def load_data(flag=None):
"""
NAME:
load_data
PURPOSE:
load_data galaxy10 data
INPUT:
None
OUTPUT:
x (ndarray): An array of images
y (ndarray): An array of answer
HISTORY:
2018-Jan-22 - Written - Henry Leung (University of Toronto)
"""
filename = 'Galaxy10.h5'
complete_url = _G10_ORIGIN + filename
datadir = os.path.join(astroNN_CACHE_DIR, 'datasets')
file_hash = '969A6B1CEFCC36E09FFFA86FEBD2F699A4AA19B837BA0427F01B0BC6DED458AF' # SHA256
# Notice python expect sha256 in lowercase
if not os.path.exists(datadir):
os.makedirs(datadir)
fullfilename = os.path.join(datadir, filename)
# Check if files exists
if os.path.isfile(fullfilename) and flag is None:
checksum = filehash(fullfilename, algorithm='sha256')
if checksum != file_hash.lower():
print(
'File corruption detected, astroNN is attempting to download again'
)
load_data(flag=1)
else:
print(fullfilename + ' was found!')
elif not os.path.isfile(fullfilename) or flag == 1:
with TqdmUpTo(unit='B',
unit_scale=True,
miniters=1,
desc=complete_url.split('/')[-1]) as t:
urllib.request.urlretrieve(complete_url,
fullfilename,
reporthook=t.update_to)
print(f'Downloaded Galaxy10 successfully to {fullfilename}')
checksum = filehash(fullfilename, algorithm='sha256')
if checksum != file_hash.lower():
load_data(flag=1)
with h5py.File(fullfilename, 'r') as F:
x = np.array(F['images'])
y = np.array(F['ans'])
return x, y
def tgas(flag=None):
"""
Get path to the Gaia TGAS DR1 files, download if files not found
:return: List of file path
:rtype: list
:History: 2017-Oct-13 - Written - Henry Leung (University of Toronto)
"""
# Check if dr arguement is provided, if none then use default
fulllist = []
# Check if directory exists
folderpath = os.path.join(gaia_env(), 'Gaia/gdr1/tgas_source/fits/')
urlbase = 'http://cdn.gea.esac.esa.int/Gaia/gdr1/tgas_source/fits/'
if not os.path.exists(folderpath):
os.makedirs(folderpath)
hash_filename = 'MD5SUM.txt'
full_hash_filename = os.path.join(folderpath, hash_filename)
if not os.path.isfile(full_hash_filename):
urllib.request.urlretrieve(urlbase + hash_filename, full_hash_filename)
hash_list = np.loadtxt(full_hash_filename, dtype='str').T
for i in range(0, 16, 1):
filename = f'TgasSource_000-000-0{i:0{2}d}.fits'
fullfilename = os.path.join(folderpath, filename)
urlstr = urlbase + filename
file_hash = (hash_list[0])[np.argwhere(hash_list[1] == filename)]
# Check if files exists
if os.path.isfile(fullfilename) and flag is None:
checksum = filehash(fullfilename, algorithm='md5')
# In some rare case, the hash cant be found, so during checking, check len(file_has)!=0 too
if checksum != file_hash and len(file_hash) != 0:
print(checksum)
print(file_hash)
print('File corruption detected, astroNN is attempting to download again')
tgas(flag=1)
else:
print(fullfilename + ' was found!')
elif not os.path.isfile(fullfilename) or flag == 1:
# progress bar
with TqdmUpTo(unit='B', unit_scale=True, miniters=1, desc=urlstr.split('/')[-1]) as t:
# Download
urllib.request.urlretrieve(urlstr, fullfilename, reporthook=t.update_to)
checksum = filehash(fullfilename, algorithm='md5')
if checksum != file_hash and len(file_hash) != 0:
print('File corruption detected, astroNN is attempting to download again')
tgas(flag=1)
print(f'Downloaded Gaia DR1 TGAS ({i:d} of 15) file catalog successfully to {fullfilename}')
fulllist.extend([fullfilename])
return fulllist
def allvisit(dr=None, flag=None):
"""
Download the allVisit file (catalog of properties from individual visit spectra)
:param dr: APOGEE DR
:type dr: int
:param flag: 0: normal, 1: force to re-download
:type flag: int
:return: full file path and download in background if not found locally, False if cannot be found on server
:rtype: str
:History: 2017-Oct-11 - Written - Henry Leung (University of Toronto)
"""
dr = apogee_default_dr(dr=dr)
if dr == 13:
file_hash = '2a3b13ccd40a2c8aea8321be9630117922d55b51'
# Check if directory exists
fullfilepath = os.path.join(apogee_env(), 'dr13/apogee/spectro/redux/r6/')
if not os.path.exists(fullfilepath):
os.makedirs(fullfilepath)
filename = 'allVisit-l30e.2.fits'
fullfilename = os.path.join(fullfilepath, filename)
url = f'https://data.sdss.org/sas/dr13/apogee/spectro/redux/r6/{filename}'
elif dr == 14:
file_hash = 'abcecbcdc5fe8d00779738702c115633811e6bbd'
# Check if directory exists
fullfilepath = os.path.join(apogee_env(), 'dr14/apogee/spectro/redux/r8/')
if not os.path.exists(fullfilepath):
os.makedirs(fullfilepath)
filename = 'allVisit-l31c.2.fits'
fullfilename = os.path.join(fullfilepath, filename)
url = f'https://data.sdss.org/sas/dr14/apogee/spectro/redux/r8/{filename}'
else:
raise ValueError('allvisit() only supports APOGEE DR13-DR15')
# check file integrity
if os.path.isfile(fullfilename) and flag is None:
checksum = filehash(fullfilename, algorithm='sha1')
if checksum != file_hash.lower():
print('File corruption detected, astroNN is attempting to download again')
allvisit(dr=dr, flag=1)
else:
print(fullfilename + ' was found!')
elif not os.path.isfile(os.path.join(fullfilepath, filename)) or flag == 1:
with TqdmUpTo(unit='B', unit_scale=True, miniters=1, desc=url.split('/')[-1]) as t:
urllib.request.urlretrieve(url, fullfilename, reporthook=t.update_to)
print(f'Downloaded DR{dr:d} allVisit file catalog successfully to {fullfilepath}')
checksum = filehash(fullfilename, algorithm='sha1')
if checksum != file_hash.lower():
print('File corruption detected, astroNN is attempting to download again')
allstar(dr=dr, flag=1)
return fullfilename
def apogee_distances(dr=None, flag=None):
"""
Download the Apogee Distances catalogue
:param dr: Apogee DR
:type dr: int
:param flag: Force to download if flag=1
:type flag: int
:return: full file path
:rtype: str
:History: 2018-Jan-24 - Written - Henry Leung (University of Toronto)
"""
dr = apogee_default_dr(dr=dr)
if dr == 14:
file_hash = 'b33c8419be784b1be3d14af3ee9696c6ac31830f'
str1 = 'https://data.sdss.org/sas/dr14/apogee/vac/apogee-distances/'
filename = f'apogee_distances-DR{dr}.fits'
urlstr = str1 + filename
fullfoldername = os.path.join(apogee_env(), 'dr14/apogee/vac/apogee-distances/')
if not os.path.exists(fullfoldername):
os.makedirs(fullfoldername)
fullfilename = os.path.join(fullfoldername, filename)
else:
raise ValueError('apogee_distances() only supports DR14')
# check file integrity
if os.path.isfile(fullfilename) and flag is None:
checksum = filehash(fullfilename, algorithm='sha1')
if checksum != file_hash.lower():
print('File corruption detected, astroNN is attempting to download again')
apogee_distances(dr=dr, flag=1)
else:
print(fullfilename + ' was found!')
