def setUp(self):
# make a Compartment & use it to make a DynamicCompartment
comp_id = 'comp_id'
self.mean_init_volume = 1E-17
self.compartment = Compartment(id=comp_id,
name='name',
init_volume=InitVolume(
mean=self.mean_init_volume,
std=self.mean_init_volume / 40.))
self.compartment.init_density = Parameter(
id='density_{}'.format(comp_id),
value=1100.,
units=unit_registry.parse_units('g l^-1'))
self.random_state = RandomStateManager.instance()
self.dynamic_compartment = DynamicCompartment(None, self.random_state,
self.compartment)
self.abstract_compartment = Compartment(
id=comp_id,
name='name',
init_volume=InitVolume(mean=self.mean_init_volume, std=0),
physical_type=onto['WC:abstract_compartment'])
self.abstract_dynamic_compartment = DynamicCompartment(
None, self.random_state, self.abstract_compartment)
def test_str(self):
dynamic_compartment = DynamicCompartment(None, self.random_state,
self.compartment)
self.assertIn("has not been initialized", str(dynamic_compartment))
self.assertIn(self.dynamic_compartment.id, str(dynamic_compartment))
dynamic_compartment.initialize_mass_and_density(self.local_species_pop)
self.assertIn("has been initialized", str(dynamic_compartment))
self.assertIn('Fold change total mass: 1.0', str(dynamic_compartment))
# test abstract compartment
self.abstract_dynamic_compartment.initialize_mass_and_density(
self.local_species_pop)
self.assertNotIn('Fraction of mass accounted for',
str(self.abstract_dynamic_compartment))
def create_dynamic_compartments(self):
""" Create the :obj:`DynamicCompartment`\ s for this simulation
"""
# create DynamicCompartments
self.temp_dynamic_compartments = {}
for compartment in self.model.get_compartments():
self.temp_dynamic_compartments[
compartment.id] = DynamicCompartment(None, self.random_state,
compartment)
def specify_init_accounted_fraction(self, desired_init_accounted_fraction):
# make a DynamicCompartment with accounted_fraction ~= desired_init_accounted_fraction
# without changing init_accounted_mass or init_volume
init_density = self.dynamic_compartment.init_accounted_mass / \
(desired_init_accounted_fraction * self.dynamic_compartment.init_volume)
self.compartment.init_density = Parameter(
id='density_x',
value=init_density,
units=unit_registry.parse_units('g l^-1'))
return DynamicCompartment(None, self.random_state, self.compartment)
def setUp(self):
comp_id = 'comp_id'
# make a LocalSpeciesPopulation
self.num_species = 100
species_nums = list(range(0, self.num_species))
self.species_ids = list(
map(lambda x: "species_{}[{}]".format(x, comp_id), species_nums))
self.all_pops = 1E6
self.init_populations = dict(
zip(self.species_ids, [self.all_pops] * len(species_nums)))
self.all_m_weights = 50
self.molecular_weights = dict(
zip(self.species_ids, [self.all_m_weights] * len(species_nums)))
self.local_species_pop = LocalSpeciesPopulation(
'test',
self.init_populations,
self.molecular_weights,
random_state=RandomStateManager.instance())
# make Compartments & use them to make a DynamicCompartments
self.mean_init_volume = 1E-17
self.compartment = Compartment(id=comp_id,
name='name',
init_volume=InitVolume(
mean=self.mean_init_volume,
std=self.mean_init_volume / 40.))
