def main():
"""
Multi-Core Markov-chain Monte Carlo (MC3) wrapper for the command-line
(shell) call.
Notes
-----
1.- To display the full list of arguments, run from the prompt:
mccubed.py -h
2.- The command line overwrites over the config file in case an argument
is defined twice.
"""
parser = mc3.mc.parse()
# Parse command-line args (right now, just interested in the config file):
args, unknown = parser.parse_known_args()
# Parse configuration file to a dictionary:
if args.cfile is not None and not os.path.isfile(args.cfile):
mu.error("Configuration file: '{:s}' not found.".format(args.cfile))
if args.cfile:
config = configparser.SafeConfigParser()
config.read([args.cfile])
defaults = dict(config.items("MCMC"))
else:
defaults = {}
# Set defaults from the configuration-file values:
parser.set_defaults(**defaults)
# Overwrite defaults with the command-line arguments:
args, unknown = parser.parse_known_args()
# Call MCMC driver:
output = mc3.mcmc(**vars(args))
def main():
"""
One function to run them all.
"""
mu.msg(
1,
"\n======= Bayesian Atmospheric Radiative Transfer (BART) ==============="
"\nA code to infer planetary atmospheric properties based on observed "
"\nspectroscopic information."
"\n\nCopyright (C) 2015-2016 University of Central Florida."
"\nAll rights reserved."
"\n\nContact: Patricio Cubillos patricio.cubillos[at]oeaw.ac.at"
"\n Jasmina Blecic jasmina[at]physics.ucf.edu"
"\n Joseph Harrington jh[at]physics.ucf.edu"
"\n======================================================================"
)
mu.msg(1, "\nInitialization:")
# Parse the config file from the command line:
cparser = argparse.ArgumentParser(
description=__doc__,
add_help=False,
formatter_class=argparse.RawDescriptionHelpFormatter)
# Add config file option:
cparser.add_argument("-c",
"--config_file",
help="Configuration file",
metavar="FILE")
# Parser for the MCMC arguments:
parser = argparse.ArgumentParser(parents=[cparser])
parser.add_argument("--justTEA", action='store_true', help="Run only TEA.")
parser.add_argument("--justOpacity",
action='store_true',
help="Run only Transit to generate the Opacity table.")
parser.add_argument("--resume",
action='store_true',
help="Resume a previous run.")
# Directories and files options:
group = parser.add_argument_group("Directories and files")
group.add_argument(
"--loc_dir",
dest="loc_dir",
help="Output directory to store results [default: %(default)s]",
type=str,
action="store",
default="outdir")
group.add_argument("--tep_name",
dest="tep_name",
help="Transiting exoplanet file name.",
type=str,
action="store",
default=None)
group.add_argument("--logfile",
dest="logfile",
help="MCMC log file [default: %(default)s]",
type=str,
action="store",
default="MCMC.log")
# Pressure layers options:
group = parser.add_argument_group("Layers pressure sampling")
group.add_argument(
"--n_layers",
dest="n_layers",
help="Number of atmospheric layers [default: %(default)s]",
type=int,
action="store",
default=100)
group.add_argument("--p_top",
dest="p_top",
help="Pressure at the top of the atmosphere (bars) "
"[default: %(default)s]",
type=np.double,
action="store",
default=1.0e-5)
group.add_argument("--p_bottom",
dest="p_bottom",
help="Pressure at the botom of the atmosphere (bars) "
"[default: %(default)s]",
type=np.double,
action="store",
default=100.0)
group.add_argument("--log",
dest="log",
help="Use log (True) or linear (False) scale sampling "
"[default: %(default)s]",
type=eval,
action="store",
default=True)
group.add_argument("--press_file",
dest="press_file",
help="Input/Output file with pressure array.",
type=str,
action="store",
default=None)
# Elemental abundance options:
group = parser.add_argument_group("Elemental abundances")
group.add_argument(
"--abun_basic",
dest="abun_basic",
help="Input elemental abundances file [default: %(default)s]",
type=str,
action="store",
default="../BART/inputs/abundances_Asplund2009.txt")
group.add_argument("--abun_file",
dest="abun_file",
help="Input/Output modified elemental abundances file",
type=str,
action="store",
default=None)
group.add_argument(
"--solar_times",
dest="solar_times",
help="Multiplication factor for metal-element abundances",
type=int,
action="store",
default=1.0)
group.add_argument(
"--COswap",
dest="COswap",
help="Swap C and O abundances if True [default: %(default)s]",
type=eval,
action="store",
default=False)
# Temperature profile options:
group = parser.add_argument_group("Temperature profile")
group.add_argument("--PTtype",
dest="PTtype",
help="Temperature profile model [default: %(default)s]",
type=str,
action="store",
default="line",
choices=("line", "madhu"))
group.add_argument("--PTinit",
dest="PTinit",
help="Temperature profile model parameters",
type=mu.parray,
action="store",
default=None)
# Atmospheric model options:
group = parser.add_argument_group("Atmospheric model")
group.add_argument(
"--in_elem",
dest="in_elem",
help="Input elements to consider in TEA [default: %(default)s]",
type=str,
action="store",
default='H He C N O')
group.add_argument(
"--out_spec",
dest="out_spec",
help="Output species to include in the atmospheric model "
"[default: %(default)s]",
type=str,
action="store",
default='H_g He_ref C_g N_g O_g H2_ref CO_g CO2_g CH4_g H2O_g')
group.add_argument(
"--preatm_file",
dest="preatm_file",
help="Pre-atmospheric file with elemental abundances per layer "
"[default: %(default)s]",
type=str,
action="store",
default="elem.atm")
group.add_argument("--atmfile",
dest="atmfile",
help="Atmospheric model file [default: %(default)s]",
type=str,
action="store",
default="")
group.add_argument(
"--uniform",
dest="uniform",
help="If not None, set uniform abundances with the specified "
