def test_backsub_all(self):
# Check the aliases:
# ====================== #
c2 = ComponentClass(name='C1', aliases=['A:=1+2', 'B:=5*A', 'C:=B+2'])
self.assertEqual(c2.aliases_map['A'].rhs_as_python_func()(), 3)
# This should assert, because its not yet back-subbed
c2.backsub_all()
self.assertEqual(c2.aliases_map['B'].rhs_as_python_func()(), 15)
# Check the ordering:
self.assertEqual(c2.aliases_map['C'].rhs_as_python_func()(), ((5 * (3)) + 2))
# ====================== #
# Check the equations:
# ====================== #
# warnings.warn('Tests not implemented')
pass
def test_get_node_addr(self):
# Signature: name(self)
# Get the namespace address of this component
d = ComponentClass(name='D',)
e = ComponentClass(name='E')
f = ComponentClass(name='F')
g = ComponentClass(name='G')
b = ComponentClass(name='B', subnodes={'d': d, 'e': e})
c = ComponentClass(name='C', subnodes={'f': f, 'g': g})
a = ComponentClass(name='A', subnodes={'b': b, 'c': c})
# Construction of the objects causes cloning to happen:
# Therefore we test by looking up and checking that there
# are the correct component names:
bNew = a.get_subnode('b')
cNew = a.get_subnode('c')
dNew = a.get_subnode('b.d')
eNew = a.get_subnode('b.e')
fNew = a.get_subnode('c.f')
gNew = a.get_subnode('c.g')
self.assertEquals(a.get_node_addr(),
NamespaceAddress.create_root())
self.assertEquals(bNew.get_node_addr(),
NamespaceAddress('b'))
self.assertEquals(cNew.get_node_addr(),
NamespaceAddress('c'))
self.assertEquals(dNew.get_node_addr(),
NamespaceAddress('b.d'))
self.assertEquals(eNew.get_node_addr(),
NamespaceAddress('b.e'))
self.assertEquals(fNew.get_node_addr(),
NamespaceAddress('c.f'))
self.assertEquals(gNew.get_node_addr(),
NamespaceAddress('c.g'))
self.assertEquals(a.name, 'A')
self.assertEquals(bNew.name, 'B')
self.assertEquals(cNew.name, 'C')
self.assertEquals(dNew.name, 'D')
self.assertEquals(eNew.name, 'E')
self.assertEquals(fNew.name, 'F')
self.assertEquals(gNew.name, 'G')
def test_backsub_all(self):
# Check the aliases:
# ====================== #
c2 = ComponentClass(name='C1', aliases=['A:=1+2', 'B:=5*A', 'C:=B+2'])
self.assertEqual(c2.aliases_map['A'].rhs_as_python_func()(), 3)
# This should assert, because its not yet back-subbed
c2.backsub_all()
self.assertEqual(c2.aliases_map['B'].rhs_as_python_func()(), 15)
# Check the ordering:
self.assertEqual(c2.aliases_map['C'].rhs_as_python_func()(),
((5 * (3)) + 2))
# ====================== #
# Check the equations:
# ====================== #
# warnings.warn('Tests not implemented')
pass
def test_get_node_addr(self):
# Signature: name(self)
# Get the namespace address of this component
d = ComponentClass(name='D', )
e = ComponentClass(name='E')
f = ComponentClass(name='F')
g = ComponentClass(name='G')
b = ComponentClass(name='B', subnodes={'d': d, 'e': e})
c = ComponentClass(name='C', subnodes={'f': f, 'g': g})
a = ComponentClass(name='A', subnodes={'b': b, 'c': c})
# Construction of the objects causes cloning to happen:
# Therefore we test by looking up and checking that there
# are the correct component names:
bNew = a.get_subnode('b')
cNew = a.get_subnode('c')
dNew = a.get_subnode('b.d')
eNew = a.get_subnode('b.e')
fNew = a.get_subnode('c.f')
gNew = a.get_subnode('c.g')
self.assertEquals(a.get_node_addr(), NamespaceAddress.create_root())
self.assertEquals(bNew.get_node_addr(), NamespaceAddress('b'))
self.assertEquals(cNew.get_node_addr(), NamespaceAddress('c'))
self.assertEquals(dNew.get_node_addr(), NamespaceAddress('b.d'))
self.assertEquals(eNew.get_node_addr(), NamespaceAddress('b.e'))
self.assertEquals(fNew.get_node_addr(), NamespaceAddress('c.f'))
self.assertEquals(gNew.get_node_addr(), NamespaceAddress('c.g'))
self.assertEquals(a.name, 'A')
self.assertEquals(bNew.name, 'B')
self.assertEquals(cNew.name, 'C')
self.assertEquals(dNew.name, 'D')
self.assertEquals(eNew.name, 'E')
self.assertEquals(fNew.name, 'F')
self.assertEquals(gNew.name, 'G')
def test_insert_subnode(self):
