# pmin, pmax, stepsize, prior, priorlow, and priorup arrays can be
# read from a text file. In this case, set the argument to be the file name.
# Each line in the 'indparams' file must contain one element of the indparams
# list, the values separated by (one or more) empty spaces.
# The other files must contain one array value per line (i.e., column-wise).
# Furthermore, the 'data' file can also contain the uncert array (as a second
# column, values separated by a empty space).
# Likewise, the 'params' file can contain the pmin, pmax, stepsize, prior,
# priorlow, and priorup arrays (as many or as few, provided that they are
# written in columns in that precise order).
# The mcutils module provides the function 'writedata' to easily make these
# files in the required format, for example:
mu.writebin([data, uncert], 'data_ex01.dat')
mu.writebin(indparams, 'indp_ex01.dat')
mu.writedata([params, pmin, pmax, stepsize], 'pars_ex01.dat')
# Check them out. These files can contain empty or comment lines without
# interfering with the routine.
# Set the arguments to the file names:
data = 'data_ex01.dat'
params = 'pars_ex01.dat'
indparams = 'indp_ex01.dat'
# Run MCMC:
allp, bp = mc3.mcmc(data=data,
func=func,
indparams=indparams,
params=params,
numit=numit,
def mcmc(data=None,
uncert=None,
func=None,
indparams=None,
params=None,
pmin=None,
pmax=None,
stepsize=None,
prior=None,
priorlow=None,
priorup=None,
numit=None,
nchains=None,
walk=None,
wlike=None,
leastsq=None,
chisqscale=None,
grtest=None,
burnin=None,
thinning=None,
plots=None,
savefile=None,
savemodel=None,
mpi=None,
resume=None,
logfile=None,
rms=None,
cfile=False):
"""
MCMC wrapper for interactive session.
Parameters:
-----------
data: 1D ndarray or string
The data array to be fitted or string with the filename where the data
array is stored (See Note 3).
uncert: string or 1D ndarray
uncertainty array of data or string with the filename where the uncert
array is stored (See Note 3).
func: Callable or string-iterable
The callable function that models data as:
model = func(params, *indparams)
Or an iterable (list, tuple, or ndarray) of 3 strings:
(funcname, modulename, path)
that specify the function name, function module, and module path.
If the module is already in the python-path scope, path can be omitted.
indparams: Tuple of 1D ndarrays or string
Tuple with additional arguments required by func (one argument per tuple
element) or filename where indparams is stored (See Note 4).
params: 1D or 2D ndarray or string
Array of initial fitting parameters for func. If 2D, of shape
(nparams, nchains), it is assumed that it is one set for each chain.
Or string with filename where params is stored (See Note 3).
pmin: 1D ndarray or string
Array with lower boundaries of the posteriors or string with filename
where pmin is stored (See Note 3).
pmax: 1D ndarray or string
Array of upper boundaries of the posteriors or string with filename
where pmax is stored (See Note 3).
stepsize: 1D ndarray or string
Array of proposal jump scales or string with filename where stepsize
array is stored (See Notes 1, 3).
prior: 1D ndarray or string
Array of parameter prior distribution means or string with filename
where the prior array is stored (See Note 2, 3).
priorlow: 1D ndarray or string
Array of lower prior uncertainty values or string with filename
where priorlow is stored (See Note 2, 3).
priorup: 1D ndarray or string
Array of upper prior uncertainty values or string with filename
where priorup is stored (See Note 2, 3).
numit: Scalar
Total number of iterations.
nchains: Scalar
Number of simultaneous chains to run.
walk: String
Random walk algorithm:
- 'mrw': Metropolis random walk.
- 'demc': Differential Evolution Markov chain.
wlike: Boolean
Calculate the likelihood in a wavelet base.
leastsq: Boolean
Perform a least-square minimization before the MCMC run.
chisqscale: Boolean
Scale the data uncertainties such that the reduced chi-squared = 1.
grtest: Boolean
Run Gelman & Rubin test.
burnin: Scalar
Burned-in (discarded) number of iterations at the beginning
of the chains.
thinning: Integer
Thinning factor of the chains (use every thinning-th iteration) used
in the GR test and plots.
plots: Boolean
If True plot parameter traces, pairwise-posteriors, and posterior
histograms.
savefile: String
If not None, filename to store allparams (with np.save).
savemodel: String
If not None, filename to store the values of the evaluated function
(with np.save).
mpi: Boolean
If True run under MPI multiprocessing protocol.
resume: Boolean
If True, resume a previous run (load outputs).
logfile: String
Filename to write log.
rms: Boolean
If True, calculate the RMS of data-bestmodel.
cfile: String
Configuration file name.
