def add_bonnefoy2014(input_path: str, database: h5py._hl.files.File) -> None:
"""
Function for adding the SINFONI spectra of young, M- and L-type dwarfs from
`Bonnefoy et al. (2014) <https://ui.adsabs.harvard.edu/abs/2014A%26A...562A.127B/abstract>`_
to the database.
Parameters
----------
input_path : str
Path of the data folder.
database : h5py._hl.files.File
The HDF5 database.
Returns
-------
NoneType
None
"""
print_text = "spectra of young M/L type objects from Bonnefoy et al. 2014"
data_url = "http://cdsarc.u-strasbg.fr/viz-bin/nph-Cat/tar.gz?J/A+A/562/A127/"
data_file = os.path.join(input_path, "J_A+A_562_A127.tar.gz")
data_folder = os.path.join(input_path, "bonnefoy+2014/")
if not os.path.isfile(data_file):
print(f"Downloading {print_text} (2.3 MB)...", end="", flush=True)
urllib.request.urlretrieve(data_url, data_file)
print(" [DONE]")
if os.path.exists(data_folder):
shutil.rmtree(data_folder)
print(f"Unpacking {print_text} (2.3 MB)...", end="", flush=True)
tar = tarfile.open(data_file)
tar.extractall(data_folder)
tar.close()
print(" [DONE]")
spec_dict = {}
with gzip.open(os.path.join(data_folder, "stars.dat.gz"),
"r") as gzip_file:
for line in gzip_file:
name = line[:13].decode().strip()
files = line[80:].decode().strip().split()
sptype = line[49:56].decode().strip()
if name == "NAME 2M1207A":
name = "2M1207A"
if len(sptype) == 0:
sptype = None
elif "." in sptype:
sptype = sptype[:4]
else:
sptype = sptype[:2]
if name == "Cha1109":
sptype = "M9"
elif name == "DH Tau B":
sptype = "M9"
elif name == "TWA 22A":
sptype = "M6"
elif name == "TWA 22B":
sptype = "M6"
elif name == "CT Cha b":
sptype = "M9"
spec_dict[name] = {"name": name, "sptype": sptype, "files": files}
database.create_group("spectra/bonnefoy+2014")
fits_folder = os.path.join(data_folder, "sp")
print_message = ""
for _, _, files in os.walk(fits_folder):
for _, filename in enumerate(files):
fname_split = filename.split("_")
data = fits.getdata(os.path.join(fits_folder, filename))
for name, value in spec_dict.items():
if filename in value["files"]:
if name == "TWA 22AB":
# Binary spectrum
continue
if "JHK.fits" in fname_split:
spec_dict[name]["JHK"] = data
elif "J" in fname_split:
spec_dict[name]["J"] = data
elif "H+K" in fname_split or "HK" in fname_split:
spec_dict[name]["HK"] = data
for name, value in spec_dict.items():
empty_message = len(print_message) * " "
print(f"\r{empty_message}", end="")
print_message = f"Adding spectra... {name}"
print(f"\r{print_message}", end="")
if "JHK" in value:
sp_data = value["JHK"]
elif "J" in value and "HK" in value:
sp_data = np.vstack((value["J"], value["HK"]))
else:
continue
dset = database.create_dataset(f"spectra/bonnefoy+2014/{name}",
data=sp_data)
dset.attrs["name"] = str(name).encode()
dset.attrs["sptype"] = str(value["sptype"]).encode()
empty_message = len(print_message) * " "
print(f"\r{empty_message}", end="")
print_message = "Adding spectra... [DONE]"
print(f"\r{print_message}")
database.close()
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}")
h_twomass = photometry.SyntheticPhotometry("2MASS/2MASS.H")
# 2MASS H band zero point for 0 mag (Cogen et al. 2003)
h_zp = 1.133e-9 # (W m-2 um-1)
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
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 = data_util.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 = data_util.update_sptype(np.array([sptype_nir]))[0]
except KeyError:
sptype_nir = None
h_flux, _ = h_twomass.magnitude_to_flux(h_mag, error=None, zp_flux=h_zp)
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 = query_util.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)
print_message = f"Adding spectra... {name}"
print(f"\r{print_message:<72}", 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"] = j_mag
dset.attrs["2MASS/2MASS.H"] = h_mag
dset.attrs["2MASS/2MASS.Ks"] = ks_mag
dset.attrs["parallax"] = parallax[0] # (mas)
dset.attrs["parallax_error"] = parallax[1] # (mas)
print_message = "Adding spectra... [DONE]"
print(f"\r{print_message:<72}")
database.close()
def add_kesseli2017(input_path: str, database: h5py._hl.files.File) -> None:
"""
Function for adding the SDSS stellar spectra from Kesseli et al. (2017) to the database.
