def saverdb(self, parameter_s='', local_ns=None):
""" Save current system's RV in a file """
try:
args = parse_arg_string('saverdb', parameter_s)
except DocoptExit:
print saverdb_usage.lstrip()
return
except SystemExit:
return
# use default system or user defined
try:
if 'default' in local_ns and not args['-n']:
system = local_ns['default']
else:
system_name = args['-n']
system = local_ns[system_name]
except KeyError:
from shell_colors import red
msg = red('ERROR: ') + 'Set a default system or provide a system '+\
'name with the -n option'
clogger.fatal(msg)
return
filename = args['<file>']
system.save(filename)
def demc(self, parameter_s='', local_ns=None):
""" Run the Differential Evolution MCMC. - stub"""
from shell_colors import red
## take care of arguments
try:
args = parse_arg_string('demc', parameter_s)
except DocoptExit:
print demc_usage.lstrip()
return
except SystemExit:
return
if 'default' in local_ns:
system = local_ns['default']
else:
msg = red('ERROR: ') + 'Set a default system or provide a system '+\
'name with the -n option'
clogger.fatal(msg)
return
print args
zfile = args.pop('<zipfile>')
results = core.do_demc(system, zfile=zfile, burnin=0)
return results
def mod(self, parameter_s='', local_ns=None):
""" Define the type of model that will be adjusted to the data.
Type 'mod -h' for more help
"""
from shell_colors import yellow, blue, red
args = parse_arg_string('mod', parameter_s)
if args == 1: # called without arguments, show how it's done
msg = yellow('Usage: ') + 'mod [k<n>] [d<n>]\n' + \
'Options: k<n> Number of keplerian signals\n' + \
' d<n> Degree of polynomial drift'
clogger.fatal(msg)
return
if 'default' in local_ns:
system = local_ns['default']
if system.model is None: system.model = {}
system.model['k'] = k = int(args[0][1])
system.model['d'] = d = int(args[1][1])
else:
msg = red('ERROR: ') + 'Set a default system or provide a system '+\
'name with the -n option'
clogger.fatal(msg)
return
# this should be logged?
print blue('Current model:'), k, 'kep,', d, 'drifts'
def gen(self, parameter_s='', local_ns=None):
""" Run the genetic algorithm minimization - stub """
from shell_colors import red
## take care of arguments
try:
args = parse_arg_string('gen', parameter_s)
except DocoptExit:
print de_usage.lstrip()
return
except SystemExit:
return
ngen = int(args.pop('--ngen'))
npop = int(args.pop('--npop'))
if 'default' in local_ns:
system = local_ns['default']
else:
msg = red('ERROR: ') + 'Set a default system or provide a system '+\
'name with the -n option'
clogger.fatal(msg)
return
core.do_genetic(system, npop=npop, ngen=ngen)
system.do_plot_fit()
def add_noise(self, parameter_s='', local_ns=None):
try:
args = parse_arg_string('add_noise', parameter_s)
except DocoptExit:
print addnoise_usage.lstrip()
return
except SystemExit:
return
# use default system or user defined
try:
if 'default' in local_ns and not args['-n']:
system = local_ns['default']
else:
system_name = args['-n']
system = local_ns[system_name]
except KeyError:
from shell_colors import red
msg = red('ERROR: ') + 'Set a default system or provide a system '+\
'name with the -n option'
clogger.fatal(msg)
return
# print args
noise = float(args['<number>'])
kms = system.error.mean() < 0.01
if kms:
system.error = sqrt(system.error**2 + (noise / 1000)**2)
else:
system.error = sqrt(system.error**2 + noise**2)
def wf(self, parameter_s='', local_ns=None):
""" Calculate the spectral window function of the observations.