elif not os.path.isfile(fullfilename) or flag == 1:
try:
with TqdmUpTo(unit='B', unit_scale=True, miniters=1, desc=urlstr.split('/')[-1]) as t:
urllib.request.urlretrieve(urlstr, fullfilename, reporthook=t.update_to)
print(f'Downloaded DR{dr} Distances successfully to {fullfilename}')
checksum = filehash(fullfilename, algorithm='sha1')
if checksum != file_hash.lower():
print('File corruption detected, astroNN is attempting to download again')
apogee_distances(dr=dr, flag=1)
except urllib.error.HTTPError:
print(f'{urlstr} cannot be found on server, skipped')
fullfilename = warning_flag
return fullfilename
def test_checksum(self):
import astroNN
from astroNN.shared.downloader_tools import filehash
anderson2017_path = os.path.join(os.path.dirname(astroNN.__path__[0]), 'astroNN', 'data',
'anderson_2017_dr14_parallax.npz')
md5_pred = filehash(anderson2017_path, algorithm='md5')
sha1_pred = filehash(anderson2017_path, algorithm='sha1')
sha256_pred = filehash(anderson2017_path, algorithm='sha256')
# read answer hashed by Windows Get-FileHash
self.assertEqual(md5_pred, '9C714F5FE22BB7C4FF9EA32F3E859D73'.lower())
self.assertEqual(sha1_pred, '733C0227CF93DB0CD6106B5349402F251E7ED735'.lower())
self.assertEqual(sha256_pred, '36C265C907F440114D747DA21D2A014D32B5E442D541F183C0EE862F5865FD26'.lower())
self.assertRaises(ValueError, filehash, anderson2017_path, algorithm='sha123')
def apogee_astronn(dr=None, flag=None):
"""
Download the apogee_astroNN file (catalog of astroNN stellar parameters, abundances, distances and orbital
parameters from combined spectra)
:param dr: APOGEE DR
:type dr: int
:param flag: 0: normal, 1: force to re-download
:type flag: int
:return: full file path and download in background if not found locally, False if cannot be found on server
:rtype: str
:History: 2019-Dec-10 - Written - Henry Leung (University of Toronto)
"""
dr = apogee_default_dr(dr=dr)
if dr == 16:
# Check if directory exists
fullfoldername = os.path.join(apogee_env(), 'dr16/apogee/vac/apogee-astronn/')
# Check if directory exists
if not os.path.exists(fullfoldername):
os.makedirs(fullfoldername)
filename = 'apogee_astroNN-DR16.fits'
fullfilename = os.path.join(fullfoldername, filename)
file_hash = '02187ef2cbe5215dc4d65df7037ecf1b8cc5853d'
url = f'https://data.sdss.org/sas/dr16/apogee/vac/apogee-astronn/{filename}'
else:
raise ValueError('apogee_astroNN() only supports APOGEE DR16')
# check file integrity
if os.path.isfile(fullfilename) and flag is None:
checksum = filehash(fullfilename, algorithm='sha1')
if checksum != file_hash.lower():
print('File corruption detected, astroNN is attempting to download again')
apogee_astronn(dr=dr, flag=1)
else:
print(fullfilename + ' was found!')
# Check if files exists
if not os.path.isfile(os.path.join(fullfoldername, filename)) or flag == 1:
with TqdmUpTo(unit='B', unit_scale=True, miniters=1, desc=url.split('/')[-1]) as t:
urllib.request.urlretrieve(url, fullfilename, reporthook=t.update_to)
print(f'Downloaded DR{dr:d} apogee_astroNN file catalog successfully to {fullfilename}')
checksum = filehash(fullfilename, algorithm='sha1')
if checksum != file_hash.lower():
print('File corruption detected, astroNN is attempting to download again')
apogee_astronn(dr=dr, flag=1)
return fullfilename
def allstar_cannon(dr=None, flag=None):
"""
Download the allStarCannon file (catalog of Cannon stellar parameters and abundances from combined spectra)
:param dr: APOGEE DR
:type dr: int
:param flag: 0: normal, 1: force to re-download
:type flag: int
:return: full file path and download in background if not found locally, False if cannot be found on server
:rtype: str
:History: 2017-Oct-24 - Written - Henry Leung (University of Toronto)
"""
dr = apogee_default_dr(dr=dr)
if dr == 14:
# Check if directory exists
fullfoldername = os.path.join(apogee_env(), 'dr14/apogee/spectro/redux/r8/stars/l31c/l31c.2/cannon/')
# Check if directory exists
if not os.path.exists(fullfoldername):
os.makedirs(fullfoldername)
filename = 'allStarCannon-l31c.2.fits'
fullfilename = os.path.join(fullfoldername, filename)
file_hash = '64d485e95b3504df0b795ab604e21a71d5c7ae45'
url = f'https://data.sdss.org/sas/dr14/apogee/spectro/redux/r8/stars/l31c/l31c.2/cannon/{filename}'
else:
raise ValueError('allstar_cannon() only supports APOGEE DR14-DR15')
# check file integrity
if os.path.isfile(fullfilename) and flag is None:
checksum = filehash(fullfilename, algorithm='sha1')
if checksum != file_hash.lower():
print('File corruption detected, astroNN is attempting to download again')
allstar_cannon(dr=dr, flag=1)
else:
print(fullfilename + ' was found!')
# Check if files exists
if not os.path.isfile(os.path.join(fullfoldername, filename)) or flag == 1:
with TqdmUpTo(unit='B', unit_scale=True, miniters=1, desc=url.split('/')[-1]) as t:
urllib.request.urlretrieve(url, fullfilename, reporthook=t.update_to)
print(f'Downloaded DR{dr:d} allStarCannon file catalog successfully to {fullfilename}')
checksum = filehash(fullfilename, algorithm='sha1')
if checksum != file_hash.lower():
print('File corruption detected, astroNN is attempting to download again')
allstar_cannon(dr=dr, flag=1)
return fullfilename
def apogee_astronn(dr=None, flag=None):
"""
Download the apogee_astroNN file (catalog of astroNN stellar parameters, abundances, distances and orbital
parameters from combined spectra)
:param dr: APOGEE DR
:type dr: int
:param flag: 0: normal, 1: force to re-download
:type flag: int
:return: full file path and download in background if not found locally, False if cannot be found on server
:rtype: str
:History: 2019-Dec-10 - Written - Henry Leung (University of Toronto)
"""
dr = apogee_default_dr(dr=dr)
if dr == 16:
# Check if directory exists
fullfoldername = os.path.join(apogee_env(),
"dr16/apogee/vac/apogee-astronn/")
# Check if directory exists
if not os.path.exists(fullfoldername):
os.makedirs(fullfoldername)
filename = "apogee_astroNN-DR16-v1.fits"
fullfilename = os.path.join(fullfoldername, filename)
file_hash = "1b81ed13eef36fe9a327a05f4a622246522199b2"
url = f"https://data.sdss.org/sas/dr16/apogee/vac/apogee-astronn/{filename}"
elif dr == 17:
# Check if directory exists
fullfoldername = os.path.join(apogee_env(),
"dr17/apogee/vac/apogee-astronn/")
# Check if directory exists
if not os.path.exists(fullfoldername):
os.makedirs(fullfoldername)
filename = "apogee_astroNN-DR17.fits"
fullfilename = os.path.join(fullfoldername, filename)
file_hash = "c422b9adba840b3415af2fe6dec6500219f1b68f"
url = f"https://data.sdss.org/sas/dr17/apogee/vac/apogee-astronn/{filename}"
else:
raise ValueError("apogee_astroNN() only supports APOGEE DR16-DR17")
# check file integrity
if os.path.isfile(fullfilename) and flag is None:
checksum = filehash(fullfilename, algorithm="sha1")
if checksum != file_hash.lower():
warnings.warn(
"File corruption detected, astroNN is attempting to download again"
)
apogee_astronn(dr=dr, flag=1)
else:
logging.info(fullfilename + " was found!")