"values for each species in out_spec [default: %(default)s]",
type=mu.parray,
action="store",
default=None)
group.add_argument(
"--refpress",
dest="refpress",
help="Reference pressure level (bar) corresponding to the pressure"
"at the planet radius [default: %(default)s]",
type=float,
action="store",
default=0.1)
# MCMC options:
group = parser.add_argument_group("MCMC")
group.add_argument("--params",
dest="params",
help="Model-fitting parameters [default: %(default)s]",
type=mu.parray,
action="store",
default=None)
group.add_argument("--molfit",
dest="molfit",
help="Molecules fit [default: %(default)s]",
type=mu.parray,
action="store",
default=None)
group.add_argument(
"--Tmin",
dest="Tmin",
help="Lower Temperature boundary [default: %(default)s]",
type=float,
action="store",
default=400.0)
group.add_argument(
"--Tmax",
dest="Tmax",
help="Higher Temperature boundary [default: %(default)s]",
type=float,
action="store",
default=3000.0)
group.add_argument("--quiet",
dest="quiet",
help="Set verbosity level to minimum",
action="store_true")
group.add_argument("--stepsize",
dest="stepsize",
help="Parameters stepsize",
type=mu.parray,
action="store",
default=None)
group.add_argument("--burnin",
dest="burnin",
help="Number of burn-in iterations per chain",
type=mu.parray,
action="store",
default=None)
group.add_argument("--data",
dest="data",
help="Transit or eclipse depths",
type=mu.parray,
action="store",
default=None)
group.add_argument("--uncert",
dest="uncert",
help="Uncertanties on transit or eclipse depths",
type=mu.parray,
action="store",
default=None)
# Input converter options:
group = parser.add_argument_group("Input Converter Options")
group.add_argument(
"--tint",
dest="tint",
help="Internal temperature of the planet [default: %(default)s].",
type=float,
action="store",
default=100.0)
# Output-Converter Options:
group = parser.add_argument_group("Output Converter Options")
group.add_argument("--filter",
action="store",
help="Waveband filter name [default: %(default)s]",
dest="filter",
type=mu.parray,
default=None)
group.add_argument("--kurucz_file",
action="store",
help="Stellar Kurucz file [default: %(default)s]",
dest="kurucz",
type=str,
default=None)
group.add_argument("--solution",
action="store",
help="Solution geometry [default: %(default)s]",
dest="solution",
type=str,
default="None",
choices=('transit', 'eclipse'))
# Transit options:
group = parser.add_argument_group("Transit variables")
group.add_argument(
"--tconfig",
dest="tconfig",
help="Transit configuration file [default: %(default)s]",
type=str,
action="store",
default="transit.cfg")
group.add_argument("--opacityfile",
dest="opacityfile",
help="Opacity table file [default: %(default)s]",
type=str,
action="store",
default=None)
group.add_argument("--outspec",
dest="outspec",
help="Output spectrum filename [default: %(default)s]",
type=str,
action="store",
default="outspec.dat")
group.add_argument(
"--shareOpacity",
dest="shareOpacity",
help="If True, use shared memory for the Transit opacity file "
"[default: %(default)s]",
type=eval,
action="store",
default=True)
# Remaining_argv contains all other command-line-arguments:
cargs, remaining_argv = cparser.parse_known_args()
# Get only the arguments defined above:
known, unknown = parser.parse_known_args(remaining_argv)
# Get configuration file from command-line:
cfile = cargs.config_file
# Default:
if cfile is None:
cfile = "./BART.cfg"
# Always require a configuration file:
if not os.path.isfile(cfile):
mu.error("Configuration file: '{:s}' not found.".format(cfile))
# Read values from configuration file:
config = ConfigParser.SafeConfigParser()
config.optionxform = str # This one enable Uppercase in arguments
config.read([cfile])
defaults = dict(config.items("MCMC"))
mu.msg(1, "The configuration file is: '{:s}'.".format(cfile), indent=2)
# Set the defaults from the configuration file:
parser.set_defaults(**defaults)
# Set values from command line:
args, unknown = parser.parse_known_args(remaining_argv)
# Unpack the variables from args:
variables = dir(args)
for var in dir(known):
if not var.startswith("_"):
exec("{:s} = args.{:s}".format(var, var))
# Make output directory:
# Make a subdirectory with the date and time
dirfmt = loc_dir + "%4d-%02d-%02d_%02d:%02d:%02d"
date_dir = dirfmt % time.localtime()[0:6]
# FINDME: Temporary hack (temporary?):
date_dir = os.path.normpath(loc_dir) + "/"
if not os.path.isabs(date_dir):
date_dir = os.getcwd() + "/" + date_dir
mu.msg(1, "Output folder: '{:s}'".format(date_dir), indent=2)
try:
os.mkdir(date_dir)
except OSError, e:
if e.errno == 17: # Allow overwritting while we debug
pass
else:
mu.error("Cannot create folder '{:s}'. {:s}.".format(
date_dir, os.strerror(e.errno)))
date_dir = os.getcwd() + "/" + date_dir
mu.msg(1, "Output folder: '{:s}'".format(date_dir), indent=2)
try:
os.mkdir(date_dir)
except OSError, e:
if e.errno == 17: # Allow overwritting while we debug
pass
else:
mu.error("Cannot create folder '{:s}'. {:s}.".format(
date_dir, os.strerror(e.errno)))
# Copy files to date dir:
# BART configuration file:
shutil.copy2(cfile, date_dir)
# TEP file:
if not os.path.isfile(tep_name):
mu.error("Tepfile ('{:s}') Not found.".format(tep_name))
else:
shutil.copy2(tep_name, date_dir + os.path.basename(tep_name))
# Check if files already exist:
runMCMC = 0 # Flag that indicate which steps to run
# Atmospheric file:
if os.path.isfile(atmfile):
atmfile = os.path.realpath(atmfile)
shutil.copy2(atmfile, date_dir + os.path.basename(atmfile))
mu.msg(1,
"Atmospheric file copied from: '{:s}'.".format(atmfile),
indent=2)
runMCMC |= 8
# Pre-atmospheric file:
if os.path.isfile(preatm_file):
def main():
"""
One function to run them all.
