class Dotter2016(Isochrone):
""" MESA isochrones from Dotter 2016:
http://waps.cfa.harvard.edu/MIST/interp_isos.html
"""
_dirname = os.path.join(get_iso_dir(), '{survey}', 'dotter2016')
defaults = (Isochrone.defaults) + (
('dirname', _dirname, 'Directory name for isochrone files'),
('hb_stage', 3, 'Horizontal branch stage name'),
('hb_spread', 0.1, 'Intrinisic spread added to horizontal branch'),
)
download_url = 'http://waps.cfa.harvard.edu/MIST'
download_defaults = copy.deepcopy(mesa_defaults_10)
abins = np.arange(1., 13.5 + 0.1, 0.1)
zbins = np.arange(1e-5, 1e-3 + 1e-5, 1e-5)
columns = dict(
des=odict([(2, ('mass_init', float)), (3, ('mass_act', float)),
(6, ('log_lum', float)), (9, ('u', float)),
(10, ('g', float)), (11, ('r', float)), (12, ('i', float)),
(13, ('z', float)), (14, ('Y', float)),
(15, ('stage', float))]),
sdss=odict([(2, ('mass_init', float)), (3, ('mass_act', float)),
(6, ('log_lum', float)), (9, ('u', float)),
(10, ('g', float)), (11, ('r', float)), (12, ('i', float)),
(13, ('z', float)), (14, ('stage', float))]),
ps1=odict([(2, ('mass_init', float)), (3, ('mass_act', float)),
(6, ('log_lum', float)), (9, ('g', float)),
(10, ('r', float)), (11, ('i', float)), (12, ('z', float)),
(13, ('y', float)), (16, ('stage', float))]),
lsst=odict([(2, ('mass_init', float)), (3, ('mass_act', float)),
(6, ('log_lum', float)), (9, ('u', float)),
(10, ('g', float)), (11, ('r', float)), (12, ('i', float)),
(13, ('z', float)), (14, ('Y', float)),
(15, ('stage', float))]),
)
def _parse(self, filename):
"""
Reads an isochrone in the Dotter 2016 format and determines
the age (Gyr), metallicity (Z), and creates arrays with the
initial stellar mass and corresponding magnitudes for each
step along the isochrone.
"""
try:
columns = self.columns[self.survey.lower()]
except KeyError as e:
logger.warning('Unrecognized survey: %s' % (self.survey))
raise (e)
kwargs = dict(comments='#',
usecols=list(columns.keys()),
dtype=list(columns.values()))
data = np.genfromtxt(filename, **kwargs)
self.mass_init = data['mass_init']
self.mass_act = data['mass_act']
self.luminosity = 10**data['log_lum']
self.mag_1 = data[self.band_1]
self.mag_2 = data[self.band_2]
self.stage = data['stage']
# Check where post-AGB isochrone data points begin
self.mass_init_upper_bound = np.max(self.mass_init)
self.index = np.nonzero(self.stage >= 4)[0][0]
self.mag = self.mag_1 if self.band_1_detection else self.mag_2
self.color = self.mag_1 - self.mag_2
@classmethod
def z2feh(cls, z):
# Section 3.1 of Choi et al. 2016 (https://arxiv.org/abs/1604.08592)
Z_init = z # Initial metal abundance
Y_p = 0.249 # Primordial He abundance (Planck 2015)
c = 1.5 # He enrichment ratio
Y_init = Y_p + c * Z_init
X_init = 1 - Y_init - Z_init
Z_solar = 0.0142 # Solar metal abundance
Y_solar = 0.2703 # Solar He abundance (Asplund 2009)
X_solar = 1 - Y_solar - Z_solar
return np.log10(Z_init / Z_solar * X_solar / X_init)
@classmethod
def feh2z(cls, feh):
# Section 3.1 of Choi et al. 2016 (https://arxiv.org/abs/1604.08592)
Y_p = 0.249 # Primordial He abundance (Planck 2015)
c = 1.5 # He enrichment ratio
Z_solar = 0.0142 # Solar metal abundance
Y_solar = 0.2703 # Solar He abundance (Asplund 2009)
X_solar = 1 - Y_solar - Z_solar
return (1 - Y_p) / ((1 + c) + (X_solar / Z_solar) * 10**(-feh))
def query_server(self, outfile, age, metallicity):
z = metallicity
feh = self.z2feh(z)
params = dict(self.download_defaults)
params['output'] = dict_output[self.survey]
params['FeH_value'] = feh
params['age_value'] = age * 1e9
if params['age_scale'] == 'log10':