# Signature: name(self, subnode, namespace)
# Insert a subnode into this component
#
#
# :param subnode: An object of type ``ComponentClass``.
# :param namespace: A `string` specifying the name of the component in
# this components namespace.
#
# :raises: ``NineMLRuntimeException`` if there is already a subcomponent at
# the same namespace location
#
# .. note::
#
# This method will clone the subnode.
d = ComponentClass(name='D')
e = ComponentClass(name='E')
f = ComponentClass(name='F')
g = ComponentClass(name='G')
b = ComponentClass(name='B')
b.insert_subnode(namespace='d', subnode=d)
b.insert_subnode(namespace='e', subnode=e)
c = ComponentClass(name='C')
c.insert_subnode(namespace='f', subnode=f)
c.insert_subnode(namespace='g', subnode=g)
a = ComponentClass(name='A')
a.insert_subnode(namespace='b', subnode=b)
a.insert_subnode(namespace='c', subnode=c)
# Construction of the objects causes cloning to happen:
# Therefore we test by looking up and checking that there
# are the correct component names:
bNew = a.get_subnode('b')
cNew = a.get_subnode('c')
dNew = a.get_subnode('b.d')
eNew = a.get_subnode('b.e')
fNew = a.get_subnode('c.f')
gNew = a.get_subnode('c.g')
self.assertEquals(a.get_node_addr(), NamespaceAddress.create_root())
self.assertEquals(bNew.get_node_addr(), NamespaceAddress('b'))
self.assertEquals(cNew.get_node_addr(), NamespaceAddress('c'))
self.assertEquals(dNew.get_node_addr(), NamespaceAddress('b.d'))
self.assertEquals(eNew.get_node_addr(), NamespaceAddress('b.e'))
self.assertEquals(fNew.get_node_addr(), NamespaceAddress('c.f'))
self.assertEquals(gNew.get_node_addr(), NamespaceAddress('c.g'))
self.assertEquals(a.name, 'A')
self.assertEquals(bNew.name, 'B')
self.assertEquals(cNew.name, 'C')
self.assertEquals(dNew.name, 'D')
self.assertEquals(eNew.name, 'E')
self.assertEquals(fNew.name, 'F')
self.assertEquals(gNew.name, 'G')
self.assertRaises(NineMLRuntimeError, a.get_subnode, 'x')
self.assertRaises(NineMLRuntimeError, a.get_subnode, 'a.')
self.assertRaises(NineMLRuntimeError, a.get_subnode, 'a.X')
self.assertRaises(NineMLRuntimeError, a.get_subnode, 'a.b.')
self.assertRaises(NineMLRuntimeError, a.get_subnode, 'a.b.X')
# Adding to the same namespace twice:
d1 = ComponentClass(name='D1')
d2 = ComponentClass(name='D2')
a = ComponentClass(name='B')
a.insert_subnode(namespace='d', subnode=d1)
self.assertRaises(NineMLRuntimeError,
a.insert_subnode,
namespace='d',
subnode=d2)
def test_connect_ports(self):
# Signature: name(self, src, sink)
# Connects the ports of 2 subcomponents.
#
# The ports can be specified as ``string`` s or ``NamespaceAddresses`` es.
#
#
# :param src: The source port of one sub-component; this should either an
# event port or analog port, but it *must* be a send port.
#
# :param sink: The sink port of one sub-component; this should either an
# event port or analog port, but it *must* be either a 'recv' or a
# 'reduce' port.
tIaf = TestableComponent('iaf')
tCoba = TestableComponent('coba_synapse')
# Should be fine:
c = ComponentClass(name='C1',
subnodes={
'iaf': tIaf(),
'coba': tCoba()
})
c.connect_ports('iaf.V', 'coba.V')
c = ComponentClass(name='C1',
subnodes={
'iaf': tIaf(),
'coba': tCoba()
},
portconnections=[('iaf.V', 'coba.V')])
# Non existant Ports:
c = ComponentClass(name='C1',
subnodes={
'iaf': tIaf(),
'coba': tCoba()
})
self.assertRaises(NineMLRuntimeError, c.connect_ports, 'iaf.V1',
'coba.V')
self.assertRaises(NineMLRuntimeError, c.connect_ports, 'iaf.V',
'coba.V1')
self.assertRaises(NineMLRuntimeError,
ComponentClass,
name='C1',
subnodes={
'iaf': tIaf(),
'coba': tCoba()
},
portconnections=[('iaf.V1', 'coba.V')])
self.assertRaises(NineMLRuntimeError,
ComponentClass,
name='C1',
subnodes={
'iaf': tIaf(),
'coba': tCoba()
},
portconnections=[('iaf.V', 'coba.V1')])
# Connect ports the wronf way around:
# [Check the wright way around works:]
c = ComponentClass(name='C1',
subnodes={
'iaf': tIaf(),
'coba': tCoba()
},
portconnections=[('coba.I', 'iaf.ISyn')])
# And the wrong way around:
c = ComponentClass(name='C1',
subnodes={
'iaf': tIaf(),
'coba': tCoba()
})
self.assertRaises(NineMLRuntimeError, c.connect_ports, 'iaf.ISyn.',
'coba.I')
self.assertRaises(NineMLRuntimeError, c.connect_ports, 'coba.V',
'iaf.V')
# Error raised on duplicate port-connection:
c = ComponentClass(
name='C1',
subnodes={
'iaf': tIaf(),
'coba': tCoba()
},
)
c.connect_ports('coba.I', 'iaf.ISyn')
self.assertRaises(NineMLRuntimeError, c.connect_ports, 'coba.I',
'iaf.ISyn')
def test_insert_subnode(self):