"""
mu.msg(1,
"\n======= Bayesian Atmospheric Radiative Transfer (BART) ==============="
"\nA code to infer planetary atmospheric properties based on observed "
"\nspectroscopic information."
"\n\nCopyright (C) 2015-2016 University of Central Florida."
"\nAll rights reserved."
"\n\nContact: Patricio Cubillos patricio.cubillos[at]oeaw.ac.at"
"\n Jasmina Blecic jasmina[at]physics.ucf.edu"
"\n Joseph Harrington jh[at]physics.ucf.edu"
"\n======================================================================")
mu.msg(1, "\nInitialization:")
# Parse the config file from the command line:
cparser = argparse.ArgumentParser(description=__doc__, add_help=False,
formatter_class=argparse.RawDescriptionHelpFormatter)
# Add config file option:
cparser.add_argument("-c", "--config_file",
help="Configuration file", metavar="FILE")
# Parser for the MCMC arguments:
parser = argparse.ArgumentParser(parents=[cparser])
parser.add_argument("--justTEA", action='store_true',
help="Run only TEA.")
parser.add_argument("--justOpacity", action='store_true',
help="Run only Transit to generate the Opacity table.")
parser.add_argument("--justPlots", action='store_true',
help="Remakes plots of BART output.")
parser.add_argument("--resume", action='store_true',
help="Resume a previous run.")
# Directories and files options:
group = parser.add_argument_group("Directories and files")
group.add_argument("--loc_dir", dest="loc_dir",
help="Output directory to store results [default: %(default)s]",
type=str, action="store", default="outdir")
group.add_argument("--tep_name", dest="tep_name",
help="Transiting exoplanet file name.",
type=str, action="store", default=None)
group.add_argument("--logfile", dest="logfile",
help="MCMC log file [default: %(default)s]",
type=str, action="store", default="MCMC.log")
# Pressure layers options:
group = parser.add_argument_group("Layers pressure sampling")
group.add_argument("--n_layers", dest="n_layers",
help="Number of atmospheric layers [default: %(default)s]",
type=int, action="store", default=100)
group.add_argument("--p_top", dest="p_top",
help="Pressure at the top of the atmosphere (bars) "
"[default: %(default)s]",
type=np.double, action="store", default=1.0e-5)
group.add_argument("--p_bottom", dest="p_bottom",
help="Pressure at the botom of the atmosphere (bars) "
"[default: %(default)s]",
type=np.double, action="store", default=100.0)
group.add_argument("--log", dest="log",
help="Use log (True) or linear (False) scale sampling "
"[default: %(default)s]",
type=eval, action="store", default=True)
group.add_argument("--press_file", dest="press_file",
help="Input/Output file with pressure array.",
type=str, action="store", default=None)
# Elemental abundance options:
group = parser.add_argument_group("Elemental abundances")
group.add_argument("--abun_basic", dest="abun_basic",
help="Input elemental abundances file [default: %(default)s]",
type=str, action="store", default="../BART/inputs/abundances_Asplund2009.txt")
group.add_argument("--abun_file", dest="abun_file",
help="Input/Output modified elemental abundances file",
type=str, action="store", default=None)
group.add_argument("--solar_times", dest="solar_times",
help="Multiplication factor for metal-element abundances",
type=int, action="store", default=1.0)
group.add_argument("--COswap", dest="COswap",
help="Swap C and O abundances if True [default: %(default)s]",
type=eval, action="store", default=False)
# Temperature profile options:
group = parser.add_argument_group("Temperature profile")
group.add_argument("--PTtype", dest="PTtype",
help="Temperature profile model [default: %(default)s]",
type=str, action="store", default="line",
choices=("line","madhu_noinv","madhu_inv","iso"))
group.add_argument("--PTinit", dest="PTinit",
help="Temperature profile model parameters",
type=mu.parray, action="store", default=None)
# Atmospheric model options:
group = parser.add_argument_group("Atmospheric model")
group.add_argument("--in_elem", dest="in_elem",
help="Input elements to consider in TEA [default: %(default)s]",
type=str, action="store", default='H He C N O')
group.add_argument("--out_spec", dest="out_spec",
help="Output species to include in the atmospheric model "
"[default: %(default)s]",
type=str, action="store",
default='H_g He_ref C_g N_g O_g H2_ref CO_g CO2_g CH4_g H2O_g')
group.add_argument("--preatm_file", dest="preatm_file",
help="Pre-atmospheric file with elemental abundances per layer "
"[default: %(default)s]",
type=str, action="store", default="elem.atm")
group.add_argument("--atmfile", dest="atmfile",
help="Atmospheric model file [default: %(default)s]",
type=str, action="store", default="")
group.add_argument("--uniform", dest="uniform",
help="If not None, set uniform abundances with the specified "
"values for each species in out_spec [default: %(default)s]",
type=mu.parray, action="store", default=None)
group.add_argument("--refpress", dest="refpress",
help="Reference pressure level (bar) corresponding to the pressure"
" at the planet radius [default: %(default)s]",
type=float, action="store", default=0.1)
# MCMC options:
group = parser.add_argument_group("MCMC")
group.add_argument("--params", dest="params",
help="Model-fitting parameters [default: %(default)s]",
type=mu.parray, action="store", default=None)
group.add_argument("--parnames", dest="parnames",
help="Labels for model-fitting parameters [default: %(default)s]",
type=mu.parray, action="store", default=None)
group.add_argument("--molfit", dest="molfit",
help="Molecules fit [default: %(default)s]",
type=mu.parray, action="store", default=None)
group.add_argument("--Tmin", dest="Tmin",
help="Lower Temperature boundary [default: %(default)s]",
type=float, action="store", default=400.0)
group.add_argument("--Tmax", dest="Tmax",
help="Higher Temperature boundary [default: %(default)s]",
type=float, action="store", default=3000.0)
group.add_argument("--quiet", dest="quiet",
help="Set verbosity level to minimum",
action="store_true")