Returns:
--------
allparams: 2D ndarray
An array of shape (nfree, numit-nchains*burnin) with the MCMC
posterior distribution of the fitting parameters.
bestp: 1D ndarray
Array of the best fitting parameters.
Notes:
------
1.- If a value is 0, keep the parameter fixed.
To set one parameter equal to another, set its stepsize to the
negative index in params (Starting the count from 1); e.g.: to set
the second parameter equal to the first one, do: stepsize[1] = -1.
2.- If any of the fitting parameters has a prior estimate, e.g.,
param[i] = p0 +up/-low,
with up and low the 1sigma uncertainties. This information can be
considered in the MCMC run by setting:
prior[i] = p0
priorup[i] = up
priorlow[i] = low
All three: prior, priorup, and priorlow must be set and, furthermore,
priorup and priorlow must be > 0 to be considered as prior.
3.- If data, uncert, params, pmin, pmax, stepsize, prior, priorlow,
or priorup are set as filenames, the file must contain one value per
line.
For simplicity, the data file can hold both data and uncert arrays.
In this case, each line contains one value from each array per line,
separated by an empty-space character.
Similarly, params can hold: params, pmin, pmax, stepsize, priorlow,
and priorup. The file can hold as few or as many array as long as
they are provided in that exact order.
4.- An indparams file works differently, the file will be interpreted
as a list of arguments, one in each line. If there is more than one
element per line (empty-space separated), it will be interpreted as
an array.
5.- See the real MCMC code in:
https://github.com/pcubillos/demc/tree/master/src/mcmc.py
Examples:
---------
>>> # See examples in: https://github.com/pcubillos/demc/tree/master/examples
Modification History:
---------------------
2014-05-02 patricio Initial implementation.
2014-05-26 patricio Call now mc3.main with subprocess.
2014-10-15 patricio Addded savemodel argument.
2015-05-15 patricio Added logfile argument.
"""
sys.argv = ['ipython']
try:
# Store arguments in a dict:
piargs = {}
piargs.update({'data': data})
piargs.update({'uncert': uncert})
piargs.update({'func': func})
piargs.update({'indparams': indparams})
piargs.update({'params': params})
piargs.update({'pmin': pmin})
piargs.update({'pmax': pmax})
piargs.update({'stepsize': stepsize})
piargs.update({'prior': prior})
piargs.update({'priorlow': priorlow})
piargs.update({'priorup': priorup})
piargs.update({'numit': numit})
piargs.update({'nchains': nchains})
piargs.update({'walk': walk})
piargs.update({'wlike': wlike})
piargs.update({'leastsq': leastsq})
piargs.update({'chisqscale': chisqscale})
piargs.update({'grtest': grtest})
piargs.update({'burnin': burnin})
piargs.update({'thinning': thinning})
piargs.update({'plots': plots})
piargs.update({'savefile': savefile})
piargs.update({'savemodel': savemodel})
piargs.update({'mpi': mpi})
piargs.update({'resume': resume})
piargs.update({'logfile': logfile})
piargs.update({'rms': rms})
# Remove None values:
for key in piargs.keys():
if piargs[key] is None:
piargs.pop(key)
# Temporary files:
tmpfiles = []
# Open ConfigParser:
config = ConfigParser.SafeConfigParser()
if not cfile:
config.add_section('MCMC') # Start new config file
else:
config.read(cfile) # Read from existing config file
# Store arguments in configuration file:
for key in piargs.keys():
value = piargs[key]
# Func:
if key == 'func':
if callable(func):
funcfile = func.__globals__['__file__']
funcpath = funcfile[:funcfile.rfind('/')]
config.set(
'MCMC', key, "%s %s %s" %
(func.__name__, func.__module__, funcpath))
else:
config.set('MCMC', key, " ".join(func))
# Arrays:
elif key in [
'data', 'uncert', 'indparams', 'params', 'pmin', 'pmax',
'stepsize', 'prior', 'priorlow', 'priorup'
]:
if isinstance(value, str):
config.set('MCMC', key, value)
else:
arrfile = "temp_mc3_mpi_%s.dat" % key # Set file name to store array
if key in ['data', 'uncert']:
mu.writebin([value], arrfile) # Write array into file
elif key in ['indparams']:
mu.writebin(value, arrfile)
else:
mu.writedata(value, arrfile)
