"""
Module for adding the SpeX Prism Spectral Libraries to the database.
"""
import os
import urllib.request
import h5py
import numpy as np
import pandas as pd
from astropy.io.votable import parse_single_table
from typeguard import typechecked
from species.phot.syn_phot import SyntheticPhotometry
from species.util.data_util import update_sptype
from species.util.query_util import get_simbad
[docs]
@typechecked
def add_spex(input_path: str, database: h5py._hl.files.File) -> None:
"""
Function for adding the SpeX Prism Spectral Library
to the database.
Parameters
----------
input_path : str
Path of the data folder.
database : h5py._hl.files.File
The HDF5 database.
Returns
-------
NoneType
None
"""
parallax_url = "https://home.strw.leidenuniv.nl/~stolker/species/parallax.dat"
parallax_file = os.path.join(input_path, "parallax.dat")
if not os.path.isfile(parallax_file):
urllib.request.urlretrieve(parallax_url, parallax_file)
parallax_data = pd.pandas.read_csv(
parallax_file,
usecols=[0, 1, 2],
names=["object", "parallax", "parallax_error"],
delimiter=",",
dtype={"object": str, "parallax": float, "parallax_error": float},
)
database.create_group("spectra/spex")
data_path = os.path.join(input_path, "spex")
if not os.path.exists(data_path):
os.makedirs(data_path)
url_all = (
"http://svo2.cab.inta-csic.es/vocats/v2/spex/cs.php?"
"RA=180.000000&DEC=0.000000&SR=180.000000&VERB=2"
)
xml_file_spex = os.path.join(data_path, "spex.xml")
if not os.path.isfile(xml_file_spex):
urllib.request.urlretrieve(url_all, xml_file_spex)
table = parse_single_table(xml_file_spex)
# name = table.array['name']
twomass = table.array["name2m"]
url = table.array["access_url"]
unique_id = []
print_message = ""
for i, item in enumerate(url):
if twomass[i] not in unique_id:
if isinstance(twomass[i], str):
xml_file_1 = os.path.join(data_path, twomass[i] + ".xml")
else:
# Use decode for backward compatibility
xml_file_1 = os.path.join(
data_path, twomass[i].decode("utf-8") + ".xml"
)
if not os.path.isfile(xml_file_1):
if isinstance(item, str):
urllib.request.urlretrieve(item, xml_file_1)
else:
urllib.request.urlretrieve(item.decode("utf-8"), xml_file_1)
table = parse_single_table(xml_file_1)
name = table.array["ID"]
url = table.array["access_url"]
if isinstance(name[0], str):
name = name[0]
else:
name = name[0].decode("utf-8")
empty_message = len(print_message) * " "
print(f"\r{empty_message}", end="")
print_message = f"Downloading SpeX Prism Spectral Library... {name}"
print(f"\r{print_message}", end="")
xml_file_2 = os.path.join(data_path, f"spex_{name}.xml")
if not os.path.isfile(xml_file_2):
if isinstance(url[0], str):
urllib.request.urlretrieve(url[0], xml_file_2)
else:
urllib.request.urlretrieve(url[0].decode("utf-8"), xml_file_2)
unique_id.append(twomass[i])
empty_message = len(print_message) * " "
print(f"\r{empty_message}", end="")
print_message = "Downloading SpeX Prism Spectral Library... [DONE]"
print(f"\r{print_message}")
# 2MASS H band zero point for 0 mag (Cogen et al. 2003)
zp_hband = 1.133e-9 # (W m-2 um-1)
h_twomass = SyntheticPhotometry("2MASS/2MASS.H", zero_point=zp_hband)
for votable in os.listdir(data_path):
if votable.startswith("spex_") and votable.endswith(".xml"):
xml_file = os.path.join(data_path, votable)
table = parse_single_table(xml_file)
wavelength = table.array["wavelength"] # (Angstrom)
flux = table.array["flux"] # Normalized units
spec_res = table.get_field_by_id("res").value
wavelength = np.array(wavelength * 1e-4) # (um)
flux = np.array(flux) # (a.u.)
error = np.full(flux.size, np.nan)
# 2MASS magnitudes
j_mag = table.get_field_by_id("jmag").value
h_mag = table.get_field_by_id("hmag").value
ks_mag = table.get_field_by_id("ksmag").value
if not isinstance(j_mag, str):
j_mag = j_mag.decode("utf-8")
if not isinstance(h_mag, str):
h_mag = h_mag.decode("utf-8")
if not isinstance(ks_mag, str):
ks_mag = ks_mag.decode("utf-8")
if j_mag == "":
j_mag = np.nan
else:
j_mag = float(j_mag)
if h_mag == "":
h_mag = np.nan
else:
h_mag = float(h_mag)
if ks_mag == "":
ks_mag = np.nan
else:
ks_mag = float(ks_mag)
name = table.get_field_by_id("name").value
if not isinstance(name, str):
name = name.decode("utf-8")
twomass_id = table.get_field_by_id("name2m").value
if not isinstance(twomass_id, str):
twomass_id = twomass_id.decode("utf-8")
# Optical spectral type
try:
sptype_opt = table.get_field_by_id("optspty").value
if not isinstance(sptype_opt, str):
sptype_opt = sptype_opt.decode("utf-8")
sptype_opt = update_sptype(np.array([sptype_opt]))[0]
except KeyError:
sptype_opt = None
# Near-infrared spectral type
try:
sptype_nir = table.get_field_by_id("nirspty").value
if not isinstance(sptype_nir, str):
sptype_nir = sptype_nir.decode("utf-8")
sptype_nir = update_sptype(np.array([sptype_nir]))[0]
except KeyError:
sptype_nir = None
h_flux, _ = h_twomass.magnitude_to_flux(h_mag, error=None)
phot = h_twomass.spectrum_to_flux(wavelength, flux) # Normalized units
flux *= h_flux / phot[0] # (W m-2 um-1)
spdata = np.column_stack([wavelength, flux, error])
simbad_id = get_simbad(f"2MASS {twomass_id}")
if simbad_id is not None:
if not isinstance(simbad_id, str):
simbad_id = simbad_id.decode("utf-8")
par_select = parallax_data[parallax_data["object"] == simbad_id]
if not par_select.empty:
parallax = (
par_select["parallax"].values[0],
par_select["parallax_error"].values[0],
)
else:
parallax = (np.nan, np.nan)
else:
parallax = (np.nan, np.nan)
empty_message = len(print_message) * " "
print(f"\r{empty_message}", end="")
print_message = f"Adding spectra... {name}"
print(f"\r{print_message}", end="")
dset = database.create_dataset(f"spectra/spex/{name}", data=spdata)
dset.attrs["name"] = str(name).encode()
if sptype_opt is not None:
dset.attrs["sptype"] = str(sptype_opt).encode()
elif sptype_nir is not None:
dset.attrs["sptype"] = str(sptype_nir).encode()
else:
dset.attrs["sptype"] = str("None").encode()
dset.attrs["simbad"] = str(simbad_id).encode()
dset.attrs["2MASS/2MASS.J"] = float(j_mag)
dset.attrs["2MASS/2MASS.H"] = float(h_mag)
dset.attrs["2MASS/2MASS.Ks"] = float(ks_mag)
dset.attrs["parallax"] = float(parallax[0]) # (mas)
dset.attrs["parallax_error"] = float(parallax[1]) # (mas)
dset.attrs["spec_res"] = float(spec_res)
empty_message = len(print_message) * " "
print(f"\r{empty_message}", end="")
print_message = "Adding spectra... [DONE]"
print(f"\r{print_message}")