group.add_argument("--nchains", dest="nchains",
help="Number of parallel chains for MCMC",
type=int, action="store", default=10)
group.add_argument("--stepsize", dest="stepsize",
help="Parameters stepsize",
type=mu.parray, action="store", default=None)
group.add_argument("--burnin", dest="burnin",
help="Number of burn-in iterations per chain",
type=int, action="store", default=None)
group.add_argument("--thinning", dest="thinning",
help="Thinning factor of the chains (use every thinning-th "
"iteration) used in the GR test and plots",
type=int, action="store", default=1)
group.add_argument("--data", dest="data",
help="Transit or eclipse depths",
type=mu.parray, action="store", default=None)
group.add_argument("--uncert", dest="uncert",
help="Uncertanties on transit or eclipse depths",
type=mu.parray, action="store", default=None)
# Input converter options:
group = parser.add_argument_group("Input Converter Options")
group.add_argument("--tint", dest="tint",
help="Internal temperature of the planet [default: %(default)s].",
type=float, action="store", default=100.0)
# Output-Converter Options:
group = parser.add_argument_group("Output Converter Options")
group.add_argument("--filters", action="store",
help="Waveband filter names [default: %(default)s]",
dest="filters", type=mu.parray, default=None)
group.add_argument("--kurucz_file", action="store",
help="Stellar Kurucz file [default: %(default)s]",
dest="kurucz", type=str, default=None)
group.add_argument("--solution", action="store",
help="Solution geometry [default: %(default)s]",
dest="solution", type=str, default="None",
choices=('transit', 'eclipse'))
# Transit options:
group = parser.add_argument_group("Transit variables")
group.add_argument("--tconfig", dest="tconfig",
help="Transit configuration file [default: %(default)s]",
type=str, action="store", default="transit.cfg")
group.add_argument("--opacityfile", dest="opacityfile",
help="Opacity table file [default: %(default)s]",
type=str, action="store", default=None)
group.add_argument("--outspec", dest="outspec",
help="Output spectrum filename [default: %(default)s]",
type=str, action="store", default="outspec.dat")
group.add_argument("--shareOpacity", dest="shareOpacity",
help="If True, use shared memory for the Transit opacity file "
"[default: %(default)s]",
type=eval, action="store", default=True)
# Remaining_argv contains all other command-line-arguments:
cargs, remaining_argv = cparser.parse_known_args()
# Get only the arguments defined above:
known, unknown = parser.parse_known_args(remaining_argv)
# Get configuration file from command-line:
cfile = cargs.config_file
# Default:
if cfile is None:
cfile = "./BART.cfg"
# Always require a configuration file:
if not os.path.isfile(cfile):
mu.error("Configuration file: '{:s}' not found.".format(cfile))
# Read values from configuration file:
config = ConfigParser.SafeConfigParser()
config.optionxform = str # This one enable Uppercase in arguments
config.read([cfile])
defaults = dict(config.items("MCMC"))
mu.msg(1, "The configuration file is: '{:s}'.".format(cfile), indent=2)
# Set the defaults from the configuration file:
parser.set_defaults(**defaults)
# Set values from command line:
args, unknown = parser.parse_known_args(remaining_argv)
# Unpack the variables from args:
variables = dir(args)
for var in dir(known):
if not var.startswith("_"):
exec("{:s} = args.{:s}".format(var, var))
# Dictionary of functions to calculate temperature for PTtype
PTfunc = {'iso' : pt.PT_iso,
'line' : pt.PT_line,
'madhu_noinv' : pt.PT_NoInversion,
'madhu_inv' : pt.PT_Inversion}
# Check that the user gave a valid PTtype:
if PTtype not in PTfunc.keys():
print("The specified 'PTtype' is not valid. Options are 'line', " + \
"'madhu_noinv', 'madhu_inv', or 'iso'. Please try again.")
sys.exit()
# Check that out_spec and uniform are valid specifications
if uniform is not None and len(uniform) != len(out_spec.split(' ')):
print('The inputs for out_spec and uniform are not compatible.')
diffuniout = len(uniform) - len(out_spec.split(' '))
if diffuniout > 0:
if diffuniout == 1:
print('uniform has ' + str(diffuniout) + 'extra entry.')
else:
print('uniform has ' + str(diffuniout) + 'extra entries.')
else:
if diffuniout == -1:
print('out_spec has ' + str(-1*diffuniout) + 'extra entry.')
else:
print('out_spec has ' + str(-1*diffuniout) + 'extra entries.')
print('Please correct this and run again.')
sys.exit()
# Make output directory:
# Make a subdirectory with the date and time
dirfmt = loc_dir + "%4d-%02d-%02d_%02d:%02d:%02d"
date_dir = dirfmt % time.localtime()[0:6]
# FINDME: Temporary hack (temporary?):
date_dir = os.path.normpath(loc_dir) + "/"
if not os.path.isabs(date_dir):
date_dir = os.getcwd() + "/" + date_dir
mu.msg(1, "Output folder: '{:s}'".format(date_dir), indent=2)
try:
os.mkdir(date_dir)
except OSError, e:
if e.errno == 17: # Allow overwritting while we debug
pass
else:
mu.error("Cannot create folder '{:s}'. {:s}.".format(date_dir,
os.strerror(e.errno)))
date_dir = os.getcwd() + "/" + date_dir
mu.msg(1, "Output folder: '{:s}'".format(date_dir), indent=2)
try:
os.mkdir(date_dir)
except OSError, e:
if e.errno == 17: # Allow overwritting while we debug
pass
else:
mu.error("Cannot create folder '{:s}'. {:s}.".format(date_dir,
os.strerror(e.errno)))
# Copy files to date dir:
# BART configuration file:
shutil.copy2(cfile, date_dir)
# TEP file:
if not os.path.isfile(tep_name):
mu.error("Tepfile ('{:s}') Not found.".format(tep_name))
else:
shutil.copy2(tep_name, date_dir + os.path.basename(tep_name))
# Check if files already exist:
runMCMC = 0 # Flag that indicate which steps to run
if justPlots:
mu.msg(1, "\nRe-making output plots.", indent=0)
runMCMC |= 16
# Atmospheric file:
if os.path.isfile(atmfile):
atmfile = os.path.realpath(atmfile)
shutil.copy2(atmfile, date_dir + os.path.basename(atmfile))
mu.msg(1, "Atmospheric file copied from: '{:s}'.".format(atmfile),indent=2)
runMCMC |= 8
# Pre-atmospheric file:
def main():
"""
One function to run them all.