params['age_value'] = np.log10(params['age_value'])
server = self.download_url
url = server + '/iso_form.php'
# First check that the server is alive
logger.debug("Accessing %s..." % url)
urlopen(url, timeout=2)
#response = requests.post(url,data=params)
q = urlencode(params).encode('utf-8')
request = Request(url, data=q)
response = urlopen(request)
try:
fname = os.path.basename(str(response.read()).split('"')[1])
except Exception as e:
logger.debug(str(e))
msg = 'Output filename not found'
raise RuntimeError(msg)
tmpdir = os.path.dirname(tempfile.NamedTemporaryFile().name)
tmpfile = os.path.join(tmpdir, fname)
out = '{0}/tmp/{1}'.format(server, fname)
cmd = 'wget --progress dot:binary %s -P %s' % (out, tmpdir)
logger.debug(cmd)
stdout = subprocess.check_output(cmd,
shell=True,
stderr=subprocess.STDOUT)
logger.debug(stdout)
cmd = 'unzip %s -d %s' % (tmpfile, tmpdir)
logger.debug(cmd)
stdout = subprocess.check_output(cmd,
shell=True,
stderr=subprocess.STDOUT)
logger.debug(stdout)
logger.debug("Creating %s..." % outfile)
shutil.move(tmpfile.replace('.zip', '.cmd'), outfile)
os.remove(tmpfile)
return outfile
@classmethod
def verify(cls, filename, survey, age, metallicity):
age = age * 1e9
nlines = 14
with open(filename, 'r') as f:
lines = [f.readline() for i in range(nlines)]
if len(lines) < nlines:
msg = "Incorrect file size"
raise Exception(msg)
try:
s = lines[2].split()[-2]
assert dict_output[survey][:4] in s
except:
msg = "Incorrect survey:\n" + lines[2]
raise Exception(msg)
try:
z = lines[5].split()[2]
assert np.allclose(metallicity, float(z), atol=1e-3)
except:
msg = "Metallicity does not match:\n" + lines[5]
raise Exception(msg)
try:
a = lines[13].split()[1]
assert np.allclose(age, float(a), atol=1e-5)
except:
msg = "Age does not match:\n" + lines[13]
raise Exception(msg)
class Bressan2012(ParsecIsochrone):
_dirname = os.path.join(get_iso_dir(), '{survey}', 'bressan2012')
defaults = (Isochrone.defaults) + (
('dirname', _dirname, 'Directory name for isochrone files'),
('hb_stage', 4, 'Horizontal branch stage name'),
('hb_spread', 0.1, 'Intrinisic spread added to horizontal branch'),
)
#download_defaults = copy.deepcopy(defaults_27)
download_defaults = copy.deepcopy(defaults_31)
download_defaults['isoc_kind'] = 'parsec_CAF09_v1.2S'
columns = dict(
des=odict([
(3, ('mass_init', float)),
(4, ('mass_act', float)),
(5, ('log_lum', float)),
(10, ('g', float)),
(11, ('r', float)),
(12, ('i', float)),
(13, ('z', float)),
(14, ('Y', float)),
(16, ('stage', int)),
]),
sdss=odict([
(3, ('mass_init', float)),
(4, ('mass_act', float)),
(5, ('log_lum', float)),
(9, ('u', float)),
(10, ('g', float)),
(11, ('r', float)),
(12, ('i', float)),
(13, ('z', float)),
(15, ('stage', int)),
]),
ps1=odict([
(3, ('mass_init', float)),
(4, ('mass_act', float)),
(5, ('log_lum', float)),
(9, ('g', float)),
(10, ('r', float)),
(11, ('i', float)),
(12, ('z', float)),
(13, ('y', float)),
(16, ('stage', int)),
]),
lsst=odict([(3, ('mass_init', float)), (4, ('mass_act', float)),
(5, ('log_lum', float)), (9, ('u', float)),
(10, ('g', float)), (11, ('r', float)), (12, ('i', float)),
(13, ('z', float)), (14, ('Y', float)),
(16, ('stage', float))]),
)
def _parse(self, filename):
"""Reads an isochrone file in the Padova (Bressan et al. 2012)
format. Creates arrays with the initial stellar mass and
corresponding magnitudes for each step along the isochrone.
"""
#http://stev.oapd.inaf.it/cgi-bin/cmd_2.7
try:
columns = self.columns[self.survey.lower()]
except KeyError as e:
logger.warning('Unrecognized survey: %s' % (self.survey))
raise (e)
