def test_ports(self):
# Signature: name
# Return an iterator over all the port (Event & Analog) in the
# component
# from nineml.abstraction.component.componentqueryer import
# ComponentClassQueryer
c = Dynamics(
name='Comp1',
regimes=[
Regime(name='r1',
transitions=[
On('spikeinput1', do=[]),
On('spikeinput2', do=OutputEvent('ev_port2'),
to='r2')]),
Regime(name='r2',
transitions=[
On('V > a', do=OutputEvent('ev_port2')),
On('spikeinput3', do=OutputEvent('ev_port3'),
to='r1')])
],
aliases=['A1:=0', 'C:=0'],
analog_ports=[AnalogSendPort('A1'), AnalogReceivePort('B'),
AnalogSendPort('C')]
)
ports = list(list(c.ports))
port_names = [p.name for p in ports]
self.assertEquals(len(port_names), 8)
self.assertEquals(set(port_names),
set(['A1', 'B', 'C', 'spikeinput1', 'spikeinput2',
'spikeinput3', 'ev_port2', 'ev_port3'])
)
def test_output_filtering(self):
"""
Tests whether the 'outputs' argument is able to filter (presumably)
unconnected nonlinear mappings from inputs and states to analog send
ports
"""
e = Dynamics(name='E',
regimes=[
Regime('dSV1/dt = -SV1 / P1',
'dSV2/dt = -SV2 / P1 + ARP1 * P2',
name='R1')
],
aliases=['A1:=SV1 * C1', 'A2:=SV1 * SV2'],
analog_ports=[
AnalogReceivePort('ARP1', dimension=un.per_time),
AnalogSendPort('A1', dimension=un.current),
AnalogSendPort('A2', dimension=un.dimensionless)
],
parameters=[
Parameter('P1', dimension=un.time),
Parameter('P2', dimension=un.dimensionless)
],
constants=[Constant('C1', 10, units=un.mA)])
self.assertFalse(e.is_linear())
self.assertTrue(e.is_linear(outputs=['A1']))
def test_nonlinear_state_assignment_in_onevent(self):
"""Test that nonlinear state assignements in on events"""
g = Dynamics(name='G',
regimes=[
Regime('dSV1/dt = -SV1 / P1',
'dSV2/dt = -SV2 / P1 + ARP1 * P2',
name='R1',
transitions=[
OnEvent('ERP1',
state_assignments=[
StateAssignment(
'SV2', 'SV2 + A2')
])
])
],
aliases=['A1:=SV1 * C1', 'A2:=P3 * P4 / ADP1'],
analog_ports=[
AnalogReceivePort('ARP1', dimension=un.per_time),
AnalogReducePort('ADP1',
operator='+',
dimension=un.dimensionless),
AnalogSendPort('A1', dimension=un.current),
AnalogSendPort('A2', dimension=un.dimensionless)
],
event_ports=[EventReceivePort('ERP1')],
parameters=[
Parameter('P1', dimension=un.time),
Parameter('P2', dimension=un.dimensionless),
Parameter('P3', dimension=un.resistance),
Parameter('P4', dimension=un.conductance)
],
constants=[Constant('C1', 10, units=un.nA)])
self.assertFalse(g.is_linear())
def duplicate_port_name_event_analog(self):
# Check different names are OK:
Dynamics(
name='C1', aliases=['A1:=1'],
event_ports=[EventReceivePort('A')],
analog_ports=[AnalogSendPort('A')])
self.assertRaises(
NineMLUsageError,
Dynamics,
name='C1',
aliases=['A1:=1'],
event_ports=[EventReceivePort('A')],
analog_ports=[AnalogSendPort('A')]
)
def test_all_expressions(self):
a = Dynamics(
name='A',
aliases=['A1:=P1 * SV2', 'A2 := ARP1 + SV2', 'A3 := SV1'],
state_variables=[
StateVariable('SV1', dimension=un.voltage),
StateVariable('SV2', dimension=un.current)],
regimes=[
Regime(
'dSV1/dt = -SV1 / P2',
'dSV2/dt = A3 / ARP2 + SV2 / P2',
transitions=[On('SV1 > P3', do=[OutputEvent('emit')]),
On('spikein', do=[OutputEvent('emit')])],
name='R1'
),
Regime(name='R2', transitions=On('(SV1 > C1) & (SV2 < P4)',
to='R1'))
],
analog_ports=[AnalogReceivePort('ARP1', dimension=un.current),
AnalogReceivePort('ARP2',
dimension=(un.resistance *
un.time)),
AnalogSendPort('A1',
dimension=un.voltage * un.current),
AnalogSendPort('A2', dimension=un.current)],
parameters=[Parameter('P1', dimension=un.voltage),
Parameter('P2', dimension=un.time),
Parameter('P3', dimension=un.voltage),
Parameter('P4', dimension=un.current)],
constants=[Constant('C1', value=1.0, units=un.mV)]
)
self.assertEqual(
set(a.all_expressions), set((
sympify('P1 * SV2'), sympify('ARP1 + SV2'), sympify('SV1'),
sympify('-SV1 / P2'), sympify('-SV1 / P2'),
sympify('A3 / ARP2 + SV2 / P2'), sympify('SV1 > P3'),