"""
mu.msg(
1,
"\n======= Bayesian Atmospheric Radiative Transfer (BART) ==============="
"\nA code to infer planetary atmospheric properties based on observed "
"\nspectroscopic information."
"\n\nCopyright (C) 2015-2016 University of Central Florida."
"\nAll rights reserved."
"\n\nContact: Patricio Cubillos patricio.cubillos[at]oeaw.ac.at"
"\n Jasmina Blecic jasmina[at]physics.ucf.edu"
"\n Joseph Harrington jh[at]physics.ucf.edu"
"\n======================================================================"
)
mu.msg(1, "\nInitialization:")
# Parse the config file from the command line:
cparser = argparse.ArgumentParser(
description=__doc__,
add_help=False,
formatter_class=argparse.RawDescriptionHelpFormatter)
# Add config file option:
cparser.add_argument("-c",
"--config_file",
help="Configuration file",
metavar="FILE")
# Parser for the MCMC arguments:
parser = argparse.ArgumentParser(parents=[cparser])
parser.add_argument("--justTEA",
dest="justTEA",
action='store_true',
help="Run only TEA.",
default=False)
parser.add_argument("--justOpacity",
dest="justOpacity",
action='store_true',
help="Run only Transit to generate the Opacity table.",
default=False)
parser.add_argument("--justPlots",
dest="justPlots",
action='store_true',
help="Remakes plots of BART output.",
default=False)
parser.add_argument("--resume",
dest="resume",
action='store_true',
help="Resume a previous run.",
default=False)
# Directories and files options:
group = parser.add_argument_group("Directories and files")
group.add_argument("--fext",
dest="fext",
help="File extension for plots [default: %(default)s]",
type=str,
action="store",
default=".png")
group.add_argument(
"--loc_dir",
dest="loc_dir",
help="Output directory to store results [default: %(default)s]",
type=str,
action="store",
default="outdir")
group.add_argument("--tep_name",
dest="tep_name",
help="Transiting exoplanet file name.",
type=str,
action="store",
default=None)
group.add_argument("--logfile",
dest="logfile",
help="MCMC log file [default: %(default)s]",
type=str,
action="store",
default="MCMC.log")
# Pressure layers options:
group = parser.add_argument_group("Layers pressure sampling")
group.add_argument(
"--n_layers",
dest="n_layers",
help="Number of atmospheric layers [default: %(default)s]",
type=int,
action="store",
default=100)
group.add_argument("--p_top",
dest="p_top",
help="Pressure at the top of the atmosphere (bars) "
"[default: %(default)s]",
type=np.double,
action="store",
default=1.0e-5)
group.add_argument("--p_bottom",
dest="p_bottom",
help="Pressure at the botom of the atmosphere (bars) "
"[default: %(default)s]",
type=np.double,
action="store",
default=100.0)
group.add_argument("--log",
dest="log",
help="Use log (True) or linear (False) scale sampling "
"[default: %(default)s]",
type=eval,
action="store",
default=True)
group.add_argument("--press_file",
dest="press_file",
help="Input/Output file with pressure array.",
type=str,
action="store",
default=None)
# Elemental abundance options:
group = parser.add_argument_group("Elemental abundances")
group.add_argument(
"--abun_basic",
dest="abun_basic",
help="Input elemental abundances file [default: %(default)s]",
type=str,
action="store",
default="../BART/inputs/abundances_Asplund2009.txt")
group.add_argument("--abun_file",
dest="abun_file",
help="Input/Output modified elemental abundances file",
type=str,
action="store",
default=None)
group.add_argument(
"--solar_times",
dest="solar_times",
help="Multiplication factor for metal-element abundances",
type=int,
action="store",
default=1.0)
group.add_argument(
"--COswap",
dest="COswap",
help="Swap C and O abundances if True [default: %(default)s]",
type=eval,
action="store",
default=False)
# Temperature profile options:
group = parser.add_argument_group("Temperature profile")
group.add_argument("--PTtype",
dest="PTtype",
help="Temperature profile model [default: %(default)s]",
type=str,
action="store",
default="line",
choices=("line", "madhu_noinv", "madhu_inv", "iso"))
group.add_argument("--PTinit",
dest="PTinit",
help="Temperature profile model parameters",
type=mu.parray,
action="store",
default=None)
# Atmospheric model options:
group = parser.add_argument_group("Atmospheric model")
group.add_argument(
"--in_elem",
dest="in_elem",
help="Input elements to consider in TEA [default: %(default)s]",
type=str,
action="store",
default='H He C N O')
group.add_argument(
"--out_spec",
dest="out_spec",
help="Output species to include in the atmospheric model "
"[default: %(default)s]",
type=str,
action="store",
default='H_g He_ref C_g N_g O_g H2_ref CO_g CO2_g CH4_g H2O_g')
group.add_argument(
"--preatm_file",
dest="preatm_file",
help="Pre-atmospheric file with elemental abundances per layer "
"[default: %(default)s]",
type=str,
action="store",
default="elem.atm")
group.add_argument("--atmfile",
dest="atmfile",
help="Atmospheric model file [default: %(default)s]",
type=str,
action="store",
default="")
group.add_argument(
"--uniform",
dest="uniform",
help="If not None, set uniform abundances with the specified "
"values for each species in out_spec [default: %(default)s]",
type=mu.parray,
action="store",
default=None)
group.add_argument(
"--refpress",
dest="refpress",
help="Reference pressure level (bar) corresponding to the pressure"
" at the planet radius [default: %(default)s]",
type=float,
action="store",
default=0.1)
group.add_argument("--cloudtop",
action="store",
help="Cloud deck top pressure [default: %(default)s]",
dest="cloudtop",
type=float,
default=None)
group.add_argument("--scattering",
action="store",
help="Rayleigh scattering [default: %(default)s]",
dest="scattering",
type=float,
default=None)
# MCMC options:
group = parser.add_argument_group("MCMC")
group.add_argument("--params",
dest="params",
help="Model-fitting parameters [default: %(default)s]",
type=mu.parray,
action="store",
default=None)
group.add_argument(
"--parnames",
dest="parnames",
help="Labels for model-fitting parameters [default: %(default)s]",
type=mu.parray,
action="store",
default=None)
group.add_argument("--molfit",
dest="molfit",
help="Molecules fit [default: %(default)s]",
type=mu.parray,
action="store",
default=None)
group.add_argument(
"--Tmin",
dest="Tmin",
help="Lower Temperature boundary [default: %(default)s]",
type=float,
action="store",
default=400.0)
group.add_argument(
"--Tmax",
dest="Tmax",