self.compartment.init_density = Parameter(
id='density_{}'.format(comp_id),
value=1100.,
units=unit_registry.parse_units('g l^-1'))
self.random_state = RandomStateManager.instance()
self.dynamic_compartment = DynamicCompartment(None, self.random_state,
self.compartment,
self.species_ids)
self.abstract_compartment = Compartment(
id=comp_id,
name='name',
init_volume=InitVolume(mean=self.mean_init_volume, std=0),
physical_type=onto['WC:abstract_compartment'])
self.abstract_dynamic_compartment = DynamicCompartment(
None, self.random_state, self.abstract_compartment)
def test_dynamic_compartment(self):
volumes = []
# test mean initial volume
for i_trial in range(10):
dynamic_compartment = DynamicCompartment(None, self.random_state,
self.compartment)
volumes.append(dynamic_compartment.init_volume)
self.assertLess(
numpy.abs((numpy.mean(volumes) - self.mean_init_volume) /
self.mean_init_volume), 0.1)
def test_initialize_mass_and_density(self):
self.dynamic_compartment.initialize_mass_and_density(
self.local_species_pop)
estimated_accounted_mass = self.num_species * self.all_pops * self.all_m_weights / Avogadro
self.assertAlmostEqual(self.dynamic_compartment.init_accounted_mass,
estimated_accounted_mass,
places=IEEE_64_BIT_FLOATING_POINT_PLACES)
self.assertTrue(0 < self.dynamic_compartment.init_mass)
self.assertAlmostEqual(self.dynamic_compartment.accounted_fraction,
self.dynamic_compartment.init_accounted_mass / \
self.dynamic_compartment.init_mass,
places=IEEE_64_BIT_FLOATING_POINT_PLACES)
# test abstract compartment
self.abstract_dynamic_compartment.initialize_mass_and_density(
self.local_species_pop)
self.assertAlmostEqual(
self.abstract_dynamic_compartment.init_accounted_mass,
estimated_accounted_mass,
places=IEEE_64_BIT_FLOATING_POINT_PLACES)
self.assertEqual(self.abstract_dynamic_compartment.init_accounted_mass,
self.abstract_dynamic_compartment.init_mass)
self.assertFalse(
hasattr(self.abstract_dynamic_compartment,
'init_accounted_density'))
empty_local_species_pop = LocalSpeciesPopulation(
'test', {}, {}, random_state=RandomStateManager.instance())
dynamic_compartment = DynamicCompartment(None, self.random_state,
self.compartment)
with self.assertRaisesRegex(MultialgorithmError,
"initial accounted ratio is 0"):
dynamic_compartment.initialize_mass_and_density(
empty_local_species_pop)
dynamic_compartment = self.specify_init_accounted_fraction(
(DynamicCompartment.MAX_ALLOWED_INIT_ACCOUNTED_FRACTION + 1) / 2)
with warnings.catch_warnings(record=True) as w:
dynamic_compartment.initialize_mass_and_density(
self.local_species_pop)
self.assertIn("initial accounted ratio (", str(w[-1].message))
self.assertIn(") greater than 1.0", str(w[-1].message))
dynamic_compartment = self.specify_init_accounted_fraction(2)
with self.assertRaises(MultialgorithmError):
dynamic_compartment.initialize_mass_and_density(
self.local_species_pop)
def test_dynamic_compartment_exceptions(self):
compartment = Compartment(id='id',
name='name',
init_volume=InitVolume(mean=0))
with self.assertRaises(MultialgorithmError):
DynamicCompartment(None, self.random_state, compartment)
self.compartment.init_density = Parameter(
id='density_{}'.format(self.compartment.id),
value=float('nan'),
units=unit_registry.parse_units('g l^-1'))
with self.assertRaises(MultialgorithmError):
DynamicCompartment(None, self.random_state, self.compartment)
self.compartment.init_density = Parameter(
id='density_{}'.format(self.compartment.id),
value=0.,
units=unit_registry.parse_units('g l^-1'))
with self.assertRaises(MultialgorithmError):
DynamicCompartment(None, self.random_state, self.compartment)
self.compartment.init_volume = None
with self.assertRaises(MultialgorithmError):
DynamicCompartment(None, self.random_state, self.compartment)
class TestInitializedDynamicCompartment(unittest.TestCase):
""" Test DynamicCompartments with species populations
"""
def setUp(self):
comp_id = 'comp_id'
# make a LocalSpeciesPopulation
self.num_species = 100
species_nums = list(range(0, self.num_species))
self.species_ids = list(
map(lambda x: "species_{}[{}]".format(x, comp_id), species_nums))
self.all_pops = 1E6
self.init_populations = dict(
zip(self.species_ids, [self.all_pops] * len(species_nums)))
self.all_m_weights = 50
self.molecular_weights = dict(
zip(self.species_ids, [self.all_m_weights] * len(species_nums)))
self.local_species_pop = LocalSpeciesPopulation(
'test',
self.init_populations,
self.molecular_weights,
random_state=RandomStateManager.instance())
# make Compartments & use them to make a DynamicCompartments
self.mean_init_volume = 1E-17
self.compartment = Compartment(id=comp_id,
name='name',
init_volume=InitVolume(
mean=self.mean_init_volume,
std=self.mean_init_volume / 40.))
