"""
Option parser for bumps command line
"""
from __future__ import print_function
import sys
import numpy as np
from .fitters import FITTERS, FIT_AVAILABLE_IDS, FIT_ACTIVE_IDS, FIT_DEFAULT_ID
# TODO: replace with standard argparse module
[docs]class ParseOpts(object):
"""
Options parser.
Subclass should define *MINARGS*, *FLAGS*, *VALUES* and *USAGE*.
*MINARGS* is the minimum number of positional arguments.
*FLAGS* is a set of arguments that may be present or absent.
*VALUES* is a set of arguments that take values. Value checking
can be done in the setter for each argument in the set. Default
values should be set in the corresponding object attribute.
*USAGE* is the help string to display for option "help".
The constructor will invoke the command line parser, leaving the
values set by the command line as attribute values. Flag options
will be True or False.
"""
MINARGS = 0
FLAGS = set()
VALUES = set()
#: Value to use if a value flag is is present without '='. This is
#: different from the default value if the flag is not present, which
#: is the default value set in the calling class.
IMPLICIT_VALUES = {}
USAGE = ""
def __init__(self, args):
if self.VALUES & self.FLAGS:
raise TypeError("option used as both a flag and a value: %s"%
",".join(self.VALUES&self.FLAGS))
self._parse(args)
def _parse(self, args):
if any(v in args for v in ('-?', '-h', '-help')):
print(self.USAGE)
sys.exit()
# Drop the "bumps" arg from the beginning of the list.
args = args[1:]
# Fill in implicit values. We need to do this to support something
# like "bumps ... --parallel=2 ... --parallel", which should have the
# later (implicit) parameter take precedence over the earlier
# parameters.
args = [
(arg + "=" + str(self.IMPLICIT_VALUES[arg[2:]])
if arg[2:] in self.IMPLICIT_VALUES else arg)
for arg in args]
# Parse options.
# Given tuples [..., (a, 1), ..., (a, 2), ...], then dict(tuples)
# will use the later value for the key rather than the earlier
# value, which is what we want for the command line interpreter.
position_args = [v for v in sys.argv[1:] if not v.startswith('--')]
flag_args = [
v[2:] # convert --flag => flag
for v in args if v.startswith('--') and not '=' in v]
value_args = dict(
v[2:].split('=', 1) # convert --flag=value => (flag, value)
for v in args if v.startswith('--') and '=' in v)
# Check that options are valid.
# TODO: move type checking from FitConfig.set_from_cli to here.
flags, values = set(flag_args), set(value_args.keys())
unknown = (flags|values) - (self.FLAGS|self.VALUES)
unexpected_value = flags - self.FLAGS
blank_values = set(
k for k, v in value_args.items() if k in self.VALUES and v == "")
missing_value = (values - self.VALUES) | blank_values
errors = []
if any(unknown):
errors.append(
"Unknown options --%s." % ", --".join(unknown))
if any(unexpected_value):
errors.append(
"Unexpected value for --%s." % ", --".join(sorted(unexpected_value)))
if any(missing_value):
errors.append(
"Missing value for --%s." % ", --".join(sorted(missing_value)))
if errors:
message = " ".join(errors + ["Use -? for help."])
raise ValueError(message)
