def testcase1():
c_light = speed_of_light * 1e-3
# TODO get better test case for this
cwd = dirname(__file__)
fname = join(cwd, "testcase1.inp")
sme = SME_Struct.load(fname)
sme = synthesize_spectrum(sme)
# Add a second segment (just for testing)
sme.spec = [sme.spec[0], sme.spec[0]]
sme.wave = [sme.wave[0], sme.wave[0]]
sme.synth = [sme.synth[0], sme.synth[0]]
sme.mask = [sme.mask[0], sme.mask[0]]
sme.wran = [sme.wran[0], sme.wran[0]]
rv = 10
x_syn = sme.wave[0] * (1 - rv / c_light)
y_syn = sme.synth[0]
x_syn = np.array([x_syn, x_syn])
y_syn = np.array([y_syn, y_syn])
return sme, x_syn, y_syn, rv
def test_run_with_nlte():
# NOTE sme structure must have long format for NLTE
sme = make_minimum_structure()
sme.nlte.set_nlte("Ca", "marcs2012p_t1.0_Ca.grd")
sme2 = synthesize_spectrum(sme)
assert isinstance(sme2.nlte.flags, np.ndarray)
assert np.issubdtype(sme2.nlte.flags.dtype, np.dtype("bool"))
assert len(sme2.nlte.flags) == len(sme2.linelist)
assert np.any(sme2.nlte.flags)
def test_synthesis_segment(sme_2segments):
sme = sme_2segments
# Out of range
with pytest.raises(IndexError):
synthesize_spectrum(sme, segments=[3])
with pytest.raises(IndexError):
synthesize_spectrum(sme, segments=[-1])
sme2 = synthesize_spectrum(sme, segments=[0])
assert len(sme2.synth[0]) != 0
assert len(sme2.synth[1]) == 0
assert len(sme2.wave[0]) != 0
assert len(sme2.wave[1]) == 0
assert sme2.wave.shape[0] == 2
assert sme2.wave.shape[1][1] == 0
orig = np.copy(sme2.synth[0])
sme2 = synthesize_spectrum(sme2, segments=[1])
assert sme2.wave.shape[1][0] != 0
assert sme2.wave.shape[1][1] != 0
assert np.all(sme2.synth[0] == orig)
def test_synthesis_simple(sme_2segments):
sme = sme_2segments
sme2 = synthesize_spectrum(sme)
# Check if a result is there it has the expected data type
assert sme2.synth is not None
assert isinstance(sme2.synth, Iliffe_vector)
assert np.all(sme2.synth.ravel() != 0)
assert sme.wave is not None
assert isinstance(sme2.wave, Iliffe_vector)
assert np.issubdtype(sme2.wave.dtype, np.floating)
assert np.all(sme2.wave.ravel() != 0)
assert sme.spec is None
def create_sme_structure(teff=5770, logg=4.4):
examples_dir = os.path.dirname(os.path.realpath(__file__))
in_file = os.path.join(examples_dir, "sun_6440_grid.inp")
# Load your existing SME structure or create your own
sme = SME.SME_Structure.load(in_file)
sme.abund = Abund(0.05, "asplund2009")
sme.linelist = ValdFile(os.path.join(examples_dir, "sun.lin"))
# Change parameters if your want
sme.vrad_flag = "none"
sme.cscale_flag = "none"
sme.cscale_type = "mask"
sme.vsini = 0
sme.vrad = 0
# Set input parameters
sme.teff = teff
sme.logg = logg
# Start SME solver
sme = synthesize_spectrum(sme)
return sme
# Start the logging to the file
makedirs(dirname(log_file), exist_ok=True)
util.start_logging(log_file)
# Load your existing SME structure or create your own
sme = SME.SME_Structure.load(in_file)
# Change parameters if your want
sme.vrad = 0.35
sme.vrad_flag = "whole"
sme.cscale_flag = "linear"
sme.cscale_type = "match"
# Apply the parameters set via the command line
sme.teff = teff
sme.logg = logg
sme.monh = monh
# Start SME solver
sme = synthesize_spectrum(sme)
# Save results
makedirs(dirname(out_file), exist_ok=True)
sme.save(out_file)
# Plot results
makedirs(dirname(plot_file), exist_ok=True)
fig = plot_plotly.FinalPlot(sme)
fig.save(filename=plot_file)
fitparameters = ["teff", "logg", "monh", "vmic"]
# Restrict the linelist to relevant lines
# for this segment
s = 18
wmin, wmax = sme.wran[s]
sme.linelist = sme.linelist.trim(wmin, wmax, rvel=100)
# Set radial velocity and continuum settings
cscale = {}
x = sme.wave[s] - sme.wave[s][0]
sme.vrad_flag = "each"
sme.cscale_type = "match"
sme.cscale_flag = "cubic"
sme = synthesize_spectrum(sme, segments=[s])
cscale["match+cubic"] = np.polyval(sme.cscale[s], x)
sme.vrad_flag = "each"
sme.cscale_type = "spline"
sme.cscale_flag = 3
sme.cscale = None
sme.vrad = None
sme = synthesize_spectrum(sme, segments=[s])
cscale["spline+3"] = np.copy(sme.cscale[s])
sme.vrad_flag = "each"
sme.cscale_flag = "none"
sme = synthesize_spectrum(sme, segments=[s])
plot_file = join(dirname(__file__), "images/cont_55cnc.png")
# Run SME
sme = SME.SME_Structure.load(in_file)
orig = sme.synth.copy()
sme.cscale_flag = "linear"
sme.cscale_type = "match+mask"
sme.cscale[0] = [0, 1]
rvel = 100
wmin, wmax = sme.wran[0]
wmin *= 1 - rvel / 3e5
wmax *= 1 + rvel / 3e5
sme.linelist = sme.linelist.trim(wmin, wmax)
sme.specific_intensities_only = True
wmod, smod, cmod = synthesize_spectrum(sme, segments=[0])
orig = readsav(in_file)["sme"]
sint = orig["SINT"][0]
wint = orig["JINT"][0]
wind = orig["WIND"][0]
sint = sint[0, 0:wind[0]]
wint = wint[0:wind[0]]
plt.plot(wint, sint)
plt.plot(wmod[0], smod[0] * cmod[0])
plt.show()
# Plot results
fig = plot_plotly.FinalPlot(sme, orig=orig)
def main(fname_in, fname_out, log_file=None):
if log_file is not None:
start_logging(log_file)
sme = SME_Structure.load(fname_in)
sme = synthesize_spectrum(sme)
sme.save(fname_out)