# Check if files exists
if not os.path.isfile(os.path.join(fullfoldername, filename)) or flag == 1:
with TqdmUpTo(unit="B",
unit_scale=True,
miniters=1,
desc=url.split("/")[-1]) as t:
try:
urllib.request.urlretrieve(url,
fullfilename,
reporthook=t.update_to)
logging.info(
f"Downloaded DR{dr:d} apogee_astroNN file catalog successfully to {fullfilename}"
)
checksum = filehash(fullfilename, algorithm="sha1")
if checksum != file_hash.lower():
warnings.warn(
"File corruption detected, astroNN is attempting to download again"
)
apogee_astronn(dr=dr, flag=1)
except urllib.error.HTTPError as emsg:
if "401" in str(emsg):
fullfilename = __apogee_credentials_downloader(
url, fullfilename)
elif "404" in str(emsg):
warnings.warn(f"{url} cannot be found on server, skipped")
fullfilename = warning_flag
else:
warnings.warn(f"Unknown error occurred - {emsg}")
fullfilename = warning_flag
return fullfilename
def allstar(dr=None, flag=None):
"""
Download the allStar file (catalog of ASPCAP stellar parameters and abundances from combined spectra)
:param dr: APOGEE DR
:type dr: int
:param flag: 0: normal, 1: force to re-download
:type flag: int
:return: full file path and download in background if not found locally, False if cannot be found on server
:rtype: str
:History: 2017-Oct-09 - Written - Henry Leung (University of Toronto)
"""
dr = apogee_default_dr(dr=dr)
if dr == 13:
file_hash = '1718723ada3018de94e1022cd57d4d950a74f91f'
# Check if directory exists
fullfoldername = os.path.join(apogee_env(), 'dr13/apogee/spectro/redux/r6/stars/l30e/l30e.2/')
if not os.path.exists(fullfoldername):
os.makedirs(fullfoldername)
filename = 'allStar-l30e.2.fits'
fullfilename = os.path.join(fullfoldername, filename)
url = f'https://data.sdss.org/sas/dr13/apogee/spectro/redux/r6/stars/l30e/l30e.2/{filename}'
elif dr == 14:
file_hash = 'a7e1801924661954da792e377ad54f412219b105'
fullfoldername = os.path.join(apogee_env(), 'dr14/apogee/spectro/redux/r8/stars/l31c/l31c.2/')
# Check if directory exists
if not os.path.exists(fullfoldername):
os.makedirs(fullfoldername)
filename = 'allStar-l31c.2.fits'
fullfilename = os.path.join(fullfoldername, filename)
url = f'https://data.sdss.org/sas/dr14/apogee/spectro/redux/r8/stars/l31c/l31c.2/{filename}'
elif dr == 16:
file_hash = '66fe854bd000ca1c0a6b50a998877e4a3e41d184'
fullfoldername = os.path.join(apogee_env(), 'dr16/apogee/spectro/aspcap/r12/l33/')
# Check if directory exists
if not os.path.exists(fullfoldername):
os.makedirs(fullfoldername)
filename = 'allStar-r12-l33.fits'
fullfilename = os.path.join(fullfoldername, filename)
url = f'https://data.sdss.org/sas/dr16/apogee/spectro/aspcap/r12/l33/{filename}'
else:
raise ValueError('allstar() only supports APOGEE DR13-DR16')
# check file integrity
if os.path.isfile(fullfilename) and flag is None:
checksum = filehash(fullfilename, algorithm='sha1')
if checksum != file_hash.lower():
print('File corruption detected, astroNN is attempting to download again')
allstar(dr=dr, flag=1)
else:
print(fullfilename + ' was found!')
# Check if files exists
if not os.path.isfile(os.path.join(fullfoldername, filename)) or flag == 1:
with TqdmUpTo(unit='B', unit_scale=True, miniters=1, desc=url.split('/')[-1]) as t:
try:
urllib.request.urlretrieve(url, fullfilename, reporthook=t.update_to)
print(f'Downloaded DR{dr:d} allStar file catalog successfully to {fullfilename}')
checksum = filehash(fullfilename, algorithm='sha1')
if checksum != file_hash.lower():
print('File corruption detected, astroNN is attempting to download again')
allstar(dr=dr, flag=1)
except urllib.error.HTTPError as emsg:
if '401' in str(emsg):
fullfilename = __apogee_credentials_downloader(url, fullfilename)
elif '404' in str(emsg):
print(f'{url} cannot be found on server, skipped')
fullfilename = warning_flag
else:
print(f"Unknown error occurred - {emsg}")
fullfilename = warning_flag
return fullfilename
def apogee_vac_rc(dr=None, flag=None):
"""
Download the red clumps catalogue
:param dr: Apogee DR
:type dr: int
:param flag: Force to download if flag=1
:type flag: int
:return: full file path
:rtype: str
:History: 2017-Nov-16 - Written - Henry Leung (University of Toronto)
"""
dr = apogee_default_dr(dr=dr)
if dr == 13:
file_hash = '5e87eb3ba202f9db24216978dafb19d39d382fc6'
str1 = 'https://data.sdss.org/sas/dr13/apogee/vac/apogee-rc/cat/'
filename = f'apogee-rc-DR{dr}.fits'
urlstr = str1 + filename
fullfoldername = os.path.join(apogee_env(), 'dr13/apogee/vac/apogee-rc/cat/')
if not os.path.exists(fullfoldername):
os.makedirs(fullfoldername)
fullfilename = os.path.join(fullfoldername, filename)
elif dr == 14:
file_hash = '104513070f1c280954f3d1886cac429dbdf2eaf6'
str1 = 'https://data.sdss.org/sas/dr14/apogee/vac/apogee-rc/cat/'
filename = f'apogee-rc-DR{dr}.fits'
urlstr = str1 + filename
fullfoldername = os.path.join(apogee_env(), 'dr14/apogee/vac/apogee-rc/cat/')
if not os.path.exists(fullfoldername):
os.makedirs(fullfoldername)
fullfilename = os.path.join(fullfoldername, filename)
elif dr == 16:
file_hash = '0bc75a230058f50ed8a5ea3fa8554d803ffc103d'
str1 = 'https://data.sdss.org/sas/dr16/apogee/vac/apogee-rc/cat/'
filename = f'apogee-rc-DR{dr}.fits'
urlstr = str1 + filename
fullfoldername = os.path.join(apogee_env(), 'dr16/apogee/vac/apogee-rc/cat/')
if not os.path.exists(fullfoldername):
os.makedirs(fullfoldername)
fullfilename = os.path.join(fullfoldername, filename)
else:
raise ValueError('apogee_vac_rc() only supports DR13 or DR14')
# check file integrity
if os.path.isfile(fullfilename) and flag is None:
checksum = filehash(fullfilename, algorithm='sha1')
if checksum != file_hash.lower():
print('File corruption detected, astroNN is attempting to download again')
apogee_vac_rc(dr=dr, flag=1)
else:
print(fullfilename + ' was found!')