Type 'wf -h' for more help. """
args = parse_arg_string('wf', parameter_s)
if args == 1: return
print args
# use default system or user defined
try:
if local_ns.has_key('default') and not args['-n']:
system = local_ns['default']
else:
system_name = args['-n']
system = local_ns[system_name]
except KeyError:
from shell_colors import red
msg = red('ERROR: ') + 'Set a default system or provide a system '+\
'name with the -n option'
clogger.fatal(msg)
return
try:
system.per
except AttributeError:
from shell_colors import green
clogger.debug('Calculating periodogram to get frequencies')
stdout_write('Calculating periodogram to get frequencies...')
system.per = periodograms.gls(system, hifac=5)
print green(' done')
try:
system.wf._plot()
except AttributeError:
system.wf = periodograms.SpectralWindow(system.per.freq, system.time)
def to_mps(self, parameter_s='', local_ns=None):
# Convert data to meters per second, if in km/s
from shell_colors import blue
args = parse_arg_string('to_mps', parameter_s)
# print args
# use default system or user defined
try:
if 'default' in local_ns and not args['-n']:
system = local_ns['default']
else:
system_name = args['SYSTEM']
system = local_ns[system_name]
except KeyError:
from shell_colors import red
msg = red('ERROR: ') + 'Set a default system or provide a system '+\
'name with the -n option'
clogger.fatal(msg)
return
if (min(system.error) < 0.01):
msg = blue('INFO: ') + 'Converting to m/s'
clogger.info(msg)
system.vrad = (system.vrad - mean(system.vrad)) * 1e3
system.error *= 1e3
system.units = 'm/s'
def do_plot_extras(self, extra):
""" Plot other observed quantities as a function of time.
Parameters
----------
extra: string
One of the quantities available in system.extras
"""
# import pyqtgraph as pg
colors = 'bgrcmykw' # lets hope for less than 9 data-sets
t = self.time
# handle inexistent field
if extra not in self.extras._fields:
from shell_colors import red
msg = red('ERROR: ') + 'The name "%s" is not available in extras.\n' % extra
clogger.fatal(msg)
return
i = self.extras._fields.index(extra) # index corresponding to this quantity
plt.figure()
# p = pg.plot()
plt.plot(t, self.extras[i], 'o', label=extra)
plt.xlabel('Time [days]')
plt.ylabel(extra + ' []')
plt.legend(loc='upper center', bbox_to_anchor=(0.5, 1.05))
plt.minorticks_on()
plt.tight_layout()
plt.show()
def plot(self, parameter_s='', local_ns=None):
""" Plot various quantities.
Type 'plot -h' for more help """
try:
args = parse_arg_string('plot', parameter_s)
except DocoptExit:
print plot_usage.lstrip()
return
except SystemExit:
return
# print args
# use default system or user defined
try:
if 'default' in local_ns and not args['-n']:
system = local_ns['default']
else:
system_name = args['-n']
system = local_ns[system_name]
except KeyError:
from shell_colors import red
msg = red('ERROR: ') + 'Set a default system or provide a system '+\
'name with the -n option'
clogger.fatal(msg)
return
together = False
if args['--together']:
together = True
second_quantity = args['--together']
# plot the observed radial velocities
if args['obs']:
if together: system.do_plot_obs_together(q=second_quantity, save=args['--save'])
else: system.do_plot_obs(save=args['--save'])
# plot residuals from fit
if args['resid']:
system.do_plot_resid(save=args['--save'])
# plot other quantities
extras_available = ['fwhm', 'contrast', 'bis_span', 'noise',
's_mw', 'sig_s', 'rhk', 'sig_rhk',
'sn_CaII', 'sn10', 'sn50', 'sn60']
extras_mapping = ['fwhm', 'contrast', 'bis', 'noise',
's', 's', 'rhk', 'rhk',
'sn', 'sn', 'sn', 'sn']
for i, e in enumerate(extras_available):
try:
if args[extras_mapping[i]]:
if together: system.do_plot_extras_together(e, save=args['--save'])
else: system.do_plot_extras(e, save=args['--save'])
return
except KeyError:
pass
def __init__(self, *filenames, **kwargs):
assert len(filenames)>=1, "Need at least one file to read"
# don't repeat files
filenames = unique(filenames)
