class TestPreserveIndices(unittest.TestCase):
def setUp(self):
self.parameters = ['P4', 'P1', 'P3', 'P5', 'P2']
self.state_variables = ['SV3', 'SV5', 'SV4', 'SV2', 'SV1']
self.regimes = ['R2', 'R3', 'R1']
self.time_derivatives = {'R1': ['SV5', 'SV1', 'SV4', 'SV3', 'SV2'],
'R2': ['SV2', 'SV4'],
'R3': ['SV4', 'SV2', 'SV1']}
self.aliases = ['A4', 'A3', 'A1', 'A2']
# Create a dynamics object with elements in a particular order
self.d = Dynamics(
name='d',
parameters=[Parameter(p) for p in self.parameters],
state_variables=[StateVariable(sv) for sv in self.state_variables],
regimes=[Regime(name=r,
time_derivatives=[
TimeDerivative(td, '{}/t'.format(td))
for td in self.time_derivatives[r]],
transitions=[
OnCondition(
'SV1 > P5',
target_regime_name=self.regimes[
self.regimes.index(r) - 1])])
for r in self.regimes],
aliases=[Alias(a, 'P{}'.format(i + 1))
for i, a in enumerate(self.aliases)])
def test_clone(self):
clone_d = self.d.clone()
self._test_indices(clone_d)
def test_serialization(self):
for ext in ext_to_format:
fname = mkstemp(suffix=ext)[1]
try:
self.d.write(fname, register=False, preserve_order=True)
except NineMLSerializerNotImportedError:
continue
reread_d = nineml.read(fname + '#d')
self._test_indices(reread_d)
def _test_indices(self, dyn):
# Set indices of parameters in non-ascending order so that they
# can be differentiated from indices on read.
for i, p in enumerate(self.parameters):
self.assertEqual(dyn.index_of(dyn.parameter(p)), i)
for i, sv in enumerate(self.state_variables):
self.assertEqual(dyn.index_of(dyn.state_variable(sv)), i)
for i, r in enumerate(self.regimes):
self.assertEqual(dyn.index_of(dyn.regime(r)), i)
for r, tds in self.time_derivatives.items():
regime = dyn.regime(r)
for i, td in enumerate(tds):
self.assertEquals(
regime.index_of(regime.time_derivative(td)), i)
for i, a in enumerate(self.aliases):
self.assertEqual(dyn.index_of(dyn.alias(a)), i)
def test_equals_with_annotations_ns(self):
a = Dynamics(name='D',
parameters=[Parameter('P', dimension=un.dimensionless)],
aliases=[Alias('A', 'P')])
b = a.clone()
c = a.clone()
d = a.clone()
e = a.clone()
a.parameter('P').annotations.set(('annot1', 'dummy_ns'), 'val1', 1.0)
b.parameter('P').annotations.set(('annot1', 'dummy_ns'), 'val1', 1.0)
c.parameter('P').annotations.set(('annot1', 'dummy_ns'), 'val1', 2.0)
e.parameter('P').annotations.set(('annot1', 'dummy_ns2'), 'val1', 1.0)
self.assertTrue(a.equals(b, annotations_ns=['dummy_ns']))
self.assertTrue(a.equals(c))
self.assertFalse(a.equals(c, annotations_ns=['dummy_ns']))
self.assertTrue(a.equals(d))
self.assertFalse(a.equals(d, annotations_ns=['dummy_ns']))
self.assertTrue(a.equals(e))
self.assertFalse(a.equals(e, annotations_ns=['dummy_ns']))
def test_equals_with_annotations_ns(self):
a = Dynamics(
name='D',
parameters=[Parameter('P', dimension=un.dimensionless)],
aliases=[Alias('A', 'P')])
b = a.clone()
c = a.clone()
d = a.clone()
e = a.clone()
a.parameter('P').annotations.set(('annot1', 'dummy_ns'), 'val1', 1.0)
b.parameter('P').annotations.set(('annot1', 'dummy_ns'), 'val1', 1.0)
c.parameter('P').annotations.set(('annot1', 'dummy_ns'), 'val1', 2.0)
e.parameter('P').annotations.set(('annot1', 'dummy_ns2'), 'val1', 1.0)
self.assertTrue(a.equals(b, annotations_ns=['dummy_ns']))
self.assertTrue(a.equals(c))
self.assertFalse(a.equals(c, annotations_ns=['dummy_ns']))
self.assertTrue(a.equals(d))
self.assertFalse(a.equals(d, annotations_ns=['dummy_ns']))
self.assertTrue(a.equals(e))
self.assertFalse(a.equals(e, annotations_ns=['dummy_ns']))
class DynamicsSubstituteAliasesTest(unittest.TestCase):
def setUp(self):
self.a = Dynamics(
name='A',
aliases=[
'A1:=P1 / P2', 'A2 := ARP2 + P3', 'A3 := A4 * P4 * P5',
'A4:=P6 ** 2 + ADP1', 'A5:=SV1 * SV2 * P8',
'A6:=SV1 * P1 / P8', 'A7:=A1 / P8'
],
regimes=[
Regime('dSV1/dt = -A1 / A2',
'dSV2/dt = -ADP1 / P7',
'dSV3/dt = -A1 * A3 / (A2 * C1)',
transitions=[