elif not os.path.isfile(fullfilename) or flag == 1:
try:
with TqdmUpTo(unit='B', unit_scale=True, miniters=1, desc=urlstr.split('/')[-1]) as t:
urllib.request.urlretrieve(urlstr, fullfilename, reporthook=t.update_to)
print(f'Downloaded DR{dr} Red Clumps Catalog successfully to {fullfilename}')
checksum = filehash(fullfilename, algorithm='sha1')
if checksum != file_hash.lower():
print('File corruption detected, astroNN is attempting to download again')
apogee_vac_rc(dr=dr, flag=1)
except urllib.error.HTTPError:
print(f'{urlstr} cannot be found on server, skipped')
fullfilename = warning_flag
return fullfilename
def visit_spectra(dr=None, location=None, field=None, apogee=None, telescope=None, verbose=1, flag=None,
commission=False):
"""
Download the required individual spectra file a.k.a apStar or asStar
:param dr: APOGEE DR
:type dr: int
:param location: Location ID [Optional]
:type location: int
:param field: Field [Optional]
:type field: str
:param apogee: Apogee ID
:type apogee: str
:param telescope: Telescope ID, for example 'apo25m' or 'lco25m'
:type telescope: str
:param verbose: verbose, set 0 to silent most logging
:type verbose: int
:param flag: 0: normal, 1: force to re-download
:type flag: int
:param commission: whether the spectra is taken during commissioning
:type commission: bool
:return: full file path and download in background if not found locally, False if cannot be found on server
:rtype: str
:History:
| 2017-Nov-11 - Written - Henry Leung (University of Toronto)
| 2018-Aug-31 - Updated - Henry Leung (University of Toronto)
"""
dr = apogee_default_dr(dr=dr)
# for DR16=<, location is expected to be none because field is used
if (location is None and dr < 16) or (field is None and dr >= 16): # try to load info if not enough info
global _ALLSTAR_TEMP
if not str(f'dr{dr}') in _ALLSTAR_TEMP:
_ALLSTAR_TEMP[f'dr{dr}'] = fits.getdata(allstar(dr=dr))
if telescope is None:
matched_idx = [np.nonzero(_ALLSTAR_TEMP[f'dr{dr}']['APOGEE_ID'] == apogee)[0]][0]
else:
matched_idx = [np.nonzero([(_ALLSTAR_TEMP[f'dr{dr}']['APOGEE_ID'] == apogee) &
(_ALLSTAR_TEMP[f'dr{dr}']['TELESCOPE'] == telescope)])][0][1]
if len(matched_idx) == 0:
raise ValueError(f"No entry found in allstar DR{dr} met with your requirement!!")
location = _ALLSTAR_TEMP[f'dr{dr}']['LOCATION_ID'][matched_idx][0] if not location else location
field = _ALLSTAR_TEMP[f'dr{dr}']['FIELD'][matched_idx][0] if not field else field
telescope = _ALLSTAR_TEMP[f'dr{dr}']['TELESCOPE'][matched_idx][0] if not telescope else telescope
if dr == 13:
reduce_prefix = 'r6'
str1 = f'https://data.sdss.org/sas/dr{dr}/apogee/spectro/redux/{reduce_prefix}/stars/apo25m/{location}/'
if commission:
filename = f'apStarC-{reduce_prefix}-{apogee}.fits'
else:
filename = f'apStar-{reduce_prefix}-{apogee}.fits'
urlstr = str1 + filename
hash_filename = f'{reduce_prefix}_stars_apo25m_{location}.sha1sum'
fullfoldername = os.path.join(apogee_env(), f'dr{dr}/apogee/spectro/redux/{reduce_prefix}/stars/apo25m/',
str(location))
if not os.path.exists(fullfoldername):
os.makedirs(fullfoldername)
elif dr == 14:
reduce_prefix = 'r8'
str1 = f'https://data.sdss.org/sas/dr{dr}/apogee/spectro/redux/{reduce_prefix}/stars/apo25m/{location}/'
if commission:
filename = f'apStarC-{reduce_prefix}-{apogee}.fits'
else:
filename = f'apStar-{reduce_prefix}-{apogee}.fits'
urlstr = str1 + filename
hash_filename = f'{reduce_prefix}_stars_apo25m_{location}.sha1sum'
fullfoldername = os.path.join(apogee_env(), f'dr{dr}/apogee/spectro/redux/{reduce_prefix}/stars/apo25m/',
str(location))
if not os.path.exists(fullfoldername):
os.makedirs(fullfoldername)
elif dr == 16:
reduce_prefix = 'r12'
str1 = f'https://data.sdss.org/sas/dr16/apogee/spectro/redux/{reduce_prefix}/stars/{telescope}/{field}/'
if telescope == 'lco25m':
if commission:
filename = f'asStarC-{reduce_prefix}-{apogee}.fits'
else:
filename = f'asStar-{reduce_prefix}-{apogee}.fits'
else:
if commission:
filename = f'apStarC-{reduce_prefix}-{apogee}.fits'
else:
filename = f'apStar-{reduce_prefix}-{apogee}.fits'
urlstr = str1 + filename
hash_filename = f'{reduce_prefix}_stars_{telescope}_{field}.sha1sum'
fullfoldername = os.path.join(apogee_env(),
f'dr{dr}/apogee/spectro/redux/{reduce_prefix}/stars/{telescope}/',
str(f'{field}'))
if not os.path.exists(fullfoldername):
os.makedirs(fullfoldername)
else:
raise ValueError('visit_spectra() only supports DR13-DR16')
# check hash file
full_hash_filename = os.path.join(fullfoldername, hash_filename)
if not os.path.isfile(full_hash_filename):
# return warning flag if the location_id cannot even be found
try:
urllib.request.urlopen(str1)
except urllib.error.HTTPError:
return warning_flag
urllib.request.urlretrieve(str1 + hash_filename, full_hash_filename)
hash_list = np.loadtxt(full_hash_filename, dtype='str').T
fullfilename = os.path.join(fullfoldername, filename)
# In some rare case, the hash cant be found, so during checking, check len(file_has)!=0 too
# visit spectra has a different filename in checksum
# handle the case where apogee_id cannot be found
hash_idx = [i for i, item in enumerate(hash_list[1]) if f'apStar-{reduce_prefix}-{apogee}' in item]
file_hash = hash_list[0][hash_idx]
if os.path.isfile(fullfilename) and flag is None:
checksum = filehash(fullfilename, algorithm='sha1')
if checksum != file_hash and len(file_hash) != 0:
print('File corruption detected, astroNN is attempting to download again')
visit_spectra(dr=dr, location=location, apogee=apogee, verbose=verbose, flag=1)
if verbose:
print(fullfilename + ' was found!')