# verbose?
try:
verbose = kwargs.pop('verbose')
except KeyError:
verbose = False
# skip header lines? (no by default)
try:
skip = kwargs.pop('skip')
except KeyError:
skip = 0
# in which format are the files? (drs35 by default)
try:
format = kwargs.pop('format').lower()
except (KeyError, AttributeError): # this way we also catch the default None
format = 'drs35'
# read data
try:
t, rv, err, self.provenance, extras = \
rvIO.read_rv(*filenames, verbose=verbose, skip=skip, format=format)
except ValueError:
from shell_colors import red
msg = red('ERROR: ') + 'If your files have header lines set --skip option.\n'
clogger.fatal(msg)
return
self.time, self.vrad, self.error = (t, rv, err)
# save the extra quantities as a namedtuple if we read them
if format == 'drs35': # default
extras_names = ['fwhm', 'contrast', 'bis_span', 'noise',
's_mw', 'sig_s', 'rhk', 'sig_rhk', 'sn_CaII',
'sn10', 'sn50', 'sn60']
elif format == 'drs34' or format == 'coralie':
extras_names = ['fwhm', 'contrast', 'bis_span', 'noise', 'sn10', 'sn50', 'sn60']
else:
extras_names = []
extra = namedtuple('Extra', extras_names, verbose=False)
self.extras = extra._make(extras)
self.extras_names = extras_names
# time, vrad and error can change,
# the *_full ones correspond always to the full set
self.time_full = self.time
self.vrad_full = self.vrad
self.error_full = self.error
# same for extras
self.extras_full = self.extras
def do_correlate(system, vars=(), verbose=False):
# just to be sure, but this should not pass through docopt in commands.py
if len(vars) != 2: return
var1 = vars[0]
var2 = vars[1]
# handle inexistent fields
available = system.extras._fields + ('vrad',)
if var1 not in available:
msg = red('ERROR: ') + 'The name "%s" is not available for correlation.\n' % var1
clogger.fatal(msg)
return
if var2 not in available:
msg = red('ERROR: ') + 'The name "%s" is not available for correlation.\n' % var2
clogger.fatal(msg)
return
if var1 == 'vrad':
v1 = system.vrad
else:
i = system.extras._fields.index(var1)
v1 = system.extras[i]
if var2 == 'vrad':
v2 = system.vrad
else:
i = system.extras._fields.index(var2)
v2 = system.extras[i]
pr = pearsonr(v1, v2)
sr = spearmanr(v1, v2)
if verbose:
print blue('[Pearson correlation]') + ' r=%f, p-value=%f' % pr
print blue('[Spearman correlation]') + ' r=%f, p-value=%f' % sr
# label =
figure()
plot(v1, v2, 'o')
xlabel(var1)
ylabel(var2)
tight_layout()
show()
def remove_rotation(self, parameter_s='', local_ns=None):
""" Remove rotation period and harmonics """
from shell_colors import red
try:
args = parse_arg_string('rrot', parameter_s)
except DocoptExit:
print rrot_usage.lstrip()
return
except SystemExit:
return
# use default system or user defined
try:
if 'default' in local_ns and not args['-n']:
system = local_ns['default']
else:
system_name = args['-n']
system = local_ns[system_name]
except KeyError:
from shell_colors import red
msg = red('ERROR: ') + 'Set a default system or provide a system '+\
'name with the -n option'
clogger.fatal(msg)
return
print args
prot = args['--prot']
nrem = int(args['--nrem'])
fwhm = args['fwhm']
rhk = args['rhk']
if 'default' in local_ns:
system = local_ns['default']
else:
msg = red('ERROR: ') + 'Set a default system or provide a system '+\
'name with the -n option'
clogger.fatal(msg)
return
core.do_remove_rotation(system, prot=prot, nrem=nrem, fwhm=fwhm, rhk=rhk)
def nest(self, parameter_s='', local_ns=None):
""" Start the MultiNest analysis and handle data interaction and IO """
from shell_colors import red
if local_ns.has_key('default'):
system = local_ns['default']
core.do_multinest(system)
else:
msg = red('ERROR: ') + 'Set a default system or provide a system '+\
'name with the -n option'
clogger.fatal(msg)
return
def detection_limits(self, parameter_s='', local_ns=None):