self.compartment.init_density = Parameter(
id='density_{}'.format(comp_id),
value=1100.,
units=unit_registry.parse_units('g l^-1'))
self.random_state = RandomStateManager.instance()
self.dynamic_compartment = DynamicCompartment(None, self.random_state,
self.compartment,
self.species_ids)
self.abstract_compartment = Compartment(
id=comp_id,
name='name',
init_volume=InitVolume(mean=self.mean_init_volume, std=0),
physical_type=onto['WC:abstract_compartment'])
self.abstract_dynamic_compartment = DynamicCompartment(
None, self.random_state, self.abstract_compartment)
def specify_init_accounted_fraction(self, desired_init_accounted_fraction):
# make a DynamicCompartment with accounted_fraction ~= desired_init_accounted_fraction
# without changing init_accounted_mass or init_volume
init_density = self.dynamic_compartment.init_accounted_mass / \
(desired_init_accounted_fraction * self.dynamic_compartment.init_volume)
self.compartment.init_density = Parameter(
id='density_x',
value=init_density,
units=unit_registry.parse_units('g l^-1'))
return DynamicCompartment(None, self.random_state, self.compartment)
def test_initialize_mass_and_density(self):
self.dynamic_compartment.initialize_mass_and_density(
self.local_species_pop)
estimated_accounted_mass = self.num_species * self.all_pops * self.all_m_weights / Avogadro
self.assertAlmostEqual(self.dynamic_compartment.init_accounted_mass,
estimated_accounted_mass,
places=IEEE_64_BIT_FLOATING_POINT_PLACES)
self.assertTrue(0 < self.dynamic_compartment.init_mass)
self.assertAlmostEqual(self.dynamic_compartment.accounted_fraction,
self.dynamic_compartment.init_accounted_mass / \
self.dynamic_compartment.init_mass,
places=IEEE_64_BIT_FLOATING_POINT_PLACES)
# test abstract compartment
self.abstract_dynamic_compartment.initialize_mass_and_density(
self.local_species_pop)
self.assertAlmostEqual(
self.abstract_dynamic_compartment.init_accounted_mass,
estimated_accounted_mass,
places=IEEE_64_BIT_FLOATING_POINT_PLACES)
self.assertEqual(self.abstract_dynamic_compartment.init_accounted_mass,
self.abstract_dynamic_compartment.init_mass)
self.assertFalse(
hasattr(self.abstract_dynamic_compartment,
'init_accounted_density'))
empty_local_species_pop = LocalSpeciesPopulation(
'test', {}, {}, random_state=RandomStateManager.instance())
dynamic_compartment = DynamicCompartment(None, self.random_state,
self.compartment)
with self.assertRaisesRegex(MultialgorithmError,
"initial accounted ratio is 0"):
dynamic_compartment.initialize_mass_and_density(
empty_local_species_pop)
dynamic_compartment = self.specify_init_accounted_fraction(
(DynamicCompartment.MAX_ALLOWED_INIT_ACCOUNTED_FRACTION + 1) / 2)
with warnings.catch_warnings(record=True) as w:
dynamic_compartment.initialize_mass_and_density(
self.local_species_pop)
self.assertIn("initial accounted ratio (", str(w[-1].message))
self.assertIn(") greater than 1.0", str(w[-1].message))
dynamic_compartment = self.specify_init_accounted_fraction(2)
with self.assertRaises(MultialgorithmError):
dynamic_compartment.initialize_mass_and_density(
self.local_species_pop)
def test_fold_changes(self):
# ensure that initial fold changes == 1
self.dynamic_compartment.initialize_mass_and_density(
self.local_species_pop)
self.assertAlmostEqual(
self.dynamic_compartment.fold_change_total_mass(0), 1.0)
self.assertAlmostEqual(
self.dynamic_compartment.fold_change_total_volume(0), 1.0)
def test_init_volume_and_eval(self):
self.dynamic_compartment.initialize_mass_and_density(
self.local_species_pop)
self.assertAlmostEqual(self.dynamic_compartment.volume(),
self.dynamic_compartment.init_volume,
places=IEEE_64_BIT_FLOATING_POINT_PLACES)
self.assertAlmostEqual(self.dynamic_compartment.eval(),