elif not os.path.isfile(fullfilename) or flag == 1:
try:
urllib.request.urlretrieve(urlstr, fullfilename)
print(f'Downloaded DR{dr} individual visit file successfully to {fullfilename}')
checksum = filehash(fullfilename, algorithm='sha1')
if checksum != file_hash and len(file_hash) != 0:
print('File corruption detected, astroNN is attempting to download again')
visit_spectra(dr=dr, location=location, apogee=apogee, verbose=verbose, flag=1)
except urllib.error.HTTPError as emsg:
if '401' in str(emsg):
fullfilename = __apogee_credentials_downloader(urlstr, fullfilename)
elif '404' in str(emsg):
print(f'{urlstr} cannot be found on server, skipped')
fullfilename = warning_flag
else:
print(f"Unknown error occurred - {emsg}")
fullfilename = warning_flag
return fullfilename
def combined_spectra(
dr=None,
location=None,
field=None,
apogee=None,
telescope=None,
verbose=1,
flag=None,
):
"""
Download the required combined spectra file a.k.a aspcapStar
:param dr: APOGEE DR
:type dr: int
:param location: Location ID [Optional]
:type location: int
:param field: Field [Optional]
:type field: str
:param apogee: Apogee ID
:type apogee: str
:param telescope: Telescope ID, for example 'apo25m' or 'lco25m'
:type telescope: str
:param verbose: verbose, set 0 to silent most logging
:type verbose: int
:param flag: 0: normal, 1: force to re-download
:type flag: int
:return: full file path and download in background if not found locally, False if cannot be found on server
:rtype: str
:History:
| 2017-Oct-15 - Written - Henry Leung (University of Toronto)
| 2018-Aug-31 - Updated - Henry Leung (University of Toronto)
"""
dr = apogee_default_dr(dr=dr)
# for DR16=<, location is expected to be none because field is used
if (location is None and dr < 16) or (
field is None and dr >= 16): # try to load info if not enough info
global _ALLSTAR_TEMP
if not str(f"dr{dr}") in _ALLSTAR_TEMP:
_ALLSTAR_TEMP[f"dr{dr}"] = fits.getdata(allstar(dr=dr))
if telescope is None:
matched_idx = [
np.nonzero(_ALLSTAR_TEMP[f"dr{dr}"]["APOGEE_ID"] == apogee)[0]
][0]
else:
matched_idx = [
np.nonzero([
(_ALLSTAR_TEMP[f"dr{dr}"]["APOGEE_ID"] == apogee)
& (_ALLSTAR_TEMP[f"dr{dr}"]["TELESCOPE"] == telescope)
])
][0][1]
if len(matched_idx) == 0:
raise ValueError(
f"No entry found in allstar DR{dr} met with your requirement!!"
)
location = (_ALLSTAR_TEMP[f"dr{dr}"]["LOCATION_ID"][matched_idx][0]
if not location else location)
field = (_ALLSTAR_TEMP[f"dr{dr}"]["FIELD"][matched_idx][0]
if not field else field)
telescope = (_ALLSTAR_TEMP[f"dr{dr}"]["TELESCOPE"][matched_idx][0]
if not telescope else telescope)
if dr == 13:
reduce_prefix = "r6"
aspcap_code = "l30e"
str1 = f"https://data.sdss.org/sas/dr{dr}/apogee/spectro/redux/{reduce_prefix}/stars/{aspcap_code}/{aspcap_code}.2/{location}/"
filename = f"aspcapStar-{reduce_prefix}-{aspcap_code}.2-{apogee}.fits"
hash_filename = f"stars_{aspcap_code}_{aspcap_code}.2_{location}.sha1sum"
urlstr = str1 + filename
# check folder existence
fullfoldername = os.path.join(
apogee_env(),
f"dr{dr}/apogee/spectro/redux/{reduce_prefix}/stars/{aspcap_code}/{aspcap_code}.2/",
str(location),
)
if not os.path.exists(fullfoldername):
os.makedirs(fullfoldername)
fullfilename = os.path.join(fullfoldername, filename)
elif dr == 14:
reduce_prefix = "r8"
aspcap_code = "l31c"
str1 = f"https://data.sdss.org/sas/dr{dr}/apogee/spectro/redux/{reduce_prefix}/stars/{aspcap_code}/{aspcap_code}.2/{location}/"
filename = f"aspcapStar-{reduce_prefix}-{aspcap_code}.2-{apogee}.fits"
hash_filename = f"stars_{aspcap_code}_{aspcap_code}.2_{location}.sha1sum"
urlstr = str1 + filename
# check folder existence
fullfoldername = os.path.join(
apogee_env(),
f"dr{dr}/apogee/spectro/redux/{reduce_prefix}/stars/{aspcap_code}/{aspcap_code}.2/",
str(location),
)
if not os.path.exists(fullfoldername):
os.makedirs(fullfoldername)
fullfilename = os.path.join(fullfoldername, filename)
elif dr == 16:
reduce_prefix = "r12"
aspcap_code = "l33"
str1 = f"https://data.sdss.org/sas/dr16/apogee/spectro/aspcap/{reduce_prefix}/{aspcap_code}/{telescope}/{field}/"
filename = f"aspcapStar-{reduce_prefix}-{apogee}.fits"
hash_filename = f"{reduce_prefix}_{reduce_prefix}_{telescope}_{field}.sha1sum"
urlstr = str1 + filename
# check folder existence
fullfoldername = os.path.join(
apogee_env(),
f"dr{dr}/apogee/spectro/aspcap/{reduce_prefix}/{aspcap_code}/{telescope}",
str(f"{field}"),
)
if not os.path.exists(fullfoldername):
os.makedirs(fullfoldername)
fullfilename = os.path.join(fullfoldername, filename)
else:
raise ValueError("combined_spectra() only supports APOGEE DR13-DR16")
# check hash file
full_hash_filename = os.path.join(fullfoldername, hash_filename)
if not os.path.isfile(full_hash_filename):
# return warning flag if the location_id cannot even be found
try:
urllib.request.urlopen(str1)
except urllib.error.HTTPError:
return warning_flag
urllib.request.urlretrieve(str1 + hash_filename, full_hash_filename)
hash_list = np.loadtxt(full_hash_filename, dtype="str").T
# In some rare case, the hash cant be found, so during checking, check len(file_has)!=0 too
file_hash = hash_list[0][np.argwhere(hash_list[1] == filename)]
if os.path.isfile(fullfilename) and flag is None:
checksum = filehash(fullfilename, algorithm="sha1")
if checksum != file_hash and len(file_hash) != 0:
warnings.warn(
"File corruption detected, astroNN is attempting to download again"
)
combined_spectra(dr=dr,
location=location,
apogee=apogee,
verbose=verbose,
flag=1)
if verbose == 1:
logging.info(fullfilename + " was found!")