Parameters
----------
input_path : str
Path of the data folder.
database : h5py._hl.files.File
The HDF5 database.
Returns
-------
NoneType
None
"""
data_url = "https://cdsarc.unistra.fr/viz-bin/nph-Cat/tar.gz?J/ApJS/230/16"
data_file = os.path.join(input_path, "J_ApJS_230_16.tar.gz")
data_folder = os.path.join(input_path, "kesseli+2017/")
if not os.path.isfile(data_file):
print(
"Downloading SDSS spectra from Kesseli et al. 2017 (145 MB)...",
end="",
flush=True,
)
urllib.request.urlretrieve(data_url, data_file)
print(" [DONE]")
if os.path.exists(data_folder):
shutil.rmtree(data_folder)
print(
"Unpacking SDSS spectra from Kesseli et al. 2017 (145 MB)...",
end="",
flush=True,
)
tar = tarfile.open(data_file)
tar.extractall(data_folder)
tar.close()
print(" [DONE]")
database.create_group("spectra/kesseli+2017")
fits_folder = os.path.join(data_folder, "fits")
print_message = ""
for _, _, files in os.walk(fits_folder):
for _, filename in enumerate(files):
with fits.open(os.path.join(fits_folder, filename)) as hdu_list:
data = hdu_list[1].data
wavelength = 1e-4 * 10.0**data["LogLam"] # (um)
flux = data["Flux"] # Normalized units
error = data["PropErr"] # Normalized units
name = filename[:-5].replace("_", " ")
file_split = filename.split("_")
file_split = file_split[0].split(".")
sptype = file_split[0]
spdata = np.column_stack([wavelength, flux, error])
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/kesseli+2017/{name}",
data=spdata)
dset.attrs["name"] = str(name).encode()
dset.attrs["sptype"] = str(sptype).encode()
empty_message = len(print_message) * " "
print(f"\r{empty_message}", end="")
print_message = "Adding spectra... [DONE]"
print(f"\r{print_message}")
database.close()
def add_irtf(input_path: str,
database: h5py._hl.files.File,
sptypes: Optional[List[str]] = None) -> None:
"""
Function for adding the IRTF Spectral Library to the database.
Parameters
----------
input_path : str
Path of the data folder.
database : h5py._hl.files.File
Database.
sptypes : list(str, ), None
List with the spectral types ('F', 'G', 'K', 'M', 'L', 'T'). All spectral types are
included if set to ``None``.
Returns
-------
NoneType
None
"""
if sptypes is None:
sptypes = ['F', 'G', 'K', 'M', 'L', 'T']
distance_url = 'https://people.phys.ethz.ch/~stolkert/species/distance.dat'
distance_file = os.path.join(input_path, 'distance.dat')
if not os.path.isfile(distance_file):
urllib.request.urlretrieve(distance_url, distance_file)
distance_data = pd.pandas.read_csv(distance_file,
usecols=[0, 3, 4],
names=['object', 'distance', 'distance_error'],
delimiter=',',
dtype={'object': str,
'distance': float,
'distance_error': float})
datadir = os.path.join(input_path, 'irtf')
if not os.path.exists(datadir):
os.makedirs(datadir)
data_file = {'F': os.path.join(input_path, 'irtf/F_fits_091201.tar'),
'G': os.path.join(input_path, 'irtf/G_fits_091201.tar'),
'K': os.path.join(input_path, 'irtf/K_fits_091201.tar'),
'M': os.path.join(input_path, 'irtf/M_fits_091201.tar'),
'L': os.path.join(input_path, 'irtf/L_fits_091201.tar'),
'T': os.path.join(input_path, 'irtf/T_fits_091201.tar')}
data_folder = {'F': os.path.join(input_path, 'irtf/F_fits_091201'),
'G': os.path.join(input_path, 'irtf/G_fits_091201'),
'K': os.path.join(input_path, 'irtf/K_fits_091201'),
'M': os.path.join(input_path, 'irtf/M_fits_091201'),
'L': os.path.join(input_path, 'irtf/L_fits_091201'),
'T': os.path.join(input_path, 'irtf/T_fits_091201')}
data_type = {'F': 'F stars (4.4 MB)',
'G': 'G stars (5.6 MB)',
'K': 'K stars (5.5 MB)',
'M': 'M stars (7.5 MB)',
'L': 'L dwarfs (850 kB)',
'T': 'T dwarfs (100 kB)'}
url_root = 'http://irtfweb.ifa.hawaii.edu/~spex/IRTF_Spectral_Library/Data/'
url = {'F': url_root+'F_fits_091201.tar',
'G': url_root+'G_fits_091201.tar',
'K': url_root+'K_fits_091201.tar',
'M': url_root+'M_fits_091201.tar',
'L': url_root+'L_fits_091201.tar',
'T': url_root+'T_fits_091201.tar'}
for item in sptypes:
if not os.path.isfile(data_file[item]):