config.set('MCMC', key, arrfile) # Set filename in config
tmpfiles.append(arrfile)
# Everything else:
else:
config.set('MCMC', key, str(value))
# Get/set the output file:
if piargs.has_key('savefile'):
savefile = piargs['savefile']
elif config.has_option('MCMC', 'savefile'):
savefile = config.get('MCMC', 'savefile')
else:
savefile = 'temp_mc3_mpi_savefile.npy'
config.set('MCMC', 'savefile', savefile)
tmpfiles.append(savefile)
if config.has_option('MCMC', 'logfile'):
logfile = config.get('MCMC', 'logfile')
else:
logfile = 'temp_mc3_mpi_logfile.npy'
config.set('MCMC', 'logfile', logfile)
tmpfiles.append(logfile)
# Save the configuration file:
cfile = 'temp_mc3_mpi_configfile.cfg'
tmpfiles.append(cfile)
with open(cfile, 'wb') as configfile:
config.write(configfile)
piargs.update({'cfile': cfile})
# Call main:
call = "mpirun {:s} -c {:s}".format(
os.path.realpath(__file__).rstrip("c"), cfile)
subprocess.call([call], shell=True)
# Read output:
allp = np.load(savefile)
nchains, nfree, niter = np.shape(allp)
# Get best-fitting values:
with open(logfile, 'r') as lfile:
lines = lfile.readlines()
# Find where the data starts and ends:
for ini in np.arange(len(lines)):
if lines[ini].startswith(' Best-fit params'):
break
# Also find the burnin iterations:
if lines[ini].startswith(' Burned'):
burnin = int(lines[ini].split()[-1])
ini += 1
# Read data:
bestp = np.zeros(nfree, np.double)
for i in np.arange(ini, ini + nfree):
bestp[i - ini] = lines[i].split()[0]
# Stack together the chains:
allstack = allp[0, :, burnin:]
for c in np.arange(1, nchains):
allstack = np.hstack((allstack, allp[c, :, burnin:]))
# Remove temporary files:
for file in tmpfiles:
os.remove(file)
return allstack, bestp
except SystemExit:
pass
# pmin, pmax, stepsize, prior, priorlow, and priorup arrays can be
# read from a text file. In this case, set the argument to be the file name.
# Each line in the 'indparams' file must contain one element of the indparams
# list, the values separated by (one or more) empty spaces.
# The other files must contain one array value per line (i.e., column-wise).
# Furthermore, the 'data' file can also contain the uncert array (as a second
# column, values separated by a empty space).
# Likewise, the 'params' file can contain the pmin, pmax, stepsize, prior,
# priorlow, and priorup arrays (as many or as few, provided that they are
# written in columns in that precise order).
# The mcutils module provides the function 'writedata' to easily make these
# files in the required format, for example:
mu.writebin([data, uncert], 'data_ex01.dat')
mu.writebin(indparams, 'indp_ex01.dat')
mu.writedata([params, pmin, pmax, stepsize], 'pars_ex01.dat')
# Check them out. These files can contain empty or comment lines without
# interfering with the routine.
# Set the arguments to the file names:
data = 'data_ex01.dat'
params = 'pars_ex01.dat'
indparams = 'indp_ex01.dat'
# Run MCMC:
allp, bp = mc3.mcmc(data=data, func=func, indparams=indparams,
params=params,
numit=numit, nchains=nchains, walk=walk, grtest=grtest,
burnin=burnin, plots=plots, savefile=savefile)
def mcmc(data=None, uncert=None, func=None, indparams=None,
params=None, pmin=None, pmax=None, stepsize=None,
prior=None, priorlow=None, priorup=None,
numit=None, nchains=None, walk=None, wlike=None,
leastsq=None, chisqscale=None, grtest=None, burnin=None,
thinning=None, plots=None, savefile=None, savemodel=None,
mpi=None, resume=None, logfile=None, rms=None,
cfile=False):
"""
MCMC wrapper for interactive session.
Parameters:
-----------
data: 1D ndarray or string
The data array to be fitted or string with the filename where the data
array is stored (See Note 3).
uncert: string or 1D ndarray
uncertainty array of data or string with the filename where the uncert
array is stored (See Note 3).
func: Callable or string-iterable
The callable function that models data as:
model = func(params, *indparams)
Or an iterable (list, tuple, or ndarray) of 3 strings:
(funcname, modulename, path)
that specify the function name, function module, and module path.