OnCondition('SV1 > 10', target_regime_name='R2')
],
aliases=[
Alias('A1', 'P1 / P2 * 2'),
Alias('A5', 'SV1 * SV2 * P8 * 2')
],
name='R1'),
Regime('dSV1/dt = -A1 / A2',
'dSV3/dt = -A1 / A2 * A4',
transitions=[
OnCondition('C2 > A6',
state_assignments=[
StateAssignment('SV1', 'SV1 - A7')
],
target_regime_name='R1')
],
name='R2')
],
analog_ports=[
AnalogReceivePort('ARP1', dimension=un.resistance),
AnalogReceivePort('ARP2', dimension=un.charge),
AnalogReducePort('ADP1', dimension=un.dimensionless),
AnalogSendPort('A5', dimension=un.current)
],
parameters=[
Parameter('P1', dimension=un.voltage),
Parameter('P2', dimension=un.resistance),
Parameter('P3', dimension=un.charge),
Parameter('P4', dimension=old_div(un.length, un.current**2)),
Parameter('P5', dimension=old_div(un.current**2, un.length)),
Parameter('P6', dimension=un.dimensionless),
Parameter('P7', dimension=un.time),
Parameter('P8', dimension=un.current)
],
constants=[
Constant('C1', value=10.0, units=un.unitless),
Constant('C2', value=1.0, units=un.ohm)
])
self.ref_substituted_a = Dynamics(
name='substituted_A',
aliases=['A5:=SV1 * SV2 * P8'],
regimes=[
Regime('dSV1/dt = -2 * (P1 / P2) / (ARP2 + P3)',
'dSV2/dt = -ADP1 / P7',
('dSV3/dt = -2 * (P1 / P2) * ((P6 ** 2 + ADP1) * P4 * '
'P5) / ((ARP2 + P3) * C1)'),
transitions=[
OnCondition('SV1 > 10', target_regime_name='R2')
],
aliases=[Alias('A5', 'SV1 * SV2 * P8 * 2')],
name='R1'),
Regime('dSV1/dt = -(P1 / P2) / (ARP2 + P3)',
'dSV3/dt = -(P1 / P2) / (ARP2 + P3) * (P6 ** 2 + ADP1)',
transitions=[
OnCondition('C2 > (SV1 * P1 / P8)',
state_assignments=[
StateAssignment(
'SV1', 'SV1 - (P1 / P2) / P8')
],
target_regime_name='R1')
],
name='R2')
],
analog_ports=[
AnalogReceivePort('ARP1', dimension=un.resistance),
AnalogReceivePort('ARP2', dimension=un.charge),
AnalogReducePort('ADP1', dimension=un.dimensionless),
AnalogSendPort('A5', dimension=un.current)
],
parameters=[
Parameter('P1', dimension=un.voltage),
Parameter('P2', dimension=un.resistance),
Parameter('P3', dimension=un.charge),
Parameter('P4', dimension=old_div(un.length, un.current**2)),
Parameter('P5', dimension=old_div(un.current**2, un.length)),
Parameter('P6', dimension=un.dimensionless),
Parameter('P7', dimension=un.time),
Parameter('P8', dimension=un.current)
],
constants=[
Constant('C1', value=10.0, units=un.unitless),
Constant('C2', value=1.0, units=un.ohm)
])
def test_substitute_aliases(self):
substituted_a = self.a.clone()
substituted_a.name = 'substituted_A'
DynamicsSubstituteAliases(substituted_a)
self.assertEqual(substituted_a, self.ref_substituted_a,
substituted_a.find_mismatch(self.ref_substituted_a))
class TestPreserveIndices(unittest.TestCase):
def setUp(self):
self.parameters = ['P4', 'P1', 'P3', 'P5', 'P2']
self.state_variables = ['SV3', 'SV5', 'SV4', 'SV2', 'SV1']
self.regimes = ['R2', 'R3', 'R1']
self.time_derivatives = {
'R1': ['SV5', 'SV1', 'SV4', 'SV3', 'SV2'],
'R2': ['SV2', 'SV4'],
'R3': ['SV4', 'SV2', 'SV1']
}
self.aliases = ['A4', 'A3', 'A1', 'A2']
# Create a dynamics object with elements in a particular order
self.d = Dynamics(
name='d',
parameters=[Parameter(p) for p in self.parameters],
state_variables=[StateVariable(sv) for sv in self.state_variables],
regimes=[
Regime(name=r,
time_derivatives=[
TimeDerivative(td, '{}/t'.format(td))
for td in self.time_derivatives[r]
],
transitions=[
OnCondition('SV1 > P5',
target_regime_name=self.regimes[
self.regimes.index(r) - 1])
]) for r in self.regimes
],
aliases=[
Alias(a, 'P{}'.format(i + 1))
for i, a in enumerate(self.aliases)
])
def test_clone(self):
clone_d = self.d.clone()
self._test_indices(clone_d)
def test_serialization(self):
for ext in ext_to_format:
fname = mkstemp(suffix=ext)[1]
try:
self.d.write(fname, register=False, preserve_order=True)
except NineMLSerializerNotImportedError:
continue
reread_d = nineml.read(fname + '#d')
self._test_indices(reread_d)
def _test_indices(self, dyn):