print(f'Downloading IRTF Spectral Library - {data_type[item]}...', end='', flush=True)
urllib.request.urlretrieve(url[item], data_file[item])
print(' [DONE]')
print('Unpacking IRTF Spectral Library...', end='', flush=True)
for item in sptypes:
tar = tarfile.open(data_file[item])
tar.extractall(path=datadir)
tar.close()
print(' [DONE]')
database.create_group('spectra/irtf')
for item in sptypes:
for root, _, files in os.walk(data_folder[item]):
for _, filename in enumerate(files):
if filename[-9:] != '_ext.fits':
fitsfile = os.path.join(root, filename)
spdata, header = fits.getdata(fitsfile, header=True)
name = header['OBJECT']
sptype = header['SPTYPE']
if name[-2:] == 'AB':
name = name[:-2]
elif name[-3:] == 'ABC':
name = name[:-3]
spt_split = sptype.split()
if item in ['L', 'T'] or spt_split[1][0] == 'V':
print_message = f'Adding IRTF Spectral Library... {name}'
print(f'\r{print_message:<70}', end='')
simbad_id = query_util.get_simbad(name)
if simbad_id is not None:
simbad_id = simbad_id.decode('utf-8')
dist_select = distance_data.loc[distance_data['object'] == simbad_id]
if not dist_select.empty:
distance = (dist_select['distance'], dist_select['distance_error'])
else:
simbad_id, distance = query_util.get_distance(name)
else:
distance = (np.nan, np.nan)
sptype = data_util.update_sptype(np.array([sptype]))[0]
dset = database.create_dataset(f'spectra/irtf/{name}',
data=spdata)
dset.attrs['name'] = str(name).encode()
dset.attrs['sptype'] = str(sptype).encode()
dset.attrs['simbad'] = str(simbad_id).encode()
dset.attrs['distance'] = distance[0]
dset.attrs['distance_error'] = distance[1]
print_message = 'Adding IRTF Spectral Library... [DONE]'
print(f'\r{print_message:<70}')
database.close()
def add_allers2013(input_path: str, database: h5py._hl.files.File) -> None:
"""
Function for adding the spectra of young, M- and L-type dwarfs from
`Allers & Liu (2013) <https://ui.adsabs.harvard.edu/abs/2013ApJ...772...79A/abstract>`_ to
the database.
Parameters
----------
input_path : str
Path of the data folder.
database : h5py._hl.files.File
The HDF5 database.
Returns
-------
NoneType
None
"""
print_text = "spectra of young M/L type objects from Allers & Liu 2013"
data_url = "https://home.strw.leidenuniv.nl/~stolker/species/allers_liu_2013.tgz"
data_file = os.path.join(input_path, "allers_liu_2013.tgz")
data_folder = os.path.join(input_path, "allers+2013/")
if not os.path.isfile(data_file):
print(f"Downloading {print_text} (173 kB)...", end="", flush=True)
urllib.request.urlretrieve(data_url, data_file)
print(" [DONE]")
if os.path.exists(data_folder):
shutil.rmtree(data_folder)
print(f"Unpacking {print_text} (173 kB)...", end="", flush=True)
tar = tarfile.open(data_file)
tar.extractall(data_folder)
tar.close()
print(" [DONE]")
sources = np.genfromtxt(
os.path.join(data_folder, "sources.csv"),
delimiter=",",
dtype=None,
encoding="ASCII",
)
source_names = sources[:, 0]
source_sptype = sources[:, 7]
database.create_group("spectra/allers+2013")
print_message = ""
for _, _, files in os.walk(data_folder):
for _, filename in enumerate(files):
if filename.endswith(".fits"):
sp_data, header = fits.getdata(os.path.join(
data_folder, filename),
header=True)
else:
continue
sp_data = np.transpose(sp_data)
# (erg s-1 cm-2 A-1) -> (W m-2 um-1)
sp_data[:, 1:] *= 10.0
name = header["OBJECT"]
index = np.argwhere(source_names == name)
if len(index) == 0:
sptype = None
else:
sptype = source_sptype[index][0][0][:2]
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/allers+2013/{name}",
data=sp_data)
dset.attrs["name"] = str(name).encode()
dset.attrs["sptype"] = str(sptype).encode()
empty_message = len(print_message) * " "
print(f"\r{empty_message}", end="")
print_message = "Adding spectra... [DONE]"
print(f"\r{print_message}")
database.close()
def add_irtf(input_path: str,
database: h5py._hl.files.File,
sptypes: Optional[List[str]] = None) -> None:
"""
Function for adding the IRTF Spectral Library to the database.