elif not os.path.isfile(fullfilename) or flag == 1:
try:
urllib.request.urlretrieve(urlstr, fullfilename)
logging.info(
f"Downloaded DR{dr} combined file successfully to {fullfilename}"
)
checksum = filehash(fullfilename, algorithm="sha1")
if checksum != file_hash and len(file_hash) != 0:
warnings.warn(
"File corruption detected, astroNN is attempting to download again"
)
combined_spectra(dr=dr,
location=location,
apogee=apogee,
verbose=verbose,
flag=1)
except urllib.error.HTTPError as emsg:
if "401" in str(emsg):
fullfilename = __apogee_credentials_downloader(
urlstr, fullfilename)
elif "404" in str(emsg):
warnings.warn(f"{urlstr} cannot be found on server, skipped")
fullfilename = warning_flag
else:
warnings.warn(f"Unknown error occurred - {emsg}")
fullfilename = warning_flag
return fullfilename
def allvisit(dr=None, flag=None):
"""
Download the allVisit file (catalog of properties from individual visit spectra)
:param dr: APOGEE DR
:type dr: int
:param flag: 0: normal, 1: force to re-download
:type flag: int
:return: full file path and download in background if not found locally, False if cannot be found on server
:rtype: str
:History: 2017-Oct-11 - Written - Henry Leung (University of Toronto)
"""
dr = apogee_default_dr(dr=dr)
if dr == 13:
file_hash = "2a3b13ccd40a2c8aea8321be9630117922d55b51"
# Check if directory exists
fullfilepath = os.path.join(apogee_env(),
"dr13/apogee/spectro/redux/r6/")
if not os.path.exists(fullfilepath):
os.makedirs(fullfilepath)
filename = "allVisit-l30e.2.fits"
fullfilename = os.path.join(fullfilepath, filename)
url = f"https://data.sdss.org/sas/dr13/apogee/spectro/redux/r6/{filename}"
elif dr == 14:
file_hash = "abcecbcdc5fe8d00779738702c115633811e6bbd"
# Check if directory exists
fullfilepath = os.path.join(apogee_env(),
"dr14/apogee/spectro/redux/r8/")
if not os.path.exists(fullfilepath):
os.makedirs(fullfilepath)
filename = "allVisit-l31c.2.fits"
fullfilename = os.path.join(fullfilepath, filename)
url = f"https://data.sdss.org/sas/dr14/apogee/spectro/redux/r8/{filename}"
elif dr == 16:
file_hash = "65befb967d8d9d6f4f87711c1fa8d0ac014b62da"
# Check if directory exists
fullfilepath = os.path.join(apogee_env(),
"dr16/apogee/spectro/aspcap/r12/l33/")
if not os.path.exists(fullfilepath):
os.makedirs(fullfilepath)
filename = "allVisit-r12-l33.fits"
fullfilename = os.path.join(fullfilepath, filename)
url = f"https://data.sdss.org/sas/dr16/apogee/spectro/aspcap/r12/l33/{filename}"
else:
raise ValueError("allvisit() only supports APOGEE DR13-DR16")
# check file integrity
if os.path.isfile(fullfilename) and flag is None:
checksum = filehash(fullfilename, algorithm="sha1")
if checksum != file_hash.lower():
warnings.warn(
"File corruption detected, astroNN is attempting to download again"
)
allvisit(dr=dr, flag=1)
else:
logging.info(fullfilename + " was found!")
elif not os.path.isfile(os.path.join(fullfilepath, filename)) or flag == 1:
with TqdmUpTo(unit="B",
unit_scale=True,
miniters=1,
desc=url.split("/")[-1]) as t:
urllib.request.urlretrieve(url,
fullfilename,
reporthook=t.update_to)
logging.info(
f"Downloaded DR{dr:d} allVisit file catalog successfully to {fullfilepath}"
)
checksum = filehash(fullfilename, algorithm="sha1")
if checksum != file_hash.lower():
warnings.warn(
"File corruption detected, astroNN is attempting to download again"
)
allvisit(dr=dr, flag=1)
return fullfilename
def gaia_source(dr=None, flag=None):
"""
NAME:
gaia_source
PURPOSE:
download the gaia_source files
INPUT:
dr (int): Gaia DR, example dr=1
flag (int): 0: normal, 1: force to re-download
OUTPUT:
list of file path
HISTORY:
2017-Oct-13 - Written - Henry Leung (University of Toronto)
2017-Nov-26 - Update - Henry Leung (University of Toronto)
"""
dr = gaia_default_dr(dr=dr)
fulllist = []
if dr == 1:
# Check if directory exists
folderpath = os.path.join(gaia_env(), 'Gaia/gdr1/gaia_source/fits/')
urlbase = 'http://cdn.gea.esac.esa.int/Gaia/gdr1/gaia_source/fits/'
if not os.path.exists(folderpath):
os.makedirs(folderpath)
hash_filename = 'MD5SUM.txt'
full_hash_filename = os.path.join(folderpath, hash_filename)
if not os.path.isfile(full_hash_filename):
urllib.request.urlretrieve(urlbase + hash_filename, full_hash_filename)
hash_list = np.loadtxt(full_hash_filename, dtype='str').T
for j in range(0, 20, 1):
for i in range(0, 256, 1):
filename = f'GaiaSource_000-0{j:0{2}d}-{i:0{3}d}.fits'
urlstr = urlbase + filename
fullfilename = os.path.join(folderpath, filename)
file_hash = (hash_list[0])[np.argwhere(hash_list[1] == filename)]
# Check if files exists
if os.path.isfile(fullfilename) and flag is None:
checksum = filehash(fullfilename, algorithm='md5')
# In some rare case, the hash cant be found, so during checking, check len(file_has)!=0 too
if checksum != file_hash and len(file_hash) != 0:
print(checksum)
print(file_hash)
print('File corruption detected, astroNN is attempting to download again')
gaia_source(dr=dr, flag=1)
else:
print(fullfilename + ' was found!')
elif not os.path.isfile(fullfilename) or flag == 1:
# progress bar
with TqdmUpTo(unit='B', unit_scale=True, miniters=1, desc=urlstr.split('/')[-1]) as t:
urllib.request.urlretrieve(urlstr, fullfilename, reporthook=t.update_to)
checksum = filehash(fullfilename, algorithm='md5')
if checksum != file_hash and len(file_hash) != 0:
print('File corruption detected, astroNN is attempting to download again')
gaia_source(dr=dr, flag=1)
print(f'Downloaded Gaia DR{dr} Gaia Source ({(j * 256 + i):d} of {(256 * 20 + 112):d}) '
f'file catalog successfully to {fullfilename}')
fulllist.extend([fullfilename])
for i in range(0, 111, 1):
filename = f'GaiaSource_000-020-{i:0{3}d}.fits'
urlstr = urlbase + filename
fullfilename = os.path.join(folderpath, filename)
file_hash = (hash_list[0])[np.argwhere(hash_list[1] == filename)]
# Check if files exists
if os.path.isfile(fullfilename) and flag is None:
checksum = filehash(fullfilename, algorithm='md5')
# In some rare case, the hash cant be found, so during checking, check len(file_has)!=0 too
if checksum != file_hash and len(file_hash) != 0:
print(checksum)
print(file_hash)
print('File corruption detected, astroNN is attempting to download again')
gaia_source(dr=dr, flag=1)
else:
print(fullfilename + ' was found!')