# Set the values into the fields.
for option in self.FLAGS:
setattr(self, option, (option in flags))
for option, value in value_args.items():
setattr(self, option, value)
self.args = position_args
# === Fitter option parsing ===
[docs]class ChoiceList(object):
def __init__(self, *choices):
self.choices = choices
def __call__(self, value):
if not value in self.choices:
raise ValueError('invalid option "%s": use %s'
% (value, '|'.join(self.choices)))
else:
return value
[docs]def yesno(value):
if value.lower() in ('true', 'yes', 'on', '1'):
return True
elif value.lower() in ('false', 'no', 'off', '0'):
return False
raise ValueError('invalid option "%s": use yes|no')
[docs]def parse_int(value):
float_value = float(value)
if int(float_value) != float_value:
raise ValueError("integer expected")
return int(float_value)
FIT_FIELDS = dict(
starts=("Starts", parse_int),
steps=("Steps", parse_int),
samples=("Samples", parse_int),
xtol=("x tolerance", float),
ftol=("f(x) tolerance", float),
alpha=("Convergence", float),
stop=("Stopping criteria", str),
thin=("Thinning", parse_int),
burn=("Burn-in steps", parse_int),
pop=("Population", float),
init=("Initializer", ChoiceList("eps", "lhs", "cov", "random")),
CR=("Crossover ratio", float),
F=("Scale", float),
nT=("# Temperatures", parse_int),
Tmin=("Min temperature", float),
Tmax=("Max temperature", float),
radius=("Simplex radius", float),
# TODO: convert --trim into a boolean flag and update docs
trim=("Burn-in trim", yesno),
outliers=("Outliers" , ChoiceList("none", "iqr", "grubbs", "mahal")),
)
# Make sure all settings are parseable
for fit in FITTERS:
assert all(opt in FIT_FIELDS for opt, _ in fit.settings), (
"Fitter %s contains unknown settings %s"
%(fit.id, ', '.join(opt for opt, _ in sorted(fit.settings)
if opt not in FIT_FIELDS)))
del fit
[docs]class FitConfig(object):
"""
Fit settings configuration object.
The command line parser will define a FitConfig object which contains
the fitter that was given on the command line and all its options. For
embedded bumps, which does not use the bumps command line parser, a
new FitConfig object can be created with its own selected options.
**Attributes**
*ids = [id, id, ...]* is a list available fitters in "preferred" order.
Depending on usage, you may want to sort them, or alternatively, sort
by long name with *[id for _,id in sorted((v,k) for k,v in self.names]*
*fitters = {id: fitclasss}* maps ids to fitters.
*names* = {id: name}* maps ids to long names
*settings = {id: [(option, default), ...]}* maps ids to default settings.
The order of the settings is the preferred order to present the settings
to the user in a GUI dialog for example.
*values = {id: {option: value, ...}}* maps ids to the settings for
each fitter. Note that in the GUI, different fitters may have there
settings recorded and preserved even when not selected.
*active_ids = [id, id, ...]* is the list of fitters to show the user in
a GUI dialog for example. The other fitters should still be available from
the command line.
*default_id = id* is the fitter to use by default.
*selected_id = id* is the fitter that was selected, either by command line
or by GUI.
*selected_values = {option: value}* returns the settings for the current
fitter.
*selected_name = name* returns the name of the selected fitter.
*selected_fitter = FitClass* returns the class of the selected fitter.
"""
def __init__(self, default=FIT_DEFAULT_ID, active=FIT_ACTIVE_IDS):
# Keep a private copy of the configure settings rather than modifying
# the global defaults
self.ids = [fit.id for fit in FITTERS]
# FITTERS is a list of FitBase classes
# Each class has:
# fit.id: the short name used on the command line
# fit.name: the long name used in the GUI
# fit.settings: available options: [(key,default value), ...]
self.fitters = dict((fit.id, fit) for fit in FITTERS)
self.names = dict((fit.id, fit.name) for fit in FITTERS)
self.settings = dict((fit.id, fit.settings) for fit in FITTERS)
self.values = dict((fit.id, dict(fit.settings)) for fit in FITTERS)
if not all(k in self.ids for k in active):
raise ValueError("Some active fitters are not available")
if default not in active:
raise ValueError("default fitter is not active")
self.active_ids = active
self.default_id = default
self.selected_id = default
[docs] def set_from_cli(self, opts):
"""
Use the BumpsOpts command line parser values to set the selected
fitter and its configuration options.
"""
fitter = opts.fit
self.selected_id = fitter
# Convert supplied options to the correct types and save them in value
for field, reset_value in self.settings[fitter]:
value = getattr(opts, field, None)
parse = FIT_FIELDS[field][1]
if value is not None:
try:
self.values[fitter][field] = parse(value)
except Exception as exc:
raise ValueError("error in --%s: %s" % (field, str(exc)))
# print("options=%s"%(str(self.options)))
@property
def selected_values(self):
return self.values[self.selected_id]
@property
def selected_name(self):
return self.names[self.selected_id]
@property
def selected_fitter(self):
return self.fitters[self.selected_id]
#: FitConfig singleton for the common case in which only one config is needed.