sympify('(SV1 > C1) & (SV2 < P4)'))),
"All expressions were not extracted from component class")
def setUp(self):
self.a = Dynamics(name='A',
aliases=['A1:=P1', 'A2 := ARP1 + SV2', 'A3 := SV1'],
regimes=[
Regime(
'dSV1/dt = -SV1 / (P2*t)',
'dSV2/dt = SV1 / (ARP1*t) + SV2 / (P1*t)',
transitions=[
On('SV1 > P1', do=[OutputEvent('emit')]),
On('spikein', do=[OutputEvent('emit')])
],
name='R1',
),
Regime(name='R2',
transitions=On('SV1 > 1', to='R1'))
],
analog_ports=[
AnalogReceivePort('ARP1'),
AnalogReceivePort('ARP2'),
AnalogSendPort('A1'),
AnalogSendPort('A2')
],
parameters=['P1', 'P2'])
self.b = Dynamics(name='B',
aliases=[
'A1:=P1', 'A2 := ARP1 + SV2', 'A3 := SV1',
'A4 := SV1^3 + SV2^3'
],
regimes=[
Regime(
'dSV1/dt = -SV1 / (P2*t)',
'dSV2/dt = SV1 / (ARP1*t) + SV2 / (P1*t)',
'dSV3/dt = -SV3/t + P3/t',
transitions=[
On('SV1 > P1', do=[OutputEvent('emit')]),
On('spikein',
do=[
OutputEvent('emit'),
StateAssignment('SV1', 'P1')
])
],
name='R1',
),
Regime(name='R2',
transitions=[
On('SV1 > 1', to='R1'),
On('SV3 < 0.001',
to='R2',
do=[StateAssignment('SV3', 1)])
])
],
analog_ports=[
AnalogReceivePort('ARP1'),
AnalogReceivePort('ARP2'),
AnalogSendPort('A1'),
AnalogSendPort('A2'),
AnalogSendPort('A3'),
AnalogSendPort('SV3')
],
parameters=['P1', 'P2', 'P3'])
self.a_props = DynamicsProperties(name="AProps",
definition=self.a,
properties={
'P1': 1,
'P2': 2
})
self.b_props = DynamicsProperties(name="BProps",
definition=self.b,
properties={
'P1': 1,
'P2': 2,
'P3': 3
})
def test_basic_flattening(self):
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'),
StateAssignment('SV1', '10')
])
],
name='r1',
),
Regime(name='r2', transitions=On('SV1>1', to='r1'))
],
analog_ports=[
AnalogReceivePort('cIn1'),
AnalogReceivePort('cIn2'),
AnalogSendPort('C1'),
AnalogSendPort('C2')
],
parameters=['cp1', 'cp2'])
d = Dynamics(name='D',
aliases=['D1:=dp1', 'D2 := dIn1', 'D3 := SV1'],
regimes=[
Regime(
'dSV1/dt = -SV1/(dp2*t)',
transitions=[
On('SV1>dp1', do=[OutputEvent('emit')]),
On('spikein', do=[OutputEvent('emit')])
],
name='r1',
),
Regime(name='r2', transitions=On('SV1>1', to='r1'))
],
analog_ports=[
AnalogReceivePort('dIn1'),
AnalogReceivePort('dIn2'),
AnalogSendPort('D1'),
AnalogSendPort('D2')
],
parameters=['dp1', 'dp2'])
e = MultiDynamics(name='E',
sub_components={
'a': c,
'b': d
},
port_connections=[('a', 'C1', 'b', 'dIn1'),
('a', 'C2', 'b', 'dIn2')],
port_exposures=[('a', 'cIn1', 'ARP1'),
('a', 'cIn2', 'ARP2'),
('a', 'spikein', 'ERP1'),
('a', 'emit', 'ESP1')])
# =====================================================================
# General properties
# =====================================================================
self.assertEqual(e.name, 'E')
self.assertEqual(set(e.parameter_names),
set(['cp1__a', 'cp2__a', 'dp1__b', 'dp2__b']))
cp1 = e.parameter('cp1__a')
self.assertEqual(cp1.dimension, un.dimensionless)
self.assertEqual(set(e.analog_receive_port_names),
set(['ARP1', 'ARP2']))
arp1 = e.analog_receive_port('ARP1')
self.assertEqual(arp1.dimension, un.dimensionless)
self.assertEqual(set(e.event_receive_port_names), set(['ERP1']))
self.assertEqual(set(e.event_send_port_names), set(['ESP1']))
self.assertEqual(
set(e.alias_names),
set([
'C1__a', 'C2__a', 'C3__a', 'D1__b', 'D2__b', 'D3__b',
'cIn1__a', 'cIn2__a', 'dIn1__b', 'dIn2__b'
]))
self.assertEqual(e.alias('C1__a').rhs, sympy.sympify('cp1__a'))
self.assertIsInstance(e.alias('cIn1__a'), _ReceivePortExposureAlias)
self.assertIsInstance(e.alias('dIn1__b'),
_LocalAnalogReceivePortConnection)
self.assertEqual(set(e.state_variable_names), set(['SV1__a',
'SV1__b']))
self.assertEqual(
e.state_variable('SV1__a').dimension, un.dimensionless)
# - Regimes and Transitions:
self.assertEqual(set(e.regime_names),
set(['r1___r1', 'r1___r2', 'r2___r1', 'r2___r2']))
# =====================================================================
# Regime a=1, b=2
# =====================================================================
r11 = e.regime('r1___r1')
