from pathlib import Path
import h5py
import numpy as np
import pooch
from typeguard import typechecked
from species.core import constants
from species.util.data_util import extract_tarfile, remove_directory
[docs]
@typechecked
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()
url = "https://cdsarc.u-strasbg.fr/viz-bin/nph-Cat/tar.gz?J/A+A/623/A85"
input_file = "J_A+A_623_A85.tar.gz"
data_file = Path(input_path) / input_file
if not data_file.exists():
print()
pooch.retrieve(
url=url,
known_hash=None,
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}")