If the module is already in the python-path scope, path can be omitted.
indparams: Tuple of 1D ndarrays or string
Tuple with additional arguments required by func (one argument per tuple
element) or filename where indparams is stored (See Note 4).
params: 1D or 2D ndarray or string
Array of initial fitting parameters for func. If 2D, of shape
(nparams, nchains), it is assumed that it is one set for each chain.
Or string with filename where params is stored (See Note 3).
pmin: 1D ndarray or string
Array with lower boundaries of the posteriors or string with filename
where pmin is stored (See Note 3).
pmax: 1D ndarray or string
Array of upper boundaries of the posteriors or string with filename
where pmax is stored (See Note 3).
stepsize: 1D ndarray or string
Array of proposal jump scales or string with filename where stepsize
array is stored (See Notes 1, 3).
prior: 1D ndarray or string
Array of parameter prior distribution means or string with filename
where the prior array is stored (See Note 2, 3).
priorlow: 1D ndarray or string
Array of lower prior uncertainty values or string with filename
where priorlow is stored (See Note 2, 3).
priorup: 1D ndarray or string
Array of upper prior uncertainty values or string with filename
where priorup is stored (See Note 2, 3).
numit: Scalar
Total number of iterations.
nchains: Scalar
Number of simultaneous chains to run.
walk: String
Random walk algorithm:
- 'mrw': Metropolis random walk.
- 'demc': Differential Evolution Markov chain.
wlike: Boolean
Calculate the likelihood in a wavelet base.
leastsq: Boolean
Perform a least-square minimization before the MCMC run.
chisqscale: Boolean
Scale the data uncertainties such that the reduced chi-squared = 1.
grtest: Boolean
Run Gelman & Rubin test.
burnin: Scalar
Burned-in (discarded) number of iterations at the beginning
of the chains.
thinning: Integer
Thinning factor of the chains (use every thinning-th iteration) used
in the GR test and plots.
plots: Boolean
If True plot parameter traces, pairwise-posteriors, and posterior
histograms.
savefile: String
If not None, filename to store allparams (with np.save).
savemodel: String
If not None, filename to store the values of the evaluated function
(with np.save).
mpi: Boolean
If True run under MPI multiprocessing protocol.
resume: Boolean
If True, resume a previous run (load outputs).
logfile: String
Filename to write log.
rms: Boolean
If True, calculate the RMS of data-bestmodel.
cfile: String
Configuration file name.
Returns:
--------
allparams: 2D ndarray
An array of shape (nfree, numit-nchains*burnin) with the MCMC
posterior distribution of the fitting parameters.
bestp: 1D ndarray
Array of the best fitting parameters.
Notes:
------
1.- If a value is 0, keep the parameter fixed.
To set one parameter equal to another, set its stepsize to the
negative index in params (Starting the count from 1); e.g.: to set
the second parameter equal to the first one, do: stepsize[1] = -1.
2.- If any of the fitting parameters has a prior estimate, e.g.,
param[i] = p0 +up/-low,
with up and low the 1sigma uncertainties. This information can be
considered in the MCMC run by setting:
prior[i] = p0
priorup[i] = up
priorlow[i] = low
All three: prior, priorup, and priorlow must be set and, furthermore,
priorup and priorlow must be > 0 to be considered as prior.
3.- If data, uncert, params, pmin, pmax, stepsize, prior, priorlow,
or priorup are set as filenames, the file must contain one value per
line.
For simplicity, the data file can hold both data and uncert arrays.
In this case, each line contains one value from each array per line,
separated by an empty-space character.
Similarly, params can hold: params, pmin, pmax, stepsize, priorlow,
and priorup. The file can hold as few or as many array as long as
they are provided in that exact order.
4.- An indparams file works differently, the file will be interpreted
as a list of arguments, one in each line. If there is more than one
element per line (empty-space separated), it will be interpreted as
an array.
5.- See the real MCMC code in:
https://github.com/pcubillos/demc/tree/master/src/mcmc.py
Examples:
---------
>>> # See examples in: https://github.com/pcubillos/demc/tree/master/examples
Modification History:
---------------------
2014-05-02 patricio Initial implementation.
2014-05-26 patricio Call now mc3.main with subprocess.
2014-10-15 patricio Addded savemodel argument.
2015-05-15 patricio Added logfile argument.