self.assertEqual(r11.num_on_conditions, 2)
self.assertEqual(r11.num_on_events, 1)
oe1 = r11.on_event('ERP1')
self.assertEqual(oe1.num_output_events, 1)
out1 = oe1.output_event('ESP1')
self.assertEqual(out1.port, e.event_send_port('ESP1'))
self.assertEqual(oe1.num_state_assignments, 1)
self.assertEqual(oe1.state_assignment('SV1__a').rhs, 10)
self.assertEqual(set(oe1.state_assignment_variables), set(
('SV1__a', )))
self.assertEqual(r11.num_on_conditions, 2)
oc1 = r11.on_condition('SV1__a > cp1__a')
self.assertEqual(oc1.num_output_events, 1)
self.assertEqual(oc1.target_regime, r11)
out1 = oc1.output_event('ESP1')
self.assertEqual(out1.port, e.event_send_port('ESP1'))
self.assertEqual(oc1.num_state_assignments, 0)
oc2 = r11.on_condition('SV1__b > dp1__b')
self.assertEqual(oc2.num_output_events, 0)
self.assertEqual(oc2.num_state_assignments, 0)
self.assertEqual(oc2.target_regime, r11)
# =====================================================================
# Regime a=1, b=2
# =====================================================================
r12 = e.regime('r1___r2')
self.assertEqual(r12.num_on_conditions, 2)
oc1 = r12.on_condition('SV1__a > cp1__a')
self.assertEqual(set(oc1.output_event_port_names), set(('ESP1', )))
self.assertEqual(oc1.target_regime, r12)
oc2 = r12.on_condition('SV1__b > 1')
self.assertEqual(oc2.num_output_events, 0)
self.assertEqual(oc2.target_regime, r11)
self.assertEqual(r12.num_on_events, 1)
self.assertEqual(
r12.on_event('ERP1').port.port, c.event_receive_port('spikein'))
# =====================================================================
# Regime a=2, b=1
# =====================================================================
r21 = e.regime('r2___r1')
self.assertEqual(r21.num_on_conditions, 2)
oc1 = r21.on_condition('SV1__a > 1')
self.assertEqual(oc1.num_output_events, 0)
self.assertEqual(oc1.num_state_assignments, 0)
self.assertEqual(oc1.target_regime, r11)
oc2 = r21.on_condition('SV1__b > dp1__b')
self.assertEqual(oc2.num_output_events, 0)
self.assertEqual(oc2.num_state_assignments, 0)
self.assertEqual(oc2.target_regime, r21)
self.assertEqual(r21.num_on_events, 0)
# =====================================================================
# Regime a=2, b=2
# =====================================================================
r22 = e.regime('r2___r2')
self.assertEqual(r21.num_on_conditions, 2)
oc1 = r22.on_condition('SV1__a > 1')
self.assertEqual(oc1.num_output_events, 0)
self.assertEqual(oc1.num_state_assignments, 0)
self.assertEqual(oc1.target_regime, r12)
oc2 = r22.on_condition('SV1__b > 1')
self.assertEqual(oc2.num_output_events, 0)
self.assertEqual(oc2.num_state_assignments, 0)
self.assertEqual(oc2.target_regime, r21)
# - Ports & Parameters:
self.assertEqual(set(e.analog_receive_port_names),
set(['ARP1', 'ARP2']))
self.assertEqual(set(e.parameter_names),
set(['cp1__a', 'cp2__a', 'dp1__b', 'dp2__b']))
self.assertEqual(set(e.state_variable_names), set(['SV1__a',
'SV1__b']))
def test_analog_ports(self):
# Signature: name
# No Docstring
c = Dynamics(name='C1')
self.assertEqual(len(list(c.analog_ports)), 0)
c = Dynamics(name='C1')
self.assertEqual(len(list(c.analog_ports)), 0)
c = Dynamics(name='C1', aliases=['A:=2'],
analog_ports=[AnalogSendPort('A')])
self.assertEqual(len(list(c.analog_ports)), 1)
self.assertEqual(list(c.analog_ports)[0].mode, 'send')
self.assertEqual(len(list(c.analog_send_ports)), 1)
self.assertEqual(len(list(c.analog_receive_ports)), 0)
self.assertEqual(len(list(c.analog_reduce_ports)), 0)
c = Dynamics(name='C1', analog_ports=[AnalogReceivePort('B')])
self.assertEqual(len(list(c.analog_ports)), 1)
self.assertEqual(list(c.analog_ports)[0].mode, 'recv')
self.assertEqual(len(list(c.analog_send_ports)), 0)
self.assertEqual(len(list(c.analog_receive_ports)), 1)
self.assertEqual(len(list(c.analog_reduce_ports)), 0)
c = Dynamics(name='C1',
analog_ports=[AnalogReducePort('B', operator='+')])