# Signature: name(self, subnode, namespace)
# Insert a subnode into this component
#
#
# :param subnode: An object of type ``ComponentClass``.
# :param namespace: A `string` specifying the name of the component in
# this components namespace.
#
# :raises: ``NineMLRuntimeException`` if there is already a subcomponent at
# the same namespace location
#
# .. note::
#
# This method will clone the subnode.
d = ComponentClass(name='D')
e = ComponentClass(name='E')
f = ComponentClass(name='F')
g = ComponentClass(name='G')
b = ComponentClass(name='B')
b.insert_subnode(namespace='d', subnode=d)
b.insert_subnode(namespace='e', subnode=e)
c = ComponentClass(name='C')
c.insert_subnode(namespace='f', subnode=f)
c.insert_subnode(namespace='g', subnode=g)
a = ComponentClass(name='A')
a.insert_subnode(namespace='b', subnode=b)
a.insert_subnode(namespace='c', subnode=c)
# Construction of the objects causes cloning to happen:
# Therefore we test by looking up and checking that there
# are the correct component names:
bNew = a.get_subnode('b')
cNew = a.get_subnode('c')
dNew = a.get_subnode('b.d')
eNew = a.get_subnode('b.e')
fNew = a.get_subnode('c.f')
gNew = a.get_subnode('c.g')
self.assertEquals(a.get_node_addr(),
NamespaceAddress.create_root())
self.assertEquals(bNew.get_node_addr(),
NamespaceAddress('b'))
self.assertEquals(cNew.get_node_addr(),
NamespaceAddress('c'))
self.assertEquals(dNew.get_node_addr(),
NamespaceAddress('b.d'))
self.assertEquals(eNew.get_node_addr(),
NamespaceAddress('b.e'))
self.assertEquals(fNew.get_node_addr(),
NamespaceAddress('c.f'))
self.assertEquals(gNew.get_node_addr(),
NamespaceAddress('c.g'))
self.assertEquals(a.name, 'A')
self.assertEquals(bNew.name, 'B')
self.assertEquals(cNew.name, 'C')
self.assertEquals(dNew.name, 'D')
self.assertEquals(eNew.name, 'E')
self.assertEquals(fNew.name, 'F')
self.assertEquals(gNew.name, 'G')
self.assertRaises(NineMLRuntimeError, a.get_subnode, 'x')
self.assertRaises(NineMLRuntimeError, a.get_subnode, 'a.')
self.assertRaises(NineMLRuntimeError, a.get_subnode, 'a.X')
self.assertRaises(NineMLRuntimeError, a.get_subnode, 'a.b.')
self.assertRaises(NineMLRuntimeError, a.get_subnode, 'a.b.X')
# Adding to the same namespace twice:
d1 = ComponentClass(name='D1')
d2 = ComponentClass(name='D2')
a = ComponentClass(name='B')
a.insert_subnode(namespace='d', subnode=d1)
self.assertRaises(
NineMLRuntimeError,
a.insert_subnode, namespace='d', subnode=d2)
def test_connect_ports(self):