"""
sys.argv = ['ipython']
try:
# Store arguments in a dict:
piargs = {}
piargs.update({'data': data})
piargs.update({'uncert': uncert})
piargs.update({'func': func})
piargs.update({'indparams':indparams})
piargs.update({'params': params})
piargs.update({'pmin': pmin})
piargs.update({'pmax': pmax})
piargs.update({'stepsize': stepsize})
piargs.update({'prior': prior})
piargs.update({'priorlow': priorlow})
piargs.update({'priorup': priorup})
piargs.update({'numit': numit})
piargs.update({'nchains': nchains})
piargs.update({'walk': walk})
piargs.update({'wlike': wlike})
piargs.update({'leastsq': leastsq})
piargs.update({'chisqscale': chisqscale})
piargs.update({'grtest': grtest})
piargs.update({'burnin': burnin})
piargs.update({'thinning': thinning})
piargs.update({'plots': plots})
piargs.update({'savefile': savefile})
piargs.update({'savemodel': savemodel})
piargs.update({'mpi': mpi})
piargs.update({'resume': resume})
piargs.update({'logfile': logfile})
piargs.update({'rms': rms})
# Remove None values:
for key in piargs.keys():
if piargs[key] is None:
piargs.pop(key)
# Temporary files:
tmpfiles = []
# Open ConfigParser:
config = ConfigParser.SafeConfigParser()
if not cfile:
config.add_section('MCMC') # Start new config file
else:
config.read(cfile) # Read from existing config file
# Store arguments in configuration file:
for key in piargs.keys():
value = piargs[key]
# Func:
if key == 'func':
if callable(func):
funcfile = func.__globals__['__file__']
funcpath = funcfile[:funcfile.rfind('/')]
config.set('MCMC', key, "%s %s %s"%(func.__name__,
func.__module__, funcpath))
else:
config.set('MCMC', key, " ".join(func))
# Arrays:
elif key in ['data', 'uncert', 'indparams', 'params', 'pmin', 'pmax',
'stepsize', 'prior', 'priorlow', 'priorup']:
if isinstance(value, str):
config.set('MCMC', key, value)
else:
arrfile = "temp_mc3_mpi_%s.dat"%key # Set file name to store array
if key in ['data', 'uncert']:
mu.writebin([value], arrfile) # Write array into file
elif key in ['indparams']:
mu.writebin(value, arrfile)
else:
mu.writedata(value, arrfile)
config.set('MCMC', key, arrfile) # Set filename in config
tmpfiles.append(arrfile)
# Everything else:
else:
config.set('MCMC', key, str(value))
# Get/set the output file:
if piargs.has_key('savefile'):
savefile = piargs['savefile']
elif config.has_option('MCMC', 'savefile'):
savefile = config.get('MCMC', 'savefile')
else:
savefile = 'temp_mc3_mpi_savefile.npy'
config.set('MCMC', 'savefile', savefile)
tmpfiles.append(savefile)
if config.has_option('MCMC', 'logfile'):
logfile = config.get('MCMC', 'logfile')
else:
logfile = 'temp_mc3_mpi_logfile.npy'
config.set('MCMC', 'logfile', logfile)
tmpfiles.append(logfile)
# Save the configuration file:
cfile = 'temp_mc3_mpi_configfile.cfg'
tmpfiles.append(cfile)
with open(cfile, 'wb') as configfile:
config.write(configfile)
piargs.update({'cfile':cfile})
# Call main:
call = "mpirun {:s} -c {:s}".format(os.path.realpath(__file__).rstrip("c"),
cfile)
subprocess.call([call], shell=True)
# Read output:
allp = np.load(savefile)
nchains, nfree, niter = np.shape(allp)
# Get best-fitting values:
with open(logfile, 'r') as lfile:
lines = lfile.readlines()
# Find where the data starts and ends:
for ini in np.arange(len(lines)):
if lines[ini].startswith(' Best-fit params'):
break
# Also find the burnin iterations:
if lines[ini].startswith(' Burned'):
burnin = int(lines[ini].split()[-1])
ini += 1
# Read data:
bestp = np.zeros(nfree, np.double)
for i in np.arange(ini, ini+nfree):
bestp[i-ini] = lines[i].split()[0]
# Stack together the chains:
allstack = allp[0, :, burnin:]
for c in np.arange(1, nchains):
allstack = np.hstack((allstack, allp[c, :, burnin:]))
# Remove temporary files:
for file in tmpfiles:
os.remove(file)
return allstack, bestp
except SystemExit:
pass