# use default system or user defined
if 'default' in local_ns:
system = local_ns['default']
else:
from shell_colors import red
msg = red('ERROR: ') + 'Set a default system or provide a system '+\
'name with the -n option'
clogger.fatal(msg)
return
core.do_detection_limits(system)
def dnest(self, parameter_s='', local_ns=None):
from shell_colors import red
if local_ns.has_key('default'):
system = local_ns['default']
else:
msg = red('ERROR: ') + 'Set a default system or provide a system '+\
'name with the -n option'
clogger.fatal(msg)
return
core.do_RJ_DNest3(system)
def genyorbit(self, parameter_s='', local_ns=None):
""" Run the genetic algorithm minimization - stub """
from shell_colors import red
if 'default' in local_ns:
system = local_ns['default']
else:
msg = red('ERROR: ') + 'Set a default system or provide a system '+\
'name with the -n option'
clogger.fatal(msg)
return
write_yorbit_macro(system)
def gen(self, parameter_s='', local_ns=None):
""" Run the genetic algorithm minimization - stub """
from shell_colors import red
if local_ns.has_key('default'):
system = local_ns['default']
core.do_genetic(system)
else:
msg = red('ERROR: ') + 'Set a default system or provide a system '+\
'name with the -n option'
clogger.fatal(msg)
return
system.do_plot_fit()
def do_fit(system, verbose):
try:
degree = system.model['d']
except TypeError:
msg = red('Error: ') + 'Need to run mod before fit. '
clogger.error(msg)
return
with warnings.catch_warnings(record=True) as w:
p = polyfit(system.time, system.vrad, degree)
if len(w):
msg = yellow('Warning: ') + 'Polyfit may be poorly conditioned. ' \
+ 'Maybe try a lower degree drift?'
clogger.info(msg)
return p
def set_fit(self, parameter_s='', local_ns=None):
from shell_colors import red
# args = parse_arg_string('fit', parameter_s)
# if args == 1: return
#print args
# verb = True if args['--verbose'] else False
if 'default' in local_ns:
system = local_ns['default']
else:
msg = red('ERROR: ') + 'Set a default system or provide a system '+\
'name with the -n option'
clogger.fatal(msg)
return
core.do_set_fit(system)
def clean(self, parameter_s='', local_ns=None):
"""
Deconvolves the LS periodogram from the window function
using the CLEAN algorithm (Roberts et al. 1985)
"""
# use default system or user defined
try:
if 'default' in local_ns:
system = local_ns['default']
except KeyError:
from shell_colors import red
msg = red('ERROR: ') + 'Set a default system or provide a system '+\
'name with the -n option'
clogger.fatal(msg)
return
core.do_clean(system)
def correlate(self, parameter_s='', local_ns=None):
from shell_colors import red
args = parse_arg_string('correlate', parameter_s)
if args == 1: return
print args
verb = True if args['--verbose'] else False
if local_ns.has_key('default'):
system = local_ns['default']
var1 = args['<var1>']
var2 = args['<var2>']
result = core.do_correlate(system, vars=(var1, var2), verbose=verb)
else:
msg = red('ERROR: ') + 'Set a default system or provide a system '+\
'name with the -n option'
clogger.fatal(msg)
return
def rotation(self, parameter_s='', local_ns=None):
""" Calculate rotation period from activity-rotation relation"""
args = parse_arg_string('rotation', parameter_s)
# print args
# use default system or user defined
try:
if 'default' in local_ns and not args['-n']:
system = local_ns['default']
else:
system_name = args['SYSTEM']
system = local_ns[system_name]
except KeyError:
from shell_colors import red
msg = red('ERROR: ') + 'Set a default system or provide a system '+\
'name with the -n option'
clogger.fatal(msg)
return
core.get_rotation_period(system)
def lowpass(self, parameter_s='', local_ns=None):
from shell_colors import blue
# try:
# args = parse_arg_string('add_noise', parameter_s)
# except DocoptExit:
# print addnoise_usage.lstrip()
# return
# except SystemExit:
# return
# use default system or user defined
try:
system = local_ns['default']
except KeyError:
from shell_colors import red
msg = red('ERROR: ') + 'Set a default system or provide a system '+\
'name with the -n option'
clogger.fatal(msg)
return
core.do_lowpass_filter(system)
def fit(self, parameter_s='', local_ns=None):
from shell_colors import red
args = parse_arg_string('fit', parameter_s)
if args == 1: return
print args
verb = True if args['--verbose'] else False
if local_ns.has_key('default'):
system = local_ns['default']
result = core.do_fit(system, verb)
if result is not None:
system.model['drift'] = result
if verb: print 'Coeff:', result
system.do_plot_drift()
else:
return
else:
msg = red('ERROR: ') + 'Set a default system or provide a system '+\
'name with the -n option'
clogger.fatal(msg)
return
def correlate(self, parameter_s='', local_ns=None):
from shell_colors import red
args = parse_arg_string('correlate', parameter_s)
if args == 1: return
#print args
verb = args['--verbose']
rem = args['--remove']
chunks = args['--chunks']
if 'default' in local_ns:
system = local_ns['default']
else:
msg = red('ERROR: ') + 'Set a default system or provide a system '+\
'name with the -n option'
clogger.fatal(msg)
return
var1 = args['<var1>']
var2 = args['<var2>']
result = core.do_correlate(system, vars=(var1, var2), verbose=verb, remove=rem, chunks=chunks)
def dawfab(self, parameter_s='', local_ns=None):
""" Run the Dawson Fabrycky algorithm to search for aliases.
Type 'dawfab -h' for more help. """
args = parse_arg_string('dawfab', parameter_s)
if args == 1: return
#print args
# use default system or user defined
try:
if 'default' in local_ns and not args['-n']:
system = local_ns['default']
else:
system_name = args['-n']
system = local_ns[system_name]
except KeyError:
from shell_colors import red
msg = red('ERROR: ') + 'Set a default system or provide a system '+\
'name with the -n option'
clogger.fatal(msg)
return
core.do_Dawson_Fabrycky(system)
return
def per(self, parameter_s='', local_ns=None):
""" Calculate periodograms of various quantities.
Type 'per -h' for more help. """
from shell_colors import red
try:
args = parse_arg_string('per', parameter_s)
except DocoptExit:
print per_usage.lstrip()
return
except SystemExit:
return
# print args
if args['--describe']:
print periodograms.help_text
return
# use default system or user defined
try:
if 'default' in local_ns and not args['-n']:
system = local_ns['default']
else:
system_name = args['-n']
system = local_ns[system_name]
except KeyError:
msg = red('ERROR: ') + 'Set a default system or provide a system '+\
'name with the -n option'
clogger.fatal(msg)
return
# verb = True if args['--verbose'] else False
hf = float(args.pop('--hifac'))
of = float(args.pop('--ofac'))
fap = args['--fap']
bfap = args['--bfap']
showplot = not args['--noplot']
# which periodogram should be calculated?
per_fcn = None
if args['--hoef']:
per_fcn = periodograms.hoeffding
name = 'Hoeffding'
elif args['--bgls']:
per_fcn = periodograms.bgls
name = 'Bayesian Generalized Lomb-Scargle'
elif args['--bayes']:
per_fcn = periodograms.bls
name = 'Bayesian Lomb-Scargle'
elif args['--ls']:
per_fcn = periodograms.ls_PressRybicki
name = 'Lomb Scargle'
elif args['--multiband']:
per_fcn = periodograms.MultiBandGLS
name = 'Multiband Lomb-Scargle'
tempmask = system.time > 57170
if (~tempmask).all():
msg = red('ERROR: ') + 'All observations are before 57170. Multiband periodogram is not appropriate'
clogger.fatal(msg)
return
elif args['--gls']:
per_fcn = periodograms.gls
name ='Generalized Lomb-Scargle'
# this is the default if user did not specify arguments
else:
per_fcn = periodograms.gls
name ='Generalized Lomb-Scargle'
if args['obs']: # periodogram of the observed RVs
try:
# are we forced to recalculate it?
if args['--force']: raise AttributeError
# it was calculated already?
system.per
# the same periodogram?
if system.per.name != name:
raise AttributeError
# system.per._output(verbose=verb) # not ready
if showplot:
system.per._plot(doFAP=fap, dobFAP=bfap, save=args['--save'])
except AttributeError:
system.per = per_fcn(system, hifac=hf, ofac=of)
# system.per._output(verbose=verb) # not ready
if showplot:
system.per._plot(doFAP=fap, dobFAP=bfap, save=args['--save'])
if args['bis']: # periodogram of the CCF's Bisector Inverse Slope
system.bis_per = per_fcn(system, hifac=hf, ofac=of, quantity='bis')
if showplot:
system.bis_per._plot(doFAP=fap, dobFAP=bfap, save=args['--save'])
if args['fwhm']: # periodogram of the CCF's fwhm
system.fwhm_per = per_fcn(system, hifac=hf, ofac=of, quantity='fwhm')
if showplot:
system.fwhm_per._plot(doFAP=fap, dobFAP=bfap, save=args['--save'])
if args['rhk']: # periodogram of rhk
system.rhk_per = per_fcn(system, hifac=hf, ofac=of, quantity='rhk')
if showplot:
system.rhk_per._plot(doFAP=fap, dobFAP=bfap, save=args['--save'])
if args['contrast']: # periodogram of contrast
system.contrast_per = per_fcn(system, hifac=hf, ofac=of, quantity='contrast')
if showplot:
system.contrast_per._plot(doFAP=fap, dobFAP=bfap, save=args['--save'])
if args['resid']: # periodogram of the residuals of the current fit
system.resid_per = per_fcn(system, hifac=hf, ofac=of, quantity='resid')
if showplot:
system.resid_per._plot(doFAP=fap, dobFAP=bfap)
def do_genetic(system, just_gen=False):
""" Carry out the fit using a genetic algorithm and if
just_gen=False try to improve it with a run of the LM algorithm """
try:
degree = system.model['d']
keplerians = system.model['k']
except TypeError:
msg = red('Error: ') + 'Need to run mod before gen. '
clogger.error(msg)
return
maxP = system.per.get_peaks(output_period=True)[1]
size_maxP = 10**(len(str(int(maxP)))-1)
system.fit = {}
msg = blue('INFO: ') + 'Initializing genetic algorithm...'
clogger.info(msg)
msg = blue(' : ') + 'Model is: %d keplerians + %d drift' % (keplerians, degree)
clogger.info(msg)
vel = zeros_like(system.time)
def chi2_1(individual):
""" Fitness function for 1 planet model """
P, K, ecc, omega, T0, gam = individual
get_rvn(system.time, P, K, ecc, omega, T0, gam, vel)
chi2 = sum(((system.vrad - vel)/system.error)**2)
#print chi2
return chi2,
def chi2_n(individual):
""" Fitness function for N planet model """
P, K, ecc, omega, T0, gam = [individual[i::6] for i in range(6)]
#print ecc
get_rvn(system.time, P, K, ecc, omega, T0, gam[0], vel)
#print 'out of get_rvn'
chi2 = sum(((system.vrad - vel)/system.error)**2)