self.assertEqual(len(list(c.analog_ports)), 1)
self.assertEqual(list(c.analog_ports)[0].mode, 'reduce')
self.assertEqual(list(c.analog_ports)[0].operator, '+')
self.assertEqual(len(list(c.analog_send_ports)), 0)
self.assertEqual(len(list(c.analog_receive_ports)), 0)
self.assertEqual(len(list(c.analog_reduce_ports)), 1)
# Duplicate Port Names:
self.assertRaises(
NineMLUsageError,
Dynamics,
name='C1',
aliases=['A1:=1'],
analog_ports=[AnalogReducePort('B', operator='+'),
AnalogSendPort('B')]
)
self.assertRaises(
NineMLUsageError,
Dynamics,
name='C1',
aliases=['A1:=1'],
analog_ports=[AnalogSendPort('A'), AnalogSendPort('A')]
)
self.assertRaises(
NineMLUsageError,
Dynamics,
name='C1',
aliases=['A1:=1'],
analog_ports=[AnalogReceivePort('A'), AnalogReceivePort('A')]
)
self.assertRaises(
NineMLUsageError,
lambda: Dynamics(name='C1', analog_ports=[AnalogReceivePort('1')])
)
self.assertRaises(
NineMLUsageError,
lambda: Dynamics(name='C1', analog_ports=[AnalogReceivePort('?')])
)
do=["tspike = t",
"V = vreset",
OutputEvent('spikeoutput')],
to="refractoryregime"),
),
Regime(
name="refractoryregime",
transitions=[On("t >= tspike + taurefrac",
to="subthresholdregime")],
)
],
state_variables=[
StateVariable('V', un.voltage),
StateVariable('tspike', un.time),
],
analog_ports=[AnalogSendPort("V", un.voltage),
AnalogReducePort("ISyn", un.current, operator="+"), ],
event_ports=[EventSendPort('spikeoutput'), ],
parameters=[Parameter('cm', un.capacitance),
Parameter('taurefrac', un.time),
Parameter('gl', un.conductance),
Parameter('vreset', un.voltage),
Parameter('vrest', un.voltage),
Parameter('vthresh', un.voltage)])
coba = Dynamics(
name="CobaSyn",
aliases=["I:=g*(vrev-V)", ],
regimes=[
Regime(
'dSV1/dt = -SV1 / P2',
'dSV2/dt = A3 / ARP2 + SV2 / P2',
transitions=[On(Trigger('SV1 > P3'),
do=[OutputEvent('ESP1')]),
On('ERP1', do=[OutputEvent('ESP2')])],
name='R1'
),
Regime(name='R2',
transitions=[
OnCondition('(SV1 > C1) & (SV2 < P4)',
target_regime_name='R1')])
],
analog_ports=[AnalogReceivePort('ARP1', dimension=un.current),
AnalogReceivePort('ARP2', dimension=(un.resistance *
un.time)),
AnalogSendPort('A1',
dimension=un.voltage * un.current),
AnalogSendPort('A2', dimension=un.current)],
parameters=[Parameter('P1', dimension=un.voltage),
Parameter('P2', dimension=un.time),
Parameter('P3', dimension=un.voltage),
Parameter('P4', dimension=un.current)],
constants=[Constant('C1', value=-71.0, units=un.mV),
Constant('C2', value=22.2, units=un.degC)])
ref.state_variable('SV2').annotations.set(('Z1', 'NS1'), 'Y1', 'X1', 2.0)
A = Dynamics(
name='dyn',
aliases=['A1:=SV2', 'A2 := ARP1 + SV2', 'A3 := SV1',
'A4 := C2 * SV1'],
state_variables=[
def _transform_full_component(self, trfrm, component_class, v, **kwargs):
# -----------------------------------------------------------------
# Remove all analog send ports with 'current' dimension so they
# don't get confused with the converted voltage time derivative
# expression
# -----------------------------------------------------------------
for port in list(trfrm.analog_send_ports):
if port.dimension == un.current:
trfrm.remove(port)
# -----------------------------------------------------------------
# Insert membrane capacitance if not present
# -----------------------------------------------------------------
# Get or guess the location of the membrane capacitance
try:
name = kwargs['membrane_capacitance']
try:
orig_cm = component_class.parameter(name)
except KeyError:
raise Pype9BuildError(
"Could not find specified membrane capacitance '{}'"
.format(name))
cm = trfrm.parameter(orig_cm.name)
except KeyError: # 'membrane_capacitance' was not specified
candidate_cms = [ccm for ccm in component_class.parameters
if ccm.dimension == un.capacitance]
if len(candidate_cms) == 1:
orig_cm = candidate_cms[0]
cm = trfrm.parameter(orig_cm.name)
logger.info("Guessing that '{}' is the membrane capacitance"
.format(orig_cm))
elif len(candidate_cms) > 1:
raise Pype9BuildError(
"Could not guess the membrane capacitance, candidates:"
" '{}'".format("', '".join(candidate_cms)))
else:
cm = Parameter("cm___pype9", dimension=un.capacitance)
trfrm.add(cm)
cm.annotations.set((BUILD_TRANS, PYPE9_NS), TRANSFORM_SRC, None)
trfrm.annotations.set((BUILD_TRANS, PYPE9_NS),
MEMBRANE_CAPACITANCE, cm.name)
# -----------------------------------------------------------------
# Replace membrane voltage equation with membrane current
# -----------------------------------------------------------------
# Determine the regimes in which each state variables has a time
# derivative in
has_td = defaultdict(list)
# List which regimes need to be clamped to their last voltage
# (as it has no time derivative)
clamped_regimes = []
# The voltage clamp equation where v_clamp is the last voltage
# value and g_clamp_ is a large conductance
clamp_i = sympy.sympify('g_clamp___pype9 * (v - v_clamp___pype9)')
memb_is = []
for regime in trfrm.regimes:
# Add an appropriate membrane current
try:
# Convert the voltage time derivative into a membrane
# current
dvdt = regime.time_derivative(v.name)
regime.remove(dvdt)
i = -dvdt.rhs * cm
memb_is.append(i)
except KeyError:
i = clamp_i
clamped_regimes.append(regime)
regime.add(Alias('i___pype9', i))
# Record state vars that have a time deriv. in this regime
for var in regime.time_derivative_variables:
if var != 'v':
has_td[var].append(regime)
# Pick the most popular membrane current to be the alias in
# the global scope
assert memb_is, "No regimes contain voltage time derivatives"
memb_i = Alias('i___pype9', max(memb_is, key=memb_is.count))
# Add membrane current along with a analog send port
trfrm.add(memb_i)
i_port = AnalogSendPort('i___pype9', dimension=un.current)
i_port.annotations.set((BUILD_TRANS, PYPE9_NS), ION_SPECIES,
NONSPECIFIC_CURRENT)
trfrm.add(i_port)
# Remove membrane currents that match the membrane current in the
# outer scope
for regime in trfrm.regimes:
if regime.alias('i___pype9') == memb_i:
regime.remove(regime.alias('i___pype9'))
# If there are clamped regimes add extra parameters and set the
# voltage to clamp to in the regimes that trfrmition to them
if clamped_regimes:
trfrm.add(StateVariable('v_clamp___pype9', un.voltage))
trfrm.add(Constant('g_clamp___pype9', 1e8, un.uS))
for trans in trfrm.transitions:
if trans.target_regime in clamped_regimes:
# Assign v_clamp_ to the value
try:
v_clamp_rhs = trans.state_assignment('v').rhs
except KeyError:
v_clamp_rhs = 'v'
trans.add(StateAssignment('v_clamp___pype9',
v_clamp_rhs))
# -----------------------------------------------------------------
trfrm.annotations.set(
(BUILD_TRANS, PYPE9_NS), NO_TIME_DERIVS,
','.join(['v'] + [sv for sv in trfrm.state_variable_names
if sv not in has_td]))
trfrm.annotations.set((BUILD_TRANS, PYPE9_NS), NUM_TIME_DERIVS,
len(has_td))
# -----------------------------------------------------------------
# Remove the external input currents
# -----------------------------------------------------------------
# Analog receive or reduce ports that are of dimension current and
# are purely additive to the membrane current and nothing else
# (actually subtractive as it is outward current)
try:
ext_is = []
for i_name in kwargs['external_currents']:
try:
ext_i = trfrm.analog_receive_port(i_name)
except KeyError:
try:
ext_i = trfrm.analog_reduce_port(i_name)
except KeyError:
raise Pype9BuildError(
"Did not find specified external current port "
"'{}'".format(i_name))
if ext_i.dimension != un.current:
raise Pype9BuildError(
"Analog receive port matching specified external "
"current '{}' does not have 'current' dimension "
"({})".format(ext_i.name, ext_i.dimension))
ext_is.append(ext_i)
except KeyError:
ext_is = []
for port in chain(component_class.analog_receive_ports,
component_class.analog_reduce_ports):
# Check to see if the receive/reduce port has current dimension
if port.dimension != un.current:
continue
# Check to see if the current appears in the membrane current
# expression
# FIXME: This test should check to to see if the port is
# additive to the membrane current and substitute all
# aliases.
if port.name not in memb_i.rhs_symbol_names:
continue
# Get the number of expressions the receive port appears in
# an expression
if len([e for e in component_class.all_expressions
if port.symbol in e.free_symbols]) > 1:
continue
# If all those conditions are met guess that port is a external
# current that can be removed (ports that don't meet these
# conditions will have to be specified separately)
ext_is.append(port)
if ext_is:
logger.info("Guessing '{}' are external currents to be removed"
.format(ext_is))
trfrm.annotations.set((BUILD_TRANS, PYPE9_NS), EXTERNAL_CURRENTS,
','.join(p.name for p in ext_is))
# Remove external input current ports (as NEURON handles them)
for ext_i in ext_is:
trfrm.remove(ext_i)
for expr in chain(trfrm.aliases, trfrm.all_time_derivatives()):
expr.subs(ext_i, 0)
expr.simplify()
def setUp(self):
liaf = Dynamics(
name='liaf',
parameters=[
Parameter(name='R', dimension=un.resistance),
Parameter(name='Vreset', dimension=un.voltage),
Parameter(name='tau', dimension=un.time),
Parameter(name='tau_rp', dimension=un.time),
Parameter(name='theta', dimension=un.voltage)
],
analog_ports=[
AnalogReducePort(name='Isyn',
dimension=un.current,
operator='+'),
AnalogSendPort(name='V', dimension=un.voltage),
AnalogSendPort(name='t_rpend', dimension=un.time)
],
event_ports=[EventSendPort(name='spikeOutput')],
state_variables=[
StateVariable(name='V', dimension=un.voltage),
StateVariable(name='t_rpend', dimension=un.time)
],
regimes=[
Regime(name='refractoryRegime',
transitions=[
OnCondition('t > t_rpend',
target_regime_name='subthresholdRegime')
]),
Regime(
name='subthresholdRegime',
time_derivatives=[TimeDerivative('V', '(Isyn*R - V)/tau')],
transitions=[
OnCondition('V > theta',
target_regime_name='refractoryRegime',
state_assignments=[
StateAssignment('V', 'Vreset'),
StateAssignment(
't_rpend', 't + tau_rp')
],
output_events=[OutputEvent('spikeOutput')])
])
])
poisson = Dynamics(
name='Poisson',
parameters=[Parameter(name='rate', dimension=un.per_time)],
event_ports=[EventSendPort(name='spikeOutput')],
state_variables=[StateVariable(name='t_next', dimension=un.time)],
regimes=[
Regime(name='default',
transitions=[
OnCondition(
't > t_next',
target_regime_name='default',
state_assignments=[
StateAssignment(
't_next', 'one_ms*random.exponential('
'rate*thousand_milliseconds) + t')
],
output_events=[OutputEvent('spikeOutput')])
])
],
constants=[
Constant(name='one_ms', units=un.ms, value=1.0),
Constant(name='thousand_milliseconds',
units=un.ms,
value=1000.0)
])
static = Dynamics(
name='StaticConnection',
analog_ports=[AnalogSendPort(name='weight', dimension=un.current)],
state_variables=[
StateVariable(name='weight', dimension=un.current)
],
regimes=[
Regime(name='default',
time_derivatives=[TimeDerivative('weight', 'zero')])
],
constants=[Constant(name='zero', units=un.A / un.s, value=0.0)])
psr = Dynamics(
name='AlphaPSR',
parameters=[Parameter(name='tau_syn', dimension=un.time)],
event_ports=[EventReceivePort(name='spike')],
analog_ports=[
AnalogReceivePort(name='weight', dimension=un.current),
AnalogSendPort(name='A', dimension=un.current),
AnalogSendPort(name='B', dimension=un.current),
AnalogSendPort(name='Isyn', dimension=un.current)
],
state_variables=[
StateVariable(name='A', dimension=un.current),
StateVariable(name='B', dimension=un.current)
],
regimes=[
Regime(name='default',
time_derivatives=[
TimeDerivative('A', '(-A + B)/tau_syn'),
TimeDerivative('B', '-B/tau_syn')
],
transitions=[
OnEvent('spike',