Parameters
----------
input_path : str
Path of the data folder.
database : h5py._hl.files.File
Database.
sptypes : list(str), None
List with the spectral types ('F', 'G', 'K', 'M', 'L', 'T'). All spectral types are
included if set to ``None``.
Returns
-------
NoneType
None
"""
if sptypes is None:
sptypes = ["F", "G", "K", "M", "L", "T"]
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
},
)
datadir = os.path.join(input_path, "irtf")
if not os.path.exists(datadir):
os.makedirs(datadir)
data_file = {
"F": os.path.join(input_path, "irtf/F_fits_091201.tar"),
"G": os.path.join(input_path, "irtf/G_fits_091201.tar"),
"K": os.path.join(input_path, "irtf/K_fits_091201.tar"),
"M": os.path.join(input_path, "irtf/M_fits_091201.tar"),
"L": os.path.join(input_path, "irtf/L_fits_091201.tar"),
"T": os.path.join(input_path, "irtf/T_fits_091201.tar"),
}
data_folder = {
"F": os.path.join(input_path, "irtf/F_fits_091201"),
"G": os.path.join(input_path, "irtf/G_fits_091201"),
"K": os.path.join(input_path, "irtf/K_fits_091201"),
"M": os.path.join(input_path, "irtf/M_fits_091201"),
"L": os.path.join(input_path, "irtf/L_fits_091201"),
"T": os.path.join(input_path, "irtf/T_fits_091201"),
}
data_type = {
"F": "F stars (4.4 MB)",
"G": "G stars (5.6 MB)",
"K": "K stars (5.5 MB)",
"M": "M stars (7.5 MB)",
"L": "L dwarfs (850 kB)",
"T": "T dwarfs (100 kB)",
}
url_root = "http://irtfweb.ifa.hawaii.edu/~spex/IRTF_Spectral_Library/Data/"
url = {
"F": url_root + "F_fits_091201.tar",
"G": url_root + "G_fits_091201.tar",
"K": url_root + "K_fits_091201.tar",
"M": url_root + "M_fits_091201.tar",
"L": url_root + "L_fits_091201.tar",
"T": url_root + "T_fits_091201.tar",
}
for item in sptypes:
if not os.path.isfile(data_file[item]):
print(
f"Downloading IRTF Spectral Library - {data_type[item]}...",
end="",
flush=True,
)
urllib.request.urlretrieve(url[item], data_file[item])
print(" [DONE]")
print("Unpacking IRTF Spectral Library...", end="", flush=True)
for item in sptypes:
tar = tarfile.open(data_file[item])
tar.extractall(path=datadir)
tar.close()
print(" [DONE]")
database.create_group("spectra/irtf")
print_message = ""
for item in sptypes:
for root, _, files in os.walk(data_folder[item]):
for _, filename in enumerate(files):
if filename[-9:] != "_ext.fits":
fitsfile = os.path.join(root, filename)
spdata, header = fits.getdata(fitsfile, header=True)
spdata = np.transpose(spdata)
name = header["OBJECT"]
sptype = header["SPTYPE"]
if name[-2:] == "AB":
name = name[:-2]
elif name[-3:] == "ABC":
name = name[:-3]
spt_split = sptype.split()
if item in ["L", "T"] or spt_split[1][0] == "V":
empty_message = len(print_message) * " "
print(f"\r{empty_message}", end="")
print_message = f"Adding spectra... {name}"
print(f"\r{print_message}", end="")
simbad_id = query_util.get_simbad(name)
if simbad_id is not None:
# For backward compatibility
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"],
par_select["parallax_error"],
)
else:
simbad_id, parallax = query_util.get_parallax(
name)
else:
parallax = (np.nan, np.nan)
sptype = data_util.update_sptype(np.array([sptype]))[0]
dset = database.create_dataset(f"spectra/irtf/{name}",
data=spdata)
dset.attrs["name"] = str(name).encode()
dset.attrs["sptype"] = str(sptype).encode()
dset.attrs["simbad"] = str(simbad_id).encode()
dset.attrs["parallax"] = parallax[0]
dset.attrs["parallax_error"] = parallax[1]
empty_message = len(print_message) * " "
print(f"\r{empty_message}", end="")
print_message = "Adding spectra... [DONE]"
print(f"\r{print_message}")
database.close()