self.dynamic_compartment.init_mass,
places=IEEE_64_BIT_FLOATING_POINT_PLACES)
# test abstract compartment
self.abstract_dynamic_compartment.initialize_mass_and_density(
self.local_species_pop)
self.assertEqual(
self.abstract_dynamic_compartment.accounted_mass(time=0),
self.abstract_dynamic_compartment.init_mass)
self.assertEqual(
self.abstract_dynamic_compartment.accounted_volume(time=0),
self.abstract_dynamic_compartment.init_volume)
self.assertEqual(self.abstract_dynamic_compartment.mass(time=0),
self.abstract_dynamic_compartment.init_mass)
self.assertEqual(self.abstract_dynamic_compartment.volume(time=0),
self.abstract_dynamic_compartment.init_volume)
def test_str(self):
dynamic_compartment = DynamicCompartment(None, self.random_state,
self.compartment)
self.assertIn("has not been initialized", str(dynamic_compartment))
self.assertIn(self.dynamic_compartment.id, str(dynamic_compartment))
dynamic_compartment.initialize_mass_and_density(self.local_species_pop)
self.assertIn("has been initialized", str(dynamic_compartment))
self.assertIn('Fold change total mass: 1.0', str(dynamic_compartment))
# test abstract compartment
self.abstract_dynamic_compartment.initialize_mass_and_density(
self.local_species_pop)
self.assertNotIn('Fraction of mass accounted for',
str(self.abstract_dynamic_compartment))
class TestUninitializedDynamicCompartment(unittest.TestCase):
""" Test DynamicCompartments that do not have a species population
"""
def setUp(self):
# make a Compartment & use it to make a DynamicCompartment
comp_id = 'comp_id'
self.mean_init_volume = 1E-17
self.compartment = Compartment(id=comp_id,
name='name',
init_volume=InitVolume(
mean=self.mean_init_volume,
std=self.mean_init_volume / 40.))
self.compartment.init_density = Parameter(
id='density_{}'.format(comp_id),
value=1100.,
units=unit_registry.parse_units('g l^-1'))
self.random_state = RandomStateManager.instance()
self.dynamic_compartment = DynamicCompartment(None, self.random_state,
self.compartment)
self.abstract_compartment = Compartment(
id=comp_id,
name='name',
init_volume=InitVolume(mean=self.mean_init_volume, std=0),
physical_type=onto['WC:abstract_compartment'])
self.abstract_dynamic_compartment = DynamicCompartment(
None, self.random_state, self.abstract_compartment)
def test_dynamic_compartment(self):
volumes = []
# test mean initial volume
for i_trial in range(10):
dynamic_compartment = DynamicCompartment(None, self.random_state,
self.compartment)
volumes.append(dynamic_compartment.init_volume)
self.assertLess(
numpy.abs((numpy.mean(volumes) - self.mean_init_volume) /
self.mean_init_volume), 0.1)
def test_abstract_dynamic_compartment(self):
self.assertTrue(self.abstract_dynamic_compartment._is_abstract())
self.assertFalse(
hasattr(self.abstract_dynamic_compartment, 'init_density'))
def test_dynamic_compartment_exceptions(self):
compartment = Compartment(id='id',
name='name',
init_volume=InitVolume(mean=0))
with self.assertRaises(MultialgorithmError):
DynamicCompartment(None, self.random_state, compartment)
self.compartment.init_density = Parameter(
id='density_{}'.format(self.compartment.id),
value=float('nan'),
units=unit_registry.parse_units('g l^-1'))
with self.assertRaises(MultialgorithmError):
DynamicCompartment(None, self.random_state, self.compartment)
self.compartment.init_density = Parameter(
id='density_{}'.format(self.compartment.id),
value=0.,
units=unit_registry.parse_units('g l^-1'))
with self.assertRaises(MultialgorithmError):
DynamicCompartment(None, self.random_state, self.compartment)
self.compartment.init_volume = None
with self.assertRaises(MultialgorithmError):
DynamicCompartment(None, self.random_state, self.compartment)