target_regime_name='default',
state_assignments=[
StateAssignment('B', 'B + weight')
])
])
],
aliases=['Isyn:=A'])
one_to_one_class = ConnectionRule(
'OneToOneClass',
standard_library=(
"http://nineml.net/9ML/1.0/connectionrules/OneToOne"))
self.one_to_one = ConnectionRuleProperties("OneToOne",
one_to_one_class, {})
random_fan_in_class = ConnectionRule(
name="RandomFanIn",
parameters=[Parameter(name="number")],
standard_library=(
"http://nineml.net/9ML/1.0/connectionrules/RandomFanIn"))
exc_random_fan_in = ConnectionRuleProperties(
name="RandomFanInProps",
definition=random_fan_in_class,
properties={'number': 100})
inh_random_fan_in = ConnectionRuleProperties(
name="RandomFanInProps",
definition=random_fan_in_class,
properties={'number': 200})
self.celltype = DynamicsProperties(name="liaf_props",
definition=liaf,
properties={
'tau': self.tau,
'theta': self.theta,
'tau_rp': 2.0 * un.ms,
'Vreset': 10.0 * un.mV,
'R': 1.5 * un.Mohm
},
initial_values={
"V": 0.0 * un.mV,
"t_rpend": 0.0 * un.ms
})
ext_stim = DynamicsProperties(name="stim",
definition=poisson,
properties={'rate': self.input_rate},
initial_values={"t_next": 0.5 * un.ms})
self.psr = DynamicsProperties(name="syn",
definition=psr,
properties={'tau_syn': self.tau_syn},
initial_values={
"A": 0.0 * un.nA,
"B": 0.0 * un.nA
})
exc = Population("Exc", self.order * 4, self.celltype)
inh = Population("Inh", self.order, self.celltype)
ext = Population("Ext", self.order * 5, ext_stim)
exc_and_inh = Selection("All", Concatenate((exc, inh)))
self.static_ext = DynamicsProperties(
"ExternalPlasticity",
static, {},
initial_values={"weight": self.Je * un.nA})
static_exc = DynamicsProperties(
"ExcitatoryPlasticity",
static, {},
initial_values={"weight": self.Je * un.nA})
static_inh = DynamicsProperties(
"InhibitoryPlasticity",
static,
initial_values={"weight": self.Ji * un.nA})
ext_prj = Projection("External",
pre=ext,
post=exc_and_inh,
response=self.psr,
plasticity=self.static_ext,
connection_rule_properties=self.one_to_one,
delay=self.delay,
port_connections=[
('response', 'Isyn', 'post', 'Isyn'),
('plasticity', 'weight', 'response', 'weight')
])
exc_prj = Projection("Excitation",
pre=exc,
post=exc_and_inh,
response=self.psr,
plasticity=static_exc,
connection_rule_properties=exc_random_fan_in,
delay=self.delay,
port_connections=[
('response', 'Isyn', 'post', 'Isyn'),
('plasticity', 'weight', 'response', 'weight')
])
inh_prj = Projection("Inhibition",
pre=inh,
post=exc_and_inh,
response=self.psr,
plasticity=static_inh,
connection_rule_properties=inh_random_fan_in,
delay=self.delay,
port_connections=[
('response', 'Isyn', 'post', 'Isyn'),
('plasticity', 'weight', 'response', 'weight')
])
self.model = Network("brunel_network")
self.model.add(ext)
self.model.add(exc)
self.model.add(inh)
self.model.add(exc_and_inh)
self.model.add(ext_prj)
self.model.add(exc_prj)
self.model.add(inh_prj)
def setUp(self):
self.pre_dynamics = Dynamics(
name='PreDynamics',
state_variables=[StateVariable('SV1', dimension=un.voltage)],
regimes=[
Regime('dSV1/dt = -SV1 / P1',
transitions=[On('SV1 > P2', do=[OutputEvent('emit')])],
name='R1'),
],
parameters=[
Parameter('P1', dimension=un.time),
Parameter('P2', dimension=un.voltage)
])
self.post_dynamics = Dynamics(
name='PostDynamics',
state_variables=[StateVariable('SV1', dimension=un.voltage)],
regimes=[
Regime('dSV1/dt = -SV1 / P1 + ARP1 / P2', name='R1'),
],
analog_ports=[AnalogReceivePort('ARP1', dimension=un.current)],
parameters=[
Parameter('P1', dimension=un.time),
Parameter('P2', dimension=un.capacitance)
])
self.response_dynamics = Dynamics(
name='ResponseDynamics',
state_variables=[StateVariable('SV1', dimension=un.current)],
regimes=[