# delimiter='\t' is used to be compatible with OldPadova...
# ADW: This should be updated, but be careful of column numbering
kwargs = dict(delimiter='\t',
usecols=list(columns.keys()),
dtype=list(columns.values()))
self.data = np.genfromtxt(filename, **kwargs)
self.mass_init = self.data['mass_init']
self.mass_act = self.data['mass_act']
self.luminosity = 10**self.data['log_lum']
self.mag_1 = self.data[self.band_1]
self.mag_2 = self.data[self.band_2]
self.stage = self.data['stage']
self.mass_init_upper_bound = np.max(self.mass_init)
self.index = len(self.mass_init)
self.mag = self.mag_1 if self.band_1_detection else self.mag_2
self.color = self.mag_1 - self.mag_2
class Marigo2017(ParsecIsochrone):
#http://stev.oapd.inaf.it/cgi-bin/cmd_31
#_dirname = '/u/ki/kadrlica/des/isochrones/v4/'
_dirname = os.path.join(get_iso_dir(), '{survey}', 'marigo2017')
defaults = (Isochrone.defaults) + (
('dirname', _dirname, 'Directory name for isochrone files'),
('hb_stage', 4, 'Horizontal branch stage name'),
('hb_spread', 0.1, 'Intrinisic spread added to horizontal branch'),
)
download_defaults = copy.deepcopy(defaults_31)
download_defaults['isoc_kind'] = 'parsec_CAF09_v1.2S_NOV13'
columns = dict(
des=odict([
(2, ('mass_init', float)),
(3, ('mass_act', float)),
(4, ('log_lum', float)),
(7, ('stage', int)),
(23, ('u', float)),
(24, ('g', float)),
(25, ('r', float)),
(26, ('i', float)),
(27, ('z', float)),
(28, ('Y', float)),
]),
sdss=odict([
(2, ('mass_init', float)),
(3, ('mass_act', float)),
(4, ('log_lum', float)),
(7, ('stage', int)),
(23, ('u', float)),
(24, ('g', float)),
(25, ('r', float)),
(26, ('i', float)),
(27, ('z', float)),
]),
ps1=odict([
(2, ('mass_init', float)),
(3, ('mass_act', float)),
(4, ('log_lum', float)),
(7, ('stage', int)),
(23, ('g', float)),
(24, ('r', float)),
(25, ('i', float)),
(26, ('z', float)),
(27, ('y', float)),
(28, ('w', float)),
]),
lsst=odict([
(2, ('mass_init', float)),
(3, ('mass_act', float)),
(4, ('log_lum', float)),
(7, ('stage', int)),
(23, ('u', float)),
(24, ('g', float)),
(25, ('r', float)),
(26, ('i', float)),
(27, ('z', float)),
(28, ('Y', float)),
]),
)
def _parse(self, filename):
"""Reads an isochrone file in the Padova (Marigo et al. 2017)
format. Creates arrays with the initial stellar mass and
corresponding magnitudes for each step along the isochrone.
"""
try:
columns = self.columns[self.survey.lower()]
except KeyError as e:
logger.warning('Unrecognized survey: %s' % (self.survey))
raise (e)
kwargs = dict(usecols=list(columns.keys()),
dtype=list(columns.values()))
self.data = np.genfromtxt(filename, **kwargs)
# cut out anomalous point:
# https://github.com/DarkEnergySurvey/ugali/issues/29
self.data = self.data[self.data['stage'] != 9]
self.mass_init = self.data['mass_init']
self.mass_act = self.data['mass_act']
self.luminosity = 10**self.data['log_lum']
self.mag_1 = self.data[self.band_1]
self.mag_2 = self.data[self.band_2]
self.stage = self.data['stage']
self.mass_init_upper_bound = np.max(self.mass_init)
self.index = len(self.mass_init)
self.mag = self.mag_1 if self.band_1_detection else self.mag_2
self.color = self.mag_1 - self.mag_2
class Dotter2008(Isochrone):
"""
KCB: currently inheriting from PadovaIsochrone because there are
several useful functions where we would basically be copying code.
"""
_dirname = os.path.join(get_iso_dir(), '{survey}', 'dotter2008')
#_zsolar = 0.0163
_zsolar = 0.0180 # Grevesse & Sauval, 1998
# KCB: What to do about horizontal branch?
defaults = (Isochrone.defaults) + (
('dirname', _dirname, 'Directory name for isochrone files'),
('hb_stage', 'BHeb', 'Horizontal branch stage name'),
('hb_spread', 0.1, 'Intrinisic spread added to horizontal branch'),
)
abins = np.arange(1., 13.5 + 0.1, 0.1)
zbins = np.arange(7e-5, 1e-3 + 1e-5, 1e-5)
download_defaults = copy.deepcopy(dartmouth_defaults)
columns = dict(
des=odict([
(1, ('mass', float)),
(4, ('log_lum', float)),
(5, ('u', float)),
(6, ('g', float)),
(7, ('r', float)),
(8, ('i', float)),
(9, ('z', float)),
]),
sdss=odict([
(1, ('mass', float)),
(4, ('log_lum', float)),
(5, ('u', float)),
(6, ('g', float)),
(7, ('r', float)),
(8, ('i', float)),
(9, ('z', float)),
]),
ps1=odict([
(1, ('mass', float)),
(4, ('log_lum', float)),
(6, ('g', float)),
(7, ('r', float)),
(8, ('i', float)),
(9, ('z', float)),
(10, ('y', float)),
]),
)
def _parse(self, filename):
"""
Reads an isochrone in the Dotter format and determines the
age (log10 yrs and Gyr), metallicity (Z and [Fe/H]), and
creates arrays with the initial stellar mass and
corresponding magnitudes for each step along the isochrone.