#: There may be other use cases, such as saving the fit config along with the
#: rest of the state so that on resume the fit options are restored, but in that
#: case the application will not be using the singleton.
FIT_CONFIG = FitConfig()
# === Bumps options parsing ===
[docs]class BumpsOpts(ParseOpts):
"""
Option parser for bumps.
"""
MINARGS = 1
# TODO: document all options in USAGE and doc/guide/options.rst
# TODO: remove application-specific options like --staj
FLAGS = set(("preview", "chisq", "profile", "time_model",
"simulate", "simrandom", "shake",
"worker", # internal, so not documented
"multiprocessing-fork", # passed in when app is a frozen image
"remote", # not active, so not documented
"batch", "noshow", "overwrite", "stepmon",
"err", "cov", "edit", "mpi", "keep_best",
"staj",
# passed when not running bumps, but instead using a
# bundled application as a python distribution with domain
# specific models pre-defined.
"i",
))
VALUES = set(("plot", "store", "resume", "entropy", "fit", "noise", "seed",
"pars", "resynth", "time",
"checkpoint", "m", "c", "p", "parallel", "view",
"trim", "alpha", "outliers",
# The following options are for remote fitting via the
# fitting service, but this is not currently active.
"transport", "notify", "queue",
))
# Add in parameters from the fitters
VALUES |= set(FIT_FIELDS.keys())
# --parallel is equivalent to --parallel=0
IMPLICIT_VALUES = {
'parallel': '0',
'entropy': 'llf',
'resume': '-',
}
pars = None
notify = ""
queue = None
resynth = "0"
noise = "5"
starts = "1"
seed = ""
time = "inf"
checkpoint = "0"
parallel = ""
entropy = None
trim = "true"
view = None
alpha = 0.0
PLOTTERS = "linear", "log", "residuals"
USAGE = """\
Usage: bumps [options] modelfile [modelargs]
The modelfile is a Python script (i.e., a series of Python commands)
which sets up the data, the models, and the fittable parameters.
The model arguments are available in the modelfile as sys.argv[1:].
Model arguments may not start with '-'.
Options:
--preview
display model but do not perform a fitting operation
--pars=filename or store path
initial parameter values; fit results are saved as path/<modelname>.par
--plot=log [%(plotter)s]
type of plot to display
--trim=true
trim any remaining burn before displaying plots [dream only]
--simulate
simulate a dataset using the initial problem parameters
--simrandom
simulate a dataset using random problem parameters
--shake
set random parameters before fitting
--noise=5%%
percent noise to add to the simulated data
--seed=integer
random number seed
--err
show uncertainty estimate from curvature at the minimum
--cov
show the covariance matrix for the model when done
--entropy=gmm|mvn|wnn|llf
compute entropy on posterior distribution [dream only]
--staj
output staj file when done [Refl1D only]
--edit
start the gui
--view=linear|log
one of the predefined problem views; reflectometry also has fresnel,
logfresnel, q4 and residuals
--store=path
output directory for plots and models
--overwrite
if store already exists, replace it
--resume=path [dream]
resume a fit from previous stored state; if path is '-' then use the
path given by --store, if it exists
--parallel=n
run fit using multiprocessing for parallelism; use --parallel=0 for all cpus
--mpi
run fit using MPI for parallelism (use command "mpirun -n cpus ...")
