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modelModulePYSB = importlib.import_module(outdir_pysb)
model_pysb = modelModulePYSB.getModel()
edata = get_data(model_pysb)
rdata_pysb = get_results(model_pysb, edata)
# -------------- SBML -----------------
sbmlFile = os.path.join(os.path.dirname(__file__), '..', 'python',
'examples', 'example_presimulation',
'model_presimulation.xml')
sbmlImporter = amici.SbmlImporter(sbmlFile)
observables = amici.assignmentRules2observables(
sbmlImporter.sbml, # the libsbml model object
filter_function=lambda variable: variable.getName() == 'pPROT_obs'
)
outdir_sbml = 'test_model_presimulation_sbml'
sbmlImporter.sbml2amici('test_model_presimulation_sbml',
outdir_sbml,
verbose=False,
observables=observables,
constantParameters=constant_parameters)
sys.path.insert(0, outdir_sbml)
modelModuleSBML = importlib.import_module(outdir_sbml)
model_sbml = modelModuleSBML.getModel()
rdata_sbml = get_results(model_sbml, edata)
# check if preequilibration fixed parameters are correctly applied:
def test_steadystate_import(self):
sbmlFile = os.path.join(os.path.dirname(__file__), '..', 'python',
'examples', 'example_steadystate',
'model_steadystate_scaled.xml')
sbmlImporter = amici.SbmlImporter(sbmlFile)
observables = amici.assignmentRules2observables(
sbmlImporter.sbml,
filter_function=lambda variable:
variable.getId().startswith('observable_') and
not variable.getId().endswith('_sigma')
)
outdir = 'test_model_steadystate_scaled'
sbmlImporter.sbml2amici('test_model_steadystate_scaled',
outdir,
observables=observables,
constantParameters=['k0'],
sigmas={'observable_x1withsigma':
'observable_x1withsigma_sigma'})
sys.path.insert(0, outdir)
import test_model_steadystate_scaled as model_module
def test_likelihoods(self):
"""
Test the custom noise distributions used to define cost functions.
"""
def assert_fun(x):
return self.assertTrue(x)
sbmlFile = os.path.join(os.path.dirname(__file__), '..', 'python',
'examples', 'example_steadystate',
'model_steadystate_scaled.xml')
sbmlImporter = amici.SbmlImporter(sbmlFile)
observables = amici.assignmentRules2observables(
sbmlImporter.sbml,
filter_function=lambda variable:
variable.getId().startswith('observable_') and
not variable.getId().endswith('_sigma')
)
# assign different noise models
obs_keys = list(observables.keys())
# exponentiate observable formulas
obs1 = observables[obs_keys[1]]
obs3 = observables[obs_keys[3]]
obs1['formula'] = '10^(' + obs1['formula'] + ')'
obs3['formula'] = 'exp(' + obs3['formula'] + ')'
def setUp(self):
self.default_path = copy.copy(sys.path)
self.resetdir = os.getcwd()
if os.path.dirname(__file__) != '':
os.chdir(os.path.dirname(__file__))
sbmlFile = os.path.join(os.path.dirname(__file__), '..', 'python',
'examples', 'example_presimulation',
'model_presimulation.xml')
sbmlImporter = amici.SbmlImporter(sbmlFile)
constantParameters = ['DRUG_0', 'KIN_0']
observables = amici.assignmentRules2observables(
sbmlImporter.sbml, # the libsbml model object
filter_function=lambda variable: variable.getName() == 'pPROT'
)
outdir = 'test_model_presimulation'
sbmlImporter.sbml2amici('test_model_presimulation',
outdir,
verbose=False,
observables=observables,
constantParameters=constantParameters)
sys.path.insert(0, outdir)
import test_model_presimulation as modelModule
self.model = modelModule.getModel()
self.model.setTimepoints(np.linspace(0, 60, 61))
self.solver = self.model.getSolver()
rdata = amici.runAmiciSimulation(self.model, self.solver)
self.edata = [amici.ExpData(rdata, 0.01, 0)]
def test_presimulation(self):
def assert_fun(x):
return self.assertTrue(x)
sbmlFile = os.path.join(os.path.dirname(__file__), '..', 'python',
'examples', 'example_presimulation',
'model_presimulation.xml')
sbmlImporter = amici.SbmlImporter(sbmlFile)
constantParameters = ['DRUG_0', 'KIN_0']
observables = amici.assignmentRules2observables(
sbmlImporter.sbml, # the libsbml model object
filter_function=lambda variable: variable.getName() == 'pPROT_obs'
)
outdir = 'test_model_presimulation'
sbmlImporter.sbml2amici('test_model_presimulation',
outdir,
verbose=False,
observables=observables,
constantParameters=constantParameters)
sys.path.insert(0, outdir)
import test_model_presimulation as modelModule
model = modelModule.getModel()
solver = model.getSolver()
solver.setNewtonMaxSteps(0)
model.setTimepoints(np.linspace(0, 60, 61))
model.setSteadyStateSensitivityMode(