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Merge pull request #358 from gyorilab/distribution_expr
Support expressions in parameter's of distributions
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Original file line number | Diff line number | Diff line change |
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import sympy | ||
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from mira.metamodel import * | ||
from mira.modeling import Model | ||
from mira.modeling.amr.petrinet import template_model_to_petrinet_json | ||
from mira.sources.amr import model_from_json | ||
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def test_distribution_expressions(): | ||
beta_mean = Parameter(name='beta_mean', | ||
distribution=Distribution(type="Beta1", | ||
parameters={'alpha': sympy.Integer(1), | ||
'beta': sympy.Integer(10)})) | ||
gamma_mean = Parameter(name='gamma_mean', | ||
distribution=Distribution(type="Beta1", | ||
parameters={'alpha': sympy.Integer(10), | ||
'beta': sympy.Integer(10)})) | ||
beta = Parameter(name='beta', | ||
distribution=Distribution(type="InverseGamma1", | ||
parameters={'shape': sympy.Symbol('beta_mean'), | ||
'scale': sympy.Float(0.01)})) | ||
gamma = Parameter(name='gamma', | ||
distribution=Distribution(type="InverseGamma1", | ||
parameters={'shape': sympy.Symbol('gamma_mean'), | ||
'scale': sympy.Float(0.01)})) | ||
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# Make an SIR model with beta and gamma in rate laws | ||
sir_model = TemplateModel( | ||
templates=[ | ||
ControlledConversion( | ||
subject=Concept(name='S'), | ||
outcome=Concept(name='I'), | ||
controller=Concept(name='I'), | ||
rate_law=sympy.Symbol('S') * sympy.Symbol('I') * sympy.Symbol('beta') | ||
), | ||
NaturalConversion( | ||
subject=Concept(name='I'), | ||
outcome=Concept(name='R'), | ||
rate_law=sympy.Symbol('I') * sympy.Symbol('gamma') | ||
), | ||
], | ||
parameters={ | ||
'beta': beta, | ||
'gamma': gamma, | ||
'beta_mean': beta_mean, | ||
'gamma_mean': gamma_mean, | ||
} | ||
) | ||
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model = Model(sir_model) | ||
pn_json = template_model_to_petrinet_json(sir_model) | ||
params = pn_json['semantics']['ode']['parameters'] | ||
assert {p['id'] for p in params} == \ | ||
{'beta_mean', 'gamma_mean', 'beta', 'gamma'} | ||
beta = [p for p in params if p['id'] == 'beta'][0] | ||
assert beta['distribution']['type'] == 'InverseGamma1' | ||
assert beta['distribution']['parameters']['shape'] == 'beta_mean' | ||
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# Now read the model back and check if it is deserialized | ||
tm = model_from_json(pn_json) | ||
assert tm.parameters['beta'].distribution.type == 'InverseGamma1' | ||
assert isinstance(tm.parameters['beta'].distribution.parameters['shape'], | ||
SympyExprStr) | ||
assert tm.parameters['beta'].distribution.parameters['shape'].args[0] == \ | ||
sympy.Symbol('beta_mean') |