def testDeserialize(self):
if IGNORE_TEST:
return
fitter = self.getFitter()
fitter.serialize(FILE_SERIALIZE)
deserializedFitter = ModelFitter.deserialize(FILE_SERIALIZE)
self.assertEqual(fitter.modelSpecification,
deserializedFitter.modelSpecification)
self.assertEqual(len(fitter.bootstrapResult.fittedStatistic.meanTS),
len(deserializedFitter.bootstrapResult.fittedStatistic.meanTS))
def __init__(self,
modelSpecification,
dataSources,
dirStudyPath=None,
instanceNames=None,
logger=Logger(),
useSerialized=True,
doSerialize=True,
isPlot=True,
**kwargs):
"""
Parameters
---------
modelSpecification: ExtendedRoadRunner/str
roadrunner model or antimony model
dataSources: list-NamedTimeseries/list-str or dict of either
str: path to CSV file
dirStudyPath: str
Path to the output directory containing the serialized fitters
for the study.
instanceNames: list-str
Names of study instances corresponds to the list of dataSources
useSerialized: bool
Use the serialization of each ModelFitter, if it exists
doSerialized: bool
Serialize each ModelFitter
isPlot: bool
Do plots
kwargs: dict
arguments passed to ModelFitter
"""
self.dirStudyPath = dirStudyPath # Path to the directory serialized ModelFitter
if self.dirStudyPath is None:
length = len(inspect.stack())
absPath = os.path.abspath((inspect.stack()[length - 1])[1])
dirCaller = os.path.dirname(absPath)
self.dirStudyPath = os.path.join(dirCaller, DIR_NAME)
self.isPlot = isPlot
self.doSerialize = doSerialize
self.useSerialized = useSerialized
self.instanceNames, self.dataSourceDct = self._mkInstanceData(
instanceNames, dataSources)
self.fitterPathDct = {
} # Path to serialized fitters; key is instanceName
self.fitterDct = {} # Fitters: key is instanceName
self.logger = logger
# Ensure that the directory exists
if not os.path.isdir(self.dirStudyPath):
os.makedirs(self.dirStudyPath)
# Construct the fitters
for name, dataSource in self.dataSourceDct.items():
filePath = self._getSerializePath(name)
self.fitterPathDct[name] = filePath
if os.path.isfile(filePath) and useSerialized:
self.fitterDct[name] = ModelFitter.deserialize(filePath)
else:
self.fitterDct[name] = ModelFitter(modelSpecification,
dataSource,
logger=self.logger,
isPlot=self.isPlot,
**kwargs)
self._serializeFitter(name)