Regime('dSV1/dt = -SV1 / P1',
transitions=[
On('receive',
do=[StateAssignment('SV1', 'SV1 + P2')])
],
name='R1'),
],
analog_ports=[AnalogSendPort('SV1', dimension=un.current)],
parameters=[
Parameter('P1', dimension=un.time),
Parameter('P2', dimension=un.current)
])
self.pre = Population(name="PrePopulation",
size=1,
cell=DynamicsProperties(
name="PreDynamicsProps",
definition=self.pre_dynamics,
properties={
'P1': 1 * un.ms,
'P2': -65 * un.mV
}))
self.post = Population(name="PostPopulation",
size=1,
cell=DynamicsProperties(
name="PostDynamicsProps",
definition=self.post_dynamics,
properties={
'P1': 1 * un.ms,
'P2': 1 * un.uF
}))
self.one_to_one = ConnectionRule(
name="OneToOne",
standard_library=(NINEML_NS + '/connectionrules/OneToOne'))
self.projection = Projection(
name="Projection",
pre=self.pre,
post=self.post,
response=DynamicsProperties(name="ResponseProps",
definition=self.response_dynamics,
properties={
'P1': 10 * un.ms,
'P2': 1 * un.nA
}),
connection_rule_properties=ConnectionRuleProperties(
name="ConnectionRuleProps", definition=self.one_to_one),
delay=1 * un.ms)
OutputEvent('spikeoutput')],
to="refractoryregime"),
),
Regime(
name="refractoryregime",
transitions=[
On("t >= tspike + taurefrac", to="subthresholdregime")
],
)
],
state_variables=[
StateVariable('V', un.voltage),
StateVariable('tspike', un.time),
],
analog_ports=[
AnalogSendPort("V", un.voltage),
AnalogReducePort("ISyn", un.current, operator="+"),
],
event_ports=[
EventSendPort('spikeoutput'),
],
parameters=[
Parameter('cm', un.capacitance),
Parameter('taurefrac', un.time),
Parameter('gl', un.conductance),
Parameter('vreset', un.voltage),
Parameter('vrest', un.voltage),
Parameter('vthresh', un.voltage)
])
coba = Dynamics(name="CobaSyn",
def get_compound_component():
"""Cannot yet be implemented in PyDSTool
"""
from nineml.abstraction.testing_utils import RecordValue
from nineml.abstraction import Dynamics, Regime, On, OutputEvent, AnalogSendPort, AnalogReducePort
emitter = Dynamics(
name='EventEmitter',
parameters=['cyclelength'],
regimes=[
Regime(transitions=On('t > tchange + cyclelength',
do=[OutputEvent('emit'), 'tchange=t'])),
])
ev_based_cc = Dynamics(
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 = Dynamics(name='pulsing_cc',
subnodes={
'evs': emitter,
'cc': ev_based_cc
},
portconnections=[('evs.emit', 'cc.inputevent')])
nrn = Dynamics(
name='LeakyNeuron',
parameters=['Cm', 'gL', 'E'],
regimes=[
Regime('dV/dt = (iInj + (E-V)*gL )/Cm'),
],
aliases=['iIn := iInj'],
analog_ports=[
AnalogSendPort('V'),
AnalogReducePort('iInj', operator='+')
],
)
combined_comp = Dynamics(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
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)
])
On(Trigger('SV1 > P3'),
do=[OutputEvent('ESP1')]),
On('ERP1', do=[OutputEvent('ESP2')])
],
name='R1'),
Regime(name='R2',
transitions=[
OnCondition('(SV1 > C1) & (SV2 < P4)',
target_regime_name='R1')
])
],
analog_ports=[
AnalogReceivePort('ARP1', dimension=un.current),
AnalogReceivePort('ARP2',
dimension=(un.resistance * un.time)),
AnalogSendPort('A1', dimension=un.voltage * un.current),
AnalogSendPort('A2', dimension=un.current)
],
parameters=[
Parameter('P1', dimension=un.voltage),
Parameter('P2', dimension=un.time),
Parameter('P3', dimension=un.voltage),
Parameter('P4', dimension=un.current)
],
constants=[
Constant('C1', value=-71.0, units=un.mV),
Constant('C2', value=22.2, units=un.degC)
])
dynB = Dynamics(
name='dynB',
def test_name(self):
# Signature: name
# The name of the port, local to the current component
self.assertEqual(AnalogReceivePort('A').name, 'A')
self.assertEqual(AnalogReducePort('B', operator='+').name, 'B')
self.assertEqual(AnalogSendPort('C').name, 'C')