help="Higher Temperature boundary [default: %(default)s]",
type=float,
action="store",
default=3000.0)
group.add_argument("--quiet",
dest="quiet",
help="Set verbosity level to minimum",
action="store_true")
group.add_argument("--nchains",
dest="nchains",
help="Number of parallel chains for MCMC",
type=int,
action="store",
default=10)
group.add_argument("--walk",
dest="walk",
help="MCMC algorithm",
type=str,
action="store",
default="snooker",
choices=('snooker', 'mrw', 'demc', 'unif'))
group.add_argument("--stepsize",
dest="stepsize",
help="Parameters stepsize",
type=mu.parray,
action="store",
default=None)
group.add_argument("--burnin",
dest="burnin",
help="Number of burn-in iterations per chain",
type=int,
action="store",
default=None)
group.add_argument(
"--thinning",
dest="thinning",
help="Thinning factor of the chains (use every thinning-th "
"iteration) used in the GR test and plots",
type=int,
action="store",
default=1)
group.add_argument("--data",
dest="data",
help="Transit or eclipse depths",
type=mu.parray,
action="store",
default=None)
group.add_argument("--uncert",
dest="uncert",
help="Uncertanties on transit or eclipse depths",
type=mu.parray,
action="store",
default=None)
group.add_argument("--savemodel",
dest="savemodel",
help="Filename to save out models.",
type=str,
action="store",
default=None)
group.add_argument("--modelper", dest="modelper",
help="Determines how to split MC3's `savemodel`. " + \
"0 makes no split, >0 sets the # of iterations per split. " + \
"If nchains=10 and modelper=5, it will save every 50 " + \
"models to a new .NPY file.",
type=int, action="store", default=0)
group.add_argument("--plots",
dest="plots",
help="Determines whether to produce plots.",
type=bool,
action="store",
default=True)
# Input converter options:
group = parser.add_argument_group("Input Converter Options")
group.add_argument(
"--tint",
dest="tint",
help="Internal temperature of the planet [default: %(default)s].",
type=float,
action="store",
default=100.0)
group.add_argument("--tint_type", dest="tint_type",
help="Method to evaluate `tint`. Options: const or thorngren. " + \
"[default: %(default)s].",
type=str, action="store", default='const',
choices=("const","thorngren"))
# Output-Converter Options:
group = parser.add_argument_group("Output Converter Options")
group.add_argument("--filters",
action="store",
help="Waveband filter names [default: %(default)s]",
dest="filters",
type=mu.parray,
default=None)
group.add_argument("--kurucz_file",
action="store",
help="Stellar Kurucz file [default: %(default)s]",
dest="kurucz",
type=str,
default=None)
group.add_argument("--solution",
action="store",
help="Solution geometry [default: %(default)s]",
dest="solution",
type=str,
default="None",
choices=('transit', 'eclipse'))
# Transit options:
group = parser.add_argument_group("Transit variables")
group.add_argument(
"--tconfig",
dest="tconfig",
help="Transit configuration file [default: %(default)s]",
type=str,
action="store",
default="transit.cfg")
group.add_argument("--opacityfile",
dest="opacityfile",
help="Opacity table file [default: %(default)s]",
type=str,
action="store",
default=None)
group.add_argument("--outspec",
dest="outspec",
help="Output spectrum filename [default: %(default)s]",
type=str,
action="store",
default="outspec.dat")
group.add_argument(
"--shareOpacity",
dest="shareOpacity",
help="If True, use shared memory for the Transit opacity file "
"[default: %(default)s]",
type=eval,
action="store",
default=True)
# Remaining_argv contains all other command-line-arguments:
cargs, remaining_argv = cparser.parse_known_args()
# Get only the arguments defined above:
known, unknown = parser.parse_known_args(remaining_argv)
# Get configuration file from command-line:
cfile = cargs.config_file
# Default:
if cfile is None:
cfile = os.path.join(os.getcwd(), "BART.cfg")
# Always require a configuration file:
if not os.path.isfile(cfile):
mu.error("Configuration file: '{:s}' not found.".format(cfile))
# Read values from configuration file:
config = ConfigParser()
config.optionxform = str # This one enable Uppercase in arguments
config.read([cfile])
defaults = dict(config.items("MCMC"))
mu.msg(1, "The configuration file is: '{:s}'.".format(cfile), indent=2)
# Set the defaults from the configuration file:
parser.set_defaults(**defaults)
# Set values from command line:
args, unknown = parser.parse_known_args(remaining_argv)
# Unpack configuration-file/command-line arguments:
justTEA = args.justTEA
justOpacity = args.justOpacity
justPlots = args.justPlots
resume = args.resume
loc_dir = args.loc_dir
fext = args.fext
tep_name = args.tep_name
logfile = args.logfile
n_layers = args.n_layers
p_top = args.p_top
p_bottom = args.p_bottom
log = args.log
press_file = args.press_file
abun_basic = args.abun_basic
abun_file = args.abun_file
solar_times = args.solar_times
COswap = args.COswap
cloud = args.cloudtop
rayleigh = args.scattering
PTtype = args.PTtype
PTinit = args.PTinit
in_elem = args.in_elem
out_spec = args.out_spec
preatm_file = args.preatm_file
atmfile = args.atmfile
uniform = args.uniform
refpress = args.refpress
params = args.params
parnames = args.parnames
molfit = args.molfit
Tmin = args.Tmin
Tmax = args.Tmax
quiet = args.quiet
nchains = args.nchains
walk = args.walk
stepsize = args.stepsize
burnin = args.burnin
thinning = args.thinning
data = args.data
uncert = args.uncert
savemodel = args.savemodel
modelper = args.modelper
plots = args.plots
tint = args.tint
tint_type = args.tint_type
filters = args.filters
kurucz = args.kurucz
solution = args.solution
tconfig = args.tconfig
opacityfile = args.opacityfile
outspec = args.outspec
shareOpacity = args.shareOpacity
# Unpack the variables from args:
'''
argd = {}
for key, val in vars(args).items():
if type(val) == str and val in ['True', 'False', 'None']:
if val == 'True':
argd.update({key:True})
elif val == 'False':
argd.update({key:False})
elif val == 'None':
argd.update({key:None})
else:
argd.update({key:val})
vars(sys.modules[__name__]).update(argd)
'''
# Dictionary of functions to calculate temperature for PTtype
PTfunc = {
'iso': pt.PT_iso,
'line': pt.PT_line,
'madhu_noinv': pt.PT_NoInversion,
'madhu_inv': pt.PT_Inversion
}
# Check that the user gave a valid PTtype:
if PTtype not in PTfunc.keys():
print("The specified 'PTtype' is not valid. Options are 'line', " + \
"'madhu_noinv', 'madhu_inv', or 'iso'. Please try again.")
