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from typing import Dict, List, Tuple, Any, Callable, Optional
from textwrap import dedent
from argparse import ArgumentTypeError
from dataclasses import dataclass, asdict
from bumps import fitters
from bumps.fitters import FIT_AVAILABLE_IDS
def get_fitter_defaults(fitters):
"""
Determines the default values for each setting of each fitter.
This comes from the Fitter.settings attribute in the fitters defined by bumps.fitter,
with an additional ("time", 0.0) setting implicit to all fitters.
"""
defaults = {f.id: dict(name=f.name, settings=dict(f.settings)) for f in fitters}
# Add an implicit time=0 for the max time on each fitter.
for k, v in defaults.items():
v["settings"]["time"] = 0.0
return defaults
FITTERS = (
fitters.SimplexFit,
fitters.DreamFit,
fitters.DEFit,
fitters.MPFit,
fitters.BFGSFit,
)
"""Fitters visible to the user. This may be a subset of bumps.fitters.FITTERS"""
DEFAULT_FITTER_ID = fitters.SimplexFit.id
"""Default fitter if none specified"""
FITTER_DEFAULTS = get_fitter_defaults(FITTERS)
"""Fitter name and default settings for the visible fitters. This list will be amended if a hidden fitter is specified on the command line."""
FIT_OPTIONS: Dict[str, "Setting"] = {}
"""Options available to the fitters."""
@dataclass(init=False)
class Setting:
name: str
label: str
description: str
stype: Callable
fitters: List[str]
defaults: List[Any]
def __init__(self, name: str, label: str, stype: type, description: str):
self.name = name
self.label = label
self.description = dedent(description)
self.stype = stype
self.fitters = []
self.defaults = []
FIT_OPTIONS[name] = self
@dataclass(frozen=True)
class Range:
"""
A floating point range which is used as an argparse type converter and validator.
"""
min: float
max: float
# def __init__(self, min, max): self.min, self.max = min, max
def __call__(self, v):
v = float(v)
if not self.min <= v <= self.max:
raise ArgumentTypeError(f"{v} not in [{self.min:g}, {self.max:g}]")
return v
def __repr__(self):
return f"float[{self.min:g},{self.max:g}]"
## Options available for the various fitters
Setting("fit", "Optimizer", [], "Fitting engine to use.")
# Stopping conditions
Setting(
"steps",
"Steps",
int,
"""\
Stop when iteration = steps.
In Dream, the number of steps is inferred from --samples as samples / (pop * pars)
if --steps is zero, otherwise it uses the value of --steps.""",
)
Setting("xtol", "x tolerance", Range(0, 1), "Stop when population diameter < xtol relative to range.")
Setting("ftol", "f(x) tolerance", float, "Stop when variation in log likelihood < ftol.")
Setting(
"alpha",
"Convergence",
Range(0, 0.1),
"""\
Stop when probability that population is varying < alpha or use default
zero for no convergence test.
(Note that while p-values vary from 0 to 1, values for alpha > 0.1 result in
an unstable check for convergence and are therefore disallowed)""",
)
Setting("time", "Max time", float, "Maximum number of hours to run the fit, or zero for no maximum.")
# Initializers
Setting(
"init",
"Initializer",
list("eps lhs cov random".split()),
"""\
Population initialization method
eps: ball around initial parameter set
lhs: latin hypercube sampling
cov: normally istributed according to covariance matrix
random: uniformly distributed within parameter range""",
)
Setting(
"pop",
"Population",
float,
"""\
Population size is pop times number of fitted parameters. If pop is
negative then set population size to -pop independent of fit parameters.""",
)
Setting("burn", "Burn-in steps", int, "Estimated number generations before convergence")
Setting("samples", "Samples", int, "Number of samples to draw = pop*pars*steps.")
Setting(
"thin",
"Thinning factor",
int,
"""\
Number of iterations between samples; use a large number here
if you find your problem is "stuck", with minimal change from
step to step in the parameter trace.""",
)
Setting(
"outliers",
"Outliers test",
list("none iqr grubbs mahal".split()),
"""\
Remove outlier Markov chains every n steps using the selected algorithm.
none: no outlier removal during fit
iqr: use interquartile range on likelihood
grubbs: use t-test on likelihood
mahal: use distance from parameter values on the best chain
At the end of the fit the iqr algorithm is used to remove any remaining
outlier chains from the statistical results and plots.""",
)
# Post processing
Setting(
"trim",
"Burn-in trim",
bool,
"""\
After fitting, trim samples from early in the Markov chains before it converged.""",
)
# Parallel tempering
Setting("nT", "# Temperatures", int, "Number of temperatures in the parallel tempering ladder")
Setting("Tmin", "Min temperature", float, "Lowest temperature in the temperture ladder")
Setting("Tmax", "Max temperature", float, "Highest temperature in the temperature ladder")
# Differential evolution
Setting("CR", "Crossover ratio", Range(0, 1), "Proportion of parameters updated in crossover step")
Setting("F", "Scale", float, "Step-size scaling on difference vector")
# TODO: DE accepts --stop=expr for bumps.mystic.stop.parse_condition(expr)
# Settings("stop", "Stopping condition", str, "Generalized stopping condition expression")
# Amoeba
Setting(
"radius",
"Simplex radius",
Range(0, 0.5),
"""\
Radius around the starting point for the initial simplex. Values are in (0, 0.5],
representing the portion of the total range of the parameter being initialized.""",
)
# Stochastic global minimization
Setting("starts", "Auto restarts", int, "Number of times to restart the amoeba fit.")