elif not os.path.isfile(fullfilename) or flag == 1:
# progress bar
with TqdmUpTo(unit='B', unit_scale=True, miniters=1, desc=urlstr.split('/')[-1]) as t:
urllib.request.urlretrieve(urlstr, fullfilename, reporthook=t.update_to)
checksum = filehash(fullfilename, algorithm='md5')
if checksum != file_hash and len(file_hash) != 0:
print('File corruption detected, astroNN is attempting to download again')
gaia_source(dr=dr, flag=1)
print(f'Downloaded Gaia DR{dr} Gaia Source ({(20 * 256 + i):d} of {(256 * 20 + 112):d}) file '
f'catalog successfully to {fullfilename}')
fulllist.extend([fullfilename])
else:
raise ValueError('gaia_source() only supports Gaia DR1 Gaia Source')
return fulllist
def apogee_rc(dr=None, flag=None):
"""
Download the APOGEE red clumps catalogue
:param dr: Apogee DR
:type dr: int
:param flag: Force to download if flag=1
:type flag: int
:return: full file path
:rtype: str
:History: 2017-Nov-16 - Written - Henry Leung (University of Toronto)
"""
dr = apogee_default_dr(dr=dr)
if dr == 13:
file_hash = "5e87eb3ba202f9db24216978dafb19d39d382fc6"
str1 = "https://data.sdss.org/sas/dr13/apogee/vac/apogee-rc/cat/"
filename = f"apogee-rc-DR{dr}.fits"
urlstr = str1 + filename
fullfoldername = os.path.join(apogee_env(),
"dr13/apogee/vac/apogee-rc/cat/")
if not os.path.exists(fullfoldername):
os.makedirs(fullfoldername)
fullfilename = os.path.join(fullfoldername, filename)
elif dr == 14:
file_hash = "104513070f1c280954f3d1886cac429dbdf2eaf6"
str1 = "https://data.sdss.org/sas/dr14/apogee/vac/apogee-rc/cat/"
filename = f"apogee-rc-DR{dr}.fits"
urlstr = str1 + filename
fullfoldername = os.path.join(apogee_env(),
"dr14/apogee/vac/apogee-rc/cat/")
if not os.path.exists(fullfoldername):
os.makedirs(fullfoldername)
fullfilename = os.path.join(fullfoldername, filename)
elif dr == 16:
file_hash = "0bc75a230058f50ed8a5ea3fa8554d803ffc103d"
str1 = "https://data.sdss.org/sas/dr16/apogee/vac/apogee-rc/cat/"
filename = f"apogee-rc-DR{dr}.fits"
urlstr = str1 + filename
fullfoldername = os.path.join(apogee_env(),
"dr16/apogee/vac/apogee-rc/cat/")
if not os.path.exists(fullfoldername):
os.makedirs(fullfoldername)
fullfilename = os.path.join(fullfoldername, filename)
elif dr == 17:
file_hash = "d54e0ea4e6a3f5cc3c02a73b93260e992d9836d0"
str1 = "https://data.sdss.org/sas/dr17/apogee/vac/apogee-rc/cat/"
filename = f"apogee-rc-DR{dr}.fits"
urlstr = str1 + filename
fullfoldername = os.path.join(apogee_env(),
"dr17/apogee/vac/apogee-rc/cat/")
if not os.path.exists(fullfoldername):
os.makedirs(fullfoldername)
fullfilename = os.path.join(fullfoldername, filename)
else:
raise ValueError("apogee_rc() only supports APOGEE DR13-DR17")
# check file integrity
if os.path.isfile(fullfilename) and flag is None:
checksum = filehash(fullfilename, algorithm="sha1")
if checksum != file_hash.lower():
warnings.warn(
"File corruption detected, astroNN is attempting to download again"
)
apogee_rc(dr=dr, flag=1)
else:
logging.info(fullfilename + " was found!")
elif not os.path.isfile(fullfilename) or flag == 1:
try:
with TqdmUpTo(unit="B",
unit_scale=True,
miniters=1,
desc=urlstr.split("/")[-1]) as t:
urllib.request.urlretrieve(urlstr,
fullfilename,
reporthook=t.update_to)
logging.info(
f"Downloaded DR{dr} Red Clumps Catalog successfully to {fullfilename}"
)
checksum = filehash(fullfilename, algorithm="sha1")
if checksum != file_hash.lower():
warnings.warn(
"File corruption detected, astroNN is attempting to download again"
)
apogee_rc(dr=dr, flag=1)
except urllib.error.HTTPError as emsg:
if "401" in str(emsg):
fullfilename = __apogee_credentials_downloader(
urlstr, fullfilename)
elif "404" in str(emsg):
warnings.warn(f"{urlstr} cannot be found on server, skipped")
fullfilename = warning_flag
else:
warnings.warn(f"Unknown error occurred - {emsg}")
fullfilename = warning_flag
return fullfilename
def combined_spectra(dr=None,
location=None,
field=None,
apogee=None,
telescope=None,
verbose=1,
flag=None):
"""
Download the required combined spectra file a.k.a aspcapStar
:param dr: APOGEE DR
:type dr: int
:param location: Location ID [Optional]
:type location: int
:param field: Field [Optional]
:type field: str
:param apogee: Apogee ID
:type apogee: str
:param telescope: Telescope ID, for example 'apo25m' or 'lco25m'
:type telescope: str
:param verbose: verbose, set 0 to silent most logging
:type verbose: int
:param flag: 0: normal, 1: force to re-download
:type flag: int
:return: full file path and download in background if not found locally, False if cannot be found on server
:rtype: str
:History:
| 2017-Oct-15 - Written - Henry Leung (University of Toronto)
| 2018-Aug-31 - Updated - Henry Leung (University of Toronto)
"""
dr = apogee_default_dr(dr=dr)
if location is None and field is None: # for DR16=<, location is expected to be none because field is used
global _ALLSTAR_TEMP
if not str(f'dr{dr}') in _ALLSTAR_TEMP:
_ALLSTAR_TEMP[f'dr{dr}'] = fits.getdata(allstar(dr=dr))
if telescope is None:
matched_idx = [
np.nonzero(_ALLSTAR_TEMP[f'dr{dr}']['APOGEE_ID'] == apogee)[0]
][0]
else:
matched_idx = [
np.nonzero([
(_ALLSTAR_TEMP[f'dr{dr}']['APOGEE_ID'] == apogee) &
(_ALLSTAR_TEMP[f'dr{dr}']['TELESCOPE'] == telescope)
])
][0][1]
if len(matched_idx) == 0:
raise ValueError(
f"No entry found in allstar DR{dr} met with your requirement!!"