#print chi2
return chi2,
## create the required types -- the fitness and the individual.
creator.create("FitnessMin", base.Fitness, weights=(-1.0,)) # minimization of a single objective
creator.create("Individual", list, fitness=creator.FitnessMin)
## create parameters by sampling from their priors
def P_prior():
return random.uniform(5, 1000)
# return random.gauss(maxP, size_maxP)
def K_prior():
return random.uniform(0, 150)
def ecc_prior():
return random.uniform(0, 0.9)
def om_prior():
return random.uniform(0, 360)
def t0_prior():
return random.uniform(2350000, 2550000)
def gamma_prior():
return random.uniform(-100, 100)
priors = [P_prior, K_prior, ecc_prior, om_prior, t0_prior, gamma_prior]
toolbox = base.Toolbox()
toolbox.register("individual", tools.initCycle, creator.Individual, priors, n=keplerians)
toolbox.register("population", tools.initRepeat, list, toolbox.individual)
def mutPrior(individual, indpb):
for i, fcn in enumerate(zip(individual, priors)):
if random.random() < indpb:
individual[i] = fcn[1]()
return individual,
toolbox.register("evaluate", chi2_n)
toolbox.register("mate", tools.cxTwoPoints)
toolbox.register("mutate", mutPrior, indpb=0.10)
toolbox.register("select", tools.selTournament, tournsize=3)
npop = 500
ngen = 150
npar = 5*keplerians+1
## build the population
pop = toolbox.population(n=npop)
## helper functions
hof = tools.HallOfFame(1)
stats = tools.Statistics(lambda ind: ind.fitness.values)
stats.register("avg", nanmean)
# stats.register("std", nanstd)
stats.register("min", np.nanmin)
# stats.register("max", np.nanmax)
# stats.register("total", sigma3)
stats.register("red", lambda v: min(v)/(len(system.time)-npar) )
msg = blue('INFO: ') + 'Created population with N=%d. Going to evolve for %d generations...' % (npop,ngen)
clogger.info(msg)
## run the genetic algorithm
algorithms.eaSimple(pop, toolbox, cxpb=0.5, mutpb=0.2, ngen=ngen, stats=stats, halloffame=hof, verbose=True)
## output results information
msg = yellow('RESULT: ') + 'Best individual is'
clogger.info(msg)
## loop over planets
print("%3s %12s %10s %10s %10s %15s %9s" % \
('', 'P[days]', 'K[km/s]', 'e', unichr(0x3c9).encode('utf-8')+'[deg]', 'T0[days]', 'gam') )
for i, planet in enumerate(list(ascii_lowercase)[:keplerians]):
P, K, ecc, omega, T0, gam = [hof[0][j::6] for j in range(6)]
print("%3s %12.1f %10.2f %10.2f %10.2f %15.2f %9.2f" % (planet, P[i], K[i], ecc[i], omega[i], T0[i], gam[i]) )
msg = yellow('RESULT: ') + 'Best fitness value: %s\n' % (hof[0].fitness)
clogger.info(msg)
if just_gen:
# save fit in the system and return, no need for LM
system.fit['params'] = hof[0]
system.fit['chi2'] = hof[0].fitness/(len(system.time)-npar)
return
msg = blue('INFO: ') + 'Calling LM to improve result...'
clogger.info(msg)
## call levenberg markardt fit
lm = do_lm(system, [hof[0][j::6] for j in range(6)])
lm_par = lm[0]
## loop over planets
msg = yellow('RESULT: ') + 'Best fit is'
clogger.info(msg)
print("%3s %12s %10s %10s %10s %15s %9s" % \
('', 'P[days]', 'K[km/s]', 'e', unichr(0x3c9).encode('utf-8')+'[deg]', 'T0[days]', 'gam') )
for i, planet in enumerate(list(ascii_lowercase)[:keplerians]):
P, K, ecc, omega, T0, gam = [lm_par[j::6] for j in range(6)]
print("%3s %12.1f %10.2f %10.2f %10.2f %15.2f %9.2f" % (planet, P[i], K[i], ecc[i], omega[i], T0[i], gam[i]) )
chi2 = chi2_n(lm_par)[0]
msg = yellow('RESULT: ') + 'Best fitness value: %f, %f' % (chi2, chi2/(len(system.time)-npar))
clogger.info(msg)
# save fit in the system
system.fit['params'] = lm_par
system.fit['chi2'] = chi2