sys.exit()
# Check that out_spec and uniform are valid specifications
if uniform is not None and len(uniform) != len(out_spec.split(' ')):
print('The inputs for out_spec and uniform are not compatible.')
diffuniout = len(uniform) - len(out_spec.split(' '))
if diffuniout > 0:
if diffuniout == 1:
print('uniform has ' + str(diffuniout) + 'extra entry.')
else:
print('uniform has ' + str(diffuniout) + 'extra entries.')
else:
if diffuniout == -1:
print('out_spec has ' + str(-1 * diffuniout) + 'extra entry.')
else:
print('out_spec has ' + str(-1 * diffuniout) +
'extra entries.')
print('Please correct this and run again.')
sys.exit()
# Make output directory:
# Make a subdirectory with the date and time
dirfmt = loc_dir + "%4d-%02d-%02d_%02d:%02d:%02d"
date_dir = dirfmt % time.localtime()[0:6]
# FINDME: Temporary hack (temporary?):
date_dir = os.path.join(os.path.normpath(loc_dir), "")
if not os.path.isabs(date_dir):
date_dir = os.path.join(os.getcwd(), date_dir)
mu.msg(1, "Output folder: '{:s}'".format(date_dir), indent=2)
try:
os.mkdir(date_dir)
except OSError as e:
if e.errno == 17: # Allow overwritting while we debug
pass
else:
mu.error("Cannot create folder '{:s}'. {:s}.".format(
date_dir, os.strerror(e.errno)))
# Copy files to date dir:
# BART configuration file:
shutil.copy2(cfile, date_dir)
# TEP file:
if not os.path.isfile(tep_name):
mu.error("Tepfile ('{:s}') Not found.".format(tep_name))
else:
shutil.copy2(tep_name, date_dir + os.path.basename(tep_name))
# Check if files already exist:
runMCMC = 0 # Flag that indicate which steps to run
if justPlots:
mu.msg(1, "\nRe-making output plots.", indent=0)
runMCMC |= 16
# Atmospheric file:
if os.path.isfile(atmfile):
fatmfile = os.path.realpath(atmfile)
shutil.copy2(fatmfile, date_dir + os.path.basename(fatmfile))
mu.msg(1,
"Atmospheric file copied from: '{:s}'.".format(fatmfile),
indent=2)
runMCMC |= 8
atmfile = date_dir + os.path.basename(atmfile)
# Pre-atmospheric file:
if os.path.isfile(preatm_file):
fpreatm_file = os.path.realpath(preatm_file)
shutil.copy2(fpreatm_file, date_dir + os.path.basename(fpreatm_file))
mu.msg(
1,
"Pre-atmospheric file copied from: '{:s}'.".format(fpreatm_file),
indent=2)
runMCMC |= 4
# Elemental-abundances file:
if abun_file is not None and os.path.isfile(abun_file):
shutil.copy2(abun_file, date_dir + os.path.basename(abun_file))
mu.msg(
1,
"Elemental abundances file copied from: '{:s}'.".format(abun_file),
indent=2)
runMCMC |= 2
# Pressure file:
if press_file is not None and os.path.isfile(press_file):
shutil.copy2(press_file, date_dir + os.path.basename(press_file))
mu.msg(1,
"Pressure file copied from: '{:s}'.".format(press_file),
indent=2)
runMCMC |= 1
press_file = date_dir + os.path.basename(press_file)
# Generate files as needed:
if runMCMC < 1: # Pressure file
mp.makeP(n_layers, p_top, p_bottom, press_file, log)
mu.msg(1, "Created new pressure file.", indent=2)
# Make uniform-abundance profiles if requested:
if uniform is not None and runMCMC < 8:
# Calculate the temperature profile:
temp = ipt.initialPT2(date_dir, PTinit, press_file, PTtype,
PTfunc[PTtype], tep_name)
# Generate the uniform-abundance profiles file:
mat.uniform(atmfile, press_file, abun_basic, tep_name, out_spec,
uniform, temp, refpress)
# Update the runMCMC flag to skip upcoming steps:
runMCMC |= 8
if runMCMC < 2: # Elemental-abundances file
mu.msg(1, "CO swap: {}".format(COswap), indent=2)
mat.makeAbun(abun_basic, date_dir + abun_file, solar_times, COswap)
mu.msg(1, "Created new elemental abundances file.", indent=2)
abun_file = date_dir + abun_file
if runMCMC < 4: # Pre-atmospheric file
# Calculate the temperature profile:
temp = ipt.initialPT2(date_dir,
PTinit,
press_file,
PTtype,
PTfunc[PTtype],
tep_name,
tint_type=tint_type)
# Choose a pressure-temperature profile
mu.msg(1, "\nChoose temperature and pressure profile:", indent=2)
raw_input(" open Initial PT profile figure and\n"
" press enter to continue or quit and choose other initial "
"PT parameters.")
