def test(obj):
newObj = _helpers.copyObject(obj)
for item in ["a", "b"]:
true = obj.__getattribute__(item) ==newObj.__getattribute__(item)
if isinstance(true, np.ndarray):
true = all(true)
self.assertTrue(true)
def update(self, other):
"""
Copies the content of other to this object.
Parameters
----------
other: Logger
"""
_ = _helpers.copyObject(other, self)
def copy(self):
return _helpers.copyObject(self)
def bootstrap(
self,
# The following must be kept in sync with ModelFitterCore.__init__
numIteration: int = 10,
reportInterval: int = 1000,
synthesizerClass=ObservationSynthesizerRandomizedResiduals,
maxProcess: int = None,
serializePath: str = None,
**kwargs: dict):
"""
Constructs a bootstrap estimate of parameter values.
Parameters
----------
numIteration: number of bootstrap iterations
reportInterval: number of iterations between progress reports
synthesizerClass: object that synthesizes new observations
Must subclass ObservationSynthesizer
maxProcess: Maximum number of processes to use. Default: numCPU
serializePath: Where to serialize the fitter after bootstrap
kwargs: arguments passed to ObservationSynthesizer
Example
-------
f.bootstrap()
f.getParameterMeans() # Mean values
f.getParameterStds() # standard deviations
Notes
1. Arguments can be overriden by the constructor using
the keyword argument bootstrapKwargs.
----
"""
def get(name, value):
if name in self.bootstrapKwargs:
if self.bootstrapKwargs[name] is not None:
return self.bootstrapKwargs[name]
else:
return value
else:
return value
# Handle overrides of arguments specified in constructor
numIteration = get("numIteration", numIteration)
reportInterval = get("reportInterval", reportInterval)
synthesizerClass = get("synthesizerClass", synthesizerClass)
maxProcess = get("maxProcess", maxProcess)
serializePath = get("serializePath", serializePath)
# Other initializations
if maxProcess is None:
maxProcess = multiprocessing.cpu_count()
if self.minimizerResult is None:
self.fitModel()
base_redchi = self.minimizerResult.redchi
# Run processes
numProcess = max(int(numIteration / ITERATION_PER_PROCESS), 1)
numProcess = min(numProcess, maxProcess)
numProcessIteration = int(np.ceil(numIteration / numProcess))
args_list = [
_Arguments(self,
numProcess,
i,
numIteration=numProcessIteration,
reportInterval=reportInterval,
synthesizerClass=synthesizerClass,
_loggerPrefix="bootstrap",
**kwargs) for i in range(numProcess)
]
msg = "Running bootstrap for %d successful iterations " % numIteration
msg += "with %d processes." % numProcess
self.logger.activity(msg)
# Run separate processes for each bootstrap
processes = []
queue = multiprocessing.Queue()
results = []
# Set to False for debug so not doing multiple processes
if True:
for args in args_list:
p = multiprocessing.Process(target=_runBootstrap,
args=(
args,
queue,
))
p.start()
processes.append(p)
timeout = MAX_ITERATION_TIME * numProcessIteration
try:
# Get rid of possible zombies
for _ in range(len(processes)):
results.append(queue.get(timeout=timeout))
# Get rid of possible zombies
for process in processes:
process.terminate()
except Exception as err:
msg = "modelFitterBootstrap/Error in process management"
self.logger.error(msg, err)
finally:
pass
else:
# Keep to debug _runBootstrap single threaded
results = []
for args in args_list:
results.append(_runBootstrap(args))
if len(results) == 0:
msg = "modelFitterBootstrap/timeout in solving model."
msg = "\nConsider increasing per timeout."
msg = "\nCurent value: %f" % MAX_ITERATION_TIME
self.logger.result(msg)
else:
self.bootstrapResult = BootstrapResult.merge(results)
# Update the logger in place
_ = _helpers.copyObject(self.bootstrapResult.fitter.logger,
self.logger)
if self.bootstrapResult.fittedStatistic is not None:
self.bootstrapResult.fittedStatistic.calculate()
self.logger.result("%d bootstrap estimates of parameters." %
self.bootstrapResult.numSimulation)
if serializePath is not None:
self.serialize(serializePath)
def bootstrap(
self,
isParallel=True,
# The following must be kept in sync with ModelFitterCore.__init__
numIteration: int = None,
maxProcess: int = None,
serializePath: str = None,
**kwargs: dict):
"""
Constructs a bootstrap estimate of parameter values.
Parameters
----------
isParallel: bool
run in parallel
numIteration: number of bootstrap iterations
maxProcess: Maximum number of processes to use. Default: numCPU
serializePath: Where to serialize the fitter after bootstrap
kwargs: arguments passed to ObservationSynthesizer
Example
-------
f.bootstrap()
f.getParameterMeans() # Mean values
f.getParameterStds() # standard deviations
Notes
1. Arguments can be overriden by the constructor using
the keyword argument bootstrapKwargs.
----
"""
def getValue(name, value, defaultValue=None):
if value is not None:
return value
# Handle arguments specified in constructor
if name in self.bootstrapKwargs:
if self.bootstrapKwargs[name] is not None:
return self.bootstrapKwargs[name]
if name in self.__dict__.keys():
return self.__dict__[name]
# None specified
return defaultValue
#
# Initialization
numIteration = getValue("numIteration", numIteration)
isParallel = getValue("_isParallel", isParallel)
isProgressBar = getValue("_isProgressBar", None, defaultValue=True)
if maxProcess is None:
maxProcess = self._maxProcess
if maxProcess is None:
maxProcess = multiprocessing.cpu_count()
serializePath = getValue("serializePath", serializePath)
# Ensure that there is a fitted model
if self.minimizerResult is None:
self.fitModel()
# Construct arguments collection
numProcess = min(maxProcess, numIteration)
batchSize = numIteration // numProcess
argumentsCol = [
RunnerArgument(self,
numIteration=batchSize,
_loggerPrefix="bootstrap",
**kwargs) for i in range(numProcess)
]
# Run separate processes for each batch
runner = ParallelRunner(BootstrapRunner,
desc="iteration",
maxProcess=numProcess)
results = runner.runSync(argumentsCol,
isParallel=isParallel,
isProgressBar=isProgressBar)
# Check the results
if len(results) == 0:
msg = "modelFitterBootstrap/timeout in solving model."
msg = "\nConsider increasing per timeout."
msg = "\nCurent value: %f" % MAX_ITERATION_TIME
self.logger.result(msg)
else:
self.bootstrapResult = BootstrapResult.merge(results, self)
# Update the logger in place
_ = _helpers.copyObject(self.bootstrapResult.fitter.logger,
self.logger)
self.bootstrapResult.fittedStatistic.calculate()
self.logger.result("%d bootstrap estimates of parameters." %
self.bootstrapResult.numSimulation)
if serializePath is not None:
self.serialize(serializePath)