Setting(
"jump",
"Jump radius",
Range(0, 0.5),
"""\
When running with multiple starts, what size of jump to take between restarts.
Values are in [0, 0.5], representing the portion of the total range of each parameter.
A value of zero uses a random starting point in the range.
""",
)
def lookup_fitter(fitter_id: str):
# Checking the complete list of fitters, not the restricted list for webview
for fitter in fitters.FITTERS:
if fitter.id == fitter_id:
return fitter
raise ValueError(f"Unknown fitter '{fitter_id}'")
def form_fit_options_associations():
"""
Builds the association list between settings and the optimizers which use them.
Rerun after changes to fit_options.FITTERS
"""
# Clear out old associations
del FIT_OPTIONS["fit"].stype[:]
for settings in FIT_OPTIONS.values():
del settings.fitters[:]
del settings.defaults[:]
# Define the new associations
for fitter in FITTERS:
fitter_id = fitter.id
settings = FIT_OPTIONS["fit"]
settings.fitters.append(fitter_id) # produces doc string for --fit [amoeba, dream, ...]
settings.stype.append(fitter_id) # does option checking for --fit=fitter
settings.defaults.append(DEFAULT_FITTER_ID)
for key, value in fitter.settings:
if key not in FIT_OPTIONS:
raise TypeError(f"Missing type and description for fit option --{key} used by {fitter_id}")
setting = FIT_OPTIONS[key]
setting.fitters.append(fitter_id)
setting.defaults.append(value)
def check_options(options: Dict[str, Any], fitter_id: Optional[str] = None) -> Tuple[Dict[str, Any], List[str]]:
"""
Check if the set of options is consistent for the fitter.
Returns an updated options dictionary and a list of warnings covering unknown options and bad types.
"""
# Note: this code is called with options set in a jupyter notebook so make
# make sure it is robust against bad inputs.
errors = []
unknown = []
if not fitter_id:
fitter_id = options.get("fit", DEFAULT_FITTER_ID)
# available = set(fitter.id for fitter in FITTERS)
# Check against all available fitters, not just the ones visibile in the interface
available = FIT_AVAILABLE_IDS
if fitter_id not in available:
errors.append(f"Fitter {fitter_id} not in {', '.join(available)}. Using {DEFAULT_FITTER_ID} instead.")
fitter_id = DEFAULT_FITTER_ID
# TODO: default from state.share.fitter_settings instead of Fitter.settings?
fitter = lookup_fitter(fitter_id)
defaults = dict(fitter.settings)
# print(f"defaults for {fitter_id}: {defaults}")
# Note: time is not one of the fit options but it is ever present.
new_options = {"fit": fitter_id, "time": 0.0, **defaults}
for key, value in options.items():
if key == "fit":
# Already added.
continue
if key not in defaults and key != "time":
# Skip unrecognized options
unknown.append(f"{key}={value}")
continue
stype = float if key == "time" else FIT_OPTIONS[key].stype
if (stype is float or isinstance(stype, Range)) and isinstance(value, int):
value = float(value) # type promotion from int to float
if isinstance(stype, list): # enumeration
if value not in stype:
# Default to first item in an enum if the enum is recognized.
errors.append(f"Expected {key}={value} to be in {{{'|'.join(stype)}}}. Using {stype[0]}")
value = stype[0]
elif isinstance(stype, Range):
if not isinstance(value, float):
# Skip values of the wrong type.
errors.append(f"Expected {key}={value} to be float. Ignored.")
continue
if not stype.min <= value <= stype.max:
# Clip values to be in range.
errors.append(f"Clipping {key}={value} to [{stype.min:g}, {stype.max:g}]")
value = min(stype.max, max(stype.min, value))
elif not isinstance(value, stype):
# Skip values of the wrong type
errors.append(f"Expected {key}={value} to have type {stype.__name__}. Ignored")
continue
new_options[key] = value
if unknown:
# Format the skipped options nicely and add to the error list
errors = [f"Unused fit options in {fitter_id}: {' '.join(unknown)}", *errors]
return new_options, errors
def _json_compatible_setting(s: Setting):
output = asdict(s)
stype = output["stype"]
if stype is int:
output["stype"] = "integer"
elif stype is float:
output["stype"] = "float"
elif stype is bool:
output["stype"] = "boolean"
return output
def get_fit_fields():
fit_fields = dict([(k, _json_compatible_setting(v)) for k, v in FIT_OPTIONS.items()])
return fit_fields
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