"""
Module with a function for adding the Linder et al. (2019)
evolutionary tracks to the database.
"""
from requests.exceptions import HTTPError, SSLError
from pathlib import Path
import h5py
import numpy as np
import pooch
from beartype import beartype
from species.core import constants
from species.util.data_util import extract_tarfile, remove_directory
[docs]
@beartype
def add_linder2019(database: h5py._hl.files.File, input_path: str) -> None:
"""
Function for adding the `Linder et al. (2019)
<https://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/623/A85#/browse>`_
isochrones data to the database.
Parameters
----------
database : h5py._hl.files.File
Database.
input_path : str
Folder where the data is located.
Returns
-------
NoneType
None
"""
filters = (
"Paranal/NACO.J",
"Paranal/NACO.H",
"Paranal/NACO.Ks",
"Paranal/NACO.Lp",
"Paranal/NACO.Mp",
"Generic/Cousins.R",
"Generic/Cousins.I",
"WISE/WISE.W1",
"WISE/WISE.W2",
"WISE/WISE.W3",
"WISE/WISE.W4",
"JWST/NIRCam.F115W",
"JWST/NIRCam.F150W",
"JWST/NIRCam.F200W",
"JWST/NIRCam.F277W",
"JWST/NIRCam.F356W",
"JWST/NIRCam.F444W",
"JWST/MIRI.F560W",
"JWST/MIRI.F770W",
"JWST/MIRI.F1000W",
"JWST/MIRI.F1280W",
"JWST/MIRI.F1500W",
"JWST/MIRI.F1800W",
"JWST/MIRI.F2100W",
"JWST/MIRI.F2550W",
"Paranal/VISIR.B87",
"Paranal/VISIR.SiC",
"Paranal/SPHERE.IRDIS_B_Y",
"Paranal/SPHERE.IRDIS_B_J",
"Paranal/SPHERE.IRDIS_B_H",
"Paranal/SPHERE.IRDIS_B_Ks",
"Paranal/SPHERE.IRDIS_D_J23_2",
"Paranal/SPHERE.IRDIS_D_J23_3",
"Paranal/SPHERE.IRDIS_D_H23_2",
"Paranal/SPHERE.IRDIS_D_H23_3",
"Paranal/SPHERE.IRDIS_D_K12_1",
"Paranal/SPHERE.IRDIS_D_K12_2",
)
data_folder = Path(input_path) / "linder_2019"
if data_folder.exists():
# The folder should be removed if the TAR file was previously
# unpacked because the file permissions are set to read-only
# such that the extract_tarfile will cause an error if the
# files need to be overwritten
remove_directory(data_folder)
data_folder.mkdir()
input_file = "J_A+A_623_A85.tar.gz"
data_file = Path(input_path) / input_file
if not data_file.exists():
print()
try:
url = "https://cdsarc.u-strasbg.fr/viz-bin/nph-Cat/tar.gz?J/A+A/623/A85"
pooch.retrieve(
url=url,
known_hash=None,
fname=input_file,
path=input_path,
progressbar=True,
)
except (HTTPError, SSLError):
url = (
"https://home.strw.leidenuniv.nl/~stolker/species/J_A+A_623_A85.tar.gz"
)
pooch.retrieve(
url=url,
known_hash="83bbc673a10207838983e0155ec21915caedd6465d6926fba23675562797923d",
fname=input_file,
path=input_path,
progressbar=True,
)
print("\nUnpacking Linder et al. (2019) isochrones (536 kB)...", end="", flush=True)
extract_tarfile(str(data_file), str(data_folder))
print(" [DONE]")
iso_folder = Path(data_folder) / "isochrones"
iso_files = sorted(iso_folder.glob("*"))
for iso_item in iso_files:
file_param = iso_item.stem.split("_")
mags_idx = file_param.index("mags")
if int(file_param[mags_idx + 1]) == -2:
atm_model = "petitCODE"
elif int(file_param[mags_idx + 1]) == -3:
atm_model = "HELIOS"
else:
raise ValueError("Atmospheric model not recognized.")
mh_idx = file_param.index("MH")
metallicity = float(file_param[mh_idx + 1])
if "brighter" in file_param or "fainter" in file_param:
# Skip _brighter and _fainter files
continue
if "fsed" in file_param:
fsed_idx = file_param.index("fsed")
fsed = float(file_param[fsed_idx + 1])
else:
fsed = None
iso_data = np.loadtxt(iso_item)
print(
f"\nAdding isochrones: Linder et al. (2019) {atm_model}...",
end="",
flush=True,
)
age = 1e-6 * 10.0 ** iso_data[:, 0] # (Myr)
mass = iso_data[:, 1] * constants.M_EARTH / constants.M_JUP # (Mjup)
radius = iso_data[:, 2] # (Rjup)
log_lum = np.log10(8.710e-10 * iso_data[:, 3]) # log(L/Lsun)
teff = iso_data[:, 4] # (K)
logg = iso_data[:, 5] # log(g/cgs)
magnitudes = iso_data[:, 6:]
if fsed is None:
tag_label = f"linder2019-{atm_model}-metal_{metallicity}"
else:
tag_label = f"linder2019-{atm_model}-metal_{metallicity}-fsed_{fsed}"
dtype = h5py.string_dtype(encoding="utf-8", length=None)
dset = database.create_dataset(
f"isochrones/{tag_label}/filters", (np.size(filters),), dtype=dtype
)
dset[...] = filters
dset = database.create_dataset(f"isochrones/{tag_label}/age", data=age) # (Myr)
database.create_dataset(f"isochrones/{tag_label}/mass", data=mass) # (Mjup)
database.create_dataset(
f"isochrones/{tag_label}/log_lum", data=log_lum
) # log(L/Lsun)
database.create_dataset(f"isochrones/{tag_label}/teff", data=teff) # (K)
database.create_dataset(f"isochrones/{tag_label}/log_g", data=logg) # log(g)
database.create_dataset(f"isochrones/{tag_label}/radius", data=radius) # (Rjup)
database.create_dataset(f"isochrones/{tag_label}/magnitudes", data=magnitudes)
dset.attrs["model"] = "linder2019"
print(" [DONE]")
print(f"Database tag: {tag_label}")