)
location = _ALLSTAR_TEMP[f'dr{dr}']['LOCATION_ID'][matched_idx][0]
field = _ALLSTAR_TEMP[f'dr{dr}']['FIELD'][matched_idx][0]
telescope = _ALLSTAR_TEMP[f'dr{dr}']['TELESCOPE'][matched_idx][0]
if dr == 13:
reduce_prefix = 'r6'
aspcap_code = 'l30e'
str1 = f'https://data.sdss.org/sas/dr{dr}/apogee/spectro/redux/{reduce_prefix}/stars/{aspcap_code}/{aspcap_code}.2/{location}/'
filename = f'aspcapStar-{reduce_prefix}-{aspcap_code}.2-{apogee}.fits'
hash_filename = f'stars_{aspcap_code}_{aspcap_code}.2_{location}.sha1sum'
urlstr = str1 + filename
# check folder existence
fullfoldername = os.path.join(
apogee_env(),
f'dr{dr}/apogee/spectro/redux/{reduce_prefix}/stars/{aspcap_code}/{aspcap_code}.2/',
str(location))
if not os.path.exists(fullfoldername):
os.makedirs(fullfoldername)
fullfilename = os.path.join(fullfoldername, filename)
elif dr == 14:
reduce_prefix = 'r8'
aspcap_code = 'l31c'
str1 = f'https://data.sdss.org/sas/dr{dr}/apogee/spectro/redux/{reduce_prefix}/stars/{aspcap_code}/{aspcap_code}.2/{location}/'
filename = f'aspcapStar-{reduce_prefix}-{aspcap_code}.2-{apogee}.fits'
hash_filename = f'stars_{aspcap_code}_{aspcap_code}.2_{location}.sha1sum'
urlstr = str1 + filename
# check folder existence
fullfoldername = os.path.join(
apogee_env(),
f'dr{dr}/apogee/spectro/redux/{reduce_prefix}/stars/{aspcap_code}/{aspcap_code}.2/',
str(location))
if not os.path.exists(fullfoldername):
os.makedirs(fullfoldername)
fullfilename = os.path.join(fullfoldername, filename)
elif dr == 16:
reduce_prefix = 'r12'
aspcap_code = 'l33'
str1 = f'https://data.sdss.org/sas/apogeework/apogee/spectro/aspcap/{reduce_prefix}/{aspcap_code}/{telescope}/{field}/'
filename = f'aspcapStar-{reduce_prefix}-{apogee}.fits'
hash_filename = f'stars_{reduce_prefix}_{reduce_prefix}.2_{location}.sha1sum'
urlstr = str1 + filename
# check folder existence
fullfoldername = os.path.join(
apogee_env(),
f'dr{dr}/apogee/spectro/aspcap/{reduce_prefix}/{aspcap_code}/{telescope}',
str(f'{field}'))
if not os.path.exists(fullfoldername):
os.makedirs(fullfoldername)
fullfilename = os.path.join(fullfoldername, filename)
else:
raise ValueError('combined_spectra() only supports DR13-DR16')
# check hash file
if dr != 16:
full_hash_filename = os.path.join(fullfoldername, hash_filename)
if not os.path.isfile(full_hash_filename):
# return warning flag if the location_id cannot even be found
try:
urllib.request.urlopen(str1)
except urllib.request.HTTPError:
return warning_flag
urllib.request.urlretrieve(str1 + hash_filename,
full_hash_filename)
hash_list = np.loadtxt(full_hash_filename, dtype='str').T
else:
# just a dummy list
hash_list = np.array(
[np.array(['yyy', 'yyy', 'yyy']),
np.array(['zzz', 'zzz', 'zzz'])])
# In some rare case, the hash cant be found, so during checking, check len(file_has)!=0 too
file_hash = hash_list[0][np.argwhere(hash_list[1] == filename)]
if os.path.isfile(fullfilename) and flag is None:
checksum = filehash(fullfilename, algorithm='sha1')
if checksum != file_hash and len(file_hash) != 0:
print(
'File corruption detected, astroNN attempting to download again'
)
combined_spectra(dr=dr,
location=location,
apogee=apogee,
verbose=verbose,
flag=1)
if verbose == 1:
print(fullfilename + ' was found!')
elif not os.path.isfile(fullfilename) or flag == 1:
try:
urllib.request.urlretrieve(urlstr, fullfilename)
print(
f'Downloaded DR{dr} combined file successfully to {fullfilename}'
)
checksum = filehash(fullfilename, algorithm='sha1')
if checksum != file_hash and len(file_hash) != 0:
print(
'File corruption detected, astroNN attempting to download again'
)
combined_spectra(dr=dr,
location=location,
apogee=apogee,
verbose=verbose,
flag=1)
except urllib.request.HTTPError as emsg:
if '401' in str(emsg):
fullfilename = __apogee_credentials_downloader(
urlstr, fullfilename)
elif '404' in str(emsg):
print(f'{urlstr} cannot be found on server, skipped')
fullfilename = warning_flag
else:
print(f"Unknown error occurred - {emsg}")
fullfilename = warning_flag
return fullfilename
def apogee_distances(dr=None, flag=None):
"""
Download the APOGEE Distances VAC catalogue (APOGEE Distances for DR14, APOGEE Starhourse for DR16)
:param dr: APOGEE DR
:type dr: int
:param flag: Force to download if flag=1
:type flag: int
:return: full file path
:rtype: str
:History:
| 2018-Jan-24 - Written - Henry Leung (University of Toronto)
| 2021-Jan-29 - Updated - Henry Leung (University of Toronto)
"""
dr = apogee_default_dr(dr=dr)
if dr == 14:
file_hash = "b33c8419be784b1be3d14af3ee9696c6ac31830f"
str1 = "https://data.sdss.org/sas/dr14/apogee/vac/apogee-distances/"
filename = f"apogee_distances-DR{dr}.fits"
urlstr = str1 + filename
fullfoldername = os.path.join(apogee_env(),
"dr14/apogee/vac/apogee-distances/")
if not os.path.exists(fullfoldername):
os.makedirs(fullfoldername)
fullfilename = os.path.join(fullfoldername, filename)
if dr == 16:
file_hash = "2502e2f7703046163f81ecc4054dce39b2038e4f"
str1 = "https://data.sdss.org/sas/dr16/apogee/vac/apogee-starhorse/"
filename = f"apogee_starhorse-DR{dr}-v1.fits"
urlstr = str1 + filename
fullfoldername = os.path.join(apogee_env(),
"dr16/apogee/vac/apogee-starhorse/")
if not os.path.exists(fullfoldername):
os.makedirs(fullfoldername)
fullfilename = os.path.join(fullfoldername, filename)
else:
raise ValueError("apogee_distances() only supports APOGEE DR14-DR16")
# check file integrity
if os.path.isfile(fullfilename) and flag is None:
checksum = filehash(fullfilename, algorithm="sha1")
if checksum != file_hash.lower():
warnings.warn(
"File corruption detected, astroNN is attempting to download again"
)
apogee_distances(dr=dr, flag=1)
else:
logging.info(fullfilename + " was found!")
elif not os.path.isfile(fullfilename) or flag == 1:
try:
with TqdmUpTo(unit="B",
unit_scale=True,
miniters=1,
desc=urlstr.split("/")[-1]) as t:
urllib.request.urlretrieve(urlstr,
fullfilename,
reporthook=t.update_to)
logging.info(
f"Downloaded DR{dr} Distances successfully to {fullfilename}"
)
checksum = filehash(fullfilename, algorithm="sha1")
if checksum != file_hash.lower():
warnings.warn(
"File corruption detected, astroNN is attempting to download again"
)
apogee_distances(dr=dr, flag=1)
except urllib.error.HTTPError:
warnings.warn(f"{urlstr} cannot be found on server, skipped")
fullfilename = warning_flag
return fullfilename