import glob
import os
import urllib.request
import h5py
import numpy as np
from species.core import constants
from species.util.data_util import extract_tarfile
[docs]
def add_atmo(database, input_path):
"""
Function for adding the AMES-Cond and AMES-Dusty
isochrone data to the database.
Parameters
----------
database : h5py._hl.files.File
Database.
input_path : str
Folder where the data is located.
Returns
-------
NoneType
None
"""
if not os.path.exists(input_path):
os.makedirs(input_path)
url_iso = (
"https://home.strw.leidenuniv.nl/~stolker/"
"species/atmo_evolutionary_tracks.tgz"
)
# iso_tags = ["ATMO-CEQ", "ATMO-NEQ-weak", , "ATMO-NEQ-strong"]
# iso_size = ["235 kB", "182 kB"]
iso_tag = "ATMO"
iso_size = "9.6 MB"
data_folder = os.path.join(input_path, "atmo_evolutionary_tracks")
if not os.path.exists(data_folder):
os.makedirs(data_folder)
input_file = url_iso.rsplit("/", maxsplit=1)[-1]
data_file = os.path.join(input_path, input_file)
if not os.path.isfile(data_file):
print(f"Downloading {iso_tag} isochrones ({iso_size})...", end="", flush=True)
urllib.request.urlretrieve(url_iso, data_file)
print(" [DONE]")
print(f"Unpacking {iso_tag} isochrones ({iso_size})...", end="", flush=True)
extract_tarfile(data_file, data_folder)
print(" [DONE]")
iso_files = [
"ATMO_CEQ",
"ATMO_NEQ_weak",
"ATMO_NEQ_strong",
]
labels = [
"ATMO equilibrium chemistry",
"ATMO non-equilibrium chemistry (weak)",
"ATMO non-equilibrium chemistry (strong)",
]
db_tags = [
"atmo-ceq",
"atmo-neq-weak",
"atmo-neq-strong",
]
for j, iso_item in enumerate(iso_files):
iso_path = os.path.join(data_folder, iso_item)
iso_path = os.path.join(iso_path, "MKO_WISE_IRAC")
file_list = sorted(glob.glob(iso_path + "/*.txt"))
for i, file_item in enumerate(file_list):
# Mass (Msun) - Age (Gyr) - Teff (K) - log(L/Lsun) - Radius (Rsun) - log(g)
if i == 0:
iso_data = np.loadtxt(file_item)
else:
iso_load = np.loadtxt(file_item)
iso_data = np.vstack((iso_data, iso_load))
with open(file_item, encoding="utf-8") as open_file:
parameters = open_file.readline()
filter_names = parameters.split()[7:]
iso_data[:, 0] *= constants.M_SUN / constants.M_JUP # (Msun) -> (Mjup)
iso_data[:, 1] *= 1e3 # (Gyr) -> (Myr)
iso_data[:, 4] *= constants.R_SUN / constants.R_JUP # (Rsun) -> (Rjup)
print(f"Adding isochrones: {labels[j]}...", end="", flush=True)
dtype = h5py.string_dtype(encoding="utf-8", length=None)
dset = database.create_dataset(
f"isochrones/{db_tags[j]}/filters", (np.size(filter_names),), dtype=dtype
)
dset[...] = filter_names
database.create_dataset(
f"isochrones/{db_tags[j]}/mass", data=iso_data[:, 0]
) # (Mjup)
dset = database.create_dataset(
f"isochrones/{db_tags[j]}/age", data=iso_data[:, 1]
) # (Myr)
database.create_dataset(
f"isochrones/{db_tags[j]}/teff", data=iso_data[:, 2]
) # (K)
database.create_dataset(
f"isochrones/{db_tags[j]}/log_lum", data=iso_data[:, 3]
) # log(L/Lsun)
database.create_dataset(
f"isochrones/{db_tags[j]}/radius", data=iso_data[:, 4]
) # (Rjup)
database.create_dataset(
f"isochrones/{db_tags[j]}/log_g", data=iso_data[:, 5]
) # log(g)
database.create_dataset(
f"isochrones/{db_tags[j]}/magnitudes", data=iso_data[:, 6:]
)
dset.attrs["model"] = "atmo"
print(" [DONE]")
print(f"Database tag: {db_tags[j]}")
