def test_if_doppler_shift_changes_quality(testing_spectrum, rv):
wavelength, flux_ = testing_spectrum[0], testing_spectrum[1]
wmin_, wmax_ = 2.1, 2.3
m1 = (wavelength < wmax_ + 0.2) * (wavelength > wmin_ - 0.2)
# shorten spectra
wavelength, flux_ = wavelength[m1], flux_[m1]
mask = (wavelength < wmax_) * (wavelength > wmin_)
wave = wavelength[mask]
flux = flux_[mask]
q1 = quality(wave, flux)
wav2 = doppler_shift_wav(wavelength, rv)
mask2 = (wav2 < wmax_) * (wav2 > wmin_)
wav2 = wav2[mask2]
flux2 = flux_[mask2]
q2 = quality(wav2, flux2)
assert q1 != q2
flux3 = doppler_shift_flux(wavelength, flux_, rv, new_wav=wave)
q3 = quality(wave, flux3)
assert len(wave) == len(flux3)
assert q1 != q3
# There are differences due to interpolation
assert q2 != q3
def test_doppler_shift_at_speed_of_light(wavelength, direction, multiplier):
r"""It is test is only valid for the non-relativistic doppler shift.
It is a test of the math but not physical (not valid at this speed)
but we are checking the math of the equation works
should result in a shift of \delta \lambda = +/- \lambda"""
c_wave = doppler_shift_wav(wavelength, direction * const.c.to("km/s").value)
assert np.all(c_wave == (wavelength * multiplier))
def main(
model: str = atmmodel,
bands: Optional[List[str]] = None,
new_name: Optional[str] = None,
data_dir: Optional[str] = None,
rv_extend: float = 100,
cutoff_depth: float = 2.0,
):
"""Split the large atmospheric model transmission spectra into the separate bands.
Keeps wavelength of atmosphere model as nanometers.
Parameters
----------
model: str
Telluric model file to load. It has columns wavelength, flux, std_flux, mask.
bands: list[str]
List bands to split model into separate files.
new_name: str
New file name base.
data_dir: Optional[str]
Directory for results. Can also be given in config.yaml "paths:atmmodel:"...
rv_extend: float (positive) (default 100)
Rv amount to extend wavelength range of telluric band. To later apply barycenter shifting.
cutoff_depth: float
Telluric line depth cutoff. Default = 2%.
"""
if (bands is None) or ("ALL" in bands):
bands_ = eniric.bands["all"]
else:
bands_ = bands
if new_name is None:
new_name = model.split(".")[0]
if data_dir is None:
data_dir_ = eniric.paths["atmmodel"]
else:
data_dir_ = str(data_dir)
model_name = join(data_dir_, model)
# If trying to obtain the provided model extract from and it doesn't yet exist
# extract from tar.gz file. (Extracted it is 230 MB which is to large for Git)
if "Average_TAPAS_2014.dat" == atmmodel:
if not os.path.exists(model_name):
print("Unpacking Average_TAPAS_2014.dat.tar.gz...")
import tarfile
with tarfile.open(str(model_name) + ".tar.gz", "r") as tar:
tar.extractall(data_dir_)
print("Unpacked")
print("Loading from_file {0}".format(model_name))
atm = Atmosphere.from_file(model_name)
# Return value from saving each band
write_status = np.empty_like(bands_, dtype=int)
for i, band in enumerate(bands_):
print("Starting {0}".format(band))
filename_band = "{0}_{1}.dat".format(new_name, band)
band_min, band_max = band_limits(band)
# * 1000 to convert into km/s
band_min = doppler_shift_wav(band_min, -rv_extend)
band_max = doppler_shift_wav(band_max, rv_extend)
split_atm = atm.wave_select(band_min, band_max)
# Apply telluric line mask
atm.mask_transmission(depth=cutoff_depth)
# Save the result to file
filename = join(data_dir_, filename_band)
header = ["# atm_wav(nm)", "atm_flux", "atm_std_flux", "atm_mask"]
print("Saving to_file {}".format(filename))
write_status[i] = split_atm.to_file(filename, header=header, fmt="%11.8f")
print("Done Splitting")
return np.sum(write_status) # If any extracts fail they will turn up here.
def doppler_shift_zero(wavelength):
"""Doppler shift of zero will give no change."""
assert np.all(doppler_shift_wav(wavelength, vel=0.0) == wavelength)