mat.make_preatm(tep_name, press_file, abun_file, in_elem, out_spec,
preatm_file, temp)
mu.msg(1, "Created new pre-atmospheric file.", indent=2)
if runMCMC < 8: # Atmospheric file
# Generate the TEA configuration file:
mc.makeTEA(cfile, TEAdir)
# Call TEA to calculate the atmospheric file:
TEAcall = os.path.join(TEAdir, "tea", "runatm.py")
TEAout = os.path.splitext(atmfile)[0] # Remove extension
# Execute TEA:
mu.msg(1, "\nExecute TEA:")
proc = subprocess.Popen([TEAcall, preatm_file, 'TEA'])
proc.communicate()
TEAres = os.path.join("TEA", "results", "TEA.tea")
shutil.copy2(os.path.join(date_dir, TEAres), atmfile)
# Add radius array:
mat.makeRadius(out_spec, atmfile, abun_file, tep_name, refpress)
mu.msg(1, "Added radius column to TEA atmospheric file.", indent=2)
# Re-format file for use with transit:
mat.reformat(atmfile)
mu.msg(1, "Atmospheric file reformatted for Transit.", indent=2)
if justTEA:
mu.msg(1, "~~ BART End (after TEA) ~~")
return
# Make the MC3 configuration file:
if runMCMC < 16: # MCMC
MCMC_cfile = os.path.join(os.path.realpath(loc_dir),
"MCMC_" + os.path.basename(cfile))
mc.makeMCMC(cfile, MCMC_cfile, logfile)
# Make transit configuration file:
mc.makeTransit(MCMC_cfile, tep_name, shareOpacity)
# Generate the opacity file if it doesn't exist:
if not os.path.isfile(opacityfile):
mu.msg(1, "Transit call to generate the Opacity grid table.")
Tcall = os.path.join(Transitdir, "transit", "transit")
subprocess.call(
["{:s} -c {:s} --justOpacity".format(Tcall, tconfig)],
shell=True,
cwd=date_dir)
else:
mu.msg(
1,
"\nTransit copies the existing opacity file from:\n '{:s}'.".
format(opacityfile),
indent=2)
shutil.copy2(opacityfile, date_dir + os.path.basename(opacityfile))
if justOpacity:
mu.msg(1, "~~ BART End (after Transit opacity calculation) ~~")
return
# Run the MCMC:
if runMCMC < 16:
MC3call = os.path.join(MC3dir, "MCcubed", "mccubed.py")
subprocess.call(["mpiexec {:s} -c {:s}".format(MC3call, MCMC_cfile)],
shell=True,
cwd=date_dir)
if walk == 'unif' and modelper > 0:
# Clean up the output directory
model_dir = os.path.join(date_dir, savemodel.replace('.npy', ''), '')
# Make directory
try:
os.mkdir(model_dir)
except OSError as e:
if e.errno == 17: # Already exists
pass
else:
mu.error("Cannot create folder '{:s}'. {:s}.".format(
model_dir, os.strerror(e.errno)))
# Move model files to subdirectory
subprocess.call(
['mv {:s} {:s}'.format('*'.join(savemodel.split('.')), model_dir)],
shell=True,
cwd=date_dir)
if plots and walk != 'unif':
# Re-plot MCMC results in prettier format
mcp.mc3plots('output.npy', burnin, thinning, nchains, uniform, molfit,
out_spec, parnames, stepsize, date_dir,
["output_trace", "output_pairwise", "output_posterior"],
fext)
# Run best-fit Transit call
mu.msg(1, "\nTransit call with the best-fitting values.")
# MCcubed output file
MCfile = date_dir + logfile
# Call bestFit submodule: make new bestFit_tconfig.cfg, run best-fit Transit
bf.callTransit(atmfile,
tep_name,
MCfile,
stepsize,
molfit,
cloud,
rayleigh,
solution,
refpress,
tconfig,
date_dir,
burnin,
abun_basic,
PTtype,
PTfunc[PTtype],
tint,
tint_type,
filters,
fext=fext)
# Plot best-fit eclipse or modulation spectrum, depending on solution:
bf.plot_bestFit_Spectrum(filters, kurucz, tep_name, solution, outspec,
data, uncert, date_dir, fext)
bestFit_atmfile = 'bestFit.atm'
# Plot abundance profiles
bf.plotabun(date_dir, bestFit_atmfile, molfit, fext)
mu.msg(1, "\nTransit call for contribution functions/transmittance.")
# Run Transit with unlimited 'toomuch' argument:
cf.cf_tconfig(date_dir)
# Call Transit with the cf_tconfig
cf_tconfig = date_dir + 'cf_tconfig.cfg'
Tcall = os.path.join(Transitdir, "transit", "transit")
subprocess.call(["{:s} -c {:s}".format(Tcall, cf_tconfig)],
shell=True,
cwd=date_dir)
# Calculate and plot contribution functions:
if solution == "eclipse":
# Compute contribution fucntions if this is a eclipse run:
mu.msg(1, "Calculating contribution functions.", indent=2)
ctfraw, ctf = cf.cf(date_dir, bestFit_atmfile, filters, fext)
else:
# Compute transmittance if this is a transmission run:
mu.msg(1, "Calculating transmittance.", indent=2)
ctf = cf.transmittance(date_dir, bestFit_atmfile, filters, fext)
# Make a plot of MCMC profiles with contribution functions/transmittance
bf.callTransit(atmfile,
tep_name,
MCfile,
stepsize,
molfit,
cloud,
rayleigh,
solution,
refpress,
tconfig,
date_dir,
burnin,
abun_basic,
PTtype,
PTfunc[PTtype],
tint,
tint_type,
filters,
ctf,
fext=fext)
mu.msg(1, "~~ BART End ~~")