# Signature: name(self, src, sink)
# Connects the ports of 2 subcomponents.
#
# The ports can be specified as ``string`` s or ``NamespaceAddresses`` es.
#
#
# :param src: The source port of one sub-component; this should either an
# event port or analog port, but it *must* be a send port.
#
# :param sink: The sink port of one sub-component; this should either an
# event port or analog port, but it *must* be either a 'recv' or a
# 'reduce' port.
tIaf = TestableComponent('iaf')
tCoba = TestableComponent('coba_synapse')
# Should be fine:
c = ComponentClass(name='C1',
subnodes={'iaf': tIaf(), 'coba': tCoba()})
c.connect_ports('iaf.V', 'coba.V')
c = ComponentClass(name='C1',
subnodes={'iaf': tIaf(), 'coba': tCoba()},
portconnections=[('iaf.V', 'coba.V')]
)
# Non existant Ports:
c = ComponentClass(name='C1',
subnodes={'iaf': tIaf(), 'coba': tCoba()})
self.assertRaises(
NineMLRuntimeError,
c.connect_ports, 'iaf.V1', 'coba.V')
self.assertRaises(
NineMLRuntimeError,
c.connect_ports, 'iaf.V', 'coba.V1')
self.assertRaises(
NineMLRuntimeError,
ComponentClass,
name='C1',
subnodes={'iaf': tIaf(), 'coba': tCoba()},
portconnections=[('iaf.V1', 'coba.V')]
)
self.assertRaises(
NineMLRuntimeError,
ComponentClass,
name='C1',
subnodes={'iaf': tIaf(), 'coba': tCoba()},
portconnections=[('iaf.V', 'coba.V1')]
)
# Connect ports the wronf way around:
# [Check the wright way around works:]
c = ComponentClass(name='C1',
subnodes={'iaf': tIaf(), 'coba': tCoba()},
portconnections=[('coba.I', 'iaf.ISyn')]
)
# And the wrong way around:
c = ComponentClass(name='C1',
subnodes={'iaf': tIaf(), 'coba': tCoba()})
self.assertRaises(
NineMLRuntimeError,
c.connect_ports, 'iaf.ISyn.', 'coba.I')
self.assertRaises(
NineMLRuntimeError,
c.connect_ports, 'coba.V', 'iaf.V')
# Error raised on duplicate port-connection:
c = ComponentClass(name='C1',
subnodes={'iaf': tIaf(), 'coba': tCoba()},
)
c.connect_ports('coba.I', 'iaf.ISyn')
self.assertRaises(
NineMLRuntimeError,
c.connect_ports, 'coba.I', 'iaf.ISyn')
def get_compound_component():
"""Cannot yet be implemented in PyDSTool
"""
from nineml.abstraction_layer.testing_utils import RecordValue
from nineml.abstraction_layer import DynamicsClass, Regime, On, OutputEvent, AnalogSendPort, AnalogReducePort
emitter = DynamicsClass(
name='EventEmitter',
parameters=['cyclelength'],
regimes=[
Regime(transitions=On('t > tchange + cyclelength',
do=[OutputEvent('emit'), 'tchange=t'])),
])
ev_based_cc = DynamicsClass(
name='EventBasedCurrentClass',
parameters=['dur', 'i'],
analog_ports=[AnalogSendPort('I')],
regimes=[
Regime(transitions=[
On('inputevent', do=['I=i', 'tchange = t']),
On('t>tchange + dur', do=['I=0', 'tchange=t'])
])
])
pulsing_emitter = DynamicsClass(name='pulsing_cc',
subnodes={
'evs': emitter,
'cc': ev_based_cc
},
portconnections=[('evs.emit',
'cc.inputevent')])
nrn = DynamicsClass(
name='LeakyNeuron',
parameters=['Cm', 'gL', 'E'],
regimes=[
Regime('dV/dt = (iInj + (E-V)*gL )/Cm'),
],
aliases=['iIn := iInj'],
analog_ports=[
AnalogSendPort('V'),
AnalogReducePort('iInj', reduce_op='+')
],
)
combined_comp = DynamicsClass(name='Comp1',
subnodes={
'nrn': nrn,
'cc1': pulsing_emitter,
'cc2': pulsing_emitter
},
portconnections=[('cc1.cc.I', 'nrn.iInj'),
('cc2.cc.I', 'nrn.iInj')])
combined_comp = al.flattening.flatten(combined_comp)
## records = [
## RecordValue(what='cc1_cc_I', tag='Current', label='Current Clamp 1'),
## RecordValue(what='cc2_cc_I', tag='Current', label='Current Clamp 2'),
## RecordValue(what='nrn_iIn', tag='Current', label='Total Input Current'),
## RecordValue(what='nrn_V', tag='Voltage', label='Neuron Voltage'),
## RecordValue(what='cc1_cc_tchange', tag='Tchange', label='tChange CC1'),
## RecordValue(what='cc2_cc_tchange', tag='Tchange', label='tChange CC2'),
## RecordValue(what='regime', tag='Regime', label='Regime'),
## ]
parameters = al.flattening.ComponentFlattener.flatten_namespace_dict({
'cc1.cc.i':
13.8,
'cc1.cc.dur':
10,
'cc1.evs.cyclelength':
30,
'cc2.cc.i':
20.8,
'cc2.cc.dur':
5.0,
'cc2.evs.cyclelength':
20,
'nrn.gL':
4.3,
'nrn.E':
-70
})
return combined_comp, parameters
