function: 'check_atm'" in captured.out
assert undefined['elements'] in captured.out
def test_atmosphere_missing_species(tmp_path, capfd, undefined, chem):
cfg = make_config(tmp_path,
f'{ROOT}tests/configs/atmosphere_{chem}_test.cfg',
remove=['species'])
pyrat = pb.run(cfg)
assert pyrat is None
captured = capfd.readouterr()
assert "Error in module: 'driver.py', function: 'check_atm'" in captured.out
assert undefined['species'] in captured.out
def test_pt_temperature_missing(tmp_path, capfd, param, undefined):
cfg = make_config(tmp_path, ROOT+'tests/configs/pt_isothermal.cfg',
remove=[param])
pyrat = pb.run(cfg)
assert pyrat is None
captured = capfd.readouterr()
assert "Error in module: 'driver.py', function: 'check_temp'" \
in captured.out
assert undefined[param] in captured.out
def test_pressure_invalid_units(tmp_path, capfd, param):
cfg = make_config(tmp_path, ROOT+'tests/configs/pt_isothermal.cfg',
reset={param:'10.0 20.0'})
pyrat = pb.run(cfg)
captured = capfd.readouterr()
assert pyrat is None
assert "Error in module: 'parser.py', function: 'parse'" in captured.out
assert f"Invalid units for value '10.0 20.0' for parameter {param}." \
in captured.out
def test_transmission_input_radius(tmp_path):
cfg = make_config(
tmp_path,
ROOT + 'tests/configs/spectrum_transmission_test.cfg',
reset={'atmfile': f'{INPUTS}atmosphere_uniform_radius.atm'},
remove=['radmodel'])
pyrat = pb.run(cfg)
atm = io.read_atm('inputs/atmosphere_uniform_radius.atm')
np.testing.assert_allclose(pyrat.atm.radius, atm[5] * pc.km, rtol=rtol)
def test_bulk_molfree_overlap(tmp_path, capfd):
cfg = make_config(tmp_path,
ROOT+'tests/configs/spectrum_transmission_test.cfg',
reset={'molmodel':'vert', 'molfree':'H2', 'bulk':'H2'})
pyrat = pb.run(cfg)
assert pyrat is None
captured = capfd.readouterr()
assert "Error in module: 'argum.py', function: 'setup'" in captured.out
assert "These species were marked as both bulk and variable-abundance: ['H2']." in captured.out
def test_units_in_value_invalid(tmp_path, capfd):
cfg = make_config(tmp_path,
ROOT + 'tests/configs/pt_isothermal.cfg',
reset={'mplanet': '1.0 nope'})
pyrat = pb.run(cfg)
assert pyrat is None
captured = capfd.readouterr()
assert "Invalid units for value '1.0 nope' for parameter mplanet." \
in captured.out
def test_spectrum_emission(tmp_path):
cfg = make_config(tmp_path,
ROOT + 'tests/configs/spectrum_transmission_test.cfg',
reset={
'rt_path': 'emission',
'cpars': '-0.5'
})
pyrat = pb.run(cfg)
assert pyrat is not None
def test_invalid_float_all_params(tmp_path, capfd, param):
cfg = make_config(tmp_path, ROOT+'tests/configs/pt_isothermal.cfg',
reset={param:'abc'})
pyrat = pb.run(cfg)
captured = capfd.readouterr()
assert pyrat is None
assert "Error in module: 'parser.py', function: 'parse'" in captured.out
assert ("Invalid data type for {:s}, could not convert string to "
"float: 'abc'".format(param)) in captured.out
def test_transmission_clear(tmp_path):
# No opacity whatsoever:
cfg = make_config(
tmp_path,
ROOT + 'tests/configs/spectrum_transmission_test.cfg',
remove=['tlifile', 'csfile', 'rayleigh', 'alkali', 'clouds'])
pyrat = pb.run(cfg)