# # print p.minFitness, p.maxFitness, p.avgFitness, p.sumFitness
# print 'Genetic:', p.bestFitIndividual, p.bestFitIndividual.fitness
# lm = do_lm(system, p.bestFitIndividual.genes)
# lm_par = lm[0]
# print 'LM:', lm_par
# # get best solution curve
# new_time = system.get_time_to_plot()
# vel = zeros_like(new_time)
# P, K, ecc, omega, t0 = p.bestFitIndividual.genes
# get_rv(new_time, P, K, ecc, omega, t0, vel)
# # plot RV with time
# plot(system.time, system.vrad, 'o')
# plot(new_time, vel, '-')
# P, K, ecc, omega, t0 = lm_par
# get_rv(new_time, P, K, ecc, omega, t0, vel)
# plot(new_time, vel, 'r-')
# show()
return
def nest(self, parameter_s='', local_ns=None):
""" Start the MultiNest analysis and handle data interaction and IO """
from shell_colors import red
try:
args = parse_arg_string('nest', parameter_s)
except DocoptExit:
print nest_usage.lstrip()
return
except SystemExit:
return
# print args
if 'default' in local_ns:
system = local_ns['default']
else:
msg = red('ERROR: ') + 'Set a default system or provide a system '+\
'name with the -n option'
clogger.fatal(msg)
return
user = args['-u']
resume = args['-r']
verbose = args['-v']
gp = args['--gp']
jitter = args['--jitter']
if gp and jitter:
msg = red('ERROR: ') + '--gp and --jitter are incompatible'
clogger.fatal(msg)
return
doplot = not args['--noplot']
saveplot = args['--saveplot']
dofeedback = args['--feed']
doMAPfeedback = args['--MAPfeed']
maxp = int(args['--maxp'])
restart = args['--restart']
nml_path = args['--nml']
startp = args['--startp']
if startp is not None:
startp = [int(i) for i in startp.split(',')]
else:
startp = []
try:
ncpu = int(args['--ncpu'])
except TypeError:
ncpu = None
train_quantity = args['--train'] if bool(args['--train']) else None
skip_train_mcmc = args['--skip-mcmc']
lin_quantity = args['--lin'] if bool(args['--lin']) else None
if bool(args['--train']) and not system.is_in_extras(train_quantity):
msg = red('ERROR: ') + 'The name "%s" is not available in extras.\n' % train_quantity
clogger.fatal(msg)
return
core.do_multinest(system, user, gp, jitter, maxp=maxp,
resume=resume, ncpu=ncpu, verbose=verbose,
training=train_quantity, skip_train_mcmc=skip_train_mcmc, lin=lin_quantity,
doplot=doplot, saveplot=saveplot, feed=dofeedback, MAPfeed=doMAPfeedback,
restart=restart, nml=nml_path, startp=startp)
def restrict(self, parameter_s='', local_ns=None):
""" Select data based on date, SNR or radial velocity accuracy.
Type 'restrict -h' for more help
"""
from shell_colors import yellow, blue, red
args = parse_arg_string('restrict', parameter_s)
if args == DocoptExit:
msg = yellow('Warning: ') + "I'm not doing anything. Type restrict -h for help"
clogger.fatal(msg)
return
# use default system or user defined
if 'default' in local_ns:
system = local_ns['default']
else:
msg = red('ERROR: ') + 'Set a default system or provide a system '+\
'name with the -n option'
clogger.fatal(msg)
return
if args['err']:
try:
maxerr = float(args['<maxerr>'])
except ValueError:
msg = red('ERROR: ') + 'maxerr shoud be a number!'
clogger.fatal(msg)
return
core.do_restrict(system, 'error', maxerr)
if args['sn']:
try:
maxsn = float(args['<maxsn>'])
except ValueError:
msg = red('ERROR: ') + 'maxsn shoud be a number!'
clogger.fatal(msg)
return
core.do_restrict(system, 'sn', maxsn)
if args['jd']:
try:
maxjd = int(args['<maxjd>'])
minjd = int(args['<minjd>'])
except ValueError:
msg = red('ERROR: ') + 'minjd and maxjd shoud be integer numbers!'
clogger.fatal(msg)
return
core.do_restrict(system, 'date', minjd, maxjd)
if args['year']:
try:
yr = int(args['<yr>'])
except ValueError:
msg = red('ERROR: ') + 'yr shoud be a number!'
clogger.fatal(msg)
return
core.do_restrict(system, 'year', yr)
if args['years']:
try:
yr1 = int(args['<yr1>'])
yr2 = int(args['<yr2>'])
except ValueError:
msg = red('ERROR: ') + 'yr1 and yr2 shoud be numbers!'
clogger.fatal(msg)
return
core.do_restrict(system, 'years', yr1, yr2)
if args['--gui']:
core.do_restrict(system, 'gui')
if args['--index']:
core.do_restrict(system, 'index', args['--index'], noask=args['--noask'])