http://stellar.dartmouth.edu/models/isolf_new.html
"""
try:
columns = self.columns[self.survey.lower()]
except KeyError as e:
logger.warning('Unrecognized survey: %s' % (survey))
raise (e)
kwargs = dict(comments='#',
usecols=list(columns.keys()),
dtype=list(columns.values()))
self.data = np.genfromtxt(filename, **kwargs)
# KCB: Not sure whether the mass in Dotter isochrone output
# files is initial mass or current mass
self.mass_init = self.data['mass']
self.mass_act = self.data['mass']
self.luminosity = 10**self.data['log_lum']
self.mag_1 = self.data[self.band_1]
self.mag_2 = self.data[self.band_2]
self.stage = np.tile('Main', len(self.data))
# KCB: No post-AGB isochrone data points, right?
self.mass_init_upper_bound = np.max(self.mass_init)
self.mag = self.mag_1 if self.band_1_detection else self.mag_2
self.color = self.mag_1 - self.mag_2
@classmethod
def z2feh(cls, z):
# Section 3 of Dotter et al. 2008
# Section 2 of Dotter et al. 2007 (0706.0847)
Z_init = z # Initial metal abundance
Y_p = 0.245 # Primordial He abundance (WMAP, 2003)
c = 1.54 # He enrichment ratio
Y_init = Y_p + c * Z_init
X_init = 1 - Y_init - Z_init
# This is not well defined...
#Z_solar/X_solar = 0.0229 # Solar metal fraction (Grevesse 1998)
ZX_solar = 0.0229
return np.log10(Z_init / X_init * 1 / ZX_solar)
@classmethod
def feh2z(cls, feh):
# Section 3 of Dotter et al. 2008
Y_p = 0.245 # Primordial He abundance (WMAP, 2003)
c = 1.54 # He enrichment ratio
# This is not well defined...
#Z_solar/X_solar = 0.0229 # Solar metal fraction (Grevesse 1998)
ZX_solar = 0.0229
return (1 - Y_p) / ((1 + c) + (1 / ZX_solar) * 10**(-feh))
def query_server(self, outfile, age, metallicity):
z = metallicity
feh = self.z2feh(z)
params = copy.deepcopy(self.download_defaults)
params['age'] = age
params['feh'] = '%.6f' % feh
params['clr'] = dict_clr[self.survey]
url = 'http://stellar.dartmouth.edu/models/isolf_new.php'
query = url + '?' + urlencode(params)
logger.debug(query)
response = urlopen(query)
page_source = response.read()
try:
file_id = int(page_source.split('tmp/tmp')[-1].split('.iso')[0])
except Exception as e:
logger.debug(str(e))
msg = 'Output filename not found'
raise RuntimeError(msg)
infile = 'http://stellar.dartmouth.edu/models/tmp/tmp%s.iso' % (
file_id)
command = 'wget -q %s -O %s' % (infile, outfile)
subprocess.call(command, shell=True)
## ADW: Old code to rename the output file based on Zeff ([a/Fe] corrected)
#tmpfile = tempfile.NamedTemporaryFile().name
#tmp = open(tmpfile,'r')
#lines = [tmp.readline() for i in range(4)]
#z_eff = float(lines[3].split()[4])
#basename = self.params2filename(age,z_eff)
#logger.info("Writing %s..."%outfile)
#mkdir(outdir)
#shutil.move(tmpfile,outfile)
@classmethod
def verify(cls, filename, survey, age, metallicity):
nlines = 8
with open(filename, 'r') as f:
lines = [f.readline() for i in range(nlines)]
if len(lines) < nlines:
msg = "Incorrect file size"
raise Exception(msg)
try:
z = lines[3].split()[4]
assert np.allclose(metallicity, float(z), atol=1e-3)
except:
msg = "Metallicity does not match:\n" + lines[3]
raise Exception(msg)
try:
s = lines[5].split()[2]
assert dict_output[survey][:4] in s
except:
msg = "Incorrect survey:\n" + lines[5]
raise Exception(msg)
try:
a = lines[7].split('=')[1].strip().split()[0]
assert np.allclose(age, float(a), atol=1e-5)
except:
msg = "Age does not match:\n" + lines[7]
raise Exception(msg)