# Set indices of parameters in non-ascending order so that they
# can be differentiated from indices on read.
for i, p in enumerate(self.parameters):
self.assertEqual(dyn.index_of(dyn.parameter(p)), i)
for i, sv in enumerate(self.state_variables):
self.assertEqual(dyn.index_of(dyn.state_variable(sv)), i)
for i, r in enumerate(self.regimes):
self.assertEqual(dyn.index_of(dyn.regime(r)), i)
for r, tds in self.time_derivatives.items():
regime = dyn.regime(r)
for i, td in enumerate(tds):
self.assertEquals(regime.index_of(regime.time_derivative(td)),
i)
for i, a in enumerate(self.aliases):
self.assertEqual(dyn.index_of(dyn.alias(a)), i)
def test_Constructor(self):
d = Dynamics(
name='D',
aliases=['D1:=dp1', 'D2 := dIn1', 'D3 := SV1'],
regimes=[
Regime('dSV1/dt = -SV1/(dp2*t)', name='r1',
transitions=On('input', 'SV1=SV1+1'))],
analog_ports=[RecvPort('dIn1'), SendPort('D1'), SendPort('D2')],
parameters=['dp1', 'dp2']
)
c = Dynamics(
name='C',
aliases=['C1:=cp1', 'C2 := cIn1', 'C3 := SV1'],
regimes=[
Regime(
'dSV1/dt = -SV1/(cp2*t)',
transitions=[On('SV1>cp1', do=[OutputEvent('emit')]),
On('spikein', do=[OutputEvent('emit')])],
name='r1',
),
Regime(name='r2', transitions=On('SV1>1', to='r1'))
],
analog_ports=[RecvPort('cIn1'), RecvPort('cIn2'), SendPort('C1'),
SendPort('C2')],
parameters=['cp1', 'cp2']
)
# Test Cloner, no hierachy
# Everything should be as before:
c_clone = Cloner(as_class=Dynamics).visit(c)
self.assertEqual(c_clone.name, 'C')
self.assertEqual(set(c_clone.alias_names), set(['C1', 'C2', 'C3']))
# - Regimes and Transitions:
self.assertEqual(set(c_clone.regime_names), set(['r1', 'r2']))
self.assertEqual(len(list(c_clone.regime('r1').on_events)), 1)
self.assertEqual(len(list(c_clone.regime('r1').on_conditions)), 1)
self.assertEqual(len(list(c_clone.regime('r2').on_events)), 0)
self.assertEqual(len(list(c_clone.regime('r2').on_conditions)), 1)
self.assertEqual(len(list(c_clone.regime('r2').on_conditions)), 1)
# - Ports & Parameters:
self.assertEqual(
set(c_clone.analog_port_names),
set(['cIn2', 'cIn1', 'C1', 'C2']))
self.assertEqual(set(c_clone.event_send_port_names),
set(['emit']))
self.assertEqual(set(c_clone.event_receive_port_names),
set(['spikein']))
self.assertEqual(set(c_clone.parameter_names),
set(['cp1', 'cp2']))
self.assertEqual(set(c_clone.state_variable_names),
set(['SV1']))
del c_clone
# Test Cloner, 1 level of hierachy
# Everything should be as before:
b = MultiDynamics(name='B',
sub_components={'c1': c, 'c2': c.clone()},
port_connections=[('c1', 'C1', 'c2', 'cIn1'),
('c2', 'emit', 'c1', 'spikein')],
port_exposures=[('c2', 'cIn2', 'cIn2_c2'),
('c1', 'cIn1', 'cIn1_c1')])
b_clone = Cloner(as_class=Dynamics).visit(b)