depth_bottom = (pyrat.atm.radius[-1] / pyrat.phy.rstar)**2
np.testing.assert_allclose(pyrat.spec.spectrum, depth_bottom, rtol=rtol)
def test_transmission_input_radius_overwrite(tmp_path):
cfg = make_config(
tmp_path,
ROOT + 'tests/configs/spectrum_transmission_test.cfg',
reset={'atmfile': f'{INPUTS}/atmosphere_uniform_radius.atm'})
pyrat = pb.run(cfg)
atm = io.read_atm('inputs/atmosphere_uniform_radius.atm')
np.testing.assert_raises(AssertionError, np.testing.assert_array_equal,
pyrat.atm.radius, atm[5] * pc.km)
def test_molfree_mismatch(tmp_path, capfd):
cfg = make_config(tmp_path,
ROOT+'tests/configs/spectrum_transmission_test.cfg',
reset={'molmodel':'vert'})
pyrat = pb.run(cfg)
assert pyrat is None
captured = capfd.readouterr()
assert "Error in module: 'argum.py', function: 'setup'" in captured.out
assert "molmodel is set, but there are no molfree." in captured.out
def test_molfree_mismatch3(tmp_path, capfd):
cfg = make_config(tmp_path,
ROOT+'tests/configs/spectrum_transmission_test.cfg',
reset={'molmodel':'vert', 'molfree':'N2'})
pyrat = pb.run(cfg)
assert pyrat is None
captured = capfd.readouterr()
assert "Error in module: 'argum.py', function: 'setup'" in captured.out
assert "These species are not present in the atmosphere: ['N2']." in captured.out
def test_pressure_invalid_type(tmp_path, capfd, param, value):
cfg = make_config(tmp_path, ROOT+'tests/configs/pt_isothermal.cfg',
reset={param:value})
pyrat = pb.run(cfg)
captured = capfd.readouterr()
assert pyrat is None
assert "Error in module: 'parser.py', function: 'parse'" in captured.out
assert "Invalid value '{:s}' for parameter {:s}.". \
format(value, param) in captured.out
def test_transmission_resolution(tmp_path):
cfg = make_config(tmp_path,
ROOT + 'tests/configs/spectrum_transmission_test.cfg',
reset={'resolution': '5000.0'},
remove=['clouds'])
pyrat = pb.run(cfg)
np.testing.assert_allclose(pyrat.spec.spectrum,
expected['resolution'],
rtol=rtol)
def test_invalid_units(tmp_path, capfd, param, var):
cfg = make_config(tmp_path, ROOT+'tests/configs/pt_isothermal.cfg',
reset={param:'invalid'})
pyrat = pb.run(cfg)
captured = capfd.readouterr()
assert pyrat is None
assert "Error in module: 'parser.py', function: 'parse'" in captured.out
assert "Invalid {:s} units ({:s}): invalid".format(var, param) \
in captured.out
def test_opacity_missing(tmp_path, capfd, param, undefined_opacity):
cfg = make_config(tmp_path, ROOT+'tests/configs/opacity_test.cfg',
reset={'extfile':str(tmp_path/'new_opacity.dat')},
remove=[param])
pyrat = pb.run(cfg)
assert pyrat is None
captured = capfd.readouterr()
assert "Error in module: 'argum.py', function: 'check_spectrum'" \
in captured.out
assert undefined_opacity[param] in captured.out
def test_kurucz_missing_pars(tmp_path, capfd, param, undefined):
cfg = make_config(tmp_path,
ROOT+'tests/configs/spectrum_transmission_test.cfg',
reset={'kurucz':f'{ROOT}/tests/inputs/fp00k0odfnew.pck'},
remove=[param])
pyrat = pb.run(cfg)
assert pyrat is None
captured = capfd.readouterr()
assert "Error in module: 'argum.py', function: 'setup'" in captured.out
assert undefined[param] in captured.out