--batch
batch mode; save output in .mon file and don't show plots after fit
--noshow
semi-batch; send output to console but don't show plots after fit
--time=inf
run for a maximum number of hours
--checkpoint=0
save fit state every n hours, or 0 for no checkpoints
--fit=amoeba [%(fitter)s]
fitting engine to use; see manual for details
--steps=0 [%(fitter)s]
number of fit iterations after any burn-in time; use samples if steps=0
--samples=1e4 [dream]
set steps=samples/(pop*#pars) so the target number of samples is drawn
--xtol=1e-4 [de, amoeba]
minimum population diameter
--ftol=1e-4 [de, amoeba]
minimum population flatness
--alpha=0.0 [dream]
p-level for rejecting convergence; with fewer samples use a stricter
stopping condition, such as --alpha=0.01 --samples=20000
--outliers=none [dream]
name of test used for removing outlier chains every N samples:
none: no outlier removal
iqr: use interquartile range on likelihood
grubbs: use t-test on likelihood
mahal: use distance from parameter values on the best chain
--pop=10 [dream, de, rl, ps]
population size is pop times number of fitted parameters; if pop is
negative, then set population size to -pop.
--burn=100 [dream, pt]
number of burn-in iterations before accumulating stats
--thin=1 [dream]
number of fit iterations between steps
--nT=25
--Tmin=0.1
--Tmax=10 [pt]
temperatures vector; use a higher maximum temperature and a larger
nT if your fit is getting stuck in local minima
--CR=0.9 [de, rl, pt]
crossover ratio for population mixing
--starts=1 [newton, rl, amoeba]
number of times to run the fit from random starting points.
--keep_best
when running with multiple starts, restart from a point near the
last minimum rather than using a completely random starting point.
--init=eps [dream]
population initialization method:
eps: ball around initial parameter set
lhs: latin hypercube sampling
cov: normally distributed according to covariance matrix
random: uniformly distributed within parameter ranges
--stepmon
show details for each step
--resynth=0
run resynthesis error analysis for n generations
--time_model
run the model --steps times in order to estimate total run time.
--profile
run the python profiler on the model; use --steps to run multiple
models for better statistics
--chisq
print the model description and chisq value and exit
-m/-c/-p command
run the python interpreter with bumps on the path:
m: command is a module such as bumps.cli, run as __main__
c: command is a python one-line command
p: command is the name of a python script
-i
start the interactive interpreter
-?/-h/--help
display this help
""" % {'fitter': '|'.join(sorted(FIT_AVAILABLE_IDS)),
'plotter': '|'.join(PLOTTERS),
}
# --remote
# queue fit to run on remote server
# --notify=user@email
# remote fit notification
# --queue=http://reflectometry.org
# remote job queue
# --transport=mp {amqp|mp|mpi}
# use amqp/multiprocessing/mpi for parallel evaluation
_plot = 'log'
def _set_plot(self, value):
if value not in set(self.PLOTTERS):
raise ValueError("unknown plot type %s; use %s"
% (value, "|".join(self.PLOTTERS)))
self._plot = value
plot = property(fget=lambda self: self._plot, fset=_set_plot)
store = None
resume = None
_fit = FIT_DEFAULT_ID
@property
def fit(self):
return self._fit
@fit.setter
def fit(self, value):
if value not in FIT_AVAILABLE_IDS:
raise ValueError("unknown fitter %s; use %s"
% (value, "|".join(sorted(FIT_AVAILABLE_IDS))))
self._fit = value
fit_config = FIT_CONFIG
TRANSPORTS = 'amqp', 'mp', 'mpi', 'celery'
_transport = 'mp'
def _set_transport(self, value):
if value not in self.TRANSPORTS:
raise ValueError("unknown transport %s; use %s"
% (value, "|".join(self.TRANSPORTS)))
self._transport = value
transport = property(fget=lambda self: self._transport, fset=_set_transport)
meshsteps = 40
[docs]def getopts():
"""
Process command line options.
Option values will be stored as attributes in the returned object.
"""
opts = BumpsOpts(sys.argv)
opts.resynth = int(opts.resynth)
# Set a random seed if none is given; want to know the seed so we can
# reproduce the run. The seed needs to be saved to the monitor file.
opts.seed = int(opts.seed) if opts.seed else np.random.randint(1000000)
opts.fit_config.set_from_cli